Temporal variations in the benthic communities at four intertidal sites in San Francisco Bay, California, 1983-85

USGS Publications Warehouse

Hopkins, D.R.

1987-01-01

Benthic core samples were collected monthly from January 1983 through January 1985 at four intertidal sites in San Francisco Bay, California, two in the northern part of the bay (North Bay) and two in the southern part of the bay (South Bay). Considerable variation was observed in numbers of species and individuals at the four sites, and abundances within species varied widely. Temporal changes in species abundances appeared to be related to freshwater inflow patterns and resultant salinity variations in the estuary. The 1982-83 winter season was extremely wet, with heavy freshwater inflow to the bay from January through March, whereas the 1983-84 winter was closer to a normal pattern, with most rainfall occurring from November through January. Species were grouped into four categories depending on their patterns of abundance during the 2-yr period. Species that showed an abundance peak in the North Bay in 1983 only were Corophium sp.B and a Chironomidae larva, apparently responding to the extended period of lowered salinity throughout spring and early summer. Species with an abundance peak only in 1984 included Corophium Acherusicum, Eteone californica, Nereis succinea, and Grandidierella japonica, typical estuarine species that might have been suppressed during the extended freshwater inflows in 1983. Species with peaks in both years were Gemma gemma and Ampelisca abdita in the South Bay; both showed strong seasonal variations. A number of species in both North and South Bays, including dominant members of the intertidal community such as Macoma balthical and Streblospio benedicti, did not show any consistent seasonal or year-to-year trends. Results of this study suggest that the intensity and timing of freshwater inflow to San Francisco Bay, particularly higher-than-normal inflow during late spring and early summer, may be an important factor in determining the composition of the intertidal benthic communities. (Author 's abstract)

A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions.

PubMed

Gao, Xiang; Lin, Huaiying; Dong, Qunfeng

2017-01-01

Dysbiosis of microbial communities is associated with various human diseases, raising the possibility of using microbial compositions as biomarkers for disease diagnosis. We have developed a Bayes classifier by modeling microbial compositions with Dirichlet-multinomial distributions, which are widely used to model multicategorical count data with extra variation. The parameters of the Dirichlet-multinomial distributions are estimated from training microbiome data sets based on maximum likelihood. The posterior probability of a microbiome sample belonging to a disease or healthy category is calculated based on Bayes' theorem, using the likelihood values computed from the estimated Dirichlet-multinomial distribution, as well as a prior probability estimated from the training microbiome data set or previously published information on disease prevalence. When tested on real-world microbiome data sets, our method, called DMBC (for Dirichlet-multinomial Bayes classifier), shows better classification accuracy than the only existing Bayesian microbiome classifier based on a Dirichlet-multinomial mixture model and the popular random forest method. The advantage of DMBC is its built-in automatic feature selection, capable of identifying a subset of microbial taxa with the best classification accuracy between different classes of samples based on cross-validation. This unique ability enables DMBC to maintain and even improve its accuracy at modeling species-level taxa. The R package for DMBC is freely available at https://github.com/qunfengdong/DMBC. IMPORTANCE By incorporating prior information on disease prevalence, Bayes classifiers have the potential to estimate disease probability better than other common machine-learning methods. Thus, it is important to develop Bayes classifiers specifically tailored for microbiome data. Our method shows higher classification accuracy than the only existing Bayesian classifier and the popular random forest method, and thus provides an alternative option for using microbial compositions for disease diagnosis.

Geographic variation in marine invasions among large estuaries: effects of ships and time.

PubMed

Ruiz, Gregory M; Fofonoff, Paul W; Ashton, Gail; Minton, Mark S; Miller, A Whitman

2013-03-01

Coastal regions exhibit strong geographic patterns of nonnative species richness. Most invasions in marine ecosystems are known from bays and estuaries, where ship-mediated transfers (on hulls or in ballasted materials) have been a dominant vector of species introductions. Conspicuous spatial differences in nonnative species richness exist among bays, but the quantitative relationship between invasion magnitude and shipping activity across sites is largely unexplored. Using data on marine invasions (for invertebrates and algae) and commercial shipping across 16 large bays in the United States, we estimated (1) geographic variation in nonnative species richness attributed to ships, controlling for effects of salinity and other vectors, (2) changes through time in geographic variation of these ship-mediated invasions, and (3) effects of commercial ship traffic and ballast water discharge magnitude on nonnative species richness. For all nonnative species together (regardless of vector, salinity, or time period), species richness differed among U.S. coasts, being significantly greater for Pacific Coast bays than Atlantic or Gulf Coast bays. This difference also existed when considering only species attributed to shipping (or ballast water), controlling for time and salinity. Variation in nonnative species richness among Pacific Coast bays was strongly affected by these same criteria. San Francisco Bay, California, had over 200 documented nonnative species, more than twice that reported for other bays, but many species were associated with other (non-shipping) vectors or the extensive low-salinity habitats (unavailable in some bays). When considering only ship- or ballast-mediated introductions in high-salinity waters, the rate of newly detected invasions in San Francisco Bay has converged increasingly through time on that for other Pacific Coast bays, appearing no different since 1982. Considering all 16 bays together, there was no relationship between either (1) number of ship arrivals (from foreign ports) and number of introductions attributed to ships since 1982 or (2) volume of foreign ballast water discharge and number of species attributed to ballast water since 1982. These shipping measures are likely poor proxies for propagule supply, although they are sometimes used as such, highlighting a fundamental gap in data needed to evaluate invasion dynamics and management strategies.

Anthropogenic activities and coastal environmental quality: a regional quantitative analysis in southeast China with management implications.

PubMed

Chen, Kai; Liu, Yan; Huang, Dongren; Ke, Hongwei; Chen, Huorong; Zhang, Songbin; Yang, Shengyun; Cai, Minggang

2018-02-01

Regional analysis of environmental issues has always been a hot topic in the field of sustainable development. Because the different levels of economic growth, urbanization, resource endowments, etc. in different regions generate apparently different ecological responses, a better description and comparison across different regions will provide more valuable implications for ecological improvement and policymaking. In this study, seven typical bays in southeast China that are a rapid developing area were selected to quantitatively analyze the relationship between socioeconomic development and coastal environmental quality. Based on the water quality data from 2007 to 2015, the multivariate statistical method was applied to analyze the potential environmental risks and to classify the seven bays based on their environmental quality status. The possible variation trends of environmental indices were predicted based on the cross-regional panel data by Environmental Kuznets Curve. The results showed that there were significant regional differences among the seven bays, especially Quanzhou, Xiamen, and Luoyuan Bays, suffered from severer artificial disturbances than other bays, despite their different development patterns. Socioeconomic development level was significantly associated with some water quality indices (pH, DIN, PO 4 -P); the association was roughly positive: the areas with higher GDP per capita have some worse water quality indices. In addition, the decreasing trend of pH values and the increasing trend of nutrient concentration in the seven bays will continue in the foreseeable future. In consideration of the variation trends, the limiting nutrient strategy should be implemented to mitigate the deterioration of the coastal environments.

Empirical Bayes scan statistics for detecting clusters of disease risk variants in genetic studies.

PubMed

McCallum, Kenneth J; Ionita-Laza, Iuliana

2015-12-01

Recent developments of high-throughput genomic technologies offer an unprecedented detailed view of the genetic variation in various human populations, and promise to lead to significant progress in understanding the genetic basis of complex diseases. Despite this tremendous advance in data generation, it remains very challenging to analyze and interpret these data due to their sparse and high-dimensional nature. Here, we propose novel applications and new developments of empirical Bayes scan statistics to identify genomic regions significantly enriched with disease risk variants. We show that the proposed empirical Bayes methodology can be substantially more powerful than existing scan statistics methods especially so in the presence of many non-disease risk variants, and in situations when there is a mixture of risk and protective variants. Furthermore, the empirical Bayes approach has greater flexibility to accommodate covariates such as functional prediction scores and additional biomarkers. As proof-of-concept we apply the proposed methods to a whole-exome sequencing study for autism spectrum disorders and identify several promising candidate genes. © 2015, The International Biometric Society.

Spatial and temporal variability of thermohaline properties in the Bay of Koper (northern Adriatic Sea)

NASA Astrophysics Data System (ADS)

Soczka Mandac, Rok; Žagar, Dušan; Faganeli, Jadran

2013-04-01

In this study influence of fresh water discharge on the spatial and temporal variability of thermohaline (TH) conditions is explored for the Bay of Koper (Bay). The Bay is subject to different driving agents: wind stress (bora, sirocco), tidal and seiches effect, buoyancy fluxes, general circulation of the Adriatic Sea and discharge of the Rizana and Badaševica rivers. These rivers have torrential characteristics that are hard to forecast in relation to meteorological events (precipitation). Therefore, during episodic events the spatial and temporal variability of TH properties in the Bay is difficult to determine [1]. Measurements of temperature, salinity and turbidity were conducted monthly on 35 sampling points in the period: June 2011 - December 2012. The data were processed and spatial interpolated with an objective analysis method. Furthermore, empirical orthogonal function analysis (EOF) [2] was applied to investigate spatial and temporal TH variations. Strong horizontal and vertical stratification was observed in the beginning of June 2011 due to high fresh water discharge of the Rizana (31 m3/s) and Badaševica (2 m3/s) rivers. The horizontal gradient (ΔT = 6°C) was noticed near the mouth of the Rizana river. Similar pattern was identified for salinity field on the boundary of the front where the gradient was ΔS = 20 PSU. Vertical temperature gradient was ΔT = 4°C while salinity gradient was ΔS = 18 PSU in the subsurface layer at depth of 3 m. Spatial analysis of the first principal component (86% of the total variance) shows uniform temperature distribution in the surface layer (1m) during the studied period. Furthermore, temporal variability of temperature shows seasonal variation with a minimum in February and maximum in August. This confirms that episodic events have a negligible effect on spatial and temporal variation of temperature in the subsurface layer. Further analysis will include application of EOF on the salinity, density and total suspended matter. Additionally, we will investigate the cross correlations between the above mentioned parameters with singular value decomposition method. Reference: 1. Faganeli, J., Planinc, R., Pezdic, J., Smodis, B., Stegnar, P., and Ogorelec, B. 1991. Marine geology of Gulf of Trieste (northern Adriatic): Geochemical aspects. Marine Geology, 99: 93-108. 2. Glover, M., Jenkins, J., and Doney, S. C. 2011. Modeling methods for marine science. Cambridge University Press, 571 p.

Modelling river discharge and precipitation from estuarine salinity in the northern Chesapeake Bay: Application to Holocene palaeoclimate

USGS Publications Warehouse

Saenger, C.; Cronin, T.; Thunell, R.; Vann, C.

2006-01-01

Long-term chronologies of precipitation can provide a baseline against which twentieth-century trends in rainfall can be evaluated in terms of natural variability and anthropogenic influence. However, there are relatively few methods to quantitatively reconstruct palaeoprecipitation and river discharge compared with proxies of other climatic factors, such as temperature. We developed autoregressive and least squares statistical models relating Chesapeake Bay salinity to river discharge and regional precipitation records. Salinity in northern and central parts of the modern Chesapeake Bay is influenced largely by seasonal, interannual and decadal variations in Susquehanna River discharge, which in turn are controlled by regional precipitation patterns. A power regressive discharge model and linear precipitation model exhibit well-defined decadal variations in peak discharge and precipitation. The utility of the models was tested by estimating Holocene palaeoprecipitation and Susquehanna River palaeodischarge, as indicated by isotopically derived palaeosalinity reconstructions from Chesapeake Bay sediment cores. Model results indicate that the early-mid Holocene (7055-5900 yr BP) was drier than the late Holocene (1500 yr BP - present), the 'Mediaeval Warm Period' (MWP) (1200-600 yr BP) was drier than the 'Little Ice Age' (LIA) (500-100 yr BP), and the twentieth century experienced extremes in precipitation possibly associated with changes in ocean-atmosphere teleconnections. ?? 2006 Edward Arnold (Publishers) Ltd.

Monitoring population status of sea otters (Enhydra lutris) in Glacier Bay National Park and Preserve, Alaska: options and considerations

USGS Publications Warehouse

Esslinger, George G.; Esler, Daniel N.; Howlin, S.; Starcevich, L.A.

2015-06-25

After many decades of absence from southeast Alaska, sea otters (Enhydra lutris) are recolonizing parts of their former range, including Glacier Bay, Alaska. Sea otters are well known for structuring nearshore ecosystems and causing community-level changes such as increases in kelp abundance and changes in the size and number of other consumers. Monitoring population status of sea otters in Glacier Bay will help park researchers and managers understand and interpret sea otter-induced ecosystem changes relative to other sources of variation, including potential human-induced impacts such as ocean acidification, vessel disturbance, and oil spills. This report was prepared for the National Park Service (NPS), Southeast Alaska Inventory and Monitoring Network following a request for evaluation of options for monitoring sea otter population status in Glacier Bay National Park and Preserve. To meet this request, we provide a detailed consideration of the primary method of assessment of abundance and distribution, aerial surveys, including analyses of power to detect interannual trends and designs to reduce variation around annual abundance estimates. We also describe two alternate techniques for evaluating sea otter population status—(1) quantifying sea otter diets and energy intake rates, and (2) detecting change in ages at death. In addition, we provide a brief section on directed research to identify studies that would further our understanding of sea otter population dynamics and effects on the Glacier Bay ecosystem, and provide context for interpreting results of monitoring activities.

Development of Dimensionless Surge Response Functions for Hazard Assessment at Panama City, Florida

NASA Astrophysics Data System (ADS)

Taylor, N. R.; Irish, J. L.; Hagen, S. C.; Kaihatu, J. M.; McLaughlin, P. W.

2013-12-01

Reliable and robust methods of extreme value analysis in hurricane surge forecasting are of high importance in the coastal engineering profession. The Joint Probability Method (JPM) has become the preferred statistical method over the Historical Surge Population (HSP) method, due to its ability to give more accurate surge predictions, as demonstrated by Irish et. al in 2011 (J. Geophys. Res.). One disadvantage to this method is its high computational cost; a single location can require hundreds of simulated storms, each needing one thousand computational hours or more to complete. One way of overcoming this issue is to use an interpolating function, called a surge response function, to reduce the required number of simulations to a manageable number. These sampling methods, which use physical scaling laws, have been shown to significantly reduce the number of simulated storms needed for application of the JPM method. In 2008, Irish et. al. (J. Phys. Oceanogr.) demonstrated that hurricane surge scales primarily as a function of storm size and intensity. Additionally, Song et. al. in 2012 (Nat. Hazards) has shown that surge response functions incorporating bathymetric variations yield highly accurate surge estimates along the Texas coastline. This study applies the Song. et. al. model to 73 stations along the open coast, and 273 stations within the bays, in Panama City, Florida. The model performs well for the open coast and bay areas; surge levels at most stations along the open coast were predicted with RMS errors below 0.40 meters, and R2 values at or above 0.80. The R2 values for surge response functions within bays were consistently at or above 0.75. Surge levels at most stations within the North Bay and East Bay were predicted with RMS errors below 0.40 meters; within the West Bay, surge was predicted with RMS errors below 0.52 meters. Accurately interpolating surge values along the Panama City coast and bays enables efficient use of the JPM model in order to develop reliable probabilistic surge estimates for use in planning and design for hurricane mitigation.

Variational Bayes method for estimating transit route OD flows using APC data.

DOT National Transportation Integrated Search

2017-01-31

The focus of this study is on the use of large quantities of APC data to estimate OD flows : for transit bus routes. Since most OD flow estimation methodologies based on boarding and : alighting counts were developed before the prevalence of APC tech...

Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay salt marshes

EPA Science Inventory

Measurement of the apparent conductivity of salt marsh sediments using electromagnetic induction (EMI) is a rapid alternative to traditional methods of salinity determination that can be used to map soil salinity across a marsh surface. Soil salinity measures can provide informat...

Determining individual variation in growth and its implication for life-history and population processes using the empirical Bayes method.

PubMed

Vincenzi, Simone; Mangel, Marc; Crivelli, Alain J; Munch, Stephan; Skaug, Hans J

2014-09-01

The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation in growth. We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth using a von Bertalanffy growth model with random effects. To illustrate the power and generality of the method, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually tagged fish have been sampled for more than 15 years. We use year-of-birth cohort, population density during the first year of life, and individual random effects as potential predictors of the von Bertalanffy growth function's parameters k (rate of growth) and L∞ (asymptotic size). Our results showed that size ranks were largely maintained throughout marble trout lifetime in both populations. According to the Akaike Information Criterion (AIC), the best models showed different growth patterns for year-of-birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. For both populations, models including density during the first year of life showed that growth tended to decrease with increasing population density early in life. Model validation showed that predictions of individual growth trajectories using the random-effects model were more accurate than predictions based on mean size-at-age of fish.

ASSESSING HABITAT QUALITY OF MOUNT HOPE BAY AND NARRAGANSETT BAY USING GROWTH, RNA:DNA, AND FEDDING HABITS OF CAGED JUVENILE WINTER FLOUNDER

EPA Science Inventory

Somatic growth rates, RNA:DNA, and feeding habits of juvenile Pseudopleuronectes americanus (Winter Flounder) were used to asses small-scale spatio-temporal variations in the habitat quality of Mount Hope Bay and Narragan-sett Bay, RI. Three successive caging experiments (14–16 d...

Causal mediation analysis with a binary outcome and multiple continuous or ordinal mediators: Simulations and application to an alcohol intervention.

PubMed

Nguyen, Trang Quynh; Webb-Vargas, Yenny; Koning, Ina M; Stuart, Elizabeth A

We investigate a method to estimate the combined effect of multiple continuous/ordinal mediators on a binary outcome: 1) fit a structural equation model with probit link for the outcome and identity/probit link for continuous/ordinal mediators, 2) predict potential outcome probabilities, and 3) compute natural direct and indirect effects. Step 2 involves rescaling the latent continuous variable underlying the outcome to address residual mediator variance/covariance. We evaluate the estimation of risk-difference- and risk-ratio-based effects (RDs, RRs) using the ML, WLSMV and Bayes estimators in Mplus. Across most variations in path-coefficient and mediator-residual-correlation signs and strengths, and confounding situations investigated, the method performs well with all estimators, but favors ML/WLSMV for RDs with continuous mediators, and Bayes for RRs with ordinal mediators. Bayes outperforms WLSMV/ML regardless of mediator type when estimating RRs with small potential outcome probabilities and in two other special cases. An adolescent alcohol prevention study is used for illustration.

Geomorphic change in Dingzi Bay, East China since the 1950s: impacts of human activity and fluvial input

NASA Astrophysics Data System (ADS)

Tian, Qing; Wang, Qing; Liu, Yalong

2017-06-01

This study examines the geomorphic evolution of Dingzi Bay, East China in response to human activity and variations in fluvial input since the 1950s. The analysis is based on data from multiple mathematical methods, along with information obtained from Remote Sensing, Geographic Information System and Global Position System technology. The results show that the annual runoff and sediment load discharged into Dingzi Bay display significant decreasing trends overall, and marked downward steps were observed in 1966 and 1980. Around 60%-80% of the decline is attributed to decreasing precipitation in the Wulong River Basin. The landform types in Dingzi Bay have changed significantly since the 1950s, especially over the period between 1981 and 1995. Large areas of tidal flats, swamp, salt fields, and paddy fields have been reclaimed, and aquaculture ponds have been constructed. Consequently, the patterns of erosion and deposition in the bay have changed substantially. Despite a reduction in sediment input of 65.68% after 1966, low rates of sediment deposition continued in the bay. However, deposition rates changed significantly after 1981 owing to large-scale development in the bay, with a net depositional area approximately 10 times larger than that during 1961-1981. This geomorphic evolution stabilized following the termination of large-scale human activity in the bay after 1995. Overall, Dingzi Bay has shown a tendency towards silting-up during 1952-2010, with the bay head migrating seaward, the number of channels in the tidal creek system decreasing, and the tidal inlet becoming narrower and shorter. In conclusion, largescale development and human activity in Dingzi Bay have controlled the geomorphic evolution of the bay since the 1950s.

Approximate method of variational Bayesian matrix factorization/completion with sparse prior

NASA Astrophysics Data System (ADS)

Kawasumi, Ryota; Takeda, Koujin

2018-05-01

We derive the analytical expression of a matrix factorization/completion solution by the variational Bayes method, under the assumption that the observed matrix is originally the product of low-rank, dense and sparse matrices with additive noise. We assume the prior of a sparse matrix is a Laplace distribution by taking matrix sparsity into consideration. Then we use several approximations for the derivation of a matrix factorization/completion solution. By our solution, we also numerically evaluate the performance of a sparse matrix reconstruction in matrix factorization, and completion of a missing matrix element in matrix completion.

Spatial and seasonal patterns of ichthyoplankton assemblages in the Haizhou Bay and its adjacent waters of China

NASA Astrophysics Data System (ADS)

Li, Zengguang; Ye, Zhenjiang; Wan, Rong

2015-12-01

Surveys were conducted in five voyages in Haizhou Bay and its adjacent coastal area from March to December 2011 during full moon spring tides. The ichthyoplankton assemblages and the environmental factors that affect their spatial and seasonal patterns were determined. Totally 35 and 12 fish egg and larvae taxa were identified, respectively. Over the past several decades, the egg and larval species composition has significantly changed in Haizhou Bay and its adjacent waters, most likely corresponding with the alteration of fishery resources, which are strongly affected by anthropogenic activities and climate change. The Bray-Curtis dissimilarity index identified four assemblages: near-shore bay assemblage, middle bay assemblage and two closely related assemblages (near-shore/middle bay assemblage and middle/edge of bay assemblage). The primary species of each assemblage principally reflected the spawning strategies of adult fish. The near-shore bay assemblage generally occurred in near-shore bay, with depths measuring <20 m, and the middle bay assemblage generally occurred in the middle of bay, with depths measuring 20 to 40 m. Spatial and seasonal variations in ichthyoplankton in each assemblage were determined by interactions between biological behavioral traits and oceanographic features, particularly the variation of local conditions within the constraint of a general reproductive strategy. The results of Spearman's rank correlation analysis indicated that both fish egg and larval abundance were positively correlated with depth, which is critical to the oceanographic features in Haizhou Bay.

Spatial and temporal characterizations of water quality in Kuwait Bay.

PubMed

Al-Mutairi, N; Abahussain, A; El-Battay, A

2014-06-15

The spatial and temporal patterns of water quality in Kuwait Bay have been investigated using data from six stations between 2009 and 2011. The results showed that most of water quality parameters such as phosphorus (PO4), nitrate (NO3), dissolved oxygen (DO), and Total Suspended Solids (TSS) fluctuated over time and space. Based on Water Quality Index (WQI) data, six stations were significantly clustered into two main classes using cluster analysis, one group located in western side of the Bay, and other in eastern side. Three principal components are responsible for water quality variations in the Bay. The first component included DO and pH. The second included PO4, TSS and NO3, and the last component contained seawater temperature and turbidity. The spatial and temporal patterns of water quality in Kuwait Bay are mainly controlled by seasonal variations and discharges from point sources of pollution along Kuwait Bay's coast as well as from Shatt Al-Arab River. Copyright © 2014 Elsevier Ltd. All rights reserved.

Seasonal and spatial variations in surface pCO2 and air-sea CO2 flux in the Chesapeake Bay

NASA Astrophysics Data System (ADS)

Cai, W. J.; Chen, B.

2017-12-01

Bay-wide observations of surface water partial pressure of carbon dioxide (pCO2) were conducted in May, June, August, and October 2016 to study the spatial and seasonal variations in surface pCO2 and to estimate air-sea CO2 flux in the Chesapeake Bay. Overall, high surface pCO2 in the upper-bay decreased downstream rapidly below the atmospheric value near the bay bridge in the mid-bay and then increased slightly to the lower-bay where pCO2 approached the atmospheric level. Over the course of a year, pCO2 was higher than 1000 µatm in the upper bay and the highest pCO2 (2500 µatm) was observed in August. Significant biologically-induced pCO2 undersaturation was observed at the upper part of the mid-bay in August with pCO2 as low as 50 µatm and oversaturated DO% of 200%. In addition to biological control, vertical mixing and upwelling controlled by wind direction and tidal stage played an important role in controlling surface pCO2 in the mid-bay as is evidenced by co-occurrence of high pCO2 with low temperature and low oxygen or high salinity from the subsurface. These physical processes occurred regularly and in short time scale of hours, suggesting they must be considered in the assessment of annual air-sea CO2 flux. Seasonally, the upper-bay acted as a source for atmospheric CO2 over the course of a year. The boundary of upper and mid bay transited from a CO2 source to a sink from May to August and was a source again in October due to strong biological production in summer. In contrast, the mid-bay represented as a CO2 source with large temporal variation due to dynamic hydrographic settings. The lower-bay transited from a weak sink in May to equilibrated with the atmosphere from June to August, while became a source again in October. Moreover, the CO2 flux could be reversed very quickly under episodic severe weather events. Thus further research, including the influence of severe weather and subsequent bloom, is needed to get better understanding of the carbon cycling in the Chesapeake Bay.

Seasonal and spatial variations in fish and macrocrustacean assemblage structure in Mad Island Marsh estuary, Texas

NASA Astrophysics Data System (ADS)

Akin, S.; Winemiller, K. O.; Gelwick, F. P.

2003-05-01

Fish and macrocrustacean assemblage structure was analyzed along an estuarine gradient at Mad Island Marsh (MIM), Matagorda Bay, TX, during March 1998-August 1999. Eight estuarine-dependent fish species accounted for 94% of the individual fishes collected, and three species accounted for 96% of macrocrustacean abundance. Consistent with evidence from other Gulf of Mexico estuarine studies, species richness and abundance were highest during late spring and summer, and lowest during winter and early spring. Sites near the bay supported the most individuals and species. Associations between fish abundance and environmental variables were examined with canonical correspondence analysis. The dominant gradient was associated with water depth and distance from the bay. The secondary gradient reflected seasonal variation and was associated with temperature, salinity, dissolved oxygen, and vegetation cover. At the scales examined, estuarine biota responded to seasonal variation more than spatial variation. Estuarine-dependent species dominated the fauna and were common throughout the open waters of the shallow lake during winter-early spring when water temperature and salinity were low and dissolved oxygen high. During summer-early fall, sub-optimal environmental conditions (high temperature, low DO) in upper reaches accounted for strong spatial variation in assemblage composition. Small estuarine-resident fishes and the blue crab ( Callinectes sapidus) were common in warm, shallow, vegetated inland sites during summer-fall. Estuarine-dependent species were common at deeper, more saline locations near the bay during this period. During summer, freshwater species, such as gizzard shad ( Dorosoma cepedianum) and gars ( Lepisosteus spp.), were positively associated with water depth and proximity to the bay. The distribution and abundance of fishes in MIM appear to result from the combined effects of endogenous, seasonal patterns of reproduction and migration operating on large spatial scales, and species-specific response to local environmental variation.

Still Bay Point-Production Strategies at Hollow Rock Shelter and Umhlatuzana Rock Shelter and Knowledge-Transfer Systems in Southern Africa at about 80-70 Thousand Years Ago

PubMed Central

Lombard, Marlize

2016-01-01

It has been suggested that technological variations associated with Still Bay assemblages of southern Africa have not been addressed adequately. Here we present a study developed to explore regional and temporal variations in Still Bay point-production strategies. We applied our approach in a regional context to compare the Still Bay point assemblages from Hollow Rock Shelter (Western Cape) and Umhlatuzana Rock Shelter (KwaZulu-Natal). Our interpretation of the point-production strategies implies inter-regional point-production conventions, but also highlights variability and intra-regional knapping strategies used for the production of Still Bay points. These strategies probably reflect flexibility in the organisation of knowledge-transfer systems at work during the later stages of the Middle Stone Age between about 80 ka and 70 ka in South Africa. PMID:27942012

Still Bay Point-Production Strategies at Hollow Rock Shelter and Umhlatuzana Rock Shelter and Knowledge-Transfer Systems in Southern Africa at about 80-70 Thousand Years Ago.

PubMed

Högberg, Anders; Lombard, Marlize

2016-01-01

It has been suggested that technological variations associated with Still Bay assemblages of southern Africa have not been addressed adequately. Here we present a study developed to explore regional and temporal variations in Still Bay point-production strategies. We applied our approach in a regional context to compare the Still Bay point assemblages from Hollow Rock Shelter (Western Cape) and Umhlatuzana Rock Shelter (KwaZulu-Natal). Our interpretation of the point-production strategies implies inter-regional point-production conventions, but also highlights variability and intra-regional knapping strategies used for the production of Still Bay points. These strategies probably reflect flexibility in the organisation of knowledge-transfer systems at work during the later stages of the Middle Stone Age between about 80 ka and 70 ka in South Africa.

The effect of long-term spatiotemporal variations in urbanization-induced eutrophication on a benthic ecosystem, Osaka Bay, Japan

USGS Publications Warehouse

Yasuhara, Moriaki; Yamazaki, Hideo; Tsujimoto, Akira; Hirose, K.

2007-01-01

Detailed spatiotemporal patterns of the influence of urbanization-induced eutrophication on a metazoan benthic community in Osaka Bay were determined using sediment cores and fossil ostracode assemblages from the last 200 yr. Results suggest that total abundance of ostracodes increased in the middle part of the bay as a result of the increase of food supply by eutrophication. Conversely, abundance decreased in the inner bay, likely because of bottom-water hypoxia by eutrophication. The variation in species composition among sites within the bay may have decreased because of the effect of eutrophication, i.e., the dominance of species that prefer food-rich environments throughout all sites. These eutrophication-induced changes occurred around 1900 as a result of Japan's industrial revolution and around 1960 as a result of rapid urbanization, depending upon location. ?? 2007, by the American Society of Limnology and Oceanography, Inc.

Spatial variations in zooplankton community structure along the Japanese coastline in the Japan Sea: influence of the coastal current

NASA Astrophysics Data System (ADS)

Kodama, Taketoshi; Wagawa, Taku; Iguchi, Naoki; Takada, Yoshitake; Takahashi, Takashi; Fukudome, Ken-Ichi; Morimoto, Haruyuki; Goto, Tsuneo

2018-06-01

This study evaluates spatial variations in zooplankton community structure and potential controlling factors along the Japanese coast under the influence of the coastal branch of the Tsushima Warm Current (CBTWC). Variations in the density of morphologically identified zooplankton in the surface layer in May were investigated for a 15-year period. The density of zooplankton (individuals per cubic meter) varied between sampling stations, but there was no consistent west-east trend. Instead, there were different zooplankton community structures in the west and east, with that in Toyama Bay particularly distinct: Corycaeus affinis and Calanus sinicus were dominant in the west and Oithona atlantica was dominant in Toyama Bay. Distance-based redundancy analysis (db-RDA) was used to characterize the variation in zooplankton community structure, and four axes (RD1-4) provided significant explanation. RD2-4 only explained < 4.8 % of variation in the zooplankton community and did not show significant spatial difference; however, RD1, which explained 89.9 % of variation, did vary spatially. Positive and negative species scores on RD1 represent warm- and cold-water species, respectively, and their variation was mainly explained by water column mean temperature, and it is considered to vary spatially with the CBTWC. The CBTWC intrusion to the cold Toyama Bay is weak and occasional due to the submarine canyon structure of the bay. Therefore, the varying bathymetric characteristics along the Japanese coast of the Japan Sea generate the spatial variation in zooplankton community structure, and dominance of warm-water species can be considered an indicator of the CBTWC.

A review of circulation and mixing studies of San Francisco Bay, California

USGS Publications Warehouse

Smith, Lawrence H.

1987-01-01

A description of the major characteristics and remaining unknowns of circulation and mixing in San Francisco Bay has been constructed from a review of published studies. From a broad perspective San Francisco Bay is an ocean-river mixing zone with a seaward flow equal to the sum of the river inflows less evaporation. Understanding of circulation and mixing within the bay requires quantification of freshwater inflows and ocean-bay exchanges, characterization of source-water variations, and separation of the within-bay components of circulation and mixing processes. Description of net circulation and mixing over a few days to a few months illustrates best the interactions of major components. Quantification of tidal circulation and mixing is also necessary because net circulation and mixing contain a large tide-induced component, and because tidal variations are dominant in measurements of stage, currents, and salinity. The discharge of the Sacramento-San Joaquin Delta into Suisun Bay is approximately 90 percent of the freshwater inflow to San Francisco Bay. Annual delta discharge is characterized by a winter season of high runoff and a summer season of low runoff. For the period 1956 to 1985 the mean of monthly discharges exceeded 1,000 cubic meters per second (35,000 cubic feet per second) for the months of December through April, whereas for July through October, it was less than 400 cubic meters per second (14,000 cubic feet per second). The months of November, May, and June commonly were transition months between these seasons. Large year-to-year deviations from this annual pattern have occurred frequently. Much less is known about the ocean-bay exchange process. Net exchanges depend on net seaward flow in the bay, tidal amplitude, and longshore coastal currents, but exchanges have not yet been measured successfully. Source-water variations are ignored by limiting discussion of mixing to salinity. The bay is composed of a northern reach, which is strongly influenced by delta discharge, and South Bay, a tributary estuary which responds to conditions in Central Bay. In the northern reach net circulation is characterized by the river-induced seaward, flow and a resulting gravitational circulation in the channels, and by a tide- and wind-induced net horizontal circulation. A surface layer of relatively fresh water in Central Bay generated by high delta discharges can induce gravitational circulation in South Bay. During low delta discharges South Bay has nearly the same salinity as Central Bay and is characterized by tide- and wind-induced net horizontal circulation. Several factors control the patterns of circulation and mixing in San Francisco Bay. Viewing circulation and mixing over different time-periods and at different geographic scales causes the influences of different factors to be emphasized. The exchange between the bay and coastal ocean and freshwater inflows determine the year-to-year behavior of San Francisco Bay as a freshwater-saltwater mixing zone. Within the bay, exchanges between the embayments control variations over a season. Circulation and mixing patterns within the embayments and the magnitude of river-induced seaward flow influence the between-bay exchanges. The within-bay patterns are in turn determined by tides, winds, and freshwater inflows. Because freshwater inflow is the only factor that can be managed, a major study focus is estimation of inflow-related effects. Most questions relate to the patterns of freshwater inflow necessary to protect valuable resources whose welfare is dependent on conditions in the bay. Among the important questions being addressed are: --What quantity of freshwater inflow is necessary to prevent salt intrusion into the Sacramento-San Joaquin Delta, and what salinity distributions in the bay would result from various inflow patterns? --What quantity of freshwater inflow is sufficient to flush pollutants through the bay? Knowledge of circul

Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method

PubMed Central

Vincenzi, Simone; Mangel, Marc; Crivelli, Alain J.; Munch, Stephan; Skaug, Hans J.

2014-01-01

The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation in growth. We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth using a von Bertalanffy growth model with random effects. To illustrate the power and generality of the method, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually tagged fish have been sampled for more than 15 years. We use year-of-birth cohort, population density during the first year of life, and individual random effects as potential predictors of the von Bertalanffy growth function's parameters k (rate of growth) and (asymptotic size). Our results showed that size ranks were largely maintained throughout marble trout lifetime in both populations. According to the Akaike Information Criterion (AIC), the best models showed different growth patterns for year-of-birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. For both populations, models including density during the first year of life showed that growth tended to decrease with increasing population density early in life. Model validation showed that predictions of individual growth trajectories using the random-effects model were more accurate than predictions based on mean size-at-age of fish. PMID:25211603

Modelling Wind Effects on Subtidal Salinity in Apalachicola Bay, Florida

NASA Astrophysics Data System (ADS)

Huang, W.; Jones, W. K.; Wu, T. S.

2002-07-01

Salinity is an important factor for oyster and estuarine productivity in Apalachicola Bay. Observations of salinity at oyster reefs have indicated a high correlation between subtidal salinity variations and the surface winds along the bay axis in an approximately east-west direction. In this paper, we applied a calibrated hydrodynamic model to examine the surface wind effects on the volume fluxes in the tidal inlets and the subtidal salinity variations in the bay. Model simulations show that, due to the large size of inlets located at the east and west ends of this long estuary, surface winds have significant effects on the volume fluxes in the estuary inlets for the water exchanges between the estuary and ocean. In general, eastward winds cause the inflow from the inlets at the western end and the outflow from inlets at the eastern end of the bay. Winds at 15 mph speed in the east-west direction can induce a 2000 m3 s-1 inflow of saline seawater into the bay from the inlets, a rate which is about 2·6 times that of the annual average freshwater inflow from the river. Due to the varied wind-induced volume fluxes in the inlets and the circulation in the bay, the time series of subtidal salinity at oyster reefs considerably increases during strong east-west wind conditions in comparison to salinity during windless conditions. In order to have a better understanding of the characteristics of the wind-induced subtidal circulation and salinity variations, the researchers also connected model simulations under constant east-west wind conditions. Results show that the volume fluxes are linearly proportional to the east-west wind stresses. Spatial distributions of daily average salinity and currents clearly show the significant effects of winds on the bay.

Ozone in the marine boundary layer of Bay of Bengal and Arabian Sea during post winter period - continental influence

NASA Astrophysics Data System (ADS)

Nair, Prabha R.; George, Susan K.; David, Liji Mary; Parameswaran, Krishnaswamy

Ozone plays a key role in controlling the oxidation capacity of the troposphere and hence the lifetime of a variety of trace gases in the atmosphere. In pristine marine boundary layer (MBL), entire chemistry is initiated by the photolysis of ozone and the subsequent formation of OH radical from water vapour. Also in such environment, photochemical destruction is considered as a major sink in global ozone budget. Even though large number of studies on near surface ozone has been carried out over land such studies are very few over oceanic environments. This paper presents the observational results on the spatial variations of near-surface ozone over Bay of Bengal and Arabian Sea as revealed by the cruise-based measurements (cruise No. SK223) conducted as part of Integrated Campaign for Aerosol gases and Radiation Budget (ICARB) under the Geosphere Biosphere Programme of Indian Space Research Organisation (IGBP). Online measurements of ozone have been carried out by using a UV Photometric Analyser (model 49C of Thermo Electron Corporation, USA). Ozone mixing ratio was observed to be significantly high over northern Bay of Bengal (20-28 ppb) compared to southern Bay of Bengal and Arabian Sea. Minimum levels of ozone ( 5 ppb) have been measured in the central Bay of Bengal region. Over Arabian Sea latitudinal variation was not prominently observed. The over all latitudinal gradient is estimated to be 1.2 ppb/o latitude over Bay of Bengal with longitudinal gradient showing variation depending on the latitude sector. It was maximum (of 1.2ppb/o longitude) over the mid Bay of Bengal region ( 15o N). Longitudinal variation was not significant over northern and southern regions. A close examination of surface airflow patterns and the air mass back trajectories revealed increase in ozone level associated with continental outflow from the northern and central parts of the subcontinent. The diurnal pattern also showed variations depending on the proximity to inhabited land mass and also with meteorological parameters.

Monitoring of oceanographic properties of Glacier Bay, Alaska 2004

USGS Publications Warehouse

Madison, Erica N.; Etherington, Lisa L.

2005-01-01

Glacier Bay is a recently (300 years ago) deglaciated fjord estuarine system that has multiple sills, very deep basins, tidewater glaciers, and many streams. Glacier Bay experiences a large amount of runoff, high sedimentation, and large tidal variations. High freshwater discharge due to snow and ice melt and the presence of the tidewater glaciers makes the bay extremely cold. There are many small- and large-scale mixing and upwelling zones at sills, glacial faces, and streams. The complex topography and strong currents lead to highly variable salinity, temperature, sediment, primary productivity, light penetration, stratification levels, and current patterns within a small area. The oceanographic patterns within Glacier Bay drive a large portion of the spatial and temporal variability of the ecosystem. It has been widely recognized by scientists and resource managers in Glacier Bay that a program to monitor oceanographic patterns is essential for understanding the marine ecosystem and to differentiate between anthropogenic disturbance and natural variation. This year’s sampling marks the 12th continuous year of monitoring the oceanographic conditions at 23 stations along the primary axes within Glacier Bay, AK, making this a very unique and valuable data set in terms of its spatial and temporal coverage.

Distribution and growth dynamics of ephemeral macroalgae in shallow bays on the Swedish west coast

NASA Astrophysics Data System (ADS)

Pihl, Leif; Magnusson, Gunilla; Isaksson, Ingela; Wallentinus, Inger

1996-02-01

Distribution and growth dynamics of ephemeral macroalgae were investigated in some shallow (0-1 m) bays on the Swedish west coast during the period 1992 to 1994. Variation in cover and biomass was assessed in nine bays, and in one of them the seasonal dynamics of these algae was followed intensively over three years. Frequent measurements were taken of algal biomass, degree of cover, in situ growth, variable fluorescence and C/N-ratios. Irradiance and water nutrient concentrations were measured concurrently with the growth measurements. Ephemeral macroalgae were dominated by Cladophora and Enteromorpha species and occurred in all sampled bays, except one, covering 10 to 100% of the bottom sediment. Generally, a rapid biomass increase was recorded from mid-May, which peaked after six weeks at 400-600 g dwt·m -2. Later in the season, strong variations in biomass, cover and species composition were observed, suggesting that these opportunistic algae form a highly dynamic community. Initial growth rates estimated from biomass samples were similar to those recorded from in situ cage experiments, and also agreed with growth rates calculated from a model. For all species studied growth rate was within the range 10 to 30 g dwt·m -2·d -1, irrespective of method used. Low algal C/N-ratios (mean = 12.7) in 1993 (cold and rainy summer) indicated that growth was not limited by nutrients, but rather by light. In 1994 (warm and sunny summer), mean C/N-ratios were 20, reflecting the opposite situation. The appearance of these opportunistic algae in shallow bays which historically had been without macroalgal communities has changed the characteristics of these areas by altering habitat complexity. This could have important consequences for trophic interactions involving many species, thereby altering community structure and function.

2017 STATE OF NARRAGANSETT BAY AND ITS WATERSHED – MAPPING DRIVERS OF CHANGE AND VARIATION

EPA Science Inventory

The Narragansett Bay Estuary Program (NBEP) developed 24 environmental indicators for its 2017 State of Narragansett Bay and Its Watershed report with the collaboration of over 50 bi-state (MA and RI) and regional partners. The report presents and tracks the 24 indicators in ord...

Regional downscaling of temporal resolution in near-surface wind from statistically downscaled Global Climate Models (GCMs) for use in San Francisco Bay coastal flood modeling

NASA Astrophysics Data System (ADS)

O'Neill, A.; Erikson, L. H.; Barnard, P.

2013-12-01

While Global Climate Models (GCMs) provide useful projections of near-surface wind vectors into the 21st century, resolution is not sufficient enough for use in regional wave modeling. Statistically downscaled GCM projections from Multivariate Adaptive Constructed Analogues (MACA) provide daily near-surface winds at an appropriate spatial resolution for wave modeling within San Francisco Bay. Using 30 years (1975-2004) of climatological data from four representative stations around San Francisco Bay, a library of example daily wind conditions for four corresponding over-water sub-regions is constructed. Empirical cumulative distribution functions (ECDFs) of station conditions are compared to MACA GFDL hindcasts to create correction factors, which are then applied to 21st century MACA wind projections. For each projection day, a best match example is identified via least squares error among all stations from the library. The best match's daily variation in velocity components (u/v) is used as an analogue of representative wind variation and is applied at 3-hour increments about the corresponding sub-region's projected u/v values. High temporal resolution reconstructions using this methodology on hindcast MACA fields from 1975-2004 accurately recreate extreme wind values within the San Francisco Bay, and because these extremes in wind forcing are of key importance in wave and subsequent coastal flood modeling, this represents a valuable method of generating near-surface wind vectors for use in coastal flood modeling.

An empirical Bayes approach to network recovery using external knowledge.

PubMed

Kpogbezan, Gino B; van der Vaart, Aad W; van Wieringen, Wessel N; Leday, Gwenaël G R; van de Wiel, Mark A

2017-09-01

Reconstruction of a high-dimensional network may benefit substantially from the inclusion of prior knowledge on the network topology. In the case of gene interaction networks such knowledge may come for instance from pathway repositories like KEGG, or be inferred from data of a pilot study. The Bayesian framework provides a natural means of including such prior knowledge. Based on a Bayesian Simultaneous Equation Model, we develop an appealing Empirical Bayes (EB) procedure that automatically assesses the agreement of the used prior knowledge with the data at hand. We use variational Bayes method for posterior densities approximation and compare its accuracy with that of Gibbs sampling strategy. Our method is computationally fast, and can outperform known competitors. In a simulation study, we show that accurate prior data can greatly improve the reconstruction of the network, but need not harm the reconstruction if wrong. We demonstrate the benefits of the method in an analysis of gene expression data from GEO. In particular, the edges of the recovered network have superior reproducibility (compared to that of competitors) over resampled versions of the data. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Temporal and spatial patterns of phytoplankton production in Tomales Bay, California, U.S.A.

USGS Publications Warehouse

Cole, B.E.

1989-01-01

Primary productivity in the water column was measured 14 times between April 1985 and April 1986 at three sites in Tomales Bay, California, USA The conditions at these three stations encompassed the range of hydrographic conditions, phytoplankton biomass, phytoplankton community composition, and turbidity typical of this coastal embayment. Linear regression of the measured daily carbon uptake against the composite parameter B Zp Io (where B is the average phytoplankton biomass in the photic zone; Zp is the photic depth; and Io is the daily surface insolation) indicates that 90% of the variability in primary productivity is explained by variations in phytoplankton biomass and light availability. The linear function derived using Tomales Bay data is essentially the same as that which explains more than 80% of the variation in productivity in four other estuarine systems. Using the linear function and measured values for B, Zp, and Io, the daily photic-zone productivity was estimated for 10 sites at monthly intervals over the annual period. The average daily photic-zone productivity for the 10 sites ranged from 0??2 to 2??2 g C m-2. The bay-wide average annual primary productivity in the water column was 400 g C m-2, with most of the uptake occuring in spring and early summer. Spatial and temporal variations in primary productivity were similar to variations in phytoplankton biomass. Productivity was highest in the seaward and central regions of the bay and lowest in the shallow landward region. ?? 1989.

Mercury accumulation in Devils Lake, North Dakota effects of environmental variation in closed-basin lakes on mercury chronologies

USGS Publications Warehouse

Lent, R.M.; Alexander, C.R.

1997-01-01

Sediment cores were collected from lakes in the Devils Lake Basin in North Dakota to determine if mercury (Hg) accumulation chronologies from sediment-core data are good indicators of variations in Hg accumulation rates in saline lakes. Sediment cores from Creel Bay and Main Bay, Devils Lake were selected for detailed analysis and interpretation. The maximum Hg concentration in the Creel Bay core was 0.15 micrograms per gram at 8 to 9 centimeters. The maximum Hg concentration in the Main Bay core was 0.07 micrograms per gram at 5 to 7 centimeters. The general decreases in Hg concentrations with depth are attributed to historic variations in atmospheric Hg deposition rate. Hg stratigraphies combined with 210Pb and 137Cs dating analyses yield Hg chronologies that indicate a general increase in Hg accumulation rates in Devils Lake since the middle of the 19th century. Mean modern Hg accumulation rates in Creel Bay were 4.9 nanograms per square centimeter per year, and rates in Main Bay were 1.8 nanograms per square centimeter per year. Mean preindustrial Hg accumulation rates in Creel Bay were 1.2 nanograms per square centimeter per year, and rates in Main Bay were 1.6 nanograms per square centimeter per year. Relatively low Hg concentrations in recent sediments in the Devils Lake Basin, along with similarities in Hg accumulation rates between lakes in the Devils Lake Basin and other lakes in the northern interior of North America, indicate that local sources of Hg are not important sources of Hg. Results of the study indicate that accurate Hg chronologies are discernible in sediment cores collected from saline lakes. However, spatial and temporal variations in lake level and water chemistry common to saline lakes make interpretation of radioisotopic and geochemical chronologies difficult. Hg geochemistry in Devils Lake, and presumably in other saline lakes, is dynamic. The results of this study indicate that the absolute amount of sediment transported to Devils Lake, along with the associated Hg and total organic carbon, and the distribution of sedimentation patterns in Devils Lake may be affected by changing lake levels.

Selenium and stable isotopes of carbon and nitrogen in the benthic clam Corbula amurensis from Northern San Francisco Bay, California: May 1995-February 2010

USGS Publications Warehouse

Kleckner, Amy E.; Stewart, A. Robin; Luoma, Samuel N.

2010-01-01

The clam-based food webs of San Francisco Bay, California efficiently bioaccumlate selenium and thus provide pathways for exposure to predators important to the estuary. This study documents changes in monthly selenium concentrations for the clam Corbula amurensis, a keystone species of the estuary, at five locations in northern San Francisco Bay from 1995 through 2010. Samples were collected from designated U.S. Geological Survey stations and prepared and analyzed by U.S. Geological Survey methods. Stable isotopes of carbon and nitrogen in soft tissues of clams also were measured as an indicator of sources of selenium for the clams. These monitoring data indicate that clam selenium concentrations ranged from a low of 2 to a high of 22 micrograms per gram dry weight with strong spatial and seasonal variation over the period of study.

Comparison of genetic and visual identification of cisco and lake whitefish larvae from Chaumont Bay, Lake Ontario

USGS Publications Warehouse

George, Ellen M.; Hare, Matthew P.; Crabtree, Darran L.; Lantry, Brian F.; Rudstam, Lars G.

2017-01-01

Cisco Coregonus artedi are an important component of native food webs in the Great Lakes, and their restoration is instrumental to the recovery of lake trout Salvelinus namaycush and Atlantic salmon Salmo salar. Difficulties with visual identification of larvae can confound early life history surveys, as cisco are often difficult to distinguish from lake whitefish C. clupeaformis. We compared traditional visual species identification methods to genetic identifications based on barcoding of the mitochondrial cytochrome C oxidase I gene for 726 coregonine larvae caught in Chaumont Bay, Lake Ontario. We found little agreement between the visual characteristics of cisco identified by genetic barcoding and the most widely used dichotomous key, and the considerable overlap in ranges of traditionally utilized metrics suggest that visual identification of coregonine larvae from Chaumont Bay is impractical. Coregonines are highly variable and plastic species, and often display wide variations in morphometric characteristics across their broad range. This study highlights the importance of developing accurate, geographically appropriate larval identification methods in order to best inform cisco restoration and management efforts.

Causal mediation analysis with a binary outcome and multiple continuous or ordinal mediators: Simulations and application to an alcohol intervention

PubMed Central

Nguyen, Trang Quynh; Webb-Vargas, Yenny; Koning, Ina M.; Stuart, Elizabeth A.

2016-01-01

We investigate a method to estimate the combined effect of multiple continuous/ordinal mediators on a binary outcome: 1) fit a structural equation model with probit link for the outcome and identity/probit link for continuous/ordinal mediators, 2) predict potential outcome probabilities, and 3) compute natural direct and indirect effects. Step 2 involves rescaling the latent continuous variable underlying the outcome to address residual mediator variance/covariance. We evaluate the estimation of risk-difference- and risk-ratio-based effects (RDs, RRs) using the ML, WLSMV and Bayes estimators in Mplus. Across most variations in path-coefficient and mediator-residual-correlation signs and strengths, and confounding situations investigated, the method performs well with all estimators, but favors ML/WLSMV for RDs with continuous mediators, and Bayes for RRs with ordinal mediators. Bayes outperforms WLSMV/ML regardless of mediator type when estimating RRs with small potential outcome probabilities and in two other special cases. An adolescent alcohol prevention study is used for illustration. PMID:27158217

A variational Bayes discrete mixture test for rare variant association

PubMed Central

Logsdon, Benjamin A.; Dai, James Y.; Auer, Paul L.; Johnsen, Jill M.; Ganesh, Santhi K.; Smith, Nicholas L.; Wilson, James G.; Tracy, Russell P.; Lange, Leslie A.; Jiao, Shuo; Rich, Stephen S.; Lettre, Guillaume; Carlson, Christopher S.; Jackson, Rebecca D.; O’Donnell, Christopher J.; Wurfel, Mark M.; Nickerson, Deborah A.; Tang, Hua; Reiner, Alexander P.; Kooperberg, Charles

2014-01-01

Recently, many statistical methods have been proposed to test for associations between rare genetic variants and complex traits. Most of these methods test for association by aggregating genetic variations within a predefined region, such as a gene. Although there is evidence that “aggregate” tests are more powerful than the single marker test, these tests generally ignore neutral variants and therefore are unable to identify specific variants driving the association with phenotype. We propose a novel aggregate rare-variant test that explicitly models a fraction of variants as neutral, tests associations at the gene-level, and infers the rare-variants driving the association. Simulations show that in the practical scenario where there are many variants within a given region of the genome with only a fraction causal our approach has greater power compared to other popular tests such as the Sequence Kernel Association Test (SKAT), the Weighted Sum Statistic (WSS), and the collapsing method of Morris and Zeggini (MZ). Our algorithm leverages a fast variational Bayes approximate inference methodology to scale to exome-wide analyses, a significant computational advantage over exact inference model selection methodologies. To demonstrate the efficacy of our methodology we test for associations between von Willebrand Factor (VWF) levels and VWF missense rare-variants imputed from the National Heart, Lung, and Blood Institute’s Exome Sequencing project into 2,487 African Americans within the VWF gene. Our method suggests that a relatively small fraction (~10%) of the imputed rare missense variants within VWF are strongly associated with lower VWF levels in African Americans. PMID:24482836

A variational Bayes discrete mixture test for rare variant association.

PubMed

Logsdon, Benjamin A; Dai, James Y; Auer, Paul L; Johnsen, Jill M; Ganesh, Santhi K; Smith, Nicholas L; Wilson, James G; Tracy, Russell P; Lange, Leslie A; Jiao, Shuo; Rich, Stephen S; Lettre, Guillaume; Carlson, Christopher S; Jackson, Rebecca D; O'Donnell, Christopher J; Wurfel, Mark M; Nickerson, Deborah A; Tang, Hua; Reiner, Alexander P; Kooperberg, Charles

2014-01-01

Recently, many statistical methods have been proposed to test for associations between rare genetic variants and complex traits. Most of these methods test for association by aggregating genetic variations within a predefined region, such as a gene. Although there is evidence that "aggregate" tests are more powerful than the single marker test, these tests generally ignore neutral variants and therefore are unable to identify specific variants driving the association with phenotype. We propose a novel aggregate rare-variant test that explicitly models a fraction of variants as neutral, tests associations at the gene-level, and infers the rare-variants driving the association. Simulations show that in the practical scenario where there are many variants within a given region of the genome with only a fraction causal our approach has greater power compared to other popular tests such as the Sequence Kernel Association Test (SKAT), the Weighted Sum Statistic (WSS), and the collapsing method of Morris and Zeggini (MZ). Our algorithm leverages a fast variational Bayes approximate inference methodology to scale to exome-wide analyses, a significant computational advantage over exact inference model selection methodologies. To demonstrate the efficacy of our methodology we test for associations between von Willebrand Factor (VWF) levels and VWF missense rare-variants imputed from the National Heart, Lung, and Blood Institute's Exome Sequencing project into 2,487 African Americans within the VWF gene. Our method suggests that a relatively small fraction (~10%) of the imputed rare missense variants within VWF are strongly associated with lower VWF levels in African Americans.

Variations of pollution sources of Cu in Jiaozhou Bay 1982-1986

NASA Astrophysics Data System (ADS)

Yang, Dongfang; Li, Haixia; Wang, Qi; Ding, Jun; Zhang, Longlei

2017-12-01

Cu pollution in marine bays has been one of the critical environmental issues in the whole world, and understanding the variations of the pollution sources is essential to environmental protection. This paper identified the sources of Cu in Jiaozhou Bay during 1982-1986, and revealed the variations of the sources. Results showed that there were five Cu sources during study years including marine current, stream flow, island top, overland runoff and marine traffic, respectively, whose source strengths were varying from 0.39-20.60 μg L-1, 0.37-10.57 μg L-1, 0.77-4.86 μg L-1, 2.28-3.56 μg L-1, 9.48 μg L-1, respectively. These findings were helpful information in decision-making of pollution control and environmental remediation practice.

Diurnal and Tidal Variation of Temperature and Salinity in the Ponta Rasa Mangrove Swamp, Mozambique

NASA Astrophysics Data System (ADS)

Hoguane, A. M.; Hill, A. E.; Simpson, J. H.; Bowers, D. G.

1999-08-01

Measurements of hydrographic conditions in the Ponta Rasa tidal mangrove swamp, Inhaca Island, Mozambique were made in August-October 1994 during the winter dry season. The Ponta Rasa swamp/creek is tidally choked on account of the narrow channel that connects it to Maputo Bay and at neap tides, a sill prevents bay water entering the creek system altogether. Temperature variation in the swamp (15-25 °C) was predominantly diurnal with an additional signal due to the tidal advection of bay waters. There is no river discharge into Ponta Rasa and during the observation period, there was no significant rainfall. The mean salinity in the swamp ( c. 38) was controlled by evaporation and transpiration by mangroves and an overall evapotranspiration rate of 0·5 cm day -1was estimated from a steady salt balance. Salinity variation ( c. 2) was predominantly due to semi-diurnal tidal advection of lower salinity Maputo Bay water into the swamp/creek. A model which incorporates tidal dynamics coupled to heat and salt balance equations reproduces many of the observed features of the system.

Worsened physical condition due to climate change contributes to the increasing hypoxia in Chesapeake Bay.

PubMed

Du, Jiabi; Shen, Jian; Park, Kyeong; Wang, Ya Ping; Yu, Xin

2018-07-15

There are increasing concerns about the impact of worsened physical condition on hypoxia in a variety of coastal systems, especially considering the influence of changing climate. In this study, an EOF analysis of the DO data for 1985-2012, a long-term numerical simulation of vertical exchange, and statistical analysis were applied to understand the underlying mechanisms for the variation of DO condition in Chesapeake Bay. Three types of analysis consistently demonstrated that both biological and physical conditions contribute equally to seasonal and interannual variations of the hypoxic condition in Chesapeake Bay. We found the physical condition (vertical exchange+temperature) determines the spatial and seasonal pattern of the hypoxia in Chesapeake Bay. The EOF analysis showed that the first mode, which was highly related to the physical forcings and correlated with the summer hypoxia volume, can be well explained by seasonal and interannual variations of physical variables and biological activities, while the second mode is significantly correlated with the estuarine circulation and river discharge. The weakened vertical exchange and increased water temperature since the 1980s demonstrated a worsened physical condition over the past few decades. Under changing climate (e.g., warming, accelerated sea-level rise, altered precipitation and wind patterns), Chesapeake Bay is likely to experience a worsened physical condition, which will amplify the negative impact of anthropogenic inputs on eutrophication and consequently require more efforts for nutrient reduction to improve the water quality condition in Chesapeake Bay. Copyright © 2018 Elsevier B.V. All rights reserved.

Time scales of circulation and mixing processes of San Francisco Bay waters

USGS Publications Warehouse

Walters, R.A.; Cheng, R.T.; Conomos, T.J.

1985-01-01

Conceptual models for tidal period and low-frequency variations in sea level, currents, and mixing processes in the northern and southern reaches of San Francisco Bay describe the contrasting characteristics and dissimilar processes and rates in these embayments: The northern reach is a partially mixed estuary whereas the southern reach (South Bay) is a tidally oscillating lagoon with density-driven exchanges with the northern reach. The mixed semidiurnal tides are mixtures of progressive and standing waves. The relatively simple oscillations in South Bay are nearly standing waves, with energy propagating down the channels and dispersing into the broad shoal areas. The tides of the northern reach have the general properties of a progressive wave but are altered at the constriction of the embayments and gradually change in an upstream direction to a mixture of progressive and standing waves. The spring and neap variations of the tides are pronounced and cause fortnightly varying tidal currents that affect mixing and salinity stratification in the water column. Wind stress on the water surface, freshwater inflow, and tidal currents interacting with the complex bay configuration are the major local forcing mechanisms creating low-frequency variations in sea level and currents. These local forcing mechanisms drive the residual flows which, with tidal diffusion, control the water-replacement rates in the estuary. In the northern reach, the longitudinal density gradient drives an estuarine circulation in the channels, and the spatial variation in tidal amplitude creates a tidally-driven residual circulation. In contrast, South Bay exhibits a balance between wind-driven circulation and tidally-driven residual circulation for most of the year. During winter, however, there can be sufficient density variations to drive multilayer (2 to 3) flows in the channel of South Bay. Mixing models (that include both diffusive and dispersive processes) are based on time scales associated with salt variations at the boundaries and those associated with the local forcing mechanisms, while the spatial scales of variations are dependent upon the configuration of the embayments. In the northern reach, where the estuarine circulation is strong, the salt flux is carried by the mean advection of the mean salt field. Where large salinity gradients are present, the tidal correlation part of the salt flux is of the same order as the advective part. Our knowledge of mixing and exchange rates in South Bay is poor. As this embayment is nearly isohaline, the salt flux is dominated entirely by the mean advection of the mean salt field. During and after peaks in river discharge, water mixing becomes more dynamic, with a strong density-driven current creating a net exchange of both water mass and salt. These exchanges are stronger during neap tides. Residence times of the water masses vary seasonally and differ between reaches. In the northern reach, residence times are on the order of days for high winter river discharge and of months for summer periods. The residence times for South Bay are fairly long (on the order of several months) during summer, and typically shorter (less than a month) during winter when density-driven exchanges occur. ?? 1985 Dr W. Junk Publishers.

Diet of a piscivorous seabird reveals spatiotemporal variation in abundance of forage fishes in the Monterey Bay region

NASA Astrophysics Data System (ADS)

Webb, Lisa A.; Harvey, James T.

2015-06-01

Brandt's Cormorant (Phalacrocorax penicillatus) diet was investigated using regurgitated pellets (n = 285) collected on 19 sampling days at three locations during the 2006-07 and 2007-08 nonbreeding seasons in the Monterey Bay region. The efficacy of using nested sieves and the all-structure technique to facilitate prey detection in the pellets was evaluated, but this method did not increase prey enumeration and greatly decreased efficiency. Although 29 prey species were consumed, northern anchovy (Engraulis mordax) dominated and speckled sanddab (Citharichthys stigmaeus) also was important in the diet. Few rockfishes (Sebastes spp.) and market squid (Doryteuthis opalescens) were consumed compared with great prevalence in previous studies during the 1970s. El Niño and La Niña during the study provided a unique opportunity to examine predator response to variation in prey availability. Patterns of prey number and diversity were not consistent among locations. Greatest number and diversity of prey occurred at locations within Monterey Bay during La Niña, results not evident at the outer coast location. Short-term specialization occurred but mean prey diversity indicated a generalist feeding mode. This study demonstrated the importance of periodic sampling at multiple locations within a region to detect spatiotemporal variability in the diet of opportunistic generalists.

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia.

PubMed

Ansmann, Ina C; Parra, Guido J; Lanyon, Janet M; Seddon, Jennifer M

2012-09-01

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small-scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine-scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F(ST) = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite-based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ(ST) = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine-scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter-related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine-scale population structure among bottlenose dolphins in Moreton Bay. © 2012 Blackwell Publishing Ltd.

Rip currents, mega-cusps, and eroding dunes

USGS Publications Warehouse

Thornton, E.B.; MacMahan, J.; Sallenger, A.H.

2007-01-01

Dune erosion is shown to occur at the embayment of beach mega-cusps O(200 m alongshore) that are associated with rip currents. The beach is the narrowest at the embayment of the mega-cusps allowing the swash of large storm waves coincident with high tides to reach the toe of the dune, to undercut the dune and to cause dune erosion. Field measurements of dune, beach, and rip current morphology are acquired along an 18 km shoreline in southern Monterey Bay, California. This section of the bay consists of a sandy shoreline backed by extensive dunes, rising to heights exceeding 40 m. There is a large increase in wave height going from small wave heights in the shadow of a headland, to the center of the bay where convergence of waves owing to refraction over the Monterey Bay submarine canyon results in larger wave heights. The large alongshore gradient in wave height results in a concomitant alongshore gradient in morphodynamic scale. The strongly refracted waves and narrow bay aperture result in near normal wave incidence, resulting in well-developed, persistent rip currents along the entire shoreline. The alongshore variations of the cuspate shoreline are found significantly correlated with the alongshore variations in rip spacing at 95% confidence. The alongshore variations of the volume of dune erosion are found significantly correlated with alongshore variations of the cuspate shoreline at 95% confidence. Therefore, it is concluded the mega-cusps are associated with rip currents and that the location of dune erosion is associated with the embayment of the mega-cusp.

Anthropogenic effects on shoreface and shoreline changes: Input from a multi-method analysis, Agadir Bay, Morocco

NASA Astrophysics Data System (ADS)

Aouiche, Ismail; Daoudi, Lahcen; Anthony, Edward J.; Sedrati, Mouncef; Ziane, Elhassane; Harti, Abderrazak; Dussouillez, Philippe

2016-02-01

In many situations, the links between shoreline fluctuations and larger-scale coastal change embracing the shoreface are not always well understood. In particular, meso-scale (years to decades) sand exchanges between the shoreface and the shoreline, considered as important on many wave-dominated coasts, are rather poorly understood and difficult to identify. Coastal systems where sediment transport is perturbed by engineering interventions on the shoreline and shoreface commonly provide fine examples liable to throw light on these links. This is especially so where shoreface bathymetric datasets, which are generally lacking, are collected over time, enabling more or less fine resolution of the meso-scale coastal sediment budget. Agadir Bay and the city of Agadir together form one of the two most important economic development poles on the Atlantic coast of Morocco. Using a combined methodological approach based on wave-current modelling, bathymetric chart-differencing, determination of shoreline fluctuations, and beach topographic surveying, we highlight the close links between variations in the bed of the inner shoreface and the bay shoreline involving both cross-shore and longshore sand transport pathways, sediment budget variations and new sediment cell patterns. We show that the significant changes that have affected the bay shoreline and shoreface since 1978 clearly reflect anthropogenic impacts, notably blocking of alongshore sand transport by Agadir harbour, completed in 1988, and the foundations of which lie well beyond the depth of wave closure. Construction of the harbour has led to the creation of a rapidly accreting beach against an original portion of rocky shoreline updrift and to a net sand loss exceeding 145,000 m3/year between 1978 and 2012 over 8.5 km2of the bay shoreface downdrift. Shoreline retreat has been further exacerbated by sand extraction from aeolian dunes and by flattening of these dunes to make space for tourist infrastructure. Digital elevation models of part of the bay beach between 2012 and 2014 confirm this on-going sand loss. These changes have involved the establishment of two divergent longshore bay sediment cells instead of the original single unidirectional cell. A prospective view of these changes suggests that perturbation of longshore drift and the on-going bay sediment budget deficit will eventual directly pose threats to the harbour access and to coastal tourism on which the economic growth of Agadir has been built.

Spatial and temporal variation in seagrass coverage in Southwest Florida: assessing the relative effects of anthropogenic nutrient load reductions and rainfall in four contiguous estuaries.

PubMed

Tomasko, D A; Corbett, C A; Greening, H S; Raulerson, G E

2005-08-01

The estuaries of Tampa Bay, Sarasota Bay, Lemon Bay, and Upper Charlotte Harbor are contiguous waterbodies located within the subtropical environment of Southwest Florida. Based on an examination of rainfall data over the period of record (1916-2001) within the watersheds of these estuaries, there is no evidence for spatial differences (at the watershed level) or monotonic trends in annual rainfall. During the 1980s, nitrogen loads into Tampa Bay and Sarasota Bay (generated primarily by domestic wastewater treatment facilities) were reduced by 57% and 46%, respectively. In response, both Tampa Bay and Sarasota Bay have lower phytoplankton concentrations, greater water clarity and more extensive seagrass coverage in 2002 than in the early 1980s. As there is no evidence of a concurrent trend in rainfall during the period of 1982-2001, it is unlikely that variation in rainfall can account for the observed increase in seagrass coverage in these two bays. In contrast, seagrass coverage has remained relatively constant since the mid 1980s in Lemon Bay and Charlotte Harbor. Domestic wastewater treatment facilities are minor sources of nitrogen to Lemon Bay, and water clarity in Charlotte Harbor varies mostly as a function of dissolved organic matter and non-chlorophyll associated turbidity, not phytoplankton levels. Even in estuaries that share boundaries and are within 100 km of each other, varied responses to anthropogenic changes and natural phenomena were observed in water quality and associated seagrass extent. Resource management strategies must take into account system-specific factors-not all strategies will result in similar results in different systems.

Spatial variation of physicochemical and bacteriological parameters elucidation with GIS in Rangat Bay, Middle Andaman, India

NASA Astrophysics Data System (ADS)

Dheenan, P. S.; Jha, Dilip Kumar; Vinithkumar, N. V.; Ponmalar, A. Angelin; Venkateshwaran, P.; Kirubagaran, R.

2014-01-01

The purpose of this study was to determine the concentration, distribution of bacteria and physicochemical property of surface seawater in Rangat Bay, Middle Andaman, Andaman Islands (India). The bay experiences tidal variations. Perhaps physicochemical properties of seawater in Rangat Bay were found not to vary significantly. The concentration of faecal streptococci was high (2.2 × 103 CFU/100 mL) at creek and harbour area, whereas total coliforms were high (7.0 × 102 CFU/100 mL) at mangrove area. Similarly, total heterotrophic bacterial concentration was high (5.92 × 104 CFU/100 mL) in mangrove and harbour area. The Vibrio cholerae and Vibrio parahaemolyticus concentration was high (4.2 × 104 CFU/100 mL and 9 × 103 CFU/100 mL) at open sea. Cluster analysis showed grouping of stations in different tidal periods. The spatial maps clearly depicted the bacterial concentration pattern in the bay. The combined approach of multivariate analysis and spatial mapping techniques was proved to be useful in the current study.

Bayesian methods for estimating GEBVs of threshold traits

PubMed Central

Wang, C-L; Ding, X-D; Wang, J-Y; Liu, J-F; Fu, W-X; Zhang, Z; Yin, Z-J; Zhang, Q

2013-01-01

Estimation of genomic breeding values is the key step in genomic selection (GS). Many methods have been proposed for continuous traits, but methods for threshold traits are still scarce. Here we introduced threshold model to the framework of GS, and specifically, we extended the three Bayesian methods BayesA, BayesB and BayesCπ on the basis of threshold model for estimating genomic breeding values of threshold traits, and the extended methods are correspondingly termed BayesTA, BayesTB and BayesTCπ. Computing procedures of the three BayesT methods using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the benefit of the presented methods in accuracy with the genomic estimated breeding values (GEBVs) for threshold traits. Factors affecting the performance of the three BayesT methods were addressed. As expected, the three BayesT methods generally performed better than the corresponding normal Bayesian methods, in particular when the number of phenotypic categories was small. In the standard scenario (number of categories=2, incidence=30%, number of quantitative trait loci=50, h2=0.3), the accuracies were improved by 30.4%, 2.4%, and 5.7% points, respectively. In most scenarios, BayesTB and BayesTCπ generated similar accuracies and both performed better than BayesTA. In conclusion, our work proved that threshold model fits well for predicting GEBVs of threshold traits, and BayesTCπ is supposed to be the method of choice for GS of threshold traits. PMID:23149458

Modelling green macroalgal blooms on the coasts of Brittany, France to enhance water quality management

NASA Astrophysics Data System (ADS)

Perrot, Thierry; Rossi, Nadège; Ménesguen, Alain; Dumas, Franck

2014-04-01

First recorded in the 1970s, massive green macroalgal blooms have since become an annual recurrence in Brittany, France. Eutrophication (in particular to anthropogenic nitrogen input) has been identified as the main factor controlling Ulva ‘green tide' events. In this study, we modelled Ulva proliferation using a two-dimensional model by coupling hydrodynamic and biological models (coined ‘MARS-Ulves') for five sites along the Brittany coastline (La Fresnaye Bay, Saint-Brieuc Bay, Lannion Bay, Guissény Bay and Douarnenez Bay). Calibration of the biological model was mainly based on the seasonal variation of the maximum nitrogen uptake rate (VmaxN) and the half-saturation constant for nitrogen (KN) to reproduce the internal nutrient quotas measured in situ for each site. In each bay, model predictions were in agreement with observed algal coverage converted into biomass. A numerical tracking method was implemented to identify the contribution of the rivers that empty into the study bays, and scenarios of decreases in nitrate concentration in rivers were simulated. Results from numerical nitrogen tracking highlighted the main nitrogen sources of green tides and also showed that each river contributes locally to green tides. In addition, dynamic modelling showed that the nitrate concentrations in rivers must be limited to between 5 and 15 mg l- 1, depending on the bay, to reduce Ulva biomass by half on the coasts. The three-step methodology developed in this study (analysing total dissolved inorganic nitrogen flux from rivers, tracking nitrogen sources in Ulva and developing scenarios for reducing nitrogen) provides qualitative and quantitative guidelines for stakeholders to define specific nitrogen reduction targets for better environmental management of water quality.

Treatment effect heterogeneity for univariate subgroups in clinical trials: Shrinkage, standardization, or else

PubMed Central

Varadhan, Ravi; Wang, Sue-Jane

2016-01-01

Treatment effect heterogeneity is a well-recognized phenomenon in randomized controlled clinical trials. In this paper, we discuss subgroup analyses with prespecified subgroups of clinical or biological importance. We explore various alternatives to the naive (the traditional univariate) subgroup analyses to address the issues of multiplicity and confounding. Specifically, we consider a model-based Bayesian shrinkage (Bayes-DS) and a nonparametric, empirical Bayes shrinkage approach (Emp-Bayes) to temper the optimism of traditional univariate subgroup analyses; a standardization approach (standardization) that accounts for correlation between baseline covariates; and a model-based maximum likelihood estimation (MLE) approach. The Bayes-DS and Emp-Bayes methods model the variation in subgroup-specific treatment effect rather than testing the null hypothesis of no difference between subgroups. The standardization approach addresses the issue of confounding in subgroup analyses. The MLE approach is considered only for comparison in simulation studies as the “truth” since the data were generated from the same model. Using the characteristics of a hypothetical large outcome trial, we perform simulation studies and articulate the utilities and potential limitations of these estimators. Simulation results indicate that Bayes-DS and Emp-Bayes can protect against optimism present in the naïve approach. Due to its simplicity, the naïve approach should be the reference for reporting univariate subgroup-specific treatment effect estimates from exploratory subgroup analyses. Standardization, although it tends to have a larger variance, is suggested when it is important to address the confounding of univariate subgroup effects due to correlation between baseline covariates. The Bayes-DS approach is available as an R package (DSBayes). PMID:26485117

Yaquina Bay, Oregon, Intertidal Sediment Temperature Database, 1998 - 2006.

EPA Science Inventory

Detailed, long term sediment temperature records were obtained and compiled in a database to determine the influence of daily, monthly, seasonal and annual temperature variation on eelgrass distribution across the intertidal habitat in Yaquina Bay, Oregon. Both currently and hi...

Weighted Regressions on Time, Discharge, and Season (WRTDS), with an application to Chesapeake Bay River inputs

USGS Publications Warehouse

Hirsch, Robert M.; Moyer, Douglas; Archfield, Stacey A.

2010-01-01

A new approach to the analysis of long-term surface water-quality data is proposed and implemented. The goal of this approach is to increase the amount of information that is extracted from the types of rich water-quality datasets that now exist. The method is formulated to allow for maximum flexibility in representations of the long-term trend, seasonal components, and discharge-related components of the behavior of the water-quality variable of interest. It is designed to provide internally consistent estimates of the actual history of concentrations and fluxes as well as histories that eliminate the influence of year-to-year variations in streamflow. The method employs the use of weighted regressions of concentrations on time, discharge, and season. Finally, the method is designed to be useful as a diagnostic tool regarding the kinds of changes that are taking place in the watershed related to point sources, groundwater sources, and surface-water nonpoint sources. The method is applied to datasets for the nine large tributaries of Chesapeake Bay from 1978 to 2008. The results show a wide range of patterns of change in total phosphorus and in dissolved nitrate plus nitrite. These results should prove useful in further examination of the causes of changes, or lack of changes, and may help inform decisions about future actions to reduce nutrient enrichment in the Chesapeake Bay and its watershed.

Diurnal and Intra-Annual Variations in Greenhouse Gases at Fixed Sites in the San Francisco Bay Area

NASA Astrophysics Data System (ADS)

Newman, S.; Guha, A.; Martien, P. T.; Bower, J.; Perkins, I.; Randall, S.; Young, A.; Stevenson, E.; Hilken, H.

2017-12-01

The Bay Area Air Quality Management District, the San Francisco Bay Area's air quality regulatory agency, has set a goal to reduce the region's greenhouse gas (GHG) emissions to 80% below 1990 levels by 2050, consistent with the State of California's climate goals. Recently, the Air District's governing board adopted a 2017 Clean Air Plan which lays out the agency's vision and includes actions to put the region on a path towards achieving the 2050 goal while also reducing air pollution and related health impacts. The Plan includes GHG rule-making efforts, policy initiatives, local government partnerships, outreach, grants, and incentives, encompassing over 250 specific implementation actions across all economic sectors to effect ambitious emission reductions in the region. To track trends in atmospheric observations of GHGs and associated species and monitor changes in regional emission patterns, the Air District has established a fixed site network (CO2, CH4, CO) of one generally upwind site (Bodega Bay - on the coast north of Marin County) and three receptor sites (Bethel Island - east of the major refineries, in the Sacramento River Delta; Livermore - east of the bulk of the East Bay cities; and San Martin - south of the major city of San Jose). Having collected over a year of data for each of the fixed sites, the Air District is now investigating spatial and temporal variations in GHG emissions. Concentrating on variations in diurnal cycles, we see the commonly observed pattern of seasonal changes in diurnal amplitude at all sites, with larger variations during the winter than the summer, consistent with seasonally varying daily changes in planetary boundary layer heights. Investigations explore the weekday/weekend effect on the diurnal patterns and the effect of seasonal wind direction changes on the intra-annual variations of the local enhancements. The Air District is beginning to investigate the ways in which the fixed site network reflects the dominant upwind GHG emissions.

Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient.

PubMed

Nunes, Vera L; Beaumont, Mark A; Butlin, Roger K; Paulo, Octávio S

2011-01-01

Identification of loci with adaptive importance is a key step to understand the speciation process in natural populations, because those loci are responsible for phenotypic variation that affects fitness in different environments. We conducted an AFLP genome scan in populations of ocellated lizards (Lacerta lepida) to search for candidate loci influenced by selection along an environmental gradient in the Iberian Peninsula. This gradient is strongly influenced by climatic variables, and two subspecies can be recognized at the opposite extremes: L. lepida iberica in the northwest and L. lepida nevadensis in the southeast. Both subspecies show substantial morphological differences that may be involved in their local adaptation to the climatic extremes. To investigate how the use of a particular outlier detection method can influence the results, a frequentist method, DFDIST, and a Bayesian method, BayeScan, were used to search for outliers influenced by selection. Additionally, the spatial analysis method was used to test for associations of AFLP marker band frequencies with 54 climatic variables by logistic regression. Results obtained with each method highlight differences in their sensitivity. DFDIST and BayeScan detected a similar proportion of outliers (3-4%), but only a few loci were simultaneously detected by both methods. Several loci detected as outliers were also associated with temperature, insolation or precipitation according to spatial analysis method. These results are in accordance with reported data in the literature about morphological and life-history variation of L. lepida subspecies along the environmental gradient. © 2010 Blackwell Publishing Ltd.

Flyway-scale variation in plasma triglyceride levels as an index of refueling rate in spring-migrating western sandpipers (Calidris mauri)

USGS Publications Warehouse

Williams, T.D.; Warnock, N.; Takekawa, John Y.; Bishop, M.A.

2007-01-01

We combined radiotelemetry, plasma metabolite analyses, and macro-invertebrate prey sampling to investigate variation in putative fattening rates (estimated as plasma triglyceride levels) at the flyway scale in Western Sandpipers (Calidris mauri) migrating between Punta Banda, Mexico (31°N), and Hartney Bay, Alaska (60°N), a distance of 4,240 km. Birds were caught at a wintering site (San Francisco Bay) and eight stopover sites along this Pacific Flyway. Body mass was higher in females than in males at six sites, but variation was not correlated with latitude for either sex, and the relationship of change in mass by date within sites was uninformative with regard to possible latitudinal variation in fattening rates. At San Francisco Bay, triglyceride levels were higher in the spring than in the winter. Mean plasma triglyceride varied among stopover sites, and there was a significant linear trend of increasing triglyceride levels with latitude as birds migrated north. At San Francisco Bay, length of stay was negatively related to triglyceride levels. However, plasma triglyceride levels at wintering or initial stopover sites (San Francisco and Punta Banda) did not predict individual variation in subsequent rates of travel during migration. We found no significant relationship between triglyceride levels and prey biomass at different stopover sites, which suggests that the latitudinal pattern is not explained by latitudinal changes in food availability. Rather, we suggest that differences in physiology of migratory birds at southern versus northern stopover sites or behavioral differences may allow birds to sustain higher fattening rates closer to the breeding grounds.

Qualitative and numerical analyses of the effects of river inflow variations on mixing diagrams in estuaries

USGS Publications Warehouse

Cifuentes, L.A.; Schemel, L.E.; Sharp, J.H.

1990-01-01

The effects of river inflow variations on alkalinity/salinity distributions in San Francisco Bay and nitrate/salinity distributions in Delaware Bay are described. One-dimensional, advective-dispersion equations for salinity and the dissolved constituents are solved numerically and are used to simulate mixing in the estuaries. These simulations account for time-varying river inflow, variations in estuarine cross-sectional area, and longitudinally varying dispersion coefficients. The model simulates field observations better than models that use constant hydrodynamic coefficients and uniform estuarine geometry. Furthermore, field observations and model simulations are consistent with theoretical 'predictions' that the curvature of propery-salinity distributions depends on the relation between the estuarine residence time and the period of river concentration variation. ?? 1990.

Chesapeake Bay Low Freshwater Inflow Study.

DTIC Science & Technology

1984-09-01

Flooding Study. The Chesapeake Bay The initial phase of the overall program Study Summary Report includes a de- involved the inventory and assessment... inventory of Chesapeake Bay’s water out put is expected to steadily increase, priority, and related land resources and an iden- There is authorized to be...daily, tation Studies. The final stages of the known, there is sufficient knowledge of seasonal, and yearly variations in salin- planning process

Spatiotemporal patterns of phytoplankton composition and abundance in the Maryland Coastal Bays: The influence of freshwater discharge and anthropogenic activities

NASA Astrophysics Data System (ADS)

Oseji, Ozuem F.; Chigbu, Paulinus; Oghenekaro, Efeturi; Waguespack, Yan; Chen, Nianhong

2018-07-01

The spatial and temporal variations in phytoplankton abundance and community structure in the northern and southern parts of the Maryland Coastal Bays (MCBs) that differ in anthropogenic activities and hydrological characteristics were studied in 2012 and 2013 using photosynthetic pigments as biomarkers. Phytoplankton pigment biomass and diversity were generally higher in the northern bays that receive high nutrient input from St. Martin River, than in the southern bays where nutrient levels were comparatively low. Sites close to the mouths of tributaries in northern and southern bays had higher nutrient levels, which favored the development of dinoflagellates, and nano- and picophytoplankton, than sites closer to the inlets. The microplankton dominated the phytoplankton community in spring (>90%) and decreased in relative abundance into fall (<60%) whereas nanoplankton peaked in summer or fall. Picoplankton relative abundance increased from late spring (<10%, March 2012 & 2013) to summer (40%, July 2012 and August 2013) and was correlated positively with NH4+ and negatively with salinity. The observed spatial and seasonal patterns of phytoplankton relative abundance and diversity are likely due to changes in nutrient concentrations and ratios, driven by variations in freshwater discharge, and selective grazing of phytoplankton. Water quality management in the MCBs should continue to focus on reducing nutrient inputs into the bays.

Occurance and survival of Vibrio alginolyticus in Tamouda Bay (Morocco).

PubMed

Sabir, M; Cohen, N; Boukhanjer, A; Ennaji, M M

2011-10-15

The objectives of this study were to investigate the spatial and seasonal fluctuations of Vibrio alginolyticus in marine environment of the Tamouda Bay on the Mediterranean coast of Morocco and to determine the dominant factors of the environment that govern these fluctuations. The samples (sea water, plankton, shellfish and sediment) were collected fortnightly for two years from three study sites on the coast Tamouda Bay in northern Morocco. The charge of Vibrio alginolyticus is determined by MPN method. The physicochemical parameters including temperature of sea water, pH, salinity, turbidity and chlorophyll a concentration were determined. Analysis of variance of specific variables and several principal component analyses showed that the temperature of seawater is the major determinant of seasonal distribution of Vibrio alginolyticus. The results showed a positive linear correlation between Vibrio alginolyticus and the water temperature, pH, turbidity and chlorophyll a. Similarly, there are seasonal variations and spatial of Vibrio alginolyticus in marine environment of the Tamouda bay and the highest concentrations were recorded in both years of study during the warm season whereas it was minimal during the cold season. Linear positive correlation was recorded between Vibrio alginolyticus populations in all ecological types of samples studied.

Genomic prediction using an iterative conditional expectation algorithm for a fast BayesC-like model.

PubMed

Dong, Linsong; Wang, Zhiyong

2018-06-11

Genomic prediction is feasible for estimating genomic breeding values because of dense genome-wide markers and credible statistical methods, such as Genomic Best Linear Unbiased Prediction (GBLUP) and various Bayesian methods. Compared with GBLUP, Bayesian methods propose more flexible assumptions for the distributions of SNP effects. However, most Bayesian methods are performed based on Markov chain Monte Carlo (MCMC) algorithms, leading to computational efficiency challenges. Hence, some fast Bayesian approaches, such as fast BayesB (fBayesB), were proposed to speed up the calculation. This study proposed another fast Bayesian method termed fast BayesC (fBayesC). The prior distribution of fBayesC assumes that a SNP with probability γ has a non-zero effect which comes from a normal density with a common variance. The simulated data from QTLMAS XII workshop and actual data on large yellow croaker were used to compare the predictive results of fBayesB, fBayesC and (MCMC-based) BayesC. The results showed that when γ was set as a small value, such as 0.01 in the simulated data or 0.001 in the actual data, fBayesB and fBayesC yielded lower prediction accuracies (abilities) than BayesC. In the actual data, fBayesC could yield very similar predictive abilities as BayesC when γ ≥ 0.01. When γ = 0.01, fBayesB could also yield similar results as fBayesC and BayesC. However, fBayesB could not yield an explicit result when γ ≥ 0.1, but a similar situation was not observed for fBayesC. Moreover, the computational speed of fBayesC was significantly faster than that of BayesC, making fBayesC a promising method for genomic prediction.

Long-term simulation of vertical transport process and its impact on bottom DO in Chesapeake Bay

NASA Astrophysics Data System (ADS)

Du, J.; Shen, J.

2016-02-01

Hypoxia in coastal waters is a widespread phenomenon that appears to have been growing globally for at least 60 years. The fact that physical transport processes and biological processes are equally important in determining the bottom DO in Chesapeake Bay is commonly agreed. However, the quantitative impact of physical transport processes is rarely documented. In this study, we use a timescale, vertical exchange time (VET), to quantify the impact of all physical processes that might have on the bottom DO. Simulation of VET from 1985 to 2012 is conducted and the monthly observed DO data along the deep channel in the Bay's main stem is collected. A conceptual bottom DO budget model is applied, using the VET to quantify the physical condition and net oxygen consumption rate to quantify biological activities. The DO budget model results show that the interannual variations of physical conditions accounts for 88.8% of the interannual variations of observed DO. The high similarity between the VET spatial pattern and the observed DO suggests that physical processes play a key role in regulating the DO condition. Model results also show that long-term VET has a slight increase in summer, but no statistically significant trend is found. Correlations among southerly wind strength, North Atlantic Oscillation index, and VET demonstrate that the physical condition in the Chesapeake Bay is highly controlled by the large-scale climate variation. The relationship is most significant during the summer, when the southerly wind dominates throughout the Chesapeake Bay.

Seasonal variations and sources of sedimentary organic carbon in Tokyo Bay.

PubMed

Kubo, Atsushi; Kanda, Jota

2017-01-30

Total organic carbon (TOC), total nitrogen (TN) contents, their stable C and N isotope ratio (δ 13 C and δ 15 N), and chlorophyll a ([Chl a] sed ) of surface sediments were investigated monthly to identify the seasonal variations and sources of organic matter in Tokyo Bay. The sedimentary TOC (TOC sed ) and TN (TN sed ) contents, and the sedimentary δ 13 C and δ 15 N (δ 13 C sed and δ 15 N sed ) values were higher in summer than other seasons. The seasonal variations were controlled by high primary production in the water column and hypoxic water in the bottom water during summer. The fraction of terrestrial and marine derived organic matter was estimated by Bayesian mixing model using stable isotope data and TOC/TN ratio. Surface sediments in Tokyo Bay are dominated by marine derived organic matter, which accounts for about 69±5% of TOC sed . Copyright © 2016 Elsevier Ltd. All rights reserved.

SEASONAL VARIATION IN THE BIOGEOCHEMICAL CYCLING OF SESTON IN GRAND TRAVERSE BAY, LAKE MICHIGAN. (R825151)

EPA Science Inventory

This study describes the biogeochemical cycling of seston in Grand Traverse Bay, Lake Michigan. Seston was characterized by carbon and nitrogen elemental and isotopic abundances. Fluorescence, temperature, light transmittance, and concentrations of dissolved inorganic nitrogen we...

Distributions and seasonal variations of dissolved carbohydrates in the Jiaozhou Bay, China

NASA Astrophysics Data System (ADS)

Yang, Gui-Peng; Zhang, Yan-Ping; Lu, Xiao-Lan; Ding, Hai-Bing

2010-06-01

Surface seawater samples were collected in the Jiaozhou Bay, a typical semi-closed basin located at the western part of the Shandong Peninsula, China, during four cruises. Concentrations of monosaccharides (MCHO), polysaccharides (PCHO) and total dissolved carbohydrates (TCHO) were measured with the 2,4,6-tripyridyl- s-triazine spectroscopic method. Concentrations of TCHO varied from 10.8 to 276.1 μM C for all samples and the ratios of TCHO to dissolved organic carbon (DOC) ranged from 1.1 to 67.9% with an average of 10.1%. This result indicated that dissolved carbohydrates were an important constituent of DOC in the surface seawater of the Jiaozhou Bay. In all samples, the concentrations of MCHO ranged from 2.9 to 65.9 μM C, comprising 46.1 ± 16.6% of TCHO on average, while PCHO ranged from 0.3 to 210.2 μM C, comprising 53.9 ± 16.6% of TCHO on average. As a major part of dissolved carbohydrates, the concentrations of PCHO were higher than those of MCHO. MCHO and PCHO accumulated in January and July, with minimum average concentration in April. The seasonal variation in the ratios of TCHO to DOC was related to water temperature, with high values in January and low values in July and October. The concentrations of dissolved carbohydrates displayed a decreasing trend from the coastal to the central areas. Negative correlations between concentrations of TCHO and salinity in July suggested that riverine input around the Jiaozhou Bay had an important effect on the concentrations of dissolved carbohydrates in surface seawater. The pattern of distributions of MCHO and PCHO reported in this study added to the global picture of dissolved carbohydrates distribution.

Seasonal and inter-annual variation in occurrence and biomass of rooted macrophytes and drift algae in shallow bays

NASA Astrophysics Data System (ADS)

Berglund, J.; Mattila, J.; Rönnberg, O.; Heikkilä, J.; Bonsdorff, E.

2003-04-01

Submerged rooted macrophytes and drift algae were studied in shallow (0-1 m) brackish soft-bottom bays in the Åland Islands, N Baltic Sea, in 1997-2000. The study was performed by aerial photography and ground-truth sampling and the compatibility of the methods was evaluated. The study provided quantitative results on seasonal and inter-annual variation in growth, distribution and biomass of submerged macrophytes and drift algae. On an average, 18 submerged macrophyte species occurred in the studied bays. The most common species, by weight and occurrence, were Chara aspera, Cladophora glomerata, Pilayella littoralis and Potamogeton pectinatus. Filamentous green algae constituted 45-70% of the biomass, charophytes 25-40% and vascular plants 3-18%. A seasonal pattern with a peak in biomass in July-August was found and the mean biomass was negatively correlated with exposure. There were statistically significant differences in coverage among years, and among levels of exposure. The coverage was highest when exposure was low. Both sheltered and exposed bays were influenced by drift algae (30 and 60% occurrence in July-August) and there was a positive correlation between exposure and occurrence of algal accumulations. At exposed sites, most of the algae had drifted in from other areas, while at sheltered ones they were mainly of local origin. Data obtained by aerial photography and ground-truth sampling showed a high concordance, but aerial photography gave a 9% higher estimate than the ground-truth samples. The results can be applied in planning of monitoring and management strategies for shallow soft-bottom areas under potential threat of drift algae.

Latitudinal variation in population structure of wintering Pacific Black Brant

USGS Publications Warehouse

Schamber, J.L.; Sedinger, J.S.; Ward, D.H.; Hagmeier, K.R.

2007-01-01

Latitudinal variation in population structure during the winter has been reported in many migratory birds, but has been documented in few species of waterfowl. Variation in environmental and social conditions at wintering sites can potentially influence the population dynamics of differential migrants. We examined latitudinal variation in sex and age classes of wintering Pacific Black Brant (Branta bernicla nigricans). Brant are distributed along a wide latitudinal gradient from Alaska to Mexico during the winter. Accordingly, migration distances for brant using different wintering locations are highly variable and winter settlement patterns are likely associated with a spatially variable food resource. We used resightings of brant banded in southwestern Alaska to examine sex and age ratios of birds wintering at Boundary Bay in British Columbia, and at San Quintin Bay, Ojo de Liebre Lagoon, and San Ignacio Lagoon in Baja California from 1998 to 2000. Sex ratios were similar among wintering locations for adults and were consistent with the mating strategy of geese. The distribution of juveniles varied among wintering areas, with greater proportions of juveniles observed at northern (San Quintin Bay and Ojo de Liebre Lagoon) than at southern (San Ignacio Lagoon) locations in Baja California. We suggest that age-related variation in the winter distribution of Pacific Black Brant is mediated by variation in productivity among individuals at different wintering locations and by social interactions among wintering family groups.

Baleen whale ecology and feeding habitat use in the Bay of Fundy, Canada

NASA Astrophysics Data System (ADS)

Davies, K. T. A.; Brown, M.; Taggart, C. T.

2016-02-01

The Bay of Fundy on the east coast of Canada contains a rich supply of zooplankton and fish that provide food for diverse baleen whales. Endangered North Atlantic right whales and other large baleen whales have been monitored in the Bay of Fundy at least weekly during every summer since the 1980s. Over the most recent years, significant declines in sightings and residency of the right whales have been observed in this habitat; hypothetically indicative of a substantial and multi-year reduction in food supply. Whether concurrent changes in other baleen whales and, by inference, their respective food supplies have also occurred is unknown. This study quantifies changes in baleen whale ecology in the Bay over three decades with a focus on comparing (1) recent declines in right whale sightings to long-term historical trends, and (2) variation in right whale sightings to other large baleen whale species who share similar zooplankton food sources (e.g., sei whales) or rely on different food sources (e.g., fin, humpback). First, survey effort is reconstructed as survey track-length and as time-on-effort, and the space-time variations in effort are quantified. Then, variation in whale density indices and residency among surveys and survey-years are examined through effort-corrected sightings of all baleen whale species, as well as effort-corrected sightings of photo-identified right whale individuals. Results are then interpreted within the context of the oceanographic and food supply variation in the habitat.

Lateral variation in crustal and mantle structure in Bay of Bengal based on surface wave data

NASA Astrophysics Data System (ADS)

Kumar, Amit; Mukhopadhyay, Sagarika; Kumar, Naresh; Baidya, P. R.

2018-01-01

Surface waves generated by earthquakes that occurred near Sumatra, Andaman-Nicobar Island chain and Sunda arc are used to estimate crustal and upper mantle S wave velocity structure of Bay of Bengal. Records of these seismic events at various stations located along the eastern coast of India and a few stations in the north eastern part of India are selected for such analysis. These stations lie within regional distance of the selected earthquakes. The selected events are shallow focused with magnitude greater than 5.5. Data of 65, 37, 36, 53 and 36 events recorded at Shillong, Bokaro, Visakhapatnam, Chennai and Trivandrum stations respectively are used for this purpose. The ray paths from the earthquake source to the recording stations cover different parts of the Bay of Bengal. Multiple Filtering Technique (MFT) is applied to compute the group velocities of surface waves from the available data. The dispersion curves thus obtained for this data set are within the period range of 15-120 s. Joint inversion of Rayleigh and Love wave group velocity is carried out to obtain the subsurface information in terms of variation of S wave velocity with depth. The estimated S wave velocity at a given depth and layer thickness can be considered to be an average value for the entire path covered by the corresponding ray paths. However, we observe variation in the value of S wave velocity and layer thickness from data recorded at different stations, indicating lateral variation in these two parameters. Thick deposition of sediments is observed along the paths followed by surface waves to Shillong and Bokaro stations. Sediment thickness keeps on decreasing as the surface wave paths move further south. Based on velocity variation the sedimentary layer is further divided in to three parts; on top lay unconsolidated sediment, underlain by consolidated sediment. Below this lies a layer which we consider as meta-sediments. The thickness and velocity of these layers decrease from north to south. The crustal material has higher velocity at the southern part compared to that at the northern part of Bay of Bengal indicating that it changes from more oceanic type in the southern part of the Bay to more continental type to its north. Both Moho and lithosphere - asthenosphere boundary (LAB) dips gently towards north. Thicknesses of both lithosphere and asthenosphere also increase in the same direction. The mantle structure shows complex variation from south to north indicating possible effect of repeated changes in type of tectonic activity in the Bay of Bengal.

Radiocarbon dating, chronologic framework, and changes in accumulation rates of holocene estuarine sediments from Chesapeake Bay

USGS Publications Warehouse

Colman, Steven M.; Baucom, P.C.; Bratton, J.F.; Cronin, T. M.; McGeehin, J.P.; Willard, D.; Zimmerman, A.R.; Vogt, P.R.

2002-01-01

Rapidly accumulating Holocene sediments in estuaries commonly are difficult to sample and date. In Chesapeake Bay, we obtained sediment cores as much as 20 m in length and used numerous radiocarbon ages measured by accelarator mass spectrometry methods to provide the first detailed chronologies of Holocene sediment accumulation in the bay. Carbon in these sediments is a complex mixture of materials from a variety of sources. Analyses of different components of the sediments show that total organic carbon ages are largely unreliable, because much of the carbon (including coal) has been transported to the bay from upstream sources and is older than sediments in which it was deposited. Mollusk shells (clams, oysters) and foraminifera appear to give reliable results, although reworking and burrowing are potential problems. Analyses of museum specimens collected alive before atmospheric nuclear testing suggest that the standard reservoir correction for marine samples is appropriate for middle to lower Chesapeake Bay. The biogenic carbonate radiocarbon ages are compatible with 210 Pb and 137 Cs data and pollen stratigraphy from the same sites. Post-settlement changes in sediment transport and accumulation is an important environmental issue in many estuaries, including the Chesapeake. Our data show that large variations in sediment mass accumulation rates occur among sites. At shallow water sites, local factors seem to control changes in accumulation rates with time. Our two relatively deep-water sites in the axial channel of the bay have different long-term average accumulation rates, but the history of sediment accumulation at these sites appears to reflect overall conditions in the bay. Mass accumulation rates at the two deep-water sites rapidly increased by about fourfold coincident with widespread land clearance for agriculture in the Chesapeake watershed.

Regional contamination versus regional dietary differences: Understanding geographic variation in brominated and chlorinated contaminant levels in polar bears

USGS Publications Warehouse

McKinney, M.A.; Letcher, R.J.; Aars, Jon; Born, E.W.; Branigan, M.; Dietz, R.; Evans, T.J.; Gabrielsen, G.W.; Muir, D.C.G.; Peacock, E.; Sonne, C.

2011-01-01

The relative contribution of regional contamination versus dietary differences to geographic variation in polar bear (Ursus maritimus) contaminant levels is unknown. Dietary variation between Alaska Canada, East Greenland, and Svalbard subpopulations was assessed by muscle nitrogen and carbon stable isotope (?? 15N, ?? 13C) and adipose fatty acid (FA) signatures relative to their main prey (ringed seals). Western and southern Hudson Bay signatures were characterized by depleted ?? 15N and ??13C, lower proportions of C20 and C22 monounsaturated FAs and higher proportions of C18 and longer chain polyunsaturated FAs. East Greenland and Svalbard signatures were reversed relative to Hudson Bay. Alaskan ?? 2011 American Chemical Society.

Age and growth of round gobies in Lake Huron: Implications for food web dynamics

USGS Publications Warehouse

Duan, You J.; Madenjian, Charles P.; Xie, Cong X.; Diana, James S.; O'Brien, Timothy P.; Zhao, Ying M.; He, Ji X.; Farha, Steve A.; Huo, Bin

2016-01-01

Although the round goby (Neogobius melanostomus) has become established throughout the Laurentian Great Lakes, information is scarce on spatial variation in round goby growth between and within lakes. Based on a sample of 754 specimens captured in 2014, age, growth, and mortality of round gobies at four locations in Lake Huron were assessed via otolith analysis. Total length (TL) of round gobies ranged from 44 to 111 mm for Saginaw Bay, from 45 to 115 mm for Rockport, from 50 to 123 mm for Hammond Bay, and from 51 to 118 mm for Thunder Bay. Estimated ages of round gobies ranged from 2 to 5 years for Saginaw Bay, from 2 to 6 years for Rockport, and from 2 to 7 years for Hammond Bay and Thunder Bay. Sex-specific, body–otolith relationships were used to back-calculate total lengths at age, which were then fitted to von Bertalanffy growth models. For each sex, round goby growth showed significant spatial variation among the four locations within Lake Huron. At all four locations in Lake Huron, males grew significantly faster than females and attained a larger asymptotic length than females. Annual mortality rate estimates were high (62 to 85%), based on catch-curve analysis, suggesting that round gobies may be under predatory control in Lake Huron.

Application of empirical Bayes methods to predict the rate of decline in ERG at the individual level among patients with retinitis pigmentosa.

PubMed

Qiu, Weiliang; Sandberg, Michael A; Rosner, Bernard

2018-05-31

Retinitis pigmentosa is one of the most common forms of inherited retinal degeneration. The electroretinogram (ERG) can be used to determine the severity of retinitis pigmentosa-the lower the ERG amplitude, the more severe the disease is. In practice for career, lifestyle, and treatment counseling, it is of interest to predict the ERG amplitude of a patient at a future time. One approach is prediction based on the average rate of decline for individual patients. However, there is considerable variation both in initial amplitude and in rate of decline. In this article, we propose an empirical Bayes (EB) approach to incorporate the variations in initial amplitude and rate of decline for the prediction of ERG amplitude at the individual level. We applied the EB method to a collection of ERGs from 898 patients with 3 or more visits over 5 or more years of follow-up tested in the Berman-Gund Laboratory and observed that the predicted values at the last (kth) visit obtained by using the proposed method based on data for the first k-1 visits are highly correlated with the observed values at the kth visit (Spearman correlation =0.93) and have a higher correlation with the observed values than those obtained based on either the population average decline rate or those obtained based on the individual decline rate. The mean square errors for predicted values obtained by the EB method are also smaller than those predicted by the other methods. Copyright © 2018 John Wiley & Sons, Ltd.

Diurnal variation in rates of calcification and carbonate sediment dissolution in Florida Bay

USGS Publications Warehouse

Yates, K.K.; Halley, R.B.

2006-01-01

Water quality and circulation in Florida Bay (a shallow, subtropical estuary in south Florida) are highly dependent upon the development and evolution of carbonate mud banks distributed throughout the Bay. Predicting the effect of natural and anthropogenic perturbations on carbonate sedimentation requires an understanding of annual, seasonal, and daily variations in the biogenic and inorganic processes affecting carbonate sediment precipitation and dissolution. In this study, net calcification rates were measured over diurnal cycles on 27 d during summer and winter from 1999 to 2003 on mud banks and four representative substrate types located within basins between mud banks. Substrate types that were measured in basins include seagrass beds of sparse and intermediate density Thalassia sp., mud bottom, and hard bottom communities. Changes in total alkalinity were used as a proxy for calcification and dissolution. On 22 d (81%), diurnal variation in rates of net calcification was observed. The highest rates of net carbonate sediment production (or lowest rates of net dissolution) generally occurred during daylight hours and ranged from 2.900 to -0.410 g CaCO3 m-2 d-1. The lowest rates of carbonate sediment production (or net sediment dissolution) occurred at night and ranged from 0.210 to -1.900 g CaCO3 m -2 night-1. During typical diurnal cycles, dissolution during the night consumed an average of 29% of sediment produced during the day on banks and 68% of sediment produced during the day in basins. Net sediment dissolution also occurred during daylight, but only when there was total cloud cover, high turbidity, or hypersalinity. Diurnal variation in calcification and dissolution in surface waters and surface sediments of Florida Bay is linked to cycling of carbon dioxide through photosynthesis and respiration. Estimation of long-term sediment accumulation rates from diurnal rates of carbonate sediment production measured in this study indicates an overall average accumulation rate for Florida Bay of 8.7 cm 1000 yr-1 and suggests that sediment dissolution plays a more important role than sediment transport in loss of sediment from Florida Bay. ?? 2006 Estuarine Research Federation.

Numerical study of water residence time in the Yueqing Bay based on the eulerian approach

NASA Astrophysics Data System (ADS)

Ying, Chao; Li, Xinwen; Liu, Yong; Yao, Wenwei; Li, Ruijie

2018-05-01

The Yueqing Bay was a semi-enclosed bay located in the southeast of Zhejiang Province, China. Due to substantial anthropogenic influences since 1964, the water quality in the bay had deteriorated seriously. Thus urgent measures should be taken to protect the water body. In this study, a numerical model was calibrated for water surface elevation and tidal current from August 14 to August 26, 2011. Comparisons of observed and simulated data showed that the model reproduced the tidal range and phase and the variations of current at different periods fairly well. The calibrated model was then applied to investigate spatial flushing pattern of the bay by calculation of residence time. The results obtained from a series of model experiments demonstrated that the residence time increased from 10 day at the bay mouth to more than 70 day at the upper bay. The average residence time over the whole bay was 49.5 day. In addition, the adaptation of flushing homogeneity curve showed that the residence time in the bay varied smoothly. This study provides a numerical tool to quantify the transport timescale in Yueqing Bay and supports adaptive management of the bay by local authorities.

Generation of periodic intrusions at Suruga Bay when the Kuroshio follows a large meandering path

NASA Astrophysics Data System (ADS)

Katsumata, Takaaki

2016-07-01

We measured the vertical profiles of currents at the eastern mouth of the Suruga Bay using a moored acoustic Doppler current profiler (ADCP). Currents vertical profiles were found to be mostly barotropic in structure when intrusions occurred at the eastern mouth of the bay. Warm-water intrusions at the Suruga Bay and sea level elevations at the bay and at islands on the Izu Ridge located off the bay have the same period of 26 days. The temporal variation in the sea levels occurs in response to Kuroshio frontal waves, and the two phases are consistent. The sea level rise propagates from Hachijo Island to the Suruga Bay via Miyake Island and Kozu Island, i.e., from off the Suruga Bay to in or near the bay. The perturbation of the sea level along the Izu Ridge occurs as waves with a period of 26 days, a wavelength of 500 km, and a phase speed of 23 cm/sec. The propagated waves and those of the Kuroshio frontal waves have the same features. This means that the periodic inflows at the eastern mouth of the Suruga Bay are caused by the passage of Kuroshio frontal waves off the bay.

Decoupling the influence of biological and physical processes on the dissolved oxygen in the Chesapeake Bay

NASA Astrophysics Data System (ADS)

Du, Jiabi; Shen, Jian

2015-01-01

is instructive and essential to decouple the effects of biological and physical processes on the dissolved oxygen condition, in order to understand their contribution to the interannual variability of hypoxia in Chesapeake Bay since the 1980s. A conceptual bottom DO budget model is applied, using the vertical exchange time scale (VET) to quantify the physical condition and net oxygen consumption rate to quantify biological activities. By combining observed DO data and modeled VET values along the main stem of the Chesapeake Bay, the monthly net bottom DO consumption rate was estimated for 1985-2012. The DO budget model results show that the interannual variations of physical conditions accounts for 88.8% of the interannual variations of observed DO. The high similarity between the VET spatial pattern and the observed DO suggests that physical processes play a key role in regulating the DO condition. Model results also show that long-term VET has a slight increase in summer, but no statistically significant trend is found. Correlations among southerly wind strength, North Atlantic Oscillation index, and VET demonstrate that the physical condition in the Chesapeake Bay is highly controlled by the large-scale climate variation. The relationship is most significant during the summer, when the southerly wind dominates throughout the Chesapeake Bay. The seasonal pattern of the averaged net bottom DO consumption rate (B'20) along the main stem coincides with that of the chlorophyll-a concentration. A significant correlation between nutrient loading and B'20 suggests that the biological processes in April-May are most sensitive to the nutrient loading.

The Mid-Latitude Positive Bay and the MPB Index of Substorm Activity

NASA Astrophysics Data System (ADS)

McPherron, Robert L.; Chu, Xiangning

2017-03-01

Substorms are a major source of magnetic activity. At substorm expansion phase onset a westward current flows through the expanding aurora. This current is the ionospheric closure of the substorm current wedge produced by diversion of tail current along magnetic field lines. At low latitudes the field-aligned currents create a systematic pattern in the north (X) and east (Y) components of the surface magnetic field. The rise and decay in X is called a midlatitude positive bay whose start is a proxy for expansion onset. In this paper we describe a new index called the midlatitude positive bay index (MPB) which monitors the power in the substorm perturbations of X and Y. The index is obtained by removing the main field, storm time variations, and the solar quiet (Sq) variation from the measured field. These are estimated with spline fits and principal component analysis. The residuals of X and Y are high pass filtered to eliminate variations with period longer than 3 hours. The sum of squares of the X and Y power is determined at each of 35 midlatitude stations. The average power in night time stations is the MPB index. The index series is standardized and intervals above a fixed threshold are taken as possible bay signatures. Post processing constrains these to have reasonable values of rise time, strength, and duration. Minima in the index before and after the peak are taken as the start and end of the bay. The MPB and AL indices can be used to identify quiet intervals in the magnetic field.

Preliminary hydrodynamic analysis of landslide-generated waves in Tidal Inlet, Glacier Bay National Park, Alaska

USGS Publications Warehouse

Geist, Eric L.; Jakob, Matthias; Wieczoreck, Gerald F.; Dartnell, Peter

2003-01-01

A landslide block perched on the northern wall of Tidal Inlet, Glacier Bay National Park (Figure 1), has the potential to generate large waves in Tidal Inlet and the western arm of Glacier Bay if it were to fail catastrophically. Landslide-generated waves are a particular concern for cruise ships transiting through Glacier Bay on a daily basis during the summer months. The objective of this study is to estimate the range of wave amplitudes and periods in the western arm of Glacier Bay from a catastrophic landslide in Tidal Inlet. This study draws upon preliminary findings of a field survey by Wieczorek et al. (2003), and evaluates the effects of variations in landslide source parameters on the wave characteristics.

Polymorphism Thr160Thr in SRD5A1, involved in the progesterone metabolism, modifies postmenopausal breast cancer risk associated with menopausal hormone therapy.

PubMed

Hein, R; Abbas, S; Seibold, P; Salazar, R; Flesch-Janys, D; Chang-Claude, J

2012-01-01

Menopausal hormone therapy (MHT) is associated with an increased breast cancer risk in postmenopausal women, with combined estrogen-progestagen therapy posing a greater risk than estrogen monotherapy. However, few studies focused on potential effect modification of MHT-associated breast cancer risk by genetic polymorphisms in the progesterone metabolism. We assessed effect modification of MHT use by five coding single nucleotide polymorphisms (SNPs) in the progesterone metabolizing enzymes AKR1C3 (rs7741), AKR1C4 (rs3829125, rs17134592), and SRD5A1 (rs248793, rs3736316) using a two-center population-based case-control study from Germany with 2,502 postmenopausal breast cancer patients and 4,833 matched controls. An empirical-Bayes procedure that tests for interaction using a weighted combination of the prospective and the retrospective case-control estimators as well as standard prospective logistic regression were applied to assess multiplicative statistical interaction between polymorphisms and duration of MHT use with regard to breast cancer risk assuming a log-additive mode of inheritance. No genetic marginal effects were observed. Breast cancer risk associated with duration of combined therapy was significantly modified by SRD5A1_rs3736316, showing a reduced risk elevation in carriers of the minor allele (p (interaction,empirical-Bayes) = 0.006 using the empirical-Bayes method, p (interaction,logistic regression) = 0.013 using logistic regression). The risk associated with duration of use of monotherapy was increased by AKR1C3_rs7741 in minor allele carriers (p (interaction,empirical-Bayes) = 0.083, p (interaction,logistic regression) = 0.029) and decreased in minor allele carriers of two SNPs in AKR1C4 (rs3829125: p (interaction,empirical-Bayes) = 0.07, p (interaction,logistic regression) = 0.021; rs17134592: p (interaction,empirical-Bayes) = 0.101, p (interaction,logistic regression) = 0.038). After Bonferroni correction for multiple testing only SRD5A1_rs3736316 assessed using the empirical-Bayes method remained significant. Postmenopausal breast cancer risk associated with combined therapy may be modified by genetic variation in SRD5A1. Further well-powered studies are, however, required to replicate our finding.

Variations in the Nd isotope composition of Late Miocene to Early Pliocene glacially derived sediments in Prydz Bay, East Antarctica

NASA Astrophysics Data System (ADS)

Mabson, M.; Pierce, E. L.; Dale, C. L.; Williams, T.; Hemming, S. R.; van de Flierdt, T.; Cook, C.; Goldstein, S. L.

2010-12-01

Michelle Mabson (Howard University), Elizabeth Pierce (Lamont-Doherty Earth Observatory, Columbia University), Cathleen Doherty (Lamont-Doherty Earth Observatory, Columbia University), Trevor Williams (Lamont-Doherty Earth Observatory), Sidney Hemming (Lamont-Doherty Earth Observatory), Tina van de Flierdt (Imperial College London), Carys Cook (Imperial College London), Steve Goldstein (Lamont-Doherty Earth Observatory) Since initiation of major ice sheets on Antarctica at about 34 Ma, Antarctica has been a major player in global climate change. Understanding the response of the East Antarctic Ice Sheet to major climate changes through the Cenozoic has fundamental importance to both Earth Sciences and Society. Previous study of Nd isotope composition of sediments at Ocean Drilling Program (ODP) Site 1166 within Prydz Bay found evidence for variations of the Nd isotope composition between -15 to -30 epsilon units through this pre-glacial to glacial record (van de Flierdt et al., 2008, GRL). The Nd isotope composition of sediments provides an estimate for the average continental crust formation age of the sources. The sources around Prydz Bay have a wide range of formation ages, from Archean to Phanerozoic, so the areas which were being preferentially eroded can be inferred. This study seeks to contribute evidence for the local variations in provenance of sediments by extending the record of Nd isotope variations to ODP Site 739 in Prydz Bay. ODP Site 1165 has an unconformity that spans ~30-3 Ma. This part of the record is much more complete in ODP site 739, located about 200 km from the coast of Prydz Bay, probably more protected from ice stream erosion in the Prydz Channel. Because of its location we can conclude that the sediment deposited into this area is derived from the Lambert Glacier, and thus the variations in epsilon Nd will allow testing whether changes in the extent of this ice stream could lead to variations in the provenance of sediment carried by this ice. Recently Williams et al. (2010, EPSL) published evidence for dramatic changes in the sources of glacially derived sediments at ODP Site 1165, further offshore from Prydz Bay, at 7, 4.8 and 3.5 Ma. Their interpretation was based on the Ar-Ar ages of detrital hornblende grains, but samples taken across the 4.8 Ma event also showed an intriguing variation of the Nd isotope composition. The older part of the event includes a significant fraction of exotic Ar-Ar ages, but with epsilon Nd similar to the background values, while the younger part of the event shows a significant decrease in epsilon Nd but Ar-Ar of local origin. The specific goal of this study is to test the hypothesis that the shift to lower epsilon Nd in the 4.8 Ma ice rafting event is due to dynamical changes in the Prydz Bay sector of the East Antarctic ice sheet. Alternatively, the Lambert glacier may have retreated far enough to allow other sources in this sector to dominate the sediment composition in core 1165.

Baltimore Harbor and Channels Deepening Study; Chesapeake Bay Hydraulic Model Investigation.

DTIC Science & Technology

1982-02-01

neap-spring salinity vari- ability. Stations within the Patapsco River (Plates 78-90), and the Magothy River station (MA-I-1, Plate 74), immediately...to-base salinity variations are found at upper bay stations above the constriction at range CB-4. Only Magothy River sta MA-l, and sta CB-7-1 have...Across the bay at the western shore Magothy River sta MA-I-I (Plate 74) no appreciable plan-to-base salinity differences are found, although during

Linking dynamics of transport timescale and variations of hypoxia in the Chesapeake Bay

NASA Astrophysics Data System (ADS)

Hong, Bo; Shen, Jian

2013-11-01

Dissolved oxygen (DO) replenishment in the bottom waters of an estuary depends on physical processes that are significantly influenced by external forcings. The vertical exchange time (VET) is introduced in this study to quantify the physical processes that regulate the DO replenishment in the Chesapeake Bay. A 3-D numerical model was applied to simulate the circulation, VET, and DO. Results indicate that VET is a suitable parameter for evaluating the bottom DO condition over both seasonal and interannual timescales. The VET is negatively correlated with the bottom DO. Hypoxia (DO <2 mg L-1) will develop in the Bay when VET is greater than 23 days in summer if mean total DO consumption rate is about 0.3 g O2 m-3 d-1. This critical VET value may vary around 23 days when the total DO consumption rate changes. The VET volume (volume of water mass with VET >23 days) can account for 77% of variations of hypoxic volume in the main Bay. The VET cannot explain all the DO variations as it can only account for the contribution of physical processes that regulate DO replenishment. It is found that the short-term vertical exchange process is highly controlled by the wind forcing. The VET volume decreases when the high-speed wind events are frequent. The summertime VET volume is less sensitive to short-term variations (pulses) of river discharge. It is sensitive to the total amount of river discharge and the high VET volume can be expected in the wet year.

Exploitation of intertidal feeding resources by the red knot Calidris canutus under megatidal conditions (Bay of Saint-Brieuc, France)

NASA Astrophysics Data System (ADS)

Sturbois, Anthony; Ponsero, Alain; Desroy, Nicolas; Le Mao, Patrick; Fournier, Jérôme

2015-02-01

The feeding ecology of the red knot has been widely studied across its wintering range. Red knots mainly select bivalves and gastropods, with differences between sites due to variation in prey availability. The shorebird's diet is also influenced or controlled by the tidal regime. The aim of this paper is to demonstrate the adaptation of foraging red knots to the megatidal environment. The variation in their diet during tidal cycles was studied in the bay of Saint-Brieuc, a functional unit for this species. The method used combined macrofauna, distribution of foraging birds and diet data. Comparative spatial analyses of macrofauna and distribution of foraging red knots have shown that the bay's four benthic assemblages are exploited by birds. By analysing droppings, we highlighted that bivalve molluscs are the main component of their diet, as shown in most overwintering sites. Fifteen types of prey were identified and Donax vittatus was discovered to be a significant prey item. The relative proportion of each main prey item differs significantly depending on the benthic assemblage used to forage. All available benthic assemblages and all potential feeding resources can be used during a single tidal cycle, reflecting an adaptation to megatidal conditions. This approach develops accurate knowledge about the feeding ecology of birds which managers need in order to identify optimal areas for the conservation of waders based on the areas and resources actually used by the birds.

Measuring the Carolina Bays Using Archetype Template Overlays on the Google Earth Virtual Globe; Planform Metrics for 25,000 Bays Extracted from LiDAR and Satellite Imagery

NASA Astrophysics Data System (ADS)

Davias, M. E.; Gilbride, J. L.

2011-12-01

Aerial photographs of Carolina bays taken in the 1930's sparked the initial research into their geomorphology. Satellite Imagery available today through the Google Earth Virtual Globe facility expands the regions available for interrogation, but reveal only part of their unique planforms. Digital Elevation Maps (DEMs), using Light Detection And Ranging (LiDAR) remote sensing data, accentuate the visual presentation of these aligned ovoid shallow basins by emphasizing their robust circumpheral rims. To support a geospatial survey of Carolina bay landforms in the continental USA, 400,000 km2 of hsv-shaded DEMs were created as KML-JPEG tile sets. A majority of these DEMs were generated with LiDAR-derived data. We demonstrate the tile generation process and their integration into Google Earth, where the DEMs augment available photographic imagery for the visualization of bay planforms. While the generic Carolina bay planform is considered oval, we document subtle regional variations. Using a small set of empirically derived planform shapes, we created corresponding Google Earth overlay templates. We demonstrate the analysis of an individual Carolina bay by placing an appropriate overlay onto the virtually globe, then orientating, sizing and rotating it by edit handles such that it satisfactorily represents the bay's rim. The resulting overlay data element is extracted from Google Earth's object directory and programmatically processed to generate metrics such as geographic location, elevation, major and minor axis and inferred orientation. Utilizing a virtual globe facility for data capture may result in higher quality data compared to methods that reference flat maps, where geospatial shape and orientation of the bays could be skewed and distorted in the orthographic projection process. Using the methodology described, we have measured over 25k distinct Carolina bays. We discuss the Google Fusion geospatial data repository facility, through which these data have been assembled and made web-accessible to other researchers. Preliminary findings from the survey are discussed, such as how bay surface area, eccentricity and orientation vary across ~800 1/4° × 1/4° grid elements. Future work includes measuring 25k additional bays, as well as interrogation of the orientation data to identify any possible systematic geospatial relationships.

Results and evaluation of a pilot primary monitoring network, San Francisco Bay, California, 1978

USGS Publications Warehouse

Bradford, W.L.; Iwatsubo, R.T.

1980-01-01

A primary monitoring network of 12 stations, with measurements at 1-meter depth intervals every 2 weeks during periods of high inflow from the Sacramento-San Joaquin River delta, and every 4-6 weeks during seasonal low delta inflows, appears adequate to observe major changes in ambient water quality in San Francisco Bay. A 1-year study tested the network operation and determined that analysis of the data could demonstrate the major changes in salinity, temperature, and light-attenuation distributions known to occur, based on earlier research, in response to variations of delta inflow and to other physical processes. Observations of eddies at two stations, of the influence of water from a river flooding in the extreme south bay, and of difference in salinity and temperature laterally across the entrance to the south bay are all new but are consistent with existing models. The pH, dissolved oxygen, and light-attenuation measurements, while adequate to observe small-scale vertical variations, are not sufficiently sensitive to detect the effects of phytoplankton blooms. (USGS)

Seasonal variation of the underground cosmic muon flux observed at Daya Bay

NASA Astrophysics Data System (ADS)

An, F. P.; Balantekin, A. B.; Band, H. R.; Bishai, M.; Blyth, S.; Cao, D.; Cao, G. F.; Cao, J.; Chan, Y. L.; Chang, J. F.; Chang, Y.; Chen, H. S.; Chen, Q. Y.; Chen, S. M.; Chen, Y. X.; Chen, Y.; Cheng, J.; Cheng, Z. K.; Cherwinka, J. J.; Chu, M. C.; Chukanov, A.; Cummings, J. P.; Ding, Y. Y.; Diwan, M. V.; Dolgareva, M.; Dove, J.; Dwyer, D. A.; Edwards, W. R.; Gill, R.; Gonchar, M.; Gong, G. H.; Gong, H.; Grassi, M.; Gu, W. Q.; Guo, L.; Guo, X. H.; Guo, Y. H.; Guo, Z.; Hackenburg, R. W.; Hans, S.; He, M.; Heeger, K. M.; Heng, Y. K.; Higuera, A.; Hsiung, Y. B.; Hu, B. Z.; Hu, T.; Huang, E. C.; Huang, H. X.; Huang, X. T.; Huber, P.; Huo, W.; Hussain, G.; Jaffe, D. E.; Jen, K. L.; Jetter, S.; Ji, X. P.; Ji, X. L.; Jiao, J. B.; Johnson, R. A.; Jones, D.; Kang, L.; Kettell, S. H.; Khan, A.; Kohn, S.; Kramer, M.; Kwan, K. K.; Kwok, M. W.; Kwok, T.; Langford, T. J.; Lau, K.; Lebanowski, L.; Lee, J.; Lee, J. H. C.; Lei, R. T.; Leitner, R.; Li, C.; Li, D. J.; Li, F.; Li, G. S.; Li, Q. J.; Li, S.; Li, S. C.; Li, W. D.; Li, X. N.; Li, X. Q.; Li, Y. F.; Li, Z. B.; Liang, H.; Lin, C. J.; Lin, G. L.; Lin, S.; Lin, S. K.; Lin, Y.-C.; Ling, J. J.; Link, J. M.; Littenberg, L.; Littlejohn, B. R.; Liu, J. L.; Liu, J. C.; Loh, C. W.; Lu, C.; Lu, H. Q.; Lu, J. S.; Luk, K. B.; Ma, X. Y.; Ma, X. B.; Ma, Y. Q.; Malyshkin, Y.; Martinez Caicedo, D. A.; McDonald, K. T.; McKeown, R. D.; Mitchell, I.; Nakajima, Y.; Napolitano, J.; Naumov, D.; Naumova, E.; Ngai, H. Y.; Ochoa-Ricoux, J. P.; Olshevskiy, A.; Pan, H.-R.; Park, J.; Patton, S.; Pec, V.; Peng, J. C.; Pinsky, L.; Pun, C. S. J.; Qi, F. Z.; Qi, M.; Qian, X.; Qiu, R. M.; Raper, N.; Ren, J.; Rosero, R.; Roskovec, B.; Ruan, X. C.; Sebastiani, C.; Steiner, H.; Sun, J. L.; Tang, W.; Taychenachev, D.; Treskov, K.; Tsang, K. V.; Tull, C. E.; Viaux, N.; Viren, B.; Vorobel, V.; Wang, C. H.; Wang, M.; Wang, N. Y.; Wang, R. G.; Wang, W.; Wang, X.; Wang, Y. F.; Wang, Z.; Wang, Z.; Wang, Z. M.; Wei, H. Y.; Wen, L. J.; Whisnant, K.; White, C. G.; Whitehead, L.; Wise, T.; Wong, H. L. H.; Wong, S. C. F.; Worcester, E.; Wu, C.-H.; Wu, Q.; Wu, W. J.; Xia, D. M.; Xia, J. K.; Xing, Z. Z.; Xu, J. L.; Xu, Y.; Xue, T.; Yang, C. G.; Yang, H.; Yang, L.; Yang, M. S.; Yang, M. T.; Yang, Y. Z.; Ye, M.; Ye, Z.; Yeh, M.; Young, B. L.; Yu, Z. Y.; Zeng, S.; Zhan, L.; Zhang, C.; Zhang, C. C.; Zhang, H. H.; Zhang, J. W.; Zhang, Q. M.; Zhang, X. T.; Zhang, Y. M.; Zhang, Y. X.; Zhang, Y. M.; Zhang, Z. J.; Zhang, Z. Y.; Zhang, Z. P.; Zhao, J.; Zhou, L.; Zhuang, H. L.; Zou, J. H.

2018-01-01

The Daya Bay Experiment consists of eight identically designed detectors located in three underground experimental halls named as EH1, EH2, EH3, with 250, 265 and 860 meters of water equivalent vertical overburden, respectively. Cosmic muon events have been recorded over a two-year period. The underground muon rate is observed to be positively correlated with the effective atmospheric temperature and to follow a seasonal modulation pattern. The correlation coefficient α, describing how a variation in the muon rate relates to a variation in the effective atmospheric temperature, is found to be αEH1 = 0.362±0.031, αEH2 = 0.433±0.038 and αEH3 = 0.641±0.057 for each experimental hall.

Variations of summer phytoplankton community related to environmental factors in a macro-tidal estuarine embayment, Hangzhou Bay, China

NASA Astrophysics Data System (ADS)

Zhang, Yuexia; Yu, Jun; Jiang, Zhibing; Wang, Qin; Wang, Hui

2015-12-01

To explore the distribution and composition of phytoplankton community and their responses to environmental changes, summer net-collected phytoplankton and physicochemical parameters in the Hangzhou Bay during 2004-2010 were investigated. A total of four phyla and 84 species were identified, including 67 diatom and 12 dinoflagellate species. The dominant species constantly consisted of the diatoms, although the dominance of dinoflagellate and cyanobacteria increased recently. Due to great spatio-temporal variations in environmental factors (salinity, suspended solids, and nutrient concentration), significant heterogeneities in community compositions among different years and subregions (inner and middle sections, and bay mouth) were found based on the analyses of multidimensional scaling and similarity. Canonical correspondence analysis showed that salinity and Si/N were the main variables associated with algal assemblage. Compared with the historical data since the 1980s, eutrophication (N, P, and N/P increased with decreasing Si/N) was exacerbated drastically. Moreover, climatic forcing and human activities resulted in a series of physical alterations, including sediment retention, temperature increase, and salinity decrease as well as reduction in water exchanges. All these changes induced obvious increases in cell density and Chl- a while decreases in species diversity and diatom-dinoflagellate ratio as well as the shifting of dominant species. Therefore, the long-term phytoplankton variations were closely related to anthropogenic and climatic perturbations in the Hangzhou Bay.

Misinterpretation of lateral acoustic variations on high-resolution seismic reflection profiles as fault offsets of Holocene bay mud beneath the southern part of San Francisco Bay, California

USGS Publications Warehouse

Marlow, M. S.; Hart, P.E.; Carlson, P.R.; Childs, J. R.; Mann, D. M.; Anima, R.J.; Kayen, R.E.

1996-01-01

We collected high-resolution seismic reflection profiles in the southern part of San Francisco Bay in 1992 and 1993 to investigate possible Holocene faulting along postulated transbay bedrock fault zones. The initial analog records show apparent offsets of reflection packages along sharp vertical boundaries. These records were originally interpreted as showing a complex series of faults along closely spaced, sharp vertical boundaries in the upper 10 m (0.013 s two-way travel time) of Holocene bay mud. A subsequent survey in 1994 was run with a different seismic reflection system, which utilized a higher power source. This second system generated records with deeper penetration (max. 20 m, 0.026 s two-way travel time) and demonstrated that the reflections originally interpreted as fault offsets by faulting were actually laterally continuous reflection horizons. The pitfall in the original interpretations was caused by lateral variations in the amplitude brightness of reflection events, coupled with a long (greater than 15 ms) source signature of the low-power system. These effects combined to show apparent offsets of reflection packages along sharp vertical boundaries. These boundaries, as shown by the second system, in fact occur where the reflection amplitude diminishes abruptly on laterally continuous reflection events. This striking lateral variation in reflection amplitude is attributable to the localized presence of biogenic(?) gas.

Mobile Bay, Alabama area seen in Skylab 4 Earth Resources Experiment Package

NASA Image and Video Library

1974-02-01

SL4-92-300 (February 1974) --- A near vertical view of the Mobile Bay, Alabama area is seen in this Skylab 4 Earth Resources Experiments Package S190-B (five-inch earth terrain camera) photograph taken from the Skylab space station in Earth orbit. North of Mobile the Tombigbee and Alabama Rivers join to form the Mobile River. Detailed configuration of the individual stream channels and boundaries can be defined as the Mobile River flows into Mobile Bay, and thence into the Gulf of Mexico. The Mobile River Valley with its numerous stream channels is a distinct light shade in contrast to the dark green shade of the adjacent areas. The red coloration of Mobile Bay reflects the sediment load carried into the Bay by the rivers. Variations in red color indicate sediment load and the current paths within Mobile Bay. The waterly movement of the along shore currents at the mouth of Mobile Bay is shown by the contrasting light blue of the sediment-laden current and the blue of the Gulf predominately. Agricultural areas east and west of Mobile Bay are characterized by a rectangular pattern in green to white shades. Color variations may reflect the type and growth cycle of crops. Agricultural areas (light gray-greens) are also clearly visible in other parts of the photograph. Interstate 10 extends from near Pascagoula, Mississippi eastward through Mobile to the outskirts of Pensacola, Florida. Analysis of the EREP photographic data will be undertaken by the U.S. Corps of Engineers to determine bay dynamic processes. Federal agencies participating with NASA on the EREP project are the Departments of Agriculture, Commerce, Interior, the Environmental Protection Agency and the Corps of Engineers. All EREP photography is available to the public through the Department of Interior's Earth Resources Observations Systems Data Center, Sioux Falls, South Dakota. 57198 Photo credit: NASA

Spatiotemporal variations in the abundance and composition of bulk and chromophoric dissolved organic matter in seasonally hypoxia-influenced Green Bay, Lake Michigan, USA.

PubMed

DeVilbiss, Stephen E; Zhou, Zhengzhen; Klump, J Val; Guo, Laodong

2016-09-15

Green Bay, Lake Michigan, USA, is the largest freshwater estuary in the Laurentian Great Lakes and receives disproportional terrestrial inputs as a result of a high watershed to bay surface area ratio. While seasonal hypoxia and the formation of "dead zones" in Green Bay have received increasing attention, there are no systematic studies on the dynamics of dissolved organic matter (DOM) and its linkage to the development of hypoxia. During summer 2014, bulk dissolved organic carbon (DOC) analysis, UV-vis spectroscopy, and fluorescence excitation-emission matrices (EEMs) coupled with PARAFAC analysis were used to quantify the abundance, composition and source of DOM and their spatiotemporal variations in Green Bay, Lake Michigan. Concentrations of DOC ranged from 202 to 571μM-C (average=361±73μM-C) in June and from 279 to 610μM-C (average=349±64μM-C) in August. In both months, absorption coefficient at 254nm (a254) was strongly correlated to bulk DOC and was most abundant in the Fox River, attesting a dominant terrestrial input. Non-chromophoric DOC comprised, on average, ~32% of bulk DOC in June with higher terrestrial DOM and ~47% in August with higher aquagenic DOM, indicating that autochthonous and more degraded DOM is of lower optical activity. PARAFAC modeling on EEM data resulted in four major fluorescent DOM components, including two terrestrial humic-like, one aquagenic humic-like, and one protein-like component. Variations in the abundance of DOM components further supported changes in DOM sources. Mixing behavior of DOM components also indicated that while bulk DOM behaved quasi-conservatively, significant compositional changes occurred during transport from the Fox River to the open bay. Copyright © 2016 Elsevier B.V. All rights reserved.

San Francisco Bay, California as seen from STS-59

NASA Image and Video Library

1994-04-14

STS059-213-009 (9-20 April 1994) --- San Francisco Bay. Orient with the sea up. The delta of the combined Sacramento and San Joaquin Rivers occupies the foreground, San Francisco Bay the middle distance, and the Pacific Ocean the rest. Variations in water color caused both by sediment load and by wind streaking strike the eye. Man-made features dominate this scene. The Lafayette/Concord complex is left of the bay head, Vallejo is to the right, the Berkeley/Oakland complex rims the shoreline of the main bay, and San Francisco fills the peninsula beyond. Salt-evaporation ponds contain differently-colored algae depending on salinity. The low altitude (less than 120 nautical miles) and unusually-clear air combine to provide unusually-strong green colors in this Spring scene. Hasselblad camera.

San Francisco Bay, California as seen from STS-59

NASA Technical Reports Server (NTRS)

1994-01-01

San Francisco Bay as seen from STS-59. View is oriented with the sea up. The delta of the combined Sacramento and San Joaquin Rivers occupies the foreground with San Francisco Bay in the middle distance, then the Pacific Ocean. Variations in water color caused both by sediment load and by wind streaking strike the eye. Man-made features dominate this scene. The Lafayette/Concord complex is left of the bay head, Vallejo is to the right, the Berkeley/Oakland complex rims the shoreline of the main bay, and San Francisco fills the peninsula beyond. Salt-evaporation ponds contain differently-colored algae depending on salinity. The low altitude (less than 120 nautical miles) and unusually-clear air combine to provide unusually-strong green colors in this Spring scene.

Does centennial morphodynamic evolution lead to higher channel efficiency in San Pablo Bay, California?

USGS Publications Warehouse

van der Wegen, M.; Jaffe, B.E.; Barnard, P.L.; Jaffee, B.E.; Schoellhamer, D.H.

2013-01-01

Measured bathymetries on 30 year interval over the past 150 years show that San Pablo Bay experienced periods of considerable deposition followed by periods of net erosion. However, the main channel in San Pablo Bay has continuously narrowed. The underlying mechanisms and consequences of this tidal channel evolution are not well understood. The central question of this study is whether tidal channels evolve towards a geometry that leads to more efficient hydraulic conveyance and sediment throughput. We applied a hydrodynamic process-based, numerical model (Delft3D), which was run on 5 San Pablo Bay bathymetries measured between 1856 and 1983. Model results shows increasing energy dissipation levels for lower water flows leading to an approximately 15% lower efficiency in 1983 compared to 1856. During the same period the relative seaward sediment throughput through the San Pablo Bay main channel increased by 10%. A probable explanation is that San Pablo Bay is still affected by the excessive historic sediment supply. Sea level rise and Delta surface water area variations over 150 years have limited effect on the model results. With expected lower sediment concentrations in the watershed and less impact of wind waves due to erosion of the shallow flats, it is possible that energy dissipations levels will decrease again in future decades. Our study suggests that the morphodynamic adaptation time scale to excessive variations in sediment supply to estuaries may be on the order of centuries.

Factors affecting suspended-solids concentrations in South San Francisco Bay, California

USGS Publications Warehouse

Schoellhamer, D.H.

1996-01-01

Measurements of suspended-solids concentration (SSC) were made at two depths at three sites in South San Francisco Bay (South Bay) to determine the factors that affect SSC. Twenty-eight segments of reliable and continuous SSC time series data longer than 14 days were collected from late 1991 or 1992 through September 1993. Spectral analysis and singular spectrum analysis were used to relate these data segments to time series of several potential forcing factors, including diurnal and semidiurnal tides, the spring-neap tidal cycle, wind shear, freshwater runoff, and longitudinal density differences. SSC is greatest during summer when a landward wind shear is applied to South Bay by the afternoon sea breeze. About one half the variance of SSC is caused by the spring-neap cycle, and SSC lags the spring-neap cycle by about 2 days. Relatively short duration of slack water limits the duration of deposition of suspended solids and consolidation of newly deposited bed sediment during the tidal cycle, so suspended solids accumulate in the water column as a spring tide is approached and slowly deposit as a neap tide is approached. Perturbations in SSC caused by wind and local runoff from winter storms during the study period were usually much smaller than SSC variations caused by the spring-neap cycle. Variations of SSC at the study sites at tidal timescales are tidally forced, and nonlinear physical processes are significant. Advective transport dominates during spring tides when water with higher SSC due to wind wave resuspension is advected to the main channel from shallow water, but during neap tides, advective transport is less significant. The findings of this and other studies indicate that the tidally averaged transport of suspended solids responds to seasonal variations of wind shear in South Bay.

Phytoplankton composition and microcystin concentrations in open and closed bays of Lake Victoria, Tanzania

PubMed Central

Mbonde, Athanasio S.; Sitoki, Lewis; Kurmayer, Rainer

2017-01-01

This study was carried out in order to investigate the spatial variation of algal toxin (microcystin) concentrations along the shoreline of Lake Victoria. A total of 16 nearshore stations differing in connectivity to the main lake basin were categorized as either closed bays (ratio of bay area to bay opening < 1) or open bays (ratio ≥ 1) and sampled during November and December 2009. Water samples were analyzed for total phosphorus (TP), chlorophyll a, phytoplankton community composition and concentrations of microcystin (MC). Open and closed bays were significantly different for phytoplankton abundance and composition: Average phytoplankton biovolume was higher for closed bays (45 mm3 L-1 ± 11 SE) than open bays (5 ± 2 mm3 L-1). Cyanobacterial biovolume (mainly Microcystis spp., Anabaena spp. and Planktolyngbya spp.) also was significantly higher in closed bays (82 ± 9% of total biovolume) than in open bays (44 ± 5%). In contrast, diatom biovolume was lower in closed bays (7 ± 1%) than in open bays (36 ± 6%). MCs were found only among sites from closed bays and concentrations ranged from 0.4 to 13 μg L-1 MC-LR equiv. and coincided with high abundance of Microcystis spp. It is concluded that the level of water exchange from individual bays to the main basin is an important factor influencing eutrophication and microcystin production in nearshore habitats of Lake Victoria. PMID:28077928

Associations between degraded benthic communities and contaminated sediments: Sabine Lake, Lake Pontchartrain, and Choctawhatchee Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Engle, V.D.; Summers, J.K.; Macauley, J.M.

1994-12-31

The Environmental Monitoring and Assessment Program for Estuaries (EMAP-E) in the Gulf of Mexico supplements its base sampling effort each year with localized, intensive spatial sampling in selected large estuarine systems. By selecting random locations within 70 km{sup 2} hexagonal areas, individual estuaries were sampled using EMAP methods but at four times the density as base sampling. In 1992, 19 sites were sampled in Lake Pontchartrain, Louisiana. In 1 993, 18 sites were sampled in Sabine Lake, Texas and 12 sites were sampled in Choctawhatchee Bay, Florida. At all sites, sediment grabs were taken and analyzed for benthic species compositionmore » and abundance, for toxicity to Ampelisca, and for organic and inorganic sediment contaminants. An indicator of biotic integrity, the benthic index, was calculated to represent the status of benthic communities. A series of statistical techniques, such as stepwise regression analysis, were employed to determine whether the variation in the benthic index could be associated with variation in sediment contaminants, sediment toxicity, or levels of dissolved oxygen. Spatial distributions of these parameters were examined to determine the geographical co-occurrence of degraded benthic communities and environmental stressors. In Lake Pontchartrain, for example, 85% of the variation in the benthic index was associated with decreased levels of dissolved oxygen, and increased concentrations of PCBs, alkanes, copper, tin, and zinc in the sediments.« less

Indicators of nitrate export from forested watersheds of the Chesapeake Bay region

Treesearch

Karl W. J. Williard

1997-01-01

Soil net nitrogen mineralization and nitrification rates were studied on nine relatively undisturbed, forested watersheds in an effort to explain the large variations in nitrate export in streamflow within the Chesapeake Bay region. The primary hypothesis tested was that nitrate export from the watersheds was positively associated with rates of net soil nitrogen...

Spatial variation in reproductive effort of a southern Australian seagrass.

PubMed

Smith, Timothy M; York, Paul H; Macreadie, Peter I; Keough, Michael J; Ross, D Jeff; Sherman, Craig D H

2016-09-01

In marine environments characterised by habitat-forming plants, the relative allocation of resources into vegetative growth and flowering is an important indicator of plant condition and hence ecosystem health. In addition, the production and abundance of seeds can give clues to local resilience. Flowering density, seed bank, biomass and epiphyte levels were recorded for the temperate seagrass Zostera nigricaulis in Port Phillip Bay, south east Australia at 14 sites chosen to represent several regions with different physicochemical conditions. Strong regional differences were found within the large bay. Spathe and seed density were very low in the north of the bay (3 sites), low in the centre of the bay (2 sites) intermediate in the Outer Geelong Arm (2 sites), high in Swan Bay (2 sites) and very high in the Inner Geelong Arm (3 sites). In the south (2 sites) seed density was low and spathe density was high. These regional patterns were largely consistent for the 5 sites sampled over the three year period. Timing of flowering was consistent across sites, occurring from August until December with peak production in October, except during the third year of monitoring when overall densities were lower and peaked in November. Seagrass biomass, epiphyte load, canopy height and stem density showed few consistent spatial and temporal patterns. Variation in spathe and seed density and morphology across Port Phillip Bay reflects varying environmental conditions and suggests that northern sites may be restricted in their ability to recover from disturbance through sexual reproduction. In contrast, sites in the west and south of the bay have greater potential to recover from disturbances due to a larger seed bank and these sites could act as source populations for sites where seed production is low. Copyright © 2016 Elsevier Ltd. All rights reserved.

Estimating parameter of Rayleigh distribution by using Maximum Likelihood method and Bayes method

NASA Astrophysics Data System (ADS)

Ardianti, Fitri; Sutarman

2018-01-01

In this paper, we use Maximum Likelihood estimation and Bayes method under some risk function to estimate parameter of Rayleigh distribution to know the best method. The prior knowledge which used in Bayes method is Jeffrey’s non-informative prior. Maximum likelihood estimation and Bayes method under precautionary loss function, entropy loss function, loss function-L 1 will be compared. We compare these methods by bias and MSE value using R program. After that, the result will be displayed in tables to facilitate the comparisons.

A Comparison of Full and Empirical Bayes Techniques for Inferring Sea Level Changes from Tide Gauge Records

NASA Astrophysics Data System (ADS)

Piecuch, C. G.; Huybers, P. J.; Tingley, M.

2016-12-01

Sea level observations from coastal tide gauges are some of the longest instrumental records of the ocean. However, these data can be noisy, biased, and gappy, featuring missing values, and reflecting land motion and local effects. Coping with these issues in a formal manner is a challenging task. Some studies use Bayesian approaches to estimate sea level from tide gauge records, making inference probabilistically. Such methods are typically empirically Bayesian in nature: model parameters are treated as known and assigned point values. But, in reality, parameters are not perfectly known. Empirical Bayes methods thus neglect a potentially important source of uncertainty, and so may overestimate the precision (i.e., underestimate the uncertainty) of sea level estimates. We consider whether empirical Bayes methods underestimate uncertainty in sea level from tide gauge data, comparing to a full Bayes method that treats parameters as unknowns to be solved for along with the sea level field. We develop a hierarchical algorithm that we apply to tide gauge data on the North American northeast coast over 1893-2015. The algorithm is run in full Bayes mode, solving for the sea level process and parameters, and in empirical mode, solving only for the process using fixed parameter values. Error bars on sea level from the empirical method are smaller than from the full Bayes method, and the relative discrepancies increase with time; the 95% credible interval on sea level values from the empirical Bayes method in 1910 and 2010 is 23% and 56% narrower, respectively, than from the full Bayes approach. To evaluate the representativeness of the credible intervals, empirical Bayes and full Bayes methods are applied to corrupted data of a known surrogate field. Using rank histograms to evaluate the solutions, we find that the full Bayes method produces generally reliable error bars, whereas the empirical Bayes method gives too-narrow error bars, such that the 90% credible interval only encompasses 70% of true process values. Results demonstrate that parameter uncertainty is an important source of process uncertainty, and advocate for the fully Bayesian treatment of tide gauge records in ocean circulation and climate studies.

Seasonal variations in the community structures of macrobenthic fauna and their health status in an estuarine bay, Gwangyang Bay in Korea

NASA Astrophysics Data System (ADS)

Seo, Jin-Young; An, Soon-Mo; Lim, Dhong-il; Choi, Jin-Woo

2017-09-01

Macrobenthic fauna in an estuarine Gwangyang Bay, southern Korean coast, were investigated to uncover recent variations in their community structures. In the study area, macrobenthic faunal communities were mainly composed of polychaete worms which were the most abundant faunal group with the highest values in species number and density, while mollusks accounted for the highest proportion in total biomass. There was no clear seasonal difference in species richness during the two year period of the investigation, but the mean density and biomass increased every spring and summer due to the mass recruitment of Theora fragilis. The Shannon's diversity index (H') was more than 2.0 during most sampling seasons and did not show any significant seasonal difference except for the data in August, 2011 when azoic conditions occurred. The community structures of macrobenthos in Gwangyang Bay did not show any remarkable change in the dominance of the two top dominant species, Scoletoma longifolia and Heteromastus filiformis, which abundantly occurred in all seasons, except for the abundance peaks associated with high occurrence of T. fragilis and Paraprionospio cordifolia, especially in spring and summer and in autumn, respectively. These fauna changes reflected the changes in the macrobenthic community health status in Gwangyang Bay, where stable conditions and a healthy status prevailed in winter, but a slightly disturbed status prevailed from spring to autumn.

Modeling investigation of the nutrient and phytoplankton variability in the Chesapeake Bay outflow plume

NASA Astrophysics Data System (ADS)

Jiang, Long; Xia, Meng

2018-03-01

The Chesapeake Bay outflow plume (CBOP) is the mixing zone between Chesapeake Bay and less eutrophic continental shelf waters. Variations in phytoplankton distribution in the CBOP are critical to the fish nursery habitat quality and ecosystem health; thus, an existing hydrodynamic-biogeochemical model for the bay and the adjacent coastal ocean was applied to understand the nutrient and phytoplankton variability in the plume and the dominant environmental drivers. The simulated nutrient and chlorophyll a distribution agreed well with field data and real-time satellite imagery. Based on the model calculation, the net dissolved inorganic nitrogen (DIN) and phosphorus (DIP) flux at the bay mouth was seaward and landward during 2003-2012, respectively. The CBOP was mostly nitrogen-limited because of the relatively low estuarine DIN export. The highest simulated phytoplankton biomass generally occurred in spring in the near field of the plume. Streamflow variations could regulate the estuarine residence time, and thus modulate nutrient export and phytoplankton biomass in the plume area; in comparison, changing nutrient loading with fixed streamflow had a less extensive impact, especially in the offshore and far-field regions. Correlation analyses and numerical experiments revealed that southerly winds on the shelf were effective in promoting the offshore plume expansion and phytoplankton accumulation. Climate change including precipitation and wind pattern shifts is likely to complicate the driving mechanisms of phytoplankton variability in the plume region.

Movements of brown bullheads in Presque Isle Bay, Lake Erie, Pennsylvania

USGS Publications Warehouse

Millard, M.J.; Smith, D.R.; Obert, E.; Grazio, J.; Bartron, M.L.; Wellington, C.; Grise, S.; Rafferty, S.; Wellington, R.; Julian, S.

2009-01-01

Presque Isle Bay, Lake Erie, was listed as an Area of Concern (AOC) by the International Joint Commission in part because of the high incidence of external tumor in brown bullheads. Verifying the source of the possible contaminant exposure is critical to addressing the AOC designation. We used telemetry tracking (n = 49 fish) to test the hypothesis that adult bullheads captured within the bay during spawning season do not exit the bay during the post-spawning summer and fall months. We analyzed genetic variation at 15 microsatellite loci for 112 adult fish from 5 locations, 4 inside the bay and 1 outside, in order to test for possible differences. Data from fixed-station receivers suggested fish did not leave Presque Isle Bay during the study period. Predicted locations outside Presque Isle Bay were only 0.1% of all predicted locations and were below the 0.2% error rate based on known manual relocations. However, there was evidence for movement within Presque Isle Bay. Most movement was between Misery Bay or Lagoons and the open bay area. Whereas telemetry results showed tendency for adult site fidelity, genetic results showed no differences among locations, indicating that there is a single panmictic population. Our telemetry data suggest that brown bullheads are likely a useful indicator species for environmental conditions in Presque Isle Bay, since adults likely are retained in the system.

Nitrogen Isotopic Study of Benthic Macroalgae and Seawater in Biscayne Bay, Florida

NASA Astrophysics Data System (ADS)

Drayer, C. L.; Lamb, K. A.; Swart, P. K.; Altabet, M. A.; Anderson, W. T.; Bellmund, S.

2006-12-01

Biscayne Bay, Florida is a complex coastal environment with many possible natural and anthropogenic sources of nitrogen. Such sources include precipitation, N fixation, nutrient regeneration/recycling, landfill soil leaching, groundwater and agricultural runoff, septic tank leakage, and treated waste water effluent. In order to understand the relative importance of these various inputs, benthic macroalgae, seagrasses, and seawater samples were collected from Biscayne Bay transecting from canals through nearshore bay to offshore reef sites Macroalgae was identified by species, decarbonated, and analyzed for δ15N and δ13C. The mean δ15N and δ13C for the algal tissue were +5.4 (±0.3‰) and -15.1 (±0.1‰), respectively. Measured nearshore algal samples differed greatly from offshore samples and had a high δ15N value of +12.0 (±0.1‰) and a mean of +8.6 (±3.0‰), in comparison to offshore samples that averaged +4.7 (±2.5‰). Despite the variation in δ15N, the δ13C values for both nearshore and offshore samples fell within the accepted parameters for algal communities. Seawater was analyzed for δ15N in DIN (dissolved inorganic nitrogen) and DON (dissolved organic nitrogen) through the cadmium reduction method (Mcllvin and Altabet, 2005). The mean δ15N for the DIN was +4.5 (±3.9‰) and the DON was +5.8 (±3.3‰). Canal DON δ15N values contained the heaviest measured values at ~+18‰, while nearshore and offshore DON values were lighter, 4.9 (±1.6‰). DIN values were more spatially variable with canal and nearshore sites ranging from ~+10‰ through ~-4.5‰. This study will continue over the next two years to examine possible temporal C and N isotope variations and will expand to include a larger geographic region focusing on areas with high nutrient levels and harmful algae blooms (HABs).

Shuttle payload bay thermal environments: Summary and conclusion report for STS Flights 1-5

NASA Technical Reports Server (NTRS)

Fu, J. H.; Graves, G. R.

1987-01-01

The thermal data for the payload bay of the first five shuttle flights is summarized and the engineering evaluation of that data is presented. After a general discussion on mission profiles and vehicle configurations, the thermal design and flight instrumentation systems of the payload bay are described. The thermal flight data sources and a categorization of the data are then presented. A thermal flight data summarization section provides temperature data for the five phases of a typical mission profile. These are: prelaunch, ascent, on-orbit, entry and postlanding. The thermal flight data characterization section encompasses this flight data for flight to flight variations, payload effects, temperature ranges, and other variations. Discussion of the thermal environment prediction models in use by industry and various NASA Centers, and the results predicted by these models, is followed by an evaluation of the correlation between the actual flight data and the results predicted by the models. Finally, the available thermal data are evaluated from the viewpoint of the user concerned with establishing the thermal environment in the payload bay. The data deficiencies are discussed and recommendations for their elimination are presented.

A variational Bayes spatiotemporal model for electromagnetic brain mapping.

PubMed

Nathoo, F S; Babul, A; Moiseev, A; Virji-Babul, N; Beg, M F

2014-03-01

In this article, we present a new variational Bayes approach for solving the neuroelectromagnetic inverse problem arising in studies involving electroencephalography (EEG) and magnetoencephalography (MEG). This high-dimensional spatiotemporal estimation problem involves the recovery of time-varying neural activity at a large number of locations within the brain, from electromagnetic signals recorded at a relatively small number of external locations on or near the scalp. Framing this problem within the context of spatial variable selection for an underdetermined functional linear model, we propose a spatial mixture formulation where the profile of electrical activity within the brain is represented through location-specific spike-and-slab priors based on a spatial logistic specification. The prior specification accommodates spatial clustering in brain activation, while also allowing for the inclusion of auxiliary information derived from alternative imaging modalities, such as functional magnetic resonance imaging (fMRI). We develop a variational Bayes approach for computing estimates of neural source activity, and incorporate a nonparametric bootstrap for interval estimation. The proposed methodology is compared with several alternative approaches through simulation studies, and is applied to the analysis of a multimodal neuroimaging study examining the neural response to face perception using EEG, MEG, and fMRI. © 2013, The International Biometric Society.

Holocene sedimentation in Richardson Bay, California

USGS Publications Warehouse

Connor, Cathy L.

1983-01-01

Examination of foraminifers, diatoms, ostracodes, clay mineralogy, and sediment-size variation from 9 borehole sites along the salt-marsh margins of Richardson Bay reveals a record of gradual infilling of fine-grained estuarine sediments. Over the past 10,000 years this area was transformed from a V-shaped Pleistocene stream valley to a flat-floored arm of the San Francisco Bay estuary. A radiocarbon date obtained from a basal peat overlying nonmarine alluvial sand near the town of Mill Valley indicates that stable salt-marsh vegetation was present in the northwestern arm of Richardson Bay 4600?165 years ago and agrees within error limits with a Holocene sea-level curve developed by Atwater, Hedel, and Helley in 1977 for southern San Francisco Bay. The average sedimentation rate over the last 4600 years is estimated to be 0.2 cm/yr for the inner part of the bay. Comparison of early maps with updated versions as well as studies of marsh plant zonations in disturbed and nondisturbed areas shows that almost half of the marsh in Richardson Bay has been leveed or filled since 1899.

Mobile Bay, Alabama area seen in Skylab 4 Earth Resources Experiment Package

NASA Technical Reports Server (NTRS)

1974-01-01

A near vertical view of the Mobile Bay, Alabama area seen in this Skylab 4 Earth Resources Experiment Package S190-B (five-inch earth terrain camera) photograph taken from the Skylab space station in earth orbit. North of Mobile the Tombigbee and Alabama Rivers join to form the Mobile River. Detailed configuration of the individual stream channels and boundaries can be defined as the Mobile River flows into Mobile Bay and into the Gulf of Mexico. The Mobile River Valley with its numerous stream channels is a distinct light shade in contrast to the dark green shade of the adjacent areas. The red coloration of Mobile Bay reflects the sediment load carried into the bay by the rivers. The westerly movement of the shore currents at the mouth of Mobile Bay is shown by the contrasting light blue of the sediment-laden current the the blue of the Gulf. Agricultural areas east and west of Mobile Bay are characterized by a rectangular pattern in green to white shades. Color variations may reflect

Spatial and temporal variation in distribution of mangroves in Moreton Bay, subtropical Australia: a comparison of pattern metrics and change detection analyses based on aerial photographs

NASA Astrophysics Data System (ADS)

Manson, F. J.; Loneragan, N. R.; Phinn, S. R.

2003-07-01

An assessment of the changes in the distribution and extent of mangroves within Moreton Bay, southeast Queensland, Australia, was carried out. Two assessment methods were evaluated: spatial and temporal pattern metrics analysis, and change detection analysis. Currently, about 15,000 ha of mangroves are present in Moreton Bay. These mangroves are important ecosystems, but are subject to disturbance from a number of sources. Over the past 25 years, there has been a loss of more than 3800 ha, as a result of natural losses and mangrove clearing (e.g. for urban and industrial development, agriculture and aquaculture). However, areas of new mangroves have become established over the same time period, offsetting these losses to create a net loss of about 200 ha. These new mangroves have mainly appeared in the southern bay region and the bay islands, particularly on the landward edge of existing mangroves. In addition, spatial patterns and species composition of mangrove patches have changed. The pattern metrics analysis provided an overview of mangrove distribution and change in the form of single metric values, while the change detection analysis gave a more detailed and spatially explicit description of change. An analysis of the effects of spatial scales on the pattern metrics indicated that they were relatively insensitive to scale at spatial resolutions less than 50 m, but that most metrics became sensitive at coarser resolutions, a finding which has implications for mapping of mangroves based on remotely sensed data.

A review on the sources and spatial-temporal distributions of Pb in Jiaozhou Bay

NASA Astrophysics Data System (ADS)

Yang, Dongfang; Zhang, Jie; Wang, Ming; Zhu, Sixi; Wu, Yunjie

2017-12-01

This paper provided a review on the source, spatial-distribution, temporal variations of Pb in Jiaozhou Bay based on investigation of Pb in surface and waters in different seasons during 1979-1983. The source strengths of Pb sources in Jiaozhou Bay were showing increasing trends, and the pollution level of Pb in this bay was slight or moderate in the early stage of reform and opening-up. Pb contents in the marine bay were mainly determined by the strength and frequency of Pb inputs from human activities, and Pb could be moving from high content areas to low content areas in the ocean interior. Surface waters in the ocean was polluted by human activities, and bottom waters was polluted by means of vertical water’s effect. The process of spatial distribution of Pb in waters was including three steps, i.e., 1), Pb was transferring to surface waters in the bay, 2) Pb was transferring to surface waters, and 3) Pb was transferring to and accumulating in bottom waters.

Detecting the spatial and temporal variability of chlorophylla concentration and total suspended solids in Apalachicola Bay, Florida using MODIS imagery

USGS Publications Warehouse

Wang, Hongqing; Hladik, C.M.; Huang, W.; Milla, K.; Edmiston, L.; Harwell, M.A.; Schalles, J.F.

2010-01-01

Apalachicola Bay, Florida, accounts for 90% of Florida's and 10% of the nation's eastern oyster (Crassostrea virginica) harvesting. Chlorophyll-a concentration and total suspended solids (TSS) are two important water quality variables, among other environmental factors such as salinity, for eastern oyster production in Apalachicola Bay. In this research, we developed regression models of the relationships between the reflectance of the Moderate-Resolution Imaging Spectroradiometer (MODIS) Terra 250 m data and the two water quality variables based on the Bay-wide field data collected during 14-17 October 2002, a relatively dry period, and 3-5 April 2006, a relatively wet period, respectively. Then we selected the best regression models (highest coefficient of determination, R2) to derive Bay-wide maps of chlorophylla concentration and TSS for the two periods. The MODIS-derived maps revealed large spatial and temporal variations in chlorophylla concentration and TSS across the entire Apalachicola Bay. ?? 2010 Taylor & Francis.

Nutrient fluxes across sediment-water interface in Bohai Bay Coastal Zone, China.

PubMed

Mu, Di; Yuan, Dekui; Feng, Huan; Xing, Fangwei; Teo, Fang Yenn; Li, Shuangzhao

2017-01-30

Sediment cores and overlying water samples were collected at four sites in Tianjin Coastal Zone, Bohai Bay, to investigate nutrient (N, P and Si) exchanges across the sediment-water interface. The exchange fluxes of each nutrient species were estimated based on the porewater profiles and laboratory incubation experiments. The results showed significant differences between the two methods, which implied that molecular diffusion alone was not the dominant process controlling nutrient exchanges at these sites. The impacts of redox conditions and bioturbation on the nutrient fluxes were confirmed by the laboratory incubation experiments. The results from this study showed that the nutrient fluxes measured directly from the incubation experiment were more reliable than that predicted from the porewater profiles. The possible impacts causing variations in the nutrient fluxes include sewage discharge and land reclamation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of benthic changes during 20 years of monitoring the Mexican Salina Cruz Bay.

PubMed

González-Macías, C; Schifter, I; Lluch-Cota, D B; Méndez-Rodríguez, L; Hernández-Vázquez, S

2009-02-01

In this work a non-parametric multivariate analysis was used to assess the impact of metals and organic compounds in the macro infaunal component of the mollusks benthic community using surface sediment data from several monitoring programs collected over 20 years in Salina Cruz Bay, Mexico. The data for benthic mollusks community characteristics (richness, abundance and diversity) were linked to multivariate environmental patterns, using the Alternating Conditional Expectations method to correlate the biological measurements of the mollusk community with the physicochemical properties of water and sediments. Mollusks community variation is related to environmental characteristics as well as lead content. Surface deposit feeders are increasing their relative density, while subsurface deposit feeders are decreasing with respect to time, these last are expected to be more related with sediment and more affected then by its quality. However gastropods with predatory carnivore as well as chemosymbiotic deposit feeder bivalves have maintained their relative densities along time.

Identification of Phragmites australis and Spartina alterniflora in the Yangtze Estuary between Bayes and BP neural network using hyper-spectral data

NASA Astrophysics Data System (ADS)

Liu, Pudong; Zhou, Jiayuan; Shi, Runhe; Zhang, Chao; Liu, Chaoshun; Sun, Zhibin; Gao, Wei

2016-09-01

The aim of this work was to identify the coastal wetland plants between Bayes and BP neural network using hyperspectral data in order to optimize the classification method. For this purpose, we chose two dominant plants (invasive S. alterniflora and native P. australis) in the Yangtze Estuary, the leaf spectral reflectance of P. australis and S. alterniflora were measured by ASD field spectral machine. We tested the Bayes method and BP neural network for the identification of these two species. Results showed that three different bands (i.e., 555 nm 711 nm and 920 nm) could be identified as the sensitive bands for the input parameters for the two methods. Bayes method and BP neural network prediction model both performed well (Bayes prediction for 88.57% accuracy, BP neural network model prediction for about 80% accuracy), but Bayes theorem method could give higher accuracy and stability.

SEASONAL AND LONGITUDINAL HOMOGENEITY OF SUSPENDED PARTICLES IN SAN FRANCISCO BAY, CA

EPA Science Inventory

Coastal environments are particularly complex due to variations in geology and upstream watersheds, and are subject to dynamic spatial and temporal changes. Their diverse characteristics result in wide variations in response to environmental stressors such as nutrient over-enrich...

Sedimentary properties of shallow marine cores collected in June and September 2006, Hanalei Bay, Kaua‘i, Hawai‘i

USGS Publications Warehouse

Draut, Amy E.; Bothner, Michael H.; Reynolds, Richard L.; Buchan, Olivia C.; Cochran, Susan A.; Casso, Michael A.; Baldwin, Sandra M.; Goldstein, Harland L.; Xiao, Jiang; Field, Michael E.; Logan, Joshua B.

2007-01-01

Sedimentary facies, short-lived isotopes 7Be, 137Cs, and 210Pb, and magnetic properties of sediment cores in Hanalei Bay, Kaua‘i, Hawai‘i, were used to assess sediment sources and patterns of deposition associated with seasonal flooding of the Hanalei River. Sediment cores were collected from the seafloor in June and September of 2006 to supplement similar data collected during the summer of 2005. The youngest and thickest terrigenous sediment was observed on the east side of the bay: near the Hanalei River mouth and in a bathymetric depression, known locally as the Black Hole, that acts as a temporary sediment sink. Deposits from floods that occurred between February and April 2006 left flood deposits in the eastern bay that, by June of 2006, were on the order of 10 cm thick. A flood occurred on August 7, 2006, that was smaller than floods that occurred the previous winter but was a substantial discharge event for the summer season. Deposits from the winter 2006 floods continued to dominate the sedimentary record in the eastern bay through early fall, even after the addition of newer sediment during the August 7 flood; this is consistent with the much higher sediment input of the winter floods compared with the August 7 flood. Broad variations in magnetic grain size and relative magnetite-hematite abundance in several sediment cores indicate many sources of upland terrigenous sediment. As a group, recent flood deposits show much less variation in these properties compared with older deposits, implying either that the 2006 winter–spring flood sediment originated from one or more distinct upland settings, or that substantial mixing of sediment from multiple sources occurred during transport. Sediment is most readily remobilized and advected out of the bay during winter, when oceanic conditions are energetic. In summer, wave and current measurements made concurrently with this study showed weak currents and little wave energy, indicating that sediment delivered during summer floods most likely remains in the bay until winter storms can remove it. Increased turbidity and sedimentation on corals resulting from floods of the Hanalei River could affect the sustainability of coral reefs and their many associated species. This possibility is of particular concern during summer months when wave energy is low and sediment is not readily remobilized and transported out of the bay. The timing (seasonality) and magnitude of sediment input to the coastal ocean relative to seasonal variations in wave and current energy could have significant ecological consequences for coral-reef communities in the Hawaiian Islands.

Daily variation characteristics at polar geomagnetic observatories

NASA Astrophysics Data System (ADS)

Lepidi, S.; Cafarella, L.; Pietrolungo, M.; Di Mauro, D.

2011-08-01

This paper is based on the statistical analysis of the diurnal variation as observed at six polar geomagnetic observatories, three in the Northern and three in the Southern hemisphere. Data are for 2006, a year of low geomagnetic activity. We compared the Italian observatory Mario Zucchelli Station (TNB; corrected geomagnetic latitude: 80.0°S), the French-Italian observatory Dome C (DMC; 88.9°S), the French observatory Dumont D'Urville (DRV; 80.4°S) and the three Canadian observatories, Resolute Bay (RES; 83.0°N), Cambridge Bay (CBB; 77.0°N) and Alert (ALE, 87.2°N). The aim of this work was to highlight analogies and differences in daily variation as observed at the different observatories during low geomagnetic activity year, also considering Interplanetary Magnetic Field conditions and geomagnetic indices.

Total petroleum hydrocarbons and heavy metals in the surface sediments of Bohai Bay, China: long-term variations in pollution status and adverse biological risk.

PubMed

Zhou, Ran; Qin, Xuebo; Peng, Shitao; Deng, Shihuai

2014-06-15

Surface sediments collected from 2001 to 2011 were analyzed for total petroleum hydrocarbons (TPH) and five heavy metals. The sediment concentration ranges of TPH, Zn, Cu, Pb, Cd and Hg were 6.3-535 μg/g, 58-332 μg/g, 7.2-63 μg/g, 4.3-138 μg/g, 0-0.98μg/g, and 0.10-0.68 μg/g, respectively. These results met the highest marine sediment quality standards in China, indicating that the sediment was fairly clean. However, based on the effects range-median (ERM) quotient method, the calculated values for all of the sampling sites were higher than 0.10, suggesting that there was a potential adverse biological risk in Bohai Bay. According to the calculated results, the biological risk decreased from 2001 to 2007 and increased afterwards. High-risk sites were mainly distributed along the coast. This study suggests that anthropogenic influences might be responsible for the potential risk of adverse biological effects from TPH and heavy metals in Bohai Bay. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spatial and temporal variations in silver contamination and toxicity in San Francisco Bay

USGS Publications Warehouse

Flegal, A.R.; Brown, C.L.; Squire, S.; Ross, J.R.M.; Scelfo, G.M.; Hibdon, S.

2007-01-01

Although San Francisco Bay has a "Golden Gate", it may be argued that it is the "Silver Estuary". For at one time the Bay was reported to have the highest levels of silver in its sediments and biota, along with the only accurately measured values of silver in solution, of any estuarine system. Since then others have argued that silver contamination is higher elsewhere (e.g., New York Bight, Florida Bay, Galveston Bay) in a peculiar form of pollution machismo, while silver contamination has measurably declined in sediments, biota, and surface waters of the Bay over the past two to three decades. Documentation of those systemic temporal declines has been possible because of long-term, ongoing monitoring programs, using rigorous trace metal clean sampling and analytical techniques, of the United States Geological Survey and San Francisco Bay Regional Monitoring Program that are summarized in this report. However, recent toxicity studies with macro-invertebrates in the Bay have indicated that silver may still be adversely affecting the health of the estuarine system, and other studies have indicated that silver concentrations in the Bay may be increasing due to new industrial inputs and/or the diagenetic remobilization of silver from historically contaminated sediments being re-exposed to overlying surface waters and benthos. Consequently, the Bay may not be ready to relinquish its title as the "Silver Estuary". ?? 2007 Elsevier Inc. All rights reserved.

Mixing to Monsoons: Air-Sea Interactions in the Bay of Bengal

NASA Astrophysics Data System (ADS)

Lucas, A. J.; Shroyer, E. L.; Wijesekera, H. W.; Fernando, H. J. S.; D'Asaro, E.; Ravichandran, M.; Jinadasa, S. U. P.; MacKinnon, J. A.; Nash, J. D.; Sharma, R.; Centurioni, L.; Farrar, J. T.; Weller, R.; Pinkel, R.; Mahadevan, A.; Sengupta, D.; Tandon, A.

2014-07-01

More than 1 billion people depend on rainfall from the South Asian monsoon for their livelihoods. Summertime monsoonal precipitation is highly variable on intraseasonal time scales, with alternating "active" and "break" periods. These intraseasonal oscillations in large-scale atmospheric convection and winds are closely tied to 1°C-2°C variations of sea surface temperature in the Bay of Bengal.

Dissolved trace elements in a nitrogen-polluted river near to the Liaodong Bay in Northeast China.

PubMed

Bu, Hongmei; Song, Xianfang; Guo, Fen

2017-01-15

Dissolved trace element concentrations (Ba, Fe, Mn, Si, Sr, and Zn) were investigated in the Haicheng River near to the Liaodong Bay in Northeast China during 2010. Dissolved Ba, Fe, Mn, and Sr showed significant spatial variation, whereas dissolved Fe, Mn, and Zn displayed seasonal variations. Conditions such as water temperature, pH, and dissolved oxygen were found to have an important impact on redox reactions involving dissolved Ba, Fe, and Zn. Dissolved Fe and Mn concentrations were regulated by adsorption or desorption of Fe/Mn oxyhydroxides and the effects of organic carbon complexation on dissolved Ba and Sr were found to be significant. The sources of dissolved trace elements were found to be mainly from domestic sewage, industrial waste, agricultural surface runoff, and natural origin, with estimated seasonal and annual river fluxes established as important inputs of dissolved trace elements from the Haicheng River into the Liaodong Bay or Bohai Sea. Copyright © 2016 Elsevier Ltd. All rights reserved.

76 FR 12356 - A Method To Assess Climate-Relevant Decisions: Application in the Chesapeake Bay

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-07

... ENVIRONMENTAL PROTECTION AGENCY [FRL-9276-3] A Method To Assess Climate-Relevant Decisions: Application in the Chesapeake Bay AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of..., ``A Method to Assess Climate-Relevant Decisions: Application in the Chesapeake Bay'' (EPA/600/R-10...

Physical property data from the ICDP-USGS Eyreville cores A and B, Chesapeake Bay impact structure, Virginia, USA, acquired using a multisensor core logger

USGS Publications Warehouse

Pierce, H.A.; Murray, J.B.

2009-01-01

The International Continental Scientific Drilling Program (ICDP) and the U.S. Geological Survey (USGS) drilled three core holes to a composite depth of 1766 m within the moat of the Chesapeake Bay impact structure. Core recovery rates from the drilling were high (??90%), but problems with core hole collapse limited the geophysical downhole logging to natural-gamma and temperature logs. To supplement the downhole logs, ??5% of the Chesapeake Bay impact structure cores was processed through the USGS GeoTek multisensor core logger (MSCL) located in Menlo Park, California. The measured physical properties included core thickness (cm), density (g cm-3), P-wave velocity (m s-1), P-wave amplitude (%), magnetic susceptibility (cgs), and resistivity (ohm-m). Fractional porosity was a secondary calculated property. The MSCL data-sampling interval for all core sections was 1 cm longitudinally. Photos of each MSCL sampled core section were imbedded with the physical property data for direct comparison. These data have been used in seismic, geologic, thermal history, magnetic, and gravity models of the Chesapeake Bay impact structure. Each physical property curve has a unique signature when viewed over the full depth of the Chesapeake Bay impact structure core holes. Variations in the measured properties reflect differences in pre-impact target-rock lithologies and spatial variations in impact-related deformation during late-stage crater collapse and ocean resurge. ?? 2009 The Geological Society of America.

Clam density and scaup feeding behavior in San Pablo Bay, California

USGS Publications Warehouse

Poulton, Victoria K.; Lovvorn, James R.; Takekawa, John Y.

2002-01-01

San Pablo Bay, in northern San Francisco Bay, California, is an important wintering area for Greater (Aythya marila) and Lesser Scaup (A. affinis). We investigated variation in foraging behavior of scaup among five sites in San Pablo Bay, and whether such variation was related to densities of their main potential prey, the clams Potamocorbula amurensis and Macoma balthica. Time-activity budgets showed that scaup spent most of their time sleeping at some sites, and both sleeping and feeding at other sites, with females feeding more than males. In the first half of the observation period (12 January–5 February 2000), percent time spent feeding increased with increasing density of P. amurensis, but decreased with increasing density of M. balthica (diet studies have shown that scaup ate mostly P. amurensis and little or no M. balthica). Densities of M. balthica stayed about the same between fall and spring benthic samples, while densities of P. amurensis declined dramatically at most sites. In the second half of the observation period (7 February–3 March 2000), percent time feeding was no longer strongly related to P. amurensis densities, and dive durations increased by 14%. These changes probably reflected declines of P. amurensis, perhaps as affected by scaup predation. The large area of potential feeding habitat, and alternative prey elsewhere in the estuary, might have resulted in the low correlations between scaup behavior and prey densities in San Pablo Bay. These low correlations made it difficult to identify specific areas of prey concentrations important to scaup.

Postimpact deposition in the Chesapeake Bay impact structure: Variations in eustasy, compaction, sediment supply, and passive-aggressive tectonism

USGS Publications Warehouse

Kulpecz, A.A.; Miller, K.G.; Browning, J.V.; Edwards, L.E.; Powars, D.S.; McLaughlin, P.P.; Harris, A.D.; Feigenson, M.D.

2009-01-01

The Eyreville and Exmore, Virginia, core holes were drilled in the inner basin and annular trough, respectively, of the Chesapeake Bay impact structure, and they allow us to evaluate sequence deposition in an impact crater. We provide new high-resolution geochronologic (<1 Ma) and sequence-stratigraphic interpretations of the Exmore core, identify 12 definite (and four possible) postimpact depositional sequences, and present comparisons with similar results from Eyreville and other mid- Atlantic core holes. The concurrence of increases in ??18O with Chesapeake Bay impact structure sequence boundaries indicates a primary glacioeustatic control on deposition. However, regional comparisons show the differential preservation of sequences across the mid-Atlantic margin. We explain this distribution by the compaction of impactites, regional sediment-supply changes, and the differential movement of basement structures. Upper Eocene strata are thin or missing updip and around the crater, but they thicken into the inner basin (and offshore to the southeast) due to rapid crater infilling and concurrent impactite compaction. Oligocene sequences are generally thin and highly dissected throughout the mid-Atlantic region due to sediment starvation and tectonism, except in southeastern New Jersey. Regional tectonic uplift of the Norfolk Arch coupled with a southward decrease in sediment supply resulted in: (1) largely absent Lower Miocene sections around the Chesapeake Bay impact structure compared to thick sections in New Jersey and Delaware; (2) thick Middle Miocene sequences across the Delmarva Peninsula that thin south of the Chesapeake Bay impact structure; and (3) upper Middle Miocene sections that pinch out just north of the Chesapeake Bay impact structure. Conversely, the Upper Miocene-Pliocene section is thick across Virginia, but it is poorly represented in New Jersey because of regional variations in relative subsidence. ?? 2009 The Geological Society of America.

Biometric, microstructural, and high-resolution trace element studies in Crassostrea gigas of Cantabria (Bay of Biscay, Spain): Anthropogenic and seasonal influences

NASA Astrophysics Data System (ADS)

Higuera-Ruiz, R.; Elorza, J.

2009-04-01

Living Crassostrea gigas oysters of different ages and sizes were collected in three estuaries of Cantabria (Bay of Biscay, Spain): San Vicente de la Barquera Estuary, Santander Bay, and Marismas de Santoña Estuary. The main objective was to determine different shell responses to variable environmental parameters. A shell morphological study, based on three biometric indices, indicates that oysters of Santander Bay have two significant shell anomalies: abnormal thickening of the right valve and loss of vital cavity volume. These shell abnormalities are related with the presence in these waters of the chemical tributyltin. In the other two estuaries, the oysters show no detectable anomalies. Four shell microstructures have been distinguished: Regular Simple Prismatic, Regular Foliated, cone-Complex Cross Foliated, and Chalk. In Santander Bay oysters, the Chalk forms a "root-type" framework, whereas in the other two estuaries it forms a more compact microstructure. It is proposed that exposure to tributyltin has produced this modification. High-spatial-resolution geochemical transects have been carried out on the Regular Foliated microstructure in the umbo region in order to evaluate the distribution of Mg, Sr, and Na. The elements analysed exhibit clear cyclic variations in San Vicente de la Barquera Estuary and Marismas de Santoña Estuary oysters, related with seasonal periods, and characterised by broad maxima during months in which the waters are warmer and have higher salinity. These patterns are buffered in Santander Bay oysters. Our results demonstrate that biometric, microstructural, and high-resolution trace element studies in oyster shells can provide information about contaminants and seasonal variations in the estuarine environment.

Applications of HCMM data to soil moisture snow and estuarine current studies. [soil moisture in Minnesota and water circulation in the Delaware Bay and Potomac River

NASA Technical Reports Server (NTRS)

Wiesnet, D. R. (Principal Investigator); Mcginnis, D. F.; Matson, M.

1979-01-01

The author has identified the following significant results. Additional analyses of Luverne, Minnesota ground data revealed that soil moisture variations are independent of elevation effects. Tidal fluctuations in the Potomac River and Delaware Bay were examined as a function of surface temperature. Preliminary findings suggest that temperature boundaries are sufficient to detect various stages of the tidal cycle in Delaware Bay, but are as yet uncertain for prediction in the Potomac River. At least three additional cases are needed to completely evaluate the tidal cycle. An alphanumeric printout at a scale of 1:1,000,000 compares closely with a 1:1,000,000 scale DMD image of the Chesapeake Bay region.

Spatial and overwinter changes in clam populations of San Pablo Bay, a semiarid estuary with highly variable freshwater inflow

USGS Publications Warehouse

Poulton, V.K.; Lovvorn, J.R.; Takekawa, John Y.

2004-01-01

In many estuaries worldwide, climate trends together with human diversion of fresh water have dramatically impacted the benthos. Such impacts have sometimes been complicated by exotic species, whose invasion and persistence can be mediated by wide variations in freshwater inflow. Monitoring such changes usually involves periodic samples at a few sites; but sampling that does not recognize variation at a range of spatial and seasonal scales may not reveal important benthic trends. San Pablo Bay, in northern San Francisco Bay, has extreme fluctuations in freshwater inflow. This bay also experienced a major benthic change with introduction of the Asian clam (Potamocorbula amurensis) in 1986. This species initially displaced the former community, but later appeared to vary in abundance depending on site and freshwater inflow. To investigate such patterns and provide guidelines for research and monitoring, we took 1746 core samples at six sites around San Pablo Bay from 19 October to 17 December 1999 and from 6 March to 19 April 2000. Most biomass consisted of the clams P. amurensis,Macoma balthica and Mya arenaria. Potamocorbula amurensis dominated the benthos at most sites in the fall and recruited a new cohort during winter, while there was weak recruitment in M. balthica and none in M. arenaria. At most but not all sites, densities of P. amurensis and M. arenaria declined dramatically over winter while M. balthica declined only slightly. The dominant clams had patch diameters >5 m at most but not all sites, and some showed inconsistent patch structure at scales of 100–1400 m. In this semiarid estuary with highly variable freshwater inflow, samples for research and monitoring should include multiple sites and seasons, and samples within sites should be ≥5 m apart to account for between-patch variation. Species abundance in winter 1999–2000 appeared to be affected by high freshwater inflows in 1997–1999, while spatial patterns were probably most affected by post-settlement dispersal and mortality.

Seasonal variations of carbonate system parameters and nutrients at the shellfish-farming bays along the south coast of Korea

NASA Astrophysics Data System (ADS)

Shim, JeongHee; Shim, Jeong-Min; Lee, Yong-Hwa

2017-04-01

About 80 90% of the annual mass production of shellfish in Korea are cultured at the inner bays including Jinhae, Tongyeong and Geoje regions, along the south coast of Korea. To understand coastal carbon and nutrients cycles and those effects/feedbacks on shellfish farming, carbonate (DIC, TA and pH) and environmental parameters were observed at Jinhae, Tongyeong and Geoje Bays 4 times (in Feb., Aug. 2014, Apr. and Oct. 2015 and are considered representative of winter, summer, spring and fall respectively). Surface temperature in the bays showed clear seasonal variation with about 6 12°C and 24 29°C in Feb. and Aug. 2014, respectively and 14 18°C and 22 26°C in Apr. and in Oct. 2015, respectively. Surface pHNBS also ranged with about 8.20 8.53 and 7.28 8.95 in Feb. and Aug. 2014, and 8.04 8.40 and 7.91 8.32 in Apr. and in Oct. 2015. High pH with low salinity in summer resulted from input of land discharge in rainy seasons, however high pH at small bays in Apr. and Oct. 2015 resulted from massive primary production by phytoplankton bloom, supported by high chlorophyll a concentrations. Seasonal variations of DIC and phosphate in the surface and bottom waters correlated largely with salinity, higher in winter and lower in summer. Specifically in shellfish (specially, oyster and mussel) growing season, aragonite saturation state (Ωarag) in bottom water ranged about 0.2 2.9 (mean 2.1) and 2.2 5.0 (mean 3.2) in Feb. 2014 and Oct. 2015, respectively, suggesting low pH environments arose seasonally in coastal area due to some mechanisms. These results suggest that seasonal ocean acidification state might seriously affect shell growth, mass production and thus shellfish industry along the south coast of Korea.

Factors affecting spatial and temporal variability in material exchange between the Southern Everglades wetlands and Florida Bay (USA)

NASA Astrophysics Data System (ADS)

Sutula, Martha A.; Perez, Brian C.; Reyes, Enrique; Childers, Daniel L.; Davis, Steve; Day, John W.; Rudnick, David; Sklar, Fred

2003-08-01

Physical and biological processes controlling spatial and temporal variations in material concentration and exchange between the Southern Everglades wetlands and Florida Bay were studied for 2.5 years in three of the five major creek systems draining the watershed. Daily total nitrogen (TN), and total phosphorus (TP) fluxes were measured for 2 years in Taylor River, and ten 10-day intensive studies were conducted in this creek to estimate the seasonal flux of dissolved inorganic nitrogen (N), phosphorus (P), total organic carbon (TOC), and suspended matter. Four 10-day studies were conducted simultaneously in Taylor, McCormick, and Trout Creeks to study the spatial variation in concentration and flux. The annual fluxes of TOC, TN, and TP from the Southern Everglades were estimated from regression equations. The Southern Everglades watershed, a 460-km 2 area that includes Taylor Slough and the area south of the C-111 canal, exported 7.1 g C m -2, 0.46 g N m -2, and 0.007 g P m -2, annually. Everglades P flux is three to four orders of magnitude lower than published flux estimates from wetlands influenced by terrigenous sedimentary inputs. These low P flux values reflect both the inherently low P content of Everglades surface water and the efficiency of Everglades carbonate sediments and biota in conserving and recycling this limiting nutrient. The seasonal variation of freshwater input to the watershed was responsible for major temporal variations in N, P, and C export to Florida Bay; approximately 99% of the export occurred during the rainy season. Wind-driven forcing was most important during the later stages of the dry season when low freshwater head coincided with southerly winds, resulting in a net import of water and materials into the wetlands. We also observed an east to west decrease in TN:TP ratio from 212:1 to 127:1. Major spatial gradients in N:P ratios and nutrient concentration and flux among the creek were consistent with the westward decrease in surface water runoff from the P-limited Everglades and increased advection of relatively P-rich Gulf of Mexico (GOM) waters into Florida Bay. Comparison of measured nutrient flux from Everglades surface water inputs from this study with published estimates of other sources of nutrients to Florida Bay (i.e. atmospheric deposition, anthropogenic inputs from the Florida Keys, advection from the GOM) show that Everglades runoff represents only 2% of N inputs and 0.5% of P input to Florida Bay.

[Atmospheric depositions of biogenic elements and their ecological effects on marine ecosystem of Jiaozhou Bay: A review].

PubMed

Xing, Jian Wei; Song, Jin Ming; Yuan, Hua Mao; Li, Xue Gang; Li, Ning; Duan, Li Qin; Qu, Bao Xiao; Kang, Xu Ming

2017-01-01

As a typical semi-closed bay, Jiaozhou Bay, is remarkably affected by human activities. Biogenic elements transported into the oceans by the atmospheric deposition of anthropogenic particles can lead to profound impacts on the ecosystem of Jiaozhou Bay. In this paper, the researches of atmospheric dry and wet depositions in the Jiaozhou Bay were systematically summarized from the following three aspects: study methods, variation characteristics of the fluxes and their influencing factors and the ecological effects of atmospheric deposition. The concentrations and fluxes of nitrogen species in atmospheric dry and wet depositions were very high in the Jiaozhou Bay compared with other bays, estuaries and marginal seas around the world. The dissolved inorganic nitrogen (DIN) was the main component of the total dissolved nitrogen (TDN) and the dissolved organic nitrogen (DON) accounted for 22%-31% of TDN. However, the concentrations and fluxes of phosphate and silicate species were very low. The atmospheric deposition fluxes of (NO 3 - -N+NO 2 - -N) were slightly higher than terrestrial inputs, while the fluxes of NH 4 + -N, PO 4 3- -P and SiO 3 2- -Si were very low compared with terrestrial inputs. The concentration of total suspended particulates (TSP) in the air, the intensity of the emission sources, precipitation amount and meteorological conditions are the major factors influencing the atmospheric depositions of biogenic elements, which can increase the primary productivity, change the structure of nutrients and the structure of phytoplankton communities in surface seawater and further promote the succession of phytoplankton dominant species from diatom to dinoflagellate in the Jiaozhou Bay. On that basis, the future research should be focused on constructing the monitoring network for atmospheric dry and wet depositions, accurately quantifying the deposition rates of aerosol particles of different forms and sizes, recognizing the ecological effects and biogeochemical mechanisms of atmospheric depositions of biogenic elements and discriminating the mechanisms, fluxes and influencing factors of atmospheric deposition biogenic elements via indirect approaches such as overland runoff, sheetflood and permeation etc. It is significant for illuminating the effects of anthropogenic activities on the coastal waters as well as understanding the bio-geochemical processes of biogenic elements in marginal seas by elucidating atmospheric depositions of biogenic elements in the Jiaozhou Bay.

Extremes in ecology: Avoiding the misleading effects of sampling variation in summary analyses

USGS Publications Warehouse

Link, W.A.; Sauer, J.R.

1996-01-01

Surveys such as the North American Breeding Bird Survey (BBS) produce large collections of parameter estimates. One's natural inclination when confronted with lists of parameter estimates is to look for the extreme values: in the BBS, these correspond to the species that appear to have the greatest changes in population size through time. Unfortunately, extreme estimates are liable to correspond to the most poorly estimated parameters. Consequently, the most extreme parameters may not match up with the most extreme parameter estimates. The ranking of parameter values on the basis of their estimates are a difficult statistical problem. We use data from the BBS and simulations to illustrate the potential misleading effects of sampling variation in rankings of parameters. We describe empirical Bayes and constrained empirical Bayes procedures which provide partial solutions to the problem of ranking in the presence of sampling variation.

Development, implementation, and validation of a modeling system for the San Francisco Bay and Estuary

NASA Astrophysics Data System (ADS)

Chao, Yi; Farrara, John D.; Zhang, Hongchun; Zhang, Yinglong J.; Ateljevich, Eli; Chai, Fei; Davis, Curtiss O.; Dugdale, Richard; Wilkerson, Frances

2017-07-01

A three-dimensional numerical modeling system for the San Francisco Bay is presented. The system is based on an unstructured grid numerical model known as Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM). The lateral boundary condition is provided by a regional coastal ocean model. The surface forcing is provided by a regional atmospheric model. The SCHISM results from a decadal hindcast run are compared with available tide gauge data, as well as a collection of temperature and salinity profiles. An examination of the observed climatological annual mean salinities at the United States Geological Survey (USGS) stations shows the highest salinities to be in the open ocean and the lowest well north (upstream) of the Central Bay, a pattern that does not change substantially with season. The corresponding mean SCHISM salinities reproduced the observed variations with location quite well, though with a fresh bias. The lowest values within the Bay occur during spring and the highest values during autumn, mirroring the seasonal variations in river discharge. The corresponding observed mean temperatures within the Bay were 2 to 3° C cooler in the Central Bay than to either the north or south. This observed pattern of a cooler Central Bay was not particularly well reproduced in the SCHISM results, which also showed a cold bias. Examination of the seasonal means revealed that the cool Central Bay pattern is found only during summer in the SCHISM results. The persistent cold and fresh biases in the model control run were nearly eliminated in a sensitivity run with modifications to the surface heat flux and river discharge. The surface atmospheric forcing and the heat flux at the western boundary are found to be the two major terms in a SCHISM-based heat budget analysis of the mean seasonal temperature cycle for the Central Bay. In the Central Bay salt budget, freshwater discharged by rivers into upstream portions of the Bay to the north balanced by the influx of salt from the west are the primary drivers of the mean seasonal salinity cycle. Concerning the interannual variability in temperatures, the warm anomalies during the period 2014-16 were the strongest and most persistent departures from normal during the period analyzed and were realistically reproduced by SCHISM. The most prominent salinity anomalies in both the observations and SCHISM results were the salty anomalies that persisted for most of the four-year California drought of 2012-2015.

Analysis of change of red tide species in Yodo River estuary by the numerical ecosystem model.

PubMed

Hayashi, Mitsuru; Yanagi, Tetsuo

2008-01-01

Occurrence number of red tides in Osaka Bay in Japan is more than 20 cases every year. Diatom red tide was dominant in Osaka Bay, but the non-diatom red tide was dominant in early 1990s. Therefore, the material cycling in Yodo River estuary in Osaka Bay during August from 1991 to 2000 was analyzed by using the numerical ecosystem model and field observation data to clarify the reasons of change in red tide species. Year-to-year variation in calculated concentration ratio of diatom to non-diatom corresponds to the variation in observed ratio of red tide days of diatom to non-diatom. Limiting nutrient of primary production is phosphate over the period. Diatom dominated from 1991 to 1993, but it was difficult for non-diatom to grow due to the limitation by physical condition. Non-diatom was able to grow because of good physical and nutrient conditions from 1994 to 1996. And diatom dominated again under the good physical condition, and phosphorus supply was not enough for non-diatom to grow from 1998 to 2000. Phosphate concentration in the lower layer of Yodo River estuary was important to the variation in red tide species in the upper layer of Yodo River estuary.

Make It Short and Easy: Username Complexity Determines Trustworthiness Above and Beyond Objective Reputation

PubMed Central

Silva, Rita R.; Chrobot, Nina; Newman, Eryn; Schwarz, Norbert; Topolinski, Sascha

2017-01-01

Can the mere name of a seller determine his trustworthiness in the eye of the consumer? In 10 studies (total N = 608) we explored username complexity and trustworthiness of eBay seller profiles. Name complexity was manipulated through variations in username pronounceability and length. These dimensions had strong, independent effects on trustworthiness, with sellers with easy-to-pronounce or short usernames being rated as more trustworthy than sellers with difficult-to-pronounce or long usernames, respectively. Both effects were repeatedly found even when objective information about seller reputation was available. We hypothesized the effect of name complexity on trustworthiness to be based on the experience of high vs. low processing fluency, with little awareness of the underlying process. Supporting this, participants could not correct for the impact of username complexity when explicitly asked to do so. Three alternative explanations based on attributions of the variations in name complexity to seller origin (ingroup vs. outgroup), username generation method (seller personal choice vs. computer algorithm) and age of the eBay profiles (10 years vs. 1 year) were tested and ruled out. Finally, we show that manipulating the ease of reading product descriptions instead of the sellers’ names also impacts the trust ascribed to the sellers. PMID:29312062

Intraspecific variation in Cryptocaryon irritans.

PubMed

Diggles, B K; Adlard, R D

1997-01-01

Intraspecific variation in the ciliate Cryptocaryon irritans was examined using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA) combined with developmental and morphological characters. Amplified rDNA sequences consisting of 151 bases of the flanking 18 S and 5.8 S regions, and the entire ITS-1 region (169 or 170 bases), were determined and compared for 16 isolates of C. irritans from Australia, Israel and the USA. There was one variable base between isolates in the 18 S region and 11 variable bases in the ITS-1 region. Despite their similar morphology, significant sequence variation (4.1% divergence) and developmental differences indicate that Australian C. irritans isolates from estuarine (Moreton Bay) and coral reef (Heron Island) environments are distinct. The Heron Island isolate was genetically closer to morphologically dissimilar isolates from Israel (1.8% divergence) and the USA (2.3% divergence) than it was to the Moreton Bay isolates. Three isolates maintained in our laboratory since February 1994 differed in sequence from earlier laboratory isolates (2.9% to 3.5% divergence), even though all were similar morphologically and originated from the same source. During this time the sequence of the isolates from wild fish in Moreton Bay remained unchanged. These genetic differences indicate the existence of a founder effect in laboratory populations of C. irritans. The genetic variation found here, combined with known morphological and developmental differences, is used to characterise four strains of C. irritans.

Seasonal and spatial variations of water quality and trophic status in Daya Bay, South China Sea.

PubMed

Wu, Mei-Lin; Wang, You-Shao; Wang, Yu-Tu; Sun, Fu-Lin; Sun, Cui-Ci; Cheng, Hao; Dong, Jun-De

2016-11-15

Coastal water quality and trophic status are subject to intensive environmental stress induced by human activities and climate change. Quarterly cruises were conducted to identify environmental characteristics in Daya Bay in 2013. Water quality is spatially and temporally dynamic in the bay. Cluster analysis (CA) groups 12 monitoring stations into two clusters. Cluster I consists of stations (S1, S2, S4-S7, S9, and S12) located in the central, eastern, and southern parts of the bay, representing less polluted regions. Cluster II includes stations (S3, S8, S10, and S11) located in the western and northern parts of the bay, indicating the highly polluted regions receiving a high amount of wastewater and freshwater discharge. Principal component analysis (PCA) identified that water quality experience seasonal change (summer, winter, and spring-autumn seasons) because of two monsoons in the study area. Eutrophication in the bay is graded as high by Assessment of Estuarine Trophic Status (ASSETS). Copyright © 2016 Elsevier Ltd. All rights reserved.

Processes of 30-90 days sea surface temperature variability in the northern Indian Ocean during boreal summer

NASA Astrophysics Data System (ADS)

Vialard, J.; Jayakumar, A.; Gnanaseelan, C.; Lengaigne, M.; Sengupta, D.; Goswami, B. N.

2012-05-01

During summer, the northern Indian Ocean exhibits significant atmospheric intraseasonal variability associated with active and break phases of the monsoon in the 30-90 days band. In this paper, we investigate mechanisms of the Sea Surface Temperature (SST) signature of this atmospheric variability, using a combination of observational datasets and Ocean General Circulation Model sensitivity experiments. In addition to the previously-reported intraseasonal SST signature in the Bay of Bengal, observations show clear SST signals in the Arabian Sea related to the active/break cycle of the monsoon. As the atmospheric intraseasonal oscillation moves northward, SST variations appear first at the southern tip of India (day 0), then in the Somali upwelling region (day 10), northern Bay of Bengal (day 19) and finally in the Oman upwelling region (day 23). The Bay of Bengal and Oman signals are most clearly associated with the monsoon active/break index, whereas the relationship with signals near Somali upwelling and the southern tip of India is weaker. In agreement with previous studies, we find that heat flux variations drive most of the intraseasonal SST variability in the Bay of Bengal, both in our model (regression coefficient, 0.9, against ~0.25 for wind stress) and in observations (0.8 regression coefficient); ~60% of the heat flux variation is due do shortwave radiation and ~40% due to latent heat flux. On the other hand, both observations and model results indicate a prominent role of dynamical oceanic processes in the Arabian Sea. Wind-stress variations force about 70-100% of SST intraseasonal variations in the Arabian Sea, through modulation of oceanic processes (entrainment, mixing, Ekman pumping, lateral advection). Our ~100 km resolution model suggests that internal oceanic variability (i.e. eddies) contributes substantially to intraseasonal variability at small-scale in the Somali upwelling region, but does not contribute to large-scale intraseasonal SST variability due to its small spatial scale and random phase relation to the active-break monsoon cycle. The effect of oceanic eddies; however, remains to be explored at a higher spatial resolution.

Dynamics of sediment carbon stocks across intertidal wetland habitats of Moreton Bay, Australia.

PubMed

Hayes, Matthew A; Jesse, Amber; Hawke, Bruce; Baldock, Jeff; Tabet, Basam; Lockington, David; Lovelock, Catherine E

2017-10-01

Coastal wetlands are known for high carbon storage within their sediments, but our understanding of the variation in carbon storage among intertidal habitats, particularly over geomorphological settings and along elevation gradients, is limited. Here, we collected 352 cores from 18 sites across Moreton Bay, Australia. We assessed variation in sediment organic carbon (OC) stocks among different geomorphological settings (wetlands within riverine settings along with those with reduced riverine influence located on tide-dominated sand islands), across elevation gradients, with distance from shore and among habitat and vegetation types. We used mid-infrared (MIR) spectroscopy combined with analytical data and partial least squares regression to quantify the carbon content of ~2500 sediment samples and provide fine-scale spatial coverage of sediment OC stocks to 150 cm depth. We found sites in river deltas had larger OC stocks (175-504 Mg/ha) than those in nonriverine settings (44-271 Mg/ha). Variation in OC stocks among nonriverine sites was high in comparison with riverine and mixed geomorphic settings, with sites closer to riverine outflow from the east and south of Moreton Bay having higher stocks than those located on the sand islands in the northwest of the bay. Sediment OC stocks increased with elevation within nonriverine settings, but not in riverine geomorphic settings. Sediment OC stocks did not differ between mangrove and saltmarsh habitats. OC stocks did, however, differ between dominant species across the research area and within geomorphic settings. At the landscape scale, the coastal wetlands of the South East Queensland catchments (17,792 ha) are comprised of approximately 4,100,000-5,200,000 Mg of sediment OC. Comparatively high variation in OC storage between riverine and nonriverine geomorphic settings indicates that the availability of mineral sediments and terrestrial derived OC may exert a strong influence over OC storage potential across intertidal wetland systems. © 2017 John Wiley & Sons Ltd.

Temporal variation of persistent organic pollutant (POP) residue concentrations in sediments from the bay of Chetumal, Mexico.

PubMed

Noreña-Barroso, E; Gold-Bouchot, G; Ceja-Moreno, V

2007-08-01

Bay of Chetumal is a transboundary priority area for the Mesoamerican Barrier Reef Systems project, which has been studied because it is the receiving body of pollutants from a large agricultural area and the city of Chetumal. Levels of persistent organic pollutants in sediments from the Bay were assessed a few years after a mass mortality event of Mayan catfish (Ariopsis assimilis) occurred in 1996. Recent sediments were collected in the rainy season (1999) and dry season (2000); results show concentrations in general lower than those reported after the fish kill, and a change of chemical profiles in chemical pollution.

From empirical Bayes to full Bayes : methods for analyzing traffic safety data.

DOT National Transportation Integrated Search

2004-10-24

Traffic safety engineers are among the early adopters of Bayesian statistical tools for : analyzing crash data. As in many other areas of application, empirical Bayes methods were : their first choice, perhaps because they represent an intuitively ap...

THREE YEAR VARIATION IN SHELL GROWTH OF THEMUSSEL, ELLIPTIO WACCAMAWENSIS (LEA), IN LAKEWACCAMAW, A BAY LAKE IN NORTH CAROLINA

EPA Science Inventory

Freshwater mussels (Bivalvia: Unionidae) are one of the most endangered animal taxa in North America, and continued research on unionids will improve management decisions regarding their conservation. One unexplored aspect of unionid ecology is the magnitude of interannual variat...

Seasonal sedimentary processes of the macrotidal flat in Gomso Bay, west coast of Korea

NASA Astrophysics Data System (ADS)

Woo, H.; Kang, J.; Choi, J.

2012-12-01

The tidal flats on the west coast of Korea have broad zones with gentle slopes and a macrotidal setting with 4 to 10 meters of tidal ranges. They are directly influenced by monsoons and heavily affected by waves in winter and tidal currents in summer. As a result, most western tidal flats show the seasonal changes of sedimentary features comprising sedimentation and/or erosion of sediments. Gomso bay in the mid-west of Korea is a funnel-shaped embayment with a wide entrance to the west. Tides are semidiurnal and macrotidal, with a mean tidal range of 433.8 cm. Digital elevation model (DEM) showed that the landward inner bay had mainly high elevations and the seaward outer bay had relatively low elevations. In particular, there are considerable gradients in the outer bay from area of high-water line to area of low-water line. The sedimentary analysis and monitoring short-term sedimentation rates were investigated to understand seasonal sedimentary processes of tidal flats in Gomso bay. The surface sediments in the bay were classified into five sedimentary facies in spring 2011. Generally, sandy sediments were dominated in the outer bay, whereas sandy mud sediments were distributed on the inner bay. The middle bay mainly consisted of muddy sand sediments. The percentages of sand decreased from outer to inner bay. The short-term sedimentation rates were obtained from three lines by burying a plate at sub-bottom depth and periodically measuring the changing sediment depth from February 2011 to February 2012. In the tidal flat at inner bay (KB- Line), the annual sedimentation rates were ranged -8.87 to 74.69 mm/year with the net deposition rate of 40.90 mm/year. The deposition occurred on KB-Line in spring, autumn and winter. The erosion was dominated on the tidal flats at middle (KH-Line) and outer bay (KM-Line) during autumn and winter with an annual erosion rate of -29.86 mm/year and -9.92 mm/year, respectively. The seasonal variations of sedimentation on these tidal flats showed that the deposition occurred with an inflow of muddy sediments in summer, whereas the erosion was dominated in autumn and winter. In August 2011, the distribution patterns of rare earth elements (REEs) relative to the upper continental crust (UCC) showed the enrichment of light REEs (LREEs: La-Nd), together with an apparent depletion of Eu in the KH- and KM-Lines. This pattern was more pronounced in the middle bay sediments (KH-Line) due to influence of muddy sediment transport from Jujin Stream during the rainy period (July and August). On the other hand, the outer bay sediments in the KM-Line were reflected more inflow of second sediment source, the Geum River. The major control factors for seasonal variations of sediments on the tidal flat could be heavy rainfall and tidal currents during summer and strong waves during winter. The net sedimentation showed that the deposition occurred in the inner tidal flat and erosion occurred in the middle and outer tidal flat of the bay.

A method for examining the geospatial distribution of CO2 storage resources applied to the Pre-Punta Gorda Composite and Dollar Bay reservoirs of the South Florida Basin, U.S.A

USGS Publications Warehouse

Roberts-Ashby, Tina; Brandon N. Ashby,

2016-01-01

This paper demonstrates geospatial modification of the USGS methodology for assessing geologic CO2 storage resources, and was applied to the Pre-Punta Gorda Composite and Dollar Bay reservoirs of the South Florida Basin. The study provides detailed evaluation of porous intervals within these reservoirs and utilizes GIS to evaluate the potential spatial distribution of reservoir parameters and volume of CO2 that can be stored. This study also shows that incorporating spatial variation of parameters using detailed and robust datasets may improve estimates of storage resources when compared to applying uniform values across the study area derived from small datasets, like many assessment methodologies. Geospatially derived estimates of storage resources presented here (Pre-Punta Gorda Composite = 105,570 MtCO2; Dollar Bay = 24,760 MtCO2) were greater than previous assessments, which was largely attributed to the fact that detailed evaluation of these reservoirs resulted in higher estimates of porosity and net-porous thickness, and areas of high porosity and thick net-porous intervals were incorporated into the model, likely increasing the calculated volume of storage space available for CO2 sequestration. The geospatial method for evaluating CO2 storage resources also provides the ability to identify areas that potentially contain higher volumes of storage resources, as well as areas that might be less favorable.

Parameter identification of civil engineering structures

NASA Technical Reports Server (NTRS)

Juang, J. N.; Sun, C. T.

1980-01-01

This paper concerns the development of an identification method required in determining structural parameter variations for systems subjected to an extended exposure to the environment. The concept of structural identifiability of a large scale structural system in the absence of damping is presented. Three criteria are established indicating that a large number of system parameters (the coefficient parameters of the differential equations) can be identified by a few actuators and sensors. An eight-bay-fifteen-story frame structure is used as example. A simple model is employed for analyzing the dynamic response of the frame structure.

Spatial variation of phytoplankton community structure in Daya Bay, China.

PubMed

Jiang, Zhao-Yu; Wang, You-Shao; Cheng, Hao; Zhang, Jian-Dong; Fei, Jiao

2015-10-01

Daya Bay is one of the largest and most important gulfs in the southern coast of China, in the northern part of the South China Sea. The phylogenetic diversity and spatial distribution of phytoplankton from the Daya Bay surface water and the relationship with the in situ water environment were investigated by the clone library of the large subunit of ribulose-1, 5-bisphosphate carboxylase (rbcL) gene. The dominant species of phytoplankton were diatoms and eustigmatophytes, which accounted for 81.9 % of all the clones of the rbcL genes. Prymnesiophytes were widely spread and wide varieties lived in Daya Bay, whereas the quantity was limited. The community structure of phytoplankton was shaped by pH and salinity and the concentration of silicate, phosphorus and nitrite. The phytoplankton biomass was significantly positively affected by phosphorus and nitrite but negatively by salinity and pH. Therefore, the phytoplankton distribution and biomass from Daya Bay were doubly affected by anthropic activities and natural factors.

Seagrass morphometrics at species level in Moreton Bay, Australia from 2012 to 2013.

PubMed

Samper-Villarreal, Jimena; Roelfsema, Chris; Kovacs, Eva M; Adi, Novi S; Lyons, Mitchell; Mumby, Peter J; Lovelock, Catherine E; Saunders, Megan I; Phinn, Stuart R

2017-05-09

Seagrass above, below and total biomass, density and leaf area, length and width were quantified at a species level for 122 sites over three sampling periods in Moreton Bay, Australia. Core samples were collected in two regions: (1) a high water quality region with varying species assemblages and canopy complexity (98 sites); and (2) along a turbidity gradient in the bay (24 sites within four locations). Core samples were collected using a 15 cm diameter×20 cm long corer. Seagrass dry biomass per component was quantified per species present in each sample. A total of 220 biomass and density data records are included, 130 from the high water quality region and 90 from the turbidity gradient. These data provide a detailed assessment of biomass, density and leaf metrics per species sampled from Moreton Bay over 2012-2013. In future, these can be used as a baseline to assess seasonal and spatial variation within the bay, within the region and among regions.

Seagrass morphometrics at species level in Moreton Bay, Australia from 2012 to 2013

PubMed Central

Samper-Villarreal, Jimena; Roelfsema, Chris; Kovacs, Eva M.; Adi, Novi S.; Lyons, Mitchell; Mumby, Peter J.; Lovelock, Catherine E.; Saunders, Megan I.; Phinn, Stuart R.

2017-01-01

Seagrass above, below and total biomass, density and leaf area, length and width were quantified at a species level for 122 sites over three sampling periods in Moreton Bay, Australia. Core samples were collected in two regions: (1) a high water quality region with varying species assemblages and canopy complexity (98 sites); and (2) along a turbidity gradient in the bay (24 sites within four locations). Core samples were collected using a 15 cm diameter×20 cm long corer. Seagrass dry biomass per component was quantified per species present in each sample. A total of 220 biomass and density data records are included, 130 from the high water quality region and 90 from the turbidity gradient. These data provide a detailed assessment of biomass, density and leaf metrics per species sampled from Moreton Bay over 2012–2013. In future, these can be used as a baseline to assess seasonal and spatial variation within the bay, within the region and among regions. PMID:28485717

Evaluation of phytoplankton community composition in the eutrophic Masan Bay by HPLC pigment analysis.

PubMed

Kim, Jeong Bae; Hong, Sokjin; Lee, Won-Chan; Lee, Yong-Woo; Kim, Hyung Chul; Cho, Yoonsik

2015-03-01

To assess the spatiotemporal changes in phytoplankton community composition in relation to the environment of Masan Bay, a semi-enclosed bay on the southern coast of Korea, photosynthetic pigments and environmental variables were analyzed in seawater, every month between March and November 2010. The level of dissolved inorganic nutrients was highest between July and September when the freshwater influx was at its peak, whereas chlorophyll a level was highest in April and August. Phosphate concentration was low in April (average: 0.22 +/- 0.17 microM), indicating the role of phosphate as a growth-limiting factor for phytoplankton. The results of pigment analysis indicate that dinoflagellate blooms occurred under favorable conditions, where competition with diatoms occurred. Fucoxanthin- and chlorophyll b-containing phytoplankton dominated the surface layer of Masan Bay from July to September. The composition of phytoplankton community in Masan Bay changed dramatically each month according to variations in the amount and composition of nutrients introduced through surface runoff.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models.

PubMed

Vallejo, Roger L; Leeds, Timothy D; Fragomeni, Breno O; Gao, Guangtu; Hernandez, Alvaro G; Misztal, Ignacy; Welch, Timothy J; Wiens, Gregory D; Palti, Yniv

2016-01-01

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models

PubMed Central

Vallejo, Roger L.; Leeds, Timothy D.; Fragomeni, Breno O.; Gao, Guangtu; Hernandez, Alvaro G.; Misztal, Ignacy; Welch, Timothy J.; Wiens, Gregory D.; Palti, Yniv

2016-01-01

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations. PMID:27303436

Time scales and mechanisms of estuarine variability, a synthesis from studies of San Francisco Bay

USGS Publications Warehouse

Cloern, J.E.; Nichols, F.H.

1985-01-01

This review of the preceding papers suggests that temporal variability in San Francisco Bay can be characterized by four time scales (hours, days-weeks, months, years) and associated with at least four mechanisms (variations in freshwater inflow, tides, wind, and exchange with coastal waters). The best understood component of temporal variability is the annual cycle, which is most obviously influenced by seasonal variations in freshwater inflow. The winter season of high river discharge is characterized by: large-scale redistribution of the salinity field (e.g. the upper estuary becomes a riverine system); enhanced density stratification and gravitational circulation with shortened residence times in the bay; decreased tissue concentrations of some contaminants (e.g. copper) in resident bivalves; increased estuarine inputs of river-borne materials such as dissolved inorganic nutrients (N, P, Si), suspended sediments, and humic materials; radical redistributions of pelagic organisms such as copepods and fish; low phutoplankton biomass and primary productivity in the upper estuary; and elimination of freshwater-intolerant species of macroalgae and benthic infauna from the upper estuary. Other mechanisms modulate this river-driven annual cycle: (1) wind speed is highly seasonal (strongest in summer) and causes seasonal variations in atmosphere-water column exchange of dissolved gases, resuspension, and the texture of surficial sediments; (2) seasonal variations in the coastal ocean (e.g. the spring-summer upwelling season) influence species composition of plankton and nutrient concentrations that are advected into the bay; and (3) the annual temperature cycle influences a few selected features (e.g. production and hatching of copepod resting eggs). Much of the interannual variability in San Francisco Bay is also correlated with freshwater inflow: wet years with persistently high river discharge are characterized by persistent winter-type conditions. Mechanisms of short-term variability are not as well understood, although some responses to storm events (pulses in residual currents from wind forcing, erosion of surficial sediments by wind waves, redistribution of fish populations) and the neap-spring tidal cycle (enhanced salinity stratification, gravitational circulation, and phytoplankton biomass during neap tides) have been quantified. In addition to these somewhat predictable features of variability are (1) largely unexplained episodic events (e.g. anomalous blooms of drift macroalgae), and (2) long-term trends directly attributable to human activities (e.g. introduction of exotic species that become permanent members of the biota). ?? 1985 Dr W. Junk Publishers.

Calibrated Bayes Factors Should Not Be Used: A Reply to Hoijtink, van Kooten, and Hulsker.

PubMed

Morey, Richard D; Wagenmakers, Eric-Jan; Rouder, Jeffrey N

2016-01-01

Hoijtink, Kooten, and Hulsker ( 2016 ) present a method for choosing the prior distribution for an analysis with Bayes factor that is based on controlling error rates, which they advocate as an alternative to our more subjective methods (Morey & Rouder, 2014 ; Rouder, Speckman, Sun, Morey, & Iverson, 2009 ; Wagenmakers, Wetzels, Borsboom, & van der Maas, 2011 ). We show that the method they advocate amounts to a simple significance test, and that the resulting Bayes factors are not interpretable. Additionally, their method fails in common circumstances, and has the potential to yield arbitrarily high Type II error rates. After critiquing their method, we outline the position on subjectivity that underlies our advocacy of Bayes factors.

Environmental influences on potential recruitment of pink shrimp, Fatlantopenaeus duorarum, from Florida Bay nursery grounds

USGS Publications Warehouse

Browder, Joan A.; Restrepo, V.R.; Rice, J.K.; Robblee, M.B.; Zein-Eldin, Z.

1999-01-01

Two modeling approaches were used to explore the basis for variation in recruitment of pink shrimp, Farfantepenaeus duorarum, to the Tortugas fishing grounds. Emphasis was on development and juvenile densities on the nursery grounds. An exploratory simulation modeling exercise demonstrated large year-to-year variations in recruitment contributions to the Tortugas rink shrimp fishery may occur on some nursery grounds, and production may differ considerably among nursery grounds within the same year, simply on the basis of differences in temperature and salinity. We used a growth and survival model to simulate cumulative harvests from a July-centered cohort of early-settlement-stage postlarvae from two parts of Florida Bay (western Florida Bay and northcentral Florida Bay), using historic temperature and salinity data from these areas. Very large year-to-year differences in simulated cumulative harvests were found for recruits from Whipray Basin. Year-to-year differences in simulated harvests of recruits from Johnson Key Basin were much smaller. In a complementary activity, generalized linear and additive models and intermittent, historic density records were used to develop an uninterrupted multi-year time series of monthly density estimates for juvenile rink shrimp in the Johnson Key Basin. The developed data series was based on relationships of density with environmental variables. The strongest relationship was with sea-surface temperature. Three other environmental variables (rainfall, water level at Everglades National Park Well P35, and mean wind speed) also contributed significantly to explaining variation in juvenile densities. Results of the simulation model and two of the three statistical models yielded similar interannual patterns for Johnson Key Basin. While it is not possible to say that one result validates the other, the concordance of the annual patterns from the two models is supportive of both approaches.

Naïve Bayes classification in R.

PubMed

Zhang, Zhongheng

2016-06-01

Naïve Bayes classification is a kind of simple probabilistic classification methods based on Bayes' theorem with the assumption of independence between features. The model is trained on training dataset to make predictions by predict() function. This article introduces two functions naiveBayes() and train() for the performance of Naïve Bayes classification.

A Comparison of Turbidity-Based and Streamflow-Based Estimates of Suspended-Sediment Concentrations in Three Chesapeake Bay Tributaries

USGS Publications Warehouse

Jastram, John D.; Moyer, Douglas; Hyer, Kenneth

2009-01-01

Fluvial transport of sediment into the Chesapeake Bay estuary is a persistent water-quality issue with major implications for the overall health of the bay ecosystem. Accurately and precisely estimating the suspended-sediment concentrations (SSC) and loads that are delivered to the bay, however, remains challenging. Although manual sampling of SSC produces an accurate series of point-in-time measurements, robust extrapolation to unmeasured periods (especially highflow periods) has proven to be difficult. Sediment concentrations typically have been estimated using regression relations between individual SSC values and associated streamflow values; however, suspended-sediment transport during storm events is extremely variable, and it is often difficult to relate a unique SSC to a given streamflow. With this limitation for estimating SSC, innovative approaches for generating detailed records of suspended-sediment transport are needed. One effective method for improved suspended-sediment determination involves the continuous monitoring of turbidity as a surrogate for SSC. Turbidity measurements are theoretically well correlated to SSC because turbidity represents a measure of water clarity that is directly influenced by suspended sediments; thus, turbidity-based estimation models typically are effective tools for generating SSC data. The U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency Chesapeake Bay Program and Virginia Department of Environmental Quality, initiated continuous turbidity monitoring on three major tributaries of the bay - the James, Rappahannock, and North Fork Shenandoah Rivers - to evaluate the use of turbidity as a sediment surrogate in rivers that deliver sediment to the bay. Results of this surrogate approach were compared to the traditionally applied streamflow-based approach for estimating SSC. Additionally, evaluation and comparison of these two approaches were conducted for nutrient estimations. Results demonstrate that the application of turbidity-based estimation models provides an improved method for generating a continuous record of SSC, relative to the classical approach that uses streamflow as a surrogate for SSC. Turbidity-based estimates of SSC were found to be more accurate and precise than SSC estimates from streamflow-based approaches. The turbidity-based SSC estimation models explained 92 to 98 percent of the variability in SSC, while streamflow-based models explained 74 to 88 percent of the variability in SSC. Furthermore, the mean absolute error of turbidity-based SSC estimates was 50 to 87 percent less than the corresponding values from the streamflow-based models. Statistically significant differences were detected between the distributions of residual errors and estimates from the two approaches, indicating that the turbidity-based approach yields estimates of SSC with greater precision than the streamflow-based approach. Similar improvements were identified for turbidity-based estimates of total phosphorus, which is strongly related to turbidity because total phosphorus occurs predominantly in particulate form. Total nitrogen estimation models based on turbidity and streamflow generated estimates of similar quality, with the turbidity-based models providing slight improvements in the quality of estimations. This result is attributed to the understanding that nitrogen transport is dominated by dissolved forms that relate less directly to streamflow and turbidity. Improvements in concentration estimation resulted in improved estimates of load. Turbidity-based suspended-sediment loads estimated for the James River at Cartersville, VA, monitoring station exhibited tighter confidence interval bounds and a coefficient of variation of 12 percent, compared with a coefficient of variation of 38 percent for the streamflow-based load.

Spatial variations in the incidence of breast cancer and potential risks associated with soil dioxin contamination in Midland, Saginaw, and Bay Counties, Michigan, USA

PubMed Central

Dai, Dajun; Oyana, Tonny J

2008-01-01

Background High levels of dioxins in soil and higher-than-average body burdens of dioxins in local residents have been found in the city of Midland and the Tittabawassee River floodplain in Michigan. The objective of this study is threefold: (1) to evaluate dioxin levels in soils; (2) to evaluate the spatial variations in breast cancer incidence in Midland, Saginaw, and Bay Counties in Michigan; (3) to evaluate whether breast cancer rates are spatially associated with the dioxin contamination areas. Methods We acquired 532 published soil dioxin data samples collected from 1995 to 2003 and data pertaining to female breast cancer cases (n = 4,604) at ZIP code level in Midland, Saginaw, and Bay Counties for years 1985 through 2002. Descriptive statistics and self-organizing map algorithm were used to evaluate dioxin levels in soils. Geographic information systems techniques, the Kulldorff's spatial and space-time scan statistics, and genetic algorithms were used to explore the variation in the incidence of breast cancer in space and space-time. Odds ratio and their corresponding 95% confidence intervals, with adjustment for age, were used to investigate a spatial association between breast cancer incidence and soil dioxin contamination. Results High levels of dioxin in soils were observed in the city of Midland and the Tittabawassee River 100-year floodplain. After adjusting for age, we observed high breast cancer incidence rates and detected the presence of spatial clusters in the city of Midland, the confluence area of the Tittabawassee, and Saginaw Rivers. After accounting for spatiotemporal variations, we observed a spatial cluster of breast cancer incidence in Midland between 1985 and 1993. The odds ratio further suggests a statistically significant (α = 0.05) increased breast cancer rate as women get older, and a higher disease burden in Midland and the surrounding areas in close proximity to the dioxin contaminated areas. Conclusion These findings suggest that increased breast cancer incidences are spatially associated with soil dioxin contamination. Aging is a substantial factor in the development of breast cancer. Findings can be used for heightened surveillance and education, as well as formulating new study hypotheses for further research. PMID:18939976

TEMPORAL AND SPATIAL VARIATION IN PLASMA THYROXINE (T4) CONCENTRATIONS IN JUVENILE ALLIGATORS COLLECTED FROM LAKE OKEECHOBEE AND THE NORTHERN EVERGLADES, FLORIDA, USA

EPA Science Inventory

We examined variation in plasma thyroxine (T4) in juvenile American alligators (Alligator mississippiensis) collected from three sites within the Kissimmee River drainage basin (FL, USA). Based on historical sediment data, Moonshine Bay served as the low contaminant exposure site...

Predictors of lung transplant survival in eurotransplant.

PubMed

Smits, J M A; Mertens, B J A; Van Houwelingen, H C; Haverich, A; Persijn, G G; Laufer, G

2003-11-01

This study was undertaken to assess the influence of patient/donor and center factors on lung transplantation outcome. Outcomes of all consecutive first cadaveric lung transplants performed at 21 Eurotransplant centers in 1997-99 were analyzed. The risk-adjusted center effect on mortality was estimated. A Cox model was built including donor and recipient age and gender, primary disease, HLA mismatches, patient's residence, cold ischemic time, donor's cause of death, serum creatinine, type of lung transplant, respiratory support status, clinical condition and percentage predicted FEV1. The center effect was calculated (expressed as the standardized difference between the observed and expected survival rates), and empirical and full Bayes methods were applied to evaluate between-center differences. A total of 590 adults underwent lung transplantation. The primary disease (p=0.01), HLA-mismatches (p = 0.02), clinical condition(p < 0.0001) and the patient's respiratory support status (p = 0.05) were significantly associated with survival. After adjusting for case-mix, no between-center differences could be found. An in-depth empirical Bayes analysis showed the between-center variation to be zero. Similar results were obtained from the full Bayes analysis. Based on these data, there is no scientific basis to support a hypothesis of possible association between center volume and lung survival rates.

A Method to Exchange Air Nitrogen Emission Reductions for Watershed Nitrogen Load Reductions

EPA Science Inventory

Presentation of the method developed for the Chesapeake Bay Program to estimate changes in nitrogen loading to Chesapeake due to changes in Bay State state-level nitrogen oxide emissions to support air-water trading by the Bay States. Type for SticsUnder AMAD Application QAPP, QA...

Glacial-marine sediments record ice-shelf retreat during the late Holocene in Beascochea Bay on the western margin of the Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Hardin, L. A.; Wellner, J. S.

2010-12-01

Beascochea Bay has an overall rapid rate of sedimentation due to retreating fast-flowing ice, and thus contains high-resolution records of Antarctica’s glacial and climate history. Beascochea Bay is a 16 km long by 8 km wide bay located on the western margin of the Antarctica Peninsula, centered between Anvers Island and Renaud Island, but open to the Bellingshausen Sea. Currently, three tidewater glaciers draining the Bruce Plateau of Graham Land enter into the fjords of Beascochea Bay, releasing terrigenous sediments which have left a record of the fluctuations of the Antarctic Peninsula Ice Cap since the grounded ice decoupled from the seafloor after the last glacial maximum. These three glaciers have played a significant role in providing sediment to the main basin, allowing a detailed sediment facies analysis to be conducted from eight sediment cores which were collected during the austral summer of 2007. Pebbly silty clay sediment cores, along with 3.5 kHz seismic data and multibeam swath bathymetry data, are integrated to reconstruct a glacial retreat timeline for the middle to late Holocene, which can be compared to the recent retreat rates over the last century. Paleoenvironment of deposition is determined by mapping lateral facies changes from the side fjords (proximal) to the outer basin (distal), as each region records the transition from glacial-marine sediments to open-marine sediments. As the ice retreated from the outer basin to the inner basin, and most recently leaving the side fjords, each facies deposited can be age-constrained by radiocarbon, 210Pb, and 137Cs dating methods. A distinct 137Cs signal is readily seen in two kasten cores from a side fjord and the inner basin of Beascochea Bay. This dating method revealed an average sedimentation rate of 2.7 mm per year for approximately the last century, which is comparable to 210Pb rates obtained in other studies. Lithology variations in each sediment core record indications of ice-shelf influence in Beascochea Bay throughout the Holocene deglaciation. The distinctively laminated sub-ice shelf facies can be clearly seen in the x-rays of these cores, and can be easily distinguished from the poorly sorted glacial-marine facies and the greenish finer-grained facies deposited in open-marine conditions. A 14 m long sediment core taken from the outer basin of Beascochea Bay recovered the greatest length of sediment and dates back to the middle Holocene. X-rays of this core show a possible mid-Holocene retreat of the ice shelf followed by intermittent advance and retreat that precedes the most recent retreat. The inner basin of Beascochea Bay has been without an ice shelf for the last 200 years, based on the sedimentation rates of the last century projected downcore.

Seasonal and annual trends in forage fish mercury concentrations, San Francisco Bay.

PubMed

Greenfield, Ben K; Melwani, Aroon R; Allen, Rachel M; Slotton, Darell G; Ayers, Shaun M; Harrold, Katherine H; Ridolfi, Katherine; Jahn, Andrew; Grenier, J Letitia; Sandheinrich, Mark B

2013-02-01

San Francisco Bay is contaminated by mercury (Hg) due to historic and ongoing sources, and has elevated Hg concentrations throughout the aquatic food web. We monitored Hg in forage fish to indicate seasonal and interannual variations and trends. Interannual variation and long-term trends were determined by monitoring Hg bioaccumulation during September-November, for topsmelt (Atherinops affinis) and Mississippi silverside (Menidia audens) at six sites, over six years (2005 to 2010). Seasonal variation was characterized for arrow goby (Clevelandia ios) at one site, topsmelt at six sites, and Mississippi silverside at nine sites. Arrow goby exhibited a consistent seasonal pattern from 2008 to 2010, with lowest concentrations observed in late spring, and highest concentrations in late summer or early fall. In contrast, topsmelt concentrations tended to peak in late winter or early spring and silverside seasonal fluctuations varied among sites. The seasonal patterns may relate to seasonal shifts in net MeHg production in the contrasting habitats of the species. Topsmelt exhibited an increase in Alviso Slough from 2005 to 2010, possibly related to recent hypoxia in that site. Otherwise, directional trends for Hg in forage fish were not observed. For topsmelt and silverside, the variability explained by year was relatively low compared to sampling station, suggesting that interannual variation is not a strong influence on Hg concentrations. Although fish Hg has shown long-term declines in some ecosystems around the world, San Francisco Bay forage fish did not decline over the six-year monitoring period examined. Copyright © 2012 Elsevier B.V. All rights reserved.

Distribution of the Euryhaline Squid Lolliguncula brevis in Chesapeake Bay: Effects of Selected Abiotic Factors

DTIC Science & Technology

2002-01-31

salinity , water temperature, dissolved oxy- gen and water clarity. Since temporal variation in the Chesapeake Bay ecosystem is high, the effects of year...temperature (p ɘ.001; ψ = 2.42) had significant impacts on squid catch probability, although the effects were con- founded by a water temperature × salinity ...commonly encountered in such waters during VIMS Trawl Surveys The synergistic and independent effects of salinity , water temperature and dissolved oxygen

Seasonal Sea-Level Variations in San Francisco Bay in Response to Atmospheric Forcing, 1980

USGS Publications Warehouse

Wang, Jingyuan; Cheng, R.T.; Smith, P.C.

1997-01-01

The seasonal response of sea level in San Francisco Bay (SFB) to atmospheric forcing during 1980 is investigated. The relations between sea-level data from the Northern Reach, Central Bay and South Bay, and forcing by local wind stresses, sea level pressure (SLP), runoff and the large scale sea level pressure field are examined in detail. The analyses show that the sea-level elevations and slopes respond to the along-shore wind stress T(V) at most times of the year, and to the cross-shore wind stress T(N) during two transition periods in spring and autumn. River runoff raises the sea-level elevation during winter. It is shown that winter precipitation in the SFB area is mainly attributed to the atmospheric circulation associated with the Alcutian Low, which transports the warm, moist air into the Bay area. A multiple linear regression model is employed to estimate the independent contributions of barometric pressure and wind stress to adjusted sea level. These calculations have a simple dynamical interpretation which confirms the importance of along-shore wind to both sea level and north-south slope within the Bay.

Alternative models of climatic effects on sockeye salmon (Oncorhynchus nerka) productivity in Bristol Bay, Alaska, and the Fraser River, British Columbia

USGS Publications Warehouse

Adkison, M.; Peterman, R.; Lapointe, M.; Gillis, D.; Korman, J.

1996-01-01

We compare alternative models of sockeye salmon (Oncorhynchus nerka) productivity (returns per spawner) using more than 30 years of catch and escapement data for Bristol Bay, Alaska, and the Fraser River, British Columbia. The models examined include several alternative forms of models that incorporate climatic influences as well as models not based on climate. For most stocks, a stationary stock-recruitment relationship explains very little of the interannual variation in productivity. In Bristol Bay, productivity co-varies among stocks and appears to be strongly related to fluctuations in climate. The best model for Bristol Bay sockeye involved a change in the 1970s in the parameters of the Ricker stock-recruitment curve; the stocks generally became more productive. In contrast, none of the models of Fraser River stocks that we examined explained much of the variability in their productivity.

Variation in hearing within a wild population of beluga whales (Delphinapterus leucas).

PubMed

Mooney, T Aran; Castellote, Manuel; Quakenbush, Lori; Hobbs, Roderick; Gaglione, Eric; Goertz, Caroline

2018-05-08

Documenting hearing abilities is vital to understanding a species' acoustic ecology and for predicting the impacts of increasing anthropogenic noise. Cetaceans use sound for essential biological functions such as foraging, navigation and communication; hearing is considered to be their primary sensory modality. Yet, we know little regarding the hearing of most, if not all, cetacean populations, which limits our understanding of their sensory ecology, population level variability and the potential impacts of increasing anthropogenic noise. We obtained audiograms (5.6-150 kHz) of 26 wild beluga whales to measure hearing thresholds during capture-release events in Bristol Bay, AK, USA, using auditory evoked potential methods. The goal was to establish the baseline population audiogram, incidences of hearing loss and general variability in wild beluga whales. In general, belugas showed sensitive hearing with low thresholds (<80 dB) from 16 to 100 kHz, and most individuals (76%) responded to at least 120 kHz. Despite belugas often showing sensitive hearing, thresholds were usually above or approached the low ambient noise levels measured in the area, suggesting that a quiet environment may be associated with hearing sensitivity and that hearing thresholds in the most sensitive animals may have been masked. Although this is just one wild population, the success of the method suggests that it should be applied to other populations and species to better assess potential differences. Bristol Bay beluga audiograms showed substantial (30-70 dB) variation among individuals; this variation increased at higher frequencies. Differences among individual belugas reflect that testing multiple individuals of a population is necessary to best describe maximum sensitivity and population variance. The results of this study quadruple the number of individual beluga whales for which audiograms have been conducted and provide the first auditory data for a population of healthy wild odontocetes. © 2018. Published by The Company of Biologists Ltd.

Bayes Error Rate Estimation Using Classifier Ensembles

NASA Technical Reports Server (NTRS)

Tumer, Kagan; Ghosh, Joydeep

2003-01-01

The Bayes error rate gives a statistical lower bound on the error achievable for a given classification problem and the associated choice of features. By reliably estimating th is rate, one can assess the usefulness of the feature set that is being used for classification. Moreover, by comparing the accuracy achieved by a given classifier with the Bayes rate, one can quantify how effective that classifier is. Classical approaches for estimating or finding bounds for the Bayes error, in general, yield rather weak results for small sample sizes; unless the problem has some simple characteristics, such as Gaussian class-conditional likelihoods. This article shows how the outputs of a classifier ensemble can be used to provide reliable and easily obtainable estimates of the Bayes error with negligible extra computation. Three methods of varying sophistication are described. First, we present a framework that estimates the Bayes error when multiple classifiers, each providing an estimate of the a posteriori class probabilities, a recombined through averaging. Second, we bolster this approach by adding an information theoretic measure of output correlation to the estimate. Finally, we discuss a more general method that just looks at the class labels indicated by ensem ble members and provides error estimates based on the disagreements among classifiers. The methods are illustrated for artificial data, a difficult four-class problem involving underwater acoustic data, and two problems from the Problem benchmarks. For data sets with known Bayes error, the combiner-based methods introduced in this article outperform existing methods. The estimates obtained by the proposed methods also seem quite reliable for the real-life data sets for which the true Bayes rates are unknown.

A Bayes linear Bayes method for estimation of correlated event rates.

PubMed

Quigley, John; Wilson, Kevin J; Walls, Lesley; Bedford, Tim

2013-12-01

Typically, full Bayesian estimation of correlated event rates can be computationally challenging since estimators are intractable. When estimation of event rates represents one activity within a larger modeling process, there is an incentive to develop more efficient inference than provided by a full Bayesian model. We develop a new subjective inference method for correlated event rates based on a Bayes linear Bayes model under the assumption that events are generated from a homogeneous Poisson process. To reduce the elicitation burden we introduce homogenization factors to the model and, as an alternative to a subjective prior, an empirical method using the method of moments is developed. Inference under the new method is compared against estimates obtained under a full Bayesian model, which takes a multivariate gamma prior, where the predictive and posterior distributions are derived in terms of well-known functions. The mathematical properties of both models are presented. A simulation study shows that the Bayes linear Bayes inference method and the full Bayesian model provide equally reliable estimates. An illustrative example, motivated by a problem of estimating correlated event rates across different users in a simple supply chain, shows how ignoring the correlation leads to biased estimation of event rates. © 2013 Society for Risk Analysis.

Bay of Fundy verification of a system for multidate Landsat measurement of suspended sediment

NASA Technical Reports Server (NTRS)

Munday, J. C., Jr.; Afoldi, T. T.; Amos, C. L.

1981-01-01

A system for automated multidate Landsat CCT MSS measurement of suspended sediment concentration (S) has been implemented and verified on nine sets (108 points) of data from the Bay of Fundy, Canada. The system employs 'chromaticity analysis' to provide automatic pixel-by-pixel adjustment of atmospheric variations, permitting reference calibration data from one or several dates to be spatially and temporally extrapolated to other regions and to other dates. For verification, each data set was used in turn as test data against the remainder as a calibration set: the average absolute error was 44 percent of S over the range 1-1000 mg/l. The system can be used to measure chlorophyll (in the absence of atmospheric variations), Secchi disk depth, and turbidity.

Oceanography of Glacier Bay, Alaska: Implications for biological patterns in a glacial fjord estuary

USGS Publications Warehouse

Etherington, L.L.; Hooge, P.N.; Hooge, Elizabeth Ross; Hill, D.F.

2007-01-01

Alaska, U.S.A, is one of the few remaining locations in the world that has fjords that contain temperate idewater glaciers. Studying such estuarine systems provides vital information on how deglaciation affects oceanographic onditions of fjords and surrounding coastal waters. The oceanographic system of Glacier Bay, Alaska, is of particular interest ue to the rapid deglaciation of the Bay and the resulting changes in the estuarine environment, the relatively high oncentrations of marine mammals, seabirds, fishes, and invertebrates, and the Bay’s status as a national park, where ommercial fisheries are being phased out. We describe the first comprehensive broad-scale analysis of physical and iological oceanographic conditions within Glacier Bay based on CTD measurements at 24 stations from 1993 to 2002. easonal patterns of near-surface salinity, temperature, stratification, turbidity, and euphotic depth suggest that freshwater nput was highest in summer, emphasizing the critical role of glacier and snowmelt to this system. Strong and persistent tratification of surface waters driven by freshwater input occurred from spring through fall. After accounting for seasonal nd spatial variation, several of the external physical factors (i.e., air temperature, precipitation, day length) explained a large mount of variation in the physical properties of the surface waters. Spatial patterns of phytoplankton biomass varied hroughout the year and were related to stratification levels, euphotic depth, and day length. We observed hydrographic atterns indicative of strong competing forces influencing water column stability within Glacier Bay: high levels of freshwater ischarge promoted stratification in the upper fjord, while strong tidal currents over the Bay’s shallow entrance sill enhanced ertical mixing. Where these two processes met in the central deep basins there were optimal conditions of intermediate tratification, higher light levels, and potential nutrient renewal. These conditions were associated with high and sustained hlorophylla levels observed from spring through fall in these zones of the Bay and provide a framework for understanding he abundance patterns of higher trophic levels within this estuarine system.

What a difference a bay makes: natural variation in dietary resources mediates growth in a recently settled herbivorous fish

NASA Astrophysics Data System (ADS)

Priest, Mark A.; Halford, Andrew R.; Clements, Kendall D.; Douglas, Emily; Abellana, Sheena L.; McIlwain, Jennifer L.

2016-12-01

Processes acting during the early stages of coral reef fish life cycles have a disproportionate influence on their adult abundance and community structure. Higher growth rates, for example, confer a major fitness advantage in larval and juvenile fishes, with larger fish undergoing significantly less mortality. The role of dietary resources in the size-structuring process has not been well validated, especially at the early post-settlement phase, where competition and predation are seen as preeminent drivers of juvenile fish assemblage structure. Here, we report on a size differential of 10-20% between recently settled Siganus spinus rabbitfish recruits from different bays around the Pacific island of Guam. This difference was maintained across multiple recruitment events within and between years. After confirming the validity of our observations through otolith increment analysis, subsequent investigation into the drivers of this variation revealed significant differences in the structure of algal assemblages between bays, congruent with the observed differences in size of the recently settled fish. Gut analyses showed a greater presence of algal types with higher levels of nitrogen and phosphorus in the stomachs of fish from Tanguisson, the bay with the largest observed recruits. To ensure this mechanism was one of causation and not correlation, we conducted a fully factorial experiment in which S. spinus recruits sampled from different bays were reared on all combinations of algal diets representative of the different bays. Recruits on the `Tanguisson' diet grew faster than recruits on other diets, regardless of their origin. We propose that the greater availability of high-quality dietary resources at this location is likely conferring benefits that impact on the population-level dynamics of this species. The spatial and temporal extent of this process clearly implicates food as a limiting resource, capable of mediating fish population dynamics at multiple spatial scales and ontogenetic phases.

Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach.

PubMed

Li, Dongmei; Le Pape, Marc A; Parikh, Nisha I; Chen, Will X; Dye, Timothy D

2013-01-01

Microarrays are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. Multiple testing methods in microarray data analysis aim at controlling both Type I and Type II error rates; however, real microarray data do not always fit their distribution assumptions. Smyth's ubiquitous parametric method, for example, inadequately accommodates violations of normality assumptions, resulting in inflated Type I error rates. The Significance Analysis of Microarrays, another widely used microarray data analysis method, is based on a permutation test and is robust to non-normally distributed data; however, the Significance Analysis of Microarrays method fold change criteria are problematic, and can critically alter the conclusion of a study, as a result of compositional changes of the control data set in the analysis. We propose a novel approach, combining resampling with empirical Bayes methods: the Resampling-based empirical Bayes Methods. This approach not only reduces false discovery rates for non-normally distributed microarray data, but it is also impervious to fold change threshold since no control data set selection is needed. Through simulation studies, sensitivities, specificities, total rejections, and false discovery rates are compared across the Smyth's parametric method, the Significance Analysis of Microarrays, and the Resampling-based empirical Bayes Methods. Differences in false discovery rates controls between each approach are illustrated through a preterm delivery methylation study. The results show that the Resampling-based empirical Bayes Methods offer significantly higher specificity and lower false discovery rates compared to Smyth's parametric method when data are not normally distributed. The Resampling-based empirical Bayes Methods also offers higher statistical power than the Significance Analysis of Microarrays method when the proportion of significantly differentially expressed genes is large for both normally and non-normally distributed data. Finally, the Resampling-based empirical Bayes Methods are generalizable to next generation sequencing RNA-seq data analysis.

Interrogating Seyferts with NebulaBayes: Spatially Probing the Narrow-line Region Radiation Fields and Chemical Abundances

NASA Astrophysics Data System (ADS)

Thomas, Adam D.; Dopita, Michael A.; Kewley, Lisa J.; Groves, Brent A.; Sutherland, Ralph S.; Hopkins, Andrew M.; Blanc, Guillermo A.

2018-04-01

NebulaBayes is a new Bayesian code that implements a general method of comparing observed emission-line fluxes to photoionization model grids. The code enables us to extract robust, spatially resolved measurements of abundances in the extended narrow-line regions (ENLRs) produced by Active Galactic Nuclei (AGN). We observe near-constant ionization parameters but steeply radially declining pressures, which together imply that radiation pressure regulates the ENLR density structure on large scales. Our sample includes four “pure Seyfert” galaxies from the S7 survey that have extensive ENLRs. NGC 2992 shows steep metallicity gradients from the nucleus into the ionization cones. An inverse metallicity gradient is observed in ESO 138-G01, which we attribute to a recent gas inflow or minor merger. A uniformly high metallicity and hard ionizing continuum are inferred across the ENLR of Mrk 573. Our analysis of IC 5063 is likely affected by contamination from shock excitation, which appears to soften the inferred ionizing spectrum. The peak of the ionizing continuum E peak is determined by the nuclear spectrum and the absorbing column between the nucleus and the ionized nebula. We cannot separate variation in this intrinsic E peak from the effects of shock or H II region contamination, but E peak measurements nevertheless give insights into ENLR excitation. We demonstrate the general applicability of NebulaBayes by analyzing a nuclear spectrum from the non-active galaxy NGC 4691 using a H II region grid. The NLR and H II region model grids are provided with NebulaBayes for use by the astronomical community.

Spatial variation in effects of temperature on Phenotypic characteristics of Phytophthora ramorum isolates from eastern Sonoma county

Treesearch

Valerie Sherron; Nathan E. Rank; Michael Cohen; Brian L. Anacker; Ross K. Meentemeyer

2008-01-01

Quantifying the growth rates of plant pathogens in the laboratory can be useful for predicting rates of disease spread and impact in nature. The purpose of this study was to examine phenotypic variation among isolates of Phytophthora ramorum collected from a foliar host plant species, Umbellularia californica (California bay laurel...

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers.

PubMed

Heidaritabar, M; Wolc, A; Arango, J; Zeng, J; Settar, P; Fulton, J E; O'Sullivan, N P; Bastiaansen, J W M; Fernando, R L; Garrick, D J; Dekkers, J C M

2016-10-01

Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population. © 2016 Blackwell Verlag GmbH.

The long-term salinity field in San Francisco Bay

USGS Publications Warehouse

Uncles, R.J.; Peterson, D.H.

1996-01-01

Data are presented on long-term salinity behaviour in San Francisco Bay, California. A two-level, width averaged model of the tidally averaged salinity and circulation has been written in order to interpret the long-term (days to decades) salinity variability. The model has been used to simulate daily averaged salinity in the upper and lower levels of a 51 segment discretization of the Bay over the 22-yr period 1967-1988. Monthly averaged surface salinity from observations and monthly-averaged simulated salinity are in reasonable agreement. Good agreement is obtained from comparison with daily averaged salinity measured in the upper reaches of North Bay. The salinity variability is driven primarily by freshwater inflow with relatively minor oceanic influence. All stations exhibit a marked seasonal cycle in accordance with the Mediterranean climate, as well as a rich spectrum of variability due to extreme inflow events and extended periods of drought. Monthly averaged salinity intrusion positions have a pronounced seasonal variability and show an approximately linear response to the logarithm of monthly averaged Delta inflow. Although few observed data are available for studies of long-term salinity stratification, modelled stratification is found to be strongly dependent on freshwater inflow; the nature of that dependence varies throughout the Bay. Near the Golden Gate, stratification tends to increase up to very high inflows. In the central reaches of North Bay, modelled stratification maximizes as a function of inflow and further inflow reduces stratification. Near the head of North Bay, lowest summer inflows are associated with the greatest modelled stratification. Observations from the central reaches of North Bay show marked spring-neap variations in stratification and gravitational circulation, both being stronger at neap tides. This spring-neap variation is simulated by the model. A feature of the modelled stratification is a hysteresis in which, for a given spring-neap tidal range and fairly steady inflows, the stratification is higher progressing from neaps to springs than from springs to neaps. The simulated responses of the Bay to perturbations in coastal sea salinity and Delta inflow have been used to further delineate the time-scales of salinity variability. Simulations have been performed about low inflow, steady-state conditions for both salinity and Delta inflow perturbations. For salinity perturbations a small, sinusoidal salinity signal with a period of 1 yr has been applied at the coastal boundary as well as a pulse of salinity with a duration of one day. For Delta inflow perturbations a small, sinusoidally varying inflow signal with a period of 1 yr has been superimposed on an otherwise constant Delta inflow, as well as a pulse of inflow with a duration of one day. Perturbations is coastal salinity dissipate as they move through the Bay. Seasonal perturbations require about 40-45 days to propagate from the coastal ocean to the Delta and to the head of South Bay. The response times of the model to perturbations in freshwater inflow are faster than this in North Bay and comparable in South Bay. In North Bay, time-scales are consistent with advection due to lower level, up-estuary transport of coastal salinity perturbations; for inflow perturbations, faster response times arise from both upper level, down-estuary advection and much faster, down-estuary migration of isohalines in response to inflow volume continuity. In South Bay, the dominant time-scales are governed by tidal dispersion.

Physical oceanographic investigation of Massachusetts and Cape Cod Bays

USGS Publications Warehouse

Geyer, W. Rockwell; Gardner, George B.; Brown, Wendell S.; Irish, James D.; Butman, Bradford; Loder, T.C.; Signell, Richard P.

1992-01-01

This physical oceanographic study of the Massachusetts Bays (fig. 1) was designed to provide for the first time a bay-wide description of the circulation and mixing processes on a seasonal basis. Most of the measurements were conducted between April 1990 and June 1991 and consisted of moored observations to study the current flow patterns (fig. 2), hydrographic surveys to document the changes in water properties (fig. 3), high-resolution surveys of velocity and water properties to provide information on the spatial variability of the flow, drifter deployments to measure the currents, and acquisition of satellite images to provide a bay-wide picture of the surface temperature and its spatial variability. A longterm objective of the Massachusetts Bays program is to develop an understanding of the transport of water, dissolved substances and particles throughout the bays. Because horizontal and vertical transport is important to biological, chemical, and geological processes in Massachusetts and Cape Cod Bays, this physical oceanographic study will have broad application and will improve the ability to manage and monitor the water and sediment quality of the Bays. Key results are:There is a marked seasonal variation in stratification in the bays, from well mixed conditions during the winter to strong stratification in the summertime. The stratification acts as a partial barrier to exchange between the surface waters and the deeper waters and causes the motion of the surface waters to be decoupled from the more sluggish flow of the deep waters. During much of the year, there is weak but persistent counterclockwise flow around the bays, made up of southwesterly flow past Cape Ann, southward flow along the western shore, and outflow north of Race Point. The data suggest that this residual flow pattern reverses in fall. Fluctuations caused by wind and density variations are typically larger than the long-term mean. With the exception of western Massachusetts Bay, flushing of the Bays is largely the result of the mean throughflow. Residence time estimates of the surface waters range from 20-45 days. The deeper water has a longer residence time, but its value is difficult to estimate. There is evidence that the deep waters in Stellwagen Basin are not renewed between the onset of stratification and the fall cooling period.Current measurements made near the new outfall site in western Massachusetts Bay suggest that water and material discharged there are not swept away in a consistent direction by a well-defined steady current but are mixed and transported by a variety of processes, including the action of tides, winds, and river inflow. One-day particle excursions are typically less than 10 km. The outfall is apparently located in a region to the west of the basin-wide residual flow pattern.Observations in western Massachusetts Bay, near the location of the future Boston sewage outfall, show that the surficial sediments are episodically resuspended from the seafloor during storms. The observations suggest onshore transport of suspended material during tranquil periods and episodic offshore and southerly alongshore transport of resuspended sediments during storms. The spatial complexity of the flow in the Massachusetts Bays is typical of nearshore areas that have irregular coastal shorelines and topography and currents that are forced locally by wind and river runoff as well as by the flow in adjacent regions. Numerical models are providing a mechanism to interpret the complex spatial flow patterns that cannot be completely resolved by field observations and to investigate key physical processes that control the physics of water and particle transport.

A Pilot Study of the Effects of Post-Hurricane Katrina Floodwater Pumping on the Chemistry and Toxicity of Violet Marsh Sediments

DTIC Science & Technology

2006-10-01

to be suitable for testing without manipulations. Survival of amphipods in the control sediment from Sequim Bay , WA was above the 90-percent level...Treatment Mean Percent Survival Coefficient of Variation (%) Negative Control ( Sequim Bay , WA) 90 ± 4 3.9 Reference (Lake Pontchartrain, LA) 95...assessed along with a perform- ance control sediment ( Sequim , WA, USA Lat. 48.0587 Long. -123.0235 and a reference sedi- ment (Lake Pontchartrain

Saco Bay, Maine: Sediment Budget for Late Twentieth Century to Present

DTIC Science & Technology

2016-02-01

determined that sediment flux was variable, depending on bathymetry and input wave conditions. Despite these variations in conditions, there is no obvious...DETAILS, SACO BAY, MAINE V3. Last update: 11 September 2014 Units are yd3/year. Source1 = bluffs, river influx, wind . Sink1 = wind -blown loss or...Beach05 (B05), Pine Point QSource1 1,600 Wind transport (from Kelley et al. 2005). DeltaV 1,600 Dune accumulation 1859–1991 (from Kelley et al. 2005

Sedimentation processes in a coral reef embayment: Hanalei Bay, Kauai

USGS Publications Warehouse

Storlazzi, C.D.; Field, M.E.; Bothner, Michael H.; Presto, M.K.; Draut, A.E.

2009-01-01

Oceanographic measurements and sediment samples were collected during the summer of 2006 as part of a multi-year study of coastal circulation and the fate of terrigenous sediment on coral reefs in Hanalei Bay, Kauai. The goal of this study was to better understand sediment dynamics in a coral reef-lined embayment where winds, ocean surface waves, and river floods are important processes. During a summer period that was marked by two wave events and one river flood, we documented significant differences in sediment trap collection rates and the composition, grain size, and magnitude of sediment transported in the bay. Sediment trap collection rates were well correlated with combined wave-current near-bed shear stresses during the non-flood periods but were not correlated during the flood. The flood's delivery of fine-grained sediment to the bay initially caused high turbidity and sediment collection rates off the river mouth but the plume dispersed relatively quickly. Over the next month, the flood deposit was reworked by mild waves and currents and the fine-grained terrestrial sediment was advected around the bay and collected in sediment traps away from the river mouth, long after the turbid surface plume was gone. The reworked flood deposits, due to their longer duration of influence and proximity to the seabed, appear to pose a greater long-term impact to benthic coral reef communities than the flood plumes themselves. The results presented here display how spatial and temporal differences in hydrodynamic processes, which result from variations in reef morphology and orientation, cause substantial variations in the deposition, residence time, resuspension, and advection of both reef-derived and fluvial sediment over relatively short spatial scales in a coral reef embayment.

Genome and Transcriptome Sequencing of the Ostreid herpesvirus 1 From Tomales Bay, California

NASA Astrophysics Data System (ADS)

Burge, C. A.; Langevin, S.; Closek, C. J.; Roberts, S. B.; Friedman, C. S.

2016-02-01

Mass mortalities of larval and seed bivalve molluscs attributed to the Ostreid herpesvirus 1 (OsHV-1) occur globally. OsHV-1 was fully sequenced and characterized as a member of the Family Malacoherpesviridae. Multiple strains of OsHV-1 exist and may vary in virulence, i.e. OsHV-1 µvar. For most global variants of OsHV-1, sequence data is limited to PCR-based sequencing of segments, including two recent genomes. In the United States, OsHV-1 is limited to detection in adjacent embayments in California, Tomales and Drakes bays. Limited DNA sequence data of OsHV-1 infecting oysters in Tomales Bay indicates the virus detected in Tomales Bay is similar but not identical to any one global variant of OsHV-1. In order to better understand both strain variation and virulence of OsHV-1 infecting oysters in Tomales Bay, we used genomic and transcriptomic sequencing. Meta-genomic sequencing (Illumina MiSeq) was conducted from infected oysters (n=4 per year) collected in 2003, 2007, and 2014, where full OsHV-1 genome sequences and low overall microbial diversity were achieved from highly infected oysters. Increased microbial diversity was detected in three of four samples sequenced from 2003, where qPCR based genome copy numbers of OsHV-1 were lower. Expression analysis (SOLiD RNA sequencing) of OsHV-1 genes expressed in oyster larvae at 24 hours post exposure revealed a nearly complete transcriptome, with several highly expressed genes, which are similar to recent transcriptomic analyses of other OsHV-1 variants. Taken together, our results indicate that genome and transcriptome sequencing may be powerful tools in understanding both strain variation and virulence of non-culturable marine viruses.

Application of the Weibull extrapolation to 137Cs geochronology in Tokyo Bay and Ise Bay, Japan.

PubMed

Lu, Xueqiang

2004-01-01

Considerable doubt surrounds the nature of processes by which 137Cs is deposited in marine sediments, leading to a situation where 137Cs geochronology cannot be always applied suitably. Based on extrapolation with Weibull distribution, the maximum concentration of 137Cs derived from asymptotic values for cumulative specific inventory was used to re-establish 137Cs geochronology, instead of original 137Cs profiles. Corresponding dating results for cores in Tokyo Bay and Ise Bay, Japan, by means of this new method, are in much closer agreement with those calculated from 210Pb method than the previous method.

Flow in water-intake pump bays: A guide for utility engineers. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ettema, R.

1998-09-01

This report is intended to serve as a guide for power-plant engineers facing problems with flow conditions in pump bays in water-intake structures, especially those located alongside rivers. The guide briefly introduces the typical prevailing flow field outside of a riverside water intake. That flow field often sets the inflow conditions for pump bays located within the water intake. The monograph then presents and discusses the main flow problems associated with pump bays. The problems usually revolve around the formation of troublesome vortices. A novel feature of this monograph is the use of numerical modeling to reveal diagnostically how themore » vortices form and their sensitivities to flow conditions, such as uniformity of approach flow entering the bay and water-surface elevation relative to pump-bell submergence. The modeling was carried out using a computer code developed specially for the present project. Pump-bay layouts are discussed next. The discussion begins with a summary of the main variables influencing bay flows. The numerical model is used to determine the sensitivities of the vortices to variations in the geometric parameters. The fixes include the use of flow-control vanes and suction scoops for ensuring satisfactory flow performance in severe flow conditions; notably flows with strong cross flow and shallow flows. The monograph ends with descriptions of modeling techniques. An extensive discussion is provided on the use of numerical model for illuminating bay flows. The model is used to show how fluid viscosity affects bay flow. The effect of fluid viscosity is an important consideration in hydraulic modeling of water intakes.« less

Coastal circulation and potential coral-larval dispersal in Maunalua Bay, O'ahu, Hawaii—Measurements of waves, currents, temperature, and salinity, June-September 2010

USGS Publications Warehouse

Presto, M. Katherine; Storlazzi, Curt D.; Logan, Joshua B.; Reiss, Thomas E.; Rosenberger, Kurt J.

2012-01-01

This report presents a summary of fieldwork conducted in Maunalua Bay, O'ahu, Hawaii to address coral-larval dispersal and recruitment from June through September, 2010. The objectives of this study were to understand the temporal and spatial variations in currents, waves, tides, temperature, and salinity in Maunalua Bay during the summer coral-spawning season of Montipora capitata. Short-term vessel surveys and satellite-tracked drifters were deployed to measure currents during the June 2010 spawning event and to supplement the longer-term measurements of currents and water-column properties by fixed, bottom-mounted instruments deployed in Maunalua Bay. These data show that currents at the surface and just below the surface where coral larvae are found are often oriented in opposite directions due primarily to tidal and trade-winds forcing as the primary mechanisms of circulation in the bay. These data extend our understanding of coral-larvae dispersal patterns due to tidal and wind-driven currents and may be applicable to larvae of other Hawaiian corals.

Intra- and inter-annual trends in phosphorus loads and comparison with nitrogen loads to Rehoboth Bay, Delaware (USA)

USGS Publications Warehouse

Volk, J.A.; Scudlark, J.R.; Savidge, K.B.; Andres, A.S.; Stenger, R.J.; Ullman, W.J.

2012-01-01

Monthly phosphorus loads from uplands, atmospheric deposition, and wastewater to Rehoboth Bay (Delaware) were determined from October 1998 to April 2002 to evaluate the relative importance of these three sources of P to the Bay. Loads from a representative subwatershed were determined and used in an areal extrapolation to estimate the upland load from the entire watershed. Soluble reactive phosphorus (SRP) and dissolved organic P (DOP) are the predominant forms of P in baseflow and P loads from the watershed are highest during the summer months. Particulate phosphorus (PP) becomes more significant in stormflow and during periods with more frequent or larger storms. Atmospheric deposition of P is only a minor source of P to Rehoboth Bay. During the period of 1998-2002, wastewater was the dominant external source of P to Rehoboth Bay, often exceeding all other P sources combined. Since 2002, however, due to technical improvements to the sole wastewater plant discharging directly to the Bay, the wastewater contribution of P has been significantly reduced and upland waters are now the principal source of P on an annualized basis. Based on comparison of N and P loads, primary productivity and biomass carrying capacity in Rehoboth Bay should be limited by P availability. However, due to the contrasting spatial and temporal patterns of N and P loading and perhaps internal cycling within the ecosystem, spatial and temporal variations in N and P-limitation within Rehoboth Bay are likely. ?? 2011 Elsevier Ltd.

Extracting Temporal and Spatial Distributions Information about Algal Glooms Based on Multitemporal Modis

NASA Astrophysics Data System (ADS)

Chunguang, L.; Qingjiu, T.

2012-07-01

Based on MODIS remote sensing data, method and technology to extraction the time and space distribution information of algae bloom is studied and established. The dynamic feature of time and space in Taihu Lake from 2009 to 2011 can be obtained by extracted method. Variation of cyanobacterial bloom in the Taihu Lake is analyzed and discussed. The algae bloom frequency index (AFI) and algae bloom sustainability index (ASI) is important criterion which can show the interannual and inter-monthly variation in the whole area or the subregion of Taihu Lake. Utilizing the AFI and ASI from 2009 to 2011, it found some phenomena that: the booming frequency decreased from the north and west to the East and South of Taihu Lake. The annual month algae bloom variation of AFI reflect the booming existing twin peaks in the high shock level and lag trend in general. In the subregion statistics, the IBD and ASI in 2011 show the abnormal condition in the border between the Gongshan Bay and Central Lake. The date is obvious earlier than that on the same subregion in previous years and that on others subregion in the same year.

The 1994 to 2008 concentration variations of atmospheric CO2 observed at Jubany Station (Antarctica)

NASA Astrophysics Data System (ADS)

Gallo, Veronica; de Simone, Sara; Ciattaglia, Luigi; Rafanelli, Claudio; Diego, Piero

2010-05-01

Since 1994 the Italian PNRA (National Research Program in Antarctica) and the Argentina DNA (Direction National de Antartico) have been collecting continuous atmospheric carbon dioxide measurements at Jubany. The Antarctic station at Jubany (62° 14'S, 58° 40'W) is located in King George Island, in the South Shetland archipelago, north of the Antarctic Peninsula. The laboratory is situated at an elevation of 15 m.s.l. on the SE slope of Potter Bay. The measurements are taken by using a Siemens U5 analyzer based on NDIR (Non Dispersive InfraRed) absorption method. Details are given on the station environment, meteorological conditions, instrumentation, and data selection strategy. The paper presents the first 14 years (1994-2008) of continuous atmospheric CO2 measurements; the interannual and seasonal variations of CO2 data are described

Simultaneous fitting of genomic-BLUP and Bayes-C components in a genomic prediction model.

PubMed

Iheshiulor, Oscar O M; Woolliams, John A; Svendsen, Morten; Solberg, Trygve; Meuwissen, Theo H E

2017-08-24

The rapid adoption of genomic selection is due to two key factors: availability of both high-throughput dense genotyping and statistical methods to estimate and predict breeding values. The development of such methods is still ongoing and, so far, there is no consensus on the best approach. Currently, the linear and non-linear methods for genomic prediction (GP) are treated as distinct approaches. The aim of this study was to evaluate the implementation of an iterative method (called GBC) that incorporates aspects of both linear [genomic-best linear unbiased prediction (G-BLUP)] and non-linear (Bayes-C) methods for GP. The iterative nature of GBC makes it less computationally demanding similar to other non-Markov chain Monte Carlo (MCMC) approaches. However, as a Bayesian method, GBC differs from both MCMC- and non-MCMC-based methods by combining some aspects of G-BLUP and Bayes-C methods for GP. Its relative performance was compared to those of G-BLUP and Bayes-C. We used an imputed 50 K single-nucleotide polymorphism (SNP) dataset based on the Illumina Bovine50K BeadChip, which included 48,249 SNPs and 3244 records. Daughter yield deviations for somatic cell count, fat yield, milk yield, and protein yield were used as response variables. GBC was frequently (marginally) superior to G-BLUP and Bayes-C in terms of prediction accuracy and was significantly better than G-BLUP only for fat yield. On average across the four traits, GBC yielded a 0.009 and 0.006 increase in prediction accuracy over G-BLUP and Bayes-C, respectively. Computationally, GBC was very much faster than Bayes-C and similar to G-BLUP. Our results show that incorporating some aspects of G-BLUP and Bayes-C in a single model can improve accuracy of GP over the commonly used method: G-BLUP. Generally, GBC did not statistically perform better than G-BLUP and Bayes-C, probably due to the close relationships between reference and validation individuals. Nevertheless, it is a flexible tool, in the sense, that it simultaneously incorporates some aspects of linear and non-linear models for GP, thereby exploiting family relationships while also accounting for linkage disequilibrium between SNPs and genes with large effects. The application of GBC in GP merits further exploration.

Chemical variations in Yellowknife Bay formation sedimentary rocks analyzed by ChemCam on board the Curiosity rover on Mars

USGS Publications Warehouse

Mangold, Nicolas; Forni, Olivier; Dromart, G.; Stack, K.M.; Wiens, Roger C.; Gasnault, Olivier; Sumner, Dawn Y.; Nachon, Marion; Meslin, Pierre-Yves; Anderson, Ryan B.; Barraclough, Bruce; Bell, J.F.; Berger, G.; Blaney, D.L.; Bridges, J.C.; Calef, F.; Clark, Brian R.; Clegg, Samuel M.; Cousin, Agnes; Edgar, L.; Edgett, Kenneth S.; Ehlmann, B.L.; Fabre, Cecile; Fisk, M.; Grotzinger, John P.; Gupta, S.C.; Herkenhoff, Kenneth E.; Hurowitz, J.A.; Johnson, J. R.; Kah, Linda C.; Lanza, Nina L.; Lasue, Jeremie; Le Mouélic, S.; Lewin, Eric; Malin, Michael; McLennan, Scott M.; Maurice, S.; Melikechi, Noureddine; Mezzacappa, Alissa; Milliken, Ralph E.; Newsome, H.L.; Ollila, A.; Rowland, Scott K.; Sautter, Violaine; Schmidt, M.E.; Schroder, S.; D'Uston, C.; Vaniman, Dave; Williams, R.A.

2015-01-01

The Yellowknife Bay formation represents a ~5 m thick stratigraphic section of lithified fluvial and lacustrine sediments analyzed by the Curiosity rover in Gale crater, Mars. Previous works have mainly focused on the mudstones that were drilled by the rover at two locations. The present study focuses on the sedimentary rocks stratigraphically above the mudstones by studying their chemical variations in parallel with rock textures. Results show that differences in composition correlate with textures and both manifest subtle but significant variations through the stratigraphic column. Though the chemistry of the sediments does not vary much in the lower part of the stratigraphy, the variations in alkali elements indicate variations in the source material and/or physical sorting, as shown by the identification of alkali feldspars. The sandstones contain similar relative proportions of hydrogen to the mudstones below, suggesting the presence of hydrous minerals that may have contributed to their cementation. Slight variations in magnesium correlate with changes in textures suggesting that diagenesis through cementation and dissolution modified the initial rock composition and texture simultaneously. The upper part of the stratigraphy (~1 m thick) displays rocks with different compositions suggesting a strong change in the depositional system. The presence of float rocks with similar compositions found along the rover traverse suggests that some of these outcrops extend further away in the nearby hummocky plains.

Investigation on growth and macro-defects of Er3+-doped BaY2F8 laser crystal

NASA Astrophysics Data System (ADS)

Wang, Shuai; Ruan, Yongfeng; Tsuboi, Taiju; Zhang, Shouchao; Wang, Youfa; Tong, Hongshuang

2013-08-01

Large BaY2F8 and Er3+-doped BaY2F8 single crystals were grown by the temperature gradient method. Three kinds of macro-defects were found in BaY2F8 single crystals. These macro-defects include cracks, growth striations and straight pipes. The morphologies and distribution regularities of these macro-defects were observed and studied using a solid polarization microscope. The formation mechanisms and the methods of eliminating these defects were discussed.

Latitudinal and stock-specific variation in size- and age-at-maturity of female winter flounder, Pseudopleuronectes americanus, as determined with gonad histology

NASA Astrophysics Data System (ADS)

McBride, Richard S.; Wuenschel, Mark J.; Nitschke, Paul; Thornton, Grace; King, Jeremy R.

2013-01-01

Female winter flounder were examined using gonad histology to determine the adequacy of routine macroscopic maturity classification methods and to determine the spatial variation in size and age of maturity in U.S. waters. Sampling occurred in spring and autumn, which was adequate to collect immature, mature, spawning-active, and non-active females. Females were collected in coastal waters from Delaware Bay, USA, to the Scotian Shelf, Canada, including in Long Island Sound and on Georges Bank, which covered all U.S. stock areas. Mature fish spawned in spring, when gonads comprised up to 30% of the total body weight. Direct comparisons of maturity assignment by macroscopic versus microscopic methods demonstrated that both schemes are compatible, but the more cost-effective macroscopic method had trouble distinguishing larger immature from smaller resting females. Spatial comparisons, using gonad histology only, supported the existence of three stocks in U.S. waters, but also revealed significant variation in age at maturity within the two coastal stocks. Age-at-maturity was more variable than size-at-maturity, which is consistent with known stock-specific patterns of growth rates and a postulated life history tradeoff to delay maturity until a size threshold is reached. The within-stock variation in median age at maturity, about one year for coastal stocks, recommends further investigation of using static, stock-specific maturity ogives to calculate reference points for management.

Alkalinity-salinity relationship in the Chesapeake Bay

NASA Astrophysics Data System (ADS)

Cintrón Del Valle, S. M.; Najjar, R.; Herrmann, M.; Goldberger, S.; Stets, E.

2016-12-01

Estuaries are a significant source of atmospheric CO2, a major greenhouse gas. However, it is not known whether the Chesapeake Bay, the largest estuary in the United States, is a source or sink of CO2. Extensive pH measurements in the Bay offer the possibility of estimating the air-water CO2 flux if robust relationships between alkalinity, the acid neutralizing capacity of a water body, and salinity can be established. Here we conduct a comprehensive analysis of the alkalinity-salinity relationship in the Chesapeake Bay based on more than 18,000 alkalinity measurements made between 1985 and 2015. It was found that seven segments of the Bay could be grouped into three different linear functions, suggesting that alkalinity is conserved in the Bay and has properties that change depending on the freshwater endmember (the riverine source). The highest freshwater endmember was 1.21 mol m-3 for the Potomac River, the lowest one was 0.41 mol m-3 for the York and Rappahannock Rivers, and an intermediate freshwater endmember was 0.79 mol m-3 for the remaining four segments. For some segments, most notably the Potomac River, the scatter of the data increases with decreasing salinity, which is due, in part, to seasonal and interannual variations in the freshwater endmember.

Patchiness of phytoplankton and primary production in Liaodong Bay, China.

PubMed

Pei, Shaofeng; Laws, Edward A; Zhang, Haibo; Ye, Siyuan; Yuan, Hongming; Liu, Haiyue

2017-01-01

A comprehensive study of water quality, phytoplankton biomass, and photosynthetic rates in Liaodong Bay, China, during June and July of 2013 revealed two large patches of high biomass and production with dimensions on the order of 10 km. Nutrient concentrations were above growth-rate-saturating concentrations throughout the bay, with the possible exception of phosphate at some stations. The presence of the patches therefore appeared to reflect the distribution of water temperature and variation of light penetration restricted by water turbidity. There was no patch of high phytoplankton biomass or production in a third, linear patch of water with characteristics suitable for rapid phytoplankton growth; the absence of a bloom in that patch likely reflected the fact that the width of the patch was less than the critical size required to overcome losses of phytoplankton to turbulent diffusion. The bottom waters of virtually all of the eastern half of the bay were below the depth of the mixed layer, and the lowest bottom water oxygen concentrations, 3-5 mg L-1, were found in that part of the bay. The water column in much of the remainder of the bay was within the mixed layer, and oxygen concentrations in both surface and bottom waters exceeded 5 mg L-1.

Patchiness of phytoplankton and primary production in Liaodong Bay, China

PubMed Central

Laws, Edward A.; Zhang, Haibo; Ye, Siyuan; Yuan, Hongming; Liu, Haiyue

2017-01-01

A comprehensive study of water quality, phytoplankton biomass, and photosynthetic rates in Liaodong Bay, China, during June and July of 2013 revealed two large patches of high biomass and production with dimensions on the order of 10 km. Nutrient concentrations were above growth-rate-saturating concentrations throughout the bay, with the possible exception of phosphate at some stations. The presence of the patches therefore appeared to reflect the distribution of water temperature and variation of light penetration restricted by water turbidity. There was no patch of high phytoplankton biomass or production in a third, linear patch of water with characteristics suitable for rapid phytoplankton growth; the absence of a bloom in that patch likely reflected the fact that the width of the patch was less than the critical size required to overcome losses of phytoplankton to turbulent diffusion. The bottom waters of virtually all of the eastern half of the bay were below the depth of the mixed layer, and the lowest bottom water oxygen concentrations, 3–5 mg L–1, were found in that part of the bay. The water column in much of the remainder of the bay was within the mixed layer, and oxygen concentrations in both surface and bottom waters exceeded 5 mg L–1. PMID:28235070

One year observations of atmospheric reactive gases (O3, CO, NOx, SO2) at Jang Bogo base in Terra Nova Bay, Antarctica

NASA Astrophysics Data System (ADS)

Siek Rhee, Tae; Seo, Sora

2016-04-01

Antarctica is a remote area surrounded by the Southern Ocean and far from the influence of human activities, giving us unique opportunity to investigate the background variation of trace gases which are sensitive to the human activities. Korean Antarctic base, Jang Bogo, was established as a unique permanent overwintering base in Terra Nova Bay in February, 2014. One year later, we installed a package of instruments to monitor atmospheric trace gases at the base, which includes long-lived greenhouse gases, CO2, CH4, and N2O, and reactive gases, O3, CO, NOx, and SO2. The atmospheric chemistry observatory, where these scientific instruments were installed, is located ca. 1 km far from the main building and power plant, minimizing the influence of pollution that may come from the operation of the base. Here we focus on the reactive gases measured in-situ at the base; O3 displays a typical seasonal variation with high in winter and low in summer with seasonal amplitude of ~18 ppb, CO was high in September at ~56 ppb, probably implying the invasion of lower latitude air mass with biomass burning, and low in late summer due to photochemical oxidation. NO did not show clear seasonal variation, but SO2 reveals larger values in summer than in winter. We will discuss potential atmospheric processes behind these first observations of reactive gases in Terra Nova Bay, Antarctica.

Life-history implications of large-scale spatial variation in adult survival of black brant (Branta bernicla nigricans)

USGS Publications Warehouse

Sedinger, James S.; Chelgren, Nathan; Lindberg, Mark S.; Obritchkewitch, Tim; Kirk, Morgan T.; Martin, Philip D.; Anderson, Betty A.; Ward, David H.

2002-01-01

We used capture-recapture methods to estimate adult survival rates for adult female Black Brant (Branta bernicla nigricans; hereafter “brant”) from three colonies in Alaska, two on the Yukon-Kuskokwim Delta, and one on Alaska's Arctic coast. Costs of migration and reproductive effort varied among those colonies, enabling us to examine variation in survival in relation to variation in these other variables. We used the Barker model in program MARK to estimate true annual survival for brant from the three colonies. Models allowing for spatial variation in survival were among the most parsimonious models but were indistinguishable from a model with no spatial variation. Point estimates of annual survival were slightly higher for brant from the Arctic (0.90 ± 0.036) than for brant from either Tutakoke River (0.85 ± 0.004) or Kokechik Bay (0.86 ± 0.011). Thus, our survival estimates do not support a hypothesis that the cost of longer migrations or harvest experienced by brant from the Arctic reduced their annual survival relative to brant from the Yukon-Kuskokwim Delta. Spatial variation in survival provides weak support for life-history theory because brant from the region with lower reproductive investment had slightly higher survival.

Development of a standardized transfusion ratio as a metric for evaluating dialysis facility anemia management practices.

PubMed

Liu, Jiannong; Li, Suying; Gilbertson, David T; Monda, Keri L; Bradbury, Brian D; Collins, Allan J

2014-10-01

Because transfusion avoidance has been the cornerstone of anemia treatment for patients with kidney disease, direct measurement of red blood cell transfusion use to assess dialysis facility anemia management performance is reasonable. We aimed to explore methods for estimating facility-level standardized transfusion ratios (STfRs) to assess provider anemia treatment practices. Retrospective cohort study. Point prevalent US hemodialysis patients on January 1, 2009, with Medicare as primary payer and dialysis duration of 90 days or longer were included (n = 223,901). All dialysis facilities with eligible patients were included (n = 5,345). Dialysis facility assignment. Receiving a red blood cell transfusion in the inpatient or outpatient setting. We evaluated 3 approaches for estimating STfR: ratio of observed to expected numbers of transfusions (STfR(obs)), a Bayesian approach (STfR(Bayes)), and a modified version of the Bayesian approach (STfR(modBayes)). The overall national transfusion rate in 2009 was 23.2 per 100 patient-years. Our model for predicting the expected number of transfusions performed well. For large facilities, all 3 STfRs worked well. However, for small facilities, while the STfR(modBayes) worked well, STfR(obs) values demonstrated instability and the STfR(Bayes) may produce more bias. Administration of transfusions to dialysis patients reflects medical practice both within and outside the dialysis unit. Some transfusions may be deemed unavoidable and transfusion practices are subject to considerable regional variation. Development of an STfR metric is feasible and reasonable for assessing anemia treatment at dialysis facilities. The STfR(obs) is simple to calculate and works well for larger dialysis facilities. The STfR(modBayes) is more analytically complex, but facilitates comparisons across all dialysis facilities, including small facilities. Copyright © 2014 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Validating Variational Bayes Linear Regression Method With Multi-Central Datasets.

PubMed

Murata, Hiroshi; Zangwill, Linda M; Fujino, Yuri; Matsuura, Masato; Miki, Atsuya; Hirasawa, Kazunori; Tanito, Masaki; Mizoue, Shiro; Mori, Kazuhiko; Suzuki, Katsuyoshi; Yamashita, Takehiro; Kashiwagi, Kenji; Shoji, Nobuyuki; Asaoka, Ryo

2018-04-01

To validate the prediction accuracy of variational Bayes linear regression (VBLR) with two datasets external to the training dataset. The training dataset consisted of 7268 eyes of 4278 subjects from the University of Tokyo Hospital. The Japanese Archive of Multicentral Databases in Glaucoma (JAMDIG) dataset consisted of 271 eyes of 177 patients, and the Diagnostic Innovations in Glaucoma Study (DIGS) dataset includes 248 eyes of 173 patients, which were used for validation. Prediction accuracy was compared between the VBLR and ordinary least squared linear regression (OLSLR). First, OLSLR and VBLR were carried out using total deviation (TD) values at each of the 52 test points from the second to fourth visual fields (VFs) (VF2-4) to 2nd to 10th VF (VF2-10) of each patient in JAMDIG and DIGS datasets, and the TD values of the 11th VF test were predicted every time. The predictive accuracy of each method was compared through the root mean squared error (RMSE) statistic. OLSLR RMSEs with the JAMDIG and DIGS datasets were between 31 and 4.3 dB, and between 19.5 and 3.9 dB. On the other hand, VBLR RMSEs with JAMDIG and DIGS datasets were between 5.0 and 3.7, and between 4.6 and 3.6 dB. There was statistically significant difference between VBLR and OLSLR for both datasets at every series (VF2-4 to VF2-10) (P < 0.01 for all tests). However, there was no statistically significant difference in VBLR RMSEs between JAMDIG and DIGS datasets at any series of VFs (VF2-2 to VF2-10) (P > 0.05). VBLR outperformed OLSLR to predict future VF progression, and the VBLR has a potential to be a helpful tool at clinical settings.

Replacement of tritiated water from irradiated fuel storage bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo, I.; Boniface, H.; Suppiah, S.

2015-03-15

Recently, AECL developed a novel method to reduce tritium emissions (to groundwater) and personnel doses at the NRU (National Research Universal) reactor irradiated fuel storage bay (also known as rod or spent fuel bay) through a water swap process. The light water in the fuel bay had built up tritium that had been transferred from the heavy water moderator through normal fuel transfers. The major advantage of the thermal stratification method was that a very effective tritium reduction could be achieved by swapping a minimal volume of bay water and warm tritiated water would be skimmed off the bay surface.more » A demonstration of the method was done that involved Computational Fluid Dynamics (CFD) modeling of the swap process and a test program that showed excellent agreement with model prediction for the effective removal of almost all the tritium with a minimal water volume. Building on the successful demonstration, AECL fabricated, installed, commissioned and operated a full-scale system to perform a water swap. This full-scale water swap operation achieved a tritium removal efficiency of about 96%.« less

Implementing a Bayes Filter in a Neural Circuit: The Case of Unknown Stimulus Dynamics.

PubMed

Sokoloski, Sacha

2017-09-01

In order to interact intelligently with objects in the world, animals must first transform neural population responses into estimates of the dynamic, unknown stimuli that caused them. The Bayesian solution to this problem is known as a Bayes filter, which applies Bayes' rule to combine population responses with the predictions of an internal model. The internal model of the Bayes filter is based on the true stimulus dynamics, and in this note, we present a method for training a theoretical neural circuit to approximately implement a Bayes filter when the stimulus dynamics are unknown. To do this we use the inferential properties of linear probabilistic population codes to compute Bayes' rule and train a neural network to compute approximate predictions by the method of maximum likelihood. In particular, we perform stochastic gradient descent on the negative log-likelihood of the neural network parameters with a novel approximation of the gradient. We demonstrate our methods on a finite-state, a linear, and a nonlinear filtering problem and show how the hidden layer of the neural network develops tuning curves consistent with findings in experimental neuroscience.

Responses of water environment to tidal flat reduction in Xiangshan Bay: Part I hydrodynamics

NASA Astrophysics Data System (ADS)

Li, Li; Guan, Weibing; Hu, Jianyu; Cheng, Peng; Wang, Xiao Hua

2018-06-01

Xiangshan Bay consists of a deep tidal channel and three shallow inlets. A large-scale tidal flat has been utilized through coastal construction. To ascertain the accumulate influences of these engineering projects upon the tidal dynamics of the channel-inlets system, this study uses FVCOM to investigate the tides and flow asymmetries of the bay, and numerically simulate the long-term variations of tidal dynamics caused by the loss of tidal flats. It was found that the reduction of tidal flat areas from 1963 to 2010 slightly dampened M2 tidal amplitudes (0.1 m, ∼6%) and advanced its phases by reducing shoaling effects, while amplified M4 tidal amplitudes (0.09 m, ∼27%) and advanced its phases by reducing bottom friction, in the inner bay. Consequently, the ebb dominance was dampened indicated by reduced absolute value of elevation skewness (∼20%) in the bay. The tides and tidal asymmetry were impacted by the locations, areas and slopes of the tidal flats through changing tidal prism, shoaling effect and bottom friction, and consequently impacted tidal duration asymmetry in the bay. Tides and tidal asymmetry were more sensitive to the tidal flat at the head of the bay than the side bank. Reduced/increased tidal flat slopes around the Tie inlet dampened the ebb dominance. Tidal flat had a role in dissipating the M4 tide rather than generating it, while the advection only play a secondary role in generating the M4 tide. The full-length tidal flats reclamation would trigger the reverse of ebb to flood dominance in the bay. This study would be applicable for similar narrow bays worldwide.

76 FR 70480 - Otay River Estuary Restoration Project, South San Diego Bay Unit of the San Diego Bay National...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-14

... River Estuary Restoration Project, South San Diego Bay Unit of the San Diego Bay National Wildlife...), intend to prepare an environmental impact statement (EIS) for the proposed Otay River Estuary Restoration... any one of the following methods. Email: [email protected] . Please include ``Otay Estuary NOI'' in the...

Reconstructing the history of eastern and central Florida Bay using mollusk-shell isotope records

USGS Publications Warehouse

Halley, R.B.; Roulier, L.M.

1999-01-01

Stable isotopic ratios of carbon and oxygen (??13C and ??18O) from mollusk shells reflect the water quality characteristics of Florida Bay and can be used to characterize the great temporal variability of the bay. Values of ?? 18O are directly influenced by temperature and evaporation and may be related to salinity. ??13C values of ??13C are sensitive to organic and inorganic sources of carbon and are influenced by productivity. Analyses of eight mollusk species from five short-core localities across Florida Bay show large ranges in the values of ??13C and ??18O, and reflect the variation of the bay over decades. Samples from southwestern Florida Bay have distinct ??13C values relative to samples collected in northeastern Florida Bay, and intermediate localities have intermediate values. 13C values of ??13C grade from marine in the southwest bay to more estuarine in the northeast. Long cores (> 1 m) with excellent chronologies were analyzed from central and eastern Florida Bay. Preliminary analyses of Brachiodontes exustus and Transenella spp. from the cores showed that both ??13C and ??18O changed during the first part of the twentieth century. After a century of relative stability during the 1800s, ??13C decreased between about 1910 and 1940, then stabilized at these new values for the next five decades. The magnitude of the reduction in ??13C values increased toward the northeast. Using a carbon budget model, reduced ??13C values are interpreted as resulting from decreased circulation in the bay, probably associated with decreased freshwater flow into the Bay. Mollusk shell ??18O values display several negative excursions during the 1800s, suggesting that the bay was less evaporitic than during the twentieth century. The isotope records indicate a fundamental change took place in Florida Bay circulation early in the twentieth century. The timing of the change links it to railroad building and early drainage efforts in South Florida rather than to flood control and water management measures initiated after World War II.

Regional distribution of the high-altitude clouds over the Indian subcontinent and surrounding oceanic regions based on seven years of satellite observations

NASA Astrophysics Data System (ADS)

Meenu, S.; Rajeev, K.; Parameswaran, K.; Suresh Raju, C.

2006-12-01

Quantitative estimates of the spatio-temporal variations in deep convective events over the Indian subcontinent, Arabian Sea, Bay of Bengal, and tropical Indian Ocean are carried out using the data obtained from Advanced Very High Resolution Radiometer (AVHRR) onboard NOAA-14 and NOAA-16 during the period 1996-2003. Pixels having thermal IR brightness temperature (BT) less than 245K are considered as high altitude clouds and those having BT<220 K are considered as very high altitude clouds. Very deep convective clouds are observed over north Bay of Bengal during the Asian summer monsoon season when the mean cloud top temperature reaches as low as 190K. Over the Head Bay of Bengal (HBoB) from June to September, more than 50% of the observed clouds are deep convective type and more than half of these deep convective clouds are very deep convective clouds. Histogram analysis of the cloud top temperatures during this period shows that over HBoB the most prominent cloud top temperature of the deep convective clouds is ~205K over the HBoB while that over southeast Arabian Sea (SEAS) is ~220K. This indicates that most probably the cloud top altitude over HBoB is ~2 km larger than that over SEAS during the Asian summer monsoon period. Another remarkable feature observed during the Asian summer monsoon period is the significantly low values of deep convective clouds observed over the south Bay of Bengal close to Srilanka, which appears as a large pool of reduced cloud amount surrounded by regions of large-scale deep convection. Over both SEAS and HBoB, the total, deep convective and very deep convective cloud amounts as well as their corresponding cloud top temperatures (or the altitude of the cloud top) undergo large seasonal variations, while such variations are less prominent over the eastern equatorial Indian Ocean.

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

DOE PAGES

An, F. P.; Balantekin, A. B.; Band, H. R.; ...

2017-06-19

Here, the Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GW th reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective 239Pu fission fractions F 239 from 0.25 to 0.35, Daya Bay measures an average IBD yield ¯σf of (5.90±0.13)×10 –43 cm 2/fission and a fuel-dependent variation in the IBDmore » yield, dσ f/dF 239, of (–1.86±0.18)×10 –43 cm 2/fission. This observation rejects the hypothesis of a constant antineutrino flux as a function of the 239Pu fission fraction at 10 standard deviations. The variation in IBD yield is found to be energy dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1σ. This discrepancy indicates that an overall deficit in the measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes 235U, 239Pu, 238U, and 241Pu. Based on measured IBD yield variations, yields of (6.17±0.17) and (4.27±0.26)×10 –43 cm 2/fission have been determined for the two dominant fission parent isotopes 235U and 239Pu. A 7.8% discrepancy between the observed and predicted 235U yields suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.« less

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay.

PubMed

An, F P; Balantekin, A B; Band, H R; Bishai, M; Blyth, S; Cao, D; Cao, G F; Cao, J; Chan, Y L; Chang, J F; Chang, Y; Chen, H S; Chen, Q Y; Chen, S M; Chen, Y X; Chen, Y; Cheng, J; Cheng, Z K; Cherwinka, J J; Chu, M C; Chukanov, A; Cummings, J P; Ding, Y Y; Diwan, M V; Dolgareva, M; Dove, J; Dwyer, D A; Edwards, W R; Gill, R; Gonchar, M; Gong, G H; Gong, H; Grassi, M; Gu, W Q; Guo, L; Guo, X H; Guo, Y H; Guo, Z; Hackenburg, R W; Hans, S; He, M; Heeger, K M; Heng, Y K; Higuera, A; Hsiung, Y B; Hu, B Z; Hu, T; Huang, E C; Huang, H X; Huang, X T; Huang, Y B; Huber, P; Huo, W; Hussain, G; Jaffe, D E; Jen, K L; Ji, X P; Ji, X L; Jiao, J B; Johnson, R A; Jones, D; Kang, L; Kettell, S H; Khan, A; Kohn, S; Kramer, M; Kwan, K K; Kwok, M W; Langford, T J; Lau, K; Lebanowski, L; Lee, J; Lee, J H C; Lei, R T; Leitner, R; Leung, J K C; Li, C; Li, D J; Li, F; Li, G S; Li, Q J; Li, S; Li, S C; Li, W D; Li, X N; Li, X Q; Li, Y F; Li, Z B; Liang, H; Lin, C J; Lin, G L; Lin, S; Lin, S K; Lin, Y-C; Ling, J J; Link, J M; Littenberg, L; Littlejohn, B R; Liu, J L; Liu, J C; Loh, C W; Lu, C; Lu, H Q; Lu, J S; Luk, K B; Ma, X Y; Ma, X B; Ma, Y Q; Malyshkin, Y; Martinez Caicedo, D A; McDonald, K T; McKeown, R D; Mitchell, I; Nakajima, Y; Napolitano, J; Naumov, D; Naumova, E; Ngai, H Y; Ochoa-Ricoux, J P; Olshevskiy, A; Pan, H-R; Park, J; Patton, S; Pec, V; Peng, J C; Pinsky, L; Pun, C S J; Qi, F Z; Qi, M; Qian, X; Qiu, R M; Raper, N; Ren, J; Rosero, R; Roskovec, B; Ruan, X C; Steiner, H; Stoler, P; Sun, J L; Tang, W; Taychenachev, D; Treskov, K; Tsang, K V; Tull, C E; Viaux, N; Viren, B; Vorobel, V; Wang, C H; Wang, M; Wang, N Y; Wang, R G; Wang, W; Wang, X; Wang, Y F; Wang, Z; Wang, Z; Wang, Z M; Wei, H Y; Wen, L J; Whisnant, K; White, C G; Whitehead, L; Wise, T; Wong, H L H; Wong, S C F; Worcester, E; Wu, C-H; Wu, Q; Wu, W J; Xia, D M; Xia, J K; Xing, Z Z; Xu, J L; Xu, Y; Xue, T; Yang, C G; Yang, H; Yang, L; Yang, M S; Yang, M T; Yang, Y Z; Ye, M; Ye, Z; Yeh, M; Young, B L; Yu, Z Y; Zeng, S; Zhan, L; Zhang, C; Zhang, C C; Zhang, H H; Zhang, J W; Zhang, Q M; Zhang, R; Zhang, X T; Zhang, Y M; Zhang, Y X; Zhang, Y M; Zhang, Z J; Zhang, Z Y; Zhang, Z P; Zhao, J; Zhou, L; Zhuang, H L; Zou, J H

2017-06-23

The Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GW_{th} reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective ^{239}Pu fission fractions F_{239} from 0.25 to 0.35, Daya Bay measures an average IBD yield σ[over ¯]_{f} of (5.90±0.13)×10^{-43}  cm^{2}/fission and a fuel-dependent variation in the IBD yield, dσ_{f}/dF_{239}, of (-1.86±0.18)×10^{-43}  cm^{2}/fission. This observation rejects the hypothesis of a constant antineutrino flux as a function of the ^{239}Pu fission fraction at 10 standard deviations. The variation in IBD yield is found to be energy dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1σ. This discrepancy indicates that an overall deficit in the measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes ^{235}U, ^{239}Pu, ^{238}U, and ^{241}Pu. Based on measured IBD yield variations, yields of (6.17±0.17) and (4.27±0.26)×10^{-43}  cm^{2}/fission have been determined for the two dominant fission parent isotopes ^{235}U and ^{239}Pu. A 7.8% discrepancy between the observed and predicted ^{235}U yields suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

NASA Astrophysics Data System (ADS)

An, F. P.; Balantekin, A. B.; Band, H. R.; Bishai, M.; Blyth, S.; Cao, D.; Cao, G. F.; Cao, J.; Chan, Y. L.; Chang, J. F.; Chang, Y.; Chen, H. S.; Chen, Q. Y.; Chen, S. M.; Chen, Y. X.; Chen, Y.; Cheng, J.; Cheng, Z. K.; Cherwinka, J. J.; Chu, M. C.; Chukanov, A.; Cummings, J. P.; Ding, Y. Y.; Diwan, M. V.; Dolgareva, M.; Dove, J.; Dwyer, D. A.; Edwards, W. R.; Gill, R.; Gonchar, M.; Gong, G. H.; Gong, H.; Grassi, M.; Gu, W. Q.; Guo, L.; Guo, X. H.; Guo, Y. H.; Guo, Z.; Hackenburg, R. W.; Hans, S.; He, M.; Heeger, K. M.; Heng, Y. K.; Higuera, A.; Hsiung, Y. B.; Hu, B. Z.; Hu, T.; Huang, E. C.; Huang, H. X.; Huang, X. T.; Huang, Y. B.; Huber, P.; Huo, W.; Hussain, G.; Jaffe, D. E.; Jen, K. L.; Ji, X. P.; Ji, X. L.; Jiao, J. B.; Johnson, R. A.; Jones, D.; Kang, L.; Kettell, S. H.; Khan, A.; Kohn, S.; Kramer, M.; Kwan, K. K.; Kwok, M. W.; Langford, T. J.; Lau, K.; Lebanowski, L.; Lee, J.; Lee, J. H. C.; Lei, R. T.; Leitner, R.; Leung, J. K. C.; Li, C.; Li, D. J.; Li, F.; Li, G. S.; Li, Q. J.; Li, S.; Li, S. C.; Li, W. D.; Li, X. N.; Li, X. Q.; Li, Y. F.; Li, Z. B.; Liang, H.; Lin, C. J.; Lin, G. L.; Lin, S.; Lin, S. K.; Lin, Y.-C.; Ling, J. J.; Link, J. M.; Littenberg, L.; Littlejohn, B. R.; Liu, J. L.; Liu, J. C.; Loh, C. W.; Lu, C.; Lu, H. Q.; Lu, J. S.; Luk, K. B.; Ma, X. Y.; Ma, X. B.; Ma, Y. Q.; Malyshkin, Y.; Martinez Caicedo, D. A.; McDonald, K. T.; McKeown, R. D.; Mitchell, I.; Nakajima, Y.; Napolitano, J.; Naumov, D.; Naumova, E.; Ngai, H. Y.; Ochoa-Ricoux, J. P.; Olshevskiy, A.; Pan, H.-R.; Park, J.; Patton, S.; Pec, V.; Peng, J. C.; Pinsky, L.; Pun, C. S. J.; Qi, F. Z.; Qi, M.; Qian, X.; Qiu, R. M.; Raper, N.; Ren, J.; Rosero, R.; Roskovec, B.; Ruan, X. C.; Steiner, H.; Stoler, P.; Sun, J. L.; Tang, W.; Taychenachev, D.; Treskov, K.; Tsang, K. V.; Tull, C. E.; Viaux, N.; Viren, B.; Vorobel, V.; Wang, C. H.; Wang, M.; Wang, N. Y.; Wang, R. G.; Wang, W.; Wang, X.; Wang, Y. F.; Wang, Z.; Wang, Z.; Wang, Z. M.; Wei, H. Y.; Wen, L. J.; Whisnant, K.; White, C. G.; Whitehead, L.; Wise, T.; Wong, H. L. H.; Wong, S. C. F.; Worcester, E.; Wu, C.-H.; Wu, Q.; Wu, W. J.; Xia, D. M.; Xia, J. K.; Xing, Z. Z.; Xu, J. L.; Xu, Y.; Xue, T.; Yang, C. G.; Yang, H.; Yang, L.; Yang, M. S.; Yang, M. T.; Yang, Y. Z.; Ye, M.; Ye, Z.; Yeh, M.; Young, B. L.; Yu, Z. Y.; Zeng, S.; Zhan, L.; Zhang, C.; Zhang, C. C.; Zhang, H. H.; Zhang, J. W.; Zhang, Q. M.; Zhang, R.; Zhang, X. T.; Zhang, Y. M.; Zhang, Y. X.; Zhang, Y. M.; Zhang, Z. J.; Zhang, Z. Y.; Zhang, Z. P.; Zhao, J.; Zhou, L.; Zhuang, H. L.; Zou, J. H.; Daya Bay Collaboration

2017-06-01

The Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 G Wth reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective 239Pu fission fractions F239 from 0.25 to 0.35, Daya Bay measures an average IBD yield σ¯f of (5.90 ±0.13 )×10-43 cm2/fission and a fuel-dependent variation in the IBD yield, d σf/d F239, of (-1.86 ±0.18 )×10-43 cm2/fission . This observation rejects the hypothesis of a constant antineutrino flux as a function of the 239Pu fission fraction at 10 standard deviations. The variation in IBD yield is found to be energy dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1 σ . This discrepancy indicates that an overall deficit in the measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes 235U, 239Pu, 238U, and 241Pu. Based on measured IBD yield variations, yields of (6.17 ±0.17 ) and (4.27 ±0.26 )×10-43 cm2 /fission have been determined for the two dominant fission parent isotopes 235U and 239Pu. A 7.8% discrepancy between the observed and predicted 235U yields suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

An, F. P.; Balantekin, A. B.; Band, H. R.

Here, the Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GW th reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective 239Pu fission fractions F 239 from 0.25 to 0.35, Daya Bay measures an average IBD yield ¯σf of (5.90±0.13)×10 –43 cm 2/fission and a fuel-dependent variation in the IBDmore » yield, dσ f/dF 239, of (–1.86±0.18)×10 –43 cm 2/fission. This observation rejects the hypothesis of a constant antineutrino flux as a function of the 239Pu fission fraction at 10 standard deviations. The variation in IBD yield is found to be energy dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1σ. This discrepancy indicates that an overall deficit in the measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes 235U, 239Pu, 238U, and 241Pu. Based on measured IBD yield variations, yields of (6.17±0.17) and (4.27±0.26)×10 –43 cm 2/fission have been determined for the two dominant fission parent isotopes 235U and 239Pu. A 7.8% discrepancy between the observed and predicted 235U yields suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.« less

The changing seascape of Galway Bay, Western Ireland

NASA Astrophysics Data System (ADS)

Mc Cullagh, D.; Benetti, S.; Plets, R. M. K.; Edwards, R.

2016-12-01

During the late Quaternary significant environmental and relative sea-level variations have contributed to shaping present day coastlines. This is particularly evident along formerly glaciated continental margins. Strong evidence of these changes are recorded in Galway Bay, Western Ireland. This research uses a multidisciplinary approach. Seismic and multibeam data, sedimentological, micropaleontological, geochemical analysis and 15 radiocarbon dates of sediment cores from the bay provide post last glacial maximum (LGM) sea level and environmental reconstructions for the region. The acoustic stratigraphy of the bay includes 3 seismic units: the deepest unit represents the acoustic basement, composed of limestone and granite bedrock; the middle unit is composed of the oldest preserved sediments, deposited during and after the LGM, and interpreted to be glacial till. The uppermost unit represents deposition and reworking after glacial retreat. The erosive action of the ice sheet that extended off the Irish coast is thought to be responsible for the removal and reworking of all sediments older that the LGM. In the sediment cores, three main lithofacies were identified: 1) a sandy silt and clay facies, 2) a distinct shell hash interlayer and, 3) a fine silty sand facies. These 3 facies are found within the uppermost seismic unit, and initial radiocarbon dating of shells in 4 cores, constrain these sediments and the uppermost seismic unit to the Holocene. Preliminary qualitative analysis on foraminifera from several cores shows a general trend of progression from estuarine to open marine conditions, inferred from indicator species. This trend is supported by X-ray fluorescence (XRF) analysis which shows increased ratios of Cl/Fe in younger deposits. Constraining dates on sea level variations in the region will be added to the sea level database for Ireland and possibly used to adjust the existing relative sea level models. These are important for understating past sea level variations and modelling future trends.

Chitosan-decorated selenium nanoparticles as protein carriers to improve the in vivo half-life of the peptide therapeutic BAY 55-9837 for type 2 diabetes mellitus.

PubMed

Rao, Lei; Ma, Yi; Zhuang, Manjiao; Luo, Tianjie; Wang, Yayu; Hong, An

2014-01-01

As a potential protein therapeutic for type 2 diabetes mellitus (T2DM), BAY 55-9837 is limited by poor stability and a very short half-life in vivo. The purpose of this study was to construct a novel nanostructured biomaterial by conjugating BAY 55-9837 to chitosan-decorated selenium nanoparticles (CS-SeNPs) to prolong the in vivo half-life of BAY 55-9837 by reducing its renal clearance rate. BAY 55-9837-loaded CS-SeNPs (BAY-CS-SeNPs) were prepared, and their surface morphology, particle size, zeta potential, and structure were characterized. The stability, protein-loading rate, and in vitro release of BAY 55-9837 from CS-SeNPs were also quantified. Additionally, a sensitive high-performance liquid chromatography (HPLC) assay was developed for the quantification of BAY 55-9837 in mouse plasma. Thereafter, mice were injected via the tail vein with either BAY 55-9837 or BAY-CS-SeNPs, and the plasma concentration of BAY 55-9837 was determined via our validated HPLC method at different time intervals postinjection. Relevant in vivo pharmacokinetic parameters (half-life, area under the curve from time 0 to last sampling point, observed clearance) were then calculated and analyzed. BAY-CS-SeNPs were successfully synthesized, with diameters of approximately 200 nm. BAY-CS-SeNPs displayed good stability with a high protein-loading rate, and the release process of BAY 55-9837 from the CS-SeNPs lasted for over 70 hours, with the cumulative release reaching 78.9%. Moreover, the conjugation of CS-SeNPs to BAY 55-9837 significantly reduced its renal clearance to a rate of 1.56 mL/h and extended its half-life to 20.81 hours. In summary, our work provides a simple method for reducing the renal clearance rate and extending the half-life of BAY 55-9837 in vivo by utilizing CS-SeNPs as nanocarriers.

Vertical Structure of Aerosols and Mineral Dust Over the Bay of Bengal From Multisatellite Observations

NASA Astrophysics Data System (ADS)

Lakshmi, N. B.; Nair, Vijayakumar S.; Suresh Babu, S.

2017-12-01

The vertical distribution of aerosol and dust extinction coefficient over the Bay of Bengal is examined using the satellite observations (Cloud Aerosol Lidar with Orthogonal Polarization (CALIOP) and Moderate Resolution Imaging Spectroradiometer (MODIS)) for the period from 2006 to 2017. Distinct seasonal pattern is observed in the vertical structure of both aerosol and dust over the Bay of Bengal with an enhancement of 24% in the aerosol extinction above 1 km from winter (December, January and February) to premonsoon (March, April, and May). Significant contribution of dust is observed over the northern Bay of Bengal during premonsoon season where 22% of the total aerosol extinction is contributed by dust aerosols transported from the nearby continental regions. During winter, dust transport is found to be less significant with fractional contribution of 10%-13% to the total aerosol optical depth over the Bay of Bengal. MODIS-derived dust fraction (fine mode based) shows an overestimation up to twofold compared to CALIOP dust fraction (depolarization based), whereas the Goddard Chemistry Aerosol Radiation and Transport-simulated dust fraction underestimates the satellite-derived dust fractions over the Bay of Bengal. Though the long-term variation in dust aerosol showed a decreasing trend over the Bay of Bengal, the confidence level is insufficient in establishing the robustness of the observed trend. However, significant dust-induced heating is observed above the boundary layer during premonsoon season. This dust-induced elevated heating can affect the convection over the Bay of Bengal which will have implication on the monsoon dynamics over the Indian region.

Stormwater impact in Guanabara Bay (Rio de Janeiro): Evidences of seasonal variability in the dynamic of the sediment heavy metals

NASA Astrophysics Data System (ADS)

Fonseca, E. M.; Baptista Neto, J. A.; Silva, C. G.; McAlister, J. J.; Smith, B. J.; Fernandez, M. A.

2013-09-01

Guanabara Bay is one of the most prominent coastal bays in Brazil. This environment is an estuary of 91 rivers and channels, surrounded by the metropolis of Rio de Janeiro. The bay receives considerable amounts of contaminants introduced from sewage effluents, industrial discharge, urban and agricultural runoff, atmospheric fallout, and the combined inputs from the rivers, making Guanabara Bay one of the most polluted coastal environments on the Brazilian coastline. The aim of this work is to study the concentration and fractionation of the heavy metals within the sediments of the bay. In order to understand the possible seasonal influence on the heavy metal fractionation, two campaigns were carried out in two different seasons of the year (rainy and dry). Twelve stations, in four different areas, with different oceanographic characteristics, where chosen. To assess the bioavailability of the metals a selective extraction procedure was used to study the geochemical fractionation and bioavailability of Zn, Cu, Cr, Ni and Pb. The rainy season was very important with respect to variation in the total concentrations of Cr, Ni and Pb and their fractionation within different "operational" phases present in Guanabara Bay sediments. The water-soluble phase showed little importance, with respect to metal adsorption and this would suggest very low mobility of metals in the water column. Nevertheless, the potentially available metals within these sediments showed a high probability for their release and therefore cause contamination of the water column, since different parts of the bay are constantly subjected to dredging projects promoted by the harbor authorities.

Spatial distribution of dinoflagellates from the tropical coastal waters of the South Andaman, India: Implications for coastal pollution monitoring.

PubMed

Narale, Dhiraj Dhondiram; Anil, Arga Chandrashekar

2017-02-15

Dinoflagellate community structure from two semi-enclosed areas along the South Andaman region, India, was investigated to assess the anthropogenic impact on coastal water quality. At the densely inhabited Port Blair Bay, the dominance of mixotrophs in water and Protoperidinoids in sediments was attributed to anthropogenic nutrient enrichment and prey availability. A significant decrease in dinoflagellate abundance from inner to outer bay emphasize the variation in nutrient availability. The dominance of autotrophs and Gonyaulacoid cysts at the North Bay highlight low nutrient conditions with less anthropogenic pressure. The occurrence of oceanic Ornithocercus steinii and Diplopsalis sp. could evince the oceanic water intrusion into the North Bay. Nine potentially harmful and red-tide-forming species including Alexandrium tamarense complex, A. minutum were identified in this study. Although there are no harmful algal bloom (HABs) incidences in this region so far, increasing coastal pollution could support their candidature towards the future HABs initiation and development. Copyright © 2016 Elsevier Ltd. All rights reserved.

Predicting the vertical structure of tidal current and salinity in San Francisco Bay, California

USGS Publications Warehouse

Ford, Michael; Wang, Jia; Cheng, Ralph T.

1990-01-01

A two-dimensional laterally averaged numerical estuarine model is developed to study the vertical variations of tidal hydrodynamic properties in the central/north part of San Francisco Bay, California. Tidal stage data, current meter measurements, and conductivity, temperature, and depth profiling data in San Francisco Bay are used for comparison with model predictions. An extensive review of the literature is conducted to assess the success and failure of previous similar investigations and to establish a strategy for development of the present model. A σ plane transformation is used in the vertical dimension to alleviate problems associated with fixed grid model applications in the bay, where the tidal range can be as much as 20–25% of the total water depth. Model predictions of tidal stage and velocity compare favorably with the available field data, and prototype salinity stratification is qualitatively reproduced. Conclusions from this study as well as future model applications and research needs are discussed.

Spatial distribution of heavy metals in surficial sediments from Guanabara Bay: Rio de Janeiro, Brazil

NASA Astrophysics Data System (ADS)

Neto, José Antônio Baptista; Gingele, Franz Xaver; Leipe, Thomas; Brehme, Isa

2006-04-01

Ninety-two surface sediment samples were collected in Guanabara Bay, one of the most prominent urban bays in SE Brazil, to investigate the spatial distribution of anthropogenic pollutants. The concentrations of heavy metals, organic carbon and particle size were examined in all samples. Large spatial variations of heavy metals and particle size were observed. The highest concentrations of heavy metals were found in the muddy sediments from the north western region of the bay near the main outlets of the most polluted rivers, municipal waste drainage systems and one of the major oil refineries. Another anomalous concentration of metals was found adjacent to Rio de Janeiro Harbour. The heavy metal concentrations decrease to the northeast, due to intact rivers and the mangrove systems in this area, and to the south where the sand fraction and open-marine processes dominate. The geochemical normalization of metal data to Li or Al has also demonstrated that the anthropogenic input of heavy metals have altered the natural sediment heavy metal distribution.

Correlation of chlorophyll, suspended matter, and related parameters of waters in the lower Chesapeake Bay area to LANDSAT-1 imagery

NASA Technical Reports Server (NTRS)

Fleischer, P. (Principal Investigator); Bowker, D. E.; Witte, W. G.; Gosink, T. A.; Hanna, W. J.; Ludwick, J. C.

1976-01-01

The author has identified the following significant results. An effort to relate water parameters of the lower Chesapeake Bay area to multispectral scanner images of LANDSAT 1 has shown that some spectral bands can be correlated to water parameters, and has demonstrated the feasibility of synoptic mapping of estuaries by satellite. Bands 5 and 6 were shown to be useful for monitoring total particles. Band 5 showed high correlation with suspended sediment concentration. Attenuation coefficients monitored continuously by ship along three baselines were cross correlated with radiance values on three days. Improved correlations resulted when tidal conditions were taken into consideration. A contouring program was developed to display sediment variation in the lower Chesapeake Bay from the MSS bands.

The holocene biochronostratigraphy and paleoenvironment in Dvina Bay from benthic foraminiferal studies of the White Sea

NASA Astrophysics Data System (ADS)

Saidova, Kh. M.

2010-08-01

The compositional changes and frequency variations in the foraminiferal communities through the sediment section across Dvina Bay allow us to identify 14 ecological-stratigraphic zones. Based on the 14C dates for the foraminiferal tests, the distinguished ecozones correspond to the appropriate Holocene stages and substages. Because most of the foraminiferal species identified in the Holocene sediments are abundant and diverse in the modern oceans, they provide a powerful tool for the reconstruction of the paleoenvironmental changes during the Holocene.

Phytoplankton assemblages within the Chesapeake Bay plume and adjacent waters of the continental shelf

NASA Technical Reports Server (NTRS)

Marshall, H. G.

1981-01-01

The Chesapeake Bay plume was identified and plotted in relation to the presence and high concentrations of phytoplankton assemblages. Seasonal differences occurred within the plume during the collection period, with Skeletonema costatum and an ultraplankton component the dominant forms. Patchiness was found along the transects, with variations in composition and concentrations common on consecutive day sampling within the plume in its movement along the shelf. The presence of 236 species is noted, with their presence indicated for plume and shelf stations during the March, June, and October 1980 collections.

A Novel Feature Selection Technique for Text Classification Using Naïve Bayes.

PubMed

Dey Sarkar, Subhajit; Goswami, Saptarsi; Agarwal, Aman; Aktar, Javed

2014-01-01

With the proliferation of unstructured data, text classification or text categorization has found many applications in topic classification, sentiment analysis, authorship identification, spam detection, and so on. There are many classification algorithms available. Naïve Bayes remains one of the oldest and most popular classifiers. On one hand, implementation of naïve Bayes is simple and, on the other hand, this also requires fewer amounts of training data. From the literature review, it is found that naïve Bayes performs poorly compared to other classifiers in text classification. As a result, this makes the naïve Bayes classifier unusable in spite of the simplicity and intuitiveness of the model. In this paper, we propose a two-step feature selection method based on firstly a univariate feature selection and then feature clustering, where we use the univariate feature selection method to reduce the search space and then apply clustering to select relatively independent feature sets. We demonstrate the effectiveness of our method by a thorough evaluation and comparison over 13 datasets. The performance improvement thus achieved makes naïve Bayes comparable or superior to other classifiers. The proposed algorithm is shown to outperform other traditional methods like greedy search based wrapper or CFS.

Probability-based estimates of site-specific copper water quality criteria for the Chesapeake Bay, USA.

PubMed

Arnold, W Ray; Warren-Hicks, William J

2007-01-01

The object of this study was to estimate site- and region-specific dissolved copper criteria for a large embayment, the Chesapeake Bay, USA. The intent is to show the utility of 2 copper saltwater quality site-specific criteria estimation models and associated region-specific criteria selection methods. The criteria estimation models and selection methods are simple, efficient, and cost-effective tools for resource managers. The methods are proposed as potential substitutes for the US Environmental Protection Agency's water effect ratio methods. Dissolved organic carbon data and the copper criteria models were used to produce probability-based estimates of site-specific copper saltwater quality criteria. Site- and date-specific criteria estimations were made for 88 sites (n = 5,296) in the Chesapeake Bay. The average and range of estimated site-specific chronic dissolved copper criteria for the Chesapeake Bay were 7.5 and 5.3 to 16.9 microg Cu/L. The average and range of estimated site-specific acute dissolved copper criteria for the Chesapeake Bay were 11.7 and 8.3 to 26.4 microg Cu/L. The results suggest that applicable national and state copper criteria can increase in much of the Chesapeake Bay and remain protective. Virginia Department of Environmental Quality copper criteria near the mouth of the Chesapeake Bay, however, need to decrease to protect species of equal or greater sensitivity to that of the marine mussel, Mytilus sp.

Reconstructing Mississippi River Deltaic Wetland Hydrostratigraphy Using Compositional Kriging Method - Implications for Groundwater, Groundwater-River Water Interaction, Subsidence and Deltaic Wetland Evolution

NASA Astrophysics Data System (ADS)

Li, A.; Tsai, F. T. C.; White, C.; Wang, J.; Bentley, S. J.; Xu, K.

2016-12-01

River deltaic wetlands are formed along coastal area where sediment-laden river water reaches ocean. A river deltaic wetland is a complex system that mainly consists of groundwater, soil and vegetation components. Groundwater makes up a large portion of the system. The wetlands are important to human being and wild life. This research focuses on hydrostratigraphic architecture of the Mississippi River deltaic wetland. Research area includes lower Barataria Bay and lower Breton Sound that located on the Mississippi River Delta in southern Louisiana. In this study, a three dimensional hydrostratigraphy model is constructed using coring survey grain size data and geostatistics approach. A three-dimensional grid system is firstly constructed to cover the whole research domain. Each cell of the grid has a dimension of 100 meters by 100 meters by 1 centimeter (length by width by depth). Then Compositional Kriging and Gaussian Sequential Simulation methods are adopted to estimate soil composition (sand, silt and clay fractions) for each cell. A result has been generated to reveal spatial hydro facies variation by cutting cross sections and extracting soil texture maps at different locations. In the result, bay silt makes a large portion of the sediments body and sandy sediments are shown at different depths in both sides of the river. In Barataria Bay, sand bodies are lenticular, relatively thick and vertical continuous, however, in Breton Sound, sand bodies are sheet-like, relatively thin and vertical non-continuous. It is likely that the sandy sediments in Barataria Bay and Breton Sound are deposited in distal distributary and overbank flow respectively. Larger sandy bodies are prone to form in the distal distributary than in the overbank flow. Sandy units formed in the distal distributary can provide better interconnection between river water and groundwater than that formed in the overbank flow. Larger sandy bodies also provides more space to store groundwater. More silty and clayey sediments in the Breton Sound side make it more subject to compactional subsidence. More sandy sediments occur at the shallow portion of the Breton Sound than Barataria Bay. And these sands are interpreted as transgressive product that is formed by reworking forces such as wind, tide, cold front and storm.

Local wind forcing of the Monterey Bay area inner shelf

USGS Publications Warehouse

Drake, P.T.; McManus, M.A.; Storlazzi, C.D.

2005-01-01

Wind forcing and the seasonal cycles of temperature and currents were investigated on the inner shelf of the Monterey Bay area of the California coast for 460 days, from June 2001 to September 2002. Temperature measurements spanned an approximate 100 km stretch of coastline from a bluff just north of Monterey Bay south to Point Sur. Inner shelf currents were measured at two sites near the bay's northern shore. Seasonal temperature variations were consistent with previous observations from the central California shelf. During the spring, summer and fall, a seasonal mean alongshore current was observed flowing northwestward in the northern bay, in direct opposition to a southeastward wind stress. A barotropic alongshore pressure gradient, potentially driving the northwestward flow, was needed to balance the alongshore momentum equation. With the exception of the winter season, vertical profiles of mean cross-shore currents were consistent with two-dimensional upwelling and existing observations from upwelling regions with poleward subsurface flow. At periods of 15-60 days, temperature fluctuations were coherent both throughout the domain and with the regional wind field. Remote wind forcing was minimal. During the spring upwelling season, alongshore currents and temperatures in the northern bay were most coherent with winds measured at a nearby land meteorological station. This wind site showed relatively low correlations to offshore buoy wind stations, indicating localized wind effects are important to the circulation along this stretch of Monterey Bay's inner shelf. ?? 2004 Elsevier Ltd. All rights reserved.

Bayesian Computation for Log-Gaussian Cox Processes: A Comparative Analysis of Methods

PubMed Central

Teng, Ming; Nathoo, Farouk S.; Johnson, Timothy D.

2017-01-01

The Log-Gaussian Cox Process is a commonly used model for the analysis of spatial point pattern data. Fitting this model is difficult because of its doubly-stochastic property, i.e., it is an hierarchical combination of a Poisson process at the first level and a Gaussian Process at the second level. Various methods have been proposed to estimate such a process, including traditional likelihood-based approaches as well as Bayesian methods. We focus here on Bayesian methods and several approaches that have been considered for model fitting within this framework, including Hamiltonian Monte Carlo, the Integrated nested Laplace approximation, and Variational Bayes. We consider these approaches and make comparisons with respect to statistical and computational efficiency. These comparisons are made through several simulation studies as well as through two applications, the first examining ecological data and the second involving neuroimaging data. PMID:29200537

Predictive performance of genomic selection methods for carcass traits in Hanwoo beef cattle: impacts of the genetic architecture.

PubMed

Mehrban, Hossein; Lee, Deuk Hwan; Moradi, Mohammad Hossein; IlCho, Chung; Naserkheil, Masoumeh; Ibáñez-Escriche, Noelia

2017-01-04

Hanwoo beef is known for its marbled fat, tenderness, juiciness and characteristic flavor, as well as for its low cholesterol and high omega 3 fatty acid contents. As yet, there has been no comprehensive investigation to estimate genomic selection accuracy for carcass traits in Hanwoo cattle using dense markers. This study aimed at evaluating the accuracy of alternative statistical methods that differed in assumptions about the underlying genetic model for various carcass traits: backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS). Accuracies of direct genomic breeding values (DGV) for carcass traits were estimated by applying fivefold cross-validation to a dataset including 1183 animals and approximately 34,000 single nucleotide polymorphisms (SNPs). Accuracies of BayesC, Bayesian LASSO (BayesL) and genomic best linear unbiased prediction (GBLUP) methods were similar for BT, EMA and MS. However, for CW, DGV accuracy was 7% higher with BayesC than with BayesL and GBLUP. The increased accuracy of BayesC, compared to GBLUP and BayesL, was maintained for CW, regardless of the training sample size, but not for BT, EMA, and MS. Genome-wide association studies detected consistent large effects for SNPs on chromosomes 6 and 14 for CW. The predictive performance of the models depended on the trait analyzed. For CW, the results showed a clear superiority of BayesC compared to GBLUP and BayesL. These findings indicate the importance of using a proper variable selection method for genomic selection of traits and also suggest that the genetic architecture that underlies CW differs from that of the other carcass traits analyzed. Thus, our study provides significant new insights into the carcass traits of Hanwoo cattle.

Geochemical studies of Fe, Mn, Co, As, Cr, Sb, Zn, Sc and V in surface sediments from Jiaozhou Bay

NASA Astrophysics Data System (ADS)

Wu, Run; Li, Pei-Quan; Miao, Lu-Tian; Zhang, Shu-Xin; Tian, Wei-Zhi

1994-12-01

The contents of nearly forty-elements in surface sediments in Jiaozhou Bay were determined using a Neutron Activation Analysis Technique (Grancini, et al., 1976; Li Peiquan et al., 1985, 1986; Li Xiuxia et al., 1986). This paper's detailed discussion on only nine elements (Fe, Mn, Co, Cr, Sc, As, Sb, Zn and V) includes their distributions, concentrations, correlationships, material sources, background, etc. Based on Zavaristski's classification method, Fe, Mn, Co, Cr and V belong to the second group; As and Sb to the eighth groups: Sc and Zn to the third and sixth groups. It was found that their notably good correlationship is mainly due to the similarity of their ionic structures and that their variation is controlled by the Fe content (except Mn). The source of sediments is mainly terristrial material, and the composition of sediment is similar to that of shale and shale+clay. The contents for a large number of elements are within the scope of the background level, but there still is pollution of Zn and Cr, at least in a few stations.

System for handling and storing radioactive waste

DOEpatents

Anderson, J.K.; Lindemann, P.E.

1982-07-19

A system and method are claimed for handling and storing spent reactor fuel and other solid radioactive waste, including canisters to contain the elements of solid waste, storage racks to hold a plurality of such canisters, storage bays to store these racks in isolation by means of shielded doors in the bays. This system also includes means for remotely positioning the racks in the bays and an access tunnel within which the remotely operated means is located to position a rack in a selected bay. The modular type of these bays will facilitate the construction of additional bays and access tunnel extension.

System for handling and storing radioactive waste

DOEpatents

Anderson, John K.; Lindemann, Paul E.

1984-01-01

A system and method for handling and storing spent reactor fuel and other solid radioactive waste, including canisters to contain the elements of solid waste, storage racks to hold a plurality of such canisters, storage bays to store these racks in isolation by means of shielded doors in the bays. This system also includes means for remotely positioning the racks in the bays and an access tunnel within which the remotely operated means is located to position a rack in a selected bay. The modular type of these bays will facilitate the construction of additional bays and access tunnel extension.

Temperature variability caused by internal tides in the coral reef ecosystem of Hanauma bay, Hawai'i

NASA Astrophysics Data System (ADS)

Smith, Katharine A.; Rocheleau, Greg; Merrifield, Mark A.; Jaramillo, Sergio; Pawlak, Geno

2016-03-01

Hanauma Bay Nature Preserve is a shallow bay (<30 m depth) on the island of O'ahu, Hawai'i, offshore of which tidal flow over deep ridge topography (500-1000 m depth) is known to generate semidiurnal frequency internal tides. A field experiment was conducted during March to June 2009 to determine whether the deep internal tides propagate shoreward to influence variability in temperature and currents in the bay environment. Temperature observations in the bay exhibit a diurnal cycle that is strongest near the surface (upper 10 m) and is associated with solar heating. In early summer (May-June), as the upper mixed layer warms and a shallow seasonal thermocline develops, temperature fluctuations in deeper bay waters (>15 m depth) become dominated by large semidiurnal variations (up to 2.7 °C) that are attributed to the internal tide. These temperature drops caused by the internal tide occur consistently twice a day under summer stratification at depths as shallow as 15 m, while smaller temperature drops (up to 1.8 °C) occur occasionally at 5 m. Although semidiurnal band temperatures vary seasonally, semidiurnal band currents exhibit similar magnitudes in spring and summer. This suggests that the weak temperature fluctuations in spring are due to the bay residing entirely in the upper mixed layer at this time of year, while internal tide energy continues to influence currents. Observations made along a cross-shore/vertical transect at the center of the bay with an autonomous underwater vehicle highlight the structure of cold intrusions that fill a large portion of the bay as well as the relationship between temperature, salinity, chlorophyll, and backscatter. Near-bottom, advective heat flux estimates at the mouth of the bay indicate that the internal tide tends to advect cold water into the bay primarily on the northeast side of the bay entrance, with cold water outflow on the opposite side. The observations highlight the role of the internal tide along with seasonal changes in stratification in temperature variability in shallow ecosystems, particularly those close to generation sites.

The nearest neighbor and the bayes error rates.

PubMed

Loizou, G; Maybank, S J

1987-02-01

The (k, l) nearest neighbor method of pattern classification is compared to the Bayes method. If the two acceptance rates are equal then the asymptotic error rates satisfy the inequalities Ek,l + 1 ¿ E*(¿) ¿ Ek,l dE*(¿), where d is a function of k, l, and the number of pattern classes, and ¿ is the reject threshold for the Bayes method. An explicit expression for d is given which is optimal in the sense that for some probability distributions Ek,l and dE* (¿) are equal.

75 FR 53298 - A Method to Assess Climate-Relevant Decisions: Application in the Chesapeake Bay

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-31

... ENVIRONMENTAL PROTECTION AGENCY [FRL-9195-4; Docket ID No. EPA-HQ-ORD-2010-0709] A Method to... comment period for the draft document titled, ``A Method to Assess Climate-Relevant Decision: Application... draft ``A Method To Assess Climate-Relevant Decisions: Application in the Chesapeake Bay'' is available...

Probabilistic combination of static and dynamic gait features for verification

NASA Astrophysics Data System (ADS)

Bazin, Alex I.; Nixon, Mark S.

2005-03-01

This paper describes a novel probabilistic framework for biometric identification and data fusion. Based on intra and inter-class variation extracted from training data, posterior probabilities describing the similarity between two feature vectors may be directly calculated from the data using the logistic function and Bayes rule. Using a large publicly available database we show the two imbalanced gait modalities may be fused using this framework. All fusion methods tested provide an improvement over the best modality, with the weighted sum rule giving the best performance, hence showing that highly imbalanced classifiers may be fused in a probabilistic setting; improving not only the performance, but also generalized application capability.

The stable oxygen and carbon isotopic record from a coral growing in Florida Bay: a 160 year record of climatic and anthropogenic influence

USGS Publications Warehouse

Swart, Peter K.; Healy, Genevieve F.; Dodge, Richard E.; Kramer, Philip; Hudson, J. Harold; Halley, Robert B.; Robblee, Michael B.

1996-01-01

A 160 year record of skeletal δ13C and δ18O was examined in a specimen of the coral Solenastrea bournonigrowing in Florida Bay. Variations in the δ18O of the skeleton can be correlated to changes in salinity while changes in the δ13C reflect cycling of organic material within the Bay. Based on the correlation between salinity and skeletal δ18O, we have concluded that there has been no long term increase in salinity in this area of Florida Bay over the past 160 years. Using salinity correlations between the various basins obtained from instrumental data, we have been able to extend our interpretations to other parts of Florida Bay reaching similar conclusions. In contrast to current ideas which have focused on changes in Florida Bay water quality over the past 20-yr history of the Bay as causative in its decline, we have determined that changes in water quality in this basin were already set in motion between 1905 and 1912 by the construction of the Florida East Coast Railway from Miami to Key West. The construction of the railway resulted in the restriction of the exchange of water between the Florida reef tract and the Gulf of Mexico causing Florida Bay to become more eutrophic. Evidence of this process is observed in the sudden shift to relatively lower δ13C values coincident with railway construction. Natural events also appear to have influenced the water in the Bay. Between 1912 and 1948 frequent hurricanes had the effect of increasing exchange of water between the Bay and reef tract and removing large quantities of organic rich sediments. However, since 1948 the number of hurricanes affecting the area has decreased and the products of the oxidation of organic material have been increasingly retained within the basin promoting the initiation of eutrophic conditions.

Environmental quality in sediments of Cadiz and Algeciras Bays based on a weight of evidence approach (southern Spanish coast).

PubMed

Usero, José Antonio; Rosado, Daniel; Usero, José; Morillo, José

2016-09-15

This research applies an integrated sediment quality assessment method using a weight of evidence approach to Cadiz and Algeciras Bays (southern Spain). The method is composed of several analyses (particle size profile, aqua regia extractable metals, acid labile metals, total organic carbon, toxicity bioassay with Photobacterium phosphoreum and macrobenthic community alteration). The proposed method provides a single result, the environmental degradation index (EDI). EDI defined samples as low degraded (outer areas of both bays) and moderately degraded (Inner Bay of Cadiz Bay, the surroundings of Algeciras port and the northern part of Algeciras Bay). These samples showed the highest concentration of aqua regia extractable metals, which exceeded effects range-low (ERL) for Zn (51-176mg/l), Cu (11-54mg/l), As (4.3-9.5mg/l), Hg (0.17-0.28mg/l), Ni (23-82mg/l), and. Cr (37-134mg/l). They also exceeded some quality criteria for total organic carbon (4.0-6.5%) and toxicity (120-240TU/g) and showed poor results for macrobenthic community. Copyright © 2016 Elsevier Ltd. All rights reserved.

Insights into Seasonal Variations in Phosphorus Concentrations and Cycling in Monterey Bay

NASA Astrophysics Data System (ADS)

Kong, M.; Defforey, D.; Paytan, A.; Roberts, K.

2014-12-01

Phosphorus (P) is an essential nutrient for life as it is a structural constituent in many cell components and a key player in cellular energy metabolism. Therefore, P availability can impact primary productivity. Here we quantify dissolved and particulate P compounds and trace P sources and cycling in Monterey Bay over the course of a year. This time series gives insights into monthly and seasonal variations in the surface water chemistry of this region. Preliminary characterization of seawater samples involves measuring total P and soluble reactive P (SRP) concentrations. 31P nuclear magnetic resonance spectroscopy (31P NMR) is used to determine the chemical structure of organic phosphorus compounds present in surface seawater. The isotopic signature of phosphatic oxygen (δ18Op) is used as a proxy for studying P cycling and sources. Oxygen isotope ratios in phosphate are determined by continuous-flow isotope mass ratio spectrometry (CF-IRMS) following purification of dissolved P from seawater samples and precipitation as silver phosphate. We expect to observe seasonal changes in P concentrations, as well as differences in organic P composition and P sources. The chemical structure of organic P compounds will affect their bioavailability and thus the extent to which they can fuel primary productivity in Monterey Bay. δ18Op will reflect source signatures and provide information on turnover rates of P in surface waters. Results from this work will provide valuable insights into seasonal changes in P cycling in surface waters and have important implications for understanding primary productivity in the Monterey Bay ecosystem.

Mono-isotope Prediction for Mass Spectra Using Bayes Network.

PubMed

Li, Hui; Liu, Chunmei; Rwebangira, Mugizi Robert; Burge, Legand

2014-12-01

Mass spectrometry is one of the widely utilized important methods to study protein functions and components. The challenge of mono-isotope pattern recognition from large scale protein mass spectral data needs computational algorithms and tools to speed up the analysis and improve the analytic results. We utilized naïve Bayes network as the classifier with the assumption that the selected features are independent to predict mono-isotope pattern from mass spectrometry. Mono-isotopes detected from validated theoretical spectra were used as prior information in the Bayes method. Three main features extracted from the dataset were employed as independent variables in our model. The application of the proposed algorithm to publicMo dataset demonstrates that our naïve Bayes classifier is advantageous over existing methods in both accuracy and sensitivity.

Bayes and the Law.

PubMed

Fenton, Norman; Neil, Martin; Berger, Daniel

2016-06-01

Although the last forty years has seen considerable growth in the use of statistics in legal proceedings, it is primarily classical statistical methods rather than Bayesian methods that have been used. Yet the Bayesian approach avoids many of the problems of classical statistics and is also well suited to a broader range of problems. This paper reviews the potential and actual use of Bayes in the law and explains the main reasons for its lack of impact on legal practice. These include misconceptions by the legal community about Bayes' theorem, over-reliance on the use of the likelihood ratio and the lack of adoption of modern computational methods. We argue that Bayesian Networks (BNs), which automatically produce the necessary Bayesian calculations, provide an opportunity to address most concerns about using Bayes in the law.

Bayes factors based on robust TDT-type tests for family trio design.

PubMed

Yuan, Min; Pan, Xiaoqing; Yang, Yaning

2015-06-01

Adaptive transmission disequilibrium test (aTDT) and MAX3 test are two robust-efficient association tests for case-parent family trio data. Both tests incorporate information of common genetic models including recessive, additive and dominant models and are efficient in power and robust to genetic model specifications. The aTDT uses information of departure from Hardy-Weinberg disequilibrium to identify the potential genetic model underlying the data and then applies the corresponding TDT-type test, and the MAX3 test is defined as the maximum of the absolute value of three TDT-type tests under the three common genetic models. In this article, we propose three robust Bayes procedures, the aTDT based Bayes factor, MAX3 based Bayes factor and Bayes model averaging (BMA), for association analysis with case-parent trio design. The asymptotic distributions of aTDT under the null and alternative hypothesis are derived in order to calculate its Bayes factor. Extensive simulations show that the Bayes factors and the p-values of the corresponding tests are generally consistent and these Bayes factors are robust to genetic model specifications, especially so when the priors on the genetic models are equal. When equal priors are used for the underlying genetic models, the Bayes factor method based on aTDT is more powerful than those based on MAX3 and Bayes model averaging. When the prior placed a small (large) probability on the true model, the Bayes factor based on aTDT (BMA) is more powerful. Analysis of a simulation data about RA from GAW15 is presented to illustrate applications of the proposed methods.

Variations in sediment texture on the northern Monterey Bay National Marine Sanctuary continental shelf

USGS Publications Warehouse

Edwards, B.D.

2002-01-01

The storm-protected continental shelf of Monterey Bay, part of the Monterey Bay National Marine Sanctuary, north-central California, is subject to abundant, episodic sediment input from fluvial sources. North of Monterey Bay, conditions of reduced sediment supply combined with the exposed nature of the shelf provide an effective laboratory for studying the contrasting effects of storm- versus fluvial-dominated conditions on modern sedimentation. Textural analyses performed on surface sediment samples collected from more than 380 box cores and MultiCores??? document the existence of a clearly defined mud belt occupying the mid-shelf throughout the region. Inshore sands combined with these mid-shelf muds represent deposits from modern sedimentation processes. In Monterey Bay, where episodic fluvial input from winter storms dominates sedimentation, the mid-shelf mud belt extends across the shelf to the shelf break. North of Monterey Bay, where sediment loads are reduced and both oceanographic and storm processes dominate, the mid-shelf mud belt is bordered by relict sediments occupying the outer shelf. In the study area, mass accumulation rates established by radiochemical studies support the contention that storm-induced along-shelf processes result in northward transport of sediment within the mud belt. The continuity of transport, however, is interrupted by topographic highs which are barriers or inhibitors to sediment transport created by wrench-style tectonics associated with the San Andreas fault system.

Gaseous exchange of polycyclic aromatic hydrocarbons across the air-water interface of lower Chesapeake Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gustafson, K.E.; Dickhut, R.M.

1995-12-31

The gaseous exchange fluxes of polycyclic aromatic hydrocarbons (PAHs) across the air-water interface of lower Chesapeake Bay were determined using a modified two-film exchange model. Sampling covered the period January 1994 to June 1995 for five sites on lower Chesapeake Bay ranging from rural to urban and highly industrialized. Simultaneous air and water samples were collected and the atmospheric gas phase and water column dissolved phase analyzed via GC/MS for 17 PAHs. The direction and magnitude of flux for each PAH was calculated using Henry`s law constants, hydrological and meteorological parameters, Temperature was observed to be an important environmental factormore » in determining both the direction and magnitude of PAH gas exchange. Nonetheless, wind speed significantly impacts mass transfer coefficients, and therefore was found to control the magnitude of flux. Spatial and temporal variation of PAH gaseous exchange fluxes were examined. Fluxes were determined to be both into and out of Chesapeake Bay. The range of gas exchange fluxes ({minus}560 to 600{micro}g/M{sup 2}*Mo) is of the same order to 10X greater than atmospheric wet and dry depositional fluxes to lower Chesapeake Bay. The results of this study support the hypothesis that gas exchange is a major transport process affecting the net loadings of PAHs in lower Chesapeake Bay.« less

Nutrient and chlorophyll a anomaly in red-tide periods of 2003-2008 in Sishili Bay, China

NASA Astrophysics Data System (ADS)

Hao, Yanju; Tang, Danling; Yu, Long; Xing, Qianguo

2011-05-01

Sishili Bay is the most important aquiculture and tourism area for the city of Yantai, China; however, red tides occurred frequently and have caused huge economic losses in this bay in recent years. To gain a better understanding of the local ecological environments in the bay, we conducted this research between 2003 and 2008 to analyze variations in nutrients and chlorophyll (chl- a) during high frequency red tide period (May to September). The results show that the chl- a concentration increased from 2.70 in 2003 to 7.26 mg/m3 in 2008, while the concentration of total inorganic nitrogen (TIN) and silicate (SiO3-Si) increased lineally from 5.18 and 1.45 μmol/L in 2003 to 18.57 and 9.52 μmol/L in 2008, respectively, and the annual phosphate (PO4-P) varied between 0.15 and 0.46 μmol/L. Special attention was given to a red tide in August 2007 occurred when water temperature was high and nutrient concentrations increased sharply because of a heavy rainfall. Overall, the results show the P limitation in Sishili Bay, and reveal that red tides were caused by eutrophication from terrestrial inputs and local warm weather, particularly during rainy periods. Therefore, to control red tide, greater efforts should be made to reduce sewage discharges into Sishili Bay, particularly during rainfall seasons.

Acoustic Doppler velocimeter backscatter for quantification of suspended sediment concentration in South San Francisco Bay, USA

USGS Publications Warehouse

Öztürk, Mehmet; Work, Paul A.

2016-01-01

A data set was acquired on a shallow mudflat in south San Francisco Bay that featured simultaneous, co-located optical and acoustic sensors for subsequent estimation of suspended sediment concentrations (SSC). The optical turbidity sensor output was converted to SSC via an empirical relation derived at a nearby site using bottle sample estimates of SSC. The acoustic data was obtained using an acoustic Doppler velocimeter. Backscatter and noise were combined to develop another empirical relation between the optical estimates of SSC and the relative backscatter from the acoustic velocimeter. The optical and acoustic approaches both reproduced similar general trends in the data and have merit. Some seasonal variation in the dataset was evident, with the two methods differing by greater or lesser amounts depending on which portion of the record was examined. It is hypothesized that this is the result of flocculation, affecting the two signals by different degrees, and that the significance or mechanism of the flocculation has some seasonal variability. In the earlier portion of the record (March), there is a clear difference that appears in the acoustic approach between ebb and flood periods, and this is not evident later in the record (May). The acoustic method has promise but it appears that characteristics of flocs that form and break apart may need to be accounted for to improve the power of the method. This may also be true of the optical method: both methods involve assuming that the sediment characteristics (size, size distribution, and shape) are constant.

Acoustic doppler velocimeter backscatter for quantification of suspended sediment concentration in South San Francisco Bay

USGS Publications Warehouse

Ozturk, Mehmet; Work, Paul A.

2016-01-01

A data set was acquired on a shallow mudflat in south San Francisco Bay that featured simultaneous, co-located optical and acoustic sensors for subsequent estimation of suspended sediment concentrations (SSC). The optical turbidity sensor output was converted to SSC via an empirical relation derived at a nearby site using bottle sample estimates of SSC. The acoustic data was obtained using an acoustic Doppler velocimeter. Backscatter and noise were combined to develop another empirical relation between the optical estimates of SSC and the relative backscatter from the acoustic velocimeter. The optical and acoustic approaches both reproduced similar general trends in the data and have merit. Some seasonal variation in the dataset was evident, with the two methods differing by greater or lesser amounts depending on which portion of the record was examined. It is hypothesized that this is the result of flocculation, affecting the two signals by different degrees, and that the significance or mechanism of the flocculation has some seasonal variability. In the earlier portion of the record (March), there is a clear difference that appears in the acoustic approach between ebb and flood periods, and this is not evident later in the record (May). The acoustic method has promise but it appears that characteristics of flocs that form and break apart may need to be accounted for to improve the power of the method. This may also be true of the optical method: both methods involve assuming that the sediment characteristics (size, size distribution, and shape) are constant

Effects of Submarine Groundwater Discharge (SGD) on the Growth of the Lobe Coral Porites lobata in Maunalua Bay, Hawaii.

NASA Astrophysics Data System (ADS)

Lubarsky, K.

2016-02-01

Submarine groundwater discharge (SGD) constitutes a large percentage of the freshwater inputs onto coastal coral reefs on high islands such as the Hawaiian Islands, although the impact of SGD on coral reef health is currently understudied. In Maunalua Bay, on Oahu, Hawaii, SGD is discharged onto shallow reef flats from discrete seeps, creating natural gradients of water chemistry across the reef flat. We used this system to investigate rates of growth of the lobe coral Porites lobata across a gradient of SGD influence at two study sites within the bay, and to characterize the variation in water chemistry gradient over space and time due to SGD. SGD input at these sites is tidally modulated, and the groundwater itself is brackish and extremely nutrient-rich (mean=190 μM NO3- at the Black Point study site, mean=40 μM NO3- at Wailupe Beach Park), with distinct carbonate signatures at both study sites. Coral nubbins were placed across the gradient for 6 months, and growth was measured using three metrics: surface area (photo analysis), buoyant weight, and linear extension. Various chemical parameters, including pH, salinity, total alkalinity, nutrients, and chlorphyll were sampled at the same locations across the gradient over 24 hour periods in the spring and fall in order to capture spatial and temporal variation in water chemistry due to the SGD plume. Spatial patterns and temporal variation in water chemistry were correlated with the observed spatial patterns in coral growth across the SGD gradient.

Facility Layout Problems Using Bays: A Survey

NASA Astrophysics Data System (ADS)

Davoudpour, Hamid; Jaafari, Amir Ardestani; Farahani, Leila Najafabadi

2010-06-01

Layout design is one of the most important activities done by industrial Engineers. Most of these problems have NP hard Complexity. In a basic layout design, each cell is represented by a rectilinear, but not necessarily convex polygon. The set of fully packed adjacent polygons is known as a block layout (Asef-Vaziri and Laporte 2007). Block layout is divided by slicing tree and bay layout. In bay layout, departments are located in vertical columns or horizontal rows, bays. Bay layout is used in real worlds especially in concepts such as semiconductor and aisles. There are several reviews in facility layout; however none of them focus on bay layout. The literature analysis given here is not limited to specific considerations about bay layout design. We present a state of art review for bay layout considering some issues such as the used objectives, the techniques of solving and the integration methods in bay.

Synoptic volumetric variations and flushing of the Tampa Bay estuary

NASA Astrophysics Data System (ADS)

Wilson, M.; Meyers, S. D.; Luther, M. E.

2014-03-01

Two types of analyses are used to investigate the synoptic wind-driven flushing of Tampa Bay in response to the El Niño-Southern Oscillation (ENSO) cycle from 1950 to 2007. Hourly sea level elevations from the St. Petersburg tide gauge, and wind speed and direction from three different sites around Tampa Bay are used for the study. The zonal (u) and meridional (v) wind components are rotated clockwise by 40° to obtain axial and co-axial components according to the layout of the bay. First, we use the subtidal observed water level as a proxy for mean tidal height to estimate the rate of volumetric bay outflow. Second, we use wavelet analysis to bandpass sea level and wind data in the time-frequency domain to isolate the synoptic sea level and surface wind variance. For both analyses the long-term monthly climatology is removed and we focus on the volumetric and wavelet variance anomalies. The overall correlation between the Oceanic Niño Index and volumetric analysis is small due to the seasonal dependence of the ENSO response. The mean monthly climatology between the synoptic wavelet variance of elevation and axial winds are in close agreement. During the winter, El Niño (La Niña) increases (decreases) the synoptic variability, but decreases (increases) it during the summer. The difference in winter El Niño/La Niña wavelet variances is about 20 % of the climatological value, meaning that ENSO can swing the synoptic flushing of the bay by 0.22 bay volumes per month. These changes in circulation associated with synoptic variability have the potential to impact mixing and transport within the bay.

Reproductive traits of the small Patagonian octopus Octopus tehuelchus

NASA Astrophysics Data System (ADS)

Storero, Lorena P.; Narvarte, Maite A.; González, Raúl A.

2012-12-01

This study evaluated the reproductive features of Octopus tehuelchus in three coastal environments of San Matías Gulf (Patagonia). Monthly samples of O. tehuelchus were used to estimate size at maturity, compare seasonal changes in oocyte size frequency distributions between sites as well as oocyte number and size between female maturity stage and sites. Females in Islote Lobos had a smaller size at maturity than females in San Antonio Bay and El Fuerte, probably as a consequence of a generally smaller body size. Males in San Antonio Bay were smaller at maturity than females. O. tehuelchus is a simultaneous terminal spawner. Fecundity (expressed as number of vitellogenic oocytes in ovary) was lower in Islote Lobos, and an increase in oocyte number in relation to female total weight was found. Females in San Antonio Bay had the largest oocytes, which may indicate higher energy reserves for the embryo and therefore higher juvenile survival. There was a close relationship between reproduction, growth and condition, represented as size at maturity, number and size of vitellogenic oocytes and period of maturity and spawning. Given the local variation in some reproductive features of O. tehuelchus, studies should focus on the environmental factors, which bring about this variation, and on how it affects the dynamics of local populations.

Seasonal variation of absorption by particles and colored dissolved organic matter (CDOM) in Funka Bay, southwestern Hokkaido, Japan

NASA Astrophysics Data System (ADS)

Sasaki, Hiroaki; Miyamura, Tsuyoshi; Saitoh, Sei-ichi; Ishizaka, Joji

2005-08-01

Between November 2000 and October 2001, the seasonal variation in absorption by particles (phytoplankton and detritus) and colored dissolved organic matter (CDOM) was measured in Funka Bay (a subarctic coastal region of Japan). In autumn-winter, chlorophyll a concentration (Chl a) near the euphotic zone remained very low (<1.0 mg m -3) but markedly increased in spring (16.8 mg m -3). Chlorophyll-specific absorption coefficient for phytoplankton ( a∗ph( λ)) was high during summer and low during the spring bloom. This is because the package effect was greater during the spring bloom due to the presence of large diatoms, while small phytoplankton dominated during summer. Absorption at 440 nm by CDOM was higher than that of phytoplankton and detritus, except during the spring bloom, and the relative contribution of CDOM absorption to the total absorption coefficient was >50%. CDOM and detritus absorption did not increase with increasing Chl a, but it showed a time lag between the spring bloom. It is suggested that phytoplankton degradation started after the spring bloom; detritus absorption increased and, then, CDOM absorption increased. River runoff was not a significant influence in Funka Bay, therefore, CDOM production may be mainly related to microbial activity.

Energy density of anchovy Engraulis encrasicolus in the Bay of Biscay.

PubMed

Dubreuil, J; Petitgas, P

2009-02-01

The energy density (E(D)) of anchovy Engraulis encrasicolus in the Bay of Biscay was determined by direct calorimetry and its evolution with size, age and season was investigated. The water content and energy density varied seasonally following opposite trends. The E(D) g(-1) of wet mass (M(W)) was highest at the end of the feeding season (autumn: c. 8 kJ g(-1)M(W)) and lowest in late winter (c. 6 kJ g(-1)M(W)). In winter, the fish lost mass, which was partially replaced by water, and the energy density decreased. These variations in water content and organic matter content may have implications on the buoyancy of the fish. The water content was the major driver of the energy density variations for a M(W) basis. A significant linear relationship was established between E(D) g(-1) (y) and the per cent dry mass (M(D); x): y =-4.937 + 0.411x. In the light of the current literature, this relationship seemed to be not only species specific but also ecosystem specific. Calibration and validation of fish bioenergetics models require energy content measurements on fish samples collected at sea. The present study provides a first reference for the energetics of E. encrasicolus in the Bay of Biscay.

Holocene climates and connections between the San Francisco Bay Estuary and its watershed: A review

USGS Publications Warehouse

Malamud-Roam, F.; Dettinger, M.; Ingram, B. Lynn; Hughes, Malcolm K.; Florsheim, Joan

2007-01-01

This review of paleoclimate records reveals a gradual warming and drying in California from about 10,000 years to about 4,000 years before present. During this period, the current Bay and Delta were inundated by rising sea level so that by 4,000 years ago the Bay and Delta had taken on much of their present shape and extent. Between about 4,000 and 2,000 years ago, cooler and wetter conditions prevailed in the watershed, lowering salinity in the Estuary and altering local ecosystems. Those wetter conditions gave way to increasing aridity during the past 2,000 years, a general trend punctuated by occasional prolonged and severe droughts and occasional unusually wet, cool periods. California’s climate since A.D. 1850 has been unusually stable and benign, compared to climate variations during the previous 2,000 or more years. Thus, climate variations in California’s future may be even more (perhaps much more) challenging than those of the past 100 years. To improve our understanding of these past examples of climate variability in California, and of the linkages between watershed climate and estuarine responses, greater emphases on paleoclimate records in and around the Estuary, improved temporal resolutions in several record types, and linked watershed-estuary paleo-modeling capabilities are needed. 

Living on the edge: latitudinal variations in the reproductive biology of two coastal species of sharks.

PubMed

Taylor, S M; Harry, A V; Bennett, M B

2016-11-01

Differences in the reproductive biology of both the Australian weasel shark Hemigaleus australiensis and the Australian sharpnose shark Rhizoprionodon taylori were apparent between individuals from the southern-most extent of their range in eastern Australia (Moreton Bay) and those from northern Australia. For H. australiensis from Moreton Bay the total length (L T ) at which 50% of individuals were mature (L T50 ) was 759 mm for females and 756 mm for males, values that were respectively 17-26% larger than reported for the species in northern Australia. The relatively low percentage (63%) of pregnant mature females and presence of small, similar-sized, embryos in utero in both May and November suggested a semi-synchronous, annual reproductive cycle in Moreton Bay, whereas a synchronous, biannual reproductive cycle occurred in northern Australia. It is likely that H. australiensis has a resting phase between gestation cycles at the southern-most extent of its range. For R. taylori from Moreton Bay the L T50 s were 588 and 579 mm for females and males, respectively, values 2-3% larger than for individuals from the mid-Queensland coast and 31-35% larger than for individuals from northern Australia. The length at which 50% of the females were maternal (611 mm L T ) in Moreton Bay was greater than the L T50 , indicating that not all sharks mate immediately after maturing. Rhizoprionodon taylori in the south had an annual reproductive cycle incorporating a 7-8 month embryonic diapause, with pups probably born in February. A mean fecundity of 7·5 was almost double that reported from northern Australia. Regional variations in the reproductive characteristics of H. australiensis and R. taylori may influence their resilience to fishing and other anthropogenic pressures. The substantial differences reported here highlight the importance of region-specific life-history parameters to successful management and conservation. © 2016 The Fisheries Society of the British Isles.

INTEGRATED ASSESSMENTS OF ANTHROPOGENIC AND NATURAL CHANGES IN CHESAPEAKE BAY WATERSHEDS

EPA Science Inventory

Both natural and anthropogenic factors affect spatial and temporal patterns in ecosystem conditions. To manage environmental change and risks, distinguishing between natural variations in ecosystem conditions and anthropogenic changes becomes important. This concept is illustrate...

Baleen whales and their prey in a coastal environment

USGS Publications Warehouse

Piatt, John F.; Methven, David A.; Burger, Alan E.; McLagan, Ruth L.; Mercer, Vicki; Creelman, Elizabeth

1989-01-01

Patterns of abundance of humpback (Megaptera novaeangliae), fin (Balaenoptera physalus), and minke (Balaenoptera acutorostrata) whales are described in relation to the abundance of their primary prey, capelin (Mallotus villosus), during 1982–1985 at Witless Bay, Newfoundland. The abundance ratio of the three whale species was 10:1:3.5, respectively. Abundance of all whale species was strongly correlated with abundance of capelin through each season and between years. Capelin abundance accounted for 63% of the variation in whale numbers in 1983 and 1984, while environmental parameters (e.g., water temperatures) accounted for little variance. The amount of capelin consumed by whales was small (< 2%) compared with the amount available. All three species overlapped temporally at Witless Bay, but spatial overlap was reduced as fins occurred primarily offshore, minkes primarily inshore, and humpbacks in bay habitats of intermediate depth.

Understanding of the naive Bayes classifier in spam filtering

NASA Astrophysics Data System (ADS)

Wei, Qijia

2018-05-01

Along with the development of the Internet, the information stream is experiencing an unprecedented burst. The methods of information transmission become more and more important and people receiving effective information is a hot topic in the both research and industry field. As one of the most common methods of information communication, email has its own advantages. However, spams always flood the inbox and automatic filtering is needed. This paper is going to discuss this issue from the perspective of Naive Bayes Classifier, which is one of the applications of Bayes Theorem. Concepts and process of Naive Bayes Classifier will be introduced, followed by two examples. Discussion with Machine Learning is made in the last section. Naive Bayes Classifier has been proved to be surprisingly effective, with the limitation of the interdependence among attributes which are usually email words or phrases.

Long-term, High Frequency, High Precision pH Measurements on the MBARI deep-water FOCE Experiment at the MARS Cabled Observatory in Monterey Bay, CA

NASA Astrophysics Data System (ADS)

Peltzer, E. T.; Maughan, T.; Barry, J. P.; Brewer, P. G.; Headley, K. L.; Herlien, R.; Kirkwood, W. J.; Matsumoto, G. I.; O'Reilly, T. C.; Salamy, K. A.; Scholfield, J.; Shane, F. F.; Walz, P. M.

2012-12-01

The MBARI deep-water FOCE experiment was deployed on the MARS cabled observatory in Monterey Bay on May 4th, 2011. It has been in continuous operation (excluding a few minor shore based power outages) ever since. During the fifteen months of deployment, we have been able to observe both the daily variation in pH in response to water mass movements associated with the semi-diurnal tides, internal waves and longer-term trends as a function of the seasonal variations in the water masses within the Monterey Bay Canyon. Our experimental site is located at 890 meters, just below the oxygen minimum for Monterey Bay, and we clearly see the anticipated inverse correlation between seawater temperature and pH. Daily variation in pH is on the order of 0.020-0.030 pH units with longer term trends adding an additional variation of similar magnitude. Instrumentation on this experiment included two CTDs with oxygen sensors (Sea-Bird 52). One CTD is mounted on the external FOCE framework to measure the background conditions, and one CTD is installed within the FOCE pH control area to monitor the experimentally manipulated conditions. In addition, 6 MBARI modified Sea-Bird 18 pH sensors were mounted on the FOCE apparatus. Four of these pH sensors monitored pH inside the experimental chamber and two monitored the external background seawater conditions. Although we originally intended to conduct several in situ CO2 enrichment experiments to study the impact of ocean acidification on the benthic biology and then recover the apparatus after one year, unanticipated changes in the ship schedule have left the FOCE experiment in place for nearly fifteen months at the time of this writing. Throughout this time period, all sensor data has been logged by the MBARI Shore-Side Data System (SSDS) resulting in the longest continuous record of high precision pH measurements in the intermediate water column. We present an analysis of the data obtained from this unique data set, and discuss our in-situ calibration techniques used to compensate for long term sensor drift associated with the reference electrode.

Performance comparison of first-order conditional estimation with interaction and Bayesian estimation methods for estimating the population parameters and its distribution from data sets with a low number of subjects.

PubMed

Pradhan, Sudeep; Song, Byungjeong; Lee, Jaeyeon; Chae, Jung-Woo; Kim, Kyung Im; Back, Hyun-Moon; Han, Nayoung; Kwon, Kwang-Il; Yun, Hwi-Yeol

2017-12-01

Exploratory preclinical, as well as clinical trials, may involve a small number of patients, making it difficult to calculate and analyze the pharmacokinetic (PK) parameters, especially if the PK parameters show very high inter-individual variability (IIV). In this study, the performance of a classical first-order conditional estimation with interaction (FOCE-I) and expectation maximization (EM)-based Markov chain Monte Carlo Bayesian (BAYES) estimation methods were compared for estimating the population parameters and its distribution from data sets having a low number of subjects. In this study, 100 data sets were simulated with eight sampling points for each subject and with six different levels of IIV (5%, 10%, 20%, 30%, 50%, and 80%) in their PK parameter distribution. A stochastic simulation and estimation (SSE) study was performed to simultaneously simulate data sets and estimate the parameters using four different methods: FOCE-I only, BAYES(C) (FOCE-I and BAYES composite method), BAYES(F) (BAYES with all true initial parameters and fixed ω 2 ), and BAYES only. Relative root mean squared error (rRMSE) and relative estimation error (REE) were used to analyze the differences between true and estimated values. A case study was performed with a clinical data of theophylline available in NONMEM distribution media. NONMEM software assisted by Pirana, PsN, and Xpose was used to estimate population PK parameters, and R program was used to analyze and plot the results. The rRMSE and REE values of all parameter (fixed effect and random effect) estimates showed that all four methods performed equally at the lower IIV levels, while the FOCE-I method performed better than other EM-based methods at higher IIV levels (greater than 30%). In general, estimates of random-effect parameters showed significant bias and imprecision, irrespective of the estimation method used and the level of IIV. Similar performance of the estimation methods was observed with theophylline dataset. The classical FOCE-I method appeared to estimate the PK parameters more reliably than the BAYES method when using a simple model and data containing only a few subjects. EM-based estimation methods can be considered for adapting to the specific needs of a modeling project at later steps of modeling.

Sources of mercury to San Francisco Bay surface sediment as revealed by mercury stable isotopes

USGS Publications Warehouse

Gehrke, Gretchen E.; Blum, Joel D.; Marvin-DePasquale, Mark

2011-01-01

Mercury (Hg) concentrations and isotopic compositions were examined in shallow-water surface sediment (0–2 cm) from San Francisco (SF) Bay to determine the extent to which historic Hg mining contributes to current Hg contamination in SF Bay, and to assess the use of Hg isotopes to trace sources of contamination in estuaries. Inter-tidal and wetland sediment had total Hg (HgT) concentrations ranging from 161 to 1529 ng/g with no simple gradients of spatial variation. In contrast, inter-tidal and wetland sediment displayed a geographic gradient of δ202Hg values, ranging from -0.30% in the southern-most part of SF Bay (draining the New Almaden Hg District) to -0.99% in the northern-most part of SF Bay near the Sacramento–San Joaquin River Delta. Similar to SF Bay inter-tidal sediment, surface sediment from the Alviso Slough channel draining into South SF Bay had a δ202Hg value of -0.29%, while surface sediment from the Cosumnes River and Sacramento–San Joaquin River Delta draining into north SF Bay had lower average δ202Hg values of -0.90% and -0.75%, respectively. This isotopic trend suggests that Hg-contaminated sediment from the New Almaden Hg District mixes with Hg-contaminated sediment from a low δ202Hg source north of SF Bay. Tailings and thermally decomposed ore (calcine) from the New Idria Hg mine in the California Coast Range had average δ202Hg values of -0.37 and +0.03%, respectively, showing that Hg calcination fractionates Hg isotopes resulting in Hg contamination from Hg(II) mine waste products with higher δ202Hg values than metallic Hg(0) produced from Hg mines. Thus, there is evidence for at least two distinct isotopic signals for Hg contamination in SF Bay: Hg associated with calcine waste materials at Hg mines in the Coast Range, such as New Almaden and New Idria; and Hg(0) produced from these mines and used in placer gold mines and/or in other industrial processes in the Sierra Nevada region and SF Bay area.

A Coastal Bay Summer Breeze Study, Part 2: High-resolution Numerical Simulation of Sea-breeze Local Influences

NASA Astrophysics Data System (ADS)

Calmet, Isabelle; Mestayer, Patrice G.; van Eijk, Alexander M. J.; Herlédant, Olivier

2018-04-01

We complete the analysis of the data obtained during the experimental campaign around the semi circular bay of Quiberon, France, during two weeks in June 2006 (see Part 1). A reanalysis of numerical simulations performed with the Advanced Regional Prediction System model is presented. Three nested computational domains with increasing horizontal resolution down to 100 m, and a vertical resolution of 10 m at the lowest level, are used to reproduce the local-scale variations of the breeze close to the water surface of the bay. The Weather Research and Forecasting mesoscale model is used to assimilate the meteorological data. Comparisons of the simulations with the experimental data obtained at three sites reveal a good agreement of the flow over the bay and around the Quiberon peninsula during the daytime periods of sea-breeze development and weakening. In conditions of offshore synoptic flow, the simulations demonstrate that the semi-circular shape of the bay induces a corresponding circular shape in the offshore zones of stagnant flow preceding the sea-breeze onset, which move further offshore thereafter. The higher-resolution simulations are successful in reproducing the small-scale impacts of the peninsula and local coasts (breeze deviations, wakes, flow divergences), and in demonstrating the complexity of the breeze fields close to the surface over the bay. Our reanalysis also provides guidance for numerical simulation strategies for analyzing the structure and evolution of the near-surface breeze over a semi-circular bay, and for forecasting important flow details for use in upcoming sailing competitions.

Wind-Driven Waves in Tampa Bay, Florida

NASA Astrophysics Data System (ADS)

Gilbert, S. A.; Meyers, S. D.; Luther, M. E.

2002-12-01

Turbidity and nutrient flux due to sediment resuspension by waves and currents are important factors controlling water quality in Tampa Bay. During December 2001 and January 2002, four Sea Bird Electronics SeaGauge wave and tide recorders were deployed in Tampa Bay in each major bay segment. Since May 2002, a SeaGauge has been continuously deployed at a site in middle Tampa Bay as a component of the Bay Regional Atmospheric Chemistry Experiment (BRACE). Initial results for the summer 2002 data indicate that significant wave height is linearly dependent on wind speed and direction over a range of 1 to 12 m/s. The data were divided into four groups according to wind direction. Wave height dependence on wind speed was examined for each group. Both northeasterly and southwesterly winds force significant wave heights that are about 30% larger than those for northwesterly and southeasterly winds. This difference is explained by variations in fetch due to basin shape. Comparisons are made between these observations and the results of a SWAN-based model of Tampa Bay. The SWAN wave model is coupled to a three-dimensional circulation model and computes wave spectra at each model grid cell under observed wind conditions and modeled water velocity. When SWAN is run without dissipation, the model results are generally similar in wave period but about 25%-50% higher in significant wave height than the observations. The impact of various dissipation mechanisms such as bottom drag and whitecapping on the wave state is being investigated. Preliminary analyses on winter data give similar results.

Transmission of hemic neoplasia in the bay mussel, Mytilus edulis, using whole cells and cell homogenate.

PubMed

Elston, R A; Kent, M L; Drum, A S

1988-01-01

Experimental studies with hemic neoplasia in the bay mussel indicated that the condition can be transmitted allogeneically with intact whole cells and cell-free homogenate. A differential pathogenesis of the disease in mussels receiving the two different inocula supports the argument that actual cell transplantation occurred. In addition to the first demonstration of the infectious nature of the disease with cell-free homogenates, it was also shown that the disease is transmitted by cohabitation. Remission of the disease occurred in some mussels indicating individual variation in recognition mechanisms.

Bayesian probability estimates are not necessary to make choices satisfying Bayes' rule in elementary situations.

PubMed

Domurat, Artur; Kowalczuk, Olga; Idzikowska, Katarzyna; Borzymowska, Zuzanna; Nowak-Przygodzka, Marta

2015-01-01

This paper has two aims. First, we investigate how often people make choices conforming to Bayes' rule when natural sampling is applied. Second, we show that using Bayes' rule is not necessary to make choices satisfying Bayes' rule. Simpler methods, even fallacious heuristics, might prescribe correct choices reasonably often under specific circumstances. We considered elementary situations with binary sets of hypotheses and data. We adopted an ecological approach and prepared two-stage computer tasks resembling natural sampling. Probabilistic relations were inferred from a set of pictures, followed by a choice which was made to maximize the chance of a preferred outcome. Use of Bayes' rule was deduced indirectly from choices. Study 1 used a stratified sample of N = 60 participants equally distributed with regard to gender and type of education (humanities vs. pure sciences). Choices satisfying Bayes' rule were dominant. To investigate ways of making choices more directly, we replicated Study 1, adding a task with a verbal report. In Study 2 (N = 76) choices conforming to Bayes' rule dominated again. However, the verbal reports revealed use of a new, non-inverse rule, which always renders correct choices, but is easier than Bayes' rule to apply. It does not require inversion of conditions [transforming P(H) and P(D|H) into P(H|D)] when computing chances. Study 3 examined the efficiency of three fallacious heuristics (pre-Bayesian, representativeness, and evidence-only) in producing choices concordant with Bayes' rule. Computer-simulated scenarios revealed that the heuristics produced correct choices reasonably often under specific base rates and likelihood ratios. Summing up we conclude that natural sampling results in most choices conforming to Bayes' rule. However, people tend to replace Bayes' rule with simpler methods, and even use of fallacious heuristics may be satisfactorily efficient.

Detection of dechallenge in spontaneous reporting systems: a comparison of Bayes methods.

PubMed

Banu, A Bazila; Alias Balamurugan, S Appavu; Thirumalaikolundusubramanian, Ponniah

2014-01-01

Dechallenge is a response observed for the reduction or disappearance of adverse drug reactions (ADR) on withdrawal of a drug from a patient. Currently available algorithms to detect dechallenge have limitations. Hence, there is a need to compare available new methods. To detect dechallenge in Spontaneous Reporting Systems, data-mining algorithms like Naive Bayes and Improved Naive Bayes were applied for comparing the performance of the algorithms in terms of accuracy and error. Analyzing the factors of dechallenge like outcome and disease category will help medical practitioners and pharmaceutical industries to determine the reasons for dechallenge in order to take essential steps toward drug safety. Adverse drug reactions of the year 2011 and 2012 were downloaded from the United States Food and Drug Administration's database. The outcome of classification algorithms showed that Improved Naive Bayes algorithm outperformed Naive Bayes with accuracy of 90.11% and error of 9.8% in detecting the dechallenge. Detecting dechallenge for unknown samples are essential for proper prescription. To overcome the issues exposed by Naive Bayes algorithm, Improved Naive Bayes algorithm can be used to detect dechallenge in terms of higher accuracy and minimal error.

Influence of marine current on vertical migration of Pb in marine bay

NASA Astrophysics Data System (ADS)

Yu, Chen; Hong, Ai; Danfeng, Yang; Huijuan, Zhao; Dongfang, Yang

2018-02-01

This paper analyzed that vertical migration of Pb contents waters in Jiaozhou Bay, and revealed the influence of marine current on vertical migration process. Results showed that Pb contents in bottom waters of Jiaozhou Bay in April and July 1988 were 1.49-18.53 μg L-1 and 12.68/-27.64 μg L-1, respectively. The pollution level of Pb in bottom waters was moderate to heavy, and were showing temporal variations and spatial heterogeneity. The vertical migration process of Pb in April 1988 included a drifting process from the southwest to the north by means of the marine current was rapid in this region. The vertical migration process of Pb in July 1988 in the open waters included no drifting process since the flow rate of marine current was relative low in this region. The vertical migration process of Pb was jointly determined by vertical water’s effect, source input and water exchange, and the influence of marine current on the vertical migration of Pb in marine bay was significant.

An historical perspective on eutrophication in the Pensacola ...

EPA Pesticide Factsheets

In this chapter, we provide a brief description of the Pensacola Bay estuary, examining the available historical data for evidence of trends in eutrophication within the estuary. Common to many industrialized estuaries, Pensacola Bay has been subjected to unregulated point sources of nutrients and other contaminants, peaking during the 1950s and 1960s. Also, over the past 60 years, the region has experienced a 5-fold increase in population in the watershed and a doubling of river nitrate concentrations. Today, the estuary exhibits classical symptoms of eutrophication, including extensive summer hypoxia, significant loss of seagrass habitat, and phytoplankton dynamics that respond strongly to seasonal and interannual variation in freshwater flow. Surprisingly, Pensacola Bay appears to have low nutrient concentrations, moderate productivity, and high water transparency; characteristics that appear to have persisted during a period of rapid human population growth. We find the lack of demonstrable changes in the distribution of phytoplankton biomass or distribution and severity of hypoxia during a period of increasing human population pressures enigmatic. This brief manuscript summarizes historical water quality data from Pensacola Bay Florida

Factors Influencing Spatial and Annual Variability in Eelgrass (Zostera marina L.) Meadows in Willapa Bay, Washington, and Coos Bay, Oregon, Estuaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thom, Ronald M.; Borde, Amy B.; Rumrill, Steven

2003-08-01

Environmental factors that influence annual variability and spatial differences in eelgrass meadows (Zostera marina L.) were examined within Willapa Bay, WA, and Coos Bay, OR, over a period of 4 years (1998-2001). A suite of eelgrass metrics were recorded annually at field sites that spanned the estuarine gradient from the marine-dominated to mesohaline regions. Growth of eelgrass plants was also monitored on a monthly basis within Sequim Bay, WA. Both the spatial cover and density of Z. marina were positively correlated with estuarine salinity and inversely correlated with temperature of the tideflat sediment. Experimental evidence verified that optimal eelgrass growthmore » occurred at highest salinities and relatively low temperatures. Eelgrass density, biomass, and the incident of flowering plants all increased substantially in Willapa Bay, and less so in Coos Bay, over the duration of the study. Warmer winters and cooler summers associated with the transition from El Ni?o to La Ni?a ocean conditions during the study period were correlated with the increase in eelgrass abundance and flowering. Anthropogenic factors (e.g., disturbance and erosion by vessel wakes and recreational shellfishing activities) may have contributed to spatial variability. Our findings indicate that large-scale changes in climate and nearshore ocean conditions can exert a strong regional influence on eelgrass abundance, which can vary annually by as much as 700% in Willapa Bay. Lower levels of variability observed in Coos Bay may be due to the stronger and more direct influence of the nearshore Pacific Ocean. We conclude that climate variation may have profound effects on the abundance and distribution of eelgrass meadows throughout the Pacific Northwest, and we anticipate that ocean conditions will emerge as a primary driving force for living estuarine resources and ecological processes that are associated with Z. marina beds within the landscape of these estuarine tidal basins.« less

Acoustic detection of ice crystals in Antarctic waters

NASA Astrophysics Data System (ADS)

Penrose, John D.; Conde, M.; Pauly, T. J.

1994-06-01

During the voyage of the RSV Aurora Australis to the region of Prydz Bay, Antarctica in January-March 1991, ice crystals were encountered at depths from the surface to 125-m in the western area of the bay. On two occasions, crystals were retrieved by netting, and echo sounder records have been used to infer additional regions of occurrence. Acoustic target strength estimates made on the ice crystal assemblies encountered show significant spatial variation, which may relate to crystal size and/or aggregation. Data from a suite of conductivity-temperature-depth casts have been used to map regions of the study area where in situ water temperatures fell below the computed freezing point. Such regions correlate well with those selected on the basis of echogram type and imply that ice crystals occurred at depth over large areas of the bay during the cruise period. The ice crystal distribution described is consistent with that expected from a plume of supercooled water emerging from under the Amery Ice Shelf and forming part of the general circulation of the bay. The magnitude of the supercooled water plume is greater than those reported previously in the Prydz Bay region. If misinterpreted as biota on echo sounder records, ice crystals could significantly bias biomass estimates based on echo integration in this and potentially other areas.

A nowcast model for tides and tidal currents in San Francisco Bay, California

USGS Publications Warehouse

Cheng, Ralph T.; Smith, Richard E.

1998-01-01

National Oceanographic and Atmospheric Administration (NOAA) installed Physical Oceanographic Real-Time System (PORTS) in San Francisco Bay, California to provide observations of tides, tidal currents, and meteorological conditions. PORTS data are used for optimizing vessel operations, increasing margin of safety for navigation, and guiding hazardous material spill prevention and response. Because tides and tidal currents in San Francisco Bay are extremely complex, limited real-time observations are insufficient to provide spatial resolution for variations of tides and tidal currents. To fill the information gaps, a highresolution, robust, semi-implicit, finite-difference nowcast numerical model has been implemented for San Francisco Bay. The model grid and water depths are defined on coordinates based on Mercator projection so the model outputs can be directly superimposed on navigation charts. A data assimilation algorithm has been established to derive the boundary conditions for model simulations. The nowcast model is executed every hour continuously for tides and tidal currents starting from 24 hours before the present time (now) covering a total of 48 hours simulation. Forty-eight hours of nowcast model results are available to the public at all times through the World Wide Web (WWW). Users can view and download the nowcast model results for tides and tidal current distributions in San Francisco Bay for their specific applications and for further analysis.

Drivers of Variability of Diel-Cycling and Episodic Hypoxia In ...

EPA Pesticide Factsheets

Eutrophication of coastal ecosystems is a longstanding environmental concern, exacerbated by population growth and associated nutrient pollution, and ultimately resulting in increased incidence of hypoxia. Shallow and highly productive estuaries and embayments are particularly susceptible to diel-cycling hypoxia, associated with day-night cycles of production and respiration, which can cause extreme excursions in dissolved oxygen (DO) concentrations from anoxia to super-saturation within a single day. Diel oxygen dynamics in these systems are complex, and may be influenced by wind forcing, vertical and horizontal mixing, variation in freshwater inflow, cloud cover, and temperature. To better understand the environmental drivers of periodic hypoxia, this study examined four northern Gulf of Mexico Estuaries (Weeks Bay, AL; Wolf Bay, AL; Fowl River, AL; and St. Louis Bay, MS). Dissolved oxygen varied strongly on a diel basis in all four systems, with periods of sustained low oxygen (>24 h) observed in both Weeks Bay and Wolf Bay. The duration and persistence of hypoxia further varied in response to changing salinity regimes and regional weather. These results underscore the dynamic nature of hypoxia in shallow estuarine systems, and highlight the importance of combining fixed site continuous monitoring data with spatial hydrographic surveys to accurately resolve DO dynamics. This abstract is submitted for presentation at the CERF conference held Nov 8-12 in Oregon

Origins of cryptic variation in the Ediacaran-Fortunian rhyolitic ignimbrites of the Saldanha Bay Volcanic Complex, Western Cape, South Africa

NASA Astrophysics Data System (ADS)

Clemens, J. D.; Stevens, G.; Frei, D.; Joseph, C. S. A.

2017-12-01

The Saldanha eruption centre, on the West Coast of South Africa, consists of 542 Ma, intracaldera, S-type, rhyolite ignimbrites divided into the basal Saldanha Ignimbrite and the partly overlying Jacob's Bay Ignimbrite. Depleted-mantle Nd model ages suggest magma sources younger than the Early Mesoproterozoic, and located within the Neoproterozoic Malmesbury Group and Swartland complex metasedimentary and metavolcanic rocks that form the regional basement. The Sr isotope systematics suggest that the dominant source rocks were metavolcaniclastic rocks and metagreywackes, and that the magmas formed from separate batches extracted from the same heterogeneous source. No apparent magma mixing trends relate the Saldanha to the Jacob's Bay Ignimbrites, or either of these to the magmas that formed the Plankiesbaai or Tsaarsbank Ignimbrites in the neighbouring Postberg eruption centre. The magmas were extracted from their source rocks carrying small but significant proportions of peritectic and restitic accessory minerals. Variations in the content of this entrained crystal cargo were responsible for most of the chemical variations in the magmas. Although we cannot construct a cogent crystal fractionation model to relate these groups of magmas, at least some crystal fractionation occurred, as an overlay on the primary signal due to peritectic assemblage entrainment (PAE). Thus, the causes of the cryptic chemical variation among the ignimbrite magmas of the Saldanha centre are variable, but dominated by the compositions of the parent melts and PAE. The preservation of clear, source-inherited chemical signatures, in individual samples, calls into question the common interpretation of silicic calderas as having been formed in large magma reservoirs, with magma compositions shaped by magma mingling, mixing, and fractional crystallization. The Saldanha rocks suggest a more intimate connection between source and erupted magma, and perhaps indicate that silicic magmas are too viscous to be significantly modified by magma-chamber processes.

Use of empirical and full Bayes before-after approaches to estimate the safety effects of roadside barriers with different crash conditions.

PubMed

Park, Juneyoung; Abdel-Aty, Mohamed; Lee, Jaeyoung

2016-09-01

Although many researchers have estimated the crash modification factors (CMFs) for specific treatments (or countermeasures), there is a lack of prior studies that have explored the variation of CMFs. Thus, the main objectives of this study are: (a) to estimate CMFs for the installation of different types of roadside barriers, and (b) to determine the changes of safety effects for different crash types, severities, and conditions. Two observational before-after analyses (i.e. empirical Bayes (EB) and full Bayes (FB) approaches) were utilized in this study to estimate CMFs. To consider the variation of safety effects based on different vehicle, driver, weather, and time of day information, the crashes were categorized based on vehicle size (passenger and heavy), driver age (young, middle, and old), weather condition (normal and rain), and time difference (day time and night time). The results show that the addition of roadside barriers is safety effective in reducing severe crashes for all types and run-off roadway (ROR) crashes. On the other hand, it was found that roadside barriers tend to increase all types of crashes for all severities. The results indicate that the treatment might increase the total number of crashes but it might be helpful in reducing injury and severe crashes. In this study, the variation of CMFs was determined for ROR crashes based on the different vehicle, driver, weather, and time information. Based on the findings from this study, the variation of CMFs can enhance the reliability of CMFs for different roadway conditions in decision making process. Also, it can be recommended to identify the safety effects of specific treatments for different crash types and severity levels with consideration of the different vehicle, driver, weather, and time of day information. Copyright © 2016 Elsevier Ltd and National Safety Council. All rights reserved.

Relationship between fabrication method and chemical stability of Ni-BaZr0.8Y0.2O3-δ membrane

NASA Astrophysics Data System (ADS)

Fang, Shumin; Wang, Siwei; Brinkman, Kyle S.; Su, Qing; Wang, Haiyan; Chen, Fanglin

2015-03-01

NiO effectively promotes the sintering of highly refractory Y-doped BaZrO3 (BZY) through the formation of BaY2NiO5, providing a simple and cost-effective method for the fabrication of dense BZY electrolyte and Ni-BZY hydrogen separation membrane at ∼1400 °C. Unfortunately, insulating BaCO3 and Y2O3 phases formed on the surface of BZY and Ni-BZY prepared by solid state reaction method with NiO after annealing in wet CO2. Ni-BZY membranes prepared from different methods suffered different degree of performance loss in wet H2 at 900 °C. The chemical instability of Ni-BZY is attributed to the formation of a secondary phase (BaY2O4) generated from the reduction of BaY2NiO5 in H2 during the sintering process. Both BaY2O4 and BaY2NiO5 react with H2O, and CO2 at elevated temperatures, generating insulating Ba(OH)2 and BaCO3 phases, respectively. The less BaY2O4 is formed in the fabrication process, the better chemical stability the Ni-BZY membranes possess. Therefore, a new Ni-BZY membrane is prepared through a judicial combination of BZY powders prepared from combined EDTA-citric and solid state reaction methods, and demonstrates exceptional chemical stability in H2O and CO2, enabling stable and even improved hydrogen flux in wet 50% CO2 at 900 °C.

A BAYESIAN SPATIAL AND TEMPORAL MODELING APPROACH TO MAPPING GEOGRAPHIC VARIATION IN MORTALITY RATES FOR SUBNATIONAL AREAS WITH R-INLA.

PubMed

Khana, Diba; Rossen, Lauren M; Hedegaard, Holly; Warner, Margaret

2018-01-01

Hierarchical Bayes models have been used in disease mapping to examine small scale geographic variation. State level geographic variation for less common causes of mortality outcomes have been reported however county level variation is rarely examined. Due to concerns about statistical reliability and confidentiality, county-level mortality rates based on fewer than 20 deaths are suppressed based on Division of Vital Statistics, National Center for Health Statistics (NCHS) statistical reliability criteria, precluding an examination of spatio-temporal variation in less common causes of mortality outcomes such as suicide rates (SRs) at the county level using direct estimates. Existing Bayesian spatio-temporal modeling strategies can be applied via Integrated Nested Laplace Approximation (INLA) in R to a large number of rare causes of mortality outcomes to enable examination of spatio-temporal variations on smaller geographic scales such as counties. This method allows examination of spatiotemporal variation across the entire U.S., even where the data are sparse. We used mortality data from 2005-2015 to explore spatiotemporal variation in SRs, as one particular application of the Bayesian spatio-temporal modeling strategy in R-INLA to predict year and county-specific SRs. Specifically, hierarchical Bayesian spatio-temporal models were implemented with spatially structured and unstructured random effects, correlated time effects, time varying confounders and space-time interaction terms in the software R-INLA, borrowing strength across both counties and years to produce smoothed county level SRs. Model-based estimates of SRs were mapped to explore geographic variation.

New subspace methods for ATR

NASA Astrophysics Data System (ADS)

Zhang, Peng; Peng, Jing; Sims, S. Richard F.

2005-05-01

In ATR applications, each feature is a convolution of an image with a filter. It is important to use most discriminant features to produce compact representations. We propose two novel subspace methods for dimension reduction to address limitations associated with Fukunaga-Koontz Transform (FKT). The first method, Scatter-FKT, assumes that target is more homogeneous, while clutter can be anything other than target and anywhere. Thus, instead of estimating a clutter covariance matrix, Scatter-FKT computes a clutter scatter matrix that measures the spread of clutter from the target mean. We choose dimensions along which the difference in variation between target and clutter is most pronounced. When the target follows a Gaussian distribution, Scatter-FKT can be viewed as a generalization of FKT. The second method, Optimal Bayesian Subspace, is derived from the optimal Bayesian classifier. It selects dimensions such that the minimum Bayes error rate can be achieved. When both target and clutter follow Gaussian distributions, OBS computes optimal subspace representations. We compare our methods against FKT using character image as well as IR data.

Role of remote sensing in Bay measurements

NASA Technical Reports Server (NTRS)

Mugler, J. P., Jr.; Godfrey, J. P.; Hickman, G. D.; Hovis, W. G.; Pearson, A. O.; Weaver, K. N.

1978-01-01

Remote measurements of a number of surface or near surface parameters for baseline definition and specialized studies, remote measurements of episodic events, and remote measurements of the Bay lithosphere are considered in terms of characterizing and understanding the ecology of the Chesapeake Bay. Geologic processes and features best suited for information enhancement by remote sensing methods are identified. These include: (1) rates of sedimentation in the Bay; (2) rates of erosion of Bay shorelines; (3) spatial distribution and geometry of aquifers; (4) mapping of Karst terrain (sinkholes); and (5) mapping of fracture patterns. Recommendations for studying problem areas identified are given.

Seasonal variations of phytoplankton assemblages and its relation to environmental variables in a scallop culture sea area of Bohai Bay, China.

PubMed

Chen, Yang-Hang; Gao, Ya-Hui; Chen, Chang-Ping; Liang, Jun-Rong; Sun, Lin; Zhen, Yu; Qiao, Ling

2016-12-15

Seasonal variations of phytoplankton assemblages were examined in a scallop culture sea area of Bohai Bay (China) with regard to some major physical and chemical variables. Samples were collected at three stations from July 2011 to September 2013. A total of 134 species belong to 4 phyla were identified, of which 104 were diatoms, 27 were dinoflagellates, 1 was euglenophyte and 2 were chrysophytes. The cells abundance in autumn (55.44×10 3 cells/L) was higher than that in summer (6.99×10 3 cells/L), spring (3.46×10 3 cells/L) and winter (2.69×10 3 cells/L). The Shannon-Wiener diversity index was higher in summer (3.06), followed by spring (3.02) and winter (2.91), and low in autumn (1.40). Results of canonical correspondence analysis showed that phosphate, salinity, temperature, silicate and DIN/SiO 2 ratio were the most important environmental factors influencing the variation of phytoplankton community structure. It is suggested that eutrophication resulted from scallop culture would cause a potential red tide risk. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of marine pollution in Izmir Bay: nutrient, heavy metal and total hydrocarbon concentrations.

PubMed

Kucuksezgin, F; Kontas, A; Altay, O; Uluturhan, E; Darilmaz, E

2006-01-01

Izmir Bay (western Turkey) is one of the great natural bays of the Mediterranean. Izmir is an important industrial and commercial centre and a cultural focal point. The main industries in the region include food processing, oil, soap and paint production, chemical industries, paper and pulp factories, textile industries and metal processing. The mean concentrations showed ranges of 0.01-0.19 and 0.01-10 microM for phosphate, 0.10-1.8 and 0.12-27 microM for nitrate+nitrite, and 0.30-5.8 and 0.43-39 microM for silicate in the outer and middle-inner bays, respectively. The TNO(x)/PO(4) ratio is significantly lower than the Redfield's ratio and nitrogen is the limiting element in the middle-inner bays. Diatoms and dinoflagellates were observed all year around in the bay and are normally nitrogen limited. Metal concentrations ranged between Hg: 0.05-1.3, Cd: 0.005-0.82, Pb: 14-113 and Cr: 29-316 microg g(-1) in the sediments. The results showed significant enrichments during sampling periods from Inner Bay. Outer and middle bays show low levels of heavy metal enrichments except estuary of Gediz River. The concentrations of Hg, Cd and Pb in the outer bay were generally similar to the background levels from the Mediterranean. The levels gradually decreased over the sampling period. Total hydrocarbons concentrations range from 427 to 7800 ng g(-1) of sediments. The highest total hydrocarbon levels were found in the inner bay due to the anthropogenic activities, mainly combustion processes of traffic and industrial activities. The concentrations of heavy metals found in fish varied for Hg: 4.5-520, Cd: 0.10-10 and Pb: 0.10-491 microg kg(-1) in Izmir Bay. There was no significant seasonal variation in metal concentrations. An increase in Hg concentration with increasing length was noted for Mullus barbatus. A person can consume more than 2, 133 and 20 meals per week of fish in human diet would represent the tolerable weekly intake of mercury, cadmium and lead, respectively, in Izmir Bay. Heavy metal levels were lower than the results in fish tissues reported from polluted areas of the Mediterranean Sea.

Variations in water clarity and bottom albedo in Florida Bay from 1985 to 1997

USGS Publications Warehouse

Stumpf, R.P.; Frayer, M.L.; Durako, M.J.; Brock, J.C.

1999-01-01

Following extensive seagrass die-offs of the late 1980s and early 1990s, Florida Bay reportedly had significant declines in water clarity due to turbidity and algal blooms. Scant information exists on the extent of the decline, as this bay was not investigated for water quality concerns before the die-offs and limited areas were sampled after the primary die-off. We use imagery from the Advanced Very High Resolution Radiometer (AVHRR) to examine water clarity in Florida Bay for the period 1985 to 1997. The AVHRR provides data on nominal water reflectance and estimated fight attenuation, which are used here to describe turbidity conditions in the bay on a seasonal basis. In situ observations on changes in seagrass abundance within the bay, combined with the satellite data, provide additional insights into losses of seagrass. The imagery shows an extensive region to the west of Florida Bay having increased reflectance and fight attenuation in both winter and summer beginning in winter of 1988. These increases are consistent with a change from dense seagrass to sparse or negligible cover. Approximately 200 km2 of these offshore seagrasses may have been lost during the primary die-off (1988 through 1991), significantly more than in the bay. The imagery shows the distribution and timing of increased turbidity that followed the die-offs in the northwestern regions of the bay, exemplified in Rankin Lake and Johnson Key Basin, and indicates that about 200 km2 of dense seagrass may have been lost or severely degraded within the bay from the start of the die-off. The decline in water clarity has continued in the northwestern bay since 1991. The area west of the Everglades National Park boundaries has shown decreases in both winter turbidity and summer reflectances, suggestive of partial seagrass recovery. Areas of low reflectance associated with a major Syringodium filiforme seagrass meadow north of Marathon (Vaca Key, in the Florida Keys) appear to have expanded westward toward Big Pine Key, indicating changes in the bottom cover from before the die-off. The southern and eastern sections of the Bay have not shown significant changes in water clarity or bottom albedo throughout the entire time period.

Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae).

PubMed

Grummer, Jared A; Bryson, Robert W; Reeder, Tod W

2014-03-01

Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal-likelihood scores of competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation (HME), smoothed harmonic mean estimation (sHME), path-sampling/thermodynamic integration (PS), and stepping-stone (SS) analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that HME and sHME perform poorly compared with PS and SS marginal-likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor delimitation (BFD) of species showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, BFD through PS and SS analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical data sets, harmonic and smoothed harmonic mean marginal-likelihood estimators provided much higher marginal-likelihood estimates than PS and SS estimators. The AICM displayed poor repeatability in both simulated and empirical data sets, and produced inconsistent model rankings across replicate runs with the empirical data. Our results suggest that species delimitation through the use of Bayes factors with marginal-likelihood estimates via PS or SS analyses provide a useful and complementary alternative to existing species delimitation methods.

Spatial variation in sediment-water exchange of phosphorus in Florida Bay: AMP as a model organic compound.

PubMed

Huang, Xiao-Lan; Zhang, Jia-Zhong

2010-10-15

Dissolved organic phosphorus (DOP) has been recognized as dominant components in total dissolved phosphorus (TDP) pools in many coastal waters, and its exchange between sediment and water is an important process in biogeochemical cycle of phosphorus. Adenosine monophosphate (AMP) was employed as a model DOP compound to simulate phosphorus exchange across sediment-water interface in Florida Bay. The sorption data from 40 stations were fitted to a modified Freundlich equation and provided a detailed spatial distribution both of the sediment's zero equilibrium phosphorus concentration (EPC(0-T)) and of the distribution coefficient (K(d-T)) with respect to TDP. The K(d-T) was found to be a function of the index of phosphorus saturation (IPS), a molar ratio of the surface reactive phosphorus to the surface reactive iron oxide content in the sediment, across the entire bay. However, the EPC(0-T) was found to correlate to the contents of phosphorus in the eastern bay only. Sediment in the western bay might act as a source of the phosphorus in the exchange process due to their high EPC(0-T) and low K(d-T), whereas sediments in the eastern bay might act as a sink because of their low EPC(0-T) and high K(d-T). These results strongly support the hypothesis that both phosphorus and iron species in calcareous marine sediments play a critical role in governing the sediment-water exchange of both phosphate and DOP in the coastal and estuarine ecosystems.

Phosphate oxygen isotope ratios as a tracer for sources and cycling of phosphate in North San Francisco Bay, California

USGS Publications Warehouse

McLaughlin, K.; Kendall, C.; Silva, S.R.; Young, M.; Paytan, A.

2006-01-01

A seasonal analysis assesing variations in the oxygen isotopic composition of dissolved inorganic phosphate (DIP) was conducted in the San Francisco Bay estuarine system, California. Isotopic fractionation of oxygen in DIP (exchange of oxygen between phosphate and environmental water) at surface water temperatures occurs only as a result of enzyme-mediated, biological reactions. Accordingly, if phospate demand is low relative to input and phosphate is not heavily cycled in the ecosystem, the oxygen isotopic composition of DIP (?? 18Op) will reflect the isotopic composition of the source of phosphate to the system. Such is the case for the North San Francisco Bay, an anthropogenically impacted estuary with high surface water phosphate concentrations. Variability in the ?? 18Op in the bay is primarily controlled by mixing of water masses with different ??18Op signatures. The ??18Op values range from 11.4??? at the Sacramento River to 20.1??? at the Golden Gate. Deviations from the two-component mixing model for the North Bay reflect additional, local sources of phosphate to the estuary that vary seasonally. Most notably, deviations from the mixing model occur at the confluence of a major river into the bay during periods of high river discharge and near wastewater treatment outlets. These data suggest that ??18Op can be an effective tool for identifying P point sources and understanding phosphate dynamics in estuarine systems. Copyright 2006 by the American Geophysical Union.

PHENOTYPIC PLASTICITY INDUCED IN TRANSPLANT EXPERIMENTS IN A MUTUALISTIC ASSOCIATION BETWEEN THE RED ALGA JANIA ADHAERENS (RHODOPHYTA, CORALLINALES) AND THE SPONGE HALICLONA CAERULEA (PORIFERA: HAPLOSCLERIDA): MORPHOLOGICAL RESPONSES OF THE ALGA(1).

PubMed

Enríquez, Susana; Ávila, Enrique; Carballo, José Luis

2009-02-01

The association between the red macroalga Jania adhaerens J. V. Lamour. and the sponge Haliclona caerulea is the most successful life-form between 2 and 4 m depth in Mazatlán Bay (Mexican Pacific). J. adhaerens colonizes the rocky intertidal area and penetrates into deeper areas only when it lives in association with H. caerulea. The aposymbiotic form of the sponge has not been reported in the bay. To understand the ecological success of this association, we examined the capacity of J. adhaerens to acclimate in Mazatlán Bay using transplant experiments. The transplanted aposymbiotic J. adhaerens did not survive the first 2 weeks; however, J. adhaerens when living in association with H. caerulea, acclimated easily to depth, showing no sign of mortality during the 103 d of the experiment. We conclude that the ability of J. adhaerens to colonize in deeper areas in this hydrodynamic environment may in part rely on the protection provided by the sponge to the algal canopy. Both species contribute to the shape of the associated form. Nevertheless, the morphological variation in the association appears to be dominated by the variation in J. adhaerens canopy to regulate pigment self-shading under light-limited conditions and/or tissue resistance under high hydrodynamics. Consequently, our results are consistent with light as the abiotic controlling factor, which regulates the lower depth distribution of the association in Mazatlán Bay, through limiting the growth rate of J. adhaerens. Hydrodynamics may determine the upper limit of the association by imposing high mass losses. © 2009 Phycological Society of America.

Crustal structure of the North Iberian continental margin from seismic refraction/wide-angle reflection profiles

NASA Astrophysics Data System (ADS)

Ruiz, M.; Díaz, J.; Pedreira, D.; Gallart, J.; Pulgar, J. A.

2017-10-01

The structure and geodynamics of the southern margin of the Bay of Biscay have been investigated from a set of 11 multichannel seismic reflection profiles, recorded also at wide angle offsets in an onshore-offshore network of 24 OBS/OBH and 46 land sites. This contribution focuses on the analysis of the wide-angle reflection/refraction data along representative profiles. The results document strong lateral variations of the crustal structure along the margin and provide an extensive test of the crustal models previously proposed for the northern part of the Iberian Peninsula. Offshore, the crust has a typical continental structure in the eastern tip of the bay, which disappears smoothly towards the NW to reach crustal thickness close to 10 km at the edge of the studied area ( 45°N, 6°W). The analysis of the velocity-depth profiles, altogether with additional information provided by the multichannel seismic data and magnetic surveys, led to the conclusion that the crust in this part of the bay should be interpreted as transitional from continental to oceanic. Typical oceanic crust has not been imaged in the investigated area. Onshore, the new results are in good agreement with previous results and document the indentation of the Bay of Biscay crust into the Iberian crust, forcing its subduction to the North. The interpreted profiles show that the extent of the southward indentation is not uniform, with an Alpine root less developed in the central and western sector of the Basque-Cantabrian Basin. N-S to NE-SW transfer structures seem to control those variations in the indentation degree.

The role of thermal stratification in tidal exchange at the mouth of San Diego Bay

USGS Publications Warehouse

Chadwick, D. B.; Largier, J. L.; Cheng, R.T.; Aubrey, D.G.; Friedrichs, C.T.; Aubrey, D.G.; Friedrichs, C.T.

1996-01-01

We have examined, from an observational viewpoint, the role of thermal stratification in the tidal exchange process at the mouth of San Diego Bay. In this region, we found that both horizontal and vertical exchange processes appear to be active. The vertical exchange in this case was apparently due to the temperature difference between the'bay water and ocean water. We found that the structure of the outflow and the nature of the tidal exchange process both appear to be influenced by thermal stratification. The tidal outflow was found to lift-off tan the bottom during the initial and later stages of the ebb flow when barotropic forcing was weak. During the peak ebb flow, the mouth section was flooded, and the outflow extended to the bottom. As the ebb flow weakened, a period of two-way exchange occurred, with the surface layer flowing seaward, and the deep layer flowing into the bay. The structure of the tidal-residual flow and the residual transport of a measured tracer were strongly influenced by this vertical exchange. Exchange appeared to occur laterally as well, in a manner consistent with the tidal-pumping mechanism described by Stommel and Farmer [1952]. Tidal cycle variations in shear and stratification were characterized by strong vertical shear and breakdown of stratification during the ebb, and weak vertical shear and build-up of stratification on the flood. Evaluation of multiple tidal-cycles from time-series records of flow and temperature indicated that the vertical variations of the flow and stratification observed during the cross-sectional measurements are a general phenomenon during the summer. Together, these observations suggest that thermal stratification can play an important role in regulating the tidal exchange of low-inflow estuaries.

Long-term variations of the riverine input of potentially toxic dissolved elements and the impacts on their distribution in Jiaozhou Bay, China.

PubMed

Wang, Changyou; Guo, Jinqiang; Liang, Shengkang; Wang, Yunfei; Yang, Yanqun; Wang, Xiulin

2018-03-01

The concentrations of the potentially toxic dissolved elements (PTEs) As, Hg, Cr, Pb, Cd, and Cu in the main rivers into Jiaozhou Bay (JZB) during 1981-2006 were measured, and the impact of the fluvial PTE fluxes on their distributions in the bay was investigated. The overall average concentration in the rivers into JZB ranged from 8.8 to 39.6 μg L -1 for As, 10.1 to 632.6 ng L -1 for Hg, 4.1 to 3003.6 μg L -1 for Cr, 8.5 to 141.9 μg L -1 for Pb, 1.1 to 34.2 μg L -1 for Cd, and 13.2 to 1042.8 μg L -1 for Cu. The interannual average concentration variations of the PTEs in these rivers were enormous, with maximum differences of 41-21,680 times, while their relative seasonal changes were far smaller with maximum differences of 3-12 times. The total annual fluvial fluxes for As, Hg, and Cr into JZB exhibited the inverse "U" pattern, while those for Pb and Cd showed the "N" pattern. As a whole, the total annual Cu flux presented a growing tendency from 1998 to 2006. In general, the changing trends of the PTE concentrations in JZB were similar to those of their annual fluxes from the rivers, indicating a great impact of their fluvial fluxes on their distributions in JZB. The annual concentration of Cd in the bay almost remained constant and differed from the fluvial flux of Cd. The diversified pattern of the environmental Kuznets curve (EKC) represented China's approach to industrialization as "improving while developing."

High Frequency Radar Observations of Tidal Current Variability in the Lower Chesapeake Bay

NASA Astrophysics Data System (ADS)

Updyke, T. G.; Dusek, G.; Atkinson, L. P.

2016-02-01

Analysis of eight years of high frequency radar surface current observations in the lower Chesapeake Bay is presented with a focus on the variability of the tidal component of the surface circulation which accounts for a majority of the variance of the surface flow (typically 70-80% for the middle of the radar footprint). Variations in amplitude and phase of the major tidal constituents are examined in the context of water level, wind and river discharge data. Comparisons are made with harmonic analysis results from long-term records of current data measured by three current profilers operated by NOAA as part of the Chesapeake Bay Physical Oceanographic Real-Time System (PORTS). Preliminary results indicate that there is significant spatial variability in the M2 amplitude over the HF radar grid as well as temporal variability when harmonic analysis is performed using bi-monthly time segments over the course of the record.

Modeling and predicting intertidal variations of the salinity field in the Bay/Delta

USGS Publications Warehouse

Knowles, Noah; Uncles, Reginald J.

1995-01-01

One approach to simulating daily to monthly variability in the bay is the development of intertidal model using tidally-averaged equations and a time step on the order of the day.  An intertidal numerical model of the bay's physics, capable of portraying seasonal and inter-annual variability, would have several uses.  Observations are limited in time and space, so simulation could help fill the gaps.  Also, the ability to simulate multi-year episodes (eg, an extended drought) could provide insight into the response of the ecosystem to such events.  Finally, such a model could be used in a forecast mode wherein predicted delta flow is used as model input, and predicted salinity distribution is output with estimates days and months in advance.  This note briefly introduces such a tidally-averaged model (Uncles and Peterson, in press) and a corresponding predictive scheme for baywide forecasting.

Mechanisms of sediment flux between shallows and marshes

USGS Publications Warehouse

Lacy, Jessica R.; Schile, L.M.; Callaway, J.C.; Ferner, M.C.

2015-01-01

We conducted a field study to investigate temporal variation and forcing mechanisms of sediment flux between a salt marsh and adjacent shallows in northern San Francisco Bay. Suspended-sediment concentration (SSC), tidal currents, and wave properties were measured over the marsh, in marsh creeks, and in bay shallows. Cumulative sediment flux in the marsh creeks was bayward during the study, and was dominated by large bayward flux during the largest tides of the year. This result was unexpected because extreme high tides with long inundation periods are commonly assumed to supply sediment to marshes, and long-term accretion estimates show that the marsh in the study site is depositional. A water mass-balance shows that some landward transport bypassed the creeks, most likely across the marsh-bay interface. An estimate of transport by this pathway based on observed SSC and inferred volume indicates that it was likely much less than the observed export.

Variation in the carbon cycle of the Sevastopol Bay (Black Sea)

NASA Astrophysics Data System (ADS)

Orekhova, N. A.; Konovalov, S. K.

2018-01-01

Continuous increase in CO2 inventory in the ocean results in dramatic changes in marine biogeochemistry, e.g. acidification. That is why temporal and spatial variabilities in atmospheric pCO2 and dissolved inorganic carbon, including CO2, pH and alkalinity in water, as well as organic and inorganic carbon in bottom sediments have to be studied together making possible to resolve the key features of the carbon cycle transformation. A 30% increase of pCO2 in the Sevastopol Bay for 2008 - 2016 evidences changes in the DIC components ratios and a significant decrease in the ability to absorb atmospheric CO2 by surface waters. High organic carbon content in the bottom sediments and predominance of organic carbon production in the biological pump at inner parts of the bay reveal ongoing transformation of the carbon cycle. This has negative consequences for recreation, social and economic potentials of the Sevastopol region.

[Fish larvae association in a Mexican Caribbean bay].

PubMed

Quintal-Lizama, C; Vásquez-Yeomans, L

2001-06-01

Interannual ichthyoplankton variation, was analyzed in Bahía de la Ascensión, Mexico, during December of four consecutive years (1994-1997). A total of 32 families, 35 genera and 21 species of fish larvae were identified. The most abundant fish larvae were the Gobiidae followed by the Callionymidae, Clupeidae and Tetraodontidae. Larval diversity was low when compared with other periods ("dry" and "rainy"). Three spatial associations (internal, medium and external) were found in December 1994 and 1995. In 1996-1997, stations of the inner and outer parts of the bay were mixed. The dominant families characterized most of the faunal associations. Egg density was highest in the external zone of the bay, whereas larvae were most abundant in the inner area. Major factors affecting the fish larval assemblages during December (1994-1997) in Bahía de la Ascensión seem to be related to the nursery areas location and to the tropical fishes reproductive period.

Core Perylene Diimide Designs via Direct Bay- and ortho-(Poly)trifluoromethylation: Synthesis, Isolation, X-Ray Structures, Optical and Electronic Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clikeman, Tyler T.; Bukovsky, Eric V.; Wang, Xue-Bin

2015-09-22

We developed an efficient solvent- and catalyst-free direct polytrifluoromethylation of solid perylene-3,4,9,10-tetracarboxylic dianhydride that produced a new family of (poly)perfluoroalkyl bay- and ortho-substituted PDIs with two different imide substituents. Direct hydrogen substitution with CN group led to the synthesis of a cyanated perfluoroalkyl PDI derivative for the first time. Absorption, steady-state and time-resolved emission, X-ray diffraction, electrochemical, and gas-phase electron affinity data allowed for systematic studies of substitution effects at bay, ortho, and imide positions in the new PDIs. Solid-state packing showed remarkable variations in the intermolecular interactions that are important for charge transport and photophysical properties. Moreover, analysis ofmore » the electrochemical data for 143 electron poor PDIs, including newly reported compounds, revealed some general trends and peculiar effects from substituting electron-withdrawing groups at all three positions.« less

Core Perylene Diimide Designs via Direct Bay and Ortho (Poly)trifluoromethylation: Synthesis, Isolation, X-ray Structures, Optical and Electronic Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clikeman, Tyler T.; Bukovsky, Eric V.; Wang, Xue B.

2015-09-22

We developed an efficient solvent- and catalyst-free direct polytrifluoromethylation of solid perylene-3,4,9,10-tetracarboxylic dianhydride that produced a new family of (poly)perfluoroalkyl bay and ortho substituted PDIs with two different imide substituents. Direct hydrogen substitution with CN group led to the synthesis of a cyanated perfluoroalkyl PDI derivative for the first time. Absorption, steady-state and time-resolved emission, X-ray diffraction, electrochemical, and gas-phase electron affinity data allowed for systematic studies of substitution effects at bay, ortho, and imide positions in the new PDIs. Solid-state packing showed remarkable variations in the intermolecular interactions that are important for charge transport and photophysical properties. Analysis ofmore » the electrochemical data for 143 electron poor PDIs, including newly reported compounds, revealed some general trends and peculiar effects of electron withdrawing group substitution at all three positions.« less

Revised method and outcomes for estimating soil phosphorus losses from agricultural land in the Chesapeake Bay watershed model

USDA-ARS?s Scientific Manuscript database

Current restoration efforts for the Chesapeake Bay watershed mandate a timeline for reducing the load of nutrients and sediment to receiving waters. The Chesapeake Bay Watershed Model (WSM) has been used for two decades to simulate hydrology and nutrient and sediment transport; however, spatial limi...

Hydrography and bottom boundary layer dynamics: Influence on inner shelf sediment mobility, Long Bay, North Carolina

USGS Publications Warehouse

Davis, L.A.; Leonard, L.A.; Snedden, G.A.

2008-01-01

This study examined the hydrography and bottom boundary-layer dynamics of two typical storm events affecting coastal North Carolina (NC); a hurricane and the passages of two small consecutive extratropical storms during November 2005. Two upward-looking 1200-kHz Acoustic Doppler Current Profilers (ADCP) were deployed on the inner shelf in northern Long Bay, NC at water depths of less than 15 m. Both instruments profiled the overlying water column in 0.35 in bins beginning at a height of 1.35 in above the bottom (mab). Simultaneous measurements of wind speed and direction, wave and current parameters, and acoustic backscatter were coupled with output from a bottom boundary layer (bbl) model to describe the hydrography and boundary layer conditions during each event. The bbl model also was used to quantify sediment transport in the boundary layer during each storm. Both study sites exhibited similar temporal variations in wave and current magnitude, however, wave heights during the November event were higher than waves associated with the hurricane. Near-bottom mean and subtidal currents, however, were of greater magnitude during the hurricane. Peak depth-integrated suspended sediment transport during the November event exceeded transport associated with the hurricane by 25-70%. Substantial spatial variations in sediment transport existed throughout both events. During both events, along-shelf sediment transport exceeded across-shelf transport and was related to the magnitude and direction of subtidal currents. Given the variations in sediment type across the bay, complex shoreline configuration, and local bathymetry, the sediment transport rates reported here are very site specific. However, the general hydrography associated with the two storms is representative of conditions across northern Long Bay. Since the beaches in the study area undergo frequent renourishment to counter the effects of beach erosion, the results of this study also are relevant to coastal management decision-making. Specifically, these issues include 1) identification of municipalities that should share the cost for renourishment given the likelihood for significant along-shelf sand movement and 2) appropriate timing of sand placement with respect to local climatology and sea-turtle nesting restrictions.

Underwater Optics in Sub-Antarctic and Antarctic Coastal Ecosystems

PubMed Central

Huovinen, Pirjo; Ramírez, Jaime; Gómez, Iván

2016-01-01

Understanding underwater optics in natural waters is essential in evaluating aquatic primary production and risk of UV exposure in aquatic habitats. Changing environmental conditions related with global climate change, which imply potential contrasting changes in underwater light climate further emphasize the need to gain insights into patterns related with underwater optics for more accurate future predictions. The present study evaluated penetration of solar radiation in six sub-Antarctic estuaries and fjords in Chilean North Patagonian region (39–44°S) and in an Antarctic bay (62°S). Based on vertical diffuse attenuation coefficients (Kd), derived from measurements with a submersible multichannel radiometer, average summer UV penetration depth (z1%) in these water bodies ranged 2–11 m for UV-B (313 nm), 4–27 m for UV-A (395 nm), and 7–30 m for PAR (euphotic zone). UV attenuation was strongest in the shallow Quempillén estuary, while Fildes Bay (Antarctica) exhibited the highest transparency. Optically non-homogeneous water layers and seasonal variation in transparency (lower in winter) characterized Comau Fjord and Puyuhuapi Channel. In general, multivariate analysis based on Kd values of UV and PAR wavelengths discriminated strongly Quempillén estuary and Puyuhuapi Channel from other study sites. Spatial (horizontal) variation within the estuary of Valdivia river reflected stronger attenuation in zones receiving river impact, while within Fildes Bay a lower spatial variation in water transparency could in general be related to closeness of glaciers, likely due to increased turbidity through ice-driven processes. Higher transparency and deeper UV-B penetration in proportion to UV-A/visible wavelengths observed in Fildes Bay suggests a higher risk for Antarctic ecosystems reflected by e.g. altered UV-B damage vs. photorepair under UV-A/PAR. Considering that damage repair processes often slow down under cool temperatures, adverse UV impact could be further exacerbated by cold temperatures in this location, together with episodes of ozone depletion. Overall, the results emphasize the marked spatial (horizontal and vertical) and temporal heterogeneity of optical characteristics, and challenges that these imply for estimations of underwater optics. PMID:27144454

[An integrated assessment method of ecological quality status in coastal waters: taking Tong'an Bay as a case].

PubMed

Chen, Zhao-hua; Wu, Hai-yan; Chen, Ke-liang; Chen, Qing-hui; Wu, Ji-chun; Zhang, Jing-fei

2011-07-01

Based on the integrated assessment methods of ecological quality status (EcoQS) in coastal waters abroad as well as the domestic related research status, 11 indices were selected from the biotic and physicochemical elements of water and sediment to built an integrated EcoQS assessment index system, and, with the comprehensive consideration of domestic and international evaluation standards, 5 levels of EcoQS classified as "high, good, moderate, poor, and bad" were determined. Then, an integrated assessment method of EcoQS in coastal waters was established by using analytic hierarchy process (AHP) and fuzzy mathematics method, and tested by the analysis of the correlations between the EcoQS grade and the major anthropogenic disturbances and pollutant concentrations of Tong' an Bay. The EcoQS of Tong' an Bay was assessed as moderate, i.e., the Bay was moderately disturbed and in transitional to poor status. The established integrated assessment method could not only reflect the major anthropogenic environmental pressure and risk factors, but also give an early warning of the pollutants satisfied by law in the study area.

Variation in spatial and temporal incidence of the crustacean pathogen Hematodinium perezi in environmental samples from Atlantic Coastal Bays

PubMed Central

2013-01-01

Background Hematodinium perezi, a parasitic dinoflagellate, infects and kills blue crabs, Callinectes sapidus, along the Atlantic and Gulf coasts of the United States. The parasite proliferates within host hemolymph and tissues, and also produces free-swimming biflagellated dinospores that emerge from infected crabs. Infections in C. sapidus recur annually, and it is not known if biotic or environmental reservoirs contribute to reinfection and outbreaks. To address this data gap, a quantitative PCR assay based on the internal transcribed spacer 2 (ITS2) region of H. perezi rRNA genes was developed to asses the temporal and spatial incidence of the parasite in Delaware and Maryland coastal bays. Results A previously-used PCR assay for H. perezi, based on the small subunit rRNA gene sequence, was found to lack adequate species specificity to discriminate non-Hematodinium sp. dinoflagellate species in environmental samples. A new ITS2-targeted assay was developed and validated to detect H. perezi DNA in sediment and water samples using E. coli carrying the H. perezi rDNA genes. Application of the method to environmental samples identified potential hotspots in sediment in Indian River Inlet, DE and Chincoteague Bay, MD and VA. H. perezi DNA was not detected in co-occurring shrimp or snails, even during an outbreak of the parasite in C. sapidus. Conclusions H. perezi is present in water and sediment samples in Maryland and Delaware coastal bays from April through November with a wide spatial and temporal variability in incidence. Sampling sites with high levels of H. perezi DNA in both bays share characteristics of silty, organic sediments and low tidal currents. The environmental detection of H. perezi in spring, ahead of peak prevalence in crabs, points to gaps in our understanding of the parasite’s life history prior to infection in crabs as well as the mode of environmental transmission. To better understand the H. perezi life cycle will require further monitoring of the parasite in habitats as well as hosts. Improved understanding of potential environmental transmission to crabs will facilitate the development of disease forecasting. PMID:23641869

A new approach to measure visual field progression in glaucoma patients using variational bayes linear regression.

PubMed

Murata, Hiroshi; Araie, Makoto; Asaoka, Ryo

2014-11-20

We generated a variational Bayes model to predict visual field (VF) progression in glaucoma patients. This retrospective study included VF series from 911 eyes of 547 glaucoma patients as test data, and VF series from 5049 eyes of 2858 glaucoma patients as training data. Using training data, variational Bayes linear regression (VBLR) was created to predict VF progression. The performance of VBLR was compared against ordinary least-squares linear regression (OLSLR) by predicting VFs in the test dataset. The total deviation (TD) values of test patients' 11th VFs were predicted using TD values from their second to 10th VFs (VF2-10), the root mean squared error (RMSE) associated with each approach then was calculated. Similarly, mean TD (mTD) of test patients' 11th VFs was predicted using VBLR and OLSLR, and the absolute prediction errors compared. The RMSE resulting from VBLR averaged 3.9 ± 2.1 (SD) and 4.9 ± 2.6 dB for prediction based on the second to 10th VFs (VF2-10) and the second to fourth VFs (VF2-4), respectively. The RMSE resulting from OLSLR was 4.1 ± 2.0 (VF2-10) and 19.9 ± 12.0 (VF2-4) dB. The absolute prediction error (SD) for mTD using VBLR was 1.2 ± 1.3 (VF2-10) and 1.9 ± 2.0 (VF2-4) dB, while the prediction error resulting from OLSLR was 1.2 ± 1.3 (VF2-10) and 6.2 ± 6.6 (VF2-4) dB. The VBLR more accurately predicts future VF progression in glaucoma patients compared to conventional OLSLR, especially in short VF series. © ARVO.

Predicting seasonal variations in coastal seabird habitats in the English Channel and the Bay of Biscay

NASA Astrophysics Data System (ADS)

Virgili, A.; Lambert, C.; Pettex, E.; Dorémus, G.; Van Canneyt, O.; Ridoux, V.

2017-07-01

Seabirds, like all animals, have to live in suitable habitats to fulfil their energetic needs for both somatic and reproductive growth and maintenance. Apart from migration trips, all coastal seabirds are linked to the coast, because they need to return daily to land for resting or breeding. Their use of marine habitats strongly depends on their biology, but also on environmental conditions, and can be described using habitat models. This study aimed to: (1) identify the processes that mostly influence seabird distributions along the coasts of the English Channel and the Bay of Biscay; (2) determine seasonal variations of these processes, (3) provide prediction maps that describe the species distributions. We collected data of coastal seabird sightings from aerial surveys carried out in the English Channel and the eastern North Atlantic in the winter 2011-2012 and summer 2012. We classified seabirds into morphological groups and described their habitats using physiographic and oceanographic variables in Generalised Additive Models (GAMs). Finally, we produced maps of predicted distributions by season for each group. The distributions of coastal seabirds were essentially determined by the distance to the nearest coast, with a weaker influence of oceanographic variables. The nature of the substrate, sand or rock, combined with the timing of reproduction, also contributed to determine seasonal at-sea distributions for some species. The highest densities were predicted near the coast, particularly in bays and estuaries for strictly coastal species with possible variations depending on the season. From this study, we were able to predict the seasonal distribution of the studied species according to varying environmental parameters that changed over time, allowing us to understand better their behaviour and ecology.

Air-water CO2 Fluxes In Seasonal Hypoxia-influenced Green Bay, Lake Michigan

NASA Astrophysics Data System (ADS)

Lin, P.; Klump, J. V.; Guo, L.

2016-02-01

Increasing anthropogenic nutrient enrichment has led to seasonal hypoxia in Green Bay, the largest freshwater estuary in the Laurentian Great Lakes, but change in carbon dynamics associated with the development of hypoxia remains poorly understood. Variations in alkalinity, abundance of carbon species, and air-water CO2 fluxes were quantified under contrasting hypoxic conditions during summer 2014. Green Bay was characterized with high pH (average 8.62 ± 0.16 in August), high DIC concentrations (2113 - 3213 µmol/kg) and high pCO2 in the water column. pCO2 was mostly >700 µatm in June, resulting in a net CO2 source to the air, while pCO2 was mostly <650 µatm in August when hypoxic conditions occurred in Green Bay. In central Green Bay, pCO2 was the highest during both sampling months, accompanying by low dissolved oxygen (DO) and lower pH in the water column. In August, pCO2 was inversely correlated with DOC concentration and increased with DOC/DOP ratio, suggesting a control by organic matter on air-water CO2 dynamics and consumption of DO in Green Bay. Positive CO2 fluxes to the atmosphere during August were only observed in northern bay but a CO2 sink was found in southern Green Bay ( 40% of study area) with high biological production and terrestrial DOM. Daily CO2 flux ranged from 10.9 to 48.5 mmol-C m-2 d-1 in June with an average of 18.29 ± 7.44 mmol-C m-2 d-1, whereas it varied from 1.82 ± 1.18 mmol m-2 d-1 in the north to -2.05 ± 1.89 mmol m-2 d-1 in the south of Green Bay in August. Even though strong biological production reduced the CO2 emission, daily CO2 fluxes from Green Bay to the air were as high as 7.4 × 107 mole-C in June and 4.6 × 106 mole-C in August, suggesting a significant role of high-DIC lakes in global CO2 budget and cycling.

Bayesian regression models outperform partial least squares methods for predicting milk components and technological properties using infrared spectral data

PubMed Central

Ferragina, A.; de los Campos, G.; Vazquez, A. I.; Cecchinato, A.; Bittante, G.

2017-01-01

The aim of this study was to assess the performance of Bayesian models commonly used for genomic selection to predict “difficult-to-predict” dairy traits, such as milk fatty acid (FA) expressed as percentage of total fatty acids, and technological properties, such as fresh cheese yield and protein recovery, using Fourier-transform infrared (FTIR) spectral data. Our main hypothesis was that Bayesian models that can estimate shrinkage and perform variable selection may improve our ability to predict FA traits and technological traits above and beyond what can be achieved using the current calibration models (e.g., partial least squares, PLS). To this end, we assessed a series of Bayesian methods and compared their prediction performance with that of PLS. The comparison between models was done using the same sets of data (i.e., same samples, same variability, same spectral treatment) for each trait. Data consisted of 1,264 individual milk samples collected from Brown Swiss cows for which gas chromatographic FA composition, milk coagulation properties, and cheese-yield traits were available. For each sample, 2 spectra in the infrared region from 5,011 to 925 cm−1 were available and averaged before data analysis. Three Bayesian models: Bayesian ridge regression (Bayes RR), Bayes A, and Bayes B, and 2 reference models: PLS and modified PLS (MPLS) procedures, were used to calibrate equations for each of the traits. The Bayesian models used were implemented in the R package BGLR (http://cran.r-project.org/web/packages/BGLR/index.html), whereas the PLS and MPLS were those implemented in the WinISI II software (Infrasoft International LLC, State College, PA). Prediction accuracy was estimated for each trait and model using 25 replicates of a training-testing validation procedure. Compared with PLS, which is currently the most widely used calibration method, MPLS and the 3 Bayesian methods showed significantly greater prediction accuracy. Accuracy increased in moving from calibration to external validation methods, and in moving from PLS and MPLS to Bayesian methods, particularly Bayes A and Bayes B. The maximum R2 value of validation was obtained with Bayes B and Bayes A. For the FA, C10:0 (% of each FA on total FA basis) had the highest R2 (0.75, achieved with Bayes A and Bayes B), and among the technological traits, fresh cheese yield R2 of 0.82 (achieved with Bayes B). These 2 methods have proven to be useful instruments in shrinking and selecting very informative wavelengths and inferring the structure and functions of the analyzed traits. We conclude that Bayesian models are powerful tools for deriving calibration equations, and, importantly, these equations can be easily developed using existing open-source software. As part of our study, we provide scripts based on the open source R software BGLR, which can be used to train customized prediction equations for other traits or populations. PMID:26387015

Bayes factors for the linear ballistic accumulator model of decision-making.

PubMed

Evans, Nathan J; Brown, Scott D

2018-04-01

Evidence accumulation models of decision-making have led to advances in several different areas of psychology. These models provide a way to integrate response time and accuracy data, and to describe performance in terms of latent cognitive processes. Testing important psychological hypotheses using cognitive models requires a method to make inferences about different versions of the models which assume different parameters to cause observed effects. The task of model-based inference using noisy data is difficult, and has proven especially problematic with current model selection methods based on parameter estimation. We provide a method for computing Bayes factors through Monte-Carlo integration for the linear ballistic accumulator (LBA; Brown and Heathcote, 2008), a widely used evidence accumulation model. Bayes factors are used frequently for inference with simpler statistical models, and they do not require parameter estimation. In order to overcome the computational burden of estimating Bayes factors via brute force integration, we exploit general purpose graphical processing units; we provide free code for this. This approach allows estimation of Bayes factors via Monte-Carlo integration within a practical time frame. We demonstrate the method using both simulated and real data. We investigate the stability of the Monte-Carlo approximation, and the LBA's inferential properties, in simulation studies.

Scale-adaptive compressive tracking with feature integration

NASA Astrophysics Data System (ADS)

Liu, Wei; Li, Jicheng; Chen, Xiao; Li, Shuxin

2016-05-01

Numerous tracking-by-detection methods have been proposed for robust visual tracking, among which compressive tracking (CT) has obtained some promising results. A scale-adaptive CT method based on multifeature integration is presented to improve the robustness and accuracy of CT. We introduce a keypoint-based model to achieve the accurate scale estimation, which can additionally give a prior location of the target. Furthermore, by the high efficiency of data-independent random projection matrix, multiple features are integrated into an effective appearance model to construct the naïve Bayes classifier. At last, an adaptive update scheme is proposed to update the classifier conservatively. Experiments on various challenging sequences demonstrate substantial improvements by our proposed tracker over CT and other state-of-the-art trackers in terms of dealing with scale variation, abrupt motion, deformation, and illumination changes.

δ15N as a Potential Paleoenvironmental Proxy for Nitrogen Loading in Chesapeake Bay

NASA Astrophysics Data System (ADS)

Black, H. D.; Andrus, C. F.; Rick, T.; Hines, A.

2013-12-01

Stable isotope analysis of Eastern Oyster (Crassostrea virginica) and other mollusk shells from archaeological sites is a useful means of acquiring paleoenvironmental data. Recently, nitrogen isotopes have been identified as a potential new proxy in these shells. δ15N content in mollusk shells is affected by numerous anthropogenic and natural influences and may be used as an environmental proxy for nitrogen loading conditions. Chesapeake Bay is well known for both historic and modern pollution problems from numerous anthropogenic sources, such as fertilizer runoff, sewage discharge, and densely populated land use and serves as an ideal study location for long-term nitrogen loading processes. Longer records of these processes may be recorded in abundant archaeological remains around the bay, however, little is known about the stability of δ15N and %N in shell material over recent geologic time. In this study, 90 archaeological C. virginica shells were collected by the Smithsonian Institution from the Rhode River Estuary within Chesapeake Bay and range in age from ~150 to 3200 years old. Twenty-two modern C. virginica shells were also collected from nearby beds in the bay. All shell samples were subsampled from the resilifer region of the calcitic shell using a hand-held micro drill and were analyzed using EA-IRMS analysis to determine the potential temporal variability of δ15N and %N as well as creating a baseline for ancient nitrogen conditions in the bay area. Modern POM water samples and C. virginica soft tissues were also analyzed in this study to determine the degree of seasonal variation of δ15N and %N in Chesapeake Bay.

Effects of nutrients and zooplankton on the phytoplankton community structure in Marudu Bay

NASA Astrophysics Data System (ADS)

Tan, Kar Soon; Ransangan, Julian

2017-07-01

Current study was carried out to provide a better understanding on spatial and temporal variations in the phytoplankton community structure in Marudu Bay, an important nursery ground for fishery resources within the Tun Mustapha Marine Park and Coral Triangle Initiative, and their relationship with environmental variables. Samplings were conducted monthly from April 2014 to April 2015 in Marudu Bay, Malaysia. Water samples were collected for nutrients analysis, zooplankton and phytoplankton counting. Moreover, the in situ environmental parameters were also examined. The field study showed a total of forty seven phytoplankton genera, representative of 33 families were identified. The nutrient concentrations in Marudu Bay was low (mesotrophic) throughout the year, where the phytoplankton community was often dominated by Chaetoceros spp. and Bacteriastrum spp. In general, increase in nitrate concentration triggered the bloom of centric diatom, Chaetoceros spp. and Bacteriastrum spp. in Marudu Bay. However, the bloom of these phytoplankton taxa did not occur in the presence of high ammonia concentration. In addition, high abundance of zooplankton also a limiting factor of the phytoplankton blooms particularly at end of southwest monsoon. High silica concentration promoted the growth of pennate diatoms, Proboscia spp. and Thallassionema spp., but the depletion of silica quickly terminated the bloom. Interestingly, our study showed that Chaetoceros spp., tolerated silica depletion condition, but the average cell size of this taxon reduced significantly. In summary, the phytoplankton community structure in mesotrophic environment is more sensitive to the changes in zooplankton abundance, nutrient concentration and its ratio than that in nutrient rich environments. This study also recommends that bivalve farming at industrial scale is not recommended in Marudu Bay because it potentially depletes the primary productivity hence jeopardizing the availability of live food for larvae of many natural fishery resources in the bay.

Spatial and temporal variation in distribution of larval lake whitefish in eastern Lake Ontario: signs of recovery?

USGS Publications Warehouse

McKenna, J.E.; Johnson, J. H.

2009-01-01

The lake whitefish (Coregonus clupeaformis) is one of the native Lake Ontario fishes that declined severely over the past century. Recent evidence of larval lake whitefish production in a historic spawning area (Chaumont Bay) might signal a recovery of this species in New York waters. We surveyed coastal and open water areas to evaluate densities and estimate total abundance of larval lake whitefish in Chaumont Bay. Other historic spawning areas and embayments with appropriate spawning and nursery habitat were also surveyed, but only a few larvae were found outside of Chaumont Bay. Lake whitefish larvae were found in every embayment sampled within Chaumont Bay, with larval densities of nearly 600/1000 m2 in some samples. Greatest abundances occurred in the northern sectors and near the mouth of the bay. Open water densities were generally less than half that of nearshore sites. The total bay-wide estimate for 2005 was approximately 644,000 lake whitefish larvae, but dropped to 230,000–400,000 in 2006 and 2007, respectively. Mean larval growth rates (0.36 mm/day) did not differ by year, but were consistently higher in early May than in late April. Lake whitefish production in Chaumont Bay is encouraging for this species, but the cause and persistence of the decline after 2005 can be determined only by continued monitoring. Other possible bottlenecks of survival may exist at juvenile and adult stages and could significantly affect recruitment dynamics. This species is sensitive to normal climatic fluctuations and increased variability associated with global climatic change could make winter nursery conditions unfavorable for this species.

A computer model of long-term salinity in San Francisco Bay: Sensitivity to mixing and inflows

USGS Publications Warehouse

Uncles, R.J.; Peterson, D.H.

1995-01-01

A two-level model of the residual circulation and tidally-averaged salinity in San Francisco Bay has been developed in order to interpret long-term (days to decades) salinity variability in the Bay. Applications of the model to biogeochemical studies are also envisaged. The model has been used to simulate daily-averaged salinity in the upper and lower levels of a 51-segment discretization of the Bay over the 22-y period 1967–1988. Observed, monthly-averaged surface salinity data and monthly averages of the daily-simulated salinity are in reasonable agreement, both near the Golden Gate and in the upper reaches, close to the delta. Agreement is less satisfactory in the central reaches of North Bay, in the vicinity of Carquinez Strait. Comparison of daily-averaged data at Station 5 (Pittsburg, in the upper North Bay) with modeled data indicates close agreement with a correlation coefficient of 0.97 for the 4110 daily values. The model successfully simulates the marked seasonal variability in salinity as well as the effects of rapidly changing freshwater inflows. Salinity variability is driven primarily by freshwater inflow. The sensitivity of the modeled salinity to variations in the longitudinal mixing coefficients is investigated. The modeled salinity is relatively insensitive to the calibration factor for vertical mixing and relatively sensitive to the calibration factor for longitudinal mixing. The optimum value of the longitudinal calibration factor is 1.1, compared with the physically-based value of 1.0. Linear time-series analysis indicates that the observed and dynamically-modeled salinity-inflow responses are in good agreement in the lower reaches of the Bay.

Feeding ecology of lake whitefish larvae in eastern Lake Ontario

USGS Publications Warehouse

Johnson, James H.; McKenna, James E.; Chalupnicki, Marc A.; Wallbridge, Tim; Chiavelli, Rich

2009-01-01

We examined the feeding ecology of larval lake whitefish (Coregonus clupeaformis) in Chaumont Bay, Lake Ontario, during April and May 2004-2006. Larvae were collected with towed ichthyoplankton nets offshore and with larval seines along the shoreline. Larval feeding periodicity was examined from collections made at 4-h intervals over one 24-h period in 2005. Inter-annual variation in diet composition (% dry weight) was low, as was spatial variation among collection sites within the bay. Copepods (81.4%), primarily cyclopoids (59.1%), were the primary prey of larvae over the 3-year period. Cladocerans (8.1%; mainly daphnids, 6.7%) and chironomids (7.3%) were the other major prey consumed. Larvae did not exhibit a preference for any specific prey taxa. Food consumption of lake whitefish larvae was significantly lower at night (i.e., 2400 and 0400 h). Substantial variation in diet composition occurred over the 24-h diel study. For the 24-h period, copepods were the major prey consumed (50.4%) and their contribution in the diet ranged from 29.3% (0400 h) to 85.9% (1200 h). Chironomids made up 33.4% of the diel diet, ranging from 8.0% (0800 h) to 69.9% (0400 h). Diel variation in the diet composition of lake whitefish larvae may require samples taken at several intervals over a 24-h period to gain adequate representation of their feeding ecology.

Hyperspectral Biofilm Classification Analysis for Carrying Capacity of Migratory Birds in the South Bay Salt Ponds

NASA Technical Reports Server (NTRS)

Hsu, Wei-Chen; Kuss, Amber Jean; Ketron, Tyler; Nguyen, Andrew; Remar, Alex Covello; Newcomer, Michelle; Fleming, Erich; Debout, Leslie; Debout, Brad; Detweiler, Angela;

The coupling of bay hydrodynamics with sediment supply and micro-tidal wetland stability under high rates of relative sea level rise

NASA Astrophysics Data System (ADS)

Wang, J.; Xu, K.; Restreppo, G. A.; Bentley, S. J.; Meng, X.; Zhang, X.

2017-12-01

Due to global sea level rise, local subsidence and sediment deficit, the Mississippi River (MR) deltaic plain has lost a total of 25% of coastal Louisiana's wetlands during the last century, leading to huge losses of ecological services, economic and social crises. Ecosystem-based restoration strategies which rely on coastal system processes and feedbacks are urgently needed. Understanding linkages between estuarine and coastal systems and the adjacent marshlands will help the designing strategies. To investigate bay hydrodynamics and its impacts on the adjacent micro-tidal wetland stability, hourly measurements of wave, tidal current, and benthic sediment concentration in summer, winter, and spring of 2015-2016 were conducted in Fourleague Bay, Louisiana, USA. The bay-marsh system has been stable for almost 80 years under high relative sea level rising rate, which is 11 km southeast of the Atchafalaya River mouth, with a water depth of 1-3 m. High-temporal resolution data indicate that benthic sediment resuspension is mainly caused by wind-driven waves with a dominant periodicity of 4.8 d. The sediment flux reaches 28 g·m-1·s-1 per unit depth in cm during the events. Net sediment transport is northwestward in summer, and southeastward in winter and spring. Sediment flux available for surrounding marsh varies from 0-500 g·m-1·s-1. An optimal inundation depth of 50 cm is estimated by the equilibrium wetland elevation change model under high relative sea level rising rate of 1.57 cm·yr-1. Seasonal variations of river discharge and wind direction (particularly speeds >3 m·s-1) greatly impact potential sediment contribution from bay to the surrounding wetlands. Three sediment transport regimes are concluded based on the seasonal variations of river discharge and wind direction: the `bypassing' season, the resuspension-accumulation season, and the combined `bypassing' and resuspension-accumulation season. The bay hydrodynamic processes and their impacts on the stability of surrounding wetlands fill in our knowledge gaps on how the micro tidal estuarine-marsh system responds to the fast relative sea level rise, and provide valuable information for future ecological restoration plans in the micro tidal deltas like the MR delta.

Variation of Strom Surge Propagation in a Shallow Estuary with Sea Level Rise

NASA Astrophysics Data System (ADS)

Herrington, T. O., Jr.; Blumberg, A. F.

2014-12-01

Hurricane Sandy made landfall along the New Jersey coast at 8pm EDT on October 29th, 2012. At landfall wind gusts of between 129 and 145 km/hr were recorded in New York and New Jersey. The large wind field associated with the storm generated an extreme storm surge north of the eye at landfall resulting in high-velocity overland storm surge along the northern barrier Islands of the Barnegat Bay followed 7 hours later by a rapid rise in water level along the bayside of the barrier islands. A high-resolution, hydrodynamic model for the Barnegat Bay estuary; including its vast intertidal areas, has been developed and validated to simulate the observed Sandy storm surge. The Barnegat Bay Inundation Model (BBIMS) has a constant 100m resolution and is nested within the three dimensional Stevens NYHOPS ocean circulation model at its offshore open boundary. Wetting and drying of land features in the model's external time step is as low as 0.1 sec in its 2D barotropic mode. This mode provides for the dynamic prediction of depth integrated flood elevations and velocities across land features during inundation events. The BBIMS was calibrated using the NYHOPS hindcast of Hurricane Sandy. The hindcast utilized Sandy over ocean wind field and atmospheric pressure data, offshore wave and tidal boundary forcing, atmospheric heat fluxes, interior stream flow data and was validated against observed water levels and measured high water marks. A comparison against 6 water level time series measured by USGS tide gauges located in the Barnegat Bay verified that the model is able to capture the spatial and temporal variation of water levels in the Bay observed during Hurricane Sandy. A comparison against the verified high water marks found that the model is capable of hincasting overland water elevation to within 0.63ft (one standard deviation) at 71% of the total water marks measured. The modeling results show that strong northerly winds along the axis of the estuary prior to landfall suppressed the storm surge in the northern portion of the Bay. A rapid shift in wind direction to southerly winds after landfall allowed the surge to propagate north up the estuary as a shallow water wave (Figure 1). The effect of future sea levels on surge propagation in the estuary is investigated through increases in model mean sea level.

An Empirical Bayes Estimate of Multinomial Probabilities.

DTIC Science & Technology

1982-02-01

multinomial probabilities has been considered from a decision theoretic point of view by Steinhaus (1957), Trybula (1958) and Rutkowska (1977). In a recent...variate Rypergeometric and Multinomial Distributions," Zastosowania Matematyki, 16, 9-21. Steinhaus , H. (1957), "The Problem of Estimation." Annals of

DOE Office of Scientific and Technical Information (OSTI.GOV)

Torrey, M S

The report is a synoptic review of data collected over the past twenty years on the chemistry of Lake Michigan. Changes in water quality and sediment chemistry, attributable to cultural and natural influences, are considered in relation to interacting processes and factors controlling the distribution and concentration of chemical substances within the Lake. Temperature, light, and mixing processes are among the important natural influences that affect nutrient cycling, dispersal of pollutants, and fate of materials entering the Lake. Characterization of inshore-offshore and longitudinal differences in chemical concentrations and sediment chemistry for the main body of the Lake is supplemented bymore » discussion of specific areas such as Green Bay and Grand Traverse Bay. Residues, specific conductance, dissolved oxygen, major and trace nutrients, and contaminants are described in the following context: biological essentiality and/or toxicity, sources to the Lake, concentrations in the water column and sediments, chemical forms, seasonal variations and variation with depth. A summary of existing water quality standards, statutes, and criteria applicable to Lake Michigan is appended.« less

Composition and temporal stability of turf sediments on inner-shelf coral reefs.

PubMed

Gordon, Sophie E; Goatley, Christopher H R; Bellwood, David R

2016-10-15

Elevated sediment loads within the epilithic algal matrix (EAM) of coral reefs can increase coral mortality and inhibit herbivory. Yet the composition, distribution and temporal variability of EAM sediment loads are poorly known, especially on inshore reefs. This study quantified EAM sediment loads (including organic particulates) and algal length across the reef profile of two bays at Orpheus Island (inner-shelf Great Barrier Reef) over a six month period. We examined the total sediment mass, organic load, carbonate and silicate content, and the particle sizes of EAM sediments. Throughout the study period, all EAM sediment variables exhibited marked variation among reef zones. However, EAM sediment loads and algal length were consistent between bays and over time, despite major seasonal variation in climate including a severe tropical cyclone. This study provides a comprehensive description of EAM sediments on inshore reefs and highlights the exceptional temporal stability of EAM sediments on coral reefs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes.

PubMed

Xia, Jun Hong; Li, Hong Lian; Zhang, Yong; Meng, Zi Ning; Lin, Hao Ran

2018-05-01

Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.

Using Bayes factors for testing hypotheses about intervention effectiveness in addictions research

PubMed Central

Dienes, Zoltan; Muirhead, Colin; West, Robert

2016-01-01

Abstract Background and Aims It has been proposed that more use should be made of Bayes factors in hypothesis testing in addiction research. Bayes factors are the ratios of the likelihood of a specified hypothesis (e.g. an intervention effect within a given range) to another hypothesis (e.g. no effect). They are particularly important for differentiating lack of strong evidence for an effect and evidence for lack of an effect. This paper reviewed randomized trials reported in Addiction between January and June 2013 to assess how far Bayes factors might improve the interpretation of the data. Methods Seventy‐five effect sizes and their standard errors were extracted from 12 trials. Seventy‐three per cent (n = 55) of these were non‐significant (i.e. P > 0.05). For each non‐significant finding a Bayes factor was calculated using a population effect derived from previous research. In sensitivity analyses, a further two Bayes factors were calculated assuming clinically meaningful and plausible ranges around this population effect. Results Twenty per cent (n = 11) of the non‐significant Bayes factors were < ⅓ and 3.6% (n = 2) were > 3. The other 76.4% (n = 42) of Bayes factors were between ⅓ and 3. Of these, 26 were in the direction of there being an effect (Bayes factor > 1 and < 3); 12 tended to favour the hypothesis of no effect (Bayes factor < 1 and > ⅓); and for four there was no evidence either way (Bayes factor = 1). In sensitivity analyses, 13.3% of Bayes Factors were < ⅓ (n = 20), 62.7% (n = 94) were between ⅓ and 3 and 24.0% (n = 36) were > 3, showing good concordance with the main results. Conclusions Use of Bayes factors when analysing data from randomized trials of interventions in addiction research can provide important information that would lead to more precise conclusions than are obtained typically using currently prevailing methods. PMID:27347846

Holocene relative sea-level change in Hiroshima Bay, Japan: A semi-quantitative reconstruction based on ostracodes

USGS Publications Warehouse

Yasuhara, Moriaki; Seto, Koji

2006-01-01

Holocene relative sea-level changes in Hiroshima Bay were reconstructed from fossil ostracodes from a core, using a semi-quantitative method. In Hiroshima Bay, relative sea level rose rapidly (about 25 m) between ca. 9000 cal yr BP and ca. 5800 cal yr BP, after which it gradually fell (about 5 m) to its present level. The peak in relative sea level occurred at ca. 5800 cal yr BP. The sea-level curve for Hiroshima Bay is similar to curves for tectonically stable areas of Japan (e.g., Osaka Bay). ?? by the Palaeontological Society of Japan.

Spatio-temporal variation of water flow and sediment discharge in the Mahanadi River, India

NASA Astrophysics Data System (ADS)

Bastia, Fakira; Equeenuddin, Sk. Md.

2016-09-01

The transport of sediments by rivers to the oceans represents an important link between the terrestrial and marine ecosystem. Therefore, this work aims to study spatio-temporal variation of the sediment discharge and erosion rate in the Mahanadi river, one of the biggest rivers in India, over past three decades vis-à-vis their controlling factors. To understand the sediment load variation, the trend analysis in the time series data of rainfall, water and sediment discharge of the Mahanadi river were also attempted. The non-parametric Mann-Kendall and Sen's methods were used to determine whether there was a positive or negative trend in the time series data with their statistical significance. The occurrence of abrupt changes was detected using Pettitt test. The trend test result represents that sediment load delivered from the Mahanadi river to the global ocean has decreased sharply at the rate of 0.515 × 106 tons/year between 1980 and 2010. Water discharge and rainfall in the basin showed no significant decreasing trend except at only one tributary. The decline in sediment discharge from the basin to the Bay of Bengal is mainly due to the increase in the number of dams, which has recorded the increase from 70 to 253 during the period of 1980 to 2010. Over the past 30 years the Mahanadi river has discharged about 49.0 ± 20.5 km3 of water and 17.4 ± 12.7 × 106 tons of sediment annually to the Bay of Bengal whereas the mean erosional rate is 265 ± 125 tons/km2/year over the period of 30 years in the basin. Based on the current data (2000-2001 to 2009-2010), sediment flux and water discharge to the ocean are 12 ± 5 × 106 tons/year and 49 ± 16 km3/year respectively; and ranking Mahanadi river second in terms of water discharge and sediment flux to the ocean among the peninsular rivers in India.

Estimating bacterial production in marine waters from the simultaneous incorporation of thymidine and leucine.

PubMed

Chin-Leo, G; Kirchman, D L

1988-08-01

We examined the simultaneous incorporation of [H]thymidine and [C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 +/- 0.2 [mean +/- standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic acid-insoluble fraction. There were no significant differences in thymidine incorporation between dual- and single-label incubations (dual/ single = 1.03 +/- 0.13). Addition of the two substrates in relatively large amounts (25 nM) did not apparently increase bacterial activity during short incubations (<5 h). With the dual-label method we found that thymidine and leucine incorporation rates covaried over depth profiles of the Chesapeake Bay. Estimates of bacterial production based on thymidine and leucine differed by less than 25%. Although the need for appropriate conversion factors has not been eliminated, the dual-label approach can be used to examine the variation in bacterial production while ensuring that the observed variation in incorporation rates is due to real changes in bacterial production rather than changes in conversion factors or introduction of other artifacts.

Regional Deformation Studies with GRACE and GPS

NASA Technical Reports Server (NTRS)

Davis, J. L.; Elosequi, P.; Tamisiea, M.; Mitrovica, J. X.

2005-01-01

GRACE data indicate large seasonal variations in gravity that have been shown to be to be related to climate-driven fluxes of surface water. Seasonal redistribution of surface mass deforms the Earth, and our previous study using GRACE data demonstrate that annual radial deformations of +/-13 mm in the region of Amazon River Basin were observed by both GRACE and ten GPS sites in the region. For the GRACE determinations, we estimate in a least-squares solution for each Stokes coefficient parameters that represent the amplitudes of the annual variation. We then filter these parameters based on a statistical test that uses the scatter of the postfit residuals. We demonstrate by comparison to the GPS amplitudes that this method is more accurate, for this region, than Gaussian smoothing. Our model for the temporal behavior of the gravity coefficients includes a rate term, and although the time series are noisy, the glacial isostatic adjustment signal over Hudson s Bay can be observed. .

Incident wave run-up into narrow sloping bays and estuaries

NASA Astrophysics Data System (ADS)

Sinan Özeren, M.; Postacioglu, Nazmi; Canlı, Umut

2015-04-01

The problem is investigated using Carrier Greenspan hodograph transformations.We perform a quasi-one-dimensional solution well into the bay, far enough of the mouth of the bay. The linearized boundary conditions at the mouth of the bay lead to an integral equation for 2-D geometry. A semi analytical optimization method has been developed to solve this integral equation. When the wavelength of the incident wave is much larger than the width of the bay, the conformalmapping of the bay and the semi infinite sea onto upper complex plane provides a solution of the integral equation in closed form. Particular emphasis is placed on the case where the frequency of the incident waves matches the real-part of the natural frequency of the oscillation of the bay. These natural frequencies are complex because of the radiation conditions imposed at the mouth of the bay. It is found that the complex part of these natural frequencies decreases with decreasing width of the bay. Thus the trapping of the waves in narrower bays leads to a strong resonance phenomenon when the frequency of the incident wave is equal to the real part of the natural frequency.

A numerical model investigation of the impacts of Hurricane Sandy on water level variability in Great South Bay, New York

USGS Publications Warehouse

Bennett, Vanessa C. C.; Mulligan, Ryan P.; Hapke, Cheryl J.

2018-01-01

Hurricane Sandy was a large and intense storm with high winds that caused total water levels from combined tides and storm surge to reach 4.0 m in the Atlantic Ocean and 2.5 m in Great South Bay (GSB), a back-barrier bay between Fire Island and Long Island, New York. In this study the impact of the hurricane winds and waves are examined in order to understand the flow of ocean water into the back-barrier bay and water level variations within the bay. To accomplish this goal, a high resolution hurricane wind field is used to drive the coupled Delft3D-SWAN hydrodynamic and wave models over a series of grids with the finest resolution in GSB. The processes that control water levels in the back-barrier bay are investigated by comparing the results of four cases that include: (i) tides only; (ii) tides, winds and waves with no overwash over Fire Island allowed; (iii) tides, winds, waves and limited overwash at the east end of the island; (iv) tides, winds, waves and extensive overwash along the island. The results indicate that strong local wind-driven storm surge along the bay axis had the largest influence on the total water level fluctuations during the hurricane. However, the simulations allowing for overwash have higher correlation with water level observations in GSB and suggest that island overwash provided a significant contribution of ocean water to eastern GSB during the storm. The computations indicate that overwash of 7500–10,000 m3s−1 was approximately the same as the inflow from the ocean through the major existing inlet. Overall, the model results indicate the complex variability in total water levels driven by tides, ocean storm surge, surge from local winds, and overwash that had a significant impact on the circulation in Great South Bay during Hurricane Sandy.

A numerical model investigation of the impacts of Hurricane Sandy on water level variability in Great South Bay, New York

NASA Astrophysics Data System (ADS)

Bennett, Vanessa C. C.; Mulligan, Ryan P.; Hapke, Cheryl J.

2018-06-01

Hurricane Sandy was a large and intense storm with high winds that caused total water levels from combined tides and storm surge to reach 4.0 m in the Atlantic Ocean and 2.5 m in Great South Bay (GSB), a back-barrier bay between Fire Island and Long Island, New York. In this study the impact of the hurricane winds and waves are examined in order to understand the flow of ocean water into the back-barrier bay and water level variations within the bay. To accomplish this goal, a high resolution hurricane wind field is used to drive the coupled Delft3D-SWAN hydrodynamic and wave models over a series of grids with the finest resolution in GSB. The processes that control water levels in the back-barrier bay are investigated by comparing the results of four cases that include: (i) tides only; (ii) tides, winds and waves with no overwash over Fire Island allowed; (iii) tides, winds, waves and limited overwash at the east end of the island; (iv) tides, winds, waves and extensive overwash along the island. The results indicate that strong local wind-driven storm surge along the bay axis had the largest influence on the total water level fluctuations during the hurricane. However, the simulations allowing for overwash have higher correlation with water level observations in GSB and suggest that island overwash provided a significant contribution of ocean water to eastern GSB during the storm. The computations indicate that overwash of 7500-10,000 m3s-1 was approximately the same as the inflow from the ocean through the major existing inlet. Overall, the model results indicate the complex variability in total water levels driven by tides, ocean storm surge, surge from local winds, and overwash that had a significant impact on the circulation in Great South Bay during Hurricane Sandy.

Bathymetry, substrate and circulation in Westcott Bay, San Juan Islands, Washington

USGS Publications Warehouse

Grossman, Eric E.; Stevens, Andrew W.; Curran, Chris; Smith, Collin; Schwartz, Andrew

2007-01-01

Nearshore bathymetry, substrate type, and circulation patterns in Westcott Bay, San Juan Islands, Washington, were mapped using two acoustic sonar systems, video and direct sampling of seafloor sediments. The goal of the project was to characterize nearshore habitat and conditions influencing eelgrass (Z. marina) where extensive loss has occurred since 1995. A principal hypothesis for the loss of eelgrass is a recent decrease in light availability for eelgrass growth due to increase in turbidity associated with either an increase in fine sedimentation or biological productivity within the bay. To explore sources for this fine sediment and turbidity, a dual-frequency Biosonics sonar operating at 200 and 430 kHz was used to map seafloor depth, morphology and vegetation along 69 linear kilometers of the bay. The higher frequency 430 kHz system also provided information on particulate concentrations in the water column. A boat-mounted 600 kHz RDI Acoustic Doppler Current Profiler (ADCP) was used to map current velocity and direction and water column backscatter intensity along another 29 km, with select measurements made to characterize variations in circulation with tides. An underwater video camera was deployed to ground-truth acoustic data. Seventy one sediment samples were collected to quantify sediment grain size distributions across Westcott Bay. Sediment samples were analyzed for grain size at the Western Coastal and Marine Geology Team sediment laboratory in Menlo Park, Calif. These data reveal that the seafloor near the entrance to Westcott Bay is rocky with a complex morphology and covered with dense and diverse benthic vegetation. Current velocities were also measured to be highest at the entrance and along a deep channel extending 1 km into the bay. The substrate is increasingly comprised of finer sediments with distance into Westcott Bay where current velocities are lower. This report describes the data collected and preliminary findings of USGS Cruise B-6-07-PS conducted between May 31, 2007 and June 5, 2007.

First Step Towards a Coastal Modelling System for South Africa: a St. Helena Bay Case Study

NASA Astrophysics Data System (ADS)

Collins, C.; Lamont, T.; Loveday, B. R.; Hermes, J. C.; Veitch, J.; Backeberg, B.

2016-02-01

St. Helena Bay, forming part of the southern Benguela ecosystem, is the largest bay on the west coast of South Africa and is a biologically important region for pelagic fish, hake, and rock lobster. To date, only a few infrequent studies have focussed on variations in the bay scale circulation. A monthly ship-based monitoring line, the St. Helena Bay Monitoring Line (SHBML), was initiated in 2000 to determine the seasonal changes in cross-shelf hydrography and biology. Even though there has been an increase in ocean modelling in and around South Africa in recent years, coastal modelling is still in its infancy. The 12-year observational data set in the St. Helena Bay region, the only long-term, cross-shelf, full water column data-set for South Africa, makes this area the perfect natural laboratory for the development of a coastal modelling system. In this study, the climatological mean temperature and salinity from three different ROMS simulations and a HYCOM simulation are evaluated against the in situ observations from the SHBML with the aim of determining the influence of different forcing products, horizontal and vertical resolution as well as vertical coordinate schemes on the vertical structure of the ocean. The model simulations tend to overestimate the temperature and salinity across the shelf, and particularly within St. Helena Bay. Furthermore, the models misrepresent the vertical salinity and temperature structures. Interestingly, below 800m, there is a better agreement between temperature in the models and the in-situ observations. This is the first detailed comparison of modelled and in-situ data for the greater St. Helena Bay area at this scale and the next phase will examine whether the model that is most congruent with the observations resolves the same interannual signals as observed in the in-situ data.

The role of surface and subsurface processes in keeping pace with sea level rise in intertidal wetlands of Moreton Bay, Queensland, Australia

USGS Publications Warehouse

Lovelock, Catherine E.; Bennion, Vicki; Grinham, Alistair; Cahoon, Donald R.

2011-01-01

Increases in the elevation of the soil surfaces of mangroves and salt marshes are key to the maintenance of these habitats with accelerating sea level rise. Understanding the processes that give rise to increases in soil surface elevation provides science for management of landscapes for sustainable coastal wetlands. Here, we tested whether the soil surface elevation of mangroves and salt marshes in Moreton Bay is keeping up with local rates of sea level rise (2.358 mm y-1) and whether accretion on the soil surface was the most important process for keeping up with sea level rise. We found variability in surface elevation gains, with sandy areas in the eastern bay having the highest surface elevation gains in both mangrove and salt marsh (5.9 and 1.9 mm y-1) whereas in the muddier western bay rates of surface elevation gain were lower (1.4 and -0.3 mm y-1 in mangrove and salt marsh, respectively). Both sides of the bay had similar rates of surface accretion (~7–9 mm y-1 in the mangrove and 1–3 mm y-1 in the salt marsh), but mangrove soils in the western bay were subsiding at a rate of approximately 8 mm y-1, possibly due to compaction of organic sediments. Over the study surface elevation increments were sensitive to position in the intertidal zone (higher when lower in the intertidal) and also to variation in mean sea level (higher at high sea level). Although surface accretion was the most important process for keeping up with sea level rise in the eastern bay, subsidence largely negated gains made through surface accretion in the western bay indicating a high vulnerability to sea level rise in these forests.

Experience of mixed-sex bays in a general hospital.

PubMed

Bryant, Debbie; Adams, John

To explore patients' and nurses' views on their experience of nursing care in mixed-sex bays. Using a descriptive exploratory method, tape-recorded semi-structured interviews were conducted with a purposive sample of patients and nurses drawn from wards where mixed-sex bays were located. The resulting transcripts were analysed to identify shared themes. The key themes identified were: communication from nursing staff, first reactions, relationships in the bay, reactions of others, awareness of organisational issues and nursing in a mixed-sex ward. While some individuals felt that the attitudes and behaviours displayed by their fellow patients were of greater significance than their gender, there was a general view that mixed-sex bays were less than ideal. Nurses also struggled to maintain patient dignity in mixed-sex bays.

Study on bayes discriminant analysis of EEG data.

PubMed

Shi, Yuan; He, DanDan; Qin, Fang

2014-01-01

In this paper, we have done Bayes Discriminant analysis to EEG data of experiment objects which are recorded impersonally come up with a relatively accurate method used in feature extraction and classification decisions. In accordance with the strength of α wave, the head electrodes are divided into four species. In use of part of 21 electrodes EEG data of 63 people, we have done Bayes Discriminant analysis to EEG data of six objects. Results In use of part of EEG data of 63 people, we have done Bayes Discriminant analysis, the electrode classification accuracy rates is 64.4%. Bayes Discriminant has higher prediction accuracy, EEG features (mainly αwave) extract more accurate. Bayes Discriminant would be better applied to the feature extraction and classification decisions of EEG data.

Pathogenicity variation in two west coast forest Phytophthoras, Phytophthora nemorosa and P. pseudosyringae, to bay laurel

Treesearch

R.E. Linzer; M. Garbelotto

2008-01-01

Two recently described pathogenic oomycetes, Phytophthora nemorosa and P. pseudosyringae, have overlapping host and geographic ranges in California and Oregon forests with P. ramorum, causal agent of ?sudden oak death? disease. Preliminary genetic evidence indicates P. nemorosa and P....

ESTUARINE PHYTOPLANKTON PRIMARY PRODUCTION AND SIZE AS DETERMINED REMOTELY FROM AIRCRAFT AND COASTAL OBSERVATION

EPA Science Inventory

We used remotely sensed estimates of chlorophyll a and sea surface temperature, incorporated into the Chesapeake Bay Productivity Model (Harding et al., 2002), to estimate the spatial and temporal variation of phytoplankton net primary production and species size in the Narragans...

Relative contributions of external forcing factors to circulation and hydrographic properties in a micro-tidal bay

NASA Astrophysics Data System (ADS)

Yoon, Seokjin; Kasai, Akihide

2017-11-01

The dominant external forcing factors influencing estuarine circulation differ among coastal environments. A three-dimensional regional circulation model was developed to estimate external influence indices and relative contributions of external forcing factors such as external oceanic forcing, surface heat flux, wind stress, and river discharge to circulation and hydrographic properties in Tango Bay, Japan. Model results show that in Tango Bay, where the Tsushima Warm Current passes offshore of the bay, under conditions of strong seasonal winds and river discharge, the water temperature and salinity are strongly influenced by surface heat flux and river discharge in the surface layer, respectively, while in the middle and bottom layers both are mainly controlled by open boundary conditions. The estuarine circulation is comparably influenced by all external forcing factors, the strong current, surface heat flux, wind stress, and river discharge. However, the influence degree of each forcing factor varies with temporal variations in external forcing factors as: the influence of open boundary conditions is higher in spring and early summer when the stronger current passes offshore of the bay, that of surface heat flux reflects the absolute value of surface heat flux, that of wind stress is higher in late fall and winter due to strong seasonal winds, and that of river discharge is higher in early spring due to snow-melting and summer and early fall due to flood events.

Effect of temperature and salinity on phosphate sorption on marine sediments.

PubMed

Zhang, Jia-Zhong; Huang, Xiao-Lan

2011-08-15

Our previous studies on the phosphate sorption on sediments in Florida Bay at 25 °C in salinity 36 seawater revealed that the sorption capacity varies considerably within the bay but can be attributed to the content of sedimentary P and Fe. It is known that both temperature and salinity influence the sorption process and their natural variations are the greatest in estuaries. To provide useful sorption parameters for modeling phosphate cycle in Florida Bay, a systematic study was carried out to quantify the effects of salinity and temperature on phosphate sorption on sediments. For a given sample, the zero equilibrium phosphate concentration and the distribution coefficient were measured over a range of salinity (2-72) and temperature (15-35 °C) conditions. Such a suite of experiments with combinations of different temperature and salinity were performed for 14 selected stations that cover a range of sediment characteristics and geographic locations of the bay. Phosphate sorption was found to increase with increasing temperature or decreasing salinity and their effects depended upon sediment's exchangeable P content. This study provided the first estimate of the phosphate sorption parameters as a function of salinity and temperature in marine sediments. Incorporation of these parameters in water quality models will enable them to predict the effect of increasing freshwater input, as proposed by the Comprehensive Everglades Restoration Plan, on the seasonal cycle of phosphate in Florida Bay.

Distribution and spawning dynamics of capelin (Mallotus villosus) in Glacier Bay, Alaska: A cold water refugium

USGS Publications Warehouse

Arimitsu, Mayumi L.; Piatt, John F.; Litzow, Michael A.; Abookire, Alisa A.; Romano, Marc D.; Robards, Martin D.

2008-01-01

Pacific capelin (Mallotus villosus) populations declined dramatically in the Northeastern Pacific following ocean warming after the regime shift of 1977, but little is known about the cause of the decline or the functional relationships between capelin and their environment. We assessed the distribution and abundance of spawning, non-spawning adult and larval capelin in Glacier Bay, an estuarine fjord system in southeastern Alaska. We used principal components analysis to analyze midwater trawl and beach seine data collected between 1999 and 2004 with respect to oceanographic data and other measures of physical habitat including proximity to tidewater glaciers and potential spawning habitat. Both spawning and non-spawning adult Pacific capelin were more likely to occur in areas closest to tidewater glaciers, and those areas were distinguished by lower temperature, higher turbidity, higher dissolved oxygen and lower chlorophyll a levels when compared with other areas of the bay. The distribution of larval Pacific capelin was not sensitive to glacial influence. Pre-spawning females collected farther from tidewater glaciers were at a lower maturity state than those sampled closer to tidewater glaciers, and the geographic variation in the onset of spawning is likely the result of differences in the marine habitat among sub-areas of Glacier Bay. Proximity to cold water in Glacier Bay may have provided a refuge for capelin during the recent warm years in the Gulf of Alaska.

An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans.

PubMed

Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B

2006-08-01

Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.

Oyster Reef Communities in the Chesapeake Bay. Virginia Institute of Marine Science Educational Series. [CD-ROM].

ERIC Educational Resources Information Center

Harding, Juliana M.; Mann, Roger; Clark, Vicki P.

This CD-ROM, Oyster Reef Communities in the Chesapeake Bay, describes oyster reefs, reef communities, and their roles in the Chesapeake Bay ecosystem. Detailed descriptions of scientific research methods and techniques used to monitor and describe oyster reef communities as well as applications of the resulting data are provided. The CD-ROM was…

How does ocean seasonality drive habitat preferences of highly mobile top predators? Part II: The eastern North-Atlantic

NASA Astrophysics Data System (ADS)

Lambert, C.; Pettex, E.; Dorémus, G.; Laran, S.; Stéphan, E.; Canneyt, O. Van; Ridoux, V.

2017-07-01

Marine ecosystems are characterised by strong heterogeneity and variability, both spatially and temporally. In particular, seasonal variations may lead to severe constraints for predators which have to cope with these variations, for example through migration to avoid unfavourable seasons, or adaptation to local modification of the ecosystem. In the Bay of Biscay and English Channel, ecosystem seasonality is well marked, especially over the shelf. Cetacean and seabird communities within the Bay of Biscay, Celtic Sea and English Channel were studied during aerial surveys conducted in winter 2011-2012 and summer 2012, following a strip-transect methodology deployed from the coast to oceanic waters. We explored seasonal variations of habitat preferences of four cetacean and six seabird groups through Generalised Additive Models, using physiographic variables and weekly- and monthly-averaged oceanographic predictors for both seasons. Our results provided the first overview at such a large scale of the variation of habitat preferences in response to the seasonality of the ocean by seabirds in that region, at such a large scale. Habitat models resulted in explained deviances from 13 to 55%. Predators answered the seasonality of their environment in different ways. Long-finned pilot whales and Risso's dolphins were the only studied group exhibiting no habitat variations between seasons, targeting the shelf break throughout the year. The other groups modulated their habitat preferences between seasons to optimise the compromise between the ocean seasonal variations and their own constraints: common and striped dolphins, bottlenose dolphins and harbour porpoises for cetaceans; northern gannets, auks, northern fulmars and kittiwakes for seabirds. For shearwaters, the seasonality had an extreme impact, inducing a complete absence from the region during the unfavourable season.

LINKING JUVENILE FISH AND THEIR HABITATS: AN EXAMPLE FROM NARRAGANSETT BAY ,RHODE ISLAND

EPA Science Inventory

We used two methods and existing field survey data to link juvenile fish and their habitats. The first method used seine survey data collected monthly from July to October 1988-1996 at fixed stations in Narragansett Bay, Rhode Island. Thirteen fish species making up 1% or more of...

Using Loss Functions for DIF Detection: An Empirical Bayes Approach.

ERIC Educational Resources Information Center

Zwick, Rebecca; Thayer, Dorothy; Lewis, Charles

2000-01-01

Studied a method for flagging differential item functioning (DIF) based on loss functions. Builds on earlier research that led to the development of an empirical Bayes enhancement to the Mantel-Haenszel DIF analysis. Tested the method through simulation and found its performance better than some commonly used DIF classification systems. (SLD)

Virioplankton dynamics are related to eutrophication levels in a tropical urbanized bay

PubMed Central

Cabral, Anderson S.; Lessa, Mariana M.; Junger, Pedro C.; Thompson, Fabiano L.; Paranhos, Rodolfo

2017-01-01

Virioplankton are an important and abundant biological component of marine and freshwater ecosystems. Often overlooked, aquatic viruses play an important role in biogeochemical cycles on a global scale, infecting both autotrophic and heterotrophic microbes. Viral diversity, abundance, and viral interactions at different trophic levels in aqueous environments are not well understood. Tropical ecosystems are less frequently studied than temperate ecosystems, but could provide new insights into how physical and chemical variability can shape or force microbial community changes. In this study, we found high viral abundance values in Guanabara Bay relative to other estuaries around the world. Viral abundance was positively correlated with bacterioplankton abundance and chlorophyll a concentrations. Moreover, prokaryotic and viral abundance were positively correlated with eutrophication, especially in surface waters. These results provide novel baseline data on the quantitative distribution of aquatic viruses in tropical estuaries. They also provide new information on a complex and dynamic relationship in which environmental factors influence the abundance of bacterial hosts and consequently their viruses. Guanabara Bay is characterized by spatial and seasonal variations, and the eutrophication process is the most important factor explaining the structuring of virioplankton abundance and distribution in this tropical urbanized bay. PMID:28362842

Greenland coastal air temperatures linked to Baffin Bay and Greenland Sea ice conditions during autumn through regional blocking patterns

NASA Astrophysics Data System (ADS)

Ballinger, Thomas J.; Hanna, Edward; Hall, Richard J.; Miller, Jeffrey; Ribergaard, Mads H.; Høyer, Jacob L.

2018-01-01

Variations in sea ice freeze onset and regional sea surface temperatures (SSTs) in Baffin Bay and Greenland Sea are linked to autumn surface air temperatures (SATs) around coastal Greenland through 500 hPa blocking patterns, 1979-2014. We find strong, statistically significant correlations between Baffin Bay freeze onset and SSTs and SATs across the western and southernmost coastal areas, while weaker and fewer significant correlations are found between eastern SATs, SSTs, and freeze periods observed in the neighboring Greenland Sea. Autumn Greenland Blocking Index values and the incidence of meridional circulation patterns have increased over the modern sea ice monitoring era. Increased anticyclonic blocking patterns promote poleward transport of warm air from lower latitudes and local warm air advection onshore from ocean-atmosphere sensible heat exchange through ice-free or thin ice-covered seas bordering the coastal stations. Temperature composites by years of extreme late freeze conditions, occurring since 2006 in Baffin Bay, reveal positive monthly SAT departures that often exceed 1 standard deviation from the 1981-2010 climate normal over coastal areas that exhibit a similar spatial pattern as the peak correlations.

Paleomagnetic investigation of late Quaternary sediments of south San Francisco Bay, California

USGS Publications Warehouse

Hillhouse, John W.

1977-01-01

Paleomagnetic inclinations of the Late Quaternary sediments of South San Francisco Bay were determined from bore hole samples collected near Dumbarton Bridge. The sediments consist of estuarine muds and nonmarine sand deposits, floored by bedrock of the Mesozoic Franciscan Formation. - Beneath Dumbarton Bridge the entire sedimentary fill is normally polarized; therefore, the fill postdates the Brunhes-Matayama polarity reversal (700,000 y. B.P.). Magnetic time lines such as the Mono Lake excursion (24,000 y. B.P.) and the reversed Blake event (110,000 y B.P.) were not found in this bore hole. In addition to Holocene and modern deposits of San Francisco Bay, an older estuarine unit occurs in the stratigraphic section. The older unit was deposited during a period of high sea level, tentatively correlated with the Sangamon interglacial period. Because evidence of the Blake event is not present in the older estuarine unit, the proposed age of this unit could not be confirmed. Although the Holocene estuarine deposits of South San Francisco Bay carry stable remanent magnetization, a reliable record of geomagnetic secular variation could not be recovered because the water-saturated sdiment was deformed by drilling.

Human and riverine impacts on the dynamics of seawater nutrient and carbon parameters in Kwangyang Bay, South Korea

NASA Astrophysics Data System (ADS)

Kim, Tae-Wook; Kim, Dongseon; Baek, Seung Ho; Kim, Young Ok

2015-04-01

We investigated seawater nutrient and carbon parameters in Kwangyang Bay, South Korea, which has been exposed to significant human influences, in each core month of four seasons for between 2010 and 2012. The survey data were analyzed using multivariate statistics analysis (cluster and factor analysis). As a result, we found that the Seomjin River (the fifth largest river in South Korea) and biological activity, including phytoplankton photosynthesis and bacterial decomposition, were the main factors determining the overall water quality of the bay. However, the impacts of these factors varied both spatially and seasonally, because the factors were linked with the geographical environments and seasonal variations in freshwater discharge. In particular, the Seomjin River was primarily responsible for nitrate, silicate, total alkalinity, and dissolved inorganic carbon, and exhibited a significant impact in the summer. During the past 10 years, nutrient loads from the river and industrial complexes to the bay have decreased. The impacts of this decrease are visible in the phosphate concentration, which has fallen to a third of its initial value. We also examined the potential role of atmospheric nitrogen deposition in nitrogen cycling in the study area.

Diagnostic modeling of trace metal partitioning in south San Francisco Bay

USGS Publications Warehouse

Wood, T. W.; Baptista, A. M.; Kuwabara, J.S.; Flegal, A.R.

1995-01-01

The numerical results indicate that aqueous speciation will control basin-scale spatial variations in the apparent distribution coefficient, Kda, if the system is close to equilibrium. However, basin-scale spatial variations in Kda are determined by the location of the sources of metal and the suspended solids concentration of the receiving water if the system is far from equilibrium. The overall spatial variability in Kda also increases as the system moves away from equilibrium.

Inherent and apparent optical properties of the complex estuarine waters of Tampa Bay: What controls light?

NASA Astrophysics Data System (ADS)

Le, Chengfeng; Hu, Chuanmin; English, David; Cannizzaro, Jennifer; Chen, Zhiqiang; Kovach, Charles; Anastasiou, Christopher J.; Zhao, Jun; Carder, Kendall L.

2013-01-01

Inherent and apparent optical properties (IOPs and AOPs) of Tampa Bay (Florida, USA) were measured during fourteen cruises between February 1998 and October 2010 to understand how these properties relate to one another and what controls light absorption and diffuse attenuation in this moderately sized (˜1000 km2), shallow estuary (average depth ˜4 m). The IOPs and AOPs included: 1) absorption coefficients of three optically significant constituents: phytoplankton pigments, detrital particles, and colored dissolved organic matter (CDOM); 2) particulate backscattering coefficients; 3) chlorophyll-a concentrations; 4) above-water remote sensing reflectance; 5) downwelling diffuse attenuation coefficients (Kd) at eight wavelengths and photosynthetically active radiation (PAR). Results showed substantial variability in all IOPs and AOPs in both space and time, with most IOPs spanning more than two orders of magnitude and showing strong co-variations. Of all four bay segments, Old Tampa Bay showed unique optical characteristics. During the wet season, the magnitude of blue-green-light absorption was dominated by CDOM, while during the dry season all three constituents contributed significantly. However, the variability in Kd (PAR, 490 nm, 555 nm) was driven mainly by the variability of detrital particles and phytoplankton as opposed to CDOM. This observation explained, at least to first order, why a nutrient reduction management strategy used by the Tampa Bay Estuary Program since the 1990s led to improved water clarity in most of Tampa Bay. The findings of this study provided the optical basis to fine tune existing or develop new algorithms to estimate the various optical water quality parameters from space.

Assessing the suitability of benthic foraminiferal morpho-groups to reconstruct paleomonsoon from Bay of Bengal

NASA Astrophysics Data System (ADS)

Manasa, M.; Saraswat, Rajeev; Nigam, Rajiv

2016-04-01

Temporal changes in benthic foraminiferal morpho-groups were suggested as an effective proxy to reconstruct past monsoon intensity from the Arabian Sea. Here, in order to test the applicability of temporal variation in morpho-groups to reconstruct past monsoon intensity from the Bay of Bengal, we have documented recent benthic foraminiferal distribution from the continental shelf region of the northwestern Bay of Bengal. Based on the external morphology, benthic foraminifera were categorized into rounded symmetrical (RSBF) and angular asymmetrical benthic foraminifera (AABF). Additionally, a few other dominant groups were also identified based on test composition (agglutinated, calcareous) and abundance (Asterorotalids and Nonions). The relative abundance of each group was compared with the ambient physico-chemical conditions, including dissolved oxygen, organic matter, salinity and temperature. We report that the RSBF are abundant in comparatively warm and well oxygenated waters of low salinity, suggesting a preference for high energy environment, whereas AABF dominate relatively cold, hypersaline deeper waters with low dissolved oxygen, indicating a low energy environment. The agglutinated foraminifera, Asterorotalids and Nonions dominate shallow water, low salinity regions, whereas the calcareous benthic foraminiferal abundance increases away from the riverine influx regions. Food availability, as estimated from organic carbon abundance in sediments, has comparatively less influence on faunal distribution in the northwestern Bay of Bengal, as compared to dissolved oxygen, temperature and salinity. We conclude that the factors associated with freshwater influx affect the distribution of benthic foraminiferal morpho-groups in the northwestern Bay of Bengal and thus it can be used to reconstruct past monsoon intensity from the Bay of Bengal.

Discontinuous hindcast simulations of estuarine bathymetric change: A case study from Suisun Bay, California

USGS Publications Warehouse

Ganju, Neil K.; Jaffe, Bruce E.; Schoellhamer, David H.

2011-01-01

Simulations of estuarine bathymetric change over decadal timescales require methods for idealization and reduction of forcing data and boundary conditions. Continuous simulations are hampered by computational and data limitations and results are rarely evaluated with observed bathymetric change data. Bathymetric change data for Suisun Bay, California span the 1867–1990 period with five bathymetric surveys during that period. The four periods of bathymetric change were modeled using a coupled hydrodynamic-sediment transport model operated at the tidal-timescale. The efficacy of idealization techniques was investigated by discontinuously simulating the four periods. The 1867–1887 period, used for calibration of wave energy and sediment parameters, was modeled with an average error of 37% while the remaining periods were modeled with error ranging from 23% to 121%. Variation in post-calibration performance is attributed to temporally variable sediment parameters and lack of bathymetric and configuration data for portions of Suisun Bay and the Delta. Modifying seaward sediment delivery and bed composition resulted in large performance increases for post-calibration periods suggesting that continuous simulation with constant parameters is unrealistic. Idealization techniques which accelerate morphological change should therefore be used with caution in estuaries where parameters may change on sub-decadal timescales. This study highlights the utility and shortcomings of estuarine geomorphic models for estimating past changes in forcing mechanisms such as sediment supply and bed composition. The results further stress the inherent difficulty of simulating estuarine changes over decadal timescales due to changes in configuration, benthic composition, and anthropogenic forcing such as dredging and channelization.

Process-based, morphodynamic hindcast of decadal deposition patterns in San Pablo Bay, California, 1856-1887

USGS Publications Warehouse

van der Wegen, M.; Jaffe, B.E.; Roelvink, J.A.

2011-01-01

This study investigates the possibility of hindcasting-observed decadal-scale morphologic change in San Pablo Bay, a subembayment of the San Francisco Estuary, California, USA, by means of a 3-D numerical model (Delft3D). The hindcast period, 1856-1887, is characterized by upstream hydraulic mining that resulted in a high sediment input to the estuary. The model includes wind waves, salt water and fresh water interactions, and graded sediment transport, among others. Simplified initial conditions and hydrodynamic forcing were necessary because detailed historic descriptions were lacking. Model results show significant skill. The river discharge and sediment concentration have a strong positive influence on deposition volumes. Waves decrease deposition rates and have, together with tidal movement, the greatest effect on sediment distribution within San Pablo Bay. The applied process-based (or reductionist) modeling approach is valuable once reasonable values for model parameters and hydrodynamic forcing are obtained. Sensitivity analysis reveals the dominant forcing of the system and suggests that the model planform plays a dominant role in the morphodynamic development. A detailed physical explanation of the model outcomes is difficult because of the high nonlinearity of the processes. Process formulation refinement, a more detailed description of the forcing, or further model parameter variations may lead to an enhanced model performance, albeit to a limited extent. The approach potentially provides a sound basis for prediction of future developments. Parallel use of highly schematized box models and a process-based approach as described in the present work is probably the most valuable method to assess decadal morphodynamic development. Copyright ?? 2011 by the American Geophysical Union.

Water resources planning for rivers draining into Mobile Bay

NASA Technical Reports Server (NTRS)

April, G. C.

1976-01-01

The application of remote sensing, automatic data processing, modeling and other aerospace related technologies to hydrological engineering and water resource management are discussed for the entire river drainage system which feeds the Mobile Bay estuary. The adaptation and implementation of existing mathematical modeling methods are investigated for the purpose of describing the behavior of Mobile Bay. Of particular importance are the interactions that system variables such as river flow rate, wind direction and speed, and tidal state have on the water movement and quality within the bay system.

Bayesian regression models outperform partial least squares methods for predicting milk components and technological properties using infrared spectral data.

PubMed

Ferragina, A; de los Campos, G; Vazquez, A I; Cecchinato, A; Bittante, G

2015-11-01

The aim of this study was to assess the performance of Bayesian models commonly used for genomic selection to predict "difficult-to-predict" dairy traits, such as milk fatty acid (FA) expressed as percentage of total fatty acids, and technological properties, such as fresh cheese yield and protein recovery, using Fourier-transform infrared (FTIR) spectral data. Our main hypothesis was that Bayesian models that can estimate shrinkage and perform variable selection may improve our ability to predict FA traits and technological traits above and beyond what can be achieved using the current calibration models (e.g., partial least squares, PLS). To this end, we assessed a series of Bayesian methods and compared their prediction performance with that of PLS. The comparison between models was done using the same sets of data (i.e., same samples, same variability, same spectral treatment) for each trait. Data consisted of 1,264 individual milk samples collected from Brown Swiss cows for which gas chromatographic FA composition, milk coagulation properties, and cheese-yield traits were available. For each sample, 2 spectra in the infrared region from 5,011 to 925 cm(-1) were available and averaged before data analysis. Three Bayesian models: Bayesian ridge regression (Bayes RR), Bayes A, and Bayes B, and 2 reference models: PLS and modified PLS (MPLS) procedures, were used to calibrate equations for each of the traits. The Bayesian models used were implemented in the R package BGLR (http://cran.r-project.org/web/packages/BGLR/index.html), whereas the PLS and MPLS were those implemented in the WinISI II software (Infrasoft International LLC, State College, PA). Prediction accuracy was estimated for each trait and model using 25 replicates of a training-testing validation procedure. Compared with PLS, which is currently the most widely used calibration method, MPLS and the 3 Bayesian methods showed significantly greater prediction accuracy. Accuracy increased in moving from calibration to external validation methods, and in moving from PLS and MPLS to Bayesian methods, particularly Bayes A and Bayes B. The maximum R(2) value of validation was obtained with Bayes B and Bayes A. For the FA, C10:0 (% of each FA on total FA basis) had the highest R(2) (0.75, achieved with Bayes A and Bayes B), and among the technological traits, fresh cheese yield R(2) of 0.82 (achieved with Bayes B). These 2 methods have proven to be useful instruments in shrinking and selecting very informative wavelengths and inferring the structure and functions of the analyzed traits. We conclude that Bayesian models are powerful tools for deriving calibration equations, and, importantly, these equations can be easily developed using existing open-source software. As part of our study, we provide scripts based on the open source R software BGLR, which can be used to train customized prediction equations for other traits or populations. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Current temporal asymmetry and the role of tides: Nan-Wan Bay vs. the Gulf of Elat

NASA Astrophysics Data System (ADS)

Ashkenazy, Yosef; Fredj, Erick; Gildor, Hezi; Gong, Gwo-Ching; Lee, Hung-Jen

2016-05-01

Nan-Wan Bay in Taiwan and the Gulf of Elat in Israel are two different coastal environments, and as such, their currents are expected to have different statistical properties. While Nan-Wan Bay is shallow, has three open boundaries, and is directly connected to the open ocean, the Gulf of Elat is deep, semi-enclosed, and connected to the Red Sea via the Straits of Tiran. Surface currents have been continuously measured with fine temporal (less than or equal to 1 h) and spatial resolution (less than or equal to 1 km) for more than a year in both environments using coastal radars (CODARs) that cover a domain of roughly 10 × 10 km. These measurements show that the currents in Nan-Wan Bay are much stronger than those in the Gulf of Elat and that the mean current field in Nan-Wan Bay exhibits cyclonic circulation, which is stronger in the summer; in the Gulf of Elat, the mean current field is directed southward and is also stronger during the summer. We have compared the statistical properties of the current speeds in both environments and found that both exhibit large spatial and seasonal variations in the shape parameter of the Weibull distribution. However, we have found fundamental and significant differences when comparing the temporal asymmetry of the current speed (i.e., the ratio between the time during which the current speed increases and the total time). While the Nan-Wan Bay currents are significantly asymmetric, those of the Gulf of Elat are not. We then extracted the tidal component of the Nan-Wan Bay currents and found that it is strongly asymmetric, while the asymmetry of tidally filtered currents is much weaker. We thus conclude that the temporal asymmetry of the Nan-Wan Bay currents reported here is due to the strong tides in the region. We show that the asymmetry ratio in Nan-Wan Bay varies spatially and seasonally: (i) the currents increase rapidly and decay slowly in the northern part of the domain and vice versa in the southern part, and (ii) the asymmetry is stronger during summer.

Current temporal asymmetry and the role of tides: Nan-Wan Bay vs. the Gulf of Elat

NASA Astrophysics Data System (ADS)

Ashkenazy, Y.; Fredj, E.; Gildor, H.; Gong, G. C.; Lee, H. J.; Wu, C. R.

2016-02-01

Nan-Wan Bay in Taiwan and the Gulf of Elat in Israel are two different coastal environments and as such are expected to have different statistical properties of their currents. While the Nan-Wan Bay is shallow, has three open boundaries, and directly connected to the open ocean, the Gulf of Elat is deep, semi-enclosed, and connected to the Red Sea via the Straits of Tiran. High temporal (less or equal one hour) and spatial (less or equal one km) surface currents have been measured continuously for more than a year in both environments using Coastal Radars (CODARs) that cover a domain of roughly 10×10 kms. These measurements show that the currents in Nan-Wan Bay are much stronger than those in the Gulf of Elat and that the mean current field in Nan-Wan Bay exhibits cyclonic circulation, which is stronger in the summer; in the Gulf of Elat the mean current field is directed to south and is stronger during the summer. We have compared the statistical properties of the CODAR current speeds in both environments and found that both exhibit large spatial and seasonal variations in the shape parameter of the Weibull distribution. However, we have found fundamental and significant differences when comparing the temporal asymmetry of the current speed (i.e., the ratio between the time during which the current speed is increasing to the total time). While the Nan-Wan Bay currents are significantly asymmetric, those of the Gulf of Elat are not significantly asymmetric. We then extracted the tidal component of the Nan-Wan Bay currents and found that it is strongly asymmetric while the asymmetry of tidally-filtered currents is much weaker. We thus conclude that the temporal asymmetry of the Nan-Wan Bay currents reported here is due to the strong tides in the region. We show that the asymmetry ratio in the Nan-Wan Bay is varied spatially and seasonally: (i) currents increase rapidly and decay slowly in the northern part of the domain and vice versa in the southern part, and that (ii) the asymmetry is stronger during summer.

Seasonal/Yearly Salinity Variations in San Francisco Bay

USGS Publications Warehouse

Peterson, David H.; Cayan, Daniel R.; Dettinger, Michael D.; DiLeo, Jeanne Sandra; Hager, Stephen E.; Knowles, Noah; Nichols, Frederic H.; Schemel, Laurence E.; Smith, Richard E.; Uncles, Reginald J.

1995-01-01

The ability of resource agencies to manage fish, wildlife and freshwater supplies of San Francisco Bay estuary requires an integrated knowledge of the relations between the biota and their physical environment. A key factor in these relations is the role of salinity in determining both the physical and the biological character of the estuary. The saltiness of the water, and particularly its seasonal and interannual patterns of variability, affects which aquatic species live where within the estuary. Salinity also determines where water can and cannot be diverted for human consumption and irrigated agriculture, and plays a role in determining the capacity of the estuary to cleanse itself of wastes. In short, salinity is a fundamental property of estuarine physics and chemistry that, in turn, determines the biological characteristics of each estuary. Freshwater is a major control on estuarine salinity. Most freshwater supplied to the Bay is from river flow through the Delta, which is primarily runoff from the Sierra Nevada. Most contaminants in San Francisco Bay are from the Sacramento/San Joaquin Valley and the local watershed around the Bay rather than the sea or atmosphere. Land is the primary source of freshwater and freshwater serves as a tracer of land-derived substances such as the trace metals (copper, lead and selenium), pesticides and plant nutrients (nitrate and phosphate). The U.S. Geological Survey is collaborating with other agencies and institutions in studying San Francisco Bay salinity using field observations and numerical simulations to define the physical processes that control salinity. The issues that arise from salinity fluctuations, however, differ in the northern and southern parts of the bay. In North Bay we need to know how salinity responds to freshwater flow through the Sacramento/San Joaquin Delta; this knowledge will benefit water managers who determine how much delta flow is needed a) to protect freshwater supplies for municipal water use and b) modulate salinity for a healthy estuary. In South Bay we need to know where the freshwater comes from (the distant Delta or local streams) to sort out the sources of a) contamination or b) dilution.

Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. II: Multivariate spike and slab priors for marker effects and derivation of approximate Bayes and fractional Bayes factors for the complete family of models.

PubMed

Martínez, Carlos Alberto; Khare, Kshitij; Banerjee, Arunava; Elzo, Mauricio A

2017-03-21

This study corresponds to the second part of a companion paper devoted to the development of Bayesian multiple regression models accounting for randomness of genotypes in across population genome-wide prediction. This family of models considers heterogeneous and correlated marker effects and allelic frequencies across populations, and has the ability of considering records from non-genotyped individuals and individuals with missing genotypes in any subset of loci without the need for previous imputation, taking into account uncertainty about imputed genotypes. This paper extends this family of models by considering multivariate spike and slab conditional priors for marker allele substitution effects and contains derivations of approximate Bayes factors and fractional Bayes factors to compare models from part I and those developed here with their null versions. These null versions correspond to simpler models ignoring heterogeneity of populations, but still accounting for randomness of genotypes. For each marker loci, the spike component of priors corresponded to point mass at 0 in R S , where S is the number of populations, and the slab component was a S-variate Gaussian distribution, independent conditional priors were assumed. For the Gaussian components, covariance matrices were assumed to be either the same for all markers or different for each marker. For null models, the priors were simply univariate versions of these finite mixture distributions. Approximate algebraic expressions for Bayes factors and fractional Bayes factors were found using the Laplace approximation. Using the simulated datasets described in part I, these models were implemented and compared with models derived in part I using measures of predictive performance based on squared Pearson correlations, Deviance Information Criterion, Bayes factors, and fractional Bayes factors. The extensions presented here enlarge our family of genome-wide prediction models making it more flexible in the sense that it now offers more modeling options. Copyright © 2017 Elsevier Ltd. All rights reserved.

Variation in tidal wetland plant diversity and composition within and among coastal estuaries: assessing the relative importance of environmental gradients

EPA Science Inventory

Question: Does wetland plant composition vary more by estuarine type (differentiated by the degree of riverine versus oceanic influence) or habitat type within estuaries (defined by US National Wetlands Inventory [NWI] marsh classes)? Location: Oregon estuaries: Netarts Bay, ...

INDICATORS OF CHANGE IN MID-ATLANTIC WATERSHEDS, AND CONSEQUENCES IN UPPER CHESAPEAKE BAY

EPA Science Inventory

The rate of change of atmospheric temperature in the Northern Hemisphere in the past century relative to the preceding millennium strongly suggests that we are in a period of rapid global climate change. The mid-Atlantic region is quite sensitive to larger-scale climate variation...

Mass spectrometric characterization of the hypoxia-inducible factor (HIF) stabilizer drug candidate BAY 85-3934 (molidustat) and its glucuronidated metabolite BAY-348, and their implementation into routine doping controls.

PubMed

Dib, Josef; Mongongu, Cynthia; Buisson, Corinne; Molina, Adeline; Schänzer, Wilhelm; Thuss, Uwe; Thevis, Mario

2017-01-01

The development of new therapeutics potentially exhibiting performance-enhancing properties implicates the risk of their misuse by athletes in amateur and elite sports. Such drugs necessitate preventive anti-doping research for consideration in sports drug testing programmes. Hypoxia-inducible factor (HIF) stabilizers represent an emerging class of therapeutics that allows for increasing erythropoiesis in patients. BAY 85-3934 is a novel HIF stabilizer, which is currently undergoing phase-2 clinical trials. Consequently, the comprehensive characterization of BAY 85-3934 and human urinary metabolites as well as the implementation of these analytes into routine doping controls is of great importance. The mass spectrometric behaviour of the HIF stabilizer drug candidate BAY 85-3934 and a glucuronidated metabolite (BAY-348) were characterized by electrospray ionization-(tandem) mass spectrometry (ESI-MS(/MS)) and multiple-stage mass spectrometry (MS n ). Subsequently, two different laboratories established different analytical approaches (one each) enabling urine sample analyses by employing either direct urine injection or solid-phase extraction. The methods were cross-validated for the metabolite BAY-348 that is expected to represent an appropriate target analyte for human urine analysis. Two test methods allowing for the detection of BAY-348 in human urine were applied and cross-validated concerning the validation parameters specificity, linearity, lower limit of detection (LLOD; 1-5 ng/mL), ion suppression/enhancement (up to 78%), intra- and inter-day precision (3-21%), recovery (29-48%), and carryover. By means of ten spiked test urine samples sent blinded to one of the participating laboratories, the fitness-for-purpose of both assays was provided as all specimens were correctly identified applying both testing methods. As no post-administration study samples were available, analyses of authentic urine specimens remain desirable. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The influence of negative training set size on machine learning-based virtual screening.

PubMed

Kurczab, Rafał; Smusz, Sabina; Bojarski, Andrzej J

2014-01-01

The paper presents a thorough analysis of the influence of the number of negative training examples on the performance of machine learning methods. The impact of this rather neglected aspect of machine learning methods application was examined for sets containing a fixed number of positive and a varying number of negative examples randomly selected from the ZINC database. An increase in the ratio of positive to negative training instances was found to greatly influence most of the investigated evaluating parameters of ML methods in simulated virtual screening experiments. In a majority of cases, substantial increases in precision and MCC were observed in conjunction with some decreases in hit recall. The analysis of dynamics of those variations let us recommend an optimal composition of training data. The study was performed on several protein targets, 5 machine learning algorithms (SMO, Naïve Bayes, Ibk, J48 and Random Forest) and 2 types of molecular fingerprints (MACCS and CDK FP). The most effective classification was provided by the combination of CDK FP with SMO or Random Forest algorithms. The Naïve Bayes models appeared to be hardly sensitive to changes in the number of negative instances in the training set. In conclusion, the ratio of positive to negative training instances should be taken into account during the preparation of machine learning experiments, as it might significantly influence the performance of particular classifier. What is more, the optimization of negative training set size can be applied as a boosting-like approach in machine learning-based virtual screening.

The influence of negative training set size on machine learning-based virtual screening

PubMed Central

2014-01-01

Background The paper presents a thorough analysis of the influence of the number of negative training examples on the performance of machine learning methods. Results The impact of this rather neglected aspect of machine learning methods application was examined for sets containing a fixed number of positive and a varying number of negative examples randomly selected from the ZINC database. An increase in the ratio of positive to negative training instances was found to greatly influence most of the investigated evaluating parameters of ML methods in simulated virtual screening experiments. In a majority of cases, substantial increases in precision and MCC were observed in conjunction with some decreases in hit recall. The analysis of dynamics of those variations let us recommend an optimal composition of training data. The study was performed on several protein targets, 5 machine learning algorithms (SMO, Naïve Bayes, Ibk, J48 and Random Forest) and 2 types of molecular fingerprints (MACCS and CDK FP). The most effective classification was provided by the combination of CDK FP with SMO or Random Forest algorithms. The Naïve Bayes models appeared to be hardly sensitive to changes in the number of negative instances in the training set. Conclusions In conclusion, the ratio of positive to negative training instances should be taken into account during the preparation of machine learning experiments, as it might significantly influence the performance of particular classifier. What is more, the optimization of negative training set size can be applied as a boosting-like approach in machine learning-based virtual screening. PMID:24976867

Parametric and Nonparametric Statistical Methods for Genomic Selection of Traits with Additive and Epistatic Genetic Architectures

PubMed Central

Howard, Réka; Carriquiry, Alicia L.; Beavis, William D.

2014-01-01

Parametric and nonparametric methods have been developed for purposes of predicting phenotypes. These methods are based on retrospective analyses of empirical data consisting of genotypic and phenotypic scores. Recent reports have indicated that parametric methods are unable to predict phenotypes of traits with known epistatic genetic architectures. Herein, we review parametric methods including least squares regression, ridge regression, Bayesian ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian LASSO, best linear unbiased prediction (BLUP), Bayes A, Bayes B, Bayes C, and Bayes Cπ. We also review nonparametric methods including Nadaraya-Watson estimator, reproducing kernel Hilbert space, support vector machine regression, and neural networks. We assess the relative merits of these 14 methods in terms of accuracy and mean squared error (MSE) using simulated genetic architectures consisting of completely additive or two-way epistatic interactions in an F2 population derived from crosses of inbred lines. Each simulated genetic architecture explained either 30% or 70% of the phenotypic variability. The greatest impact on estimates of accuracy and MSE was due to genetic architecture. Parametric methods were unable to predict phenotypic values when the underlying genetic architecture was based entirely on epistasis. Parametric methods were slightly better than nonparametric methods for additive genetic architectures. Distinctions among parametric methods for additive genetic architectures were incremental. Heritability, i.e., proportion of phenotypic variability, had the second greatest impact on estimates of accuracy and MSE. PMID:24727289

Empirical Bayes methods for smoothing data and for simultaneous estimation of many parameters.

PubMed Central

Yanagimoto, T; Kashiwagi, N

1990-01-01

A recent successful development is found in a series of innovative, new statistical methods for smoothing data that are based on the empirical Bayes method. This paper emphasizes their practical usefulness in medical sciences and their theoretically close relationship with the problem of simultaneous estimation of parameters, depending on strata. The paper also presents two examples of analyzing epidemiological data obtained in Japan using the smoothing methods to illustrate their favorable performance. PMID:2148512

Power System Reliability Assessment by Analysing Voltage Dips on the Blue Horizon Bay 22KV Overhead Line in the Nelson Mandela Bay Municipality

NASA Astrophysics Data System (ADS)

Lamour, B. G.; Harris, R. T.; Roberts, A. G.

2010-06-01

Power system reliability problems are very difficult to solve because the power systems are complex and geographically widely distributed and influenced by numerous unexpected events. It is therefore imperative to employ the most efficient optimization methods in solving the problems relating to reliability of the power system. This paper presents a reliability analysis and study of the power interruptions resulting from severe power outages in the Nelson Mandela Bay Municipality (NMBM), South Africa and includes an overview of the important factors influencing reliability, and methods to improve the reliability. The Blue Horizon Bay 22 kV overhead line, supplying a 6.6 kV residential sector has been selected. It has been established that 70% of the outages, recorded at the source, originate on this feeder.

Biogeochemical study of water and bottom sediments from the Khai river - Nha Trang Bay estuarine system, South China Sea

NASA Astrophysics Data System (ADS)

Shulga, Natalia; Lobys, Nikolay; Drozdova, Anastasia; Peresypkin, Valery

2014-05-01

The present study was carried out in Nha Trang Bay (Southern Vietnam, the South China Sea). The samples of water, suspended matter and bottom sediments were collected in summer 2010-2012 in section from the estuary of the Khai River to the marine part of the bay. The samples were analyzed in the stationary lab of IO RAS, Moscow, by TOC-V-CPH, GC/MS and pirolysis methods. We report here the novel data on sources, transformation and burial of OM coming from the Khai river waters. The investigation is focused on ontent and distribution of suspended matter (SM) in the estuary, dissolved organic carbon (DOC), particulated organic carbon (POC); molecular and group composition of hydrocarbons (n-alkanes, steranes, hopanes) and mercury content in water, SM and bottom sediments. It was found that concentration of POC and SM decrease in the Nha Trang Bay waters from estuary to the open part of the bay. However, major changes in the concentration of SM and POC belong to the zone of salinity gradient.DOC behavior is more stable throughout the study area. Organic-geochemical indicators estimation allowed recognition of genesis and transformation degree of organic matter in the study area. The estuary is characterized by mixed genesis of SM with a predominance of allochthonous organic matter whereas outlying parts of the Nha Trang bay are characterized by autochthonous OM. Composition of OM in sediments reflects regularities identified above, despite of the interannual and seasonal variability in the study area. The investigation reveals a predominance of terrestrial organic matter in the silt sediments of the estuary, transported by the Khai river. Distribution of OM in sediments of marine part of the bay is mosaic, with a predominance of planktonogenic, bacterial or terrestrial input at their complex combination. Local anthropogenic pollution as well as an impact of industrial city effluents are found in river- and seaport areas. According to obtained data sedimentation rate in Nha Trang bay area is 36-118 g/m^2/day in summer season. Sedimentary TOC (%) in samples varies in the range 0.50 - 1.95 in 2010, 0.22 - 1.84 in 2011 and 0.27 - 1.94 in 2012. This variations associated with differences in grain size distribution of sediments and intensity of anthropogenic influence. Mercury (Hg) concentration in the bottom sediments of aquatic systems varies from 2 to 108 ng/g of dry weight. Low concentration of the metal is typical for sediments, where OM is mainly represented by remains of aquatic organisms, while high concentration are common for river- and seaport areas with mainly terrestrial origin. Our study shows terrigenous organic matter is an important agent in the transfer of mercury from land to water ecosystems and Hg migrates in dissolved forms mainly. The reported study was supported by RFBR, research project No:14-05-31059-mol_a.

Bayes' Theorem: An Old Tool Applicable to Today's Classroom Measurement Needs. ERIC/AE Digest.

ERIC Educational Resources Information Center

Rudner, Lawrence M.

This digest introduces ways of responding to the call for criterion-referenced information using Bayes' Theorem, a method that was coupled with criterion-referenced testing in the early 1970s (see R. Hambleton and M. Novick, 1973). To illustrate Bayes' Theorem, an example is given in which the goal is to classify an examinee as being a master or…

Using soil surveys to target riparian buffers in the Chesapeake Bay watershed

Treesearch

Michael G. Dosskey

2008-01-01

The efficacy of vegetative buffers for improving water quality could be enhanced by distinguishing differences in buffer capability across watersheds and accounting for them in buffer planning. A soil survey-based method was applied to riparian areas in the Chesapeake Bay watershed. The method is based on soil attributes that are important in determining buffer...

A Bayesian antedependence model for whole genome prediction.

PubMed

Yang, Wenzhao; Tempelman, Robert J

2012-04-01

Hierarchical mixed effects models have been demonstrated to be powerful for predicting genomic merit of livestock and plants, on the basis of high-density single-nucleotide polymorphism (SNP) marker panels, and their use is being increasingly advocated for genomic predictions in human health. Two particularly popular approaches, labeled BayesA and BayesB, are based on specifying all SNP-associated effects to be independent of each other. BayesB extends BayesA by allowing a large proportion of SNP markers to be associated with null effects. We further extend these two models to specify SNP effects as being spatially correlated due to the chromosomally proximal effects of causal variants. These two models, that we respectively dub as ante-BayesA and ante-BayesB, are based on a first-order nonstationary antedependence specification between SNP effects. In a simulation study involving 20 replicate data sets, each analyzed at six different SNP marker densities with average LD levels ranging from r(2) = 0.15 to 0.31, the antedependence methods had significantly (P < 0.01) higher accuracies than their corresponding classical counterparts at higher LD levels (r(2) > 0. 24) with differences exceeding 3%. A cross-validation study was also conducted on the heterogeneous stock mice data resource (http://mus.well.ox.ac.uk/mouse/HS/) using 6-week body weights as the phenotype. The antedependence methods increased cross-validation prediction accuracies by up to 3.6% compared to their classical counterparts (P < 0.001). Finally, we applied our method to other benchmark data sets and demonstrated that the antedependence methods were more accurate than their classical counterparts for genomic predictions, even for individuals several generations beyond the training data.

A Bayesian Nonparametric Approach to Image Super-Resolution.

PubMed

Polatkan, Gungor; Zhou, Mingyuan; Carin, Lawrence; Blei, David; Daubechies, Ingrid

2015-02-01

Super-resolution methods form high-resolution images from low-resolution images. In this paper, we develop a new Bayesian nonparametric model for super-resolution. Our method uses a beta-Bernoulli process to learn a set of recurring visual patterns, called dictionary elements, from the data. Because it is nonparametric, the number of elements found is also determined from the data. We test the results on both benchmark and natural images, comparing with several other models from the research literature. We perform large-scale human evaluation experiments to assess the visual quality of the results. In a first implementation, we use Gibbs sampling to approximate the posterior. However, this algorithm is not feasible for large-scale data. To circumvent this, we then develop an online variational Bayes (VB) algorithm. This algorithm finds high quality dictionaries in a fraction of the time needed by the Gibbs sampler.

Effects of local geology on ground motion in the San Francisco Bay region, California—A continued study

USGS Publications Warehouse

Gibbs, James F.; Borcherdt, Roger D.

1974-01-01

Measurements of ground motion generated by nuclear explosions in Nevada have been completed for 99 locations in the San Francisco Bay region, California. The seismograms, Fourier amplitude spectra, spectral amplification curves for the signal, and the Fourier amplitude spectra of the seismic noise are presented for 60 locations. Analog amplifications, based on the maximum signal amplitude, are computed for an additional 39 locations. The recordings of the nuclear explosions show marked amplitude variations which are consistently related to the local geologic conditions of the recording site. The average spectral amplifications observed for vertical and horizontal ground motions are, respectively: (1, 1) for granite, (1.5, 1.6) for the Franciscan Formation, (2.3, 2.3), for other pre-Tertiary and Tertiary rocks, (3.0, 2.7) for the Santa Clara Formation, (3.3, 4.4) for older bay sediments, and (3.7, 11.3) for younger bay mud. Spectral amplification curves define predominant ground frequencies for younger bay mud sites and for some older bay sediment sites. The predominant frequencies for most sites were not clearly defined by the amplitude spectra computed from the seismic background noise. The intensities ascribed to various sites in the San Francisco Bay region for the California earthquake of April 18, 1906, are strongly dependent on distance from the zone of surface faulting and the geological character of the ground. Considering only those sites (approximately one square city block in size) for which there is good evidence for the degree of ascribed intensity, the intensities for 917 sites on Franciscan rocks generally decrease with the logarithm of distance as Intensity = 2.69 - 1.90 log (Distance Km). For sites on other geologic units, intensity increments, derived from this empirical rela.tion, correlate strongly with the Average Horizontal Spectral Amplifications (MISA) according to the empirical relation Intensity Increment= 0.27 + 2.70 log(AHSA). Average intensity increments predicted for various geologic units are -0.3 for granite, 0.2 for Franciscan Formation, 0.6 for other pre-Tertiary, Tertiary bedrock, 0.8 for Santa Clara Formation, 1 .3 for older bay sediments, 2.4 for younger bay mud. These empirical relations, together with detailed geologic maps, delineate areas in the San Francisco Bay region of potentially high intensity from future earthquakes on either the San Andreas fault or the Hayward fault.

Automatic registration of terrestrial point clouds based on panoramic reflectance images and efficient BaySAC

NASA Astrophysics Data System (ADS)

Kang, Zhizhong

2013-10-01

This paper presents a new approach to automatic registration of terrestrial laser scanning (TLS) point clouds utilizing a novel robust estimation method by an efficient BaySAC (BAYes SAmpling Consensus). The proposed method directly generates reflectance images from 3D point clouds, and then using SIFT algorithm extracts keypoints to identify corresponding image points. The 3D corresponding points, from which transformation parameters between point clouds are computed, are acquired by mapping the 2D ones onto the point cloud. To remove false accepted correspondences, we implement a conditional sampling method to select the n data points with the highest inlier probabilities as a hypothesis set and update the inlier probabilities of each data point using simplified Bayes' rule for the purpose of improving the computation efficiency. The prior probability is estimated by the verification of the distance invariance between correspondences. The proposed approach is tested on four data sets acquired by three different scanners. The results show that, comparing with the performance of RANSAC, BaySAC leads to less iterations and cheaper computation cost when the hypothesis set is contaminated with more outliers. The registration results also indicate that, the proposed algorithm can achieve high registration accuracy on all experimental datasets.

Natural and anthropogenic nitrogen uptake by bloom-forming macroalgae.

PubMed

Thornber, Carol S; DiMilla, Peter; Nixon, Scott W; McKinney, Richard A

2008-02-01

The frequency and duration of macroalgal blooms have increased in many coastal waters over the past several decades. We used field surveys and laboratory culturing experiments to examine the nitrogen content and delta(15)N values of Ulva and Gracilaria, two bloom-forming algal genera in Narragansett Bay, RI (USA). The northern end of this bay is densely populated with large sewage treatment plant nitrogen inputs; the southern end is more lightly populated and opens to the Atlantic Ocean. Field-collected Ulva varied in delta(15)N among sites, but with two exceptions had delta(15)N above 10 per thousand, reflecting a significant component of heavy anthropogenic N. This variation was not correlated with a north-south gradient. Both Ulva and Gracilaria cultured in water from across Narragansett Bay also had high signals (delta(15)N= approximately 14-17 per thousand and 8-12 per thousand, respectively). These results indicate that inputs of anthropogenic N can have far-reaching impacts throughout estuaries.

Effects of hypoxia caused by mussel farming on benthic foraminifera in semi-closed Gamak Bay, South Korea.

PubMed

Lee, Yeon Gyu; Jeong, Da Un; Lee, Jung Sick; Choi, Yang Ho; Lee, Moon Ok

2016-08-15

Seawater monitoring and geochemical and benthic foraminiferal analysis of sediments were conducted to identify the effects of hypoxia created by a mussel farm on benthic foraminifera in a semi-closed bay. Extremely polluted reductive conditions with a high content of organic matter (OM) at >12.0% and oxygen minimum zones (OMZs) with dissolved oxygen (DO) <0.4mg∙L(-1) were formed below the mussel farm in the northwest area of Gamak Bay, and gradually diffused toward the south. Highly similar patterns of variation were observed in species diversity, abundance frequency, and benthic foraminiferal assemblage distributed from Elphidium subarcticum-Ammonia beccarii in the northwest area through E. subarcticum-A. beccarii-Trochammina hadai, E. subarcticum-A. beccarii-Elphidiumclavatum, and E. clavatum-Ammonia ketienziensis in the southern area. These phenomena were caused by hydrodynamics in the current water mass. It was thought that E. subarcticum is a bioindicator of organic pollution caused by the mussel farm. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Accidental Tide Gauge: A GPS Reflection Case Study from Kachemak Bay, Alaska

NASA Technical Reports Server (NTRS)

Larson, Kristine M.; Ray, Richard D.; Nievinski, Felipe G..; Freymueller, Jeffrey T.

2013-01-01

For the last decade, it has been known that reflected GPS signals observed with specialized instruments could be used to measure sea level. In this letter, data from an existing geodeticquality GPS site near Kachemak Bay, Alaska, are analyzed for a one-year time period. Daily sea-level variations are more than 7 m. Tidal coefficients have been estimated and compared with coefficients estimated from records from a traditional tide gauge at Seldovia Harbor, approximately 30 km away. The GPS and Seldovia estimates of M(sub 2) and S(sub 2) coefficients agree to better than 2%; much of this residual can be attributed to true differences in the tide over 30 km as it propagates up Kachemak Bay. For daily mean sea levels the agreement is 2.3 cm. Because a standard geodetic GPS receiver/antenna is used, this GPS instrument can measure long-term sea-level changes in a stable terrestrial reference frame.

Spatio-temporal variations in bloom of the red-tide dinoflagellate Karenia mikimotoi in Imari Bay, Japan, in 2014: Factors controlling horizontal and vertical distribution.

PubMed

Aoki, Kazuhiro; Kameda, Takahiko; Yamatogi, Toshifumi; Ishida, Naoya; Hirae, Sou; Kawaguchi, Mayumi; Syutou, Toshio

2017-11-15

A massive bloom of the dinoflagellate Karenia mikimotoi appeared in 2014 in Imari Bay, Japan. Bloom dynamics and hydrographical conditions were examined by field survey. The bloom initially developed in the eastern area of Imari Bay, subsequently after rainfall during the neap tides, cell density exceeded over 10,000cellsml. Vertical distribution of K. mikimotoi was primarily controlled by the light intensity and secondarily by the water quality during the daytime. Almost all cell-density maxima occurred in depths with weak daytime light intensities of <300μmolm -2 s -1 . In some cases of weak light intensity, cell-density maxima occurred in depths with favorable hydrodynamic conditions for the growth. Spatially classified areas were identified by cluster analysis using the growth rate calculated from seawater temperature and salinity. This study quantitatively evaluated the environmental factors of the eastern area, where the bloom initially occurred, during the development of the bloom. Copyright © 2017 Elsevier Ltd. All rights reserved.

Approximated adjusted fractional Bayes factors: A general method for testing informative hypotheses.

PubMed

Gu, Xin; Mulder, Joris; Hoijtink, Herbert

2018-05-01

Informative hypotheses are increasingly being used in psychological sciences because they adequately capture researchers' theories and expectations. In the Bayesian framework, the evaluation of informative hypotheses often makes use of default Bayes factors such as the fractional Bayes factor. This paper approximates and adjusts the fractional Bayes factor such that it can be used to evaluate informative hypotheses in general statistical models. In the fractional Bayes factor a fraction parameter must be specified which controls the amount of information in the data used for specifying an implicit prior. The remaining fraction is used for testing the informative hypotheses. We discuss different choices of this parameter and present a scheme for setting it. Furthermore, a software package is described which computes the approximated adjusted fractional Bayes factor. Using this software package, psychological researchers can evaluate informative hypotheses by means of Bayes factors in an easy manner. Two empirical examples are used to illustrate the procedure. © 2017 The British Psychological Society.

Characterizing submarine ground‐water discharge using fiber‐optic distributed temperature sensing and marine electrical resistivity

USGS Publications Warehouse

Henderson, Rory; Day-Lewis, Frederick D.; Lane, John W.; Harvey, Charles F.; Liu, Lanbo

2008-01-01

Submarine ground‐water discharge (SGD) contributes important solute fluxes to coastal waters. Pollutants are transported to coastal ecosystems by SGD at spatially and temporally variable rates. New approaches are needed to characterize the effects of storm‐event, tidal, and seasonal forcing on SGD. Here, we evaluate the utility of two geophysical methods‐fiber‐optic distributed temperature sensing (FO‐DTS) and marine electrical resistivity (MER)—for observing the spatial and temporal variations in SGD and the configuration of the freshwater/saltwater interface within submarine sediments. FO‐DTS and MER cables were permanently installed into the estuary floor on a transect extending 50 meters offshore under Waquoit Bay, Massachusetts, at the Waquoit Bay National Estuarine Research Reserve, and nearly continuous data were collected for 4 weeks in summer 2007. Initial results indicate that the methods are extremely useful for monitoring changes in the complex estuarine environment. The FO‐DTS produced time‐series data at approximately 1‐meter increments along the length of the fiber at approximately 29‐second intervals. The temperature time‐series data show that the temperature at near‐shore locations appears to be dominated by a semi‐diurnal (tidal) signal, whereas the temperature at off‐shore locations is dominated by a diurnal signal (day/night heating and cooling). Dipole‐dipole MER surveys were completed about every 50 minutes, allowing for production of high‐resolution time‐lapse tomograms, which provide insight into the variations of the subsurface freshwater/saltwater interface. Preliminary results from the MER data show a high‐resistivity zone near the shore at low tide, indicative of SGD, and consistent with the FO‐DTS results.

Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers

PubMed Central

2010-01-01

Background The information provided by dense genome-wide markers using high throughput technology is of considerable potential in human disease studies and livestock breeding programs. Genome-wide association studies relate individual single nucleotide polymorphisms (SNP) from dense SNP panels to individual measurements of complex traits, with the underlying assumption being that any association is caused by linkage disequilibrium (LD) between SNP and quantitative trait loci (QTL) affecting the trait. Often SNP are in genomic regions of no trait variation. Whole genome Bayesian models are an effective way of incorporating this and other important prior information into modelling. However a full Bayesian analysis is often not feasible due to the large computational time involved. Results This article proposes an expectation-maximization (EM) algorithm called emBayesB which allows only a proportion of SNP to be in LD with QTL and incorporates prior information about the distribution of SNP effects. The posterior probability of being in LD with at least one QTL is calculated for each SNP along with estimates of the hyperparameters for the mixture prior. A simulated example of genomic selection from an international workshop is used to demonstrate the features of the EM algorithm. The accuracy of prediction is comparable to a full Bayesian analysis but the EM algorithm is considerably faster. The EM algorithm was accurate in locating QTL which explained more than 1% of the total genetic variation. A computational algorithm for very large SNP panels is described. Conclusions emBayesB is a fast and accurate EM algorithm for implementing genomic selection and predicting complex traits by mapping QTL in genome-wide dense SNP marker data. Its accuracy is similar to Bayesian methods but it takes only a fraction of the time. PMID:20969788

Diurnal temperature asymmetries and fog at Churchill, Manitoba

NASA Astrophysics Data System (ADS)

Gough, William A.; He, Dianze

2015-07-01

A variety of methods are available to calculate daily mean temperature. We explore how the difference between two commonly used methods provides insight into the local climate of Churchill, Manitoba. In particular, we found that these differences related closely to seasonal fog. A strong statistically significant correlation was found between the fog frequency (hours per day) and the diurnal temperature asymmetries of the surface temperature using the difference between the min/max and 24-h methods of daily temperature calculation. The relationship was particularly strong for winter, spring and summer. Autumn appears to experience the joint effect of fog formation and the radiative effect of snow cover. The results of this study suggests that subtle variations of diurnality of temperature, as measured in the difference of the two mean temperature methods of calculation, may be used as a proxy for fog detection in the Hudson Bay region. These results also provide a cautionary note for the spatial analysis of mean temperatures using data derived from the two different methods particularly in areas that are fog prone.

Studies on Anthropogenic Impact on Water Quality in Hilo (Hawaii) Bay and Mapping the Study Stations Using Geospatial Technologies

NASA Astrophysics Data System (ADS)

Cartier, A. J.; Williams, M. S.; Adolf, J.; Sriharan, S.

2015-12-01

Hilo Bay has uncharacteristically brown waters compared to other waters found in Hawai'i. The majority of the freshwater entering Hilo Bay is from storm and surface water runoff. The anthropogenic impact on water quality at Hilo Bay is due to sediment entrance, cesspools (Bacteria), and invasive species (Albizia). This poster presentation will focus on the water quality and phytoplankton collected on a weekly basis at a buoy positioned one meter from the shore of Hilo Bay, preserving the phytoplankton intact, concentrating and dehydrating the sample with ethanol, and viewing the phytoplankton with a scanning electron microscope (Hitachi S-3400NII). The GPS (Global Positioning System) points were collected at the sampling stations. Three transects on three separate dates were performed in Hilo Bay with salinity, percent dissolved oxygen, turbidity, secchi depth, temperature, and chlorophyll fluorescence data collected at each sampling station. A consistent trend observed in all transects was as distance from the river increased turbidity decreased and salinity increased. The GPS data on June 30, 2015 showed a major correlation between stations and their distance from shore. There is a decrease in the turbidity but not the temperature for these stations. The GPS points collected on July 7, 2015 at thirteen stations starting with station one being at the shore to the water, showed that the salinity concentration fluctuate noticeably at the first 6 stations. As we proceed further away from the shore, the salinity concentration increases from stations seven through thirteen. The water temperature shows little variation throughout the thirteen stations. The turbidity level was high at the shore and shows a noticeable drop at station thirteen.

Effects of small-scale hydrogeologic heterogeneity on submarine groundwater discharge (SGD) dynamics in river dominated estuaries: example of Mobile Bay, Alabama

NASA Astrophysics Data System (ADS)

Montiel, D.; Dimova, N.

2017-12-01

Submarine groundwater discharge (SGD) is known to be an important pathway for nutrients and dissolved constituents in estuarine environments worldwide. Despite its limited contribution to the total fresh water flux to the ocean (5 - 10 %), SGD-derived material loadings can rival riverine inputs. Therefore, a good understanding of the coastal hydrogeology and subsequent SGD dynamics is crucial to further investigate constituent fluxes and its implications on small and large scale coastal ecosystems. We evaluated SGD in Mobile Bay (Alabama), the fourth largest estuary in the US, using a combination of radiotracer techniques (223Ra, 226Ra, and 222Rn), stable isotopes (δ 18O and δ 2H), geophysical surveys (continuous resistivity profiling (CRP) and electrical resistivity tomography (ERT)), and seepage meters during three consecutive years. A detailed examination of the entire shoreline of Mobile Bay using CRP, ERT imaging, and multiple sediment cores collection unveiled a heterogeneous (horizontal and vertical) distribution of the surficial coastal aquifer. This was reflected and confirmed by groundwater tracer measurements and direct measurements of SGD in the coastal zone. We found that SGD occurs mainly in the northeast section of Mobile Bay with a total flux that ranged between 0.9 and 13 × 105 m3 d-1 during dry and wet periods, which represents 0.4 - 2 % of the total fresh water inputs into the Bay. While total SGD is insignificant when accounting the whole water budget of Mobile Bay, we found that small-scale geology variations produce groundwater flow preferential pathways in particular areas where SGD inputs play an important role in the water and nutrient budgets.

Geochemical analysis of sediments from a semi-enclosed bay (Dongshan Bay, southeast China) to determine the anthropogenic impact and source.

PubMed

Xu, Yonghang; Sun, Qinqin; Ye, Xiang; Yin, Xijie; Li, Dongyi; Wang, Liang; Wang, Aijun; Li, Yunhai

2017-05-01

The geochemical compositions of sediments in the Dongshan Bay, a semi-enclosed bay on the southeast coast of China, were obtained to identify pollutant sources and evaluate the anthropogenic impacts over the last 100 years. The results indicated that the metal flux had been increasing since the 1980s. Enrichment factor values (Pb, Zn and Cu) suggested only slight enrichment. The proportion of anthropogenic Pb changed from 9% to 15% during 2000-2014. Coal combustion might be an important contamination source in the Dongshan Bay. The historical variation in the metal flux reflected the economic development and urbanization in the Zhangjiang drainage area in the past 30 years. According to the Landsat satellite remote sensing data, the urbanization area expanded approximately three times from 1995 to 2010. The δ 13 C values (-21‰ to -23‰) of the organic matter (OM) in the sediments indicated that the OM was primarily sourced from aquatic, terrigenous and marsh C 3 plants. Nitrogen was mainly derived from aquatic plants and terrigenous erosion before the 1980s. However, the total organic carbon (TOC) contents, total nitrogen (TN) contents and δ 15 N had been increasing since the 1980s, which suggested that the sources of nitrogen were soil erosion, fertilizer and sewage. In addition, the TOC and TN fluxes in the Dongshan Bay had significantly increased since the 1980s, which reflected the use of N fertilizer. However, the TOC and TN fluxes significantly decreased in the past decade because environmental awareness increased and environmental protection policies were implemented. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of naïve Bayes and logistic regression for computer-aided diagnosis of breast masses using ultrasound imaging

NASA Astrophysics Data System (ADS)

Cary, Theodore W.; Cwanger, Alyssa; Venkatesh, Santosh S.; Conant, Emily F.; Sehgal, Chandra M.

2012-03-01

This study compares the performance of two proven but very different machine learners, Naïve Bayes and logistic regression, for differentiating malignant and benign breast masses using ultrasound imaging. Ultrasound images of 266 masses were analyzed quantitatively for shape, echogenicity, margin characteristics, and texture features. These features along with patient age, race, and mammographic BI-RADS category were used to train Naïve Bayes and logistic regression classifiers to diagnose lesions as malignant or benign. ROC analysis was performed using all of the features and using only a subset that maximized information gain. Performance was determined by the area under the ROC curve, Az, obtained from leave-one-out cross validation. Naïve Bayes showed significant variation (Az 0.733 +/- 0.035 to 0.840 +/- 0.029, P < 0.002) with the choice of features, but the performance of logistic regression was relatively unchanged under feature selection (Az 0.839 +/- 0.029 to 0.859 +/- 0.028, P = 0.605). Out of 34 features, a subset of 6 gave the highest information gain: brightness difference, margin sharpness, depth-to-width, mammographic BI-RADs, age, and race. The probabilities of malignancy determined by Naïve Bayes and logistic regression after feature selection showed significant correlation (R2= 0.87, P < 0.0001). The diagnostic performance of Naïve Bayes and logistic regression can be comparable, but logistic regression is more robust. Since probability of malignancy cannot be measured directly, high correlation between the probabilities derived from two basic but dissimilar models increases confidence in the predictive power of machine learning models for characterizing solid breast masses on ultrasound.

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus)

USGS Publications Warehouse

Wood, Dustin A.; Bui, Thuy-Vy D.; Overton, Cory T.; Vandergast, Amy; Casazza, Michael L.; Hull, Joshua M.; Takekawa, John Y.

2016-01-01

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.

Numerical experiments based on a coupled physical-biochemical ocean model to study the Kuroshio-induced nutrient supply on the shelf-slope region off the southwestern coast of Japan

NASA Astrophysics Data System (ADS)

Kuroda, Hiroshi; Takasuka, Akinori; Hirota, Yuichi; Kodama, Taketoshi; Ichikawa, Tadafumi; Takahashi, Daisuke; Aoki, Kazuhiro; Setou, Takashi

2018-03-01

We developed a triply nested 1/50° ocean model coupled with a NPZD-type lower trophic level ecosystem model and used it to conduct numerical experiments to identify the major processes that supply nutrients on the shelf-slope region north of the Kuroshio. Tosa Bay, an open-type bay facing the Kuroshio, was selected for our experiment. Comparisons of numerical simulations using different grid sizes revealed that a grid size no larger than 1/50° was essential to reproduce a time-independent density structure related to the Kuroshio jet that uplifted nitrate from subsurface waters into the euphotic zone north of the Kuroshio front. The monthly mean budget of nitrate within the euphotic zone on the shelf showed that primary production was nearly balanced by physical advection and the biochemical supply of nitrate via mechanisms such as remineralization of detritus. Eddy advection of nitrate based on Reynolds decomposition, attributable primarily to submesoscale variations, had both positive and negative values within the bay, the indication being that eddy advection functioned regionally to supply or remove nitrate. Lagrangian particle-tracking experiments were performed to examine the major pathways of the nitrate used for primary production in Tosa Bay during the summer, when subsurface maxima of primary production typically appeared. The experiments revealed that when the Kuroshio took a stable nearshore path, nitrate was frequently uplifted around the Kuroshio front and horizontally transported along the front and into the bay via the counterclockwise circulation within the bay; it was sometimes further uplifted onto the shelf.

Sources of nitrate in Xiangshan Bay (China), as identified using nitrogen and oxygen isotopes

NASA Astrophysics Data System (ADS)

Yang, Zhi; Chen, Jianfang; Li, Hongliang; Jin, Haiyan; Gao, Shenquan; Ji, Zhongqiang; Zhu, Yong; Ran, Lihua; Zhang, Jingjing; Liao, Yibo; Bai, Youcheng

2018-07-01

Eutrophication, mainly caused by the oversupply of nitrate (NO3-) and phosphate, has become a serious environmental problem in Xiangshan Bay (east China), but the sources of the nitrate are poorly understood. In this study, the estuarine distributions of dual stable isotopes (δ15N and δ18O) of NO3- measured in May 2012 were used in combination with concurrent measurements of salinity, pH, dissolved oxygen, and nutrients (nitrate, nitrite, ammonium, and phosphate) to investigate NO3- sources and the processes that control NO3- distributions within the bay. In the lower bay, high concentrations of NO3- (up to 60.6 μmol L-1), an N/P ratio of 52, and low values of nitrate δ15N (δ15NNO3 = 5.7‰-6.7‰) and δ18O (δ18ONO3 = 1.8‰-3.5‰) indicate that NO3- in this area was likely from the Changjiang and Qiantangjiang rivers as well as local nitrification-associated inputs. In the upper bay, constituent concentrations and high values of δ15NNO3 (up to 8.8‰) and δ18ONO3 (up to 6.8‰) suggest that NO3- distributions here were controlled mainly by the mixing of coastal and fresh waters, phytoplankton assimilation, and inputs of riverine NO3-, possibly derived from manure and sewage. Spatial variations of Δ(15,18), the nitrate δ15N-to-δ18O anomaly, is possibly resulted from the different water residence times across the bay, which could in turn lead to different degrees of nitrification or variable amounts of NO3- from atmospheric deposition.

Disease dynamics of Montipora white syndrome within Kaneohe Bay, Oahu, Hawaii: distribution, seasonality, virulence, and transmissibility.

PubMed

Aeby, G S; Ross, M; Williams, G J; Lewis, T D; Works, T M

2010-07-26

We report on an investigation of Montipora white syndrome (MWS), which is a coral disease reported from Hawaii, U.S.A., that results in tissue loss. Disease surveys of Montipora capitata within Kaneohe Bay (Oahu) found colonies that were affected by MWS on 9 reefs within 3 regions of Kaneohe Bay (south, central, north). Mean MWS prevalence ranged from 0.02 to 0.87% and average number of MWS cases per survey site ranged from 1 to 28 colonies. MWS prevalence and number of cases were significantly lower in the central region as compared to those in the north and south regions of Kaneohe Bay. There was a positive relationship between host abundance and MWS prevalence, and differences in host abundance between sites explained approximately 27% of the variation in MWS prevalence. Reefs in central Kaneohe Bay had lower M. capitata cover and lower MWS levels. MWS prevalence on reefs was neither significantly different between seasons (spring versus fall) nor among 57 tagged colonies that were monitored through time. MWS is a chronic and progressive disease causing M. capitata colonies to lose an average of 3.1% of live tissue mo(-1). Case fatality rate was 28% after 2 yr but recovery occurred in some colonies (32%). Manipulative experiments showed that the disease is acquired through direct contact. This is the first study to examine the dynamics of MWS within Hawaii, and our findings suggest that MWS has the potential to degrade Hawaii's reefs through time.

The effects of exposure in sandy beach surf zones on larval fishes.

PubMed

Pattrick, P; Strydom, N A

2014-05-01

The influence of wind and wave exposure on larval fish assemblages within a large bay system was investigated. Larval fishes were sampled from two areas with vastly different exposure to waves and wind, namely the windward and leeward sectors of Algoa Bay. In total, 5702 larval fishes were collected using a modified larval seine. Of these, 4391 were collected in the leeward and 1311 in the windward sector of the bay, representing a total of 23 families and 57 species. Dominant fish families included Clinidae, Engraulidae, Kyphosidae, Mugilidae, Soleidae and Sparidae, similar to the situation elsewhere, highlighting continuity in the composition of larval fish assemblages and the utilization of surf zones by a specific group of larval fishes. Nineteen estuary-associated marine species occurred within the surf zones of Algoa Bay and dominated catches (86·7%) in terms of abundance. Postflexion larvae comprised > 80% of the catch, indicating the importance of the seemingly inhospitable surf zone environment for the early life stages of many fish species. The greatest species diversity was observed within the windward sector of the bay. Distance-based linear modelling identified wave period as the environmental variable explaining the largest proportion of the significant variation in the larval fish assemblage. The physical disturbance generated by breaking waves could create a suitable environment for fish larvae, sheltered from predators and with an abundance of food resources. © 2014 The Fisheries Society of the British Isles.

MrBayes tgMC3++: A High Performance and Resource-Efficient GPU-Oriented Phylogenetic Analysis Method.

PubMed

Ling, Cheng; Hamada, Tsuyoshi; Gao, Jingyang; Zhao, Guoguang; Sun, Donghong; Shi, Weifeng

2016-01-01

MrBayes is a widespread phylogenetic inference tool harnessing empirical evolutionary models and Bayesian statistics. However, the computational cost on the likelihood estimation is very expensive, resulting in undesirably long execution time. Although a number of multi-threaded optimizations have been proposed to speed up MrBayes, there are bottlenecks that severely limit the GPU thread-level parallelism of likelihood estimations. This study proposes a high performance and resource-efficient method for GPU-oriented parallelization of likelihood estimations. Instead of having to rely on empirical programming, the proposed novel decomposition storage model implements high performance data transfers implicitly. In terms of performance improvement, a speedup factor of up to 178 can be achieved on the analysis of simulated datasets by four Tesla K40 cards. In comparison to the other publicly available GPU-oriented MrBayes, the tgMC 3 ++ method (proposed herein) outperforms the tgMC 3 (v1.0), nMC 3 (v2.1.1) and oMC 3 (v1.00) methods by speedup factors of up to 1.6, 1.9 and 2.9, respectively. Moreover, tgMC 3 ++ supports more evolutionary models and gamma categories, which previous GPU-oriented methods fail to take into analysis.

Improved fine-scale transport model performance using AUV and HSI feedback in a tidally dominated system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hibler, Lyle F.; Maxwell, Adam R.; Miller, Lee M.

2008-08-22

Applied numerical circulation and transport modeling study of Sequim Bay, WA focused on the simulation of the redistribution of rhodamine dye release at the water surface. Model sensitivity to bathymetric variation, side-wall boundary conditions, and thermal stratification is examined. Model results compared to observational datasets.

VARIATION OF KOC IN SURFACE SEDIMENTS FROM NARRAGANSETT BAY AND LONG ISLAND SOUND: ANALYSIS OF THE ROLE OF OTHER PARTICULATE CHARACTERISTICS

EPA Science Inventory

In the first part of this investigation, we examined whether differences in the Kocs of three nonpolar organic chemicals (Lindane, fluoranthene, tetrachlorinated biphenyl (PCB)) from five sites along the New England coast were statistically significant. Although no statistical di...

EXTRACELLULAR ENZYME ACTIVITY IN A RIVER-BAY-SHELF TRANSECT: VARIATIONS IN POLYSACCHARIDE HYDROLYSIS RATES WITH SUBSTRATE AND SIZE CLASS. (R825159)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

DEVELOPING NUTRIENT CRIETERIA FOR ESTUARIES WITH VARIABLE OCEAN INPUTS: AN EXAMPLE FROM THE PACIFIC NORTHWEST

EPA Science Inventory

Estuaries in the Pacific Northwest have major intraannual and within estuary variation in sources and magnitudes of nutrient inputs. To develop an approach for setting nutrient criteria for these systems, we conducted a case study for Yaquina Bay, OR based on a synthesis of resea...

Effects of microtopographic variation and macroalgal cover on morphometrics and survival of the annual form of eelgrass (Zostera marina)

EPA Science Inventory

A disjunct population of the annual form of the seagrass Zostera marina that occurred in the upper intertidal zone of Yaquina Bay, Oregon was sampled to determine whether there were differences in recruitment, growth, survivorship and morphology associated with microtopographic l...

INDICATORS OF CHANGE IN THE MID-ATLANTIC WATERSHEDS AND CONSEQUENCES OF CLIMATE IN UPPER CHESAPEAKE BAY

EPA Science Inventory

The rate of change in Northern Hemisphere atmospheric temperature in the past century relative to the preceding millennium strongly suggests that we are in a period of rapid global climate change. The mid-Atlantic region is quite sensitive to larger scale climate variation, which...

Bayes and the Law

PubMed Central

Fenton, Norman; Neil, Martin; Berger, Daniel

2016-01-01

Although the last forty years has seen considerable growth in the use of statistics in legal proceedings, it is primarily classical statistical methods rather than Bayesian methods that have been used. Yet the Bayesian approach avoids many of the problems of classical statistics and is also well suited to a broader range of problems. This paper reviews the potential and actual use of Bayes in the law and explains the main reasons for its lack of impact on legal practice. These include misconceptions by the legal community about Bayes’ theorem, over-reliance on the use of the likelihood ratio and the lack of adoption of modern computational methods. We argue that Bayesian Networks (BNs), which automatically produce the necessary Bayesian calculations, provide an opportunity to address most concerns about using Bayes in the law. PMID:27398389

Annual variation in neustonic micro- and meso-plastic particles and zooplankton in the Bay of Calvi (Mediterranean-Corsica).

PubMed

Collignon, Amandine; Hecq, Jean-Henri; Galgani, François; Collard, France; Goffart, Anne

2014-02-15

The annual variation in neustonic plastic particles and zooplankton was studied in the Bay of Calvi (Corsica) between 30 August 2011 and 7 August 2012. Plastic particles were classified into three size classes, small microplastics (0.2-2mm), large microplastics (2-5mm) and mesoplastics (5-10mm). 74% of the 38 samples contained plastic particles of varying composition: e.g. filaments, polystyrene, thin plastic films. An average concentration of 6.2 particles/100 m(2) was observed. The highest abundance values (69 particles/100 m(2)) observed occurred during periods of low offshore wind conditions. These values rose in the same order of magnitude as in previous studies in the North Western Mediterranean. The relationships between the abundance values of the size classes between zooplankton and plastic particles were then examined. The ratio for the intermediate size class (2-5mm) reached 2.73. This would suggest a potential confusion for predators regarding planktonic prey of this size class. Copyright © 2013 Elsevier Ltd. All rights reserved.

Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.

PubMed

Cleary, D F R; Polónia, A R M; Renema, W; Hoeksema, B W; Rachello-Dolmen, P G; Moolenbeek, R G; Budiyanto, A; Yahmantoro; Tuti, Y; Giyanto; Draisma, S G A; Prud'homme van Reine, W F; Hariyanto, R; Gittenberger, A; Rikoh, M S; de Voogd, N J

2016-09-30

Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay-Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Climate variability in an estuary: Effects of riverflow on San Francisco Bay

USGS Publications Warehouse

Peterson, David H.; Cayan, Daniel R.; Festa, John F.; Nichols, Frederic H.; Walters, Roy A.; Slack, James V.; Hager, Stephen E.; Schemel, Laurence E.; Peterson, David H.

1989-01-01

A simple conceptual model of estuarine variability in the context of climate forcing has been formulated using up to 65 years of estimated mean-monthly delta flow, the cumulative freshwater flow to San Francisco Bay from the Sacramento-San Joaquin River, and salinity observations near the mouth, head, mid-estuary, and coastal ocean. Variations in delta flow, the principal source of variability in the bay, originate from anomalous changes in northern and central California streamflow, much of which is linked to anomalous winter sea level pressure (“CPA”) in the eastern Pacific. In years when CPA is strongly negative, precipitation in the watershed is heavy, delta flow is high, and the bay's salinity is low; similarly, when CPA is strongly positive, precipitation is light, delta flow is low, and the bay's salinity is high. Thus the pattern of temporal variability in atmospheric pressure anomalies is reflected in the streamflow, then in delta flow, then in estuarine variability. Estuarine salinity can be characterized by river to ocean patterns in annual cycles of salinity in relation to delta flow. Salinity (total dissolved solids) data from the relatively pristine mountain streams of the Sierra Nevada show that for a given flow, one observes higher salinities during the rise in winter flow than on the decline. Salinity at locations throughout San Francisco Bay estuary are also higher during the rise in winter flow than the decline (because it takes a finite time for salinity to fully respond to changes in freshwater flow). In the coastal ocean, however, the annual pattern of sea surface salinity is reversed: lower salinities during the rise in winter flow than on the decline due to effects associated with spring upwelling. Delta flow in spring masks these effects of coastal upwelling on estuarine salinity, including near the mouth of the estuary and, in fact, explains in a statistical sense 86 percent of the variance in salinity at the mouth of the estuary. Some of the variations in residual salinity in the bay not explained by delta flow appear to correlate with variability in coastal ocean properties. Interestingly CPA correlates also with anomalous sea surface salinity in the coastal ocean adjacent to the bay, especially in spring (albeit through a different mechanism than streamflow). For instance, when the atmospheric pressure anomaly as indicated for streamflow is high, the coastal ocean upper-layer Ekman transport is probably in the offshore direction resultingin higher sea surface salinities along the coast (with a phase lag). This circulation corresponds, in direction, to density driven estuarine circulation. In contrast a low atmospheric pressure regime leads to an onshore surface transport, and therefore opposes estuarine circulation. The influence of variations in delta flow on estuarine/phytoplankton/biochemical dynamics can be illustrated with numerical simulation models. For example, when riverflow is high the resulting low estuarine water residence time limits phytoplankton biomass and the observed effects of phytoplankton productivity on estuarine biochemistry are minimal. When riverflow is low but suspended sediment concentrations are high, light becomes a more important factor limiting phytoplankton biomass than residence time and effects of phytoplankton productivity on estuarine biochemistry are also minimal. When both riverflow and suspended sediment concentrations are low, phytoplankton biomass increases and phytoplankton productivity emerges as a major control on estuarine biochemistry: phytoplankton activity draws down and maintains very low ambient concentrations of dissolved silica and partial pressures of carbon dioxide (shifting pH to higher values). However, after an extended period of very low delta flow the major controls on estuarine biochemistry appear to change, possibly because benthic exchange processes (both sources and sinks) strengthen as salinity rises and benthic filter-feeding invertebrates migrate upstream with increasing salinity.

Time evolution of atmospheric parameters and their influence on sea level pressure over the head Bay of Bengal

NASA Astrophysics Data System (ADS)

Patra, Anindita; Bhaskaran, Prasad K.; Jose, Felix

2018-06-01

A zonal dipole in the observed trends of wind speed and significant wave height over the Head Bay of Bengal region was recently reported in the literature attributed due to the variations in sea level pressure (SLP). The SLP in turn is governed by prevailing atmospheric conditions such as local temperature, humidity, rainfall, atmospheric pressure, wind field distribution, formation of tropical cyclones, etc. The present study attempts to investigate the inter-annual variability of atmospheric parameters and its role on the observed zonal dipole trend in sea level pressure, surface wind speed and significant wave height. It reports on the aspects related to linear trend as well as its spatial variability for several atmospheric parameters: air temperature, geopotential height, omega (vertical velocity), and zonal wind, over the head Bay of Bengal, by analyzing National Centers for Environmental Prediction (NCEP) Reanalysis 2 dataset covering a period of 38 years (1979-2016). Significant warming from sea level to 200 mb pressure level and thereafter cooling above has been noticed during all the seasons. Warming within the troposphere exhibits spatial difference between eastern and western side of the domain. This led to fall in lower tropospheric geopotential height and its east-west variability, exhibiting a zonal dipole pattern across the Head Bay. In the upper troposphere, uplift in geopotential height was found as a result of cooling in higher levels (10-100 mb). Variability in omega also substantiated the observed variations in geopotential height. The study also finds weakening in the upper level westerlies and easterlies. Interestingly, a linear trend in lower tropospheric u-wind component also reveals an east-west dipole pattern over the study region. Further, the study corroborates the reported dipole in trends of sea level pressure, wind speed and significant wave height by evaluating the influence of atmospheric variability on these parameters.

Variations in population exposure and evacuation potential to multiple tsunami evacuation phases on Alameda and Bay Farm Islands, California

NASA Astrophysics Data System (ADS)

Peters, J.

2015-12-01

Planning for a tsunami evacuation is challenging for California communities due to the variety of earthquake sources that could generate a tsunami. A maximum tsunami inundation zone is currently the basis for all tsunami evacuations in California, although an Evacuation Playbook consisting of specific event-based evacuation phases relating to flooding severity is in development. We chose to investigate the Evacuation Playbook approach for the island community of Alameda, CA since past reports estimated a significant difference in numbers of residents in the maximum inundation zone when compared to an event-based inundation zone. In order to recognize variations in the types of residents and businesses within each phase, a population exposure analysis was conducted for each of the four Alameda evacuation phases. A pedestrian evacuation analysis using an anisotropic, path distance model was also conducted to understand the time it would take for populations to reach high ground by foot. Initial results suggest that the two islands of the City of Alameda have different situations when it comes to the four tsunami evacuation phases. Pedestrian evacuation results suggest that Bay Farm Island would have more success evacuating by vehicle due to limited nearby high ground for pedestrians to reach safety. Therefore, agent-based traffic simulation software was used to model vehicle evacuation off Bay Farm Island. Initial results show that Alameda Island could face challenges evacuating numerous boat docks and a large beach for phases 1 and 2, whereas Bay Farm Island is unaffected at these phases but might be challenged with evacuating by vehicle for phases 3 and maximum due to congestion on limited egress routes. A better understanding of the population exposure within each tsunami Evacuation Playbook phase and the time it would take to evacuate out of each phase by foot or vehicle will help emergency managers implement the evacuation phases during an actual tsunami event.

Temporal and spatial distributions of sediment mercury at salt pond wetland restoration sites, San Francisco Bay, CA, USA

USGS Publications Warehouse

Miles, A.K.; Ricca, M.A.

2010-01-01

Decommissioned agricultural salt ponds within south San Francisco Bay, California, are in the process of being converted to habitat for the benefit of wildlife as well as water management needs and recreation. Little is known of baseline levels of contaminants in these ponds, particularly mercury (Hg), which has a well established legacy in the Bay. In this study we described spatial and short-term temporal variations in sediment Hg species concentrations within and among the Alviso and Eden Landing salt ponds in the southern region of San Francisco Bay. We determined total Hg (Hgt) and methylmercury (MeHg) in the top 5 cm of sediment of most ponds in order to establish baseline conditions prior to restoration, sediment Hgt concentrations in a subset of these ponds after commencement of restoration, and variation in MeHg concentrations relative to sediment Hgt, pH, and total Fe concentrations and water depth and salinity in the subset of Alviso ponds. Inter-pond differences were greatest within the Alviso pond complex, where sediment Hgt concentrations averaged (arithmetic mean) 0.74 ??g/g pre and 1.03 ??g/g post-restoration activity compared to 0.11 ??g/g pre and post at Eden Landing ponds. Sediment Hgt levels at Alviso were fairly stable temporally and spatially, whereas MeHg levels were variable relative to restoration activities across time and space. Mean (arithmetic) sediment MeHg concentrations increased (2.58 to 3.03 ng/g) in Alviso and decreased (2.20 to 1.03 ng/g) in Eden Landing restoration ponds during the study. Differences in MeHg levels were related to water depth and pH, but these relationships were not consistent between years or among ponds and were viewed with caution. Factors affecting MeHg levels in these ponds (and in general) are highly complex and require in-depth study to understand.

Spatial and temporal variation of Shelf Water and its connection with Antarctic Bottom Water in Prydz Bay, East Antarctica

NASA Astrophysics Data System (ADS)

Sun, Y.; Shi, J.; Yuan, X.

2016-02-01

Hydrographic surveys from 1981 to 2015, instrumented seal data from 2004 to 2014, and mooring data were used to reveal spatial and temporal variation of Shelf Water (SW) and the connection between SW and Antarctic Bottom Water (AABW) in Prydz Bay. The basic spatial pattern of the SW properties was presented and 5 subregions were distinguished based on the pattern and the topography. The change of water masses and the processes on the shelf are investigated in these subregions. A high salinity SW(S>34.6) is observed in the central and northern part of the Amery Basin in summer, which is like to be caused by the Circumpolar Deep Water (CDW) intrusion, and the eddy activities could be the primary impact to the CDW intrusion. There could be less CDW intrusion in winter because of the ice cover in this subregion, which is supported by the mooring in Prydz Bay Channel. A high salinity SW is observed near the Mackenzie polynya in winter, which is caused by brine rejection in ice production process. But the high salinity SW seems unlikely to form the overflow denser SW and locally form AABW. A dense water mass with low salinity, low temperature and high oxygen was observed on the shelf break in the 70.5°E section, which could be caused by the Ice Shelf Water (ISW) export from Amery Shelf. According to the hydrographic data, the dense water can form overflow DSW and flow downslope to west, which can be observed in the bottom of slope near 1500m in the 70°E section. The water will form AABW if it can flow downslope to the deep basin and keep mixing with CDW, suggesting a new type of DSW overflow in Prydz Bay.

Automatic Bayes Factors for Testing Equality- and Inequality-Constrained Hypotheses on Variances.

PubMed

Böing-Messing, Florian; Mulder, Joris

2018-05-03

In comparing characteristics of independent populations, researchers frequently expect a certain structure of the population variances. These expectations can be formulated as hypotheses with equality and/or inequality constraints on the variances. In this article, we consider the Bayes factor for testing such (in)equality-constrained hypotheses on variances. Application of Bayes factors requires specification of a prior under every hypothesis to be tested. However, specifying subjective priors for variances based on prior information is a difficult task. We therefore consider so-called automatic or default Bayes factors. These methods avoid the need for the user to specify priors by using information from the sample data. We present three automatic Bayes factors for testing variances. The first is a Bayes factor with equal priors on all variances, where the priors are specified automatically using a small share of the information in the sample data. The second is the fractional Bayes factor, where a fraction of the likelihood is used for automatic prior specification. The third is an adjustment of the fractional Bayes factor such that the parsimony of inequality-constrained hypotheses is properly taken into account. The Bayes factors are evaluated by investigating different properties such as information consistency and large sample consistency. Based on this evaluation, it is concluded that the adjusted fractional Bayes factor is generally recommendable for testing equality- and inequality-constrained hypotheses on variances.

Application of acoustical methods for estimating water flow and constituent loads in Perdido Bay, Florida

USGS Publications Warehouse

Grubbs, J.W.; Pittman, J.R.

1997-01-01

Water flow and quality data were collected from December 1994 to September 1995 to evaluate variations in discharge, water quality, and chemical fluxes (loads) through Perdido Bay, Florida. Data were collected at a cross section parallel to the U.S. Highway 98 bridge. Discharges measured with an acoustic Doppler current profiler (ADCP) and computed from stage-area and velocity ratings varied roughly between + or - 10,000 cubic feet per second during a typical tidal cycle. Large reversals in flow direction occurred rapidly (less than 1 hour), and complete reversals (resulting in near peak net-upstream or downstream discharges) occurred within a few hours of slack water. Observations of simultaneous upstream and downstream flow (bidirectional flow) were quite common in the ADCP measurements, with opposing directions of flow occurring predominantly in vertical layers. Continuous (every 15 minutes) discharge data were computed for the period from August 18, 1995, to September 28, 1995, and filtered daily mean discharge values were computed for the period from August 19 to September 26, 1995. Data were not computed prior to August 18, 1995, either because of missing data or because the velocity rating was poorly defined (because of insufficient data) for the period prior to landfall of hurricane Erin (August 3, 1995). The results of the study indicate that acoustical techniques can yield useful estimates of continuous (instantaneous) discharge in Perdido Bay. Useful estimates of average daily net flow rates can also be obtained, but the accuracy of these estimates will be limited by small rating shifts that introduce bias into the instantaneous values that are used to compute the net flows. Instantaneous loads of total nitrogen ranged from -180 to 220 grams per second for the samples collected during the study, and instantaneous loads of total phosphorous ranged from -10 to 11 grams per second (negative loads indicate net upstream transport). The chloride concentrations from the water samples collected from Perdido Bay indicated a significant amount of mixing of saltwater and freshwater. Mixing effects could greatly reduce the accuracy of estimates of net loads of nutrients or other substances. The study results indicate that acoustical techniques can yield acceptable estimates of instantaneous loads in Perdido Bay. However, estimates of net loads should be interpreted with great caution and may have unacceptably large errors, especially when saltwater and freshwater concentrations differ greatly.

Machine Learning for Information Extraction in Informal Domains

DTIC Science & Technology

1998-11-01

Bayes algorithm (BayeslDF), a hybrid of BayeslDF and the grammatical inference algo- rithm Alergia (BayesGI), and a relational learner (SRV). It...State-Merging Methods 59 4.1.3 Alergia 61 4.2 Inferring Transducers 62 4.3 Experiments 66 4.4 Discussion 72 Relational Learning for...65 4.5 Precision/recall results for Alergia and BayesG I on the speaker field, with the alphabet transducer produced using m-estimates, at various

Variability in home mechanical ventilation prescription.

PubMed

Escarrabill, Joan; Tebé, Cristian; Espallargues, Mireia; Torrente, Elena; Tresserras, Ricard; Argimón, J

2015-10-01

Few studies have analyzed the prevalence and accessibility of home mechanical ventilation (HMV). The aim of this study was to characterize the prevalence of HMV and variability in prescriptions from administrative data. Prescribing rates of HMV in the 37 healthcare sectors of the Catalan Health Service were compared from billing data from 2008 to 2011. Crude accumulated activity rates (per 100,000 population) were calculated using systematic component of variation (SCV) and empirical Bayes (EB) methods. Standardized activity ratios (SAR) were described using a map of healthcare sectors. A crude rate of 23 HMV prescriptions per 100,000 population was observed. Rates increase with age and have increased by 39%. Statistics measuring variation not due to chance show a high variation in women (CSV=0.20 and EB=0.30) and in men (CSV=0.21 and EB=0.40), and were constant over time. In a multilevel Poisson model, hospitals with a chest unit were associated with a greater number of cases (beta=0.68, P<.0001). High variability in prescribing HMV can be explained, in part, by the attitude of professionals towards treatment and accessibility to specialist centers with a chest unit. Analysis of administrative data and variability mapping help identify unexplained variations and, in the absence of systematic records, are a feasible way of tracking treatment. Copyright © 2014 SEPAR. Published by Elsevier Espana. All rights reserved.

Spacelab Accomplishments Forum 4

NASA Technical Reports Server (NTRS)

Emond, J. (Editor); Bennet, N. (Compiler); McCauley, D. (Compiler); Murphy, K. (Compiler); Baugher, Charles R. (Technical Monitor)

1999-01-01

The Spacelab Module, exposed platforms, and supporting instrumentation were designed and developed by the European Space Agency to house advanced experiments inside the Space Shuttle cargo bay. The Spacelab program has hosted a cross-disciplinary research agenda over a 17-year flight history. Several variations of Spacelab were used to host payloads for almost every space research discipline that NASA pursues-life sciences, microgravity research, space sciences, and earth observation studies. After seventeen years of flight, Spacelab modules, pallets, or variations thereof flew on the Shuttle 36 times for a total of 375 flight days.

Oil slick studies using photographic and multispectral scanner data.

NASA Technical Reports Server (NTRS)

Munday, J. C., Jr.; Macintyre, W. G.; Penney, M. E.; Oberholtzer, J. D.

1971-01-01

Field studies of spills of Nos. 6 (Bunker C), 4, and 2 fuel oils and menhaden fish oil in the southern Chesapeake Bay have been supplemented with aerial photographic and multispectral scanner data. Thin films showed best in ultraviolet and blue bands and thick films in the green. Color film was effective for all thicknesses. Thermal infrared imagery provided clear detection, but required field temperature and thickness data to distinguish thickness/emissivity variations from temperature variations. Slick spreading rates agree with the theory of Fay (1969); further study of spreading is in progress.

On the spatial-temporal variations in the chlorophyll- a concentration on the Peter the Great Bay shelf during the winter-spring phytoplankton bloom according to satellite and subsatellite data

NASA Astrophysics Data System (ADS)

Shtraikhert, E. A.; Zakharkov, S. P.

2016-12-01

Chlorophyll- a concentration ( C chl) variations in the cross section within and outside the Peter the Great Bay shelf during different stages of the winter-spring phytoplankton bloom in 2003-2005 has been considered based on a ship (obtained during the R/V Akademik M.A. Lavrent'ev voyage of February 26 to March 9, 2003) and MODIS-Aqua spectroradiometer and the SeaWiFS color-scanner satellite data. A comparison of the C chl variability obtained from the ship and satellite data indicates that these data are inconsistent. According to satellite data obtained at the MUMM atmospheric correction, the C chl variability is distorted less than the NIR-correction data. Studying the variations in the coefficients of light absorption by the detritus and yellow substance ( a dg) and light backscattering by suspended particles ( b bp), C chl, chlorophyll- a fluorescence ( F chl) according to the satellite data allow us to state that the variations in the discrepancy between the satellite and ship C chl values are mainly caused by the variations in the content of the detritus and yellow substance in water. Based on the satellite data, it has been revealed that the a dg values increase with increasing wind mixing after the phytoplankton bloom (about 2-5 km areas where the a dg, C chl, F chl, and bbp values abruptly increased in 2005, apparently due to eddy formation). It has been indicated that the F chl characteristic, which is close to C chl, increases when the favorable conditions for the phytoplankton bloom deteriorate. Therefore, this characteristic cannot be used to identify C chl under the indicated conditions.

Parameter estimation for a cohesive sediment transport model by assimilating satellite observations in the Hangzhou Bay: Temporal variations and spatial distributions

NASA Astrophysics Data System (ADS)

Wang, Daosheng; Zhang, Jicai; He, Xianqiang; Chu, Dongdong; Lv, Xianqing; Wang, Ya Ping; Yang, Yang; Fan, Daidu; Gao, Shu

2018-01-01

Model parameters in the suspended cohesive sediment transport models are critical for the accurate simulation of suspended sediment concentrations (SSCs). Difficulties in estimating the model parameters still prevent numerical modeling of the sediment transport from achieving a high level of predictability. Based on a three-dimensional cohesive sediment transport model and its adjoint model, the satellite remote sensing data of SSCs during both spring tide and neap tide, retrieved from Geostationary Ocean Color Imager (GOCI), are assimilated to synchronously estimate four spatially and temporally varying parameters in the Hangzhou Bay in China, including settling velocity, resuspension rate, inflow open boundary conditions and initial conditions. After data assimilation, the model performance is significantly improved. Through several sensitivity experiments, the spatial and temporal variation tendencies of the estimated model parameters are verified to be robust and not affected by model settings. The pattern for the variations of the estimated parameters is analyzed and summarized. The temporal variations and spatial distributions of the estimated settling velocity are negatively correlated with current speed, which can be explained using the combination of flocculation process and Stokes' law. The temporal variations and spatial distributions of the estimated resuspension rate are also negatively correlated with current speed, which are related to the grain size of the seabed sediments under different current velocities. Besides, the estimated inflow open boundary conditions reach the local maximum values near the low water slack conditions and the estimated initial conditions are negatively correlated with water depth, which is consistent with the general understanding. The relationships between the estimated parameters and the hydrodynamic fields can be suggestive for improving the parameterization in cohesive sediment transport models.

Genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay

USGS Publications Warehouse

Duda, T. F.

1994-01-01

The genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay was described using starch gel electrophoresis at eight presumptive loci. Specimens were taken from five environmentally distinct sites located throughout the bay. The population maintains a high degree of genetic variation, with a mean heterozygosity of 0.295, a mean polymorphism of 0.75, and an average of 3.70 alleles per locus. The population is genetically homogeneous, as evidenced from genetic distance values and F-statistics. However, heterogeneity of populations was indicated from a contingency chi-square test. Significant deviations from Hardy-Weinberg equilibrium and heterozygote deficiencies were found at the Lap-1 locus for all populations and at the Lap-2 locus for a single population. High levels of variability could represent a universal characteristic of invading species, the levels of variability in the source population(s), and/or the dynamics of the introduction. Lack of differentiation between subpopulations may be due to the immaturity of the San Francisco Bay population, the “general purpose” phenotype genetic strategy of the species, high rates of gene flow in the population, and/or the selective neutrality of the loci investigated.

Past leaded gasoline emissions as a nonpoint source tracer in riparian systems: A study of river inputs to San Francisco Bay

USGS Publications Warehouse

Dunlap, C.E.; Bouse, R.; Flegal, A.R.

2000-01-01

Variations in the isotopic composition of lead in 1995-1998 river waters flowing into San Francisco Bay trace the washout of lead deposited in the drainage basin from leaded gasoline combustion. At the confluence of the Sacramento and San Joaquin rivers where they enter the Bay, the isotopic compositions of lead in the waters define a linear trend away from the measured historical compositions of leaded gas in California. The river waters are shifted away from leaded gasoline values and toward an isotopic composition similar to Sierra Nevadan inputs which became the predominant source of sedimentation in San Francisco Bay following the onset of hydraulic gold mining in 1853. Using lead isotopic compositions of hydraulic mine sediments and average leaded gasoline as mixing end members, we calculate that more than 50% of the lead in the present river water originated from leaded gasoline combustion. The strong adsorption of lead (log K(d) > 7.4) to particulates appears to limit the flushing of gasoline lead from the drainage basin, and the removal of that lead from the system may have reached an asymptotic limit. Consequently, gasoline lead isotopes should prove to be a useful nonpoint source tracer of the environmental distribution of particle- reactive anthropogenic metals in freshwater systems.

Evaluating Aquatic Life Benefits of Reducing Nutrient Loading ...

EPA Pesticide Factsheets

Theoretical linkages between excess nutrient loading, nutrient-enhanced community metabolism (i.e., production and respiration), and hypoxia in estuaries are well-understood. In seasonally-stratified estuaries and coastal systems (e.g., Chesapeake Bay, northern Gulf of Mexico), hypoxia is predominantly seasonal, such that the spatial extent indicates potential aquatic life impacts. However, in relatively small and shallow Gulf of Mexico bays and bayous, hypoxia frequently occurs episodically or on a diel basis. This study utilized continuous DO monitoring and 3-D hydrodynamic (Environmental Fluid Dynamics Code) and water quality (Water Quality Analysis Simulation Program) models to examine physical and biological controls on DO dynamics and ecosystem metabolism in Weeks Bay, AL. Observed vertical DO gradients varied on a diel basis, with larger amplitude variations at depth relative to the surface, underscoring the importance of benthic production and respiration as a driver of ecosystem metabolism in shallow estuaries. Hydrodynamic and water quality models simulated seasonal and event-driven dynamics, but struggled to resolve the amplitude of daily DO fluctuations, particularly in bottom waters. Using these data in conjunction with the 10-year continuous O2 record from Weeks Bay, we applied empirical relationships and simple scaling relations to predict how reducing nutrient loading may affect the frequency, severity and duration of hypoxia. We further applied

Migration and stopover strategies of individual Dunlin along the Pacific coast of North America

USGS Publications Warehouse

Warnock, N.; Takekawa, John Y.; Bishop, M.A.

2004-01-01

We radio-marked 18 Dunlin, Calidris alpina (L., 1758), at San Francisco Bay, California, and 11 Dunlin at Grays Harbor, Washington, and relocated 90% of them along the 4200 km long coastline from north of San Francisco Bay to the Yukon-Kuskokwim Delta, Alaska. The Copper River Delta, Alaska, was the single most important stopover site, with 79% of the marked birds detected there. Our second most important site was the Willapa Bay and Grays Harbor complex of wetlands in Washington. The mean length of stay past banding sites ranged from 1.0 to 3.8 days. Controlling for date of departure, birds banded at San Francisco Bay had higher rates of travel to the Copper River Delta than those banded at Grays Harbor. The later a bird left a capture site, the faster it traveled to the Copper River Delta. Length of stay at the Copper River Delta was inversely related to arrival date. We did not find any effect of sex on travel rate or length of stay. Combining the results of this study with our previous work on Western Sandpipers, Calidris mauri (Cabanis, 1875), reveals variation of migration strategies used within and among shorebird species along the eastern Pacific Flyway. ?? 2004 NRC.

Coastal circulation and sediment dynamics in Maunalua Bay, Oahu, Hawaii, measurements of waves, currents, temperature, salinity, and turbidity; November 2008-February 2009

USGS Publications Warehouse

Storlazzi, Curt D.; Presto, M. Katherine; Logan, Joshua B.; Field, Michael E.

2010-01-01

High-resolution measurements of waves, currents, water levels, temperature, salinity and turbidity were made in Maunalua Bay, southern Oahu, Hawaii, during the 2008-2009 winter to better understand coastal circulation, water-column properties, and sediment dynamics during a range of conditions (trade winds, kona storms, relaxation of trade winds, and south swells). A series of bottom-mounted instrument packages were deployed in water depths of 20 m or less to collect long-term, high-resolution measurements of waves, currents, water levels, temperature, salinity, and turbidity. These data were supplemented with a series of profiles through the water column to characterize the vertical and spatial variability in water-column properties within the bay. These measurements support the ongoing process studies being done as part of the U.S. Geological Survey (USGS) Coastal and Marine Geology Program's Pacific Coral Reef Project; the ultimate goal of these studies is to better understand the transport mechanisms of sediment, larvae, pollutants, and other particles in coral reef settings. Project Objectives The objective of this study was to understand the temporal variations in currents, waves, tides, temperature, salinity and turbidity within a coral-lined embayment that receives periodic discharges of freshwater and sediment from multiple terrestrial sources in the Maunalua Bay. Instrument packages were deployed for a three-month period during the 2008-2009 winter and a series of vertical profiles were collected in November 2008, and again in February 2009, to characterize water-column properties within the bay. Measurements of flow and water-column properties in Maunalua Bay provided insight into the potential fate of terrestrial sediment, nutrient, or contaminant delivered to the marine environment and coral larval transport within the embayment. Such data are useful for providing baseline information for future watershed decisions and for establishing guidelines for the U.S. Coral Reef Task Force's (USCRTF) Hawaiian Local Action Strategy to address Land-Based Pollution (LAS-LBP) threats to coral reefs adjacent to the urbanized watersheds of Manualua Bay. Study Area Maunalua Bay is on the south side of Oahu, Hawaii, and is approximately 10 km long and 3 km wide. The bay is flanked by two large, dormant craters: Koko Head to the east and Diamond Head to the west. Rainfall in the watersheds that drain into Maunalua Bay ranges from more than 200 cm/year at the top of the Ko'olau Range that borders the northwestern part of the bay to less than 70 cm/year to the east at Koko Head. Seven major channels flow into the bay, and all but one have been altered by engineering structures.

Reconstruction of Missing Pixels in Satellite Images Using the Data Interpolating Empirical Orthogonal Function (DINEOF)

NASA Astrophysics Data System (ADS)

Liu, X.; Wang, M.

2016-02-01

For coastal and inland waters, complete (in spatial) and frequent satellite measurements are important in order to monitor and understand coastal biological and ecological processes and phenomena, such as diurnal variations. High-frequency images of the water diffuse attenuation coefficient at the wavelength of 490 nm (Kd(490)) derived from the Korean Geostationary Ocean Color Imager (GOCI) provide a unique opportunity to study diurnal variation of the water turbidity in coastal regions of the Bohai Sea, Yellow Sea, and East China Sea. However, there are lots of missing pixels in the original GOCI-derived Kd(490) images due to clouds and various other reasons. Data Interpolating Empirical Orthogonal Function (DINEOF) is a method to reconstruct missing data in geophysical datasets based on Empirical Orthogonal Function (EOF). In this study, the DINEOF is applied to GOCI-derived Kd(490) data in the Yangtze River mouth and the Yellow River mouth regions, the DINEOF reconstructed Kd(490) data are used to fill in the missing pixels, and the spatial patterns and temporal functions of the first three EOF modes are also used to investigate the sub-diurnal variation due to the tidal forcing. In addition, DINEOF method is also applied to the Visible Infrared Imaging Radiometer Suite (VIIRS) on board the Suomi National Polar-orbiting Partnership (SNPP) satellite to reconstruct missing pixels in the daily Kd(490) and chlorophyll-a concentration images, and some application examples in the Chesapeake Bay and the Gulf of Mexico will be presented.

A large CO2 sink enhanced by eutrophication in a tropical coastal embayment (Guanabara Bay, Rio de Janeiro, Brazil)

NASA Astrophysics Data System (ADS)

Cotovicz, L. C., Jr.; Knoppers, B. A.; Brandini, N.; Costa Santos, S. J.; Abril, G.

2015-03-01

In contrast to its small surface area, the coastal zone plays a disproportionate role in the global carbon cycle. Carbon production, transformation, emission and burial rates at the land-ocean interface are still poorly known, especially in tropical regions. Surface water pCO2 and ancillary parameters were monitored during nine field campaigns between April 2013 and April 2014 in Guanabara Bay, a tropical eutrophic to hypertrophic semi-enclosed estuarine embayment surrounded by the city of Rio de Janeiro, SE-Brazil. Water pCO2 varied between 22 and 3715 ppmv in the Bay showing spatial, diurnal and seasonal trends that mirrored those of dissolved oxygen (DO) and Chlorophyll a (Chl a). Marked pCO2 undersaturation was prevalent in the shallow, confined and thermally stratified waters of the upper bay, whereas pCO2 oversaturation was restricted to sites close to the small river mouths and small sewage channels, which covered only 10% of the bay's area. Substantial daily variations in pCO2 (up to 395 ppmv between dawn and dusk) were also registered and could be integrated temporally and spatially for the establishment of net diurnal, seasonal and annual CO2 fluxes. In contrast to other estuaries worldwide, Guanabara Bay behaved as a net sink of atmospheric CO2, a property enhanced by the concomitant effects of strong radiation intensity, thermal stratification, and high availability of nutrients, which promotes phytoplankton development and net autotrophy. In the inner part of the bay, the calculated annual CO2 sink (-19.6 mol C m2 yr-1) matched the organic carbon burial in the sediments reported in the literature. The carbon sink and autotrophy of Guanabara Bay was driven by planktonic primary production promoted by eutrophication, and by its typology of marine embayment lacking the classical extended estuarine mixing zone, in contrast to river-dominated estuarine systems, which are generally net heterotrophic and CO2 emitters. Our results show that global CO2 budgetary assertions still lack information on tropical estuarine embayments and lagoons, which are affected by thermal stratification and eutrophication and behave specifically with respect to atmospheric CO2.

Microbial biogeography of San Francisco Bay sediments

NASA Astrophysics Data System (ADS)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess whether patterns of diversity observed at the broadest of taxonomic scales also apply to patterns observed within a single extremely diverse gene (nirS). In sum, this project provides a first look at the forces driving the migration and selection of microbial communities in San Francisco Bay.

A strong CO2 sink enhanced by eutrophication in a tropical coastal embayment (Guanabara Bay, Rio de Janeiro, Brazil)

NASA Astrophysics Data System (ADS)

Cotovicz, L. C., Jr.; Knoppers, B. A.; Brandini, N.; Costa Santos, S. J.; Abril, G.

2015-10-01

In contrast to its small surface area, the coastal zone plays a disproportionate role in the global carbon cycle. Carbon production, transformation, emission and burial rates at the land-ocean interface are significant at the global scale but still poorly known, especially in tropical regions. Surface water pCO2 and ancillary parameters were monitored during nine field campaigns between April 2013 and April 2014 in Guanabara Bay, a tropical eutrophic to hypertrophic semi-enclosed estuarine embayment surrounded by the city of Rio de Janeiro, southeast Brazil. Water pCO2 varied between 22 and 3715 ppmv in the bay, showing spatial, diurnal and seasonal trends that mirrored those of dissolved oxygen (DO) and chlorophyll a (Chl a). Marked pCO2 undersaturation was prevalent in the shallow, confined and thermally stratified waters of the upper bay, whereas pCO2 oversaturation was restricted to sites close to the small river mouths and small sewage channels, which covered only 10 % of the bay's area. Substantial daily variations in pCO2 (up to 395 ppmv between dawn and dusk) were also registered and could be integrated temporally and spatially for the establishment of net diurnal, seasonal and annual CO2 fluxes. In contrast to other estuaries worldwide, Guanabara Bay behaved as a net sink of atmospheric CO2, a property enhanced by the concomitant effects of strong radiation intensity, thermal stratification, and high availability of nutrients, which promotes phytoplankton development and net autotrophy. The calculated CO2 fluxes for Guanabara Bay ranged between -9.6 and -18.3 mol C m-2 yr-1, of the same order of magnitude as the organic carbon burial and organic carbon inputs from the watershed. The positive and high net community production (52.1 mol C m-2 yr-1) confirms the high carbon production in the bay. This autotrophic metabolism is apparently enhanced by eutrophication. Our results show that global CO2 budgetary assertions still lack information on tropical, marine-dominated estuarine systems, which are affected by thermal stratification and eutrophication and behave specifically with respect to atmospheric CO2.

Modern sedimentary environments in a large tidal estuary, Delaware Bay

USGS Publications Warehouse

Knebel, H.J.

1989-01-01

Data from an extensive grid of sidescan-sonar records reveal the distribution of sedimentary environments in the large, tidally dominated Delaware Bay estuary. Bathymetric features of the estuary include large tidal channels under the relatively deep (> 10 m water depth) central part of the bay, linear sand shoals (2-8 m relief) that parallel the sides of the tidal channels, and broad, low-relief plains that form the shallow bay margins. The two sedimentary environments that were identified are characterized by either (1) bedload transport and/or erosion or (2) sediment reworking and/or deposition. Sand waves and sand ribbons, composed of medium to coarse sands, define sites of active bedload transport within the tidal channels and in gaps between the linear shoals. The sand waves have spacings that vary from 1 to 70 m, amplitudes of 2 m or less, and crestlines that are usually straight. The orientations of the sand waves and ribbons indicate that bottom sediment movement may be toward either the northwest or southeast along the trends of the tidal channels, although sand-wave asymmetry indicates that the net bottom transport is directed northwestward toward the head of the bay. Gravelly, coarse-grained sediments, which appear as strongly reflective patterns on the sonographs, are also present along the axes and flanks of the tidal channels. These coarse sediments are lag deposits that have developed primarily where older strata were eroded at the bay floor. Conversely, fine sands that compose the linear shoals and muddy sands that cover the shallow bay margins appear mainly on the sonographs either as smooth featureless beds that have uniform light to moderate shading or as mosaics of light and dark patches produced by variations in grain size. These acoustic and textural characteristics are the result of sediment deposition and reworking. Data from this study (1) support the hypothesis that bed configurations under deep tidal flows are functions of current velocity, sediment size, and depth; (2) suggest criteria that could be used to distinguish between open estuarine tidal deposits in the geologic record; and (3) provide a guide to future utilization of the bay floor. ?? 1989.

Comparison of land-based sources with ambient estuarine concentrations of total dissolved nitrogen in Jiaozhou Bay (China)

NASA Astrophysics Data System (ADS)

Lu, Dongliang; Yang, Nannan; Liang, Shengkang; Li, Keqiang; Wang, Xiulin

2016-10-01

Seasonal, land-sea synchronous surveys were conducted from 2012 to 2013 to characterize the relationship between the composition of land-based total dissolved nitrogen (TDN) and the concentration of dissolved inorganic nitrogen (DIN) in Jiaozhou Bay (JZB). A total of 11 freshwater riverine sampling sites were selected at the river mouths and at waste water outfalls around JZB, while a total 23 Bay stations were established in JZB. Among them, 11 Bay stations were located near the 11 outfalls. Each land-sea sampling was conducted synchronously during a semi-tidal cycle. The contribution of NO3sbnd N, NO2sbnd N, NH4sbnd N, and dissolved organic nitrogen (DON) to TDN in land-based freshwater were similar to those in JZB seawater, while the contribution of the sum of NO3sbnd N and NO2sbnd N to TDN and the contribution of DON to TDN were about 3.2 and 4.1 times higher than the contribution of NH4sbnd N to TDN, respectively. These results showed that inputs of all land-based forms of nitrogen impact the DIN in seawater. Spatial distributions of DIN and DON, showing a gradual decrease from inner bay to the mouth of the bay, were negatively correlated with S in different seasons. In summer and winter, the ratio of DIN to DON in seawater (Rs) gradually decreased from the inner bay to the center of the bay, and the ratio of land-based DIN to DON (RL) was less than RS, indicating net transformation from land-based DON into marine DIN. However, in spring and autumn, the distribution of Rs was opposite to that in summer and winter, and RL was greater than RS, indicating net conversion from land-based DIN into marine DON. Throughout the whole year, net land-based DON was transformed into marine DIN. We provided direct evidence that the variation in DIN concentration in JZB was affected both by land-based TDN inputs and by their hydrodynamic transport and biogeochemical transformation processes.

Seasonal variation of early diagenesis and greenhouse gas production in coastal sediments of Cadiz Bay: Influence of anthropogenic activities

NASA Astrophysics Data System (ADS)

Burgos, Macarena; Ortega, Teodora; Bohórquez, Julio; Corzo, Alfonso; Rabouille, Christophe; Forja, Jesús M.

2018-01-01

Greenhouse gas production in coastal sediments is closely associated with the early diagenesis processes of organic matter and nutrients. Discharges from anthropogenic activities, particularly agriculture, fish farming and waste-water treatment plants supply large amounts of organic matter and inorganic nutrients that affect mineralization processes. Three coastal systems of Cadiz Bay (SW Spain) (Guadalete River, Rio San Pedro Creek and Sancti Petri Channel) were chosen to determine the seasonal variation of organic matter mineralization. Two sampling stations were selected in each system; one in the outer part, close to the bay, and another more inland, close to a discharge point of effluent related to anthropogenic activities. Seasonal variation revealed that metabolic reactions were driven by the annual change of temperature in the outer station of the systems. In contrast, these reactions depended on the amount of organic matter reaching the sediments in the outermost part of the systems, which was higher during winter. Oxygen is consumed in the first 0.5 cm indicating that suboxic and anoxic processes, such as denitrification, sulfate reduction and methanogenesis are important in these sediments. Sulfate reduction seems to account for most of the mineralization of organic matter at the marine stations, while methanogenesis is the main pathway at the sole freshwater station of this study, located inside the estuary of the Guadalete River, because of the lack of sulfate as electron acceptor. Results point to denitrification being the principal process of N2O formation. Diffusive fluxes varied between 2.6 and 160 mmol m-2 d-1 for dissolved inorganic carbon (DIC); 0.9 and 164.3 mmol m-2 d-1 for TA; 0.8 and 17.4 μmol m-2 d-1 for N2O; and 0.1 μmol and 13.1 mmol m-2 d-1 for CH4, indicating that these sediments act as a source of greenhouse gases to the water column.

A chemostratigraphic method to determine the end of impact-related sedimentation at marine-target impact craters (Chesapeake Bay, Lockne, Tvären)

USGS Publications Warehouse

Ormö, Jens; Hill, Andrew C.; Self-Trail, Jean M.

2010-01-01

To better understand the impact cratering process and its environmental consequences at the local to global scale, it is important to know when in the geological record of an impact crater the impact-related processes cease. In many instances, this occurs with the end of early crater modification, leaving an obvious sedimentological boundary between impactites and secular sediments. However, in marine-target craters the transition from early crater collapse (i.e., water resurge) to postimpact sedimentation can appear gradual. With the a priori assumption that the reworked target materials of the resurge deposits have a different chemical composition to the secular sediments we use chemostratigraphy (δ13Ccarb, %Corg, major elements) of sediments from the Chesapeake Bay, Lockne, and Tvären craters, to define this boundary. We show that the end of impact-related sedimentation in these cases is fairly rapid, and does not necessarily coincide with a visual boundary (e.g., grain size shift). Therefore, in some cases, the boundary is more precisely determined by chemostratigraphy, especially carbonate carbon isotope variations, rather than by visual inspection. It is also shown how chemostratigraphy can confirm the age of marine-target craters that were previously determined by biostratigraphy; by comparing postimpact carbon isotope trends with established regional trends.

Marine electrical resistivity imaging of submarine groundwater discharge: Sensitivity analysis and application in Waquoit Bay, Massachusetts, USA

USGS Publications Warehouse

Henderson, Rory; Day-Lewis, Frederick D.; Abarca, Elena; Harvey, Charles F.; Karam, Hanan N.; Liu, Lanbo; Lane, John W.

2010-01-01

Electrical resistivity imaging has been used in coastal settings to characterize fresh submarine groundwater discharge and the position of the freshwater/salt-water interface because of the relation of bulk electrical conductivity to pore-fluid conductivity, which in turn is a function of salinity. Interpretation of tomograms for hydrologic processes is complicated by inversion artifacts, uncertainty associated with survey geometry limitations, measurement errors, and choice of regularization method. Variation of seawater over tidal cycles poses unique challenges for inversion. The capabilities and limitations of resistivity imaging are presented for characterizing the distribution of freshwater and saltwater beneath a beach. The experimental results provide new insight into fresh submarine groundwater discharge at Waquoit Bay National Estuarine Research Reserve, East Falmouth, Massachusetts (USA). Tomograms from the experimental data indicate that fresh submarine groundwater discharge may shut down at high tide, whereas temperature data indicate that the discharge continues throughout the tidal cycle. Sensitivity analysis and synthetic modeling provide insight into resolving power in the presence of a time-varying saline water layer. In general, vertical electrodes and cross-hole measurements improve the inversion results regardless of the tidal level, whereas the resolution of surface arrays is more sensitive to time-varying saline water layer.

Geographic relatedness and predictability of Escherichia coli along a peninsular beach complex of Lake Michigan

USGS Publications Warehouse

Nevers, M.B.; Shively, D.A.; Kleinheinz, G.T.; McDermott, C.M.; Schuster, W.; Chomeau, V.; Whitman, R.L.

2009-01-01

To determine more accurately the real-time concentration of fecal indicator bacteria (FIB) in beach water, predictive modeling has been applied in several locations around the Great Lakes to individual or small groups of similar beaches. Using 24 beaches in Door County, Wisconsin, we attempted to expand predictive models to multiple beaches of complex geography. We examined the importance of geographic location and independent variables and the consequential limitations for potential beach or beach group models. An analysis of Escherichia coli populations over 4 yr revealed a geographic gradient to the beaches, with mean E. coli concentrations decreasing with increasing distance from the city of Sturgeon Bay. Beaches grouped strongly by water type (lake, bay, Sturgeon Bay) and proximity to one another, followed by presence of a storm or creek outfall or amount of shoreline enclosure. Predictive models developed for beach groups commonly included wave height and cumulative 48-h rainfall but generally explained little E. coli variation (adj. R2 = 0.19-0.36). Generally low concentrations of E. coli at the beaches influenced the effectiveness of model results presumably because of low signal-to-noise ratios and the rarity of elevated concentrations. Our results highlight the importance of the sensitivity of regressors and the need for careful methods evaluation. Despite the attractiveness of predictive models as an alternative beach monitoring approach, it is likely that FIB fluctuations at some beaches defy simple prediction approaches. Regional, multi-beach, and individual beach predictive models should be explored alongside other techniques for improving monitoring reliability at Great Lakes beaches. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Occurrence and seasonal variations of per- and polyfluoroalkyl substances (PFASs) including fluorinated alternatives in rivers, drain outlets and the receiving Bohai Sea of China.

PubMed

Chen, Hong; Han, Jianbo; Zhang, Can; Cheng, Jiayi; Sun, Ruijun; Wang, Xiaomeng; Han, Gengchen; Yang, Wenchao; He, Xin

2017-12-01

A simultaneous sampling campaign was undertaken to study the pollution by 21 per- and polyfluoroalkyl substances (PFASs) in rivers, drain outlets and their receiving Bohai Sea of China. Chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) are being used as fluorinated alternatives and they were included in this study. In comparison with other regions and countries, high concentrations of ∑ 21 PFASs in seawater samples from the Bohai Sea, ranging from 5.03 to 41 700 ng/L (median: 64.8 ng/L), were observed. The spatial distribution of PFAS levels in this sea area was in the ranking of Laizhou Bay > Liaodong Bay > Bohai Bay > other sea areas. By comparing the levels and composition profiles of PFASs in the seawater and their sources (rivers and drain outlets), it was concluded that rivers and drain outlets are the primary sources of PFAS contamination to the Bohai Sea. These PFAS levels varied seasonally among the rivers and drain outlets, but statistically significant changes were not observed. Levels of 6:2 and 8:2 Cl-PFESAs in rivers, drain outlets and receiving sea were firstly reported in the present study. Relatively high concentrations of 6:2 Cl-PFESA were found in drain outlets, ranging from below method limits of quantification (MLQ) to 7600 ng/L, but 8:2 Cl-PFAES detection was infrequent and all median concentration below MLQ. Mass discharges to the sea of 6:2 Cl-PFESA from rivers and drain outlets to the sea were estimated to be 37 and 17 kg/y, respectively. Copyright © 2017. Published by Elsevier Ltd.

Phosphorus speciation and its bioavailability in sediments of the Jiaozhou Bay

NASA Astrophysics Data System (ADS)

Kang, Xuming; Song, Jinming; Yuan, Huamao; Shi, Xin; Yang, Weifeng; Li, Xuegang; Li, Ning; Duan, Liqin

2017-03-01

Phosphorus (P) is an important macronutrient that can limit primary productivity in coastal marine ecosystems. In this study, four sediment cores were collected in the Jiaozhou Bay to study the phosphorus forms and their bioavailability, including exchangeable or loosely sorbed P (Ex-P), iron-bound P (Fe-P), authigenic P (Ca-P), detrital P (De-P) and organic P (OP), which were separated and quantified using a sequential extraction method (SEDEX). The results showed that the concentration of total P (TP) in core sediments ranged from 6.23 to 10.46 μmol/g, and inorganic P (IP) was the dominated P form. Fe-P and De-P were the main chemical forms of IP in core sediments. The profile variation of OP presented the most significant among the phosphorus forms. Whereas the concentrations of Ex-P, Fe-P, and Ca-P varied slightly with depth, indicating that the transformation of Ex-P, Fe-P, Ca-P, and OP could occur during sedimentary P burial. Moreover, the distribution of P species was influenced by many factors, including terrigenous input, biological processes, organic matter degradation and increasing human activities. High total organic carbon (TOC)/OP ratio occurred in the Jiaozhou Bay, ranging from 73 to 472 (average, 180 ± 81) in core sediments, which was caused by the increasing terrestrial organic matter. The ratio of TOC/Preactive ranged from 24 to 101 (average 46 ± 15) in core sediments (lower than the Redfield ratio), implying a surplus of sedimentary reactive P compared with TOC. Potential bioavailable P (BAP) accounted for about 28.2-60.8% (average, 47.1 ± 7.4%) of TP in core sediments, and presented an increasing trend since 1980s, which might be responsible for the shift of phytoplankton community composition during these decades.

Estimating Bacterial Production in Marine Waters from the Simultaneous Incorporation of Thymidine and Leucine

PubMed Central

Chin-Leo, Gerardo; Kirchman, David L.

1988-01-01

We examined the simultaneous incorporation of [3H]thymidine and [14C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 ± 0.2 [mean ± standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic acid-insoluble fraction. There were no significant differences in thymidine incorporation between dual- and single-label incubations (dual/ single = 1.03 ± 0.13). Addition of the two substrates in relatively large amounts (25 nM) did not apparently increase bacterial activity during short incubations (<5 h). With the dual-label method we found that thymidine and leucine incorporation rates covaried over depth profiles of the Chesapeake Bay. Estimates of bacterial production based on thymidine and leucine differed by less than 25%. Although the need for appropriate conversion factors has not been eliminated, the dual-label approach can be used to examine the variation in bacterial production while ensuring that the observed variation in incorporation rates is due to real changes in bacterial production rather than changes in conversion factors or introduction of other artifacts. PMID:16347706

Distribution of polycyclic aromatic hydrocarbons in southern Chesapeake Bay surface water: Evaluation of three methods for determining freely dissolved water concentrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gustafson, K.E.; Dickhut, R.M.

1997-03-01

Gas sparging, semipermeable-membrane devices (SPMDs), and filtration with sorption of dissolved polycyclic aromatic hydrocarbons (PAHs) to XAD-2 resin were evaluated for determining the concentrations of freely dissolved PAHs in estuarine waters of southern Chesapeake Bay at sites ranging from rural to urban and highly industrialized. Gas sparging had significant sampling artifacts due to particle scavenging by rising bubbles, and SPMDs were kinetically limited for four-ring and larger PAHs relative to short-term temporal changes in water concentrations. Filtration with sorption of the dissolved contaminant fraction to XAD-2 resin was found to be the most accurate and feasible method for determining concentrationsmore » of freely dissolved PAHs in estuarine water. Concentrations and distribution coefficients of dissolved and particulate PAHs were measured using the filtration/XAD-2 method. Concentrations of PAHs in surface waters of southern Chesapeake Bay were higher than those reported for the northern bay; concentrations in the Elizabeth River were elevated relative to all other sites. A gradient for particulate PAHs was observed from urban to remote sites. No seasonal trends were observed in dissolved or particle-bound PAH fractions at any site. Distributions of dissolved and particulate PAHs in surface waters of the Chesapeake Bay are near equilibrium at all locations and during all seasons.« less

Removing tidal-period variations from time-series data using low-pass digital filters

USGS Publications Warehouse

Walters, Roy A.; Heston, Cynthia

1982-01-01

Several low-pass, digital filters are examined for their ability to remove tidal Period Variations from a time-series of water surface elevation for San Francisco Bay. The most efficient filter is the one which is applied to the Fourier coefficients of the transformed data, and the filtered data recovered through an inverse transform. The ability of the filters to remove the tidal components increased in the following order: 1) cosine-Lanczos filter, 2) cosine-Lanczos squared filter; 3) Godin filter; and 4) a transform fitter. The Godin fitter is not sufficiently sharp to prevent severe attenuation of 2–3 day variations in surface elevation resulting from weather events.

Collaborating at a Regional Scale for Climate Literacy and Action

NASA Astrophysics Data System (ADS)

Carlton, C.; Shcherba, O.

2016-12-01

Since 2014, the Bay Area Climate Literacy Impact Collaborative (Bay-CLIC) has been the leading regional consortium dedicated to improving climate education and action. Collectively, Bay-CLIC members reach over 3 million individuals through their educational programming, serve counties all throughout the Bay Area, offer multiple methods of climate communication like place-based school programs and visitor centers, and serve audiences representing all age groups. With over 30 organizations ranging from park agencies to science museums and nonprofits promoting energy efficiency, Bay-CLIC is preparing to push out climate change messaging through a suite of projects. Currently, Bay-CLIC's work is centered on building connections between educators and local scientists and region-specific climate data, implementing joint campaigns to promote the social norming of sustainable behavior change, and developing a toolkit and trainings targeted to the needs of Bay Area environmental educators. Meeting the needs of this diverse group offers many opportunities for increasing impact, growing new, strategic partnerships, as well as overcoming a few challenges along the way. Come learn more about what we've accomplished so far and what new, exciting projects are coming down the pike.

Comparison of safety effect estimates obtained from empirical Bayes before-after study, propensity scores-potential outcomes framework, and regression model with cross-sectional data.

PubMed

Wood, Jonathan S; Donnell, Eric T; Porter, Richard J

2015-02-01

A variety of different study designs and analysis methods have been used to evaluate the performance of traffic safety countermeasures. The most common study designs and methods include observational before-after studies using the empirical Bayes method and cross-sectional studies using regression models. The propensity scores-potential outcomes framework has recently been proposed as an alternative traffic safety countermeasure evaluation method to address the challenges associated with selection biases that can be part of cross-sectional studies. Crash modification factors derived from the application of all three methods have not yet been compared. This paper compares the results of retrospective, observational evaluations of a traffic safety countermeasure using both before-after and cross-sectional study designs. The paper describes the strengths and limitations of each method, focusing primarily on how each addresses site selection bias, which is a common issue in observational safety studies. The Safety Edge paving technique, which seeks to mitigate crashes related to roadway departure events, is the countermeasure used in the present study to compare the alternative evaluation methods. The results indicated that all three methods yielded results that were consistent with each other and with previous research. The empirical Bayes results had the smallest standard errors. It is concluded that the propensity scores with potential outcomes framework is a viable alternative analysis method to the empirical Bayes before-after study. It should be considered whenever a before-after study is not possible or practical. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mineral compositions of plutonic rocks from the Lewis Hills massif, Bay of Islands ophiolite

NASA Technical Reports Server (NTRS)

Smith, Susan E.; Elthon, Don

1988-01-01

Mineral compositions of residual and cumulate rocks from the Lewis Hills massif of the Bay of Islands ophiolite complex are reported and interpreted in the context of magnetic processes involved in the geochemical evolution of spatially associated diabase dikes. The mineral compositions reflect greater degrees of partial melting than most abyssal peridotites do and appear to represent the most depleted end of abyssal peridotite compositions. Subsolidus equilibration between Cr-Al spinal and olivine generally has occurred at temperatures of 700 to 900 C. The spinel variations agree with the overall fractionation of basaltic magmas producing spinels with progressively lower Cr numbers. The compositions of clinopyroxenes suggest that the fractionation of two different magma series produced the various cumulate rocks.

Constancy of the relation between floc size and density in San Francisco Bay

USGS Publications Warehouse

Ganju, N.K.; Schoellhamer, D.H.; Murrell, M.C.; Gartner, J.W.; Wright, S.A.; ,

2007-01-01

The size and density of fine-sediment aggregates, or flocs, govern their transport and depositional properties. While the mass and volume concentrations of flocs can be measured directly or by optical methods, they must be determined simultaneously to gain an accurate density measurement. Results are presented from a tidal cycle study in San Francisco Bay, where mass concentration was determined directly, and volume concentration was measured in 32 logarithmically spaced size bins by laser-diffraction methods. The relation between floc size and density is investigated assuming a constant primary particle size and fractal floc dimension. This relation is validated with measurements from several sites throughout San Francisco Bay. The constancy of this relation implies a uniform primary particle size throughout the Bay, as well as uniform aggregation/disaggregation mechanisms (which modify fractal dimension). The exception to the relation is identified during near-bed measurements, when advected flocs mix with recently resuspended flocs from the bed, which typically have a higher fractal dimension than suspended flocs. The constant relation for suspended flocs simplifies monitoring and numerical modeling of suspended sediment in San Francisco Bay. ?? 2007 Elsevier B.V. All rights reserved.

Classifying emotion in Twitter using Bayesian network

NASA Astrophysics Data System (ADS)

Surya Asriadie, Muhammad; Syahrul Mubarok, Mohamad; Adiwijaya

2018-03-01

Language is used to express not only facts, but also emotions. Emotions are noticeable from behavior up to the social media statuses written by a person. Analysis of emotions in a text is done in a variety of media such as Twitter. This paper studies classification of emotions on twitter using Bayesian network because of its ability to model uncertainty and relationships between features. The result is two models based on Bayesian network which are Full Bayesian Network (FBN) and Bayesian Network with Mood Indicator (BNM). FBN is a massive Bayesian network where each word is treated as a node. The study shows the method used to train FBN is not very effective to create the best model and performs worse compared to Naive Bayes. F1-score for FBN is 53.71%, while for Naive Bayes is 54.07%. BNM is proposed as an alternative method which is based on the improvement of Multinomial Naive Bayes and has much lower computational complexity compared to FBN. Even though it’s not better compared to FBN, the resulting model successfully improves the performance of Multinomial Naive Bayes. F1-Score for Multinomial Naive Bayes model is 51.49%, while for BNM is 52.14%.

New Inlet in Great South Bay: Changes in Circulation Dynamics, Residence Time, and Salt Balance in Response to Low Frequency Forcing from Observations and FCVOM Simulations

NASA Astrophysics Data System (ADS)

Hinrichs, C.; Flagg, C. N.; Wilson, R. E.; Flood, R. D.

2016-02-01

The Great South Bay is a shallow, multi-inlet estuary at the south shore of Long Island. It is sheltered from the Atlantic by its barrier island Fire Island. Sufficient freshwater input in form of river flow, runoff, and groundwater input combined with restricted ocean-bay-exchange through few narrow inlets produce significant horizontal salinity and temperature gradients. A new inlet was cut into Fire Island during Hurricane Sandy in October 2012, and thanks to the ongoing monitoring program observational data is available from before and after Sandy to investigate changes in the bay induced by this new inlet.The data show a persistent increase in salinity in the bay, and residents, fishermen and scientists report decreased turbidity, improved water quality and a healthier ecosystem in the eastern part of bay. Calculation of residence time based on the freshwater fraction method showed a decrease from 25 to ten days for Bellport Bay near the new breach. From tide gauge data we see, that while tidal range in the bay has not increased significantly with the new inlet, water level response to low frequency forcing did. In general, water levels within the bay responds to both coastal Ekman set-up/set-down and to local wind forcing over the bay itself. Data analysis shows that the relative importance of those two drivers did change with the new inlet. In concert with data analysis, the finite element model FVCOM is applied on a high-resolution Great South Bay grid to further investigate changes in salinity distribution, circulation, and bay-ocean volume-exchange induced by the new breach as well as to examine the degree of interaction between the existing inlets and the new breach.

Variations of trace gases over the Bay of Bengal during the summer monsoon

NASA Astrophysics Data System (ADS)

Girach, I. A.; Ojha, Narendra; Nair, Prabha R.; Tiwari, Yogesh K.; Kumar, K. Ravi

2018-02-01

In situ measurements of near-surface ozone (O3), carbon monoxide (CO), and methane (CH4) were carried out over the Bay of Bengal (BoB) as a part of the Continental Tropical Convergence Zone (CTCZ) campaign during the summer monsoon season of 2009. O3, CO and CH4 mixing ratios varied in the ranges of 8-54 ppbv, 50-200 ppbv and 1.57-2.15 ppmv, respectively during 16 July-17 August 2009. The spatial distribution of mean tropospheric O3 from satellite retrievals is found to be similar to that in surface O3 observations, with higher levels over coastal and northern BoB as compared to central BoB. The comparison of in situ measurements with the Monitoring Atmospheric Composition & Climate (MACC) global reanalysis shows that MACC simulations reproduce the observations with small mean biases of 1.6 ppbv, -2.6 ppbv and 0.07 ppmv for O3, CO and CH4, respectively. The analysis of diurnal variation of O3 based on observations and the simulations from Weather Research and Forecasting coupled with Chemistry (WRF-Chem) at a stationary point over the BoB did not show a net photochemical build up during daytime. Satellite retrievals show limitations in capturing CH4 variations as measured by in situ sample analysis highlighting the need of more shipborne in situ measurements of trace gases over this region during monsoon.

Recruitment variation of eastern Bering Sea crabs: Climate-forcing or top-down effects?

NASA Astrophysics Data System (ADS)

Zheng, Jie; Kruse, Gordon H.

2006-02-01

During the last three decades, population abundances of eastern Bering Sea (EBS) crab stocks fluctuated greatly, driven by highly variable recruitment. In recent years, abundances of these stocks have been very low compared to historical levels. This study aims to understand recruitment variation of six stocks of red king ( Paralithodes camtschaticus), blue king ( P. platypus), Tanner ( Chionoecetes bairdi), and snow ( C. opilio) crabs in the EBS. Most crab recruitment time series are not significantly correlated with each other. Spatial distributions of three broadly distributed crab stocks (EBS snow and Tanner crabs and Bristol Bay red king crab) have changed considerably over time, possibly related in part to the regime shift in climate and physical oceanography in 1976-1977. Three climate-forcing hypotheses on larval survival have been proposed to explain crab recruitment variation of Bristol Bay red king crab and EBS Tanner and snow crabs. Some empirical evidence supports speculation that groundfish predation may play an important role in crab recruitment success in the EBS. However, spatial dynamics in the geographic distributions of groundfish and crabs over time make it difficult to relate crab recruitment strength to groundfish biomass. Comprehensive field and spatially explicit modeling studies are needed to test the hypotheses and better understand the relative importance and compound effects of bottom-up and top-down controls on crab recruitment.

Seasonal variations in erodibility and sediment transport potential in a mesotidal channel-flat complex, Willapa Bay, WA

NASA Astrophysics Data System (ADS)

Wiberg, Patricia L.; Law, Brent A.; Wheatcroft, Robert A.; Milligan, Timothy G.; Hill, Paul S.

2013-06-01

Measurements of erodibility, porosity and sediment size were made three times over the course of a year at sites within a muddy, mesotidal flat-channel complex in southern Willapa Bay, WA, to examine spatial and seasonal variations in sediment properties and transport potential. Average critical shear stress profiles, the metric we used for erodibility, were quantified using a power-law fit to cumulative eroded mass vs. shear stress for the flats and channel. Laboratory erosion measurements of deposits made from slurries of flat and channel sediment were used to quantify erodibility over consolidation time scales ranging from 6 to 96h. Erodibility of the tidal flats was consistently low, with spatial variability comparable to seasonal variability despite seasonal changes in biological activity. In contrast, channel-bed erodibility underwent large seasonal variations, with mobile sediment present in the channel thalweg during winter that was absent in the spring and summer, when channel-bed erodibility was low and comparable to that of the tidal flats. Sediment on the northern (left) channel flank was mobile in summer and winter, whereas sediment on the southern flank was not. Seasonal changes in channel-bed erodibility are sufficient to produce order-of-magnitude changes in suspended sediment concentrations during peak tidal flows. Porosity just below the sediment surface was the best predictor of erodibility in our study area.

Organic carbon balance and net ecosystem metabolism in Chesapeake Bay

USGS Publications Warehouse

Kemp, W.M.; Smith, E.M.; Marvin-DiPasquale, M.; Boynton, W.R.

1997-01-01

The major fluxes of organic carbon associated with physical transport and biological metabolism were compiled, analyzed and compared for the mainstem portion of Chesapeake Bay (USA). In addition, 5 independent methods were used to calculate the annual mean net ecosystem metabolism (NEM = production - respiration) for the integrated Bay. These methods, which employed biogeochemical models, nutrient mass-balances anti summation of individual organic carbon fluxes, yielded remarkably similar estimates, with a mean NEM of +50 g C m-2 yr-1 (?? SE = 751, which is approximately 8% of the estimated annual average gross primary production. These calculations suggest a strong cross-sectional pattern in NEM throughout the Bay, wherein net heterotrophic metabolism prevails in the pelagic zones of the main channel, while net autotrophy occurs in the littoral zones which flank the deeper central area. For computational purposes, the estuary was separated into 3 regions along the land-sea gradient: (1) the oligohaline Upper Bay (11% of total area); (2) the mesohaline Mid Bay (36% of area); and (3) the polyhaline Lower Bay (53% of area). A distinct regional trend in NEM was observed along this salinity gradient, with net here(atrophy (NEM = 87 g C m-2 yr-1) in the Upper Bay, balanced metabolism in the Mid Bay and net autotrophy (NEM = +92 g C m-2 yr-1) in the Lower Bay. As a consequence of overall net autotrophy, the ratio of dissolved inorganic nitrogen (DIN) to total organic nitrogen (TON) changed from DIN:TON = 5.1 for riverine inputs to DIN:TON = 0.04 for water exported to the ocean. A striking feature of this organic C mass-balance was the relative dominance of biologically mediated metabolic fluxes compared to physical transport fluxes. The overall ratio of physical TOC inputs (1) to biotic primary production (P) was 0.08 for the whole estuary, but varied dramatically from 2.3 in the Upper Bay to 0.03 in the Mid and Lower Bay regions. Similarly, ecosystem respiration was some 6-fold higher than the sum of all physical carbon sinks. This general negative correspondence between I:P ratio and NEM, which occurred among Bay regions, was also evident in data available for organic C fluxes in other coastal ecosystems. An inverse relationship between NEM and P, postulated in a previous study, did not apply to Chesapeake Bay, and closer examination of available data revealed the importance of the loading ratio of DIN:TOC as a key control on coastal NEM. It is proposed here that the general global trend of coastal eutrophication will lead to increasing values of NEM in estuaries worldwide. The management implications of this trend are complex, involving both increased potential fisheries harvest and decreased demersal habitat.

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles.

PubMed

Kitchen, Robert R; Sabine, Vicky S; Sims, Andrew H; Macaskill, E Jane; Renshaw, Lorna; Thomas, Jeremy S; van Hemert, Jano I; Dixon, J Michael; Bartlett, John M S

2010-02-24

Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data.

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles

PubMed Central

2010-01-01

Background Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. Results A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. Conclusion In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data. PMID:20181233

Heritability of body size in the polar bears of Western Hudson Bay.

PubMed

Malenfant, René M; Davis, Corey S; Richardson, Evan S; Lunn, Nicholas J; Coltman, David W

2018-04-18

Among polar bears (Ursus maritimus), fitness is dependent on body size through males' abilities to win mates, females' abilities to provide for their young and all bears' abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449-individual pedigree and an array of 5,433 single nucleotide polymorphisms (SNPs) to provide the first quantitative genetic study of polar bears. We used animal models to estimate heritability (h 2 ) among polar bears handled between 1966 and 2011, obtaining h 2 estimates of 0.34-0.48 for strictly skeletal traits and 0.18 for axillary girth (which is also dependent on fatness). We genotyped 859 individuals with the SNP array to test for marker-trait association and combined p-values over genetic pathways using gene-set analysis. Variation in all traits appeared to be polygenic, but we detected one region of moderately large effect size in body length near a putative noncoding RNA in an unannotated region of the genome. Gene-set analysis suggested that variation in body length was associated with genes in the regulatory cascade of cyclin expression, which has previously been associated with body size in mice. A greater understanding of the genetic architecture of body size variation will be valuable in understanding the potential for adaptation in polar bear populations challenged by climate change. © 2018 John Wiley & Sons Ltd.

Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

PubMed Central

Barbeau, Myriam A.

2016-01-01

Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

HISTORICAL CHANGES IN GLOBAL SCALE CIRCULATION PATTERNS, MID-ATLANTIC CLIMATE STREAM FLOW AND NUTRIENT FLUXES TO THE CHESAPEAKE BAY

EPA Science Inventory

The rate of change in Northern Hemisphere temperature in the past century strongly suggests that we are now in a period of rapid global climate change. Also, the climate in the mid-Atlantic is quite sensitive to larger scale climate variation, which affects the frequency and seve...

77 FR 35431 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-13

...-007, Ecology Department, Montana State University, 310 Lewis Hall, Bozeman, MT 59715. Activity for... heterogeneity in life-history tactics of Weddell seals in Erebus Bay, Antarctica. A breeding population of... evaluate how temporal variation in the marine environment affects a long-lived mammal's population dynamics...

Natural environment design requirements for the space tug

NASA Technical Reports Server (NTRS)

West, G. S., Jr.

1973-01-01

The natural environment design requirements for the space tug are presented. Since the Space Tug is carried as cargo to orbital altitudes in the space shuttle bay, orbital environmental impacts and short-period atmospheric density variations are the main concerns. The subjects discussed are: (1) natural environment, (2) neutral environment, (3) charged particles, (4) radiation, and (5) meteoroid hazards.

Study of the possible role of pollution in the prevalence of sea nettles in the Chesapeake Bay and the development of a census taking method

NASA Technical Reports Server (NTRS)

1971-01-01

A study of the effect of pollutants on the sea nettle population of Chesapeake Bay was conducted. The effects of pollutants on the polyp stage of the nettle were stressed. Methods of detecting adult sea nettles by remote sensing are discussed. The effects of phosphate, nitrate, ammonium, and combinations of these pollutants were investigated.

Mercury concentrations in estuarine sediments, Lavaca and Matagorda bays, Texas, 1992

USGS Publications Warehouse

Brown, David S.; Snyder, Grant L.; Taylor, R. Lynn

1998-01-01

U.S. Environmental Protection Agency Method 7471 (Cold Vapor Atomic Absorption) was an acceptable analytical method for determining the total mercury concentrations in the Lavaca-Matagorda Bays estuarine sediment samples. Measurement of additional trace metals would aid in the characterization of total mercury concentrations and in the identification of concentrator/collector relations that are principally responsible for the adsorption of mercurous compounds to particulates in the bottom sediments.

Biological baseline data Youngs Bay, Oregon, 1974

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMechan, K.J.; Higley, D.L.; Holton, R.L.

1975-04-01

This report presents biological baseline information gathered during the research project, Physical, Chemical and Biological Studies on Youngs Bay.'' Youngs Bay is a shallow embayment located on the south shore of the Columbia River, near Astoria, Oregon. Research on Youngs Bay was motivated by the proposed construction by Alumax Pacific Aluminum Corporation of an aluminum reduction plant at Warrenton, Oregon. The research was designed to provide biological baseline information on Youngs Bay in anticipation of potential harmful effects from plant effluents. The information collected concerns the kinds of animals found in the Youngs Bay area, and their distribution and seasonalmore » patterns of abundance. In addition, information was collected on the feeding habits of selected fish species, and on the life history and behavioral characteristics of the most abundant benthic amphipod, Corophium salmonis. Sampling was conducted at approximately three-week intervals, using commonly accepted methods of animal collection. Relatively few stations were sampled for fish, because of the need to standardize conditions of capture. Data on fish capture are reported in terms of catch-per-unit effort by a particular sampling gear at a specific station. Methods used in sampling invertebrates were generally more quantitative, and allowed sampling at a greater variety of places, as well as a valid basis for the computation of densities. Checklists of invertebrate species and fish species were developed from these samples, and are referred to throughout the report. The invertebrate checklist is more specific taxonomically than are tables reporting invertebrate densities. This is because the methods employed in identification were more precise than those used in counts. 9 refs., 27 figs., 25 tabs.« less

Linking Structural Equation Modelling with Bayesian Network and Coastal Phytoplankton Dynamics in Bohai Bay

NASA Astrophysics Data System (ADS)

Chu, Jiangtao; Yang, Yue

2018-06-01

Bayesian networks (BN) have many advantages over other methods in ecological modelling and have become an increasingly popular modelling tool. However, BN are flawed in regard to building models based on inadequate existing knowledge. To overcome this limitation, we propose a new method that links BN with structural equation modelling (SEM). In this method, SEM is used to improve the model structure for BN. This method was used to simulate coastal phytoplankton dynamics in Bohai Bay. We demonstrate that this hybrid approach minimizes the need for expert elicitation, generates more reasonable structures for BN models and increases the BN model's accuracy and reliability. These results suggest that the inclusion of SEM for testing and verifying the theoretical structure during the initial construction stage improves the effectiveness of BN models, especially for complex eco-environment systems. The results also demonstrate that in Bohai Bay, while phytoplankton biomass has the greatest influence on phytoplankton dynamics, the impact of nutrients on phytoplankton dynamics is larger than the influence of the physical environment in summer. Furthermore, despite the Redfield ratio indicating that phosphorus should be the primary nutrient limiting factor, our results indicate that silicate plays the most important role in regulating phytoplankton dynamics in Bohai Bay.

Sea otter studies in Glacier Bay National Park and Preserve: Aerial surveys, foraging observations, and intertidal clam sampling

USGS Publications Warehouse

Bodkin, James L.; Kloecker, Kimberly A.; Esslinger, George G.; Monson, Daniel H.; DeGroot, J.D.

2001-01-01

Following translocations to the outer coast of Southeast Alaska in 1965, sea otters have been expanding their range and increasing in abundance. We began conducting surveys for sea otters in Cross Sound, Icy Strait and Glacier Bay, Alaska in 1994, following initial reports of their presence in Glacier Bay in 1993. Since 1995, the number of sea otters in Glacier Bay proper has increased from about 5 to more than 500. Between 1993 and 1997 sea otters were apparently only occasional visitors to Glacier Bay, but in 1998 long-term residence was established as indicated by the presence of adult females and their dependent pups. Sea otter distribution is limited to the Lower Bay, south of Sandy Cove, and is not continuous within that area. Concentration occur in the vicinity of Sita Reef and Boulder Island and between Pt. Carolus and Rush Pt. on the west side of the Bay (Figure 1). We describe the diet of sea otters in Glacier Bay and south Icy Strait through visual observations of prey during >4,000 successful forage dives. In 2,399 successful foraging dives observed in Glacier Bay proper, diet consisted of 40% clam, 21% urchins, 18% mussel, 4% crab, 5% other and 12% unidentified. Most prey recovered by sea otters are commercially, socially, or ecological important species. Species of clam are primarily Saxidomus gigantea, Protothaca staminea, and Serripes groenlandicus. Urchins are primarily Strongylocentrotus droebachiensis while both mussles, Modiolus modiolus and Mytilus trossulus, are taken. Crabs include species of Cancer, Chinoecetes, Paralithodes, and Telmessus. Although we characterize diet at broad geographic scales, we found diet to vary between sites separated by as little as several hundred meters. Dietary variation among and within sites can reflect differences in prey availability and individual choice.We estimated species composition, density, biomass, and sizes of intertidal clams at 59 sites in Glacier Bay, 14 sites in Idaho Inlet, 12 sites in Port Althorp and 2 sites in Dundas Bay. There is no direct evidence of otter foraging at any of our clam sampling sites except at Port Althorp where sea otters have been present for >20 years and regularly forage intertidally. There is some indication of intertidal foraging in Idaho Inlet, based on reduced mean size of preferred clam species. Sea otters have been present in Idaho Inlet for at least 12 years. We sampled 48 systematically selected sites to allow inference throughout Glacier Bay intertidal areas and 12 preferred habitat intertidal sites to estimate maximum clam densities in the Bay. We also sampled 14 and 12 random sites in Idaho Inlet and Port Althorp, respectively, to provide contrast between sites with and without sea otters. Densities and biomass of intertidal clams were greater in the Lower Bay than either the East or West Arms. Mean densities (#/0.25m2) of all species of clams > 10.0 mm total length were 96.5 at preferred sites, 32.8 in the Lower Bay, 12.2 in the East Arm, 6.6 in the West Arm, 11.32 at Port Althorp and 27.1 at Idaho Inlet. Clam densities were lower in the Upper Arms of Glacier Bay, compared to the Lower Bay and were similar to densities at Port Althorp. In the Lower Bay, clam densities were nearly twice as high at preferred clam sites compared to those systematically sampled. Species of Macoma were the numerically dominant intertidal clam at most sites in Glacier Bay, while Protothaca staminea was dominant at Idaho Inlet and Port Althorp. Biomas (g/0.25m2) was higher in the Lower Bay (23.5) than either Arm (2.1 and .91) and higher at preferred sites (73.4) than systematically selected sites in Glacier Bay. Biomass estimates at Port Althorp were 5.2 and 9.7 at Idaho Inlet. Biomass estimates were dominated by species of Saxidomus, Protothaca and Mya in Glacier Bay and by Protothaca and Saxidomus at Idaho Inlet and Port Althrop. We suspect differences in density and biomass relate to habitat differences between areas within Glacier Bay

Marine magnetic survey and onshore gravity and magnetic survey, San Pablo Bay, northern California

USGS Publications Warehouse

Ponce, David A.; Denton, Kevin M.; Watt, Janet T.

2016-09-12

IntroductionFrom November 2011 to August 2015, the U.S. Geological Survey (USGS) collected more than 1,000 line-kilometers (length of lines surveyed in kilometers) of marine magnetic data on San Pablo Bay, 98 onshore gravity stations, and over 27 line-kilometers of ground magnetic data in northern California. Combined magnetic and gravity investigations were undertaken to study subsurface geologic structures as an aid in understanding the geologic framework and earthquake hazard potential in the San Francisco Bay Area. Furthermore, marine magnetic data illuminate local subsurface geologic features in the shallow crust beneath San Pablo Bay where geologic exposure is absent.Magnetic and gravity methods, which reflect contrasting physical properties of the subsurface, are ideal for studying San Pablo Bay. Exposed rock units surrounding San Pablo Bay consist mainly of Jurassic Coast Range ophiolite, Great Valley sequence, Franciscan Complex rocks, Miocene sedimentary rocks, and unconsolidated alluvium (Graymer and others, 2006). The contrasting magnetic and density properties of these rocks enable us to map their subsurface extent.

Summary of suspended-sediment concentration data, San Francisco Bay, California, water year 2010

USGS Publications Warehouse

Buchanan, Paul A.; Morgan, Tara L.

2014-01-01

Suspended-sediment concentration data were collected by the U.S. Geological Survey in San Francisco Bay during water year 2010 (October 1, 2009–September 30, 2010). Turbidity sensors and water samples were used to monitor suspended-sediment concentration at two sites in Suisun Bay, one site in San Pablo Bay, three sites in Central San Francisco Bay, and one site in South San Francisco Bay. Sensors were positioned at two depths at most sites to help define the vertical variability of suspended sediments. Water samples were collected periodically and analyzed for concentrations of suspended sediment. The results of the analyses were used to calibrate the output of the turbidity sensors so that a record of suspended-sediment concentrations could be computed. This report presents the data-collection methods used and summarizes, in graphs, the suspended-sediment concentration data collected from October 2009 through September 2010. Calibration curves and plots of the processed data for each sensor also are presented.

Metabarcoding reveals environmental factors influencing spatio-temporal variation in pelagic micro-eukaryotes.

PubMed

Brannock, Pamela M; Ortmann, Alice C; Moss, Anthony G; Halanych, Kenneth M

2016-08-01

Marine environments harbour a vast diversity of micro-eukaryotic organisms (protists and other small eukaryotes) that play important roles in structuring marine ecosystems. However, micro-eukaryote diversity is not well understood. Likewise, knowledge is limited regarding micro-eukaryote spatial and seasonal distribution, especially over long temporal scales. Given the importance of this group for mobilizing energy from lower trophic levels near the base of the food chain to larger organisms, assessing community stability, diversity and resilience is important to understand ecosystem health. Herein, we use a metabarcoding approach to examine pelagic micro-eukaryote communities over a 2.5-year time series. Bimonthly surface sampling (July 2009 to December 2011) was conducted at four locations within Mobile Bay (Bay) and along the Alabama continental shelf (Shelf). Alpha-diversity only showed significant differences in Shelf sites, with the greatest differences observed between summer and winter. Beta-diversity showed significant differences in community composition in relation to season and the Bay was dominated by diatoms, while the Shelf was characterized by dinoflagellates and copepods. The northern Gulf of Mexico is heavily influenced by the Mobile River Basin, which brings low-salinity nutrient-rich water mostly during winter and spring. Community composition was correlated with salinity, temperature and dissolved silicate. However, species interactions (e.g. predation and parasitism) may also contribute to the observed variation, especially on the Shelf, which warrants further exploration. Metabarcoding revealed clear patterns in surface pelagic micro-eukaryote communities that were consistent over multiple years, demonstrating how these techniques could be greatly beneficial to ecological monitoring and management over temporal scales. © 2016 John Wiley & Sons Ltd.

Shipborne Magnetic Survey of San Pablo Bay and Implications on the Hayward-Rodgers Creek Fault Junction

NASA Astrophysics Data System (ADS)

Ponce, D. A.; Athens, N. D.; Denton, K.

2012-12-01

A shipborne magnetic survey of San Pablo Bay reveals a steep magnetic gradient as well as several prominent magnetic anomalies along the offshore extension of the Hayward Fault. The Hayward Fault enters San Pablo Bay at Pinole Point and potentially extends beneath San Pablo Bay for 15 km. About 1,000 line-km of shipborne magnetometer data were collected in San Pablo Bay along approximately north-east and north-west trending traverses. Shiptrack lines were spaced 200-m apart in a N55oE direction and tie-lines were spaced 500- and 1,000-m apart in a N145oE direction. Magnetometer and Geographic Positioning System (GPS) data were collected simultaneously at one-second intervals using a Geometrics G858 cesium vapor magnetometer with the sensor attached to a nonmagnetic pole extended about 2 m over the bow. Diurnal variations of the Earth's magnetic field were recorded at a ground magnetic base station and shipborne data were corrected for diurnal variations, International Geomagnetic Reference Field, cultural noise, heading errors, and leveling errors. The heading correction applied to the shipborne magnetic data accounts for a systematic shift in the magnetic readings due to the magnetic field produced by the boat and the orientation of the boat. The heading correction was determined by traversing several shiptrack lines in various azimuths in opposite directions. Magnetic measurements off the main survey lines (e.g., turns) were removed from the survey. After applying the heading correction, crossing values or the difference in values where two survey lines intersect were compared and the survey was leveled. Shipborne magnetic data reveal a prominent magnetic anomaly immediately offshore of Point Pinole that probably reflects ultramafic rocks (e.g. serpentinite), similar to those exposed in the northern part of the onshore Hayward Fault. Further to the northwest, shipborne magnetic data enhance two prominent aeromagnetic anomalies along the Hayward Fault in the central part of San Pablo Bay. These magnetic anomalies appear to represent two separate features, one on either side of the Hayward Fault. Likely sources for these anomalies are probably mafic, ultramafic, or volcanic rocks along the fault. Indeed, the more prominent, higher amplitude anomaly, which occurs on the west side of the Hayward Fault, could reflect an offset counterpart to the San Leandro gabbro body in the central part of the onshore portion of the Hayward Fault (Jachens et al., 2002). If so, the apparent offset is about 43 km. Although a magnetic ridge of possible volcanic rock origin (Wright and Smith, 1992) occurs between the Hayward and Rodgers Creek Faults, the Rodgers Creek Fault itself may be expressed by a steep gradient in the shipborne magnetic data. Analysis of these high-resolution shipborne magnetic data afford us the opportunity to image the detailed structure beneath San Pablo Bay and its implications on earthquake hazards.

Bayesian Statistics for Biological Data: Pedigree Analysis

ERIC Educational Resources Information Center

Stanfield, William D.; Carlton, Matthew A.

2004-01-01

The use of Bayes' formula is applied to the biological problem of pedigree analysis to show that the Bayes' formula and non-Bayesian or "classical" methods of probability calculation give different answers. First year college students of biology can be introduced to the Bayesian statistics.

External impacts of an intraurban air transportation system in the San Francisco Bay area

NASA Technical Reports Server (NTRS)

Lu, J. Y.; Gebman, J. R.; Kirkwood, T. F.; Mcclure, P. T.; Stucker, J. P.

1972-01-01

The effects are studied of an intraurban V/STOL commuter system on the economic, social, and physical environment of the San Francisco Bay Area. The Bay Area was chosen mainly for a case study; the real intent of the analysis is to develop methods by which the effects of such a system could be evaluated for any community. Aspects of the community life affected include: income and employment, benefits and costs, noise, air pollution, and road congestion.

Atmospheric deposition of organochlorine contaminants to Galveston Bay, Texas

NASA Astrophysics Data System (ADS)

Park, June-Soo; Wade, Terry L.; Sweet, Stephen

Atmospheric monitoring of PCBs and chlorinated pesticides (e.g., HCHs, chlordanes, and DDTs) in Galveston Bay was conducted at Seabrook, Texas. Air and wet deposition samples were collected from 2 February 1995 and continued through 6 August 1996. Vapor total PCB ( tPCB) concentrations in air ranged from 0.21 to 4.78 ng m -3 with a dominance of tri-chlorinated PCBs. Dissolved tPCBs in rain ranged from 0.08 to 3.34 ng l -1, with tetra-chlorinated PCBs predominating. The predominant isomers found in air and rain were α- and γ-HCH, α- and γ-chlordanes, 4,4'-DDT, and dieldrin. The concentrations of PCBs and pesticides in the air and rain revealed no clear seasonal trend. Elevated levels of PCBs in the air occurred when temperatures were high and wind came from urban and industrialized areas (S, SW, NW, and W of the site). Concentrations of HCHs were elevated in April, May, and October, perhaps due to local and/or regional applications of γ-HCH (lindane). Other pesticides showed no notable temporal variation. When winds originated from the Gulf of Mexico (southeasterly), lower concentrations of organochlorines were detected in the air. The direct deposition rate (wet+dry) of PCBs to Galveston Bay (6.40 μg m -2 yr -1) was significantly higher than that of pesticides by a factor of 5-10. The net flux from gas exchange estimated for PCBs was from Galveston Bay water to the atmosphere (78 μg m -2 yr -1). Gas exchange of PCBs from bay water to the atmosphere was the dominant flux.

Time series models of decadal trends in the harmful algal species Karlodinium veneficum in Chesapeake Bay.

PubMed

Lin, Chih-Hsien Michelle; Lyubchich, Vyacheslav; Glibert, Patricia M

2018-03-01

The harmful dinoflagellate, Karlodnium veneficum, has been implicated in fish-kill and other toxic, harmful algal bloom (HAB) events in waters worldwide. Blooms of K. veneficum are known to be related to coastal nutrient enrichment but the relationship is complex because this HAB taxon relies not only on dissolved nutrients but also particulate prey, both of which have also changed over time. Here, applying cross-correlations of climate-related physical factors, nutrients and prey, with abundance of K. veneficum over a 10-year (2002-2011) period, a synthesis of the interactive effects of multiple factors on this species was developed for Chesapeake Bay, where blooms of the HAB have been increasing. Significant upward trends in the time series of K. veneficum were observed in the mesohaline stations of the Bay, but not in oligohaline tributary stations. For the mesohaline regions, riverine sources of nutrients with seasonal lags, together with particulate prey with zero lag, explained 15%-46% of the variation in the K. veneficum time series. For the oligohaline regions, nutrients and particulate prey generally showed significant decreasing trends with time, likely a reflection of nutrient reduction efforts. A conceptual model of mid-Bay blooms is presented, in which K. veneficum, derived from the oceanic end member of the Bay, may experience enhanced growth if it encounters prey originating from the tributaries with different patterns of nutrient loading and which are enriched in nitrogen. For all correlation models developed herein, prey abundance was a primary factor in predicting K. veneficum abundance. Copyright © 2018 Elsevier B.V. All rights reserved.

Geology, geochemistry, and geochronology of the East Bay gold trend, Red Lake, Ontario, Canada

NASA Astrophysics Data System (ADS)

Gallagher, Shaun; Camacho, Alfredo; Fayek, Mostafa; Epp, Mark; Spell, Terry L.; Armstrong, Richard

2018-01-01

The Red Lake greenstone belt is situated in northwestern Ontario within the Uchi Subprovince, Superior Province. Most gold deposits therein are associated with major deformation corridors; the east-west oriented "Mine trend" hosts most of the large deposits and the northeast-southwest "East Bay trend" hosts several small deposits and showings. Gold along the East Bay trend typically occurs in quartz replacement veins that were emplaced into pre-existing quartz-carbonate veins. Gold can occur as free gold or along vein margins associated with pyrite and pyrrhotite. Most primary fluid inclusions, preserved in relatively undeformed portions of veins, are carbonaceous with lesser quantities of aqueous inclusions. The average homogenization temperature of aqueous fluids is 250 °C; however, the abundance of three-phase inclusions, variation in liquid-vapor ratios, and a wide range in homogenization temperatures indicate that immiscibility, effervescence, and fluid mixing are mechanisms associated with gold deposition. The age ( 2550 Ma) of alteration minerals in the Abino area is considerably younger (by 100 Myr) than alteration minerals in other deposits in the Red Lake district, indicating that the mineralizing fluid history was more protracted than previously thought. Along the East Bay trend, barren veins generally have lower δ18OVSMOW values (0.0 to 8.5‰) relative to auriferous veins (9.6 and 13.1‰). Consequently, the oxygen isotopic composition of quartz could be used as a vector for gold mineralization. The genetic model for the East Bay trend involves several stages of vein formation. Auriferous veins formed near the upper boundary of the mesozonal regime (depth of 5-6 km).

Stable isotope tracing of anaerobic methane oxidation in the gassy sediments of Eckernfoerde Bay, German Baltic Sea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martens, C.S.; Albert, D.B.; Alperin, M.J.

Methane concentrations in the pore waters of Eckernfoerde Bay in the German Baltic Sea generally reach gas bubble saturation values within the upper meter of the sediment column. The depth at which saturation occurs is controlled by a balance between rates of methane production, consumption (oxidation), and transport. The relative importance of anaerobic methane oxidation (AMO) in controlling dissolved and gas bubble methane distributions in the bay's sediments is indirectly revealed through methane concentration versus depth profiles, depth variations in the stable C and H isotope composition of methane, and the C isotope composition of total dissolved inorganic carbon ({Sigma}CO{submore » 2}). Direct radiotracer measurements indicate that AMO rates of over 15 mM/yr are focused at the base of the sulfate reduction zone. Diagenetic equations that describe the depth destructions of the {delta}{sup 13}C and {delta}D values of methane reproduce isotopic shifts observed throughout the methane oxidation zone and are best fit with kinetic isotope fractionation factors of 1.012 {+-} 0.001 and 1.120 {plus{underscore}minus} 0.020 respectively.« less

Historical trend in heavy metal pollution in core sediments from the Masan Bay, Korea.

PubMed

Cho, Jinhyung; Hyun, Sangmin; Han, J-H; Kim, Suhyun; Shin, Dong-Hyeok

2015-06-15

The spatiotemporal distribution and their mass accumulation rate (MAR) of heavy metals were investigated to evaluate the time-dependent historical trends of heavy metal concentration. The three short cores used for this study were collected from the catchment area (MS-PC5, 60cm length), the central part (MS-PC4, 40cm length) and the offshore (MS-PC2, 60cm length) of the Masan Bay, Korea. The concentration of heavy metals (Co, Ni, Cu, Zn, Cr and Pb) in catchment area is as much as 1.5-2 times higher than central part of the Bay, and about 2 times higher than offshore area approximately. In particular, MAR of metals (Cu, Zn and Pb) show clear spatiotemporal variation, so that MAR's of heavy metal may provide more accurate information in evaluating the degree of pollution. Temporally, the heavy metal concentration had been increased since the late 1970s, but it seems to decrease again since the 2004yr in catchment area. This may came from concentrated efforts for the government to reduce industrial waste release. Copyright © 2015 Elsevier Ltd. All rights reserved.

Oxygenation variability in Mejillones Bay, off northern Chile, during the last two centuries

NASA Astrophysics Data System (ADS)

Díaz-Ochoa, J. A.; Pantoja, S.; de Lange, G. J.; Lange, C. B.; Sánchez, G. E.; Acuña, V. R.; Muñoz, P.; Vargas, G.

2011-01-01

The Peru Chile Current ecosystem is characterized by high biological productivity and important fisheries. Although this system is likely to be severely affected by climate change, its response to current global warming is still uncertain. In this paper, we analyze 10-166 year-old sediments in two cores collected from Mejillones Bay, an anoxic sedimentary setting favorable for the preservation of proxies. Based on a 166-year chronology, we used proxies of bottom-water oxygenation (Mo, V, S, and the (lycopane + n-C35)/n-C31 ratio) and surface water productivity (biogenic opal, counts of diatom valves, biogenic Ba, organic carbon, and chlorins) to reconstruct environmental variations in Mejillones Bay. During the last two centuries, a shift took place in the coastal marine ecosystem of Bahia Mejillones at decadal scales. This shift was characterized by intense ENSO-like activity, large-scale fluctuations in biological export productivity and bottom water oxygenation, and increased eolian activity (inferred from Ti/Al and Zr/Al). This short-term variability was accompanied by a gradual increase of sulfidic conditions that has intensified since the early 1960s.

Aragonite saturation state in a tropical coastal embayment dominated by phytoplankton blooms (Guanabara Bay - Brazil).

PubMed

Cotovicz, Luiz C; Knoppers, Bastiaan A; Brandini, Nilva; Poirier, Dominique; Costa Santos, Suzan J; Abril, Gwenaël

2018-04-01

The dynamics of the aragonite saturation state (Ω arag ) were investigated in the eutrophic coastal waters of Guanabara Bay (RJ-Brazil). Large phytoplankton blooms stimulated by a high nutrient enrichment promoted the production of organic matter with strong uptake of dissolved inorganic carbon (DIC) in surface waters, lowering the concentrations of dissolved carbon dioxide (CO 2aq ), and increasing the pH, Ω arag and carbonate ion (CO 3 2- ), especially during summer. The increase of Ω arag related to biological activity was also evident comparing the negative relationship between the Ω arag and the apparent utilization of oxygen (AOU), with a very close behavior between the slopes of the linear regression and the Redfield ratio. The lowest values of Ω arag were found at low-buffered waters in regions that receive direct discharges from domestic effluents and polluted rivers, with episodic evidences of corrosive waters (Ω arag <1). This study showed that the eutrophication controlled the variations of Ω arag in Guanabara Bay. Copyright © 2017 Elsevier Ltd. All rights reserved.

Naive Bayes as opinion classifier to evaluate students satisfaction based on student sentiment in Twitter Social Media

NASA Astrophysics Data System (ADS)

Candra Permana, Fahmi; Rosmansyah, Yusep; Setiawan Abdullah, Atje

2017-10-01

Students activity on social media can provide implicit knowledge and new perspectives for an educational system. Sentiment analysis is a part of text mining that can help to analyze and classify the opinion data. This research uses text mining and naive Bayes method as opinion classifier, to be used as an alternative methods in the process of evaluating studentss satisfaction for educational institution. Based on test results, this system can determine the opinion classification in Bahasa Indonesia using naive Bayes as opinion classifier with accuracy level of 84% correct, and the comparison between the existing system and the proposed system to evaluate students satisfaction in learning process, there is only a difference of 16.49%.

ORGANIC COMPOUNDS IN SURFACE SEDIMENTS AND OYSTER TISSUES FROM THE CHESAPEAKE BAY. APPENDICES

EPA Science Inventory

Detailed in the first part of this report is a development and discussion of the methodology used to extract and analyze sediment and oyster tissue samples from Chesapeake Bay for organic compounds. The method includes extraction, fractionation, and subsequent analysis using glas...

Empirical constrained Bayes predictors accounting for non-detects among repeated measures.

PubMed

Moore, Reneé H; Lyles, Robert H; Manatunga, Amita K

2010-11-10

When the prediction of subject-specific random effects is of interest, constrained Bayes predictors (CB) have been shown to reduce the shrinkage of the widely accepted Bayes predictor while still maintaining desirable properties, such as optimizing mean-square error subsequent to matching the first two moments of the random effects of interest. However, occupational exposure and other epidemiologic (e.g. HIV) studies often present a further challenge because data may fall below the measuring instrument's limit of detection. Although methodology exists in the literature to compute Bayes estimates in the presence of non-detects (Bayes(ND)), CB methodology has not been proposed in this setting. By combining methodologies for computing CBs and Bayes(ND), we introduce two novel CBs that accommodate an arbitrary number of observable and non-detectable measurements per subject. Based on application to real data sets (e.g. occupational exposure, HIV RNA) and simulation studies, these CB predictors are markedly superior to the Bayes predictor and to alternative predictors computed using ad hoc methods in terms of meeting the goal of matching the first two moments of the true random effects distribution. Copyright © 2010 John Wiley & Sons, Ltd.

A Pairwise Naïve Bayes Approach to Bayesian Classification.

PubMed

Asafu-Adjei, Josephine K; Betensky, Rebecca A

2015-10-01

Despite the relatively high accuracy of the naïve Bayes (NB) classifier, there may be several instances where it is not optimal, i.e. does not have the same classification performance as the Bayes classifier utilizing the joint distribution of the examined attributes. However, the Bayes classifier can be computationally intractable due to its required knowledge of the joint distribution. Therefore, we introduce a "pairwise naïve" Bayes (PNB) classifier that incorporates all pairwise relationships among the examined attributes, but does not require specification of the joint distribution. In this paper, we first describe the necessary and sufficient conditions under which the PNB classifier is optimal. We then discuss sufficient conditions for which the PNB classifier, and not NB, is optimal for normal attributes. Through simulation and actual studies, we evaluate the performance of our proposed classifier relative to the Bayes and NB classifiers, along with the HNB, AODE, LBR and TAN classifiers, using normal density and empirical estimation methods. Our applications show that the PNB classifier using normal density estimation yields the highest accuracy for data sets containing continuous attributes. We conclude that it offers a useful compromise between the Bayes and NB classifiers.

A naive Bayes algorithm for tissue origin diagnosis (TOD-Bayes) of synchronous multifocal tumors in the hepatobiliary and pancreatic system.

PubMed

Jiang, Weiqin; Shen, Yifei; Ding, Yongfeng; Ye, Chuyu; Zheng, Yi; Zhao, Peng; Liu, Lulu; Tong, Zhou; Zhou, Linfu; Sun, Shuo; Zhang, Xingchen; Teng, Lisong; Timko, Michael P; Fan, Longjiang; Fang, Weijia

2018-01-15

Synchronous multifocal tumors are common in the hepatobiliary and pancreatic system but because of similarities in their histological features, oncologists have difficulty in identifying their precise tissue clonal origin through routine histopathological methods. To address this problem and assist in more precise diagnosis, we developed a computational approach for tissue origin diagnosis based on naive Bayes algorithm (TOD-Bayes) using ubiquitous RNA-Seq data. Massive tissue-specific RNA-Seq data sets were first obtained from The Cancer Genome Atlas (TCGA) and ∼1,000 feature genes were used to train and validate the TOD-Bayes algorithm. The accuracy of the model was >95% based on tenfold cross validation by the data from TCGA. A total of 18 clinical cancer samples (including six negative controls) with definitive tissue origin were subsequently used for external validation and 17 of the 18 samples were classified correctly in our study (94.4%). Furthermore, we included as cases studies seven tumor samples, taken from two individuals who suffered from synchronous multifocal tumors across tissues, where the efforts to make a definitive primary cancer diagnosis by traditional diagnostic methods had failed. Using our TOD-Bayes analysis, the two clinical test cases were successfully diagnosed as pancreatic cancer (PC) and cholangiocarcinoma (CC), respectively, in agreement with their clinical outcomes. Based on our findings, we believe that the TOD-Bayes algorithm is a powerful novel methodology to accurately identify the tissue origin of synchronous multifocal tumors of unknown primary cancers using RNA-Seq data and an important step toward more precision-based medicine in cancer diagnosis and treatment. © 2017 UICC.

Default "Gunel and Dickey" Bayes factors for contingency tables.

PubMed

Jamil, Tahira; Ly, Alexander; Morey, Richard D; Love, Jonathon; Marsman, Maarten; Wagenmakers, Eric-Jan

2017-04-01

The analysis of R×C contingency tables usually features a test for independence between row and column counts. Throughout the social sciences, the adequacy of the independence hypothesis is generally evaluated by the outcome of a classical p-value null-hypothesis significance test. Unfortunately, however, the classical p-value comes with a number of well-documented drawbacks. Here we outline an alternative, Bayes factor method to quantify the evidence for and against the hypothesis of independence in R×C contingency tables. First we describe different sampling models for contingency tables and provide the corresponding default Bayes factors as originally developed by Gunel and Dickey (Biometrika, 61(3):545-557 (1974)). We then illustrate the properties and advantages of a Bayes factor analysis of contingency tables through simulations and practical examples. Computer code is available online and has been incorporated in the "BayesFactor" R package and the JASP program ( jasp-stats.org ).

High-Frequency Observation of Water Spectrum and Its Application in Monitoring of Dynamic Variation of Suspended Materials in the Hangzhou Bay.

PubMed

Dai, Qian; Pan, De-lu; He, Xian-qiang; Zhu, Qian-kun; Gong, Fang; Huang, Hai-qing

2015-11-01

In situ measurement of water spectrum is the basis of the validation of the ocean color remote sensing. The traditional method to obtain the water spectrum is based on the shipboard measurement at limited stations, which is difficult to meet the requirement of validation of ocean color remote sensing in the highly dynamic coastal waters. To overcome this shortage, continuously observing systems of water spectrum have been developed in the world. However, so far, there are still few high-frequency observation systems of the water spectrum in coastal waters, especially in the highly turbid and high-dynamic waters. Here, we established a high-frequency water-spectrum observing system based on tower in the Hangzhou Bay. The system measures the water spectrum at a step of 3 minutes, which can fully match the satellite observation. In this paper, we primarily developed a data processing method for the tower-based high-frequency water spectrum data, to realize automatic judgment of clear sky, sun glint, platform shadow, and weak illumination, etc. , and verified the processing results. The results show that the normalized water-leaving radiance spectra obtained through tower observation have relatively high consistency with the shipboard measurement results, with correlation coefficient of more than 0. 99, and average relative error of 9.96%. In addition, the long-term observation capability of the tower-based high-frequency water-spectrum observing system was evaluated, and the results show that although the system has run for one year, the normalized water-leaving radiance obtained by this system have good consistency with the synchronously measurement by Portable spectrometer ASD in respect of spectral shape and value, with correlation coefficient of more than 0.90 and average relative error of 6.48%. Moreover, the water spectra from high-frequency observation by the system can be used to effectively monitor the rapid dynamic variation in concentration of suspended materials with tide. The tower-based high-frequency water-spectrum observing system provided rich in situ spectral data for the validation of ocean color remote sensing in turbid waters, especially for validation of the high temporal-resolution geostationary satellite ocean color remote sensing.

Effects of climate variability and human activities on Chesapeake Bay and the implications for ecosystem restoration

USGS Publications Warehouse

Cronin, Thomas M.; Willard, Debra A.; Phillips, Scott

2000-01-01

Chesapeake Bay, the Nation’s largest and most productive estuary (fig. 1), faces complex environmental issues related to nutrients and oxygen, turbidity and sedimentation, toxic dinoflagellates, sea-level rise, and coastal erosion. The Chesapeake Bay Program (CBP) is a partnership among the Chesapeake Bay Commission, the Federal Government, the District of Columbia, and the States of Maryland, Virginia, and Pennsylvania. The CBP is working to preserve, restore, and protect the bay’s living resources, vital habitats, and water quality, to protect human health, and to promote sound land-use policies in the watershed. The CBP began to set restoration goals for the ecosystem in the mid-1980’s and is now refining current goals and setting new ones as part of a new bay agreement— Chesapeake 2000. As the CBP sets restoration goals for the next 10–20 years, it will be critical to understand the long-term changes of the bay ecosystem due to climate variability and the influence of past and future human activities.For the past 4 years, the U.S. Geological Survey (USGS) has been engaged in research designed to provide objective scientific answers to questions about long-term changes in the bay ecosystem: What paleoecological and geochemical methods are best for documenting trends in the bay ecosystem?How does climate variability, including drought, affect the bay?What are historical trends in dissolved oxygen?What is the relationship between sedimentation and water clarity, and what is the effect of turbidity on living resources?How have past land-use changes affected bay habitats and living resources?

Geographic variation in marine turtle fibropapillomatosis

USGS Publications Warehouse

Greenblatt, R.J.; Work, Thierry M.; Dutton, P.; Sutton, C.A.; Spraker, T.R.; Casey, R.N.; Diez, C.E.; Parker, Dana C.; St. Ledger, J.; Balazs, G.H.; Casey, J.W.

2005-01-01

We document three examples of fibropapillomatosis by histology, quantitative polymerase chain reaction (qPCR), and sequence analysis from three different geographic areas. Tumors compatible in morphology with fibropapillomatosis were seen in green turtles from Puerto Rico and San Diego (California) and in a hybrid loggerhead/ hawksbill turtle from Florida Bay (Florida). Tumors were confirmed as fibropapillomas on histology, although severity of disease varied between cases. Polymerase chain reaction (PCR) analyses revealed infection with the fibropapilloma-associated turtle herpesvirus (FPTHV) in all cases, albeit at highly variable copy numbers per cell. Alignment of a portion of the polymerase gene from each fibropapilloma-associated turtle herpesvirus isolate demonstrated geographic variation in sequence. These cases illustrate geographic variation in both the pathology and the virology of fibropapillomatosis.

Geographic variation in marine turtle fibropapillomatosis.

PubMed

Greenblatt, Rebecca J; Work, Thierry M; Dutton, Peter; Sutton, Claudia A; Spraker, Terry R; Casey, Rufina N; Diez, Carlos E; Parker, Denise; St Leger, Judy; Balazs, George H; Casey, James W

2005-09-01

We document three examples of fibropapillomatosis by histology, quantitative polymerase chain reaction (qPCR), and sequence analysis from three different geographic areas. Tumors compatible in morphology with fibropapillomatosis were seen in green turtles from Puerto Rico and San Diego (California) and in a hybrid loggerhead/ hawksbill turtle from Florida Bay (Florida). Tumors were confirmed as fibropapillomas on histology, although severity of disease varied between cases. Polymerase chain reaction (PCR) analyses revealed infection with the fibropapilloma-associated turtle herpesvirus (FPTHV) in all cases, albeit at highly variable copy numbers per cell. Alignment of a portion of the polymerase gene from each fibropapilloma-associated turtle herpesvirus isolate demonstrated geographic variation in sequence. These cases illustrate geographic variation in both the pathology and the virology of fibropapillomatosis.

[Estimation and experiment of carbon sequestration by oysters attached to the enhancement artificial reefs in Laizhou Bay, Shandong, China].

PubMed

Gong, Pi-Hai; Li, Jiao; Guan, Chang-Tao; Li, Meng-Jie; Liu, Chao

2014-10-01

Through sampling investigation of fouling organisms on the enhancement artificial reefs set up in Laizhou Bay, it was proved that oyster (Ostrea plicatula) was the dominant fouling species. Therefore the dry mass of shell (Ms), total fresh mass (Mt) and thickness (T) of oyster attached on the reefs were analyzed. The results showed that the Mt and Ms presented seasonal variation (P < 0.01), that is, the values were the lowest in April and the highest in December. The reef age and the length of the time the enhancement reefs placed in the sea had significant effect on Mt, Ms and T. With the increment of reef ages, all indices increased obviously. The carbon sinks of oysters attaching to the tube enhancement reefs constructed in 2009, 2010 and 2011 in Laizhou Bay were 17.61, 16.33 and 10.45 kg · m(-3), respectively. The oysters on the enhancement reefs of Jincheng marine ranch with an area of 64.25 hm2 had fixed carbon of 297.5 t C (equivalent to 1071 t of CO2) from 2009 to 2013 in Laizhou Bay. To capture and store the same amount of CO2 would cost about 1.6 x 10(5)-6.4 x 10(5) US dollars. Therefore, oysters attaching to the enhancement reefs bring about remarkable ecological benefits.

Long-term evolution (1988-2008) of Zostera spp. meadows in Arcachon Bay (Bay of Biscay)

NASA Astrophysics Data System (ADS)

Martin, Plus; Sébastien, Dalloyau; Gilles, Trut; Isabelle, Auby; de Montaudouin, Xavier; Emery, Éric; Claire, Noël; Christophe, Viala

2010-04-01

The spatial variability of seagrass meadows in Arcachon Bay, was studied between 1988 and 2008 using a combination of mapping techniques based on aerial photographs for intertidal dwarf-grass ( Zostera noltii) beds and acoustic sonar for permanently submerged eelgrass ( Zostera marina) populations. The results show a severe decline over the period for both species, as well as an acceleration of the decline since 2005 for Z. noltii. The total surface regression over the studied period is estimated to be 22.8 km 2 for Z. noltii and 2.7 km 2 for Z. marina, which represent declines of 33 and 74% respectively. Environmental data time series spanning the same period were investigated in order to seek the causes for such a decline. The calculated inter-annual trends for temperature, salinity, nitrate plus nitrite, ammonia, suspended sediment and chlorophyll a did not identify any clear environmental change capable of explaining the observed seagrass regression. For instance, no evident sign of eutrophication was observed over the study period. On the other hand, we suggest that the observed variations of ammonia in the inner part of the lagoon are a symptom of the seagrasses' disappearance and thus, a first sign indicating a change of the Arcachon Bay ecosystem towards more instability and vulnerability. Several hypotheses to explain the observed seagrass decay are proposed.

Daily variation in ingress of fall-spawned larval fishes into Delaware Bay in relation to alongshore and along-estuary wind components

NASA Astrophysics Data System (ADS)

Schieler, Brittany M.; Hale, Edward A.; Targett, Timothy E.

2014-12-01

Identifying factors that affect ingress of larval fishes from offshore spawning areas into estuarine nurseries is important to improve understanding of variability in recruitment of many coastal marine species. This study investigated the ingress of larval Atlantic croaker (Micropogonias undulatus), Atlantic menhaden (Brevoortia tyrannus), and summer flounder (Paralichthys dentatus) at Roosevelt Inlet, near the mouth of Delaware Bay, USA in relation to short-term wind events. Nightly abundances, from November 15 to December 15, 2010, were analyzed with alongshore and along-estuary wind components (direction and speed) using cross-correlation analysis to determine if winds affect larval ingress. Ingress of Atlantic croaker and summer flounder correlated with along-estuary winds, whereas Atlantic menhaden showed no significant correlations with either alongshore or along-estuary winds. Although along-estuary winds during this period were predominantly down-estuary, Atlantic croaker ingress was correlated with positive along-estuary winds (blowing up-estuary), with a three-day lag; and a particularly large ingress peak occurred following the largest up-estuary wind peak. Ingress of summer flounder was correlated with negative along-estuary winds (blowing down-estuary), with a two-day lag. These results suggest that species-specific vertical position in the water column influenced ingress into Delaware Bay. The lag results also suggest that ingressing Atlantic croaker and summer flounder may have a pooling stage outside the mouth of Delaware Bay.

Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds.

PubMed

Cannon, Edward O; Amini, Ata; Bender, Andreas; Sternberg, Michael J E; Muggleton, Stephen H; Glen, Robert C; Mitchell, John B O

2007-05-01

We investigate the classification performance of circular fingerprints in combination with the Naive Bayes Classifier (MP2D), Inductive Logic Programming (ILP) and Support Vector Inductive Logic Programming (SVILP) on a standard molecular benchmark dataset comprising 11 activity classes and about 102,000 structures. The Naive Bayes Classifier treats features independently while ILP combines structural fragments, and then creates new features with higher predictive power. SVILP is a very recently presented method which adds a support vector machine after common ILP procedures. The performance of the methods is evaluated via a number of statistical measures, namely recall, specificity, precision, F-measure, Matthews Correlation Coefficient, area under the Receiver Operating Characteristic (ROC) curve and enrichment factor (EF). According to the F-measure, which takes both recall and precision into account, SVILP is for seven out of the 11 classes the superior method. The results show that the Bayes Classifier gives the best recall performance for eight of the 11 targets, but has a much lower precision, specificity and F-measure. The SVILP model on the other hand has the highest recall for only three of the 11 classes, but generally far superior specificity and precision. To evaluate the statistical significance of the SVILP superiority, we employ McNemar's test which shows that SVILP performs significantly (p < 5%) better than both other methods for six out of 11 activity classes, while being superior with less significance for three of the remaining classes. While previously the Bayes Classifier was shown to perform very well in molecular classification studies, these results suggest that SVILP is able to extract additional knowledge from the data, thus improving classification results further.

Improved method for calibration of exchange flows for a physical transport box model of Tampa Bay, FL USA

EPA Science Inventory

Results for both sequential and simultaneous calibration of exchange flows between segments of a 10-box, one-dimensional, well-mixed, bifurcated tidal mixing model for Tampa Bay are reported. Calibrations were conducted for three model options with different mathematical expressi...

ASSESSMENT OF GROUNDWATER DISCHARGE AND SEWAGE IMPACT INTO SARASOTA BAY AND SUWANNEE RIVER ESTUARY

EPA Science Inventory

The ongoing objectives in Sarasota Bay are to 1) determine if the reduced water clarity and enriched 15N seagrass values are due to groundwater N inputs, 2) determine the effectiveness of geophysical reconnaissance methods in identifying zones of groundwater discharge under a var...