Science.gov

Sample records for naive bayes models

  1. Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes

    PubMed Central

    Jiang, Tao; Shan, Guogen

    2016-01-01

    Residue fluctuations in protein structures have been shown to be highly associated with various protein functions. Gaussian network model (GNM), a simple representative coarse-grained model, was widely adopted to reveal function-related protein dynamics. We directly utilized the high frequency modes generated by GNM and further performed Gaussian Naive Bayes (GNB) to identify hot spot residues. Two coding schemes about the feature vectors were implemented with varying distance cutoffs for GNM and sliding window sizes for GNB based on tenfold cross validations: one by using only a single high mode and the other by combining multiple modes with the highest frequency. Our proposed methods outperformed the previous work that did not directly utilize the high frequency modes generated by GNM, with regard to overall performance evaluated using F1 measure. Moreover, we found that inclusion of more high frequency modes for a GNB classifier can significantly improve the sensitivity. The present study provided additional valuable insights into the relation between the hot spots and the residue fluctuations. PMID:27882325

  2. A Naive-Bayes model observer for detection and localization of perfusion defects in cardiac SPECT-MPI

    NASA Astrophysics Data System (ADS)

    Parages, Felipe M.; O'Connor, J. Michael; Pretorius, P. Hendrik; Brankov, Jovan G.

    2014-03-01

    Model observers (MO) are widely used in medical imaging to act as surrogates of human observers in task-based image quality evaluation, frequently towards optimization of reconstruction algorithms. In SPECT myocardial perfusion imaging (MPI), a realistic task-based approach involves detection and localization of perfusion defects, as well as a subsequent assessment of defect severity. In this paper we explore a machine-learning MO based on Naive- Bayes classification (NB-MO). NB-MO uses a set of polar-map image features to predict lesion detection, localization and severity scores given by five human readers for a set of simulated 3D SPECT-MPI patients. The simulated dataset included lesions with different sizes, perfusion-reduction ratios, and locations. Simulated projections were reconstructed using two readily used methods namely: FBP and OSEM. For validation, a multireader multi-case (MRMC) analysis of alternative free-response ROC (AFROC) curve was performed for NB-MO and human observers. For comparison, we also report performances of a statistical Hotelling Observer applied on polar-map images. Results show excellent agreement between NB-MO and humans, as well as model's good generalization between different reconstruction treatments.

  3. Hierarchical Naive Bayes for genetic association studies

    PubMed Central

    2012-01-01

    Background Genome Wide Association Studies represent powerful approaches that aim at disentangling the genetic and molecular mechanisms underlying complex traits. The usual "one-SNP-at-the-time" testing strategy cannot capture the multi-factorial nature of this kind of disorders. We propose a Hierarchical Naïve Bayes classification model for taking into account associations in SNPs data characterized by Linkage Disequilibrium. Validation shows that our model reaches classification performances superior to those obtained by the standard Naïve Bayes classifier for simulated and real datasets. Methods In the Hierarchical Naïve Bayes implemented, the SNPs mapping to the same region of Linkage Disequilibrium are considered as "details" or "replicates" of the locus, each contributing to the overall effect of the region on the phenotype. A latent variable for each block, which models the "population" of correlated SNPs, can be then used to summarize the available information. The classification is thus performed relying on the latent variables conditional probability distributions and on the SNPs data available. Results The developed methodology has been tested on simulated datasets, each composed by 300 cases, 300 controls and a variable number of SNPs. Our approach has been also applied to two real datasets on the genetic bases of Type 1 Diabetes and Type 2 Diabetes generated by the Wellcome Trust Case Control Consortium. Conclusions The approach proposed in this paper, called Hierarchical Naïve Bayes, allows dealing with classification of examples for which genetic information of structurally correlated SNPs are available. It improves the Naïve Bayes performances by properly handling the within-loci variability. PMID:23095471

  4. Naive Bayes-guided bat algorithm for feature selection.

    PubMed

    Taha, Ahmed Majid; Mustapha, Aida; Chen, Soong-Der

    2013-01-01

    When the amount of data and information is said to double in every 20 months or so, feature selection has become highly important and beneficial. Further improvements in feature selection will positively affect a wide array of applications in fields such as pattern recognition, machine learning, or signal processing. Bio-inspired method called Bat Algorithm hybridized with a Naive Bayes classifier has been presented in this work. The performance of the proposed feature selection algorithm was investigated using twelve benchmark datasets from different domains and was compared to three other well-known feature selection algorithms. Discussion focused on four perspectives: number of features, classification accuracy, stability, and feature generalization. The results showed that BANB significantly outperformed other algorithms in selecting lower number of features, hence removing irrelevant, redundant, or noisy features while maintaining the classification accuracy. BANB is also proven to be more stable than other methods and is capable of producing more general feature subsets.

  5. A NAIVE BAYES SOURCE CLASSIFIER FOR X-RAY SOURCES

    SciTech Connect

    Broos, Patrick S.; Getman, Konstantin V.; Townsley, Leisa K.; Feigelson, Eric D.; Garmire, Gordon P.; Povich, Matthew S.

    2011-05-01

    The Chandra Carina Complex Project (CCCP) provides a sensitive X-ray survey of a nearby starburst region over >1 deg{sup 2} in extent. Thousands of faint X-ray sources are found, many concentrated into rich young stellar clusters. However, significant contamination from unrelated Galactic and extragalactic sources is present in the X-ray catalog. We describe the use of a naive Bayes classifier to assign membership probabilities to individual sources, based on source location, X-ray properties, and visual/infrared properties. For the particular membership decision rule adopted, 75% of CCCP sources are classified as members, 11% are classified as contaminants, and 14% remain unclassified. The resulting sample of stars likely to be Carina members is used in several other studies, which appear in this special issue devoted to the CCCP.

  6. Improving Naive Bayes with Online Feature Selection for Quick Adaptation to Evolving Feature Usefulness

    SciTech Connect

    Pon, R K; Cardenas, A F; Buttler, D J

    2007-09-19

    The definition of what makes an article interesting varies from user to user and continually evolves even for a single user. As a result, for news recommendation systems, useless document features can not be determined a priori and all features are usually considered for interestingness classification. Consequently, the presence of currently useless features degrades classification performance [1], particularly over the initial set of news articles being classified. The initial set of document is critical for a user when considering which particular news recommendation system to adopt. To address these problems, we introduce an improved version of the naive Bayes classifier with online feature selection. We use correlation to determine the utility of each feature and take advantage of the conditional independence assumption used by naive Bayes for online feature selection and classification. The augmented naive Bayes classifier performs 28% better than the traditional naive Bayes classifier in recommending news articles from the Yahoo! RSS feeds.

  7. Naive Probability: A Mental Model Theory of Extensional Reasoning.

    ERIC Educational Resources Information Center

    Johnson-Laird, P. N.; Legrenzi, Paolo; Girotto, Vittorio; Legrenzi, Maria Sonino; Caverni, Jean-Paul

    1999-01-01

    Outlines a theory of naive probability in which individuals who are unfamiliar with the probability calculus can infer the probabilities of events in an "extensional" way. The theory accommodates reasoning based on numerical premises, and explains how naive reasoners can infer posterior probabilities without relying on Bayes's theorem.…

  8. The Naive Intuitive Statistician: A Naive Sampling Model of Intuitive Confidence Intervals

    ERIC Educational Resources Information Center

    Juslin, Peter; Winman, Anders; Hansson, Patrik

    2007-01-01

    The perspective of the naive intuitive statistician is outlined and applied to explain overconfidence when people produce intuitive confidence intervals and why this format leads to more overconfidence than other formally equivalent formats. The naive sampling model implies that people accurately describe the sample information they have but are…

  9. Using an Integrated Naive Bayes Calssifier for Crawling Relevent Data on the Web

    NASA Astrophysics Data System (ADS)

    Mihsra, A.

    2015-12-01

    In our experiments (at JPL, NASA) for DARPA Memex project, we wanted to crawl a large amount of data for various domains. A big challenge was data relevancy in the crawled data. More than 50% of the data was irrelevant to the domain at hand. One immediate solution was to use good seeds (seeds are the initial urls from where the program starts to crawl) and make sure that the crawl remains into the original host urls. This although a very efficient technique, fails under two conditions. One when you aim to reach deeper into the web; into new hosts (not in the seed list) and two when the website hosts myriad content types eg. a News website.The relevancy calculation used to be a post processing step i.e. once we had finished crawling, we trained a NaiveBayes Classifier and used it to find a rough relevancy of the web pages that we had. Integrating the relevancy into the crawling rather than after it was very important because crawling takes resources and time. To save both we needed to get an idea of relevancy of the whole crawl during run time and be able to steer its course accordingly. We use Apache Nutch as the crawler, which uses a plugin system to incorporate any new implementations and hence we built a plugin for Nutch.The Naive Bayes Parse Plugin works in the following way. It parses every page and decides, using a trained model (which is built in situ only once using the positive and negative examples given by the user in a very simple format), if it is relevant; If true, then it allows all the outlinks from that page to go to the next round of crawling; If not, then it gives the urls a second chance to prove themselves by checking some commonly expected words in the url relevant to that domain. This two tier system is very intuitive and efficient in focusing the crawl. In our initial test experiments over 100 seed urls, the results were astonishingly good with a recall of 98%.The same technique can be applied to geo-informatics. This will help scientists

  10. A Naive Bayes machine learning approach to risk prediction using censored, time-to-event data.

    PubMed

    Wolfson, Julian; Bandyopadhyay, Sunayan; Elidrisi, Mohamed; Vazquez-Benitez, Gabriela; Vock, David M; Musgrove, Donald; Adomavicius, Gediminas; Johnson, Paul E; O'Connor, Patrick J

    2015-09-20

    Predicting an individual's risk of experiencing a future clinical outcome is a statistical task with important consequences for both practicing clinicians and public health experts. Modern observational databases such as electronic health records provide an alternative to the longitudinal cohort studies traditionally used to construct risk models, bringing with them both opportunities and challenges. Large sample sizes and detailed covariate histories enable the use of sophisticated machine learning techniques to uncover complex associations and interactions, but observational databases are often 'messy', with high levels of missing data and incomplete patient follow-up. In this paper, we propose an adaptation of the well-known Naive Bayes machine learning approach to time-to-event outcomes subject to censoring. We compare the predictive performance of our method with the Cox proportional hazards model which is commonly used for risk prediction in healthcare populations, and illustrate its application to prediction of cardiovascular risk using an electronic health record dataset from a large Midwest integrated healthcare system.

  11. Using naive Bayes classifier for classification of convective rainfall intensities based on spectral characteristics retrieved from SEVIRI

    NASA Astrophysics Data System (ADS)

    Hameg, Slimane; Lazri, Mourad; Ameur, Soltane

    2016-07-01

    This paper presents a new algorithm to classify convective clouds and determine their intensity, based on cloud physical properties retrieved from the Spinning Enhanced Visible and Infrared Imager (SEVIRI). The convective rainfall events at 15 min, 4 × 5 km spatial resolution from 2006 to 2012 are analysed over northern Algeria. The convective rain classification methodology makes use of the relationship between cloud spectral characteristics and cloud physical properties such as cloud water path (CWP), cloud phase (CP) and cloud top height (CTH). For this classification, a statistical method based on `naive Bayes classifier' is applied. This is a simple probabilistic classifier based on applying `Bayes' theorem with strong (naive) independent assumptions. For a 9-month period, the ability of SEVIRI to classify the rainfall intensity in the convective clouds is evaluated using weather radar over the northern Algeria. The results indicate an encouraging performance of the new algorithm for intensity differentiation of convective clouds using SEVIRI data.

  12. Building Models with Bayes

    NASA Astrophysics Data System (ADS)

    Hart, Gus; Nelson, Lance J.; Reese, Shane

    2011-10-01

    The whole of modern Bayesian statistical methods is founded on the simple idea of Bayes rule, stated by the Reverend Thomas Bayes, and presented in 1763. Bayes rule is merely a simple statement of conditional probablility but can be used to make strong inferences. However, the application of Bayes rule to all but the simplest problems requires significant computation. As a result, Baysian-based approaches have been largely impractical until high-speed computing became inexpensive in the recent in the last 20 years or so. We discuss the general idea behind Bayes rule, how to use it to build physical models, and illustrate the approach for a simple case of lattice gas models.

  13. Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds

    NASA Astrophysics Data System (ADS)

    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.

  14. Detection of Cardiovascular Disease Risk's Level for Adults Using Naive Bayes Classifier

    PubMed Central

    Miranda, Eka; Amelga, Alowisius Y.; Maribondang, Marco M.; Salim, Mulyadi

    2016-01-01

    Objectives The number of deaths caused by cardiovascular disease and stroke is predicted to reach 23.3 million in 2030. As a contribution to support prevention of this phenomenon, this paper proposes a mining model using a naïve Bayes classifier that could detect cardiovascular disease and identify its risk level for adults. Methods The process of designing the method began by identifying the knowledge related to the cardiovascular disease profile and the level of cardiovascular disease risk factors for adults based on the medical record, and designing a mining technique model using a naïve Bayes classifier. Evaluation of this research employed two methods: accuracy, sensitivity, and specificity calculation as well as an evaluation session with cardiologists and internists. The characteristics of cardiovascular disease are identified by its primary risk factors. Those factors are diabetes mellitus, the level of lipids in the blood, coronary artery function, and kidney function. Class labels were assigned according to the values of these factors: risk level 1, risk level 2 and risk level 3. Results The evaluation of the classifier performance (accuracy, sensitivity, and specificity) in this research showed that the proposed model predicted the class label of tuples correctly (above 80%). More than eighty percent of respondents (including cardiologists and internists) who participated in the evaluation session agree till strongly agreed that this research followed medical procedures and that the result can support medical analysis related to cardiovascular disease. Conclusions The research showed that the proposed model achieves good performance for risk level detection of cardiovascular disease. PMID:27525161

  15. A Similarity-Based Adaptation of Naive Bayes for Label Ranking: Application to the Metalearning Problem of Algorithm Recommendation

    NASA Astrophysics Data System (ADS)

    Aiguzhinov, Artur; Soares, Carlos; Serra, Ana Paula

    The problem of learning label rankings is receiving increasing attention from several research communities. A number of common learning algorithms have been adapted for this task, including k-Nearest Neighbours (k-NN) and decision trees. Following this line, we propose an adaptation of the naive Bayes classification algorithm for the label ranking problem. Our main idea lies in the use of similarity between the rankings to replace the concept of probability. We empirically test the proposed method on some metalearning problems that consist of relating characteristics of learning problems to the relative performance of learning algorithms. Our method generally performs better than the baseline indicating that it is able to identify some of the underlying patterns in the data.

  16. Opinion mining feature-level using Naive Bayes and feature extraction based analysis dependencies

    NASA Astrophysics Data System (ADS)

    Sanda, Regi; Baizal, Z. K. Abdurahman; Nhita, Fhira

    2015-12-01

    Development of internet and technology, has major impact and providing new business called e-commerce. Many e-commerce sites that provide convenience in transaction, and consumers can also provide reviews or opinions on products that purchased. These opinions can be used by consumers and producers. Consumers to know the advantages and disadvantages of particular feature of the product. Procuders can analyse own strengths and weaknesses as well as it's competitors products. Many opinions need a method that the reader can know the point of whole opinion. The idea emerged from review summarization that summarizes the overall opinion based on sentiment and features contain. In this study, the domain that become the main focus is about the digital camera. This research consisted of four steps 1) giving the knowledge to the system to recognize the semantic orientation of an opinion 2) indentify the features of product 3) indentify whether the opinion gives a positive or negative 4) summarizing the result. In this research discussed the methods such as Naï;ve Bayes for sentiment classification, and feature extraction algorithm based on Dependencies Analysis, which is one of the tools in Natural Language Processing (NLP) and knowledge based dictionary which is useful for handling implicit features. The end result of research is a summary that contains a bunch of reviews from consumers on the features and sentiment. With proposed method, accuration for sentiment classification giving 81.2 % for positive test data, 80.2 % for negative test data, and accuration for feature extraction reach 90.3 %.

  17. Missisquoi Bay Phosphorus Model Addendum

    EPA Pesticide Factsheets

    This technical memorandum provides results of an extended load reduction simulation. The memorandum serves as an addendum to the main Missisquoi Bay Phosphorus Mass Balance Model report prepared for the Lake Champlain Basin Program by LimnoTech in 2012

  18. Antibiotic Activity against Naive and Induced Streptococcus pneumoniae Biofilms in an In Vitro Pharmacodynamic Model

    PubMed Central

    Vandevelde, Nathalie M.; Tulkens, Paul M.

    2014-01-01

    Biofilms play a role in the pathogenicity of pneumococcal infections. A pharmacodynamic in vitro model of biofilm was developed that allows characterization of the activity of antibiotics against viability and biomass by using in parallel capsulated (ATCC 49619) and noncapsulated (R6) reference strains. Naive biofilms were obtained by incubating fresh planktonic cultures for 2 to 11 days in 96-well polystyrene plates. Induced biofilms were obtained using planktonic bacteria collected from the supernatant of 6-day-old naive biofilms. Biomass production was more rapid and intense in the induced model, but the levels were similar for both strains. Full concentration responses fitting sigmoidal regressions allowed calculation of maximal efficacies and relative potencies of drugs. All antibiotics tested (amoxicillin, clarithromycin, solithromycin, levofloxacin, and moxifloxacin) were more effective against young naive biofilms than against old or induced biofilms, except macrolides/ketolides, which were as effective at reducing viability in 2-day-old naive biofilms and in 11-day-old induced biofilms of R6. Macrolides/ketolides, however, were less potent than fluoroquinolones against R6 (approximately 5- to 20-fold-higher concentrations needed to reduction viability of 20%). However, at concentrations obtainable in epithelial lining fluid, the viabilities of mature or induced biofilms were reduced 15 to 45% (amoxicillin), 17 to 44% (macrolides/ketolides), and 12 to 64% (fluoroquinolones), and biomasses were reduced 5 to 45% (amoxicillin), 5 to 60% (macrolides/ketolides), and 10 to 76% (fluoroquinolones), with solithromycin and moxifloxacin being the most effective and the most potent agents (due to lower MICs) in their respective classes. This study allowed the ranking of antibiotics with respect to their potential effectiveness in biofilm-related infections, underlining the need to search for still more effective options. PMID:24342635

  19. Naive Probability: Model-Based Estimates of Unique Events.

    PubMed

    Khemlani, Sangeet S; Lotstein, Max; Johnson-Laird, Philip N

    2015-08-01

    We describe a dual-process theory of how individuals estimate the probabilities of unique events, such as Hillary Clinton becoming U.S. President. It postulates that uncertainty is a guide to improbability. In its computer implementation, an intuitive system 1 simulates evidence in mental models and forms analog non-numerical representations of the magnitude of degrees of belief. This system has minimal computational power and combines evidence using a small repertoire of primitive operations. It resolves the uncertainty of divergent evidence for single events, for conjunctions of events, and for inclusive disjunctions of events, by taking a primitive average of non-numerical probabilities. It computes conditional probabilities in a tractable way, treating the given event as evidence that may be relevant to the probability of the dependent event. A deliberative system 2 maps the resulting representations into numerical probabilities. With access to working memory, it carries out arithmetical operations in combining numerical estimates. Experiments corroborated the theory's predictions. Participants concurred in estimates of real possibilities. They violated the complete joint probability distribution in the predicted ways, when they made estimates about conjunctions: P(A), P(B), P(A and B), disjunctions: P(A), P(B), P(A or B or both), and conditional probabilities P(A), P(B), P(B|A). They were faster to estimate the probabilities of compound propositions when they had already estimated the probabilities of each of their components. We discuss the implications of these results for theories of probabilistic reasoning.

  20. Naïve Bayes classification in R

    PubMed Central

    2016-01-01

    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. PMID:27429967

  1. Tsunami Inundation modeling for Tolaga Bay, Tokomaru Bay, Hicks Bay and Te Araroa communities

    NASA Astrophysics Data System (ADS)

    Barberopoulou, A.; Wang, X.; Power, W. L.

    2012-12-01

    We assess the tsunami hazard to four communities in Raukumara Peninsula (Northeastern region of North Island of New Zealand): Tokomaru Bay, Tolaga Bay, Hicks Bay and Te Araroa. Representative severe but realistic scenarios that could affect the Raukumara peninsula are earthquakes that rupture the interface between the Australian and Pacific plates, earthquakes that rupture faults within the overlying Australian plate or the subducting Pacific plate (location is not always well constrained). Earthquakes that rupture both the plate interface and simultaneously faults within the crust of the Australian plate are also a possibility. Tsunamis may also be caused by submarine landslides that occur near the edge of the continental shelf, but these are not considered here. For this study four scenario events were constructed, including a distant event from South America (offshore Peru), outer rise events and a thrust event in the Hikurangi region off the east coast of New Zealand. The sources are not exhaustive but representative of the types of significant events that could occur in the region and were either improved from earlier sources or derived from recent studies. Available high resolution LiDAR and RTK data were combined with topographic and LINZ data for the development of bathymetric/topographic grids. Our modelling results show that Tolaga Bay appears most vulnerable to tsunami inundation although Hicks Bay and Te Araroa are also significantly inundated in several of the scenarios. Tokomaru Bay is naturally well protected because the rapid change in elevation limits the range of inundation. The worst scenario for Tokomaru Bay was an earthquake in the Hikurangi subduction zone resulting in large flow depths, whereas for Tolaga Bay inundation is severe from most scenarios. Hicks Bay and Te Araroa get the most severe flooding from earthquakes in South America and on the Hikurangi subduction zone. Inundation extent is similar for Tolaga Bay during the Outer Rise and

  2. Chesapeake Bay sediment flux model. Final report

    SciTech Connect

    Di Toro, D.M.; Fitzpatrick, J.J.

    1993-06-01

    Formulation and application of a predictive diagenetic sediment model are described in this report. The model considers two benthic sediment layers: a thin aerobic layer in contact with the water column and a thicker anaerobic layer. Processes represented include diagenesis, diffusion, particle mixing, and burial. Deposition of organic matter, water column concentrations, and temperature are treated as independent variables that influence sediment-water fluxes. Sediment oxygen demand and sediment-water fluxes of sulfide, ammonium, nitrate, phosphate, and silica are predicted. The model was calibrated using sediment-water flux observations collected in Chesapeake Bay 1985-1988. When independent variables were specified based on observations, the model correctly represented the time series of sediment-water fluxes observed at eight stations in the Bay and tributaries.... Chesapeake Bay, Models, Sediments, Dissolved oxygen, Nitrogen Eutrophication, Phosphorus.

  3. Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation.

    PubMed

    Sahakyan, Anna; Kim, Rachel; Chronis, Constantinos; Sabri, Shan; Bonora, Giancarlo; Theunissen, Thorold W; Kuoy, Edward; Langerman, Justin; Clark, Amander T; Jaenisch, Rudolf; Plath, Kathrin

    2017-01-05

    Naive human embryonic stem cells (hESCs) can be derived from primed hESCs or directly from blastocysts, but their X chromosome state has remained unresolved. Here, we show that the inactive X chromosome (Xi) of primed hESCs was reactivated in naive culture conditions. Like cells of the blastocyst, the resulting naive cells contained two active X chromosomes with XIST expression and chromosome-wide transcriptional dampening and initiated XIST-mediated X inactivation upon differentiation. Both establishment of and exit from the naive state (differentiation) happened via an XIST-negative XaXa intermediate. Together, these findings identify a cell culture system for functionally exploring the two X chromosome dosage compensation processes in early human development: X dampening and X inactivation. However, remaining differences between naive hESCs and embryonic cells related to mono-allelic XIST expression and non-random X inactivation highlight the need for further culture improvement. As the naive state resets Xi abnormalities seen in primed hESCs, it may provide cells better suited for downstream applications.

  4. Modeling the seasonal circulation in Massachusetts Bay

    USGS Publications Warehouse

    Signell, Richard P.; Jenter, Harry L.; Blumberg, Alan F.; ,

    1994-01-01

    An 18 month simulation of circulation was conducted in Massachusetts Bay, a roughly 35 m deep, 100??50 km embayment on the northeastern shelf of the United States. Using a variant of the Blumberg-Mellor (1987) model, it was found that a continuous 18 month run was only possible if the velocity field was Shapiro filtered to remove two grid length energy that developed along the open boundary due to mismatch in locally generated and climatologically forced water properties. The seasonal development of temperature and salinity stratification was well-represented by the model once ??-coordinate errors were reduced by subtracting domain averaged vertical profiles of temperature, salinity and density before horizontal differencing was performed. Comparison of modeled and observed subtidal currents at fixed locations revealed that the model performance varies strongly with season and distance from the open boundaries. The model performs best during unstratified conditions, and in the interior of the bay. The model performs poorest during stratified conditions and in the regions where the bay is driven predominantly by remote fluctuations from the Gulf of Maine.

  5. Topobathymetric model of Mobile Bay, Alabama

    USGS Publications Warehouse

    Danielson, Jeffrey J.; Brock, John C.; Howard, Daniel M.; Gesch, Dean B.; Bonisteel-Cormier, Jamie M.; Travers, Laurinda J.

    2013-01-01

    Topobathymetric Digital Elevation Models (DEMs) are a merged rendering of both topography (land elevation) and bathymetry (water depth) that provides a seamless elevation product useful for inundation mapping, as well as for other earth science applications, such as the development of sediment-transport, sea-level rise, and storm-surge models. This 1/9-arc-second (approximately 3 meters) resolution model of Mobile Bay, Alabama was developed using multiple topographic and bathymetric datasets, collected on different dates. The topographic data were obtained primarily from the U.S. Geological Survey (USGS) National Elevation Dataset (NED) (http://ned.usgs.gov/) at 1/9-arc-second resolution; USGS Experimental Advanced Airborne Research Lidar (EAARL) data (2 meters) (http://pubs.usgs.gov/ds/400/); and topographic lidar data (2 meters) and Compact Hydrographic Airborne Rapid Total Survey (CHARTS) lidar data (2 meters) from the U.S. Army Corps of Engineers (USACE) (http://www.csc.noaa.gov/digitalcoast/data/coastallidar/). Bathymetry was derived from digital soundings obtained from the National Oceanic and Atmospheric Administration’s (NOAA) National Geophysical Data Center (NGDC) (http://www.ngdc.noaa.gov/mgg/geodas/geodas.html) and from water-penetrating lidar sources, such as EAARL and CHARTS. Mobile Bay is ecologically important as it is the fourth largest estuary in the United States. The Mobile and Tensaw Rivers drain into the bay at the northern end with the bay emptying into the Gulf of Mexico at the southern end. Dauphin Island (a barrier island) and the Fort Morgan Peninsula form the mouth of Mobile Bay. Mobile Bay is 31 miles (50 kilometers) long by a maximum width of 24 miles (39 kilometers) with a total area of 413 square miles (1,070 square kilometers). The vertical datum of the Mobile Bay topobathymetric model is the North American Vertical Datum of 1988 (NAVD 88). All the topographic datasets were originally referenced to NAVD 88 and no transformations

  6. Hydraulic model of the Chesapeake Bay

    NASA Technical Reports Server (NTRS)

    Robinson, A. E., Jr.

    1978-01-01

    Preliminary planning for the formulation of the first year of hydraulic studies on the Chesapeake Bay model was recently completed. The primary purpose of this initial effort was to develop a study program that is both responsive to problems of immediate importance and at the same time ensure that from the very beginning of operation maximum economical use is made of the model. The formulation of this preliminary study plan involved an extensive analysis of the environmental, economic, and social aspects of a series of current problems in order to establish a priority listing of their importance. The study program that evolved is oriented towards the analysis of the effects of some of the works of man on the Chesapeake Bay estuarine environment.

  7. Modeling nitrogen cycling in forested watersheds of Chesapeake Bay

    SciTech Connect

    Hunsaker, C.T.; Garten, C.T.; Mulholland, P.J.

    1995-03-01

    The Chesapeake Bay Agreement calls for a 40% reduction of controllable phosphorus and nitrogen to the tidal Bay by the year 2000. To accomplish this goal the Chesapeake Bay Program needs accurate estimates of nutrient loadings, including atmospheric deposition, from various land uses. The literature was reviewed on forest nitrogen pools and fluxes, and nitrogen data from research catchments in the Chesapeake Basin were identified. The structure of a nitrogen module for forests is recommended for the Chesapeake Bay Watershed Model along with the possible functional forms for fluxes.

  8. Sediment calibration strategies of Phase 5 Chesapeake Bay watershed model

    USGS Publications Warehouse

    Wu, J.; Shenk, G.W.; Raffensperger, J.; Moyer, D.; Linker, L.C.; ,

    2005-01-01

    Sediment is a primary constituent of concern for Chesapeake Bay due to its effect on water clarity. Accurate representation of sediment processes and behavior in Chesapeake Bay watershed model is critical for developing sound load reduction strategies. Sediment calibration remains one of the most difficult components of watershed-scale assessment. This is especially true for Chesapeake Bay watershed model given the size of the watershed being modeled and complexity involved in land and stream simulation processes. To obtain the best calibration, the Chesapeake Bay program has developed four different strategies for sediment calibration of Phase 5 watershed model, including 1) comparing observed and simulated sediment rating curves for different parts of the hydrograph; 2) analyzing change of bed depth over time; 3) relating deposition/scour to total annual sediment loads; and 4) calculating "goodness-of-fit' statistics. These strategies allow a more accurate sediment calibration, and also provide some insightful information on sediment processes and behavior in Chesapeake Bay watershed.

  9. Nonparametric Bayes Stochastically Ordered Latent Class Models

    PubMed Central

    Yang, Hongxia; O’Brien, Sean; Dunson, David B.

    2012-01-01

    Latent class models (LCMs) are used increasingly for addressing a broad variety of problems, including sparse modeling of multivariate and longitudinal data, model-based clustering, and flexible inferences on predictor effects. Typical frequentist LCMs require estimation of a single finite number of classes, which does not increase with the sample size, and have a well-known sensitivity to parametric assumptions on the distributions within a class. Bayesian nonparametric methods have been developed to allow an infinite number of classes in the general population, with the number represented in a sample increasing with sample size. In this article, we propose a new nonparametric Bayes model that allows predictors to flexibly impact the allocation to latent classes, while limiting sensitivity to parametric assumptions by allowing class-specific distributions to be unknown subject to a stochastic ordering constraint. An efficient MCMC algorithm is developed for posterior computation. The methods are validated using simulation studies and applied to the problem of ranking medical procedures in terms of the distribution of patient morbidity. PMID:22505787

  10. Ecological modeling for water quality management of Kwangyang Bay, Korea.

    PubMed

    Lee, Dae In; Park, Chung Kil; Cho, Hyeon Seo

    2005-03-01

    This study estimated the appropriate pollutant load reduction from point sources in Kwangyang Bay, Korea, using an eco-hydrodynamic model. The total chemical oxygen demand (COD), nitrogen (TN), and phosphorus (TP) loads from rivers and ditches that provide input to the bay were approximately 2.8x10(4), 2.5x10(4), and 5.9x10(2) kg day-1, respectively. Wastewater discharge from industrial complexes was the greatest contributor to pollutant loads in the inner part of the bay. COD values in the inner part of the bay were greater than 3.0 mg l-1, and exceeded Korean seawater quality grade III limits. A residual current was simulated, using a hydrodynamic model, to have a slightly complicated pattern in the inner part of the bay, ranging from 0.001 to 8 cm s-1. In the outer part of the bay, the simulated current flowed out to the South Sea with a southward flow at a maximum of 15 cm s-1. The results of the ecological model simulation of COD levels showed high concentrations, exceeding 4 mg l-1, in the southwest of the Myodo, an area of wastewater discharge, and lower levels, approaching less than 1 mg l-1, closer to the outer part of the bay. Engineering countermeasures to reduce the organic and inorganic material loads from point sources by more than 45% were required to keep the COD levels below 2 mg l-1.

  11. Modeling Total Suspended Solids (TSS) Concentrations in Narragansett Bay.

    EPA Science Inventory

    This work covers mechanistic modeling of suspended particulates in estuarine systems with an application to Narragansett Bay, RI. Suspended particles directly affect water clarity and attenuate light in the water column. Water clarity affects both phytoplankton and submerged aqua...

  12. Tampa Bay Water Clarity Model (TBWCM): As a Predictive Tool

    EPA Science Inventory

    The Tampa Bay Water Clarity Model was developed as a predictive tool for estimating the impact of changing nutrient loads on water clarity as measured by secchi depth. The model combines a physical mixing model with an irradiance model and nutrient cycling model. A 10 segment bi...

  13. Model for carbonate deposition in an Epicontinental Bay

    SciTech Connect

    Carney, C.; Smosna, R.

    1986-05-01

    By mapping the distribution of correlative sediments across the north-central region of the Appalachian basin, a paleogeographic model has been generated for part of the Mississippian period. During the Chesterian, the upper Greenbrier Limestone was deposited in an embayment that extended northward into parts of West Virginia, Ohio, Pennsylvanian, and Maryland. The bay, only a few hundred kilometers wide, was surrounded by lowlands to the west and north, and deltaic sediments shed from nearby highlands diluted the easternmost facies. In the bay, several different shallow-water carbonate environments are distinguished. Muddy skeletal sand was deposited in the central part, which was characterized by normal marine circulation and salinity. This open-bay facies supported a moderately diverse fauna of forams, brachiopods, and mollusks. From the central facies to the bay margins, water depth decreased, circulation became more restricted, and salinity was slightly higher. A restricted-bay facies developed closer to shore, with sediment consisting of pelletal mud and scattered skeletal grains. Diversity was lower, and the fauna was composed primarily of forams and ostracodes. A tidal mud flat surrounded the embayment on all three sides where partly to totally dolomitized mud containing cryptalgal structures formed. Oolite shoals, present on the eastern side of the bay near its mouth, mark areas where tidal currents were concentrated. Eventually, the epicontinental sea flooded the small enclosed bay, replacing the shallow-water facies with an open-marine facies. The new environment supported a highly diverse fauna including crinoids, brachiopods, mollusks, forams, and ostracods.

  14. An Amorphous Model for Morphological Processing in Visual Comprehension Based on Naive Discriminative Learning

    ERIC Educational Resources Information Center

    Baayen, R. Harald; Milin, Petar; Durdevic, Dusica Filipovic; Hendrix, Peter; Marelli, Marco

    2011-01-01

    A 2-layer symbolic network model based on the equilibrium equations of the Rescorla-Wagner model (Danks, 2003) is proposed. The study first presents 2 experiments in Serbian, which reveal for sentential reading the inflectional paradigmatic effects previously observed by Milin, Filipovic Durdevic, and Moscoso del Prado Martin (2009) for unprimed…

  15. Dynamic modeling of Tampa Bay urban development using parallel computing

    USGS Publications Warehouse

    Xian, G.; Crane, M.; Steinwand, D.

    2005-01-01

    Urban land use and land cover has changed significantly in the environs of Tampa Bay, Florida, over the past 50 years. Extensive urbanization has created substantial change to the region's landscape and ecosystems. This paper uses a dynamic urban-growth model, SLEUTH, which applies six geospatial data themes (slope, land use, exclusion, urban extent, transportation, hillside), to study the process of urbanization and associated land use and land cover change in the Tampa Bay area. To reduce processing time and complete the modeling process within an acceptable period, the model is recoded and ported to a Beowulf cluster. The parallel-processing computer system accomplishes the massive amount of computation the modeling simulation requires. SLEUTH calibration process for the Tampa Bay urban growth simulation spends only 10 h CPU time. The model predicts future land use/cover change trends for Tampa Bay from 1992 to 2025. Urban extent is predicted to double in the Tampa Bay watershed between 1992 and 2025. Results show an upward trend of urbanization at the expense of a decline of 58% and 80% in agriculture and forested lands, respectively. ?? 2005 Elsevier Ltd. All rights reserved.

  16. Dynamic modeling of Tampa Bay urban development using parallel computing

    NASA Astrophysics Data System (ADS)

    Xian, George; Crane, Mike; Steinwand, Dan

    2005-08-01

    Urban land use and land cover has changed significantly in the environs of Tampa Bay, Florida, over the past 50 years. Extensive urbanization has created substantial change to the region's landscape and ecosystems. This paper uses a dynamic urban-growth model, SLEUTH, which applies six geospatial data themes (slope, land use, exclusion, urban extent, transportation, hillside), to study the process of urbanization and associated land use and land cover change in the Tampa Bay area. To reduce processing time and complete the modeling process within an acceptable period, the model is recoded and ported to a Beowulf cluster. The parallel-processing computer system accomplishes the massive amount of computation the modeling simulation requires. SLEUTH calibration process for the Tampa Bay urban growth simulation spends only 10 h CPU time. The model predicts future land use/cover change trends for Tampa Bay from 1992 to 2025. Urban extent is predicted to double in the Tampa Bay watershed between 1992 and 2025. Results show an upward trend of urbanization at the expense of a decline of 58% and 80% in agriculture and forested lands, respectively.

  17. 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.

  18. San Francisco Bay test case for 3-D model verification

    USGS Publications Warehouse

    Smith, Peter E.

    1994-01-01

    This paper describes a field test case for 3-D hydrodynamic model verification using data from Carquinez Strait in San Francisco Bay, California. It will be disseminated by the ASCE Computational Hydraulics task committee on 3-D Free-Surface Hydrodynamic Model Verifications during late 1994.

  19. Impact of Glider Data Assimilation on the Monterey Bay Model

    DTIC Science & Technology

    2009-01-01

    Assimilation on the Monterey Bay Model 6. AUTHOR(S) Igor Shulman, Clark Rowley, Stephanie Anderson, Sergio DeRada, John Kindle, Paul Martin, James...Impact of glider data assimilation on the Monterey Bay model Igor Shulman3*, Clark Rowley3, Stephanie Andersona, Sergio DeRadaa, John Kindlea, Paul ...support of the AOSN-II field campaign. Deep-Sea Research II, this issue |doi:10.1016/j.dsr2.2008 08.009). Kundu. P.K.. 1976. Ekman veering observed

  20. Hydrodynamic characterization of Corpus Christi Bay through modeling and observation.

    PubMed

    Islam, Mohammad S; Bonner, James S; Edge, Billy L; Page, Cheryl A

    2014-11-01

    Christi Bay is a relatively flat, shallow, wind-driven system with an average depth of 3-4 m and a mean tidal range of 0.3 m. It is completely mixed most of the time, and as a result, depth-averaged models have, historically, been applied for hydrodynamic characterization supporting regulatory decisions on Texas coastal management. The bay is highly stratified during transitory periods of the summer with low wind conditions. This has important implications on sediment transport, nutrient cycling, and water quality-related issues, including hypoxia which is a key water quality concern for the bay. Detailed hydrodynamic characterization of the bay during the summer months included analysis of simulation results of 2-D hydrodynamic model and high-frequency (HF) in situ observations. The HF radar system resolved surface currents, whereas an acoustic Doppler current profiler (ADCP) measured current at different depths of the water column. The developed model successfully captured water surface elevation variation at the mouth of the bay (i.e., onshore boundary of the Gulf of Mexico) and at times within the bay. However, large discrepancies exist between model-computed depth-averaged water currents and observed surface currents. These discrepancies suggested the presence of a vertical gradient in the current structure which was further substantiated by the observed bi-directional current movement within the water column. In addition, observed vertical density gradients proved that the water column was stratified. Under this condition, the bottom layer became hypoxic due to inadequate mixing with the aerated surface water. Understanding the disparities between observations and model predictions provides critical insights about hydrodynamics and physical processes controlling water quality.

  1. Modeling tidal hydrodynamics of San Diego Bay, California

    USGS Publications Warehouse

    Wang, P.-F.; Cheng, R.T.; Richter, K.; Gross, E.S.; Sutton, D.; Gartner, J.W.

    1998-01-01

    In 1983, current data were collected by the National Oceanic and Atmospheric Administration using mechanical current meters. During 1992 through 1996, acoustic Doppler current profilers as well as mechanical current meters and tide gauges were used. These measurements not only document tides and tidal currents in San Diego Bay, but also provide independent data sets for model calibration and verification. A high resolution (100-m grid), depth-averaged, numerical hydrodynamic model has been implemented for San Diego Bay to describe essential tidal hydrodynamic processes in the bay. The model is calibrated using the 1983 data set and verified using the more recent 1992-1996 data. Discrepancies between model predictions and field data in beth model calibration and verification are on the order of the magnitude of uncertainties in the field data. The calibrated and verified numerical model has been used to quantify residence time and dilution and flushing of contaminant effluent into San Diego Bay. Furthermore, the numerical model has become an important research tool in ongoing hydrodynamic and water quality studies and in guiding future field data collection programs.

  2. A model for the geomorphology of the Carolina Bays

    NASA Astrophysics Data System (ADS)

    Zamora, Antonio

    2017-04-01

    Geometrical analysis of the Carolina Bays using Google Earth in combination with LiDAR data makes it possible to postulate that the bays formed as the result of impacts, rather than from eolian and lacustrine processes. The Carolina Bays are elliptical conic sections with width-to-length ratios averaging 0.58 that are radially oriented toward the Great Lakes region. The radial distribution of ejecta is one characteristic of impacts, and the width-to-length ratios of the ellipses correspond to cones inclined at approximately 35°, which is consistent with ballistic trajectories from the point of convergence. These observations, and the fact that these geomorphological features occur only on unconsolidated soil close to the water table, make it plausible to propose that the Carolina Bays are the remodeled remains of oblique conical craters formed on ground liquefied by the seismic shock waves of secondary impacts of glacier ice boulders ejected by an extraterrestrial impact on the Laurentide Ice Sheet. Mathematical analysis using ballistic equations and scaling laws relating yield energy to crater size provide clues about the magnitude of the extraterrestrial event. An experimental model elucidates the remodeling mechanisms and provides an explanation for the morphology and the diverse dates of the bays.

  3. Modeling Fecal Indicator Bacteria Like Salt in Newport Bay

    NASA Astrophysics Data System (ADS)

    Ciglar, A. M.; Rippy, M.; Grant, S. B.

    2015-12-01

    Newport Bay is a harbor and estuary located in Orange County, CA that provides many water sports and recreational activities for millions of southern California residents and tourists. The aim of this study is to quickly assess exceedances of FIB in the Newport Bay which pose a health risk to recreational users. The ability to quickly assess water quality is made possible with an advection-diffusion mass transport model that uses easily measurable parameters such as volumetric flow rate from tributaries. Current FIB assessment methods for Newport Bay take a minimum of 24 hours to evaluate health risk by either culturing for FIB or running a more complex fluid dynamics model. By this time the FIB may have already reached the ocean outlet thus no longer posing a risk in the bay or recreationists may have already come in close contact with contaminated waters. The advection-diffusion model can process and disseminate health risk information within a few hours of flow rate measurements, minimizing time between an FIB exceedance and public awareness about the event. Data used to calibrate and validate the model was collected from January 2006 through February 2007. Salinity data was used for calibration and FIB data was used for validation. Both steady-state and transient conditions were assessed to determine if dry weather patterns can be simplified to the steady-state condition.

  4. Naive Conceptions of Motion.

    ERIC Educational Resources Information Center

    McCloskey, Michael

    Two experiments were conducted to characterize the system of beliefs that make up the naive impetus theory of motion and to determine what effects physics instruction has on students' conceptions of motion. Thirteen college students were asked to solve several quantitative problems and were interviewed about their answers in the first experiment.…

  5. Using simple models to describe the kinetics of growth, glucose consumption, and monoclonal antibody formation in naive and infliximab producer CHO cells.

    PubMed

    López-Meza, Julián; Araíz-Hernández, Diana; Carrillo-Cocom, Leydi Maribel; López-Pacheco, Felipe; Rocha-Pizaña, María Del Refugio; Alvarez, Mario Moisés

    2016-08-01

    Despite their practical and commercial relevance, there are few reports on the kinetics of growth and production of Chinese hamster ovary (CHO) cells-the most frequently used host for the industrial production of therapeutic proteins. We characterize the kinetics of cell growth, substrate consumption, and product formation in naive and monoclonal antibody (mAb) producing recombinant CHO cells. Culture experiments were performed in 125 mL shake flasks on commercial culture medium (CD Opti CHO™ Invitrogen, Carlsbad, CA, USA) diluted to different glucose concentrations (1.2-4.8 g/L). The time evolution of cell, glucose, lactic acid concentration and monoclonal antibody concentrations was monitored on a daily basis for mAb-producing cultures and their naive counterparts. The time series were differentiated to calculate the corresponding kinetic rates (rx = d[X]/dt; rs = d[S]/dt; rp = d[mAb]/dt). Results showed that these cell lines could be modeled by Monod-like kinetics if a threshold substrate concentration value of [S]t = 0.58 g/L (for recombinant cells) and [S]t = 0.96 g/L (for naïve cells), below which growth is not observed, was considered. A set of values for μmax, and Ks was determined for naive and recombinant cell cultures cultured at 33 and 37 °C. The yield coefficient (Yx/s) was observed to be a function of substrate concentration, with values in the range of 0.27-1.08 × 10(7) cell/mL and 0.72-2.79 × 10(6) cells/mL for naive and recombinant cultures, respectively. The kinetics of mAb production can be described by a Luedeking-Piret model (d[mAb]/dt = αd[X]/dt + β[X]) with values of α = 7.65 × 10(-7) µg/cell and β = 7.68 × 10(-8) µg/cell/h for cultures conducted in batch-agitated flasks and batch and instrumented bioreactors operated in batch and fed-batch mode.

  6. Modeling the tides of Massachusetts and Cape Cod bays

    USGS Publications Warehouse

    Jenter, H.L.; Signell, R.P.; Blumberg, A.F.; ,

    1993-01-01

    A time-dependent, three-dimensional numerical modeling study of the tides of Massachusetts and Cape Code Bays, motivated by construction of a new sewage treatment plant and ocean outfall for the city of Boston, has been undertaken by the authors. The numerical model being used is a hybrid version of the Blumberg and Mellor ECOM3D model, modified to include a semi-implicit time-stepping scheme and transport of a non-reactive dissolved constituent. Tides in the bays are dominated by the semi-diurnal frequencies, in particular by the M2 tide, due to the resonance of these frequencies in the Gulf of Maine. The numerical model reproduces, well, measured tidal ellipses in unstratified wintertime conditions. Stratified conditions present more of a problem because tidal-frequency internal wave generation and propagation significantly complicates the structure of the resulting tidal field. Nonetheless, the numerical model reproduces qualitative aspects of the stratified tidal flow that are consistent with observations in the bays.

  7. Consistent Safety and Infectivity in Sporozoite Challenge Model of Plasmodium vivax in Malaria-Naive Human Volunteers

    PubMed Central

    Herrera, Sócrates; Solarte, Yezid; Jordán-Villegas, Alejandro; Echavarría, Juan Fernando; Rocha, Leonardo; Palacios, Ricardo; Ramírez, Óscar; Vélez, Juan D.; Epstein, Judith E.; Richie, Thomas L.; Arévalo-Herrera, Myriam

    2011-01-01

    A safe and reproducible Plasmodium vivax infectious challenge method is required to evaluate the efficacy of malaria vaccine candidates. Seventeen healthy Duffy (+) and five Duffy (−) subjects were randomly allocated into three (A–C) groups and were exposed to the bites of 2–4 Anopheles albimanus mosquitoes infected with Plasmodium vivax derived from three donors. Duffy (−) subjects were included as controls for each group. Clinical manifestations of malaria and parasitemia were monitored beginning 7 days post-challenge. All Duffy (+) volunteers developed patent malaria infection within 16 days after challenge. Prepatent period determined by thick smear, was longer for Group A (median 14.5 d) than for Groups B and C (median 10 d/each). Infected volunteers recovered rapidly after treatment with no serious adverse events. The bite of as low as two P. vivax-infected mosquitoes provides safe and reliable infections in malaria-naive volunteers, suitable for assessing antimalarial and vaccine efficacy trials. PMID:21292872

  8. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

    PubMed

    Höhna, Sebastian; Landis, Michael J; Heath, Tracy A; Boussau, Bastien; Lartillot, Nicolas; Moore, Brian R; Huelsenbeck, John P; Ronquist, Fredrik

    2016-07-01

    Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.].

  9. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

    PubMed Central

    Höhna, Sebastian; Landis, Michael J.

    2016-01-01

    Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com. [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.] PMID:27235697

  10. Observations and a linear model of water level in an interconnected inlet-bay system

    USGS Publications Warehouse

    Aretxabaleta, Alfredo; Ganju, Neil Kamal; Butman, Bradford; Signell, Richard

    2017-01-01

    A system of barrier islands and back-barrier bays occurs along southern Long Island, New York, and in many coastal areas worldwide. Characterizing the bay physical response to water level fluctuations is needed to understand flooding during extreme events and evaluate their relation to geomorphological changes. Offshore sea level is one of the main drivers of water level fluctuations in semienclosed back-barrier bays. We analyzed observed water levels (October 2007 to November 2015) and developed analytical models to better understand bay water level along southern Long Island. An increase (∼0.02 m change in 0.17 m amplitude) in the dominant M2 tidal amplitude (containing the largest fraction of the variability) was observed in Great South Bay during mid-2014. The observed changes in both tidal amplitude and bay water level transfer from offshore were related to the dredging of nearby inlets and possibly the changing size of a breach across Fire Island caused by Hurricane Sandy (after December 2012). The bay response was independent of the magnitude of the fluctuations (e.g., storms) at a specific frequency. An analytical model that incorporates bay and inlet dimensions reproduced the observed transfer function in Great South Bay and surrounding areas. The model predicts the transfer function in Moriches and Shinnecock bays where long-term observations were not available. The model is a simplified tool to investigate changes in bay water level and enables the evaluation of future conditions and alternative geomorphological settings.

  11. Modelling a storm surge event in Liverpool Bay with FVCOM.

    NASA Astrophysics Data System (ADS)

    Hall, P.

    2012-04-01

    A model of the Irish Sea/Liverpool Bay area has been developed using the finite volume, unstructured mesh code FVCOM. The model has been run with meteorological forcing to simulate the storm surge event of January 2007. This event has previously been modelled with the POLCOMS code, the results of which were used for a comparison of accuracy and computational efficiency of the two approaches. The wind speed (and hence wind stress) together with atmospheric pressure have been applied to the model as surface boundary conditions for a period of a few days to allow the model to settle down, and then the results for the peak of the storm on January 18th 2007 have been analysed to give metrics for the accuracy of the sea surface elevation that is predicted against measurements taken at Hilbre Island, near the mouth of the River Dee in Liverpool Bay. It was found that by changing the wind stress formulation within the FVCOM code a significant improvement in the accuracy of the model results could be obtained for the period of this surge event.

  12. Projected 2050 Model Simulations for the Chesapeake Bay ...

    EPA Pesticide Factsheets

    The Chesapeake Bay Program as has been tasked with assessing how changes in climate systems are expected to alter key variables and processes within the Watershed in concurrence with land use changes. EPA’s Office of Research and Development will be conducting historic and future, 2050, Weather Research and Forecast (WRF) metrological and Community Multiscale Air Quality (CMAQ) chemical transport model simulations to provide meteorological and nutrient deposition estimates for inclusion of the Chesapeake Bay Program’s assessment of how climate and land use change may impact water quality and ecosystem health. This presentation will present the timeline and research updates. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, decision-support tools, and models to be applied to media-specific or receptor-specific problem areas. CED uses modeling-based approaches to characterize exposures, evaluate fate and transport, and support environmental diagnostics/forensics with input from multiple data sources. It also develops media- and receptor-specific models, process models, and decision support tools for use both within and outside of EPA.

  13. Restoration Lessons Learned from Bay Scallop Habitat Models

    EPA Science Inventory

    Habitat quality and quantity are important factors to consider when restoring bay scallop (Argopecten irradians) populations; however, data linking habitat attributes to bay scallop populations are lacking. This information is essential to guide restoration efforts to reverse sc...

  14. The outflow of radionuclides from Novaya Zemlya bays--modeling and monitoring strategies.

    PubMed

    Harms, I H; Povinec, P P

    1999-09-30

    Hydrodynamic model results are used to evaluate possible monitoring strategies for a continuous survey of underwater dump sites. The Hamburg Shelf Ocean Model (HAMSOM) is applied to Abrosimov Bay and forced with realistic, transient wind fields and air temperatures. The three-dimensional circulation model is coupled to a dynamic-thermodynamic ice model that accounts for surface heat fluxes, fractional ice cover and ice thickness. Model results show significant variations in the bay circulation due to a pronounced seasonality in the wind forcing and the ice cover. The circulation is weakest in early summer when wind speeds are low and the ice still covers most parts of the bay. In autumn, circulation and flushing of the bay is most enhanced, due to increasing wind speeds and the absence of an ice cover. Dispersion scenarios were carried out assuming a leakage at dumped objects. During most of the year the obtained tracer concentrations in the bay are higher in the upper layers than close to the bottom, indicating an outflow at the surface and a compensatory inflow below. This general pattern is only reversed during spring and early summer, when the wind directions change. Since ice problems make it almost impossible to monitor surface waters or even the whole water column in a shallow bay, the only way to install a monitoring system, is at the bottom of the bay, as close as possible to dumped objects. Data transmission via satellite or radio could be realized from a small station located on the bay's edge.

  15. Spatial estimation from remotely sensed data via empirical Bayes models

    NASA Technical Reports Server (NTRS)

    Hill, J. R.; Hinkley, D. V.; Kostal, H.; Morris, C. N.

    1984-01-01

    Multichannel satellite image data, available as LANDSAT imagery, are recorded as a multivariate time series (four channels, multiple passovers) in two spatial dimensions. The application of parametric empirical Bayes theory to classification of, and estimating the probability of, each crop type at each of a large number of pixels is considered. This theory involves both the probability distribution of imagery data, conditional on crop types, and the prior spatial distribution of crop types. For the latter Markov models indexed by estimable parameters are used. A broad outline of the general theory reveals several questions for further research. Some detailed results are given for the special case of two crop types when only a line transect is analyzed. Finally, the estimation of an underlying continuous process on the lattice is discussed which would be applicable to such quantities as crop yield.

  16. Spatially and Temporally Detailed Modeling of Water Quality in Narragansett Bay (AGU)

    EPA Science Inventory

    Nutrient loading to Narragansett Bay has led to eutrophication, resulting in hypoxia and anoxia, finfish and shellfish kills, loss of seagrass, and reductions in the recreational and economic value of the Bay. We are developing a model that simulates the effects of external nutri...

  17. Spatially and Temporally Detailed Modeling of Water Quality in Narragansett Bay

    EPA Science Inventory

    Nutrient loading to Narragansett Bay has led to eutrophication, resulting in hypoxia and anoxia, finfish and shellfish kills, loss of seagrass, and reductions in the recreational and economic value of the Bay. We are developing a model that simulates the effects of external nutri...

  18. A Variational Bayes Approach to the Analysis of Occupancy Models

    PubMed Central

    Clark, Allan E.; Altwegg, Res; Ormerod, John T.

    2016-01-01

    Detection-nondetection data are often used to investigate species range dynamics using Bayesian occupancy models which rely on the use of Markov chain Monte Carlo (MCMC) methods to sample from the posterior distribution of the parameters of the model. In this article we develop two Variational Bayes (VB) approximations to the posterior distribution of the parameters of a single-season site occupancy model which uses logistic link functions to model the probability of species occurrence at sites and of species detection probabilities. This task is accomplished through the development of iterative algorithms that do not use MCMC methods. Simulations and small practical examples demonstrate the effectiveness of the proposed technique. We specifically show that (under certain circumstances) the variational distributions can provide accurate approximations to the true posterior distributions of the parameters of the model when the number of visits per site (K) are as low as three and that the accuracy of the approximations improves as K increases. We also show that the methodology can be used to obtain the posterior distribution of the predictive distribution of the proportion of sites occupied (PAO). PMID:26928878

  19. An Adaptive Model of Student Performance Using Inverse Bayes

    ERIC Educational Resources Information Center

    Lang, Charles

    2014-01-01

    This article proposes a coherent framework for the use of Inverse Bayesian estimation to summarize and make predictions about student behaviour in adaptive educational settings. The Inverse Bayes Filter utilizes Bayes theorem to estimate the relative impact of contextual factors and internal student factors on student performance using time series…

  20. Naive CD8 T-Cells Initiate Spontaneous Autoimmunity to a Sequestered Model Antigen of the Central Nervous System

    ERIC Educational Resources Information Center

    Na, Shin-Young; Cao, Yi; Toben, Catherine; Nitschke, Lars; Stadelmann, Christine; Gold, Ralf; Schimpl, Anneliese; Hunig, Thomas

    2008-01-01

    In multiple sclerosis, CD8 T-cells are thought play a key pathogenetic role, but mechanistic evidence from rodent models is limited. Here, we have tested the encephalitogenic potential of CD8 T-cells specific for the model antigen ovalbumin (OVA) sequestered in oligodendrocytes as a cytosolic molecule. We show that in these "ODC-OVA" mice, the…

  1. Development of a Hydrodynamic and Transport model of Bellingham Bay in Support of Nearshore Habitat Restoration

    SciTech Connect

    Wang, Taiping; Yang, Zhaoqing; Khangaonkar, Tarang

    2010-04-22

    In this study, a hydrodynamic model based on the unstructured-grid finite volume coastal ocean model (FVCOM) was developed for Bellingham Bay, Washington. The model simulates water surface elevation, velocity, temperature, and salinity in a three-dimensional domain that covers the entire Bellingham Bay and adjacent water bodies, including Lummi Bay, Samish Bay, Padilla Bay, and Rosario Strait. The model was developed using Pacific Northwest National Laboratory’s high-resolution Puget Sound and Northwest Straits circulation and transport model. A sub-model grid for Bellingham Bay and adjacent coastal waters was extracted from the Puget Sound model and refined in Bellingham Bay using bathymetric light detection and ranging (LIDAR) and river channel cross-section data. The model uses tides, river inflows, and meteorological inputs to predict water surface elevations, currents, salinity, and temperature. A tidal open boundary condition was specified using standard National Oceanic and Atmospheric Administration (NOAA) predictions. Temperature and salinity open boundary conditions were specified based on observed data. Meteorological forcing (wind, solar radiation, and net surface heat flux) was obtained from NOAA real observations and National Center for Environmental Prediction North American Regional Analysis outputs. The model was run in parallel with 48 cores using a time step of 2.5 seconds. It took 18 hours of cpu time to complete 26 days of simulation. The model was calibrated with oceanographic field data for the period of 6/1/2009 to 6/26/2009. These data were collected specifically for the purpose of model development and calibration. They include time series of water-surface elevation, currents, temperature, and salinity as well as temperature and salinity profiles during instrument deployment and retrieval. Comparisons between model predictions and field observations show an overall reasonable agreement in both temporal and spatial scales. Comparisons of

  2. Random Parameter Markov Population Process Models and Their Likelihood, Bayes and Empirical Bayes Analysis.

    DTIC Science & Technology

    1985-09-01

    XW Dr. Douglas de Priest Statistics & Probability Program Code 411(SP) Office of Naval Research Arlington, VA 22217 Dr. Morris DeGroot Statistics...consult Morris (1983) for a review of parametric empirical Bayes methods, Robbins (1983) and in much previous work, has elucidated the non-parametric...South Street Morris Township, NJ 07960 Dr. David L. Wallace Statistics Dept. University of Chicago 5734 S. University Ave. Chicago, IL 60637 Dr. F

  3. Acute and chronic stress models differentially impact the inflammatory and antibody titer responses to respiratory vaccination in naive beef steers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this research was to determine the effect of an acute vs. chronic stress model on serum antibody titer and acute phase responses. Seronegative beef steers (n=32; 209 +/- 8 kg) were stratified by body weight and assigned randomly to 1 of 3 treatments: 1) Chronic stress (CHR), 0.5 mg/...

  4. Modulation of the metabolic response to vaccination in naive beef steers using an acute versus chronic stress model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Available energy plays a critical role in the initiation and maintenance of an immune response to a pathogen a process that is further altered by activation of stress system. This study was designed to determine the effect of an acute versus chronic stress model on the metabolic response to vaccinat...

  5. Spatially and Temporally Detailed Modeling of Water Quality in Narragansett Bay

    NASA Astrophysics Data System (ADS)

    Charlestra, L.; Dettmann, E. H.; Abdelrhman, M.

    2014-12-01

    Nutrient loading to Narragansett Bay has led to eutrophication, resulting in hypoxia and anoxia, finfish and shellfish kills, loss of seagrass, and reductions in the recreational and economic value of the Bay. We are developing a model that simulates the effects of external nutrient and hydrologic loading on water quality in Narragansett Bay. Extensive field monitoring programs and process studies by the Narragansett Bay Commission, Federal and State agencies, municipalities, and university groups have been measuring physical parameters, nutrient concentrations and other water quality parameters in the Bay and its tributaries, nutrient inputs from wastewater treatment facilities, and process kinetic parameters. We are using data for existing nutrient concentrations, river flow and wastewater treatment facility effluent flow to estimate nutrient loading for non-sampled days using the U.S. Geological Survey's Load Estimator (LOADEST) software. The time-variable data so generated will be used as input to the U.S. Environmental Protection Agency's WASPEUTRO model linked with a calibrated three-dimensional hydrodynamic model, the Environmental Fluid Dynamics Code (EFDC). The primary objectives of the modeling effort are to simulate the effects of nutrient loading on dissolved oxygen concentrations and chlorophyll-a, an important parameter for water clarity and seagrass viability, to estimate the sensitivity of the Bay to changes in nutrient loading and freshwater inflow, and to explore the potential effects of management actions and other factors such as climate change on these water quality parameters in the Bay.

  6. Modeling biogeochemical cycles in Chesapeake Bay with a coupled physical biological model

    NASA Astrophysics Data System (ADS)

    Xu, Jiangtao; Hood, Raleigh R.

    2006-08-01

    In this paper we describe the development and validation of a relatively simple biogeochemical model of Chesapeake Bay. This model consists of a 3-dimensional, prognostic hydrodynamic model that is coupled to an NPZD-type open ocean ecosystem model, which has been modified by adding additional compartments and parameterizations of biogeochemical processes that are important in estuarine systems. These modifications include an empirical optical model for predicting the diffuse attenuation coefficient Kd, compartments for representing oxygen and suspended sediment concentrations, and parameterizations of phosphorus limitation, denitrification, and seasonal changes in ecosystem structure and temperature effects. To show the overall performance of the coupled physical-biological model, the modeled dissolved inorganic nitrogen, phytoplankton, dissolved oxygen, total suspended solids and light attenuation coefficient in 1995 (a dry year) and 1996 (a very wet year) are examined and compared with observations obtained from the Chesapeake Bay Program. We demonstrate that this relatively simple model is capable of producing the general distribution of each field (both the mean and variability) in the main stem of the Bay. And the model is robust enough to generate reasonable results under both wet and dry conditions. Some significant discrepancies are also observed, such as overestimation of phytoplankton concentrations in shoal regions and overestimation of oxygen concentrations in deep channels, which reveal some deficiencies in the model formulation. Some potential improvements and remedies are suggested. Sensitivity studies on selected parameters are also reported.

  7. THE ROLE OF PLAUSIBLE REASONING WITHIN MILITARY INTELLIGENCE: AN APPLICATION OF BAYES THEOREM AS A MODEL FOR PROBLEM SOLVING,

    DTIC Science & Technology

    followed with the introduction of Bayes Theorem as a model for intelligence analysis. The conjecture is made that Bayes Theorem can also serve as the...nucleus of a formal methodology. The application of Bayes Theorem to several types of problems is demonstrated. However, the implementation of such a

  8. Circulation and effluent dilution modeling in Massachusetts Bay : model implementation, verification and results

    USGS Publications Warehouse

    Signell, Richard P.; Jenter, Harry L.; Blumberg, Alan F.

    1996-01-01

    A three-dimensional hydrodynamic model was developed as part of a cooperative U.S. Geological Survey/Massachusetts Water Resources Authority program to study contaminated sediment accumulation and transport in Massachusetts Bay. This report details the development of the model and assesses how well the model represents observed currents and water properties in the bay. It also summarizes circulation and comparative effluent dilution simulations from existing and future Boston sewage outfalls over a three-year period from October 1, 1989 to December 31, 1992. The ECOM-si model, a semi-implicit version of the Blumberg and Mellor (1987) Estuarine, Coastal and Ocean Model, is shown to reproduce many of the important hydrodynamical features of Massachusetts Bay: the seasonal evolution of the pycnocline, the mean flow pattern, and the strength of sub-tidal current fluctuations. Throughout the simulation period, during both vertically well-mixed and stratified conditions, the seasonal statistics of observed currents are well-represented by the model. The model is therefore appropriate for studying the average dilution of sewage effluent and other continuously discharged substances over seasonal time scales. The ability of the model to reproduce individual flow events varies with season and location within the bay. Flow events during unstratified conditions in western Massachusetts Bay are particularly well-represented, indicating that the model is appropriate for studying processes such as the transport of suspended material from the future outfall site due to winter storms. Individual flow events during stratified conditions and in the offshore Stellwagen Bank region, however, are less well-represented due to small length scales (caused by upwelling and river discharge events) coupled with insufficient data to specify open boundary forcing from the Gulf of Maine. Thus while the model might be used to answer issues such as the frequency with which Gulf of Maine river

  9. Empirical Bayes Estimation of Coefficients in the General Linear Model from Data of Deficient Rank.

    ERIC Educational Resources Information Center

    Braun, Henry I.; And Others

    1983-01-01

    Empirical Bayes methods are shown to provide a practical alternative to standard least squares methods in fitting high dimensional models to sparse data. An example concerning prediction bias in educational testing is presented as an illustration. (Author)

  10. Using Bayes Model Averaging for Wind Power Forecasts

    NASA Astrophysics Data System (ADS)

    Preede Revheim, Pål; Beyer, Hans Georg

    2014-05-01

    For operational purposes predictions of the forecasts of the lumped output of groups of wind farms spread over larger geographic areas will often be of interest. A naive approach is to make forecasts for each individual site and sum them up to get the group forecast. It is however well documented that a better choice is to use a model that also takes advantage of spatial smoothing effects. It might however be the case that some sites tends to more accurately reflect the total output of the region, either in general or for certain wind directions. It will then be of interest giving these a greater influence over the group forecast. Bayesian model averaging (BMA) is a statistical post-processing method for producing probabilistic forecasts from ensembles. Raftery et al. [1] show how BMA can be used for statistical post processing of forecast ensembles, producing PDFs of future weather quantities. The BMA predictive PDF of a future weather quantity is a weighted average of the ensemble members' PDFs, where the weights can be interpreted as posterior probabilities and reflect the ensemble members' contribution to overall forecasting skill over a training period. In Revheim and Beyer [2] the BMA procedure used in Sloughter, Gneiting and Raftery [3] were found to produce fairly accurate PDFs for the future mean wind speed of a group of sites from the single sites wind speeds. However, when the procedure was attempted applied to wind power it resulted in either problems with the estimation of the parameters (mainly caused by longer consecutive periods of no power production) or severe underestimation (mainly caused by problems with reflecting the power curve). In this paper the problems that arose when applying BMA to wind power forecasting is met through two strategies. First, the BMA procedure is run with a combination of single site wind speeds and single site wind power production as input. This solves the problem with longer consecutive periods where the input data

  11. Study on the Calculation Models of Bus Delay at Bays Using Queueing Theory and Markov Chain

    PubMed Central

    Sun, Li; Sun, Shao-wei; Wang, Dian-hai

    2015-01-01

    Traffic congestion at bus bays has decreased the service efficiency of public transit seriously in China, so it is crucial to systematically study its theory and methods. However, the existing studies lack theoretical model on computing efficiency. Therefore, the calculation models of bus delay at bays are studied. Firstly, the process that buses are delayed at bays is analyzed, and it was found that the delay can be divided into entering delay and exiting delay. Secondly, the queueing models of bus bays are formed, and the equilibrium distribution functions are proposed by applying the embedded Markov chain to the traditional model of queuing theory in the steady state; then the calculation models of entering delay are derived at bays. Thirdly, the exiting delay is studied by using the queueing theory and the gap acceptance theory. Finally, the proposed models are validated using field-measured data, and then the influencing factors are discussed. With these models the delay is easily assessed knowing the characteristics of the dwell time distribution and traffic volume at the curb lane in different locations and different periods. It can provide basis for the efficiency evaluation of bus bays. PMID:25759720

  12. Study on the calculation models of bus delay at bays using queueing theory and Markov chain.

    PubMed

    Sun, Feng; Sun, Li; Sun, Shao-Wei; Wang, Dian-Hai

    2015-01-01

    Traffic congestion at bus bays has decreased the service efficiency of public transit seriously in China, so it is crucial to systematically study its theory and methods. However, the existing studies lack theoretical model on computing efficiency. Therefore, the calculation models of bus delay at bays are studied. Firstly, the process that buses are delayed at bays is analyzed, and it was found that the delay can be divided into entering delay and exiting delay. Secondly, the queueing models of bus bays are formed, and the equilibrium distribution functions are proposed by applying the embedded Markov chain to the traditional model of queuing theory in the steady state; then the calculation models of entering delay are derived at bays. Thirdly, the exiting delay is studied by using the queueing theory and the gap acceptance theory. Finally, the proposed models are validated using field-measured data, and then the influencing factors are discussed. With these models the delay is easily assessed knowing the characteristics of the dwell time distribution and traffic volume at the curb lane in different locations and different periods. It can provide basis for the efficiency evaluation of bus bays.

  13. Modeling of Waves, Hydrodynamics and Sediment Transport for Protection of Wetlands at Braddock Bay, New York

    DTIC Science & Technology

    2015-03-01

    Support Program Modeling of Waves, Hydrodynamics and Sediment Transport for Protection of Wetlands at Braddock Bay, New York En gi ne er R es ea...Operations Technical Support Program ERDC TR-14-8 March 2015 Modeling of Waves, Hydrodynamics and Sediment Transport for Protection of Wetlands...Corps of Engineers (USACE), Buffalo Dis- trict, is conducting a study to evaluate shoreline protection measures for coastal wetlands at Braddock Bay

  14. Flexible Modeling of Epidemics with an Empirical Bayes Framework

    PubMed Central

    Brooks, Logan C.; Farrow, David C.; Hyun, Sangwon; Tibshirani, Ryan J.; Rosenfeld, Roni

    2015-01-01

    Seasonal influenza epidemics cause consistent, considerable, widespread loss annually in terms of economic burden, morbidity, and mortality. With access to accurate and reliable forecasts of a current or upcoming influenza epidemic’s behavior, policy makers can design and implement more effective countermeasures. This past year, the Centers for Disease Control and Prevention hosted the “Predict the Influenza Season Challenge”, with the task of predicting key epidemiological measures for the 2013–2014 U.S. influenza season with the help of digital surveillance data. We developed a framework for in-season forecasts of epidemics using a semiparametric Empirical Bayes framework, and applied it to predict the weekly percentage of outpatient doctors visits for influenza-like illness, and the season onset, duration, peak time, and peak height, with and without using Google Flu Trends data. Previous work on epidemic modeling has focused on developing mechanistic models of disease behavior and applying time series tools to explain historical data. However, tailoring these models to certain types of surveillance data can be challenging, and overly complex models with many parameters can compromise forecasting ability. Our approach instead produces possibilities for the epidemic curve of the season of interest using modified versions of data from previous seasons, allowing for reasonable variations in the timing, pace, and intensity of the seasonal epidemics, as well as noise in observations. Since the framework does not make strict domain-specific assumptions, it can easily be applied to some other diseases with seasonal epidemics. This method produces a complete posterior distribution over epidemic curves, rather than, for example, solely point predictions of forecasting targets. We report prospective influenza-like-illness forecasts made for the 2013–2014 U.S. influenza season, and compare the framework’s cross-validated prediction error on historical data to

  15. Flexible Modeling of Epidemics with an Empirical Bayes Framework.

    PubMed

    Brooks, Logan C; Farrow, David C; Hyun, Sangwon; Tibshirani, Ryan J; Rosenfeld, Roni

    2015-08-01

    Seasonal influenza epidemics cause consistent, considerable, widespread loss annually in terms of economic burden, morbidity, and mortality. With access to accurate and reliable forecasts of a current or upcoming influenza epidemic's behavior, policy makers can design and implement more effective countermeasures. This past year, the Centers for Disease Control and Prevention hosted the "Predict the Influenza Season Challenge", with the task of predicting key epidemiological measures for the 2013-2014 U.S. influenza season with the help of digital surveillance data. We developed a framework for in-season forecasts of epidemics using a semiparametric Empirical Bayes framework, and applied it to predict the weekly percentage of outpatient doctors visits for influenza-like illness, and the season onset, duration, peak time, and peak height, with and without using Google Flu Trends data. Previous work on epidemic modeling has focused on developing mechanistic models of disease behavior and applying time series tools to explain historical data. However, tailoring these models to certain types of surveillance data can be challenging, and overly complex models with many parameters can compromise forecasting ability. Our approach instead produces possibilities for the epidemic curve of the season of interest using modified versions of data from previous seasons, allowing for reasonable variations in the timing, pace, and intensity of the seasonal epidemics, as well as noise in observations. Since the framework does not make strict domain-specific assumptions, it can easily be applied to some other diseases with seasonal epidemics. This method produces a complete posterior distribution over epidemic curves, rather than, for example, solely point predictions of forecasting targets. We report prospective influenza-like-illness forecasts made for the 2013-2014 U.S. influenza season, and compare the framework's cross-validated prediction error on historical data to that of a

  16. Naive Theories of Social Groups

    ERIC Educational Resources Information Center

    Rhodes, Marjorie

    2012-01-01

    Four studies examined children's (ages 3-10, Total N = 235) naive theories of social groups, in particular, their expectations about how group memberships constrain social interactions. After introduction to novel groups of people, preschoolers (ages 3-5) reliably expected agents from one group to harm members of the other group (rather than…

  17. Modelling sea ice formation in the Terra Nova Bay polynya

    NASA Astrophysics Data System (ADS)

    Sansiviero, M.; Morales Maqueda, M. Á.; Fusco, G.; Aulicino, G.; Flocco, D.; Budillon, G.

    2017-02-01

    Antarctic sea ice is constantly exported from the shore by strong near surface winds that open leads and large polynyas in the pack ice. The latter, known as wind-driven polynyas, are responsible for significant water mass modification due to the high salt flux into the ocean associated with enhanced ice growth. In this article, we focus on the wind-driven Terra Nova Bay (TNB) polynya, in the western Ross Sea. Brine rejected during sea ice formation processes that occur in the TNB polynya densifies the water column leading to the formation of the most characteristic water mass of the Ross Sea, the High Salinity Shelf Water (HSSW). This water mass, in turn, takes part in the formation of Antarctic Bottom Water (AABW), the densest water mass of the world ocean, which plays a major role in the global meridional overturning circulation, thus affecting the global climate system. A simple coupled sea ice-ocean model has been developed to simulate the seasonal cycle of sea ice formation and export within a polynya. The sea ice model accounts for both thermal and mechanical ice processes. The oceanic circulation is described by a one-and-a-half layer, reduced gravity model. The domain resolution is 1 km × 1 km, which is sufficient to represent the salient features of the coastline geometry, notably the Drygalski Ice Tongue. The model is forced by a combination of Era Interim reanalysis and in-situ data from automatic weather stations, and also by a climatological oceanic dataset developed from in situ hydrographic observations. The sensitivity of the polynya to the atmospheric forcing is well reproduced by the model when atmospheric in situ measurements are combined with reanalysis data. Merging the two datasets allows us to capture in detail the strength and the spatial distribution of the katabatic winds that often drive the opening of the polynya. The model resolves fairly accurately the sea ice drift and sea ice production rates in the TNB polynya, leading to

  18. Therapeutic effect of the triazole Bay R 3783 in mouse models of coccidioidomycosis, blastomycosis, and histoplasmosis.

    PubMed

    Pappagianis, D; Zimmer, B L; Theodoropoulos, G; Plempel, M; Hector, R F

    1990-06-01

    A new triazole, Bay R 3783, was compared with ketoconazole, itraconazole, and fluconazole, which were given via the alimentary tract at three dosages, and amphotericin B, which was given at 1 mg/kg intraperitoneally, in murine models of the systemic mycoses coccidioidomycosis, histoplasmosis, and blastomycosis. In a pulmonary coccidioidomycosis model, Bay R 3783, fluconazole, and itraconazole were essentially equally efficacious and more active than ketoconazole in protecting mice against death; but they were inferior to amphotericin B. In a short-term organ load experiment, Bay R 3783 and amphotericin B were equally effective and were more effective than the other drugs in reducing the amount of Coccidioides immitis in the lungs. Against meningocerebral coccidioidomycosis, Bay R 3783, itraconazole, and fluconazole at 25 mg/kg and amphotericin B prevented death only during therapy, with mortalities ensuing shortly thereafter. In mice with systemic histoplasmosis, Bay R 3783 and itraconazole at 25 mg/kg and amphotericin B prevented death in all mice through a 44-day observation period. Clearance of Histoplasma capsulatum from organs was similar in mice treated with Bay R 3783 and itraconazole; this clearance was greater than that in mice treated with ketoconazole and fluconazole but less than that in mice treated with amphotericin B. In mice with systemic blastomycosis, Bay R 3783 at 25 mg/kg yielded 90% survivors at 60 days, which was greater than that achieved with amphotericin B (60%) or itraconazole (30%). Clearance of Blastomyces dermatitidis from the lungs was greatest with Bay R 3783, followed by that with amphotericin B, itraconazole, fluconazole, and ketoconazole, in that order. Therefore, Bay R 3783 showed effectiveness comparable to or exceeding those of itraconazole and fluconazole and exceeding that of ketoconazole against these systemic mycoses in mice.

  19. The predictive validity of the drug-naive bilaterally MPTP-treated monkey as a model of Parkinson's disease: effects of L-DOPA and the D1 agonist SKF 82958.

    PubMed

    Andringa, G; Lubbers, L; Drukarch, B; Stoof, J C; Cools, A R

    1999-03-01

    The aim of this study was twofold: (1) to study the predictive validity of the drug-naive, bilaterally MPTP-treated monkey as an animal model of Parkinson's disease (PD), and (2) to investigate the therapeutic and undesired effects of the D1 agonist SKF 82958 as compared to L-DOPA treatment, in drug-naive and L-DOPA pretreated monkeys. A detailed ethogram was used, allowing the separation of therapeutic and undesired effects. Eight weeks after bilateral intracarotid MPTP administration, SKF 82958 (1 mg/kg, n = 4, SKF 82958, naive group) or methyl-L-DOPA + carbi-dopa (10 + 2.5 mg/kg, n = 4, L-DOPA group) was administered intramuscularly for 22 days. After a drug-free period of eight weeks, the L-DOPA group was treated with SKF 82958 for 22 days (SKF 82959, 1 mg/kg, n=4, pretreated). All drug treatments increased the parameters used classically to evaluate dopaminergic drugs, namely body displacement, dyskinesia and dystonia. However, the new detailed analysis revealed that L-DOPA, but not SKF 82958, had therapeutic effects, reflected by an increase in goal-directed fore-limb use. SKF 82958, but not L-DOPA, induced additional undesired effects; including epileptoid behaviours in both drug-naive and drug-pretreated monkeys. In one L-DOPA-unresponsive monkey, SKF 82958 did induce minor therapeutic effects, as well as undesired effects. Although the effects of SKF 82958 on fore-limb movements, rotational behaviours and body displacement were comparable in the naive and pretreated group, SKF 82958 re-initiated undesired effects in the L-DOPA pretreated group from day one. It is concluded that the bilaterally MPTP-treated monkey is an animal model with predictive validity for PD: it adequately predicts the therapeutic effects and undesired effects of L-DOPA. Furthermore, it is concluded that SKF 82958 is less effective than L-DOPA in the treatment of PD, because it did not induce therapeutic effects, but instead elicited several undesired effects.

  20. Challenges associated with modeling low-oxygen waters in Chesapeake Bay: a multiple model comparison

    NASA Astrophysics Data System (ADS)

    Irby, I. D.; Friedrichs, M. A. M.; Friedrichs, C. T.; Bever, A. J.; Hood, R. R.; Lanerolle, L. W. J.; Scully, M. E.; Sellner, K.; Shen, J.; Testa, J.; Li, M.; Wang, H.; Wang, P.; Linker, L.; Xia, M.

    2015-12-01

    As three-dimensional (3-D) aquatic ecosystem models are becoming used more frequently for operational water quality forecasts and ecological management decisions, it is important to understand the relative strengths and limitations of existing 3-D models of varying spatial resolution and biogeochemical complexity. To this end, two-year simulations of the Chesapeake Bay from eight hydrodynamic-oxygen models have been statistically compared to each other and to historical monitoring data. Results show that although models have difficulty resolving the variables typically thought to be the main drivers of dissolved oxygen variability (stratification, nutrients, and chlorophyll), all eight models have significant skill in reproducing the mean and seasonal variability of dissolved oxygen. In addition, models with constant net respiration rates independent of nutrient supply and temperature reproduced observed dissolved oxygen concentrations about as well as much more complex, nutrient-dependent biogeochemical models. This finding has significant ramifications for short-term hypoxia forecasts in the Chesapeake Bay, which may be possible with very simple oxygen parameterizations, in contrast to the more complex full biogeochemical models required for scenario-based forecasting. However, models have difficulty simulating correct density and oxygen mixed layer depths, which are important ecologically in terms of habitat compression. Observations indicate a much stronger correlation between the depths of the top of the pycnocline and oxycline than between their maximum vertical gradients, highlighting the importance of the mixing depth in defining the region of aerobic habitat in the Chesapeake Bay when low-oxygen bottom waters are present. Improvement in hypoxia simulations will thus depend more on the ability of models to reproduce the correct mean and variability of the depth of the physically driven surface mixed layer than the precise magnitude of the vertical density

  1. Challenges associated with modeling low-oxygen waters in Chesapeake Bay: a multiple model comparison

    NASA Astrophysics Data System (ADS)

    Irby, Isaac D.; Friedrichs, Marjorie A. M.; Friedrichs, Carl T.; Bever, Aaron J.; Hood, Raleigh R.; Lanerolle, Lyon W. J.; Li, Ming; Linker, Lewis; Scully, Malcolm E.; Sellner, Kevin; Shen, Jian; Testa, Jeremy; Wang, Hao; Wang, Ping; Xia, Meng

    2016-04-01

    As three-dimensional (3-D) aquatic ecosystem models are used more frequently for operational water quality forecasts and ecological management decisions, it is important to understand the relative strengths and limitations of existing 3-D models of varying spatial resolution and biogeochemical complexity. To this end, 2-year simulations of the Chesapeake Bay from eight hydrodynamic-oxygen models have been statistically compared to each other and to historical monitoring data. Results show that although models have difficulty resolving the variables typically thought to be the main drivers of dissolved oxygen variability (stratification, nutrients, and chlorophyll), all eight models have significant skill in reproducing the mean and seasonal variability of dissolved oxygen. In addition, models with constant net respiration rates independent of nutrient supply and temperature reproduced observed dissolved oxygen concentrations about as well as much more complex, nutrient-dependent biogeochemical models. This finding has significant ramifications for short-term hypoxia forecasts in the Chesapeake Bay, which may be possible with very simple oxygen parameterizations, in contrast to the more complex full biogeochemical models required for scenario-based forecasting. However, models have difficulty simulating correct density and oxygen mixed layer depths, which are important ecologically in terms of habitat compression. Observations indicate a much stronger correlation between the depths of the top of the pycnocline and oxycline than between their maximum vertical gradients, highlighting the importance of the mixing depth in defining the region of aerobic habitat in the Chesapeake Bay when low-oxygen bottom waters are present. Improvement in hypoxia simulations will thus depend more on the ability of models to reproduce the correct mean and variability of the depth of the physically driven surface mixed layer than the precise magnitude of the vertical density gradient.

  2. Empirical Bayes Estimation in the Rasch Model: A Simulation.

    ERIC Educational Resources Information Center

    de Gruijter, Dato N. M.

    In a situation where the population distribution of latent trait scores can be estimated, the ordinary maximum likelihood estimator of latent trait scores may be improved upon by taking the estimated population distribution into account. In this paper empirical Bayes estimators are compared with the liklihood estimator for three samples of 300…

  3. Numerical Modeling of Storm Surges in Chesapeake Bay

    DTIC Science & Technology

    2008-01-01

    bathymetry grid was developed from several data sources, including the National Ocean Service (NOS) Digital Navigation Charts ( DNC ), bathymetry data from...of Virginia and Maryland coasts. This grid was refined in Chesapeake Bay (Figure 5) using the NOS/ DNC data, a composite dataset from VIMS, GEODAS

  4. Projected 2050 Model Simulations for the Chesapeake Bay Program

    EPA Science Inventory

    The Chesapeake Bay Program as has been tasked with assessing how changes in climate systems are expected to alter key variables and processes within the Watershed in concurrence with land use changes. EPA’s Office of Research and Development will be conducting historic and...

  5. Risk of Erectile Dysfunction in Transfusion-naive Thalassemia Men

    PubMed Central

    Chen, Yu-Guang; Lin, Te-Yu; Lin, Cheng-Li; Dai, Ming-Shen; Ho, Ching-Liang; Kao, Chia-Hung

    2015-01-01

    Abstract Based on the mechanism of pathophysiology, thalassemia major or transfusion-dependent thalassemia patients may have an increased risk of developing organic erectile dysfunction resulting from hypogonadism. However, there have been few studies investigating the association between erectile dysfunction and transfusion-naive thalassemia populations. We constructed a population-based cohort study to elucidate the association between transfusion-naive thalassemia populations and organic erectile dysfunction This nationwide population-based cohort study involved analyzing data from 1998 to 2010 obtained from the Taiwanese National Health Insurance Research Database, with a follow-up period extending to the end of 2011. We identified men with transfusion-naive thalassemia and selected a comparison cohort that was frequency-matched with these according to age, and year of diagnosis thalassemia at a ratio of 1 thalassemia man to 4 control men. We analyzed the risks for transfusion-naive thalassemia men and organic erectile dysfunction by using Cox proportional hazards regression models. In this study, 588 transfusion-naive thalassemia men and 2337 controls were included. Total 12 patients were identified within the thalassaemia group and 10 within the control group. The overall risks for developing organic erectile dysfunction were 4.56-fold in patients with transfusion-naive thalassemia men compared with the comparison cohort after we adjusted for age and comorbidities. Our long-term cohort study results showed that in transfusion-naive thalassemia men, there was a higher risk for the development of organic erectile dysfunction, particularly in those patients with comorbidities. PMID:25837766

  6. Modeling spatial and temporal variation of suitable nursery habitats for Atlantic sturgeon in the Chesapeake Bay

    NASA Astrophysics Data System (ADS)

    Niklitschek, Edwin J.; Secor, David H.

    2005-07-01

    For rare and endangered species, bioenergetics modeling can represent a valuable approach for understanding issues of habitat value and connectivity among potential habitats within nurseries in restoration programs. We used multivariable bioenergetics and survival models for Atlantic sturgeon to generate spatially explicit maps of potential production in the Chesapeake Bay. For the period 1993-2002, spatial and temporal patterns in water quality effects (temperature, dissolved oxygen [DO] and salinity) on potential production were evaluated. In addition, two forecasted scenarios were modeled: one implementing newly revised U.S. Environmental Protection Agency (EPA) DO-criteria for the Chesapeake Bay, and the other assuming a bay-wide increase of 1 °C due to an underlying trend in regional climate. Atlantic sturgeon's low (survival/growth) tolerance to temperatures >28 °C was a critical constraint during their first 1-2 summers of life. Hatched in freshwater (spring to mid-summer), young-of-the-year were predicted to occupy cooler (deeper) areas as temperature approached sub-lethal levels. While most thermal refuges were located down-estuary, a large fraction of potential refuges were unsuitable due to persistent hypoxia and/or salinity levels beyond the limited osmoregulatory capabilities of early juvenile Atlantic sturgeon. As a result, suitable summer habitats for juvenile Atlantic sturgeons in the Chesapeake Bay were predicted to be spatially restricted and variable between years, ranging from 0 to 35% of the modeled bay surface area. In critical (drought) years, almost no summer habitat was predicted to be available for juvenile Atlantic sturgeon. Value and size of nursery habitat was highly sensitive to climatic oscillations and anthropogenic interventions affecting freshwater inflow, water temperature and/or DO. Achieving EPA DO-criteria for the Chesapeake Bay was predicted to increase total suitable habitat by 13% for an average year, while increasing

  7. A trophic model of fringing coral reefs in Nanwan Bay, southern Taiwan suggests overfishing.

    PubMed

    Liu, Pi-Jen; Shao, Kwang-Tsao; Jan, Rong-Quen; Fan, Tung-Yung; Wong, Saou-Lien; Hwang, Jiang-Shiou; Chen, Jen-Ping; Chen, Chung-Chi; Lin, Hsing-Juh

    2009-09-01

    Several coral reefs of Nanwan Bay, Taiwan have recently undergone shifts to macroalgal or sea anemone dominance. Thus, a mass-balance trophic model was constructed to analyze the structure and functioning of the food web. The fringing reef model was comprised of 18 compartments, with the highest trophic level of 3.45 for piscivorous fish. Comparative analyses with other reef models demonstrated that Nanwan Bay was similar to reefs with high fishery catches. While coral biomass was not lower, fish biomass was lower than those of reefs with high catches. Consequently, the sums of consumption and respiratory flows and total system throughput were also decreased. The Nanwan Bay model potentially suggests an overfished status in which the mean trophic level of the catch, matter cycling, and trophic transfer efficiency are extremely reduced.

  8. A system dynamics model for the environmental management of the Sepetiba Bay Watershed, Brazil.

    PubMed

    Leal Neto, Alexandre de C; Legey, Luiz F L; González-Araya, Marcela Cecilia; Jablonski, Silvio

    2006-11-01

    In the recent past, the Sepetiba Bay watershed, located in the Rio de Janeiro State, Brazil has experienced rapid industrial development and population growth, as well as an increase in water pollution and environmental degradation. To analyze the complex interrelationships among the agents affecting the Sepetibza Bay environment, a system dynamics model was developed. The model builds on extensive studies conducted for the watershed, and simulates different hypotheses of economic growth and of demographic expansion. Thus, it can be used as a decision support tool for the identification of investment priorities and policy analyses under various scenarios. In order to provide a comprehensive approach to the environmental management of the Sepetiba Bay watershed, the model had to consider only the most relevant aspects of the behavior and the key interactions among agents operating in the watershed. In this article, the model's structure is presented together with some of its main results.

  9. Low Freshwater Inflow Study. Chesapeake Bay Hydraulic Model Investigation.

    DTIC Science & Technology

    1982-01-01

    47 discharge from other main bay tributaries such as the Elizabeth, Back (Virginia), Piankatank, Saint Mary’s, South, Magothy , Back (Maryland), Bush...Proto Ft) James R. (Continued) J- 10-01 26 2, 13, 24 Little Choptank R. LC-01-01 17 4, 12 LC-02-01 22 4, 12, 21 Magothy R. MA-01-01 21 4, 12, 18 MA-02

  10. Diagnostic model construction and example analysis of habitat degradation in enclosed bay: III. Sansha Bay habitat restoration strategy

    NASA Astrophysics Data System (ADS)

    Sun, Peng; Yu, Ge; Chen, Zhaozhang; Hu, Jianyu; Liu, Guangxing; Xu, Donghui

    2015-03-01

    Unbalanced inputs and outputs of material are the root cause of habitat degradation in Sansha Bay, Fujian Province, China. However, the cumulative pollution varies in different geographic locations and natural conditions in the enclosed bay. In this study, hydrodynamic conditions, sediment characteristics, and aquaculture methods were recognized as the underlying causes of spatial heterogeneity in the distribution of nitrogen and phosphorous pollutants, the two major controlling factors of habitat degradation in the bay area. In order to achieve the goal of balancing nutrient inputs and outputs in Sansha Bay, we developed a feasible and practical zone restoration strategy for reasonable adjustment and arrangement of aquaculture species and production scale in accordance with varying hydrodynamic conditions and sediment characteristics in six sub-bay areas (sub-systems). The proposed zone restoration strategy lays a solid foundation for habitat restoration and management in Sansha Bay.

  11. Diagnostic model construction and example analysis of habitat degradation in enclosed bay: III. Sansha Bay habitat restoration strategy

    NASA Astrophysics Data System (ADS)

    Sun, Peng; Yu, Ge; Chen, Zhaozhang; Hu, Jianyu; Liu, Guangxing; Xu, Donghui

    2014-09-01

    Unbalanced inputs and outputs of material are the root cause of habitat degradation in Sansha Bay, Fujian Province, China. However, the cumulative pollution varies in different geographic locations and natural conditions in the enclosed bay. In this study, hydrodynamic conditions, sediment characteristics, and aquaculture methods were recognized as the underlying causes of spatial heterogeneity in the distribution of nitrogen and phosphorous pollutants, the two major controlling factors of habitat degradation in the bay area. In order to achieve the goal of balancing nutrient inputs and outputs in Sansha Bay, we developed a feasible and practical zone restoration strategy for reasonable adjustment and arrangement of aquaculture species and production scale in accordance with varying hydrodynamic conditions and sediment characteristics in six sub-bay areas (sub-systems). The proposed zone restoration strategy lays a solid foundation for habitat restoration and management in Sansha Bay.

  12. Derivation of novel human ground state naive pluripotent stem cells.

    PubMed

    Gafni, Ohad; Weinberger, Leehee; Mansour, Abed AlFatah; Manor, Yair S; Chomsky, Elad; Ben-Yosef, Dalit; Kalma, Yael; Viukov, Sergey; Maza, Itay; Zviran, Asaf; Rais, Yoach; Shipony, Zohar; Mukamel, Zohar; Krupalnik, Vladislav; Zerbib, Mirie; Geula, Shay; Caspi, Inbal; Schneir, Dan; Shwartz, Tamar; Gilad, Shlomit; Amann-Zalcenstein, Daniela; Benjamin, Sima; Amit, Ido; Tanay, Amos; Massarwa, Rada; Novershtern, Noa; Hanna, Jacob H

    2013-12-12

    of cross-species chimaeric mouse embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas. Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo.

  13. Wind-forced circulation model and water exchanges through the channel in the Bay of Toulon

    NASA Astrophysics Data System (ADS)

    Dufresne, Christiane; Duffa, Céline; Rey, Vincent

    2014-01-01

    A hydrodynamic model of the Bay of Toulon has been developed for use as a post-accident radionuclide dispersion simulation tool. Located in a Mediterranean urban area, the Bay of Toulon is separated into two basins by a 1.4-km long seawall. The Little Bay is semi-enclosed and connected to the Large Bay by a fairway channel. This channel is the site of significant water mass exchange as a result of both wind-driven currents and bathymetry. It is therefore a focal point for marine contamination. As part of the model calibration and validation process, the first step consisted of studying the water mass exchange between the two basins. An Acoustic Doppler Current Profiler was moored in the channel for 1 year. The present study analyses in situ data to determine the current intensity and direction, and also to better understand the vertical current profile, which is highly correlated with meteorological forcing. Comparisons of model-generated and measured data are presented, and various atmospheric forcing datasets are used to enhance computed results. It appears that accurate meteorological forcing data is needed to enhance the accuracy of the hydrodynamic model. This channel is an important location for water mass renewal in the Bay of Toulon, and model results are used to quantify these exchanges. The mean calculated annual water exchange time is approximately 3.4 days. However, this duration is strongly wind dependent and shortens during windy winter months. It ranges from 1.5 days during strong wind periods to 7.5 days during calm weather. Residence time values calculated through tracer dispersion modelling after release at the back of the Little Bay are found to be comparable to the mean exchange time values, especially for windy conditions.

  14. Pelagic nitrogen cycling in Jiaozhou Bay, a model study I: The conceptual model

    NASA Astrophysics Data System (ADS)

    Ren, Ling; Zhang, Manping; Brockmann, Uwe H.; Feng, Shizuo

    2003-12-01

    A zero-dimensional box model (PNCMjzb) with six state variables (ammonium, nitrate, dissolved organic nitrogen, phytoplankton, zooplankton and detritus) was developed to study nitrogen cycling in the Jiaozhou Bay pelagic ecosystem. The dominant processes within these compartments are considered with nitrogen as flow currency. Phytoplankton and zooplankton are treated as separate state variables, assuming that the species composition was dominated by two or three species the dynamic constants of which are similar and that they represent the entire plankton community. The microbial loop has not been integrated explicitly in the model. The turnover of bacteria is included implicitly in processes such as detritus decomposition, DON remineralization, pelagic nitrification and denitrification. The model is driven by two forcing variables, viz. water temperature and light intensity. Historical data from the 1980s and 1990s were compiled and used for model calibration. In this paper (part I), the consideration of every main compartment in the model is interpreted in detail. And the applied equations and parameters are presented. The main results from the simulations together with discussion about phytoplankton dynamics and primary production in Jiaozhou Bay are presented in the next paper (part II).

  15. Nowcast model for hazardous material spill prevention and response, San Francisco Bay, California

    USGS Publications Warehouse

    Cheng, Ralph T.; Wilmot, Wayne L.; Galt, Jerry A.

    1997-01-01

    The National Oceanic and Atmospheric Administration (NOAA) installed the Physical Oceanographic Real-time System (PORTS) in San Francisco Bay, California, to provide real-time observations of tides, tidal currents, and meteorological conditions to, among other purposes, guide hazardous material spill prevention and response. Integrated with nowcast modeling techniques and dissemination of real-time data and the nowcasting results through the Internet on the World Wide Web, emerging technologies used in PORTS for real-time data collection forms a nowcast modeling system. Users can download tides and tidal current distribution in San Francisco Bay for their specific applications and/or for further analysis.

  16. Bayes factor between Student t and Gaussian mixed models within an animal breeding context

    PubMed Central

    Casellas, Joaquim; Ibáñez-Escriche, Noelia; García-Cortés, Luis Alberto; Varona, Luis

    2008-01-01

    The implementation of Student t mixed models in animal breeding has been suggested as a useful statistical tool to effectively mute the impact of preferential treatment or other sources of outliers in field data. Nevertheless, these additional sources of variation are undeclared and we do not know whether a Student t mixed model is required or if a standard, and less parameterized, Gaussian mixed model would be sufficient to serve the intended purpose. Within this context, our aim was to develop the Bayes factor between two nested models that only differed in a bounded variable in order to easily compare a Student t and a Gaussian mixed model. It is important to highlight that the Student t density converges to a Gaussian process when degrees of freedom tend to infinity. The twomodels can then be viewed as nested models that differ in terms of degrees of freedom. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling of the complex model (Student t mixed model). The performance of this Bayes factor was tested under simulation and on a real dataset, using the deviation information criterion (DIC) as the standard reference criterion. The two statistical tools showed similar trends along the parameter space, although the Bayes factor appeared to be the more conservative. There was considerable evidence favoring the Student t mixed model for data sets simulated under Student t processes with limited degrees of freedom, and moderate advantages associated with using the Gaussian mixed model when working with datasets simulated with 50 or more degrees of freedom. For the analysis of real data (weight of Pietrain pigs at six months), both the Bayes factor and DIC slightly favored the Student t mixed model, with there being a reduced incidence of outlier individuals in this population. PMID:18558073

  17. Carcinogen metabolism, cigarette smoking, and breast cancer risk: a Bayes model averaging approach

    PubMed Central

    2010-01-01

    Background Standard logistic regression with or without stepwise selection has the disadvantage of not incorporating model uncertainty and the dependency of estimates on the underlying model into the final inference. We explore the use of a Bayes Model Averaging approach as an alternative to analyze the influence of genetic variants, environmental effects and their interactions on disease. Methods Logistic regression with and without stepwise selection and Bayes Model Averaging were applied to a population-based case-control study exploring the association of genetic variants in tobacco smoke-related carcinogen pathways with breast cancer. Results Both regression and Bayes Model Averaging highlighted a significant effect of NAT1*10 on breast cancer, while regression analysis also suggested a significant effect for packyears and for the interaction of packyears and NAT2. Conclusions Bayes Model Averaging allows incorporation of model uncertainty, helps reduce dimensionality and avoids the problem of multiple comparisons. It can be used to incorporate biological information, such as pathway data, into the analysis. As with all Bayesian analysis methods, careful consideration must be given to prior specification. PMID:21080951

  18. 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.

  19. Hybrid modeling of the mega-tsunami runup in Lituya Bay after half a century

    NASA Astrophysics Data System (ADS)

    Weiss, Robert; Fritz, Hermann M.; Wünnemann, Kai

    2009-05-01

    The largest mega-tsunami dates back half a century to 10 July 1958, when almost unnoticed by the general public, an earthquake of M w 8.3 at the Fairweather Fault triggered a rockslide into Lituya Bay. The rockslide impact generated a giant tsunami at the head of Lituya Bay resulting in an unprecedented tsunami runup of 524 m on a spur ridge in direct prolongation of the slide axis. A forest trim line and erosion down to bedrock mark the largest runup in recorded history. While these observations have not been challenged directly, they have been largely ignored in hazard mitigation studies, because of the difficulties of even posing - much less solving - a well-defined physical problem for investigation. We study the mega-tsunami runup with a hybrid modeling approach applying physical and numerical models of slide processes of deformable bodies into a U-shaped trench similar to the geometry found at Lituya Bay.

  20. Modelling larval dispersal of the king scallop ( Pecten maximus) in the English Channel: examples from the bay of Saint-Brieuc and the bay of Seine

    NASA Astrophysics Data System (ADS)

    Nicolle, Amandine; Dumas, Franck; Foveau, Aurélie; Foucher, Eric; Thiébaut, Eric

    2013-06-01

    The king scallop ( Pecten maximus) is one of the most important benthic species of the English Channel as it constitutes the first fishery in terms of landings in this area. To support strategies of spatial fishery management, we develop a high-resolution biophysical model to study scallop dispersal in two bays along the French coasts of the English Channel (i.e. the bay of Saint-Brieuc and the bay of Seine) and to quantify the relative roles of local hydrodynamic processes, temperature-dependent planktonic larval duration (PLD) and active swimming behaviour (SB). The two bays are chosen for three reasons: (1) the distribution of the scallop stocks in these areas is well known from annual scallop stock surveys, (2) these two bays harbour important fisheries and (3) scallops in these two areas present some differences in terms of reproductive cycle and spawning duration. The English Channel currents and temperature are simulated for 10 years (2000-2010) with the MARS-3D code and then used by the Lagrangian module of MARS-3D to model the transport. Results were analysed in terms of larval distribution at settlement and connectivity rates. While larval transport in the two bays depended both on the tidal residual circulation and the wind-induced currents, the relative role of these two hydrodynamic processes varied among bays. In the bay of Saint-Brieuc, the main patterns of larval dispersal were due to tides, the wind being only a source of variability in the extent of larval patch and the local retention rate. Conversely, in the bay of Seine, wind-induced currents altered both the direction and the extent of larval transport. The main effect of a variable PLD in relation to the thermal history of each larva was to reduce the spread of dispersal and consequently increase the local retention by about 10 % on average. Although swimming behaviour could influence larval dispersal during the first days of the PLD when larvae are mainly located in surface waters, it has a

  1. Mid-Bay Islands Hydrodynamics and Sedimentation Modeling Study, Chesapeake Bay

    DTIC Science & Technology

    2006-08-01

    B3 Hydrodynamic and sediment transport modeling with M2D ................. B7 Hydrodynamics...maximum current field, normal tide ............................... B6 Figure B6. Alt JI-7 M2D model grid...B7 Figure B7. Alt JI-7 maximum current field, NE33 ........................................ B9 Figure B8. Alt JI-7 M2D

  2. Linking selenium sources to ecosystems: San Francisco Bay-Delta Model

    USGS Publications Warehouse

    Presser, Theresa S.; Luoma, Samuel N.

    2004-01-01

    Marine sedimentary rocks of the Coast Ranges contribute selenium to soil, surface water, and ground water in the western San Joaquin Valley, California. Irrigation funnels selenium into a network of subsurface drains and canals. Proposals to build a master drain (i.e., San Luis Drain) to discharge into the San Francisco Bay-Delta Estuary remain as controversial today as they were in the 1950s, when drainage outside the San Joaquin Valley was first considered. An existing 85-mile portion of the San Luis Drain was closed in 1986 after fish mortality and deformities in ducks, grebes and coots were discovered at Kesterson National Wildlife Refuge, the temporary terminus of the drain. A 28-mile portion of the drain now conveys drainage from 100,000 acres into the San Joaquin River and eventually into the Bay-Delta. If the San Luis Drain is extended directly to the Bay-Delta, as is now being proposed as an alternative to sustain agriculture, it could receive drainage from an estimated one-million acres of farmland affected by rising water tables and increasing salinity. In addition to agricultural sources, oil refineries also discharge selenium to the Bay-Delta, although those discharges have declined in recent years. To understand the effects of changing selenium inputs, scientists have developed the Bay-Delta Selenium Model.

  3. Development and application of econometric demand and supply models for selected Chesapeake Bay seafood products

    SciTech Connect

    Nieves, L.A.; Moe, R.J.

    1984-12-01

    Five models were developed to forecast future Chesapeake seafood product prices, harvest quantities, and resulting income. Annual econometric models are documented for oysters, hard and soft blue crabs, and hard and soft clams. To the degree that data permit, these models represent demand and supply at the retail, wholesale, and harvest levels. The resulting models have broad applications in environmental policy issues and regulatory analyses for the Chesapeake Bay. 37 references, 10 figures, 99 tables.

  4. Hydrodynamic properties of San Quintin Bay, Baja California: Merging models and observations.

    PubMed

    Melaku Canu, Donata; Aveytua-Alcázar, Leslie; Camacho-Ibar, Victor F; Querin, Stefano; Solidoro, Cosimo

    2016-07-15

    We investigated the physical dynamics of San Quintin Bay, a coastal lagoon located on the Pacific coast of northern Baja California, Mexico. We implemented, validated and used a finite element 2-D hydrodynamic model to characterize the spatial and temporal variability of the hydrodynamic of the bay in response to variability in the tidal regime and in meteorological forcing patterns. Our analysis of general circulation, residual currents, residence times, and tidal propagation delays allowed us to characterize spatial variability in the hydrodynamic basin features. The eulerian water residence time is -on average and under reference conditions- approximately 7days, although this can change significantly by region and season and under different tidal and meteorological conditions. Ocean upwelling events that bring colder waters into the bay mouth affect hydrodynamic properties in all areas of the lagoon and may affect ecological dynamics. A return to pre-upwelling conditions would take approximately 10days.

  5. Geomorphic modeling of macro-tidal embayment with extensive tidal flats: Skagit Bay, Washington

    DTIC Science & Technology

    2012-09-30

    DISTRIBUTION A: Distribution approved for public release; distribution is unlimited. Geomorphic modeling of macro- tidal embayment with extensive... tidal flats: Skagit Bay, Washington Lyle Hibler Battelle-Pacific Northwest Division Marine Sciences Laboratory Sequim, WA 98382 phone: (360) 681...of muddy tidal flats and to quantify the effects of tidal action, river discharge, and shoreline development (e.g. dikes and jetties) on these

  6. MODELING FISH AND SHELLFISH DISTRIBUTIONS IN THE MOBILE BAY ESTUARY, USA

    EPA Science Inventory

    Estuaries in the Gulf of Mexico provide rich habitat for many fish and shellfish, including those that have been identified as economically and ecologically important. For the Mobile Bay estuary, we developed statistical models to relate distributions of individual species and sp...

  7. A Tidally Averaged Sediment-Transport Model for San Francisco Bay, California

    USGS Publications Warehouse

    Lionberger, Megan A.; Schoellhamer, David H.

    2009-01-01

    A tidally averaged sediment-transport model of San Francisco Bay was incorporated into a tidally averaged salinity box model previously developed and calibrated using salinity, a conservative tracer (Uncles and Peterson, 1995; Knowles, 1996). The Bay is represented in the model by 50 segments composed of two layers: one representing the channel (>5-meter depth) and the other the shallows (0- to 5-meter depth). Calculations are made using a daily time step and simulations can be made on the decadal time scale. The sediment-transport model includes an erosion-deposition algorithm, a bed-sediment algorithm, and sediment boundary conditions. Erosion and deposition of bed sediments are calculated explicitly, and suspended sediment is transported by implicitly solving the advection-dispersion equation. The bed-sediment model simulates the increase in bed strength with depth, owing to consolidation of fine sediments that make up San Francisco Bay mud. The model is calibrated to either net sedimentation calculated from bathymetric-change data or measured suspended-sediment concentration. Specified boundary conditions are the tributary fluxes of suspended sediment and suspended-sediment concentration in the Pacific Ocean. Results of model calibration and validation show that the model simulates the trends in suspended-sediment concentration associated with tidal fluctuations, residual velocity, and wind stress well, although the spring neap tidal suspended-sediment concentration variability was consistently underestimated. Model validation also showed poor simulation of seasonal sediment pulses from the Sacramento-San Joaquin River Delta at Point San Pablo because the pulses enter the Bay over only a few days and the fate of the pulses is determined by intra-tidal deposition and resuspension that are not included in this tidally averaged model. The model was calibrated to net-basin sedimentation to calculate budgets of sediment and sediment-associated contaminants. While

  8. Empirical Bayes Point Estimates of True Score Using a Compound Binomial Error Model. Research Memorandum 74-11.

    ERIC Educational Resources Information Center

    Kearns, Jack

    Empirical Bayes point estimates of true score may be obtained if the distribution of observed score for a fixed examinee is approximated in one of several ways by a well-known compound binomial model. The Bayes estimates of true score may be expressed in terms of the observed score distribution and the distribution of a hypothetical binomial test.…

  9. A Combined Modeling Approach to Evaluate Water Quality Benefits of Riparian Buffers in the Jobos Bay Watershed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Jobos Bay Watershed, located in south-central Puerto Rico, is a tropical Conservation Effects Assessment Project (CEAP) Special Emphasis Watershed. The purpose of CEAP is to quantify environmental benefits of conservation practices and includes field and watershed modeling. In Jobos Bay, the goa...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. Vitalism in naive biological thinking.

    PubMed

    Morris, S C; Taplin, J E; Gelman, S A

    2000-09-01

    Vitalism is the belief that internal bodily organs have agency and that they transmit or exchange a vital force or energy. Three experiments investigated the use of vitalistic explanations for biological phenomena by 5- and 10-year-old English-speaking children and adults, focusing on 2 components: the notion that bodily organs have intentions and the notion that some life force or energy is transmitted. The original Japanese finding of vitalistic thinking was replicated in Experiment 1 with English-speaking 5-year-olds. Experiment 2 indicated that the more active component of vitalism for these children is a belief in the transfer of energy during biological processes, and Experiment 3 suggested an additional, albeit lesser, role for organ intentionality. A belief in vital energy may serve a causal placeholder function within a naive theory of biology until a more precisely formulated mechanism is known.

  12. Observations and Modeling of the Shelf Circulation North of the Monterey Bay during August 2006

    DTIC Science & Technology

    2007-06-01

    the three ocean models (HOPS, ROMS and NCOM/ICON) used during the MB06 real-time operations diffusivities estimated using (i) a simple turbulent ... MODELING OF THE SHELF CIRCULATION NORTH OF THE MONTEREY BAY DURING AUGUST 2006 by Rebecca E. Wolf June 2007 Thesis Advisor: Steven R...ONLY (Leave blank) 2. REPORT DATE June 2007 3. REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE Observations and Modeling of

  13. Finite-difference model for 3-D flow in bays and estuaries

    USGS Publications Warehouse

    Smith, Peter E.; Larock, Bruce E.; ,

    1993-01-01

    This paper describes a semi-implicit finite-difference model for the numerical solution of three-dimensional flow in bays and estuaries. The model treats the gravity wave and vertical diffusion terms in the governing equations implicitly, and other terms explicitly. The model achieves essentially second-order accurate and stable solutions in strongly nonlinear problems by using a three-time-level leapfrog-trapezoidal scheme for the time integration.

  14. Workplan for tributary refinements to Chesapeake Bay eutrophication model package. Final report

    SciTech Connect

    Cerco, C.F.

    1994-05-01

    The Corps of Engineers, in partnership with the U.S. Environmental Protection Agency Chesapeake Bay Program Office, recently completed a three-dimensional model study of eutrophication in Chesapeake Bay and tributaries. The model package applied included an intratidal hydrodynamic model, an intertidal water-quality model, and a benthic sediment diagenesis model. This report comprises a workplan to improve model representation of Chesapeake Bay tributaries and to incorporate living resources directly into the model framework. Four tributaries have been selected for emphasis under this tributary refinements program. They are the James, York, and Rappahannock rivers, and Baltimore Harbor. The James, York, and Rappahannock were specified because tributary-specific models are required to address water-quality and living-resource benefits to be derived from nutrient reductions. Baltimore Harbor was specified because it presents unique management problems, coupled with long-term toxic impacts, which cannot be addressed in the current model framework. The time scale for the project is 4 years from initiation to completion. Anticipated commencement is April 1, 1994.

  15. Predicting tidal currents in San Francisco Bay using a spectral model

    USGS Publications Warehouse

    Burau, Jon R.; Cheng, Ralph T.

    1988-01-01

    This paper describes the formulation of a spectral (or frequency based) model which solves the linearized shallow water equations. To account for highly variable basin bathymetry, spectral solutions are obtained using the finite element method which allows the strategic placement of the computation points in the specific areas of interest or in areas where the gradients of the dependent variables are expected to be large. Model results are compared with data using simple statistics to judge overall model performance in the San Francisco Bay estuary. Once the model is calibrated and verified, prediction of the tides and tidal currents in San Francisco Bay is accomplished by applying astronomical tides (harmonic constants deduced from field data) at the prediction time along the model boundaries.

  16. 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.

  17. Using a food-web model to assess the trophic structure and energy flows in Daya Bay, China

    NASA Astrophysics Data System (ADS)

    Chen, Zuozhi; Xu, Shannan; Qiu, Yongsong

    2015-12-01

    Daya Bay, is one of the largest and most important semi-closed bays along the southern coast of China. Due to the favorable geomorphological and climatic conditions, this bay has become an important conservation zone of aquatic germplasm resources in South China Sea. To characterize the trophic structure, ecosystem properties and keystone species, a food-web model for Daya Bay has been developed by the means of a mass-balance approach using the Ecopath with Ecosim software. The mean trophic transfer efficiency for the entire ecosystem as a whole is 10.9% while the trophic level II is 5.1%. The primary- and secondary-producers, including phytoplankton, zooplankton and micro-zoobenthos demonstrated the important overall impacts on the rest of the groups based on mixed trophic impact (MIT) analysis and are classified as the keystone groups. The analysis of ecosystem attributes indicated that ecosystem of Daya Bay can be categorized as an immature one and/or is in the degraded stage. A comparison of this model with other coastal ecosystems, including Kuosheng Bay, Tongoy Bay, Beibu Gulf and Cadiz Gulf, underpinned that the ecosystem of Daye Bay is an obviously stressed system and is more vulnerable to the external disturbance. In general, our study indicates that a holistic approach is needed to minimize the impacts of anthropogenic activities to ensure the sustainability of the ecosystem in the future.

  18. Modeling the Effect of Hypoxia on Macrobenthos Production in the Lower Rappahannock River, Chesapeake Bay, USA

    PubMed Central

    Sturdivant, Samuel Kersey; Brush, Mark J.; Diaz, Robert J.

    2013-01-01

    Hypoxia in Chesapeake Bay has substantially increased in recent decades, with detrimental effects on macrobenthic production; the production of these fauna link energy transfer from primary consumers to epibenthic and demersal predators. As such, the development of accurate predictive models that determine the impact of hypoxia on macrobenthic production is important. A continuous-time, biomass-based model was developed for the lower Rappahannock River, a Bay tributary prone to seasonal hypoxia. Phytoplankton, zooplankton, and macrobenthic state variables were modeled, with a focus on quantitatively constraining the effect of hypoxia on macrobenthic biomass. This was accomplished through regression with Z': a sigmoidal function between macrobenthic biomass and dissolved oxygen concentration, derived using macrobenthic data collected from the Rappahannock River during the summers of 2007 and 2008, and applied to compute hypoxia-induced mortality as a rate process. The model was verified using independent monitoring data collected by the Chesapeake Bay Program. Simulations showed that macrobenthic biomass was strongly linked to dissolved oxygen concentrations, with fluctuations in biomass related to the duration and severity of hypoxia. Our model demonstrated that hypoxia negatively affected macrobenthic biomass, as longer durations of hypoxia and greater hypoxic severity resulted in an increasing loss in biomass. This exercise represents an important contribution to modeling anthropogenically impacted coastal ecosystems, by providing an empirically constrained relationship between hypoxia and macrobenthic biomass, and applying that empirical relationship in a mechanistic model to quantify the effect of the severity, duration, and frequency of hypoxia on benthic biomass dynamics. PMID:24391904

  19. Dopamine induces IL-6-dependent IL-17 production via D1-like receptor on CD4 naive T cells and D1-like receptor antagonist SCH-23390 inhibits cartilage destruction in a human rheumatoid arthritis/SCID mouse chimera model.

    PubMed

    Nakano, Kazuhisa; Yamaoka, Kunihiro; Hanami, Kentaro; Saito, Kazuyoshi; Sasaguri, Yasuyuki; Yanagihara, Nobuyuki; Tanaka, Shinya; Katsuki, Ichiro; Matsushita, Sho; Tanaka, Yoshiya

    2011-03-15

    A major neurotransmitter dopamine transmits signals via five different seven-transmembrane G protein-coupled receptors termed D1-D5. Several studies have shown that dopamine not only mediates interactions into the nervous system, but can contribute to the modulation of immunity via receptors expressed on immune cells. We have previously shown an autocrine/paracrine release of dopamine by dendritic cells (DCs) during Ag presentation to naive CD4(+) T cells and found efficacious results of a D1-like receptor antagonist SCH-23390 in the experimental autoimmune encephalomyelitis mouse model of multiple sclerosis and in the NOD mouse model of type I diabetes, with inhibition of Th17 response. This study aimed to assess the role of dopaminergic signaling in Th17-mediated immune responses and in the pathogenesis of rheumatoid arthritis (RA). In human naive CD4(+) T cells, dopamine increased IL-6-dependent IL-17 production via D1-like receptors, in response to anti-CD3 plus anti-CD28 mAb. Furthermore, dopamine was localized with DCs in the synovial tissue of RA patients and significantly increased in RA synovial fluid. In the RA synovial/SCID mouse chimera model, although a selective D2-like receptor antagonist haloperidol significantly induced accumulation of IL-6(+) and IL-17(+) T cells with exacerbated cartilage destruction, SCH-23390 strongly suppressed these responses. Taken together, these findings indicate that dopamine released by DCs induces IL-6-Th17 axis and causes aggravation of synovial inflammation of RA, which is the first time, to our knowledge, that actual evidence has shown the pathological relevance of dopaminergic signaling with RA.

  20. Hydrodynamic modeling and ecohydrological analysis of river inflow effects on Apalachicola Bay, Florida, USA

    NASA Astrophysics Data System (ADS)

    Huang, Wenrui

    2010-02-01

    This paper presents an integrated hydrodynamic modeling and probability analysis approach to assess the long-term effects of changing river inflows on the estuarine ecosystem. The probability analysis method, which is popularly used in advanced hydrological frequency analysis of river flows and rainfalls, has been applied to analyze the effects of changing inflow on salinity and thus on oyster ecology in Apalachicola Bay. Long-term salinity data were predicted through the application of a calibrated 3D hydrodynamic model under two river inflow conditions over a 10-year period. The first flow represents the historic flow. The 2nd flow condition, called Scenario-1, represents a regulated flow scenario to account for the potential increasing upstream water demands. Two stations, Mid Bay and Dry Bar, in the bay were selected to examine the estuarine responses. Under the historic flow condition, the maximum probability salinity at Dry Bar in the rich oyster reef is near 24 ppt, within the optimal salinity range for oyster growth of 16-26 ppt (Harned et al., 1996); the maximum probability salinity at Mid Bay station is 27 ppt, beyond the optimal salinity for oyster growth in mid-bay area where there is no oyster reef around. While it is difficult to examine the difference between two scenarios by conventional time series analysis of river flows and salinity, probability analysis reasonably characterizes and quantifies the changes of river flow and salinity patterns over the 10-year period. The Scenario-1 has caused the increase of the probability in low flows. Higher probability of low flows for the regulated flow scenario shortens the period of optimal salinity in the oyster reef, and cause substantial increase of exceedance probability of higher salinity in the oyster reef to the level beyond the optimal salinity range for oyster growth. The probability analysis approach has demonstrated its advantage for the risk assessments of the long-term estuarine ecohydrological

  1. Modelling the response of Placentia Bay to hurricanes Igor and Leslie

    NASA Astrophysics Data System (ADS)

    Ma, Zhimin; Han, Guoqi; de Young, Brad

    2017-04-01

    A three-dimensional, baroclinic, finite-volume ocean model (FVCOM) is used to examine hurricane induced responses in Placentia Bay, Newfoundland. Hurricane Igor (2010) and Hurricane Leslie (2012) made landfall within 100 km of the mouth of the bay, with the former to the eastern side and the latter on the western side. The model results have reasonable agreement with field observations on sea level, near-surface currents and sea surface temperature (SST). During landfall the two hurricanes cause the opposite shifts in inner bay circulation. Hurricane Igor overwhelms the mean inflow into the inner bay and shifts the currents to outflow. Hurricane Leslie reinforces the inflow into the inner bay. The peak storm surge is significantly influenced by local wind and air pressure during Leslie, accounting for 34% and 62% at the Argentia and St. Lawrence tide-gauge stations respectively, but predominately due to remote forcing entering the upstream eastern open boundary during Igor. There is a strong near-surface near-inertial response during Leslie, but a weak one during Igor. Stratification plays an important role in both generation and dissipation of near-inertial oscillation. A strong pre-storm stratification during Leslie favours the generation of near-inertia oscillation. Strong turbulent mixing induced on the right side of Leslie generates large vertical movement of the thermocline and thus contributes to strong near-inertia oscillation inside the mixed layer. The barotropic simulation results in a significant underestimation of near-surface currents and near-inertial oscillation. The baroclinic simulation shows a large increase of the current gradient in the vertical, as the first baroclinic mode in response to the hurricane forcing.

  2. Norfolk Harbor and Channels Deepening Study. Report 1. Physical Model Results. Chesapeake Bay Hydraulic Model Investigation.

    DTIC Science & Technology

    1983-06-01

    Susquehanna River Valley to form the bay. Sedimentation from the tributaries as well as erosion of the banks has contributed to maintaining the bay’s broad... Anacostia River 1,663 532 10 Potomac River 21,997 7,699 11 Patuxent River 2,517 88l 12 Severn River 660 23i 13 Patapsco River 1,751 613 14 Gunpowder River ...Chesapeake Bay system with the vast majority being located near the project area in the lower bay anti James River areas. A 2-1/2-year weekly stepped

  3. Simulation model of Skeletonema costatum population dynamics in northern San Francisco Bay, California

    USGS Publications Warehouse

    Cloern, J.E.; Cheng, R.T.

    1981-01-01

    A pseudo-two-dimensional model is developed to simulate population dynamics of one dominant phytoplankton species (Skeletonema costatum) in northern San Francisco Bay. The model is formulated around a conceptualization of this estuary as two distinct but coupled subsystems-a deep (10-20 m) central channel and lateral areas with shallow (<2 m) water and slow circulation. Algal growth rates are governed by solar irradiation, temperature and salinity, while population losses are assumed to result from grazing bycalanoid copepods. Consequences of estuarine gravitational circulation are approximated simply by reducing convective-dispersive transport in that section of the channel (null zone) where residual bottom currents are near zero, and lateral mixing is treated as a bulkexchange process between the channel and the shoals. Model output is consistent with the hypothesis that, because planktonic algae are light-limited, shallow areas are the sites of active population growth. Seasonal variation in the location of the null zone (a response to variable river discharge) is responsible for maintaining the spring bloom of neritic diatoms in the seaward reaches of the estuary (San Pablo Bay) and the summer bloom upstream (Suisun Bay). Model output suggests that these spring and summer blooms result from the same general process-establishment of populations over the shoals, where growth rates are rapid, coupled with reduced particulate transport due to estuarine gravitational circulation. It also suggests, however, that the relative importance of physical and biological processes to phytoplankton dynamics is different in San Pablo and Suisun Bays. Finally, the model has helped us determine those processes having sufficient importance to merit further refinement in the next generation of models, and it has given new direction to field studies. ?? 1981 Academic Press Inc. (London) Ltd.

  4. Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

    USGS Publications Warehouse

    McGowan, Conor P.; Smith, David; Sweka, John A.; Martin, Julien; Nichols, James D.; Wong, Richard; Lyons, James E.; Niles, Lawrence J.; Kalasz, Kevin; Brust, Jeffrey; Klopfer, Michelle; Spear, Braddock

    2011-01-01

    Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

  5. Water resources planning for rivers draining into Mobile Bay. Part 2: Non-conservative species transport models

    NASA Technical Reports Server (NTRS)

    April, G. C.; Liu, H. A.

    1975-01-01

    Total coliform group bacteria were selected to expand the mathematical modeling capabilities of the hydrodynamic and salinity models to understand their relationship to commercial fishing ventures within bay waters and to gain a clear insight into the effect that rivers draining into the bay have on water quality conditions. Parametric observations revealed that temperature factors and river flow rate have a pronounced effect on the concentration profiles, while wind conditions showed only slight effects. An examination of coliform group loading concentrations at constant river flow rates and temperature shows these loading changes have an appreciable influence on total coliform distribution within Mobile Bay.

  6. Observed and modeled tsunami current velocities in Humboldt Bay and Crescent City Harbor, northern California

    NASA Astrophysics Data System (ADS)

    Admire, A. R.; Dengler, L.; Crawford, G. B.; uslu, B. U.; Montoya, J.

    2012-12-01

    Crescent City were compared to calculated velocities from the Method of Splitting Tsunamis (MOST) numerical model. For Humboldt Bay, the 2010 model tsunami frequencies matched the actual values for the first two hours after the initial arrival however the amplitudes were underestimated by approximately 65%. MOST replicated the first four hours of the 2011 tsunami signal in Humboldt Bay quite well although the peak flood currents were underestimated by about 50%. MOST predicted attenuation of the signal after four hours but the actual signal persisted at a nearly constant level for more than 48 hours. In Crescent City, the model prediction of the 2011 frequency agreed quite well with the observed signal for the first two and a half hours after the initial arrival with a 50% underestimation of the peak amplitude. The results from this project demonstrate that ADCPs can effectively record tsunami currents for small to moderate events and can be used to calibrate and validate models (i.e. MOST) in order to better predict hazardous tsunami conditions and improve planned responses to protect lives and property, especially within harbors. An ADCP will be installed in Crescent City Harbor and four additional ADCPs are being deployed in Humboldt Bay during the fall of 2012.

  7. A Multilayer Naïve Bayes Model for Analyzing User's Retweeting Sentiment Tendency

    PubMed Central

    Wang, Mengmeng; Zuo, Wanli; Wang, Ying

    2015-01-01

    Today microblogging has increasingly become a means of information diffusion via user's retweeting behavior. Since retweeting content, as context information of microblogging, is an understanding of microblogging, hence, user's retweeting sentiment tendency analysis has gradually become a hot research topic. Targeted at online microblogging, a dynamic social network, we investigate how to exploit dynamic retweeting sentiment features in retweeting sentiment tendency analysis. On the basis of time series of user's network structure information and published text information, we first model dynamic retweeting sentiment features. Then we build Naïve Bayes models from profile-, relationship-, and emotion-based dimensions, respectively. Finally, we build a multilayer Naïve Bayes model based on multidimensional Naïve Bayes models to analyze user's retweeting sentiment tendency towards a microblog. Experiments on real-world dataset demonstrate the effectiveness of the proposed framework. Further experiments are conducted to understand the importance of dynamic retweeting sentiment features and temporal information in retweeting sentiment tendency analysis. What is more, we provide a new train of thought for retweeting sentiment tendency analysis in dynamic social networks. PMID:26417367

  8. Ecological Forecasting in Chesapeake Bay: Using a Mechanistic-Empirical Modelling Approach

    SciTech Connect

    Brown, C. W.; Hood, Raleigh R.; Long, Wen; Jacobs, John M.; Ramers, D. L.; Wazniak, C.; Wiggert, J. D.; Wood, R.; Xu, J.

    2013-09-01

    The Chesapeake Bay Ecological Prediction System (CBEPS) automatically generates daily nowcasts and three-day forecasts of several environmental variables, such as sea-surface temperature and salinity, the concentrations of chlorophyll, nitrate, and dissolved oxygen, and the likelihood of encountering several noxious species, including harmful algal blooms and water-borne pathogens, for the purpose of monitoring the Bay's ecosystem. While the physical and biogeochemical variables are forecast mechanistically using the Regional Ocean Modeling System configured for the Chesapeake Bay, the species predictions are generated using a novel mechanistic empirical approach, whereby real-time output from the coupled physical biogeochemical model drives multivariate empirical habitat models of the target species. The predictions, in the form of digital images, are available via the World Wide Web to interested groups to guide recreational, management, and research activities. Though full validation of the integrated forecasts for all species is still a work in progress, we argue that the mechanistic–empirical approach can be used to generate a wide variety of short-term ecological forecasts, and that it can be applied in any marine system where sufficient data exist to develop empirical habitat models. This paper provides an overview of this system, its predictions, and the approach taken.

  9. Hydraulic modeling and scour analysis for the San Francisco - Oakland Bay Bridge

    USGS Publications Warehouse

    Shelden, J.G.; Smith, E.D.; Sheppard, D.M.; Odeh, M.

    2004-01-01

    A study was conducted to determine potential maximum scour depths for the foundations of the replacement east span of the San Francisco-Oakland Bay Bridge, as part of the ongoing structural design. This effort presented unique challenges as strong tidal currents, large depths, and cohesive bottom sediments characterize the site. The authors met these challenges with a multi-faceted approach to the problem. First, design current velocities were determined using a two-dimensional hydrodynamic model of San Francisco Bay in conjunction with ADCP hydrographic surveys. Analytical scour calculations were performed and live-bed flume tests of the proposed foundations were also conducted. Finally, two separate methodologies were used to interpret the physical model tests in order to calculate potential scour depths around the foundations. Copyright ASCE 2004.

  10. Extending radiative transfer models by use of Bayes rule. [in atmospheric science

    NASA Technical Reports Server (NTRS)

    Whitney, C.

    1977-01-01

    This paper presents a procedure that extends some existing radiative transfer modeling techniques to problems in atmospheric science where curvature and layering of the medium and dynamic range and angular resolution of the signal are important. Example problems include twilight and limb scan simulations. Techniques that are extended include successive orders of scattering, matrix operator, doubling, Gauss-Seidel iteration, discrete ordinates and spherical harmonics. The procedure for extending them is based on Bayes' rule from probability theory.

  11. Mitigation Modelling of the Leeuwin Class Hydrographic Sonars in Shoalwater Bay

    DTIC Science & Technology

    2009-12-01

    The welfare of dolphins and dugongs is the main concern in Shoalwater Bay in reference to hydrographic sonar frequencies. Modelling therefore...considered all sonars capable of radiating signals within the auditory frequency range of dolphins, 1 to 150 kHz, and dugongs , 1 to 8 kHz. Sonar operations...at frequencies above 200 kHz were not considered since the effects on dolphins and dugongs were assumed inconsequential. The sonar with the lowest

  12. A self-modifying cellular automaton model of historical urbanization in the San Francisco Bay area

    USGS Publications Warehouse

    Clarke, K.C.; Hoppen, S.; Gaydos, L.

    1997-01-01

    In this paper we describe a cellular automaton (CA) simulation model developed to predict urban growth as part of a project for estimating the regional and broader impact of urbanization on the San Francisco Bay area's climate. The rules of the model are more complex than those of a typical CA and involve the use of multiple data sources, including topography, road networks, and existing settlement distributions, and their modification over time. In addition, the control parameters of the model are allowed to self-modify: that is, the CA adapts itself to the circumstances it generates, in particular, during periods of rapid growth or stagnation. In addition, the model was written to allow the accumulation of probabilistic estimates based on Monte Carlo methods. Calibration of the model has been accomplished by the use of historical maps to compare model predictions of urbanization, based solely upon the distribution in year 1900, with observed data for years 1940, 1954, 1962, 1974, and 1990. The complexity of this model has made calibration a particularly demanding step. Lessons learned about the methods, measures, and strategies developed to calibrate the model may be of use in other environmental modeling contexts. With the calibration complete, the model is being used to generate a set of future scenarios for the San Francisco Bay area along with their probabilities based on the Monte Carlo version of the model. Animated dynamic mapping of the simulations will be used to allow visualization of the impact of future urban growth.

  13. Chesapeake Bay nitrogen fluxes derived from a land‐estuarine ocean biogeochemical modeling system: Model description, evaluation, and nitrogen budgets

    PubMed Central

    Friedrichs, Marjorie A. M.; Wilkin, John; Tian, Hanqin; Yang, Qichun; Hofmann, Eileen E.; Wiggert, Jerry D.; Hood, Raleigh R.

    2015-01-01

    Abstract The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land‐estuarine‐ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within‐estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite‐derived data, and a simulation using environmental conditions for 2001–2005 was conducted to quantify the Chesapeake Bay nitrogen budget. The 5 year simulation was characterized by large riverine inputs of nitrogen (154 × 109 g N yr−1) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 109 g N yr−1) and buried (46 × 109 g N yr−1) within the estuarine system. A positive net annual ecosystem production for the bay further contributed to a large advective export of organic nitrogen to the shelf (91 × 109 g N yr−1) and negligible inorganic nitrogen export. Interannual variability was strong, particularly for the riverine nitrogen fluxes. In years with higher than average riverine nitrogen inputs, most of this excess nitrogen (50–60%) was exported from the bay as organic nitrogen, with the remaining split between burial, denitrification, and inorganic export to the coastal ocean. In comparison to previous simulations using generic shelf biogeochemical model formulations inside the estuary, the estuarine biogeochemical model described here produced more realistic and significantly greater exports of organic nitrogen and lower exports of inorganic nitrogen to the shelf. PMID:27668137

  14. Chesapeake Bay nitrogen fluxes derived from a land-estuarine ocean biogeochemical modeling system: Model description, evaluation, and nitrogen budgets.

    PubMed

    Feng, Yang; Friedrichs, Marjorie A M; Wilkin, John; Tian, Hanqin; Yang, Qichun; Hofmann, Eileen E; Wiggert, Jerry D; Hood, Raleigh R

    2015-08-01

    The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001-2005 was conducted to quantify the Chesapeake Bay nitrogen budget. The 5 year simulation was characterized by large riverine inputs of nitrogen (154 × 10(9) g N yr(-1)) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 10(9) g N yr(-1)) and buried (46 × 10(9) g N yr(-1)) within the estuarine system. A positive net annual ecosystem production for the bay further contributed to a large advective export of organic nitrogen to the shelf (91 × 10(9) g N yr(-1)) and negligible inorganic nitrogen export. Interannual variability was strong, particularly for the riverine nitrogen fluxes. In years with higher than average riverine nitrogen inputs, most of this excess nitrogen (50-60%) was exported from the bay as organic nitrogen, with the remaining split between burial, denitrification, and inorganic export to the coastal ocean. In comparison to previous simulations using generic shelf biogeochemical model formulations inside the estuary, the estuarine biogeochemical model described here produced more realistic and significantly greater exports of organic nitrogen and lower exports of inorganic nitrogen to the shelf.

  15. Models for Holocene valley-fill sequences from high-resolution seismic facies of Galveston Bay

    SciTech Connect

    Smyth, W.; Thomas, M.A.; Anderson, J.B.

    1988-01-01

    Reconstructions of the northern Gulf of Mexico shelf for the Holocene have relied on the dating of isolated bathymetric banks. These banks, which are interpreted as former shorelines, provide snapshots of the shelf during periods of relative sea level stillstand. A more complete sedimentary record of the Holocene transgression is likely preserved in the incised valley-fill sequences. The first step in deciphering the record of Holocene valley-fill sequences is development of high-resolution seismic facies models based on modern environments. The modern incised valley-estuarine system of Galveston Bay has been seismically surveyed. Important environments include bayhead delta (Trinity River delta), tidal inlet, flood tidal delta (Bolivar Roads), and estuarine sediments (central bay). Additionally, fluvial sediments partially infill the entrenched Trinity River valley. Seismic facies interpretation was corroborated by information obtained from sediment cores.

  16. Modelled trends in oceanic conditions of Pine Island Bay between 1991 and 2014

    NASA Astrophysics Data System (ADS)

    Kimuras, Satoshi; Holland, Paul; Regan, Heather; Jenkins, Adrian; Van Wessem, Melchior

    2016-04-01

    Two ice shelves in Pine Island Bay, Pine Island Glacier and its neighbour Thwaites Glacier, have been highlighted as major drainage pathways for the West Antarctic Ice Sheet. We quantify the melting of these ice shelves and oceanic conditions between 1991 and 2014 using a general circulation model. Two different atmospheric forcing scenarios (RACMO2.3 and ERA-Interim) are used as a surface boundary. The ocean heat content of the Pine Island Bay from the simulations shows periodic decrease in the late 1990s and 2012-2014, but the magnitude of cooling is different between RACMO2.3 and ERA-Interim forced simulations. The brine rejection of the sea ice production causes enhanced overturning and cools the water north of Pine Island Glacier Ice Shelf. This cold water flows southward along the coastline, resulting in lower melt rate in the late 1990s and 2012-2014.

  17. Impact of Stratification on Summer Hypoxia in Narragansett Bay, RI: Time-Series Observations and Numerical Modeling

    NASA Astrophysics Data System (ADS)

    Bergondo, D. L.; Kincaid, C. R.; Kester, D. R.

    2003-12-01

    Determining water column structure in a partially-mixed estuary, such as Narragansett Bay, is important for understanding the impact stratification has on phytoplankton productivity and dissolved oxygen concentrations. Stratification reduces vertical mixing and influences the vertical flux of ecologically important variables such as phytoplankton, heat, oxygen, and nutrients. We utilize a combination of buoy data and numerical modeling to better understand processes surrounding the evolution and breakdown in stratification in Narragansett Bay for a range of environmental conditions. Autonomous sensors have been deployed in Narragansett Bay to collect continuous high temporal resolution chemical and hydrographic data. Data were collected every fifteen minutes 0.5 m below the surface and 1 m from the bottom from July 2001 to December 2001 and from July 2002 to December 2002 at two locations in Narragansett Bay and the Providence River, RI. The suite of water column variables measured were surface and bottom temperature, salinity, dissolved oxygen and pH, and surface chlorophyll. Results show that stratification events occur intermittently in the Providence River and Narragansett Bay and that increased phytoplankton productivity and hypoxia were associated with summertime stratification events. The Regional Ocean Modeling System (ROMS) model, a three-dimensional hydrodynamic model developed by Rutgers University, New Jersey, has been applied to Narragansett Bay to determine how the basic layered flow can be perturbed by runoff events and variable winds. For instance, in the basic stratified flow pattern in Narragansett Bay there is an outward flow of fresher water at the surface and an inward flow of deep denser water within the channel, however, strong south winds shutdown the deep return flow. Time series observations combined with model relationships have been able to enhance the understanding of the development and breakdown of stratification and the impact

  18. Broadband Waveform Modeling to Evaluate the USGS Seismic Velocity Model for the San Francisco Bay Area

    NASA Astrophysics Data System (ADS)

    Rodgers, A.; Petersson, A.; Nilsson, S.; Sjogreen, B.; McCandless, K.

    2006-12-01

    As part of the 1906 San Francisco earthquake centenary, the USGS developed a three-dimensional seismic velocity and attenuation model for Northern California based on detailed geologic and geophysical constraints. The model was used to predict ground motions for the 1906 rupture. In this study we evaluate the model to assess its ability to accurately predict ground motions from moderate earthquakes recorded on broadband stations. Satisfactory prediction of ground motions from these events will provide hope for accurate modeling of future scenario earthquakes. Simulations were performed on large parallel computer(s) with a new elastic finite difference code developed at LLNL. We simulated broadband ground motions (0-0.25 Hz) for several moderate (magnitude 3.5-5.0) earthquakes in the region observed at Berkeley Digital Seismic Network (BDSN) broadband stations. These events are well located and can be modeled with simple point moment tensor sources (taken from the Berkeley Seismological Laboratory catalog), helping to isolate the effects of structure on the waveforms. These data sample the region's diverse tectonic structures, such as the bay muds, sedimentary basins and hard rock complexes. Preliminary results indicate that the simulations reproduce many important features in the data. For example, observed long duration surface waves are often predicted for complex paths (traveling across contrasting structures) and through sedimentary basins. Excellent waveform fits were frequently obtained for long-period comparisons (0.02-0.1) and good fits were often obtained for shorter periods. We will attempt higher frequency simulations to test the ability of the model to match the high frequency response. Finally, we performed large scenario earthquake simulations for the Hayward Fault. These simulations predict large amplifications across the Santa Clara and San Ramon/Livermore Valley sedimentary basins and with the Sacramento/San Joaquin River Delta.

  19. Uncertainty in model predictions of Vibrio vulnificus response to climate variability and change: a Chesapeake Bay case study.

    PubMed

    Urquhart, Erin A; Zaitchik, Benjamin F; Waugh, Darryn W; Guikema, Seth D; Del Castillo, Carlos E

    2014-01-01

    The effect that climate change and variability will have on waterborne bacteria is a topic of increasing concern for coastal ecosystems, including the Chesapeake Bay. Surface water temperature trends in the Bay indicate a warming pattern of roughly 0.3-0.4°C per decade over the past 30 years. It is unclear what impact future warming will have on pathogens currently found in the Bay, including Vibrio spp. Using historical environmental data, combined with three different statistical models of Vibrio vulnificus probability, we explore the relationship between environmental change and predicted Vibrio vulnificus presence in the upper Chesapeake Bay. We find that the predicted response of V. vulnificus probability to high temperatures in the Bay differs systematically between models of differing structure. As existing publicly available datasets are inadequate to determine which model structure is most appropriate, the impact of climatic change on the probability of V. vulnificus presence in the Chesapeake Bay remains uncertain. This result points to the challenge of characterizing climate sensitivity of ecological systems in which data are sparse and only statistical models of ecological sensitivity exist.

  20. Uncertainty in Model Predictions of Vibrio Vulnificus Response to Climate Variability and Change: A Chesapeake Bay Case Study

    NASA Technical Reports Server (NTRS)

    Urquhart, Erin A.; Zaitchik, Benjamin F.; Waugh, Darryn W.; Guikema, Seth D.; Del Castillo, Carlos E.

    2014-01-01

    The effect that climate change and variability will have on waterborne bacteria is a topic of increasing concern for coastal ecosystems, including the Chesapeake Bay. Surface water temperature trends in the Bay indicate a warming pattern of roughly 0.3-0.4 C per decade over the past 30 years. It is unclear what impact future warming will have on pathogens currently found in the Bay, including Vibrio spp. Using historical environmental data, combined with three different statistical models of Vibrio vulnificus probability, we explore the relationship between environmental change and predicted Vibrio vulnificus presence in the upper Chesapeake Bay. We find that the predicted response of V. vulnificus probability to high temperatures in the Bay differs systematically between models of differing structure. As existing publicly available datasets are inadequate to determine which model structure is most appropriate, the impact of climatic change on the probability of V. vulnificus presence in the Chesapeake Bay remains uncertain. This result points to the challenge of characterizing climate sensitivity of ecological systems in which data are sparse and only statistical models of ecological sensitivity exist.

  1. Development of wavelet-ANN models to predict water quality parameters in Hilo Bay, Pacific Ocean.

    PubMed

    Alizadeh, Mohamad Javad; Kavianpour, Mohamad Reza

    2015-09-15

    The main objective of this study is to apply artificial neural network (ANN) and wavelet-neural network (WNN) models for predicting a variety of ocean water quality parameters. In this regard, several water quality parameters in Hilo Bay, Pacific Ocean, are taken under consideration. Different combinations of water quality parameters are applied as input variables to predict daily values of salinity, temperature and DO as well as hourly values of DO. The results demonstrate that the WNN models are superior to the ANN models. Also, the hourly models developed for DO prediction outperform the daily models of DO. For the daily models, the most accurate model has R equal to 0.96, while for the hourly model it reaches up to 0.98. Overall, the results show the ability of the model to monitor the ocean parameters, in condition with missing data, or when regular measurement and monitoring are impossible.

  2. San Francisco Central Bay Suspended Sediment Movement. Report 1. Summer Condition Data Collection Program and Numerical Model Verification

    DTIC Science & Technology

    1990-09-01

    79 PLATES 1-21 APPENDIX A: BIBLIOGRAPHY ON SAN FRANCISCO BAY SEDIMENTATION ......... Al APPENDIX B: THE TABS-2...north, the Farallon Islands to the west, and Half Moon Bay to the south, which are all approximately 22 nautical miles from the Golden Cate Bridge...physical model 58 results for water levels and velocities are compared in Plates 1-7. The sta- tion locations for comparisons are shown in Figure 22

  3. Numerical modeling of landslide generated tsunamis in the bay of Biscay

    NASA Astrophysics Data System (ADS)

    Frere, Antoine; Hebert, Helene

    2016-04-01

    Tsunami hazard in metropolitan France is poorly known. The TANDEM (Tsunamis in northern AtlaNtic : Definition of Effects by Modeling) project is a French initiative to draw lessons from the 2011 catastrophic tsunami in Japan on French coastlines, in order to provide guidance for risk assessment on the nuclear facilities in the area. This project is aimed at adapting numerical methods of tsunami hazard assessment against the outstanding observation database of the 2011 tsunami, in order to apply these validated methods to the definition of the tsunami hazard for the French Atlantic and Channel coastlines. Landslide induced tsunami hazard in the Bay of Biscay France (NE Atlantic ocean) is poorly known. Investigation on the continental slope of the Bay show the existence of numerous landslide scars, but no real risk assessment studies were made to determine the potential tsunami hazard from those landslide. This work focuses on tsunami induced by landslides, and aims to assess the threat using numerical simulation. We assumes that the landslide has a fluid-like behaviour and applies shallow water/thin layer approximations to both aspect. The similarity of the resulting equations of momentum and mass conservation enables to use a single Godunov-like numerical scheme for both parts of the model. The model results are then carried into a multigrid dispersive model in order to get better estimation of the water height near the coast. This second model uses the Boussinesq equations for larger scale grids and the Saint-Venant equations near the coast, and is resolved using a Crank-Nicholson scheme. The first study zone is located in the Cap Breton canyon region in the south of the Bay. Investigation is carried out to identify scenarios that could have caused paleo-tsunamis, with a special interest on a large scar off the canyon(~70 km3). 4 scenarios of varying volumes (from 17 to 70 km3) and depth are carried into the model and the result show maximum water heights of up to

  4. Acquiring a naive theory of kinship through inference.

    PubMed

    Springer, K

    1995-04-01

    The present study focused on how children acquire a naive theory of kinship. Young children appear to have theoretical beliefs about the biological meaning of kinship relations. It was argued here that these beliefs reflect inductive inferences from simple facts about prenatal growth (e.g, where babies grow). An informal model of the inferences linking facts to theory was proposed and tested. In Experiment 1, 4-7-year-olds who knew the basic facts of prenatal growth were most likely to also express the naive theory of kinship. Virtually none of the children who expressed the theory were unaware of the basic facts. In Experiment 2, teaching the facts to a sample of preschoolers led to some increase in their acceptance of the kinship theory. Overall, the results implicate a type of theory building that involves inferences from preexisting knowledge rather than structural change, use of analogy, or acquisition of new knowledge.

  5. Model for isopaching Jurassic-age Norphlet Formation in Mobile Bay, Alabama area

    SciTech Connect

    Torres, L.F.

    1989-03-01

    Deep gas was discovered in the Norphlet Sandstone of Mobile Bay Alabama in 1979. Sixteen wells, of which Exxon Company, U.S.A. has had an interest in eight, have tested gas from depths greater than 20,000 ft and at an average rate of 19 million ft/sub 3/ of gas per day. The dominant structural features in Mobile Bay are large east-west-trending salt-supported anticlines associated with salt pull-apart listric normal faulting. Throws on these faults measure up to 1000 ft. Individual structures have dimensions as large as 15 mi in an east-west strike direction and 8 mi in a north-south dip direction. The Jurassic age (Callovian) Norphlet of Mobile Bay is characterized by eolian dune sand deposits up to 700 ft thick. An important factor affecting future development drilling is the accurate prediction of reservoir thickness. This presentation shows that an integrated study of seismic and well data has facilitated the development of a geological model for isopaching the Norphlet Formation. The isopach exhibits a strong north-northwest-south-southeast orientation of parallel thicks and thins. These trends are believed to be the result of original eolian deposition of complex linear dunes in the Norphlet Sandstone. The major east-west structural grain of faults and anticlines overprints this preserved depositional trend.

  6. 2010 bathymetric survey and digital elevation model of Corte Madera Bay, California

    USGS Publications Warehouse

    Foxgrover, Amy C.; Finlayson, David P.; Jaffe, Bruce E.; Takekawa, John Y.; Thorne, Karen M.; Spragens, Kyle A.

    2011-01-01

    A high-resolution bathymetric survey of Corte Madera Bay, California, was collected in early 2010 in support of a collaborative research project initiated by the San Francisco Bay Conservation and Development Commission and funded by the U.S. Environmental Protection Agency. The primary objective of the Innovative Wetland Adaptation in the Lower Corte Madera Creek Watershed Project is to develop shoreline adaptation strategies to future sea-level rise based upon sound science. Fundamental to this research was the development of an of an up-to-date, high-resolution digital elevation model (DEM) extending from the subtidal environment through the surrounding intertidal marsh. We provide bathymetric data collected by the U.S. Geological Survey and have merged the bathymetry with a 1-m resolution aerial lidar data set that was collected by the National Oceanic and Atmospheric Administration during the same time period to create a seamless, high-resolution DEM of Corte Madera Bay and the surrounding topography. The bathymetric and DEM surfaces are provided at both 1 m and 10 m resolutions formatted as both X, Y, Z text files and ESRI Arc ASCII files, which are accompanied by Federal Geographic Data Committee compliant metadata.

  7. Chesapeake Bay Study. Supplement A. Problem Identification. Supplement B. Public Involvement. Supplement C. The Chesapeake Bay Hydraulic Model.

    DTIC Science & Technology

    1984-09-01

    which are located in the area are not considered to be major water users (i.e., chemicals, pulp and paper, metals, petroleum refining, and food and...concentrated on the Eastern Shore, in the Washington SMSA, and in Norfolk. The only major pulp and paper mill in the Bay Region is located at West Point...finishing, and packaging of light products to heavy manufacturing activities such as steel, pulp , or lumber milling, electric power generating, oil

  8. Modeling Trace Element Concentrations in the San Francisco Bay Estuary from Remote Measurement of Suspended Solids

    NASA Astrophysics Data System (ADS)

    Press, J.; Broughton, J.; Kudela, R. M.

    2014-12-01

    Suspended and dissolved trace elements are key determinants of water quality in estuarine and coastal waters. High concentrations of trace element pollutants in the San Francisco Bay estuary necessitate consistent and thorough monitoring to mitigate adverse effects on biological systems and the contamination of water and food resources. Although existing monitoring programs collect annual in situ samples from fixed locations, models proposed by Benoit, Kudela, & Flegal (2010) enable calculation of the water column total concentration (WCT) and the water column dissolved concentration (WCD) of 14 trace elements in the San Francisco Bay from a more frequently sampled metric—suspended solids concentration (SSC). This study tests the application of these models with SSC calculated from remote sensing data, with the aim of validating a tool for continuous synoptic monitoring of trace elements in the San Francisco Bay. Using HICO imagery, semi-analytical and empirical SSC algorithms were tested against a USGS dataset. A single-band method with statistically significant linear fit (p < 0.001) was chosen as the proxy for SSC values. The numerical models for WCT and the distribution ratio D were applied in MATLAB with terms to account for regional and seasonal effects, and results were used to calculate WCD. The modeled results were assessed against in situ data from the San Francisco Estuary Regional Monitoring Program. Quantile regression was used to evaluate model sensitivity to the distribution of regions, and outliers displaying regional aberrations were removed before robust regression was applied. Statistically significant and highly correlated results for WCT were found for 10 elements, with goodness of fit greater than or equal to that of the original models of seven elements. WCD was successfully modeled for six elements, with goodness of fit for each exceeding that of the original models. Concentrations of Arsenic, Iron, and Lead in the southern region of the

  9. Development of a data-driven numerical model for San Francisco Bay marsh habitat sustainability

    NASA Astrophysics Data System (ADS)

    Swanson, K.; Drexler, J. Z.; Schoellhamer, D. H.; Thorne, K.; Spragens, K.; Takekawa, J.

    2011-12-01

    Marsh species have specific requirements for marsh elevation relative to sea level. As sea level rises and sediment and organic matter accumulate within a marsh, the effect of changes in relative elevation on habitat for specific species will differ. The Wetland Accretion Rate Model for Ecosystem Resilience, WARMER, is a 1-D model of elevation that incorporates both biological and physical processes of vertical marsh accretion at a point representative of wetland habitat. It is currently being developed in order to better understand the threat of rising sea level on marsh sustainability and habitat quality. WARMER incorporates dynamic processes of relative sea-level rise, inorganic sediment deposition and organic matter production, decomposition, and compaction to evaluate changes in marsh surface elevation and the impact of these elevation changes on marsh habitat for specific species of concern. WARMER builds upon existing wetland vertical accretion models by improving upon the sediment input relationship as well as including a more realistic biomass production routine. Sediment input is determined from elevation-dependent marsh inundation and temporal suspended sediment concentration variability and is calibrated to accumulation rates in sediment cores determined from 210Pb dating. Organic matter accumulation is also an elevation-dependent parabolic function defined by the tidal range of San Francisco Bay marsh vegetation and calibrated to measured organic matter accumulation. Both above ground and below ground organic matter accumulation are accounted for within the model. The cohort-based model is also parametrized with measurements of elevation, porosity, tidal inundation patterns measured in San Francisco Bay marshes and a single scenario of modeled sea level within the Bay from Cayan et al. (2008) and Cayan et al. (2009) based on the IPCC A2 emissions scenario. Model results are compared to elevation-based habitat evaluation criteria developed for marsh

  10. Research on Bayes matting algorithm based on Gaussian mixture model

    NASA Astrophysics Data System (ADS)

    Quan, Wei; Jiang, Shan; Han, Cheng; Zhang, Chao; Jiang, Zhengang

    2015-12-01

    The digital matting problem is a classical problem of imaging. It aims at separating non-rectangular foreground objects from a background image, and compositing with a new background image. Accurate matting determines the quality of the compositing image. A Bayesian matting Algorithm Based on Gaussian Mixture Model is proposed to solve this matting problem. Firstly, the traditional Bayesian framework is improved by introducing Gaussian mixture model. Then, a weighting factor is added in order to suppress the noises of the compositing images. Finally, the effect is further improved by regulating the user's input. This algorithm is applied to matting jobs of classical images. The results are compared to the traditional Bayesian method. It is shown that our algorithm has better performance in detail such as hair. Our algorithm eliminates the noise well. And it is very effectively in dealing with the kind of work, such as interested objects with intricate boundaries.

  11. Storm and fair-weather driven sediment-transport within Poverty Bay, New Zealand, evaluated using coupled numerical models

    NASA Astrophysics Data System (ADS)

    Bever, Aaron J.; Harris, Courtney K.

    2014-09-01

    The Waipaoa River Sedimentary System in New Zealand, a focus site of the MARGINS Source-to-Sink program, contains both a terrestrial and marine component. Poverty Bay serves as the interface between the fluvial and oceanic portions of this dispersal system. This study used a three-dimensional hydrodynamic and sediment-transport numerical model, the Regional Ocean Modeling System (ROMS), coupled to the Simulated WAves Nearshore (SWAN) wave model to investigate sediment-transport dynamics within Poverty Bay and the mechanisms by which sediment travels from the Waipaoa River to the continental shelf. Two sets of model calculations were analyzed; the first represented a winter storm season, January-September, 2006; and the second an approximately 40 year recurrence interval storm that occurred on 21-23 October 2005. Model results indicated that hydrodynamics and sediment-transport pathways within Poverty Bay differed during wet storms that included river runoff and locally generated waves, compared to dry storms driven by oceanic swell. During wet storms the model estimated significant deposition within Poverty Bay, although much of the discharged sediment was exported from the Bay during the discharge pulse. Later resuspension events generated by Southern Ocean swell reworked and modified the initial deposit, providing subsequent pulses of sediment from the Bay to the continental shelf. In this manner, transit through Poverty Bay modified the input fluvial signal, so that the sediment characteristics and timing of export to the continental shelf differed from the Waipaoa River discharge. Sensitivity studies showed that feedback mechanisms between sediment-transport, currents, and waves were important within the model calculations.

  12. Acoustic Modeling of the Monterey Bay Tomography Experiment

    DTIC Science & Technology

    1990-12-01

    26 A. INTRODUCTION TO EIGENRAY SEARCH TECHNIQ .; 3,S ......... 26 B. SEARCHING FOR EIGENRAYS...match measured arrivals times with the model raypaths. 8 3. Large enough temporal separation of eigenray arrivals to resolve individual rays (this...meters depth. [Ref. 6] Separating the MSC from the Soquel Submarine Canyon along the line-of- sight is a south-eastwardly sloping fan-like feature which

  13. Conceptual ecosystem model of the Corpus Christi Bay National Estuary Program study area. Final report

    SciTech Connect

    Montagna, P.A.; Li, J.; Street, G.T.

    1996-01-01

    This report developed a conceptual ecosystem model, both pictorial and narrative, of the Corpus Christi Bay National Estuary Program (CCBNEP) study area. The model demonstrates ecosystem linkages at all trophic levels and substrate types, and provides a conceptual framework with which to assess ecological and environmental impacts (both episodic and cumulative) associated with external influences. The model is based on current scientific consensus regarding the modeling of estuarine ecosystem components, and data and information regarding these relationships within the study area. The model was developed to two levels of detail: (1) a detailed model suitable for the scientific and technical community; and, (2) a simple model suitable for use in CCBNEP public documents and management conference deliberations.

  14. Tidal, Residual, Intertidal Mudflat (TRIM) Model and its Applications to San Francisco Bay, California

    USGS Publications Warehouse

    Cheng, R.T.; Casulli, V.; Gartner, J.W.

    1993-01-01

    A numerical model using a semi-implicit finite-difference method for solving the two-dimensional shallow-water equations is presented. The gradient of the water surface elevation in the momentum equations and the velocity divergence in the continuity equation are finite-differenced implicitly, the remaining terms are finite-differenced explicitly. The convective terms are treated using an Eulerian-Lagrangian method. The combination of the semi-implicit finite-difference solution for the gravity wave propagation, and the Eulerian-Lagrangian treatment of the convective terms renders the numerical model unconditionally stable. When the baroclinic forcing is included, a salt transport equation is coupled to the momentum equations, and the numerical method is subject to a weak stability condition. The method of solution and the properties of the numerical model are given. This numerical model is particularly suitable for applications to coastal plain estuaries and tidal embayments in which tidal currents are dominant, and tidally generated residual currents are important. The model is applied to San Francisco Bay, California where extensive historical tides and current-meter data are available. The model calibration is considered by comparing time-series of the field data and of the model results. Alternatively, and perhaps more meaningfully, the model is calibrated by comparing the harmonic constants of tides and tidal currents derived from field data with those derived from the model. The model is further verified by comparing the model results with an independent data set representing the wet season. The strengths and the weaknesses of the model are assessed based on the results of model calibration and verification. Using the model results, the properties of tides and tidal currents in San Francisco Bay are characterized and discussed. Furthermore, using the numerical model, estimates of San Francisco Bay's volume, surface area, mean water depth, tidal prisms, and

  15. Nonparametric Bayes modeling for case control studies with many predictors.

    PubMed

    Zhou, Jing; Herring, Amy H; Bhattacharya, Anirban; Olshan, Andrew F; Dunson, David B

    2016-03-01

    It is common in biomedical research to run case-control studies involving high-dimensional predictors, with the main goal being detection of the sparse subset of predictors having a significant association with disease. Usual analyses rely on independent screening, considering each predictor one at a time, or in some cases on logistic regression assuming no interactions. We propose a fundamentally different approach based on a nonparametric Bayesian low rank tensor factorization model for the retrospective likelihood. Our model allows a very flexible structure in characterizing the distribution of multivariate variables as unknown and without any linear assumptions as in logistic regression. Predictors are excluded only if they have no impact on disease risk, either directly or through interactions with other predictors. Hence, we obtain an omnibus approach for screening for important predictors. Computation relies on an efficient Gibbs sampler. The methods are shown to have high power and low false discovery rates in simulation studies, and we consider an application to an epidemiology study of birth defects.

  16. CALMET/CALPUFF modeling of nitrogen deposition to Sarasota Bay, Florida

    SciTech Connect

    Weaver, R.; Poor, N.; Iranipour, G.; Kalch, R.; Shell, P.

    1999-07-01

    The dispersion, transport, chemical transformation and deposition of southern Florida nitrogen oxide emissions were modeled using CALMET/CALPUFF to estimate nitrogen deposition to Sarasota Bay. The domain modeled was 390 km x 400 km with a 10-km grid size, and included emissions from the metropolitan areas of Tampa Bay, Orlando, Miami, and Ft. Myers. Utility emissions were modeled as 67 point sources (150,000 metric tons/year), industrial emissions as 90 point sources (18,000 metric tons/year), and combined mobile and area sources as 13 volume and 20 line sources (320,000 metric tons/year). CALMET/CALPUFF modeling was done month-by-month, and each source category was modeled separately. Annually averaged ambient air concentrations predicted over Sarasota Bay for NO{sub x}, HNO{sub 3} and NO{sub 3} were 9 {micro}g m{sup {minus}3}, 1 {micro}g m{sup {minus}3}, and 0.7 {micro}g m{sup {minus}3}, respectively. Mobile plus area sources contributed 86%, 69% and 78% to the average annual ambient air NO{sub x}, HNO{sub 3} and NO{sub 3} concentrations, respectively. The total predicted nitrogen deposition to Sarasota Bay from these species was 23 metric tons/year, and this represents a deposition rate of 1.8 kg-N/ha/year. Of this total predicted nitrogen deposition, 11% was from wet deposition and 89% from dry deposition. Mobile and area sources accounted for 80%, utility sources 16% and industrial sources 4%, of the total nitrogen deposition. By species, NO{sub x} contributed 69%, HNO{sub 3} 29%, and NO{sub 3} 2%, to the total nitrogen deposited. The modeled wet deposition rate of 0.2 kg-N/ha/year is well below the 1.9 kg-N/ha/year NO{sub 3} wet deposition rate measured in 1990 at a National Atmospheric Deposition Program site in Sarasota County.

  17. Nonparametric Bayes Conditional Distribution Modeling With Variable Selection.

    PubMed

    Chung, Yeonseung; Dunson, David B

    2009-12-01

    This article considers a methodology for flexibly characterizing the relationship between a response and multiple predictors. Goals are (1) to estimate the conditional response distribution addressing the distributional changes across the predictor space, and (2) to identify important predictors for the response distribution change both within local regions and globally. We first introduce the probit stick-breaking process (PSBP) as a prior for an uncountable collection of predictor-dependent random distributions and propose a PSBP mixture (PSBPM) of normal regressions for modeling the conditional distributions. A global variable selection structure is incorporated to discard unimportant predictors, while allowing estimation of posterior inclusion probabilities. Local variable selection is conducted relying on the conditional distribution estimates at different predictor points. An efficient stochastic search sampling algorithm is proposed for posterior computation. The methods are illustrated through simulation and applied to an epidemiologic study.

  18. Numerical study on pollutant transport in Dalian bay based on hydrodynamic model

    NASA Astrophysics Data System (ADS)

    Qiao, Huiting; Li, Jin; Zhang, Hongxing; Zhao, Kaibin; Zhang, Mingliang

    2017-01-01

    Based on the depth-averaged two-dimensional shallow water and pollutant transport equation, the coupling model of water flow and water quality with explicit scheme is developed in this study. The unstructured triangular grid is adopted to locally refine the mesh around sewage outlet or in high-gradient regions of terrain change for the coupling model. The finite volume method is applied to ensure the conservation of mass for each element. This hydrodynamic model applies the Roe solver approximate Riemann solution with second-order accuracy to compute the water momentum flux on the grid interface. Taking Dalian Bay as the research object, the numerical model established is used to simulate the hydrodynamic characteristics and pollutant transport process. The computed results of the tide level, flow current and flow direction agree well with the measured data in Dalian Bay. The spatial and temporal distribution of pollutant in water are analyzed and discussed in this study. Simulated results show that the two-dimensional hydrodynamic and pollutant transport model can accurately simulate the mass transport in coastal waters, and it can provide a scientific basis on coastal water environment protection for the research water.

  19. Final report for sea-level rise response modeling for San Francisco Bay estuary tidal marshes

    USGS Publications Warehouse

    Takekawa, John Y.; Thorne, Karen M.; Buffington, Kevin J.; Spragens, Kyle A.; Swanson, Kathleen M.; Drexler, Judith Z.; Schoellhamer, David H.; Overton, Cory T.; Casazza, Michael L.

    2013-01-01

    The International Panel on Climate Change has identified coastal ecosystems as areas that will be disproportionally affected by climate change. Current sea-level rise projections range widely with 0.57 to 1.9 meters increase in mea sea level by 2100. The expected accelerated rate of sea-level rise through the 21st century will put many coastal ecosystems at risk, especially those in topographically low-gradient areas. We assessed marsh accretion and plant community state changes through 2100 at 12 tidal salt marshes around San Francisco Bay estuary with a sea-level rise response model. Detailed ground elevation, vegetation, and water level data were collected at all sites between 2008 and 2011 and used as model inputs. Sediment cores (taken by Callaway and others, 2012) at four sites around San Francisco Bay estuary were used to estimate accretion rates. A modification of the Callaway and others (1996) model, the Wetland Accretion Rate Model for Ecosystem Resilience (WARMER), was utilized to run sea-level rise response models for all sites. With a mean sea level rise of 1.24 m by 2100, WARMER projected that the vast majority, 95.8 percent (1,942 hectares), of marsh area in our study will lose marsh plant communities by 2100 and to transition to a relative elevation range consistent with mudflat habitat. Three marshes were projected to maintain marsh vegetation to 2100, but they only composed 4.2 percent (85 hectares) of the total marsh area surveyed.

  20. Estimating the input of submarine groundwater discharge (SGD) and SGD-derived nutrients in Geoje Bay, Korea using (222)Rn-Si mass balance model.

    PubMed

    Hwang, Dong-Woon; Lee, In-Seok; Choi, Minkyu; Kim, Tae-Hoon

    2016-09-15

    In order to evaluate the main source of nutrients for maintaining the high production in shellfish farming bay, we have measured (222)Rn activities and the concentrations of nutrients in stream water, seawater, and coastal groundwater around Geoje Bay, one of the largest cultivation areas of oyster in the southern sea of Korea in April 2013. Using the (222)Rn and Si mass balance model, the residence time of bay seawater was about 5days and the submarine groundwater discharge (SGD) into the bay was estimated to be approximately 1.8×10(6)m(3) d(-1). The SGD-derived nutrient fluxes contributed approximately 54% for DIN, 5% for DIP, and 50% for DSi of total nutrient input entering into the bay. Thus, our results suggest that SGD is the major source of nutrients in Geoje Bay, and SGD-derived nutrients are very important to support the biological production of this shellfish farming bay.

  1. Modification of the vertically generalized production model for the turbid waters of Ariake Bay, southwestern Japan

    NASA Astrophysics Data System (ADS)

    Tripathy, S. C.; Ishizaka, J.; Siswanto, E.; Shibata, T.; Mino, Y.

    2012-01-01

    The vertically generalized production model (VGPM), which was designed for open ocean waters ( Behrenfeld and Falkowski, 1997a; henceforth BF), was evaluated using in situ measurements of primary productivity (PP) in the characteristically turbid coastal waters of Ariake Bay, southwestern Japan, to develop a regionally modified version of the model. The euphotic depth ( Z eu)-integrated PP (IPP) calculated from the VGPM using in situ chlorophyll a (Chl a) and sea surface temperature (SST) was significantly overestimated (by factors of 2-3), but 52% of the observed variability was explained. The weak correlation could have partially resulted from overestimations by the sub-models embedded in the original VGPM model for estimation of Z eu ( Morel and Berthon, 1989; henceforth MB) and the optimal Chl a-normalized PP ( poptB). The sub-model estimates of poptB and Z eu with in situpoptB and Z eu showed significant improvement, accounting for 84% of the variability and causing less overestimation. Z eu was the most important parameter influencing the modeled IPP variation in Ariake Bay. Previous research suggested that the Z eu model, which was based on surface Chl a, overestimated in situ Z eu by a factor of 2-3, resulting in weak correlation between the modeled and in situ IPP. The Z eu sub-model was not accurate in the present study area because it was basically developed for clear (case 1) waters. A better estimation of Z eu could be obtained from the in situ remote sensing reflectance ( R rs) using a quasi-analytical algorithm (QAA) in this turbid water ecosystem. Among the parameters of PP models, poptB is conventionally considered the most important. However, in this study poptB was of secondary importance because the contribution of poptB to the variation in modeled IPP was less than the contribution of Z eu. The modeled and in situpoptB were weakly correlated with 50% of the data points that overestimated the in situ values. The estimation of Chl a was improved

  2. Naive Juveniles Are More Likely to Become Breeders after Witnessing Predator Mobbing.

    PubMed

    Griesser, Michael; Suzuki, Toshitaka N

    2017-01-01

    Responding appropriately during the first predatory attack in life is often critical for survival. In many social species, naive juveniles acquire this skill from conspecifics, but its fitness consequences remain virtually unknown. Here we experimentally demonstrate how naive juvenile Siberian jays (Perisoreus infaustus) derive a long-term fitness benefit from witnessing knowledgeable adults mobbing their principal predator, the goshawk (Accipiter gentilis). Siberian jays live in family groups of two to six individuals that also can include unrelated nonbreeders. Field observations showed that Siberian jays encounter predators only rarely, and, indeed, naive juveniles do not respond to predator models when on their own but do when observing other individuals mobbing them. Predator exposure experiments demonstrated that naive juveniles had a substantially higher first-winter survival after observing knowledgeable group members mobbing a goshawk model, increasing their likelihood of acquiring a breeding position later in life. Previous research showed that naive individuals may learn from others how to respond to predators, care for offspring, or choose mates, generally assuming that social learning has long-term fitness consequences without empirical evidence. Our results demonstrate a long-term fitness benefit of vertical social learning for naive individuals in the wild, emphasizing its evolutionary importance in animals, including humans.

  3. Work Plan for Three-Dimensional Time-Varying, Hydrodynamic and Water Quality Model of Chesapeake Bay

    DTIC Science & Technology

    1988-08-01

    The MEXAMS model is also a potential candidate for application to the Bay. This model ( Felmy et al., 1984) was developed by USEPA by coupling MINTEQ...Oxygen Demand - Processes, Modelling, and Measurement, K. Hatcher ed., University of Georgia, Athens, pp 171-208. Felmy , A. R. et al. 1984. "Project

  4. Modeling of Selenium for the San Diego Creek Watershed and Newport Bay, California

    USGS Publications Warehouse

    Presser, Theresa S.; Luoma, Samuel N.

    2009-01-01

    The San Diego Creek watershed and Newport Bay in southern California are contaminated with selenium (Se) as a result of groundwater associated with urban development overlying a historical wetland, the Swamp of the Frogs. The primary Se source is drainage from surrounding seleniferous marine sedimentary formations. An ecosystem-scale model was employed as a tool to assist development of a site-specific Se objective for the region. The model visualizes outcomes of different exposure scenarios in terms of bioaccumulation in predators using partitioning coefficients, trophic transfer factors, and site-specific data for food-web inhabitants and particulate phases. Predicted Se concentrations agreed well with field observations, validating the use of the model as realistic tool for testing exposure scenarios. Using the fish tissue and bird egg guidelines suggested by regulatory agencies, allowable water concentrations were determined for different conditions and locations in the watershed and the bay. The model thus facilitated development of a site-specific Se objective that was locally relevant and provided a basis for step-by-step implementation of source control.

  5. Modeling the periodic stratification and gravitational circulation in San Francisco Bay, California

    USGS Publications Warehouse

    Cheng, Ralph T.; Casulli, Vincenzo

    1996-01-01

    A high resolution, three-dimensional (3-D) hydrodynamic numerical model is applied to San Francisco Bay, California to simulate the periodic tidal stratification caused by tidal straining and stirring and their long-term effects on gravitational circulation. The numerical model is formulated using fixed levels in the vertical and uniform computational mesh on horizontal planes. The governing conservation equations, the 3-D shallow water equations, are solved by a semi-implicit finite-difference scheme. Numerical simulations for estuarine flows in San Francisco Bay have been performed to reproduce the hydrodynamic properties of tides, tidal and residual currents, and salt transport. All simulations were carried out to cover at least 30 days, so that the spring-neap variance in the model results could be analyzed. High grid resolution used in the model permits the use of a simple turbulence closure scheme which has been shown to be sufficient to reproduce the tidal cyclic stratification and well-mixed conditions in the water column. Low-pass filtered 3-D time-series reveals the classic estuarine gravitational circulation with a surface layer flowing down-estuary and an up-estuary flow near the bottom. The intensity of the gravitational circulation depends upon the amount of freshwater inflow, the degree of stratification, and spring-neap tidal variations.

  6. Empirical model of Skeletonema costatum photosynthetic rate, with applications in the San Francisco Bay estuary

    USGS Publications Warehouse

    Cloern, J.E.

    1978-01-01

    An empirical model of Skeletonema costatum photosynthetic rate is developed and fit to measurements of photosynthesis selected from the literature. Because the model acknowledges existence of: 1) a light-temperature interaction (by allowing optimum irradiance to vary with temperature), 2) light inhibition, 3) temperature inhibition, and 4) a salinity effect, it accurately estimates photosynthetic rates measured over a wide range of temperature, light intensity, and salinity. Integration of predicted instantaneous rate of photosynthesis with time and depth yields daily net carbon assimilation (pg C cell-1 day-1) in a mixed layer of specified depth, when salinity, temperature, daily irradiance and extinction coefficient are known. The assumption of constant carbon quota (pg C cell-1) allows for prediction of mean specific growth rate (day-1), which can be used in numerical models of Skeletonema costatum population dynamics. Application of the model to northern San Francisco Bay clearly demonstrates the limitation of growth by low light availability, and suggests that large population densities of S. costatum observed during summer months are not the result of active growth in the central deep channels (where growth rates are consistently predicted to be negative). But predicted growth rates in the lateral shallows are positive during summer and fall, thus offering a testable hypothesis that shoals are the only sites of active population growth by S. costatum (and perhaps other neritic diatoms) in the northern reach of San Francisco Bay. ?? 1978.

  7. Observations and modelling of fast ice growth in the Tiksi Bay, Laptev Sea

    NASA Astrophysics Data System (ADS)

    Bogorodsky, Petr; Makshtas, Aleksandr; Grubiy, Andrey; Kustov, Vasiliy

    2016-04-01

    Fast ice is one of the main features of sea ice cover in the Laptev Sea. The formation of this immobile ice which occupies up to 30% of the sea area and significantly affects the intensity of air-sea energy exchange in the coastal zones had been investigated during winter 2014-2015 in the Tiksi Bay (Buor-Khaya Gulf). The temperature measurements within sea ice thickness and under-ice sea layer using GeoPrecision thermistor string of 10 sensors together with measurements of snow and ice thicknesses were carried out at the distance of 0.5 km from the shore at the 3.5 m water depth. According to measurements temperature variations qualitatively repeat air temperature variations and, damping with depth, approach to sea water freezing temperature. Vertical temperature distributions allow to recognize snow, ice and water layers by profile inclination in each layer. The temperature profiles within growing ice were quasi-linear, indicating permanence of heat flux inside ice. The linearity of temperature profiles increased during ice growth. For calculations of fast ice evolution one-dimensional thermodynamic model was used. Besides the empirical formulae, based on frost degree-days, developed in 1930th for the Tiksi Bay was applied. Numerical experiments were carried out with constant values of thermal properties of all media and 10 ppt water salinity, as initial condition. The daily average data from Hydrometeorological Observatory Tiksi, located approximately 1 km from the site of ice observations, were used as atmospheric forcing. For the examined area evolutions of ice cover thickness estimated from direct measurements, the thermodynamic model and the empirical formulae were almost identical. The result indicates stability of hydrological and meteorological conditions, determining fast ice growth in the Tiksi Bay during last 75 years. Model simulations showed that in shallow waters the growth of ice thickness is stabilized due to increase of sub-ice water layer

  8. Inference for dynamic and latent variable models via iterated, perturbed Bayes maps

    PubMed Central

    Ionides, Edward L.; Nguyen, Dao; Atchadé, Yves; Stoev, Stilian; King, Aaron A.

    2015-01-01

    Iterated filtering algorithms are stochastic optimization procedures for latent variable models that recursively combine parameter perturbations with latent variable reconstruction. Previously, theoretical support for these algorithms has been based on the use of conditional moments of perturbed parameters to approximate derivatives of the log likelihood function. Here, a theoretical approach is introduced based on the convergence of an iterated Bayes map. An algorithm supported by this theory displays substantial numerical improvement on the computational challenge of inferring parameters of a partially observed Markov process. PMID:25568084

  9. Verification by remote sensing of an oil slick movement prediction model. [Delaware Bay

    NASA Technical Reports Server (NTRS)

    Klemas, V. (Principal Investigator); Davis, G.; Wang, H.

    1976-01-01

    The author has identified the following significant results. LANDSAT, aircraft, ships, and air-dropped current drogues were deployed to determine current circulation and to track oil slick movement on four different dates in Delaware Bay. The results were used to verify a predictive model for oil slicks given their size, location, tidal stage (current), weather (wind), and nature of crude. Both LANDSAT satellites provided valuable data on gross circulation patterns and convergent coastal fronts which by capturing oil slicks significantly influence their movement and dispersion.

  10. Detecting adverse drug events in discharge summaries using variations on the simple Bayes model.

    PubMed

    Visweswaran, Shyam; Hanbury, Paul; Saul, Melissa; Cooper, Gregory F

    2003-01-01

    Detection and prevention of adverse events and, in particular, adverse drug events (ADEs), is an important problem in health care today. We describe the implementation and evaluation of four variations on the simple Bayes model for identifying ADE-related discharge summaries. Our results show that these probabilistic techniques achieve an ROC curve area of up to 0.77 in correctly determining which patient cases should be assigned an ADE-related ICD-9-CM code. These results suggest a potential for these techniques to contribute to the development of an automated system that helps identify ADEs, as a step toward further understanding and preventing them.

  11. A three-dimensional, time-dependent model of Mobile Bay

    NASA Technical Reports Server (NTRS)

    Pitts, F. H.; Farmer, R. C.

    1976-01-01

    A three-dimensional, time-variant mathematical model for momentum and mass transport in estuaries was developed and its solution implemented on a digital computer. The mathematical model is based on state and conservation equations applied to turbulent flow of a two-component, incompressible fluid having a free surface. Thus, bouyancy effects caused by density differences between the fresh and salt water, inertia from thare river and tidal currents, and differences in hydrostatic head are taken into account. The conservation equations, which are partial differential equations, are solved numerically by an explicit, one-step finite difference scheme and the solutions displayed numerically and graphically. To test the validity of the model, a specific estuary for which scaled model and experimental field data are available, Mobile Bay, was simulated. Comparisons of velocity, salinity and water level data show that the model is valid and a viable means of simulating the hydrodynamics and mass transport in non-idealized estuaries.

  12. Dispersal of lobster larvae within and between coastal bays in the eastern Gulf of Maine: Preliminary model studies

    NASA Astrophysics Data System (ADS)

    Brooks, D.

    2003-04-01

    The lobster (Homarus americanus) supports the most important coastal fishery in the Gulf of Maine. Over the last decade, lobster landing rates have roughly doubled, leading to concerns about sustainable levels of the fishery. Informed management requires better understanding of the physical processes responsible for the dispersal of lobster larvae by shelf and coastal currents and the exchange of post-larvae between offshore waters and coastal bays, where settlement and eventual harvest can occur. The issues are international, because the Gulf currents link Canadian and U.S. waters. The eastern Maine coastal current, a seasonal component of the prevailing circulation, is influenced by river run-off, the winds, tidal mixing, and the hydrographic structure of the deeper offshore waters. Circulation models show that increased run-off in wet years produces river plumes with strong thermohaline fronts that deflect the coastal current offshore, which may reduce the probability of larval settlement in bays. Fine-scale models applied to several bays at the eastern end of the Maine coast show that the pathways of neutral particles approximating larvae entering the region are strongly dependent on the vigorous semidiurnal tidal currents and complex topography. Residence times of particles within the bays range from one tidal cycle to greater than a week, and particles may be exchanged between bays. Ejected particles may enter the coastal current and subsequently be carried southwestward to other bays. Ongoing model studies will quantify the bay-shelf larval exchange rates under different climatological conditions. This work is part of a multidisciplinary project entitled "Impact of Transport Processes on Lobster Fishery Patterns," funded by the U.S. NOAA Coastal Ocean Program, grant number NA160P2658.

  13. Sedimentology models from activity concentration measurements: application to the "Bay of Cadiz" Natural Park (SW Spain).

    PubMed

    Ligero, R A; Vidal, J; Meléndez, M J; Hamani, M; Casas-Ruiz, M

    2009-03-01

    A previous study on seabed sediments of the Bay of Cadiz (SW of Spain) enabled us to identify several relations between sedimentological variables and activity concentrations of environmental radionuclides such as (137)Cs, (226)Ra, (232)Th and (40)K. In this paper the study has been extended to a large neighbouring inter-tidal area in order to establish if the above mentioned models can be generalized. As a result we have determined that the measured activity concentrations are closely to the values predicted by the theoretical models (correlation coefficient range=0.85-0.93). Furthermore, the proposal model for granulometric facies as a function of activity concentrations of the abovementioned radionuclides provides for the sediments distribution a representation which agrees with the values of the tidal energy distribution obtained using numeric models calibrated with experimental data from current meters and water level recorders.

  14. Naive Optics: Acting on Mirror Reflections

    ERIC Educational Resources Information Center

    Hecht, Heiko; Bertamini, Marco; Gamer, Matthias

    2005-01-01

    It is known that naive observers have striking misconceptions about mirror reflections. In 5 experiments, this article systematically extends the findings to graphic stimuli, to interactive visual tasks, and finally to tasks involving real mirrors. The results show that the perceptual knowledge of nonexpert adults is far superior to their…

  15. Towards improved storm surge models in the northern Bay of Bengal

    NASA Astrophysics Data System (ADS)

    Krien, Y.; Testut, L.; Islam, A. K. M. S.; Bertin, X.; Durand, F.; Mayet, C.; Tazkia, A. R.; Becker, M.; Calmant, S.; Papa, F.; Ballu, V.; Shum, C. K.; Khan, Z. H.

    2017-03-01

    The northern Bay of Bengal is home to some of the deadliest cyclones recorded during the last decades. Storm surge models developed for this region significantly improved in recent years, but they still fail to predict patterns of coastal flooding with sufficient accuracy. In the present paper, we make use of a state-of-the art numerical modeling system with improved bathymetric and topographic data to identify the strengths, weaknesses, and to suggest areas for improvement of current storm surge models in this area. The new model is found to perform relatively well in reproducing waves characteristics and maximum water levels for the two extreme cyclones studied here: Phailin (2013) and Sidr (2007). The wave setup turns out to be small compared to the wind-driven surge, although it still plays a significant role for inland flooding. Relatively large tide-surge interactions mainly due to shallow water effects are also evidenced by the model. These findings plead in favor of further efforts to improve the representation of the bathymetry, especially in the nearshore area, and the implementation of models including tides and radiation stresses explicitly. The main limit of the model is its inability to predict the detailed patterns of coastal flooding satisfactorily. The reason lies mainly in the fact that topographic data also need to be further improved. In particular, a good knowledge of embankments characteristics (crest elevation and their condition) is found to be of primary importance to represent inland flooding correctly. Public authorities should take urgent action to ensure that better data are available to the scientific community, so that state-of-the-art storm surge models reaching a sufficiently high level of confidence can be used for emergency preparedness and to implement mitigation strategies in the northern Bay of Bengal.

  16. Bed composition generation for morphodynamic modeling: Case study of San Pablo Bay in California, USA

    USGS Publications Warehouse

    van der Wegen, M.; Dastgheib, A.; Jaffe, B.E.; Roelvink, D.

    2011-01-01

    Applications of process-based morphodynamic models are often constrained by limited availability of data on bed composition, which may have a considerable impact on the modeled morphodynamic development. One may even distinguish a period of "morphodynamic spin-up" in which the model generates the bed level according to some ill-defined initial bed composition rather than describing the realistic behavior of the system. The present paper proposes a methodology to generate bed composition of multiple sand and/or mud fractions that can act as the initial condition for the process-based numerical model Delft3D. The bed composition generation (BCG) run does not include bed level changes, but does permit the redistribution of multiple sediment fractions over the modeled domain. The model applies the concept of an active layer that may differ in sediment composition above an underlayer with fixed composition. In the case of a BCG run, the bed level is kept constant, whereas the bed composition can change. The approach is applied to San Pablo Bay in California, USA. Model results show that the BCG run reallocates sand and mud fractions over the model domain. Initially, a major sediment reallocation takes place, but development rates decrease in the longer term. Runs that take the outcome of a BCG run as a starting point lead to more gradual morphodynamic development. Sensitivity analysis shows the impact of variations in the morphological factor, the active layer thickness, and wind waves. An important but difficult to characterize criterion for a successful application of a BCG run is that it should not lead to a bed composition that fixes the bed so that it dominates the "natural" morphodynamic development of the system. Future research will focus on a decadal morphodynamic hindcast and comparison with measured bathymetries in San Pablo Bay so that the proposed methodology can be tested and optimized. ?? 2010 The Author(s).

  17. Chesapeake Bay study

    NASA Technical Reports Server (NTRS)

    Love, W. J.

    1972-01-01

    The objectives and scope of the Chesapeake Bay study are discussed. The physical, chemical, biological, political, and social phenomena of concern to the Chesapeake Bay area are included in the study. The construction of a model of the bay which will provide a means of accurately studying the interaction of the ecological factors is described. The application of the study by management organizations for development, enhancement, conservation, preservation, and restoration of the resources is examined.

  18. Models for Holocene valley-fill sequences from high-resolution seismic facies of Galveston Bay

    SciTech Connect

    Smyth, W.; Thomas, M.A.; Anderson, J.B. )

    1988-02-01

    Reconstructions of the northern Gulf of Mexico shelf for the Holocene have relied on the dating of isolated bathymetric banks. These banks, which are interpreted as former shorelines, provide snapshots of the shelf during periods of relative sea level stillstand. A more complete sedimentary record of the Holocene transgression is likely preserved in the incised valley-fill sequences. The first step in deciphering the record of Holocene valley-fill sequences is development of high-resolution seismic facies models based on modern environments. The modern incised valley-estuarine system of Galveston Bay has been seismically surveyed. Important environments include bayhead delta (Trinity River delta), tidal inlet, flood tidal delta (Bolivar Roads), and estuarine sediments (central bay). Additionally, fluvial sediments partially infill the entrenched Trinity River valley. Seismic facies interpretation was corroborated by information obtained from sediment cores. The influence of the rate of relative sea level rise on incised valley-fill facies architecture is demonstrated in hypothetical sequence models which are applied to the interpretation of high-resolution surveys of Holocene shelf deposits.

  19. Network-based empirical Bayes methods for linear models with applications to genomic data.

    PubMed

    Li, Caiyan; Wei, Zhi; Li, Hongzhe

    2010-03-01

    Empirical Bayes methods are widely used in the analysis of microarray gene expression data in order to identify the differentially expressed genes or genes that are associated with other general phenotypes. Available methods often assume that genes are independent. However, genes are expected to function interactively and to form molecular modules to affect the phenotypes. In order to account for regulatory dependency among genes, we propose in this paper a network-based empirical Bayes method for analyzing genomic data in the framework of linear models, where the dependency of genes is modeled by a discrete Markov random field defined on a predefined biological network. This method provides a statistical framework for integrating the known biological network information into the analysis of genomic data. We present an iterated conditional mode algorithm for parameter estimation and for estimating the posterior probabilities using Gibbs sampling. We demonstrate the application of the proposed methods using simulations and analysis of a human brain aging microarray gene expression data set.

  20. Modeling the 1958 Lituya Bay mega-tsunami with a PVM-IFCP GPU-based model

    NASA Astrophysics Data System (ADS)

    González-Vida, José M.; Arcas, Diego; de la Asunción, Marc; Castro, Manuel J.; Macías, Jorge; Ortega, Sergio; Sánchez-Linares, Carlos; Titov, Vasily

    2013-04-01

    In this work we present a numerical study, performed in collaboration with the NOAA Center for Tsunami Research (USA), that uses a GPU version of the PVM-IFCP landslide model for the simulation of the 1958 landslide generated tsunami of Lituya Bay. In this model, a layer composed of fluidized granular material is assumed to flow within an upper layer of an inviscid fluid (e. g. water). The model is discretized using a two dimensional PVM-IFCP [Fernández - Castro - Parés. On an Intermediate Field Capturing Riemann Solver Based on a Parabolic Viscosity Matrix for the Two-Layer Shallow Water System, J. Sci. Comput., 48 (2011):117-140] finite volume scheme implemented on GPU cards for increasing the speed-up. This model has been previously validated by using the two-dimensional physical laboratory experiments data from H. Fritz [Lituya Bay Landslide Impact Generated Mega-Tsunami 50th Anniversary. Pure Appl. Geophys., 166 (2009) pp. 153-175]. In the present work, the first step was to reconstruct the topobathymetry of the Lituya Bay before this event ocurred, this is based on USGS geological surveys data. Then, a sensitivity analysis of some model parameters has been performed in order to determine the parameters that better fit to reality, when model results are compared against available event data, as run-up areas. In this presentation, the reconstruction of the pre-tsunami scenario will be shown, a detailed simulation of the tsunami presented and several comparisons with real data (runup, wave height, etc.) shown.

  1. Estimation of environmental capacity of phosphorus in Gorgan Bay, Iran, via a 3D ecological-hydrodynamic model.

    PubMed

    Ranjbar, Mohammad Hassan; Hadjizadeh Zaker, Nasser

    2016-11-01

    Gorgan Bay is a semi-enclosed basin located in the southeast of the Caspian Sea in Iran and is an important marine habitat for fish and seabirds. In the present study, the environmental capacity of phosphorus in Gorgan Bay was estimated using a 3D ecological-hydrodynamic numerical model and a linear programming model. The distribution of phosphorus, simulated by the numerical model, was used as an index for the occurrence of eutrophication and to determine the water quality response field of each of the pollution sources. The linear programming model was used to calculate and allocate the total maximum allowable loads of phosphorus to each of the pollution sources in a way that eutrophication be prevented and at the same time maximum environmental capacity be achieved. In addition, the effect of an artificial inlet on the environmental capacity of the bay was investigated. Observations of surface currents in Gorgan Bay were made by GPS-tracked surface drifters to provide data for calibration and verification of numerical modeling. Drifters were deployed at five different points across the bay over a period of 5 days. The results indicated that the annual environmental capacity of phosphorus is approximately 141 t if a concentration of 0.0477 mg/l for phosphorus is set as the water quality criterion. Creating an artificial inlet with a width of 1 km in the western part of the bay would result in a threefold increase in the environmental capacity of the study area.

  2. Equivalence of multibreed animal models and hierarchical Bayes analysis for maternally influenced traits

    PubMed Central

    2010-01-01

    Background It has been argued that multibreed animal models should include a heterogeneous covariance structure. However, the estimation of the (co)variance components is not an easy task, because these parameters can not be factored out from the inverse of the additive genetic covariance matrix. An alternative model, based on the decomposition of the genetic covariance matrix by source of variability, provides a much simpler formulation. In this study, we formalize the equivalence between this alternative model and the one derived from the quantitative genetic theory. Further, we extend the model to include maternal effects and, in order to estimate the (co)variance components, we describe a hierarchical Bayes implementation. Finally, we implement the model to weaning weight data from an Angus × Hereford crossbred experiment. Methods Our argument is based on redefining the vectors of breeding values by breed origin such that they do not include individuals with null contributions. Next, we define matrices that retrieve the null-row and the null-column pattern and, by means of appropriate algebraic operations, we demonstrate the equivalence. The extension to include maternal effects and the estimation of the (co)variance components through the hierarchical Bayes analysis are then straightforward. A FORTRAN 90 Gibbs sampler was specifically programmed and executed to estimate the (co)variance components of the Angus × Hereford population. Results In general, genetic (co)variance components showed marginal posterior densities with a high degree of symmetry, except for the segregation components. Angus and Hereford breeds contributed with 50.26% and 41.73% of the total direct additive variance, and with 23.59% and 59.65% of the total maternal additive variance. In turn, the contribution of the segregation variance was not significant in either case, which suggests that the allelic frequencies in the two parental breeds were similar. Conclusion The multibreed

  3. Role of wetlands in attenuation of storm surges using coastal circulation model (ADCIRC), Chesapeake Bay region

    NASA Astrophysics Data System (ADS)

    Deb, Mithun; Ferreira, Celso; Lawler, Seth

    2014-05-01

    The Chesapeake Bay, Virginia is subject to storm surge from extreme weather events nearly year-round; from tropical storms and hurricanes during the summer and fall, (e.g., hurricanes Isabel [2003] and Sandy [2012]), and from nor'easters during the winter (e.g., winter storms Nemo and Saturn [2013]). Coastal wetlands can deliver acute fortification against incoming hurricane storm surges. Coastal wetlands and vegetation shape the hydrodynamics of storm surge events by retaining water and slowing the propagation of storm surge, acting as a natural barrier to flooding. Consequently, a precise scheme to quantify the effect of wetlands on coastal surge levels was also prerequisite. Two wetland sites were chosen in the Chesapeake Bay region for detailed cataloging of vegetation characteristics, including: height, stem diameter, and density. A framework was developed combining these wetlands characterizations with numerical simulations. Storms surges were calculated using Coastal circulation model (ADCIRC) coupled to a wave model (SWAN) forced by an asymmetric hurricane vortex model using an unstructured mesh (comprised of 1.8 million nodes) under a High Performance Computing environment. The Hurricane Boundary Layer (HBL) model was used to compute wind and pressure fields for historical tropical storms and for all of the synthetic storms. Wetlands were characterized in the coupled numerical models by bathymetric and frictional resistance. Multiple model simulations were performed using historical hurricane data and hypothetical storms to compare the predicted storm surge inundation resulting from various levels of wetlands expansion or reduction. The results of these simulations demonstrate the efficacy of wetlands in storm surge attenuation and also the outcome will scientifically support planning of wetlands restoration projects with multi-objective benefits for society.

  4. Three-dimensional eutrophication model of Chesapeake Bay. Volume 1: Main report. Final report

    SciTech Connect

    Cerco, C.F.; Cole, T.M.

    1994-05-01

    A three-dimensional, time-variable, eutrophication model, CE-QUAL-ICM, was applied to Chesapeake Bay. The model incorporated 22 state variables that included physical properties, multiple forms of algae, carbon, nitrogen, phosphorus, and silica, and dissolved oxygen. The model was part of a larger package that included a three-dimensional hydrodynamic model and a benthic sediment diagenesis model. The model was initially applied to a 3-year period, 1984-1986. The model successfully simulated water-column and sediment processes that affected water quality. Phenomena simulated include formation of the spring algal bloom subsequent to the annual peak in nutrient runoff, onset and breakup of summer anoxia, and coupling of organic particle deposition with sediment-water nutrient and oxygen fluxes. The model was next applied in a 30-year simulation of water quality, 1959-1988. The model indicated longterm trends in water quality and affirmed the role of stratification in determining anoxia. Final application of the model was in a series of nutrient load-reduction sensitivity analyses. The study demonstrated that complex eutrophication problems can be addressed with coupled three-dimensional hydrodynamic and water quality models.

  5. Ecological niche modeling of sympatric krill predators around Marguerite Bay, Western Antarctic Peninsula

    NASA Astrophysics Data System (ADS)

    Friedlaender, Ari S.; Johnston, David W.; Fraser, William R.; Burns, Jennifer; Halpin, Patrick N.; Costa, Daniel P.

    2011-07-01

    Adélie penguins ( Pygoscelis adeliae), carabeater seals ( Lobodon carcinophagus), humpback ( Megaptera novaeangliae), and minke whales ( Balaenoptera bonaernsis) are found in the waters surrounding the Western Antarctic Peninsula. Each species relies primarily on Antarctic krill ( Euphausia superba) and has physiological constraints and foraging behaviors that dictate their ecological niches. Understanding the degree of ecological overlap between sympatric krill predators is critical to understanding and predicting the impacts on climate-driven changes to the Antarctic marine ecosystem. To explore ecological relationships amongst sympatric krill predators, we developed ecological niche models using a maximum entropy modeling approach (Maxent) that allows the integration of data collected by a variety of means (e.g. satellite-based locations and visual observations). We created spatially explicit probability distributions for the four krill predators in fall 2001 and 2002 in conjunction with a suite of environmental variables. We find areas within Marguerite Bay with high krill predator occurrence rates or biological hot spots. We find the modeled ecological niches for Adélie penguins and crabeater seals may be affected by their physiological needs to haul-out on substrate. Thus, their distributions may be less dictated by proximity to prey and more so by physical features that over time provide adequate access to prey. Humpback and minke whales, being fully marine and having greater energetic demands, occupy ecological niches more directly proximate to prey. We also find evidence to suggest that the amount of overlap between modeled niches is relatively low, even for species with similar energetic requirements. In a rapidly changing and variable environment, our modeling work shows little indication that krill predators maintain similar ecological niches across years around Marguerite Bay. Given the amount of variability in the marine environment around the

  6. A comparative study on entrepreneurial attitudes modeled with logistic regression and Bayes nets.

    PubMed

    López Puga, Jorge; García García, Juan

    2012-11-01

    Entrepreneurship research is receiving increasing attention in our context, as entrepreneurs are key social agents involved in economic development. We compare the success of the dichotomic logistic regression model and the Bayes simple classifier to predict entrepreneurship, after manipulating the percentage of missing data and the level of categorization in predictors. A sample of undergraduate university students (N = 1230) completed five scales (motivation, attitude towards business creation, obstacles, deficiencies, and training needs) and we found that each of them predicted different aspects of the tendency to business creation. Additionally, our results show that the receiver operating characteristic (ROC) curve is affected by the rate of missing data in both techniques, but logistic regression seems to be more vulnerable when faced with missing data, whereas Bayes nets underperform slightly when categorization has been manipulated. Our study sheds light on the potential entrepreneur profile and we propose to use Bayesian networks as an additional alternative to overcome the weaknesses of logistic regression when missing data are present in applied research.

  7. Identification of spatiotemporal nutrient patterns in a coastal bay via an integrated k-means clustering and gravity model.

    PubMed

    Chang, Ni-Bin; Wimberly, Brent; Xuan, Zhemin

    2012-03-01

    This study presents an integrated k-means clustering and gravity model (IKCGM) for investigating the spatiotemporal patterns of nutrient and associated dissolved oxygen levels in Tampa Bay, Florida. By using a k-means clustering analysis to first partition the nutrient data into a user-specified number of subsets, it is possible to discover the spatiotemporal patterns of nutrient distribution in the bay and capture the inherent linkages of hydrodynamic and biogeochemical features. Such patterns may then be combined with a gravity model to link the nutrient source contribution from each coastal watershed to the generated clusters in the bay to aid in the source proportion analysis for environmental management. The clustering analysis was carried out based on 1 year (2008) water quality data composed of 55 sample stations throughout Tampa Bay collected by the Environmental Protection Commission of Hillsborough County. In addition, hydrological and river water quality data of the same year were acquired from the United States Geological Survey's National Water Information System to support the gravity modeling analysis. The results show that the k-means model with 8 clusters is the optimal choice, in which cluster 2 at Lower Tampa Bay had the minimum values of total nitrogen (TN) concentrations, chlorophyll a (Chl-a) concentrations, and ocean color values in every season as well as the minimum concentration of total phosphorus (TP) in three consecutive seasons in 2008. The datasets indicate that Lower Tampa Bay is an area with limited nutrient input throughout the year. Cluster 5, located in Middle Tampa Bay, displayed elevated TN concentrations, ocean color values, and Chl-a concentrations, suggesting that high values of colored dissolved organic matter are linked with some nutrient sources. The data presented by the gravity modeling analysis indicate that the Alafia River Basin is the major contributor of nutrients in terms of both TP and TN values in all seasons

  8. Modeling selenium bioaccumulation through arthropod food webs in San Francisco Bay, California, USA

    USGS Publications Warehouse

    Schlekat, C.E.; Purkerson, D.G.; Luoma, S.N.

    2004-01-01

    Trophic transfer is the main process by which upper trophic level wildlife are exposed to selenium. Transfers through lower levels of a predator's food web thus can be instrumental in determining the threat of selenium in an ecosystem. Little is known about Se transfer through pelagic, zooplankton-based food webs in San Francisco Bay ([SFB], CA, USA), which serve as an energy source for important predators such as striped bass. A dynamic multipathway bioaccumulation model was used to model Se transfer from phytoplankton to pelagic copepods to carnivorous mysids (Neomysis mercedis). Uptake rates of dissolved Se, depuration rates, and assimilation efficiencies (AE) for the model were determined for copepods and mysids in the laboratory. Small (73-250 ??m) and large (250-500 ??m) herbivorous zooplankton collected from SFB (Oithona/Limnoithona and Acartia sp.) assimilated Se with similar efficiencies (41-52%) from phytoplankton. Mysids assimilated 73% of Se from small herbivorous zooplankton; Se AE was significantly lower (61%) than larger herbivorous zooplankton. Selenium depuration rates were high for both zooplankton and mysids (12-25% d-1), especially compared to bivalves (2-3% d-1). The model predicted steady state Se concentrations in mysids similar to those observed in the field. The predicted concentration range (1.5-5.4 ??g g -1) was lower than concentrations of 4.5 to 24 ??g g-1 observed in bivalves from the bay. Differences in efflux between mysids and bivalves were the best explanation for the differences in uptake. The results suggest that the risk of selenium toxicity to predators feeding on N. mercedis would be less than the risk to predators feeding on bivalves. Management of selenium contamination should include food webs analyses to focus on the most important exposure pathways identified for a given watershed.

  9. Shuttle measured contaminant environment and modeling for payloads. Preliminary assessment of the space telescope environment in the shuttle bay

    NASA Technical Reports Server (NTRS)

    Scialdone, J. J.

    1983-01-01

    A baseline gaseous and particulate environment of the Shuttle bay was developed based on the various measurements which were made during the first four flights of the Shuttle. The environment is described by the time dependent pressure, density, scattered molecular fluxes, the column densities and including the transient effects of water dumps, engine firings and opening and closing of the bay doors. The particulate conditions in the ambient and on surfaces were predicted as a function of the mission time based on the available data. This basic Shuttle environment when combined with the outgassing and the particulate contributions of the payloads, can provide a description of the environment of a payload in the Shuttle bay. As an example of this application, the environment of the Space Telescope in the bay, which may be representative of the environment of several payloads, was derived. Among the many findings obtained in the process of modeling the environment, one is that the payloads environment in the bay is not substantially different or more objectionable than the self-generated environment of a large payload or spacecraft. It is, however, more severe during ground facilities operations, the first 15 to 20 hours of the flight, during and for a short period after ater was dumped overboard, and the reaction control engines are being fired.

  10. 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.

  11. User's guide for SAMMY: a computer model for multilevel r-matrix fits to neutron data using Bayes' equations

    SciTech Connect

    Larson, N. M.; Perey, F. G.

    1980-11-01

    A method is described for determining the parameters of a model from experimental data based upon the utilization of Bayes' theorem. This method has several advantages over the least-squares method as it is commonly used; one important advantage is that the assumptions under which the parameter values have been determined are more clearly evident than in many results based upon least squares. Bayes' method has been used to develop a computer code which can be utilized to analyze neutron cross-section data by means of the R-matrix theory. The required formulae from the R-matrix theory are presented, and the computer implementation of both Bayes' equations and R-matrix theory is described. Details about the computer code and compelte input/output information are given.

  12. Delta de l'Ebre is a natural bay model for Marteilia spp. (Paramyxea) dynamics and life-cycle studies.

    PubMed

    Carrasco, N; Arzul, I; Berthe, F C J; Fernández-Tejedor, M; Durfort, M; Furones, M D

    2008-03-03

    Marteilia spp. are paramyxean parasites that affect several bivalve species of economic interest, such as Ostrea edulis and Mytilus galloprovincialis. Certain aspects of Marteilia spp., such as their life cycle and host affinity and infection dynamics, still remain unknown. The 'Delta de l'Ebre' constitutes a natural model for the study of the life cycle of the parasite Marteilia, since uninfected mussels and flat oysters immersed in the bays can become infected. This, along with the geographical and ecological characteristics of the bays, make it a very interesting location to study the Marteilia life cycle. Preliminary results concerning marteiliosis, mainly in mussels, such as prevalence dynamics, infectious periods, host affinity and host intermediate candidates are reported in the present paper. This information will be required for further, more exhaustive, studies in the bays of the Ebre delta.

  13. Tidal simulation of a bay with a very large floating structure using a multi-level model

    SciTech Connect

    Hu, C.H.; Kyozuka, Y.

    1996-12-31

    Accurate tidal flow simulation is necessary for environmental assessment of a large-scale ocean development in a bay, because the flow plays an important role in mass-transport and other physical phenomena. In this paper the authors present a method to simulate tidal flows of a bay with a very large floating structure using a multi-level model. Pressure under the pontoon-type floating structure is obtained by solving the Poisson equation. Effects of vertical displacement of the pontoon due to tidal force are considered in the tidal simulation. Tidal currents, residual currents and wind driven currents in a bay with/without the structure are presented graphically and discussed.

  14. Modeling and forecasting the distribution of Vibrio vulnificus in Chesapeake Bay

    SciTech Connect

    Jacobs, John M.; Rhodes, M.; Brown, C. W.; Hood, Raleigh R.; Leight, A.; Long, Wen; Wood, R.

    2014-11-01

    The aim is to construct statistical models to predict the presence, abundance and potential virulence of Vibrio vulnificus in surface waters. A variety of statistical techniques were used in concert to identify water quality parameters associated with V. vulnificus presence, abundance and virulence markers in the interest of developing strong predictive models for use in regional oceanographic modeling systems. A suite of models are provided to represent the best model fit and alternatives using environmental variables that allow them to be put to immediate use in current ecological forecasting efforts. Conclusions: Environmental parameters such as temperature, salinity and turbidity are capable of accurately predicting abundance and distribution of V. vulnificus in Chesapeake Bay. Forcing these empirical models with output from ocean modeling systems allows for spatially explicit forecasts for up to 48 h in the future. This study uses one of the largest data sets compiled to model Vibrio in an estuary, enhances our understanding of environmental correlates with abundance, distribution and presence of potentially virulent strains and offers a method to forecast these pathogens that may be replicated in other regions.

  15. The East Bay Center for the Performing Arts: A Model for Community-Based Multicultural Arts Education

    ERIC Educational Resources Information Center

    Engdahl, Eric

    2012-01-01

    This article highlights the East Bay Center for the Performing Arts in Richmond, California, which is one successful model of a community-based arts education organization whose central mission is to provide these deep art-rich experiences for students from low socio-economic status (SES) communities, who in this instance are predominately African…

  16. Modeling the Role of Zebra Mussels in the Proliferation of Blue-green Algae in Saginaw Bay, Lake Huron

    EPA Science Inventory

    Under model assumptions from Saginaw Bay 1991, selective rejection of blue-green algae by zebra mussels appears to be a necessary factor in the enhancement of blue-green algae production in the presence of zebra mussels. Enhancement also appears to depend on the increased sedime...

  17. Application of spatially referenced regression modeling for the evaluation of total nitrogen loading in the Chesapeake Bay watershed

    USGS Publications Warehouse

    Preston, Stephen D.; Brakebill, John W.

    1999-01-01

    The reduction of stream nutrient loads is an important part of current efforts to improve water quality in the Chesapeake Bay. To design programs that will effectively reduce stream nutrient loading, resource managers need spatially detailed information that describes the location of nutrient sources and the watershed factors that affect delivery of nutrients to the Bay. To address this need, the U.S. Geological Survey has developed a set of spatially referenced regression models for the evaluation of nutrient loading in the watershed. The technique applied for this purpose is referred to as ?SPARROW? (SPAtially Referenced Regressions On Watershed attributes), which is a statistical modeling approach that retains spatial referencing for illustrating predictions, and for relating upstream nutrient sources to downstream nutrient loads. SPARROW is based on a digital stream-network data set that is composed of stream segments (reaches) that are attributed with traveltime and connectivity information. Drainage-basin boundaries are defined for each stream reach in the network data set through the use of a digital elevation model. For the Chesapeake Bay watershed, the spatial network was developed using the U.S. Environmental Protection Agency?s River Reach File 1 digital stream network, and is composed of 1,408 stream reaches and watershed segments. To develop a SPARROW model for total nitrogen in the Chesapeake Bay watershed, data sets for sources and basin characteristics were incorporated into the spatial network and related to stream-loading information by using a nonlinear regression model approach. Total nitrogen source variables that were statistically significant in the model include point sources, urban area, fertilizer application, manure generation and atmospheric deposition. Total nitrogen loss variables that were significant in the model include soil permeability and instream-loss rates for four stream-reach classes. Applications of SPARROW for evaluating

  18. A parametric multiclass Bayes error estimator for the multispectral scanner spatial model performance evaluation

    NASA Technical Reports Server (NTRS)

    Mobasseri, B. G.; Mcgillem, C. D.; Anuta, P. E. (Principal Investigator)

    1978-01-01

    The author has identified the following significant results. The probability of correct classification of various populations in data was defined as the primary performance index. The multispectral data being of multiclass nature as well, required a Bayes error estimation procedure that was dependent on a set of class statistics alone. The classification error was expressed in terms of an N dimensional integral, where N was the dimensionality of the feature space. The multispectral scanner spatial model was represented by a linear shift, invariant multiple, port system where the N spectral bands comprised the input processes. The scanner characteristic function, the relationship governing the transformation of the input spatial, and hence, spectral correlation matrices through the systems, was developed.

  19. Use of salinity mixing models to estimate the contribution of creek water fecal indicator bacteria to an estuarine environment: Newport Bay, California.

    PubMed

    McLaughlin, Karen; Ahn, Jong Ho; Litton, Rachel M; Grant, Stanley B

    2007-08-01

    The contribution of freshwater discharge to fecal indicator bacteria (FIB) impairment of an estuarine environment can be approximated from simple, two end-member mixing models using salinity as a tracer. We conducted a yearlong time series investigation of Newport Bay, a regionally important estuarine embayment in southern California, assessing the concentrations of FIB, specifically Escherichia coli and enterococci bacteria, and salinity. In total, eight within-bay stations and one offshore control site were sampled nearly once per week and the three tributaries draining into Newport Bay were sampled approximately daily. Using salinity as a conservative tracer for water mass mixing and determining the end-member values of FIB in both the creek sites and the offshore site, we created a linear, two end-member mixing model of FIB within Newport Bay. Deviations from the mixing model suggest either an additional source of FIB to the bay (e.g. bird feces, storm drain discharge) or regrowth and/or die-off of FIB within the bay. Our results indicate that salinity mixing models can be useful in predicting changes in FIB concentrations in the estuarine environments and can help narrow the search for sources of FIB to the bay and enhance our understanding of the fate of FIB within the bay.

  20. Development of a seamless multisource topographic/bathymetric elevation model of Tampa Bay

    USGS Publications Warehouse

    Gesch, D.; Wilson, R.

    2001-01-01

    Many applications of geospatial data in coastal environments require knowledge of the nearshore topography and bathymetry. However, because existing topographic and bathymetric data have been collected independently for different purposes, it has been difficult to use them together at the land/water interface owing to differences in format, projection, resolution, accuracy, and datums. As a first step toward solving the problems of integrating diverse coastal datasets, the U.S. Geological Survey (USGS) and the National Oceanic and Atmospheric Administration (NOAA) are collaborating on a joint demonstration project to merge their data for the Tampa Bay region of Florida. The best available topographic and bathymetric data were extracted from the USGS National Elevation Dataset and the NOAA hydrographic survey database, respectively. Before being merged, the topographic and bathymetric datasets were processed with standard geographic information system tools to place them in a common horizontal reference frame. Also, a key part of the preprocessing was transformation to a common vertical reference through the use of VDatum, a new tool created by NOAA's National Geodetic Survey for vertical datum conversions. The final merged product is a seamless topographic/bathymetric model covering the Tampa Bay region at a grid spacing of 1 arc-second. Topographic LIDAR data were processed and merged with the bathymetry to demonstrate the incorporation of recent third party data sources for several test areas. A primary application of a merged topographic/bathymetric elevation model is for user-defined shoreline delineation, in which the user decides on the tidal condition (for example, low or high water) to be superimposed on the elevation data to determine the spatial position of the water line. Such a use of merged topographic/bathymetric data could lead to the development of a shoreline zone, which could reduce redundant mapping efforts by federal, state, and local agencies

  1. A hydrologic network supporting spatially referenced regression modeling in the Chesapeake Bay watershed

    USGS Publications Warehouse

    Brakebill, J.W.; Preston, S.D.

    2003-01-01

    The U.S. Geological Survey has developed a methodology for statistically relating nutrient sources and land-surface characteristics to nutrient loads of streams. The methodology is referred to as SPAtially Referenced Regressions On Watershed attributes (SPARROW), and relates measured stream nutrient loads to nutrient sources using nonlinear statistical regression models. A spatially detailed digital hydrologic network of stream reaches, stream-reach characteristics such as mean streamflow, water velocity, reach length, and travel time, and their associated watersheds supports the regression models. This network serves as the primary framework for spatially referencing potential nutrient source information such as atmospheric deposition, septic systems, point-sources, land use, land cover, and agricultural sources and land-surface characteristics such as land use, land cover, average-annual precipitation and temperature, slope, and soil permeability. In the Chesapeake Bay watershed that covers parts of Delaware, Maryland, Pennsylvania, New York, Virginia, West Virginia, and Washington D.C., SPARROW was used to generate models estimating loads of total nitrogen and total phosphorus representing 1987 and 1992 land-surface conditions. The 1987 models used a hydrologic network derived from an enhanced version of the U.S. Environmental Protection Agency's digital River Reach File, and course resolution Digital Elevation Models (DEMs). A new hydrologic network was created to support the 1992 models by generating stream reaches representing surface-water pathways defined by flow direction and flow accumulation algorithms from higher resolution DEMs. On a reach-by-reach basis, stream reach characteristics essential to the modeling were transferred to the newly generated pathways or reaches from the enhanced River Reach File used to support the 1987 models. To complete the new network, watersheds for each reach were generated using the direction of surface-water flow derived

  2. Extreme Crustal Thinning in a Transtensional Setting (Bay of Biscay - Western Pyrenees): from Observations to Modelling

    NASA Astrophysics Data System (ADS)

    Jammes, S.; Manatschal, G.; Lavier, L.; Tiberi, C.

    2008-12-01

    What are the processes controlling extreme crustal thinning observed in front of a propagating ocean? Young V-shaped basins such as the Gulf of California, the Woodlark basin, the Red Sea, or the ancient Bay of Biscay-Western Pyrenees are natural laboratories where such processes can be studied. In the case of the Bay of Biscay, previous studies suggested late Cretaceous rifting associated with at least 400 km of left lateral movements between Iberia and Europe. However using the latest plate reconstructions from the Iberian/Newfoundland margins, we propose that oblique rifting initiated in latest Jurassic-Early Cretaceous time and predated the anticlockwise rotation of Iberia during Late Aptian to Early Albian time. This reinterpretation of the kinematics has major implications for the formation of the Parentis and Mauléon basins located at the termination of the Bay of Biscay, both presenting evidence for extreme crustal thinning. In this study we develop a model for the evolution of the Bay of Biscay based on seismic and field evidence for extreme thinning and exhumation of the crust and mantle. In the Parentis basin, geophysical surveys (reflection, refraction and gravity) and well data show evidence for extreme crustal thinning, an important asymmetry of the basin and only little evidence for normal faulting. A major E-W trending fault, named the Ibis fault, separates a sag basin to the north from a more complex basin geometry that is strongly affected by salt tectonics to the south. The Mauléon basin, in contrast, is exposed onshore in the western Pyrenees and affected by a mild reactivation during the Pyrenean compression. Our field investigations show that the base of this basin was formed by mantle peridotites and lower crustal rocks that were exhumed, reworked and overlain either by extensional allochthons, today preserved in "chaînons Béarnais", or upper Aptian to Albian sediments. Structures that document the exhumation are exposed in the Labourd

  3. Development and adoption of a simple nonpoint source pollution model for Port Phillip Bay, Australia.

    PubMed

    Argent, Robert M; Mitchell, V Grace

    2003-09-01

    New computing tools and approaches allow tailored development of software to meet the needs of environmental managers. The processes required for such tailoring fit well with adaptive management concepts where, as knowledge and system understanding develop among managers, the software can be developed or replaced to match. This paper reports on development and adoption of a simple nonpoint source pollution modeling tool, including technical aspects of data support for modeling and social aspects of software design. The software, named FILTER, used a unit load model to generate expected pollutant loads from subcatchments of Port Phillip Bay, Australia. Monitoring data were used for calibration to modify the delivery of generated pollutants to receiving waters. Spatial, tabular, and charting software components were used to provide alternative forms of output visualization. FILTER was developed using a process that resulted in manager-stakeholders taking responsibility for setting of model parameter values and operation of the user interface, thereby encouraging uptake. The inclusive development process, tailoring of the software to manager needs and styles of usage, and matching of model complexity to data and knowledge, resulted in a successful application that has become the current agreed system representation among disparate stakeholder organizations.

  4. Modeling hydrodynamics, water quality, and benthic processes to predict ecological effects in Narragansett Bay

    EPA Science Inventory

    The environmental fluid dynamics code (EFDC) was used to study the three dimensional (3D) circulation, water quality, and ecology in Narragansett Bay, RI. Predictions of the Bay hydrodynamics included the behavior of the water surface elevation, currents, salinity, and temperatur...

  5. Periodic Matrix Model to Evaluate Management Strategies for Bay Scallop (Argopectin iraddians) Populations

    EPA Science Inventory

    Within the last twenty years total harvests of bay scallops (Argopecten irradians) have dwindled in the southern New England Region, and one of the reasons often cited for this decline is drastic changes to their habitat, specifically eelgrass. To counteract these declines, bay ...

  6. Model for the incorporation of plant detritus within clastic accumulating interdistributary bays

    SciTech Connect

    Gastaldo, R.A.; McCarroll, S.M.; Douglass, D.P.

    1985-01-01

    Plant-bearing clastic lithologies interpreted as interdistributary bay deposits are reported from rocks Devonian to Holocene in age. Often, these strata preserve accumulations of discrete, laterally continuous leaf beds or coaly horizons. Investigations within two modern inter-distributary bays in the lower delta plain of the Mobile Delta, Alabama have provided insight into the phytotaphonomic processes responsible for the generation of carbonaceous lithologies, coaly horizons and laterally continuous leaf beds. Delvan and Chacalooche Bays lie adjacent to the Tensaw River distributary channel and differ in the mode of clastic and plant detrital accumulation. Delvan Bay, lying west of the distributary channel, is accumulating detritus solely by overbank deposition. Chacaloochee Bay, lying east of the channel, presently is accumulating detritus by active crevasse-splay activity. Plant detritus is accumulating as transported assemblages in both bays, but the mode of preservation differs. In Delvan Bay, the organic component is highly degraded and incorporated within the clastic component resulting in a carbonaceous silt. Little identifiable plant detritus can be recovered. On the other hand, the organic component in Chacaloochee Bay is accumulating in locally restricted allochthonous peat deposits up to 2 m in thickness, and discrete leaf beds generated by flooding events. In addition, autochthonous plant accumulations occur on subaerially and aerially exposed portions of the crevasse. The resultant distribution of plant remains is a complicated array of transported and non-transported organics.

  7. Modeling Diel Oxygen Dynamics and Ecosystem Metabolism in Weeks Bay, Alabama.

    EPA Science Inventory

    Weeks Bay is a shallow eutrophic estuary that exhibits frequent summertime diel-cycling hypoxia and periods of dissolved oxygen (DO) oversaturation during the day. Diel DO dynamics in shallow estuaries like Weeks Bay are complex, and may be influenced by wind forcing, vertical an...

  8. ECOSYSTEM MODELING IN COBSCOOK BAY, MAINE:A SUMMARY, PERSPECTIVE, AND LOOK FORWARD

    EPA Science Inventory

    In the mid-1990s, an interdisciplinary, multi-institutional team of scientists was assembled to address basic issues concerning biological productivity and the unique co-occurrence of many unusual ecological features in Cobscook Bay, Maine. Cobscook Bay is a geologically complex,...

  9. Linking structural equation modeling with Bayesian network and its application to coastal phytoplankton dynamics in the Bohai Bay

    NASA Astrophysics Data System (ADS)

    Xu, Xiao-fu; Sun, Jian; Nie, Hong-tao; Yuan, De-kui; Tao, Jian-hua

    2016-10-01

    Bayesian networks (BN) have many advantages over other methods in ecological modeling, and have become an increasingly popular modeling 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 modeling (SEM). In this method, SEM is used to improve the model structure for BN. This method was used to simulate coastal phytoplankton dynamics in the 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 the 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, although the Redfield ratio indicates that phosphorus should be the primary nutrient limiting factor, our results show that silicate plays the most important role in regulating phytoplankton dynamics in the Bohai Bay.

  10. Horseshoe crab spawning activity in Delaware Bay, USA, after harvest reduction: A mixed-model analysis

    USGS Publications Warehouse

    Smith, David; Robinson, Timothy J.

    2015-01-01

    A Delaware Bay, USA, standardized survey of spawning horseshoe crabs, Limulus polyphemus, was carried out in 1999 − 2013 through a citizen science network. Previous trend analyses of the data were at the state (DE or NJ) or bay-wide levels. Here, an alternative mixed-model regression analysis was used to estimate trends in female and male spawning densities at the beach level (n = 26) with the objective of inferring their causes. For females, there was no overall trend and no single explanation applies to the temporal and spatial patterns in their densities. Individual beaches that initially had higher densities tended to experience a decrease, while beaches that initially had lower densities tended to experience an increase. As a result, densities of spawning females at the end of the study period were relatively similar among beaches, suggesting a redistribution of females among the beaches over the study period. For males, there was a positive overall trend in spawning abundance from 1999 to 2013, and this increase occurred broadly among beaches. Moreover, the beaches with below-average initial male density tended to have the greatest increases. Possible explanations for these patterns include harvest reduction, sampling artifact, habitat change, density-dependent habitat selection, or mate selection. The broad and significant increase in male spawning density, which occurred after enactment of harvest controls, is consistent with the harvest reduction explanation, but there is no single explanation for the temporal or spatial pattern in female densities. These results highlight the continued value of a citizen-science-based spawning survey in understanding horseshoe crab ecology and conservation.

  11. Analyses of phosphorus and nitrogen cyclings in the estuarine ecosystem of Hiroshima Bay by a pelagic and benthic coupled model

    NASA Astrophysics Data System (ADS)

    Kittiwanich, J.; Yamamoto, T.; Kawaguchi, O.; Hashimoto, T.

    2007-10-01

    A pelagic and benthic coupled model expressing both phosphorus and nitrogen cyclings in the ecosystem of Hiroshima Bay, Japan was developed to investigate the fate and transportation of these elements and their annual budgets. The Bay was divided into eight (8) boxes, wherein two (2) areas ran horizontally and four (4) layers vertically. The model consists of equations representing all the concerned physical and biological processes. The results revealed that internal regeneration of materials is an important source of bio-available nutrients for phytoplankton growth. The study indicated that Hiroshima Bay's sediment functions as source of dissolved phosphorus and nitrogen for phytoplankton in the pelagic system, which is supported by calculated results indicating that the releasing rates of dissolved phosphorus and nitrogen from the sediment exceeded 100% of TP and TN loadings in the southern area. As for the northern area which is known to have significant loading via the river, the releasing rates were found to be up to 56% of TP and TN loadings. With regards to the denitrification process, the results revealed that 48% and 37% of NO 3- produced by nitrification was denitrified in the northern and southern areas, respectively. More than 10% of the total nitrogen loaded to the northern area of Hiroshima Bay was estimated to be denitrified. A similar trend was also found in the southern area where the figure was more than 14%. Such findings suggested that the process taking place in the sediment is an important natural purification mechanism that helps remove nitrogen from land. Whereas, almost all phosphorus in the sediment is remineralized, it subsequently goes back to the pelagic system and is repeatedly utilized for the growth of phytoplankton. The model used, therefore, provides a basis and tool to describe the dynamics of phosphorus and nitrogen cyclings in Hiroshima Bay.

  12. A Bayes network approach to uncertainty quantification in hierarchically developed computational models

    SciTech Connect

    Urbina, Angel; Mahadevan, Sankaran; Paez, Thomas L.

    2012-03-01

    Here, performance assessment of complex systems is ideally accomplished through system-level testing, but because they are expensive, such tests are seldom performed. On the other hand, for economic reasons, data from tests on individual components that are parts of complex systems are more readily available. The lack of system-level data leads to a need to build computational models of systems and use them for performance prediction in lieu of experiments. Because their complexity, models are sometimes built in a hierarchical manner, starting with simple components, progressing to collections of components, and finally, to the full system. Quantification of uncertainty in the predicted response of a system model is required in order to establish confidence in the representation of actual system behavior. This paper proposes a framework for the complex, but very practical problem of quantification of uncertainty in system-level model predictions. It is based on Bayes networks and uses the available data at multiple levels of complexity (i.e., components, subsystem, etc.). Because epistemic sources of uncertainty were shown to be secondary, in this application, aleatoric only uncertainty is included in the present uncertainty quantification. An example showing application of the techniques to uncertainty quantification of measures of response of a real, complex aerospace system is included.

  13. A Bayes network approach to uncertainty quantification in hierarchically developed computational models

    DOE PAGES

    Urbina, Angel; Mahadevan, Sankaran; Paez, Thomas L.

    2012-03-01

    Here, performance assessment of complex systems is ideally accomplished through system-level testing, but because they are expensive, such tests are seldom performed. On the other hand, for economic reasons, data from tests on individual components that are parts of complex systems are more readily available. The lack of system-level data leads to a need to build computational models of systems and use them for performance prediction in lieu of experiments. Because their complexity, models are sometimes built in a hierarchical manner, starting with simple components, progressing to collections of components, and finally, to the full system. Quantification of uncertainty inmore » the predicted response of a system model is required in order to establish confidence in the representation of actual system behavior. This paper proposes a framework for the complex, but very practical problem of quantification of uncertainty in system-level model predictions. It is based on Bayes networks and uses the available data at multiple levels of complexity (i.e., components, subsystem, etc.). Because epistemic sources of uncertainty were shown to be secondary, in this application, aleatoric only uncertainty is included in the present uncertainty quantification. An example showing application of the techniques to uncertainty quantification of measures of response of a real, complex aerospace system is included.« less

  14. Estimation of regional hydrogeological properties for use in a hydrologic model of the Chesapeake Bay watershed

    NASA Astrophysics Data System (ADS)

    Seck, A.; Welty, C.

    2012-12-01

    Characterization of subsurface hydrogeologic properties in three dimensions and at large scales for use in groundwater flow models can remain a challenge owing to the lack of regional data sets and scatter in coverage, type, and format of existing small-scale data sets. This is the case for the Chesapeake Bay watershed, where numerous studies have been carried out to quantify groundwater processes at small scales but limited information is available on subsurface characteristics and groundwater fluxes at regional scales. One goal of this work is to synthesize disparate information on subsurface properties for the Chesapeake Bay watershed for use in a 3D integrated ParFlow model over an area of 400,000 km2 with a horizontal resolution of 1 km and a vertical resolution of 5 m. We combined different types of data at various scales to characterize hydrostratigraphy and hydrogeological properties. The conceptual hydrogeologic model of the study area is composed of two major regions. One region extends from the Valley and Ridge physiographic province south of New York to the Piedmont physiographic province in Maryland and Virginia. This region is generally characterized by fractured rock overlain by a mantle of regolith. Soil thickness and hydraulic conductivity values were obtained from the U.S. General Soil Map (STATSGO2). Saprolite thickness was evaluated using casing depth information from well completion reports from four state agencies. Geostatistical methods were used to generalize point data to the model extent and resolution. A three-dimensional hydraulic conductivity field for fractured bedrock was estimated using a published national map of permeability and depth- varying functions from literature. The Coastal Plain of Maryland, Virginia, Delaware and New Jersey constitutes the second region and is characterized by layered sediments. In this region, the geometry of 20 aquifers and confining units was constructed using interpolation of published contour maps of

  15. A 3D, cross-scale, baroclinic model with implicit vertical transport for the Upper Chesapeake Bay and its tributaries

    NASA Astrophysics Data System (ADS)

    Ye, Fei; Zhang, Yinglong J.; Friedrichs, Marjorie A. M.; Wang, Harry V.; Irby, Isaac D.; Shen, Jian; Wang, Zhengui

    2016-11-01

    We develop a new vertically implicit transport solver, based on two total variation diminishing (TVD) limiters in space and time, inside a 3D unstructured-grid model (SCHISM), and apply it to the Upper Chesapeake Bay (UCB), which has complex geometry and sharp pycnocline. We show that the model is able to accurately and efficiently capture the elevation, velocity, salinity and temperature in both the deep and shallow regions of UCB. Compared with all available CTD casts, the overall model skills have the mean absolute error of 1.08 PSU and 0.85 °C, and correlation coefficient of 0.97 and 0.99 for salinity and temperature respectively. More importantly, the new implicit solver better captures the density stratification, which has great implications on biogeochemistry in this estuarine system. The cross-scale capability of the model is demonstrated by extending the high-resolution grids into a tributary (Chester River) and its sub-tributary (Corsica River), with minimal impact on the model efficiency. The model is also able to capture complex 3D structures at the transition zone between the main bay and the tributary, including the three-layered circulation in Baltimore Harbor. As more and more attention is being paid to the productive shallows in the Chesapeake Bay and other estuaries, the model can serve as a very powerful management tool to understand the impact of both local and remote forcing functions.

  16. Examining features of enhanced phytoplankton biomass in the Bay of Bengal using a coupled physical-biological model

    NASA Astrophysics Data System (ADS)

    Gomes, Helga do Rosário; deRada, Sergio; Goes, Joaquim I.; Chai, Fei

    2016-07-01

    A coupled bio-physical ocean model is used to describe areas of enhanced phytoplankton biomass, seen in remotely sensed observations, in the otherwise oligotrophic environment of the Bay of Bengal. The model is based on the Naval Coastal Ocean Model (NCOM), which is one-way coupled to the 13-component Carbon, Silicate, and Nitrogen Ecosystem (CoSiNE) model and configured for the Indian Ocean. Model results are compared and evaluated against a set of in situ shipboard observations as well as ocean color data acquired from several remote sensing platforms. The model is shown to successfully simulate the seasonal cycle of phytoplankton, the markedly contrasting scenarios of phytoplankton distribution in the north versus the south Bay of Bengal, and the biological impact from the 1997/1998 Indian Ocean Dipole (IOD) event. The model simulation provides us with vertical cross sections of phytoplankton biomass from summer and winter blooms in the southwest of the bay, information not found in remotely sensed data. It also successfully reproduces the timing of the onset of the blooms and their spatial extent, thereby providing a measure of its potential for augmenting in situ and remotely sensed observations to improve understanding of the dynamics of primary producers and carbon cycling in one of the most poorly sampled regions of the world's oceans.

  17. Development of baseline water quality stormwater detention pond model for Chesapeake Bay catchments

    SciTech Connect

    Musico, W.J.; Yoon, J.

    1999-07-01

    An environmental impact assessment is required for every proposed development in the Commonwealth of Virginia to help identify areas of potential concerns. The purpose of the Chesapeake Bay Local Assistance Department (CBLAD), Guidance Calculation Procedures is to ensure that development of previously constructed areas do not further exacerbate current problems of stormwater-induced eutrophication and downstream flooding. The methodology is based on the post development conditions that will not generate greater peak flows and will result in a 10% overall reduction of total phosphorus. Currently, several well-known models can develop hydrographs and pollutographs that accurately model the real response of a given watershed to any given rainfall event. However, conventional method of achieving the desired peak flow reduction and pollutant removal is not a deterministic procedure, and is inherently a trail and error process. A method of quickly and accurately determining the required size of stormwater easements was developed to evaluate the effectiveness of alternative stormwater collection and treatment systems. In this method, predevelopment conditions were modeled first to estimate the peak flows and subsequent pollutants generation that can be used as a baseline for post development plan. Resulting stormwater easement estimates facilitate decision-making processes during the planning and development phase of a project. The design can be optimized for the minimum cost or the smallest-possible pond size required for peak flow reduction and detention time given the most basic data such as: inflow hydrograph and maximum allowable pond depth.

  18. Comparison of objective Bayes factors for variable selection in parametric regression models for survival analysis.

    PubMed

    Cabras, Stefano; Castellanos, Maria Eugenia; Perra, Silvia

    2014-11-20

    This paper considers the problem of selecting a set of regressors when the response variable is distributed according to a specified parametric model and observations are censored. Under a Bayesian perspective, the most widely used tools are Bayes factors (BFs), which are undefined when improper priors are used. In order to overcome this issue, fractional (FBF) and intrinsic (IBF) BFs have become common tools for model selection. Both depend on the size, Nt , of a minimal training sample (MTS), while the IBF also depends on the specific MTS used. In the case of regression with censored data, the definition of an MTS is problematic because only uncensored data allow to turn the improper prior into a proper posterior and also because full exploration of the space of the MTSs, which includes also censored observations, is needed to avoid bias in model selection. To address this concern, a sequential MTS was proposed, but it has the drawback of an increase of the number of possible MTSs as Nt becomes random. For this reason, we explore the behaviour of the FBF, contextualizing its definition to censored data. We show that these are consistent, providing also the corresponding fractional prior. Finally, a large simulation study and an application to real data are used to compare IBF, FBF and the well-known Bayesian information criterion.

  19. Integrated geostatistics for modeling fluid contacts and shales in Prudhoe Bay

    SciTech Connect

    Perez, G.; Chopra, A.K.; Severson, C.D.

    1997-12-01

    Geostatistics techniques are being used increasingly to model reservoir heterogeneity at a wide range of scales. A variety of techniques is now available with differing underlying assumptions, complexity, and applications. This paper introduces a novel method of geostatistics to model dynamic gas-oil contacts and shales in the Prudhoe Bay reservoir. The method integrates reservoir description and surveillance data within the same geostatistical framework. Surveillance logs and shale data are transformed to indicator variables. These variables are used to evaluate vertical and horizontal spatial correlation and cross-correlation of gas and shale at different times and to develop variogram models. Conditional simulation techniques are used to generate multiple three-dimensional (3D) descriptions of gas and shales that provide a measure of uncertainty. These techniques capture the complex 3D distribution of gas-oil contacts through time. The authors compare results of the geostatistical method with conventional techniques as well as with infill wells drilled after the study. Predicted gas-oil contacts and shale distributions are in close agreement with gas-oil contacts observed at infill wells.

  20. Investigation of Spatial Variation of Sea States Offshore of Humboldt Bay CA Using a Hindcast Model.

    SciTech Connect

    Dallman, Ann Renee; Neary, Vincent Sinclair

    2014-10-01

    Spatial variability of sea states is an important consideration when performing wave resource assessments and wave resource characterization studies for wave energy converter (WEC) test sites and commercial WEC deployments. This report examines the spatial variation of sea states offshore of Humboldt Bay, CA, using the wave model SWAN . The effect of depth and shoaling on bulk wave parameters is well resolved using the model SWAN with a 200 m grid. At this site, the degree of spatial variation of these bulk wave parameters, with shoaling generally perpendicular to the depth contours, is found to depend on the season. The variation in wave height , for example, was higher in the summer due to the wind and wave sheltering from the protruding land on the coastline north of the model domain. Ho wever, the spatial variation within an area of a potential Tier 1 WEC test site at 45 m depth and 1 square nautical mile is almost negligible; at most about 0.1 m in both winter and summer. The six wave characterization parameters recommended by the IEC 6 2600 - 101 TS were compared at several points along a line perpendicular to shore from the WEC test site . As expected, these parameters varied based on depth , but showed very similar seasonal trends.

  1. Informing Marine Spatial Planning (MSP) with numerical modelling: A case-study on shellfish aquaculture in Malpeque Bay (Eastern Canada).

    PubMed

    Filgueira, Ramón; Guyondet, Thomas; Bacher, Cédric; Comeau, Luc A

    2015-11-15

    A moratorium on further bivalve leasing was established in 1999-2000 in Prince Edward Island (Canada). Recently, a marine spatial planning process was initiated explore potential mussel culture expansion in Malpeque Bay. This study focuses on the effects of a projected expansion scenario on productivity of existing leases and available suspended food resources. The aim is to provide a robust scientific assessment using available datasets and three modelling approaches ranging in complexity: (1) a connectivity analysis among culture areas; (2) a scenario analysis of organic seston dynamics based on a simplified biogeochemical model; and (3) a scenario analysis of phytoplankton dynamics based on an ecosystem model. These complementary approaches suggest (1) new leases can affect existing culture both through direct connectivity and through bay-scale effects driven by the overall increase in mussel biomass, and (2) a net reduction of phytoplankton within the bounds of its natural variation in the area.

  2. The Preference for Symmetry in Flower-Naive and Not-so-Naive Bumblebees

    ERIC Educational Resources Information Center

    Plowright, C. M. S.; Evans, S. A.; Leung, J. Chew; Collin, C. A.

    2011-01-01

    Truly flower-naive bumblebees, with no prior rewarded experience for visits on any visual patterns outside the colony, were tested for their choice of bilaterally symmetric over asymmetric patterns in a radial-arm maze. No preference for symmetry was found. Prior training with rewarded black and white disks did, however, lead to a significant…

  3. Do the Naive Know Best? The Predictive Power of Naive Ratings of Couple Interactions

    ERIC Educational Resources Information Center

    Baucom, Katherine J. W.; Baucom, Brian R.; Christensen, Andrew

    2012-01-01

    We examined the utility of naive ratings of communication patterns and relationship quality in a large sample of distressed couples. Untrained raters assessed 10-min videotaped interactions from 134 distressed couples who participated in both problem-solving and social support discussions at each of 3 time points (pre-therapy, post-therapy, and…

  4. The use of computer models to predict temperature and smoke movement in high bay spaces

    NASA Astrophysics Data System (ADS)

    Notarianni, Kathy A.; Davis, William D.

    1993-12-01

    The Building and Fire Research Laboratory (BFRL) was given the opportunity to make measurements during fire calibration tests of the heat detection system in an aircraft hangar with a nominal 30.4 (100 ft) ceiling height near Dallas, TX. Fire gas temperatures resulting from an approximately 8250 kW isopropyl alcohol pool fire were measured above the fire and along the ceiling. The results of the experiments were then compared to predictions from the computer fire models DETACT-QS, FPETOOL, and LAVENT. In section A of the analysis conducted, DETACT-QS AND FPETOOL significantly underpredicted the gas temperature. LAVENT at the position below the ceiling corresponding to maximum temperature and velocity provided better agreement with the data. For large spaces, hot gas transport time and an improved fire plume dynamics model should be incorporated into the computer fire model activation routines. A computational fluid dynamics (CFD) model, HARWELL FLOW3D, was then used to model the hot gas movement in the space. Reasonable agreement was found between the temperatures predicted from the CFD calculations and the temperatures measured in the aircraft hangar. In section B, an existing NASA high bay space was modeled using the CFD model. The NASA space was a clean room, 27.4 m (90 ft) high with forced horizontal laminar flow. The purpose of this analysis is to determine how the existing fire detection devices would respond to various size fires in the space. The analysis was conducted for 32 MW, 400 kW, and 40 kW fires.

  5. Forward Bay Cover Separation Modeling and Testing for the Orion Multi-Purpose Crew Vehicle

    NASA Technical Reports Server (NTRS)

    Ali, Yasmin; Radke, Tara; Chuhta, Jesse; Hughes, Michael

    2014-01-01

    Spacecraft multi-body separation events during atmospheric descent require complex testing and analysis to validate the flight separation dynamics model and to verify no recontact. NASA Orion Multi-Purpose Crew Vehicle (MPCV) teams examined key model parameters and risk areas to develop a robust but affordable test campaign in order to validate and verify the Forward Bay Cover (FBC) separation event for Exploration Flight Test-1 (EFT-1). The FBC jettison simulation model is highly complex, consisting of dozens of parameters varied simultaneously, with numerous multi-parameter interactions (coupling and feedback) among the various model elements, and encompassing distinct near-field, mid-field, and far-field regimes. The test campaign was composed of component-level testing (for example gas-piston thrusters and parachute mortars), ground FBC jettison tests, and FBC jettison air-drop tests that were accomplished by a highly multi-disciplinary team. Three ground jettison tests isolated the testing of mechanisms and structures to anchor the simulation models excluding aerodynamic effects. Subsequently, two air-drop tests added aerodynamic and parachute parameters, and served as integrated system demonstrations, which had been preliminarily explored during the Orion Pad Abort-1 (PA-1) flight test in May 2010. Both ground and drop tests provided extensive data to validate analytical models and to verify the FBC jettison event for EFT-1, but more testing is required to support human certification, for which NASA and Lockheed Martin are applying knowledge from Apollo and EFT-1 testing and modeling to develop a robust but affordable human spacecraft capability.

  6. Forward Bay Cover Separation Modeling and Testing for the Orion Multi-Purpose Crew Vehicle

    NASA Technical Reports Server (NTRS)

    Ali, Yasmin; Chuhta, Jesse D.; Hughes, Michael P.; Radke, Tara S.

    2015-01-01

    Spacecraft multi-body separation events during atmospheric descent require complex testing and analysis to validate the flight separation dynamics models used to verify no re-contact. The NASA Orion Multi-Purpose Crew Vehicle (MPCV) architecture includes a highly-integrated Forward Bay Cover (FBC) jettison assembly design that combines parachutes and piston thrusters to separate the FBC from the Crew Module (CM) and avoid re-contact. A multi-disciplinary team across numerous organizations examined key model parameters and risk areas to develop a robust but affordable test campaign in order to validate and verify the FBC separation event for Exploration Flight Test-1 (EFT-1). The FBC jettison simulation model is highly complex, consisting of dozens of parameters varied simultaneously, with numerous multi-parameter interactions (coupling and feedback) among the various model elements, and encompassing distinct near-field, mid-field, and far-field regimes. The test campaign was composed of component-level testing (for example gas-piston thrusters and parachute mortars), ground FBC jettison tests, and FBC jettison air-drop tests that were accomplished by a highly multi-disciplinary team. Three ground jettison tests isolated the testing of mechanisms and structures to anchor the simulation models excluding aerodynamic effects. Subsequently, two air-drop tests added aerodynamic and parachute elements, and served as integrated system demonstrations, which had been preliminarily explored during the Orion Pad Abort-1 (PA-1) flight test in May 2010. Both ground and drop tests provided extensive data to validate analytical models and to verify the FBC jettison event for EFT-1. Additional testing will be required to support human certification of this separation event, for which NASA and Lockheed Martin are applying knowledge from Apollo and EFT-1 testing and modeling to develop a robust human-rated FBC separation event.

  7. Modeling of Tsunamis Induced by Landslides: Application in the Bay of Biscay.

    NASA Astrophysics Data System (ADS)

    Frere, A.; Gailler, A.; Loevenbruck, A.; Hebert, H.; Le Friant, A.

    2014-12-01

    Tsunami hazard in metropolitan France is poorly known. The TANDEM (Tsunamis in northern AtlaNtic : Definition of Effects by Modeling) project is a French initiative to draw lessons from the 2011 catastrophic tsunami in Japan on French coastlines, in order to provide guidance for risk assessment on the nuclear facilities in the area. This project is aimed at adapting numerical methods of tsunami hazard assessment against the outstanding observation database of the 2011 tsunami, in order to apply these validated methods to the definition of the tsunami hazard for the French Atlantic and Channel coastlines. As part of the TANDEM project, this work focuses on tsunami induced by landslides, and uses the CEA's model named AVALANCHE that can model simultaneously model a landslide and the resulting tsunami. AVALANCHE assumes that the landslide has a fluid-like behavior and applies shallow water/thin layer approximations to both aspect. The similarity of the resulting equations of momentum and mass conservation enables to use a single numerical scheme for both parts of the model. The model is being submitted to several benchmarks to compare its response to analytical or experimental results. The first case compares the simulation result to the analytical result obtain by a fixed slide movement in one dimension and introduces the importance of the shallow water assumption in our results. The second case consists in the modeling of a wedge going down a slope and is compared to experimental results. The last part of this work focuses on the continental slope of the Bay of Biscay off the South of France (NE Atlantic ocean). The slope presents scars left by large scale landslides. Investigation is carried out to identify the scenarios that could have caused paleo-tsunamis, with a special interest on the large scar of the Cap Breton (~100 millions m3). Several scenarios in this area are tested using the AVANLANCHE method in order to determine the potential threat.

  8. The use of computer models to predict temperature and smoke movement in high bay spaces

    NASA Technical Reports Server (NTRS)

    Notarianni, Kathy A.; Davis, William D.

    1993-01-01

    The Building and Fire Research Laboratory (BFRL) was given the opportunity to make measurements during fire calibration tests of the heat detection system in an aircraft hangar with a nominal 30.4 (100 ft) ceiling height near Dallas, TX. Fire gas temperatures resulting from an approximately 8250 kW isopropyl alcohol pool fire were measured above the fire and along the ceiling. The results of the experiments were then compared to predictions from the computer fire models DETACT-QS, FPETOOL, and LAVENT. In section A of the analysis conducted, DETACT-QS AND FPETOOL significantly underpredicted the gas temperature. LAVENT at the position below the ceiling corresponding to maximum temperature and velocity provided better agreement with the data. For large spaces, hot gas transport time and an improved fire plume dynamics model should be incorporated into the computer fire model activation routines. A computational fluid dynamics (CFD) model, HARWELL FLOW3D, was then used to model the hot gas movement in the space. Reasonable agreement was found between the temperatures predicted from the CFD calculations and the temperatures measured in the aircraft hangar. In section B, an existing NASA high bay space was modeled using the CFD model. The NASA space was a clean room, 27.4 m (90 ft) high with forced horizontal laminar flow. The purpose of this analysis is to determine how the existing fire detection devices would respond to various size fires in the space. The analysis was conducted for 32 MW, 400 kW, and 40 kW fires.

  9. Modeling Salinity Exchanges Between the Equatorial Indian Ocean and the Bay of Bengal

    DTIC Science & Technology

    2016-06-01

    of high-salinity water from the equatorial Indian Ocean into the Bay of Bengal during the northeast monsoon, although it is weaker than during the...southwest monsoon. On average, salt is transported into the Bay of Bengal between 83°E and 95°E, and low-salinity water flows southward near the...that a strong subsurface current with a speed of about 1 m s–1 intrudes into the Bay of Bengal beneath southward-flowing low-salinity water during the

  10. 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.

  11. Relation of landslides triggered by the Kiholo Bay earthquake to modeled ground motion

    USGS Publications Warehouse

    Harp, Edwin L.; Hartzell, Stephen H.; Jibson, Randall W.; Ramirez-Guzman, L.; Schmitt, Robert G.

    2014-01-01

    The 2006 Kiholo Bay, Hawaii, earthquake triggered high concentrations of rock falls and slides in the steep canyons of the Kohala Mountains along the north coast of Hawaii. Within these mountains and canyons a complex distribution of landslides was triggered by the earthquake shaking. In parts of the area, landslides were preferentially located on east‐facing slopes, whereas in other parts of the canyons no systematic pattern prevailed with respect to slope aspect or vertical position on the slopes. The geology within the canyons is homogeneous, so we hypothesize that the variable landslide distribution is the result of localized variation in ground shaking; therefore, we used a state‐of‐the‐art, high‐resolution ground‐motion simulation model to see if it could reproduce the landslide‐distribution patterns. We used a 3D finite‐element analysis to model earthquake shaking using a 10 m digital elevation model and slip on a finite‐fault model constructed from teleseismic records of the mainshock. Ground velocity time histories were calculated up to a frequency of 5 Hz. Dynamic shear strain also was calculated and compared with the landslide distribution. Results were mixed for the velocity simulations, with some areas showing correlation of landslide locations with peak modeled ground motions but many other areas showing no such correlation. Results were much improved for the comparison with dynamic shear strain. This suggests that (1) rock falls and slides are possibly triggered by higher frequency ground motions (velocities) than those in our simulations, (2) the ground‐motion velocity model needs more refinement, or (3) dynamic shear strain may be a more fundamental measurement of the decoupling process of slope materials during seismic shaking.

  12. A physical model for strain accumulation in the San Francisco Bay region: Stress evolution since 1838

    USGS Publications Warehouse

    Pollitz, F.; Bakun, W.H.; Nyst, M.

    2004-01-01

    Understanding of the behavior of plate boundary zones has progressed to the point where reasonably comprehensive physical models can predict their evolution. The San Andreas fault system in the San Francisco Bay region (SFBR) is dominated by a few major faults whose behavior over about one earthquake cycle is fairly well understood. By combining the past history of large ruptures on SFBR faults with a recently proposed physical model of strain accumulation in the SFBR, we derive the evolution of regional stress from 1838 until the present. This effort depends on (1) an existing compilation of the source properties of historic and contemporary SFBR earthquakes based on documented shaking, geodetic data, and seismic data (Bakun, 1999) and (2) a few key parameters of a simple regional viscoelastic coupling model constrained by recent GPS data (Pollitz and Nyst, 2004). Although uncertainties abound in the location, magnitude, and fault geometries of historic ruptures and the physical model relies on gross simplifications, the resulting stress evolution model is sufficiently detailed to provide a useful window into the past stress history. In the framework of Coulomb failure stress, we find that virtually all M ??? 5.8 earthquakes prior to 1906 and M ??? 5.5 earthquakes after 1906 are consistent with stress triggering from previous earthquakes. These events systematically lie in zones of predicted stress concentration elevated 5-10 bars above the regional average. The SFBR is predicted to have emerged from the 1906 "shadow" in about 1980, consistent with the acceleration in regional seismicity at that time. The stress evolution model may be a reliable indicator of the most likely areas to experience M ??? 5.5 shocks in the future.

  13. Modeling the fate of p,p'-DDT in water and sediment of two typical estuarine bays in South China: Importance of fishing vessels' inputs.

    PubMed

    Fang, Shu-Ming; Zhang, Xianming; Bao, Lian-Jun; Zeng, Eddy Y

    2016-05-01

    Antifouling paint applied to fishing vessels is the primary source of dichloro-diphenyl-trichloroethane (DDT) to the coastal marine environments of China. With the aim to provide science-based support of potential regulations on DDT use in antifouling paint, we utilized a fugacity-based model to evaluate the fate and impact of p,p'-DDT, the dominant component of DDT mixture, in Daya Bay and Hailing Bay, two typical estuarine bays in South China. The emissions of p,p'-DDT from fishing vessels to the aquatic environments of Hailing Bay and Daya Bay were estimated as 9.3 and 7.7 kg yr(-1), respectively. Uncertainty analysis indicated that the temporal variability of p,p'-DDT was well described by the model if fishing vessels were considered as the only direct source, i.e., fishing vessels should be the dominant source of p,p'-DDT in coastal bay areas of China. Estimated hazard quotients indicated that sediment in Hailing Bay posed high risk to the aquatic system, and it would take at least 21 years to reduce the hazards to a safe level. Moreover, p,p'-DDT tends to migrate from water to sediment in the entire Hailing Bay and Daya Bay. On the other hand, our previous research indicated that p,p'-DDT was more likely to migrate from sediment to water in the maricultured zones located in shallow waters of these two bays, where fishing vessels frequently remain. These findings suggest that relocating mariculture zones to deeper waters would reduce the likelihood of farmed fish contamination by p,p'-DDT.

  14. Understanding redox conditions in the mid-Cretaceous Baffin Bay - a combined model-data approach

    NASA Astrophysics Data System (ADS)

    Lenniger, M.; Bjerrum, C. J.; Pedersen, G. K.; Azhar, M. Al

    2012-04-01

    the fact that the proto-Baffin Bay would have been preconditioned for anoxia because of basin geometry and high river nutrient discharge. This ongoing work aims to test and validate different hypotheses in a three dimensional regional ocean model (ROMS). The most important question going forward is how different palaeogeographic and ocean gateway configurations affect the regional ocean circulation and consequently the redox conditions in the proto-Baffin Bay area.

  15. Development, calibration, and analysis of a hydrologic and water-quality model of the Delaware Inland Bays watershed

    USGS Publications Warehouse

    Gutierrez-Magness, Angelica L.; Raffensperger, Jeffrey Peter

    2003-01-01

    Excessive nutrients and sediment are among the most significant environmental stressors in the Delaware Inland Bays (Rehoboth, Indian River, and Little Assawoman Bays). Sources of nutrients, sediment, and other contaminants within the Inland Bays watershed include point-source discharges from industries and wastewater-treatment plants, runoff and infiltration to ground water from agricultural fields and poultry operations, effluent from on-site wastewater disposal systems, and atmospheric deposition. To determine the most effective restoration methods for the Inland Bays, it is necessary to understand the relative distribution and contribution of each of the possible sources of nutrients, sediment, and other contaminants. A cooperative study involving the Delaware Department of Natural Resources and Environmental Control, the Delaware Geological Survey, and the U.S. Geological Survey was initiated in 2000 to develop a hydrologic and water-quality model of the Delaware Inland Bays watershed that can be used as a water-resources planning and management tool. The model code Hydrological Simulation Program - FORTRAN (HSPF) was used. The 719-square-kilometer watershed was divided into 45 model segments, and the model was calibrated using streamflow and water-quality data for January 1999 through April 2000 from six U.S. Geological Survey stream-gaging stations within the watershed. Calibration for some parameters was accomplished using PEST, a model-independent parameter estimator. Model parameters were adjusted systematically so that the discrepancies between the simulated values and the corresponding observations were minimized. Modeling results indicate that soil and aquifer permeability, ditching, dominant land-use class, and land-use practices affect the amount of runoff, the mechanism or flow path (surface flow, interflow, or base flow), and the loads of sediment and nutrients. In general, the edge-of-stream total suspended solids yields in the Inland Bays

  16. Quantitative Models for Ecosystem Assessment in Narragansett Bay: Response to Nutrient Loading and Other Stressors

    EPA Science Inventory

    Multiple drivers, including nutrient loading and climate change, affect the Narragansett Bay ecosystem. Managers are interested in understanding the timing and magnitude of these effects, as well as ecosystem responses to restoration actions, such as the capacity and potential fo...

  17. Quantitative Models for the Narragansett Bay Estuary, Rhode Island/Massachusetts, USA

    EPA Science Inventory

    Multiple drivers, including nutrient loading and climate change, affect the Narragansett Bay ecosystem in Rhode Island/Massachusetts, USA. Managers are interested in understanding the timing and magnitude of these effects, and ecosystem responses to restoration actions. To provid...

  18. A landscape based, systems dynamic model for assessing impacts of urban development on water quality for sustainable seagrass growth in Tampa Bay, Florida

    EPA Science Inventory

    We present an integrated assessment model to predict potential unintended consequences of urban development on the sustainability of seagrasses and preservation of ecosystem services, such as catchable fish, in Tampa Bay. Ecosystem services are those ecological functions and pro...

  19. Linear models and empirical bayes methods for assessing differential expression in microarray experiments.

    PubMed

    Smyth, Gordon K

    2004-01-01

    The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model. The purpose of this paper is to develop the hierarchical model of Lonnstedt and Speed (2002) into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples. The model is reset in the context of general linear models with arbitrary coefficients and contrasts of interest. The approach applies equally well to both single channel and two color microarray experiments. Consistent, closed form estimators are derived for the hyperparameters in the model. The estimators proposed have robust behavior even for small numbers of arrays and allow for incomplete data arising from spot filtering or spot quality weights. The posterior odds statistic is reformulated in terms of a moderated t-statistic in which posterior residual standard deviations are used in place of ordinary standard deviations. The empirical Bayes approach is equivalent to shrinkage of the estimated sample variances towards a pooled estimate, resulting in far more stable inference when the number of arrays is small. The use of moderated t-statistics has the advantage over the posterior odds that the number of hyperparameters which need to estimated is reduced; in particular, knowledge of the non-null prior for the fold changes are not required. The moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom. The moderated t inferential approach extends to accommodate tests of composite null hypotheses through the use of moderated F-statistics. The performance of the methods is demonstrated in a simulation study. Results are presented for two publicly available data sets.

  20. Applications of 3D hydrodynamic and particle tracking models in the San Francisco bay-delta estuary

    USGS Publications Warehouse

    Smith, P.E.; Donovan, J.M.; Wong, H.F.N.

    2005-01-01

    Three applications of three-dimensional hydrodynamic and particle-tracking models are currently underway by the United States Geological Survey in the San Francisco Bay-Delta Estuary. The first application is to the San Francisco Bay and a portion of the coastal ocean. The second application is to an important, gated control channel called the Delta Cross Channel, located within the northern portion of the Sacramento-San Joaquin River Delta. The third application is to a reach of the San Joaquin River near Stockton, California where a significant dissolved oxygen problem exists due, in part, to conditions associated with the deep-water ship channel for the Port of Stockton, California. This paper briefly discusses the hydrodynamic and particle tracking models being used and the three applications. Copyright ASCE 2005.

  1. An empirical model for earthquake probabilities in the San Francisco Bay region, California, 2002-2031

    USGS Publications Warehouse

    Reasenberg, P.A.; Hanks, T.C.; Bakun, W.H.

    2003-01-01

    The moment magnitude M 7.8 earthquake in 1906 profoundly changed the rate of seismic activity over much of northern California. The low rate of seismic activity in the San Francisco Bay region (SFBR) since 1906, relative to that of the preceding 55 yr, is often explained as a stress-shadow effect of the 1906 earthquake. However, existing elastic and visco-elastic models of stress change fail to fully account for the duration of the lowered rate of earthquake activity. We use variations in the rate of earthquakes as a basis for a simple empirical model for estimating the probability of M ≥6.7 earthquakes in the SFBR. The model preserves the relative magnitude distribution of sources predicted by the Working Group on California Earthquake Probabilities' (WGCEP, 1999; WGCEP, 2002) model of characterized ruptures on SFBR faults and is consistent with the occurrence of the four M ≥6.7 earthquakes in the region since 1838. When the empirical model is extrapolated 30 yr forward from 2002, it gives a probability of 0.42 for one or more M ≥6.7 in the SFBR. This result is lower than the probability of 0.5 estimated by WGCEP (1988), lower than the 30-yr Poisson probability of 0.60 obtained by WGCEP (1999) and WGCEP (2002), and lower than the 30-yr time-dependent probabilities of 0.67, 0.70, and 0.63 obtained by WGCEP (1990), WGCEP (1999), and WGCEP (2002), respectively, for the occurrence of one or more large earthquakes. This lower probability is consistent with the lack of adequate accounting for the 1906 stress-shadow in these earlier reports. The empirical model represents one possible approach toward accounting for the stress-shadow effect of the 1906 earthquake. However, the discrepancy between our result and those obtained with other modeling methods underscores the fact that the physics controlling the timing of earthquakes is not well understood. Hence, we advise against using the empirical model alone (or any other single probability model) for estimating the

  2. Assessing past and present P Retention in Sediments in Lake Ontario (Bay of Quinte) by Reaction-Transport Diagenetic Modeling

    NASA Astrophysics Data System (ADS)

    Doan, Phuong; Berry, Sandra; Markovic, Stefan; Watson, Sue; Mugalingam, Shan; Dittrich, Maria

    2016-04-01

    Phosphorus (P) is an important macronutrient that can limit aquatic primary production and the risk of harmful algal blooms. Although there is considerable evidence that P release from sediments can represent a significant source of P and burial in sediments returns P to the geological sink; these processes have been poorly characterised. In this study, we applied a non-steady state reactive transport diagenetic model to gain insights into the dynamics of phosphorus binding forms in sediments and the phosphorus cycling of the Bay of Quinte, an embayment of Lake Ontario, Canada. The three basins of the bay (Belleville, Hay Bay and Napanee) that we investigated had differences in their phosphorus binding forms and phosphorus release, reflecting the distinct spatial temporal patterns of land use and urbanization levels in the watershed. Sediment cores from the three stations were collected during summer and under ice cover in 2013-14. Oxygen, pH and redox potential were monitored by microsensors; porewater and sediment solid matter were analyzed for P content, and a sequential extraction was used to analyze P binding forms. In the reaction-transport model, total phosphorus was divided into adsorbed phosphorus, phosphorus bound with aluminium, organic phosphorus, redox sensitive and apatite phosphorus. Using the fluxes of organic and inorganic matter as dynamic boundary conditions, we simulated the depth profiles of solute and solid components. The model closely reproduced the fractionation data of phosphorus binding forms and soluble reactive phosphorus. The past and present P fluxes were calculated and estimated; they related to geochemical conditions, and P binding forms in sediments. Our results show that P release from sediments is dominated by the redox-sentive P fraction accounting for higher percentage at Napanee station. The main P binding form that can be immobilized through diagenesis is apatite P contributing highest P retention at HayBay station. The mass

  3. Three-dimensional P wave velocity model for the San Francisco Bay region, California

    USGS Publications Warehouse

    Thurber, C.H.; Brocher, T.M.; Zhang, H.; Langenheim, V.E.

    2007-01-01

    A new three-dimensional P wave velocity model for the greater San Francisco Bay region has been derived using the double-difference seismic tomography method, using data from about 5,500 chemical explosions or air gun blasts and approximately 6,000 earthquakes. The model region covers 140 km NE-SW by 240 km NW-SE, extending from 20 km south of Monterey to Santa Rosa and reaching from the Pacific coast to the edge of the Great Valley. Our model provides the first regional view of a number of basement highs that are imaged in the uppermost few kilometers of the model, and images a number of velocity anomaly lows associated with known Mesozoic and Cenozoic basins in the study area. High velocity (Vp > 6.5 km/s) features at ???15-km depth beneath part of the edge of the Great Valley and along the San Francisco peninsula are interpreted as ophiolite bodies. The relocated earthquakes provide a clear picture of the geometry of the major faults in the region, illuminating fault dips that are generally consistent with previous studies. Ninety-five percent of the earthquakes have depths between 2.3 and 15.2 km, and the corresponding seismic velocities at the hypocenters range from 4.8 km/s (presumably corresponding to Franciscan basement or Mesozoic sedimentary rocks of the Great Valley Sequence) to 6.8 km/s. The top of the seismogenic zone is thus largely controlled by basement depth, but the base of the seismogenic zone is not restricted to seismic velocities of ???6.3 km/s in this region, as had been previously proposed. Copyright 2007 by the American Geophysical Union.

  4. Simulation of Tropical Cyclones over Bay of Bengal with NCMRWF Regional Unified Model

    NASA Astrophysics Data System (ADS)

    Routray, A.; Singh, Vivek; George, John P.; Mohandas, Saji; Rajagopal, E. N.

    2016-12-01

    This study delineates the relative performance of the 12-km resolution NCMRWF regional Unified Model (NCUM-R) over the operational global NCUM (NCUM-G) model. Forecasts of four Bay of Bengal (BoB) landfalling tropical cyclones (TCs) using several different initial conditions (ICs) are used to compare the performance of two models. The position and intensity errors of the TCs are estimated with respect to the India Meteorological Department (IMD) and Joint Typhoon Warning Center (JTWC) best-track datasets and an inter-comparison study is also carried out between IMD and JTWC. The overall results suggest that the NCUM-R simulates the position and intensity of TCs more accurately compared to the NCUM-G. A majority of the TC tracks in the NCUM-G diverge more from the IMD track when compared to NCUM-R simulated tracks. It is also clearly noticed that both the models are more skillful in track prediction when initialized at intensity stages greater than "cyclone" category. However, the mean position errors at different forecast hours and landfall errors of TCs are reduced by approximately 31 and 47% in the NCUM-R simulations compared to NCUM-G simulations, respectively. The mean gain in skill of the NCUM-R in cross track (CT) and along track (AT) error is around 29 and 24% over NCUM-G, respectively. The intensity errors are less in the NCUM-R simulations. The mean rainfall skill scores are considerably improved in the NCUM-R simulations in day-1 and day-2 as compared to the NCUM-G simulations. It is noticed that the mean position errors of the TCs are approximately 8% lower when compared against the JTWC tracks than the IMD tracks. However, the intensity errors are higher against the JTWC than that of IMD most likely due to the averaging period of the wind speed.

  5. Simulation of Tropical Cyclones over Bay of Bengal with NCMRWF Regional Unified Model

    NASA Astrophysics Data System (ADS)

    Routray, A.; Singh, Vivek; George, John P.; Mohandas, Saji; Rajagopal, E. N.

    2017-03-01

    This study delineates the relative performance of the 12-km resolution NCMRWF regional Unified Model (NCUM-R) over the operational global NCUM (NCUM-G) model. Forecasts of four Bay of Bengal (BoB) landfalling tropical cyclones (TCs) using several different initial conditions (ICs) are used to compare the performance of two models. The position and intensity errors of the TCs are estimated with respect to the India Meteorological Department (IMD) and Joint Typhoon Warning Center (JTWC) best-track datasets and an inter-comparison study is also carried out between IMD and JTWC. The overall results suggest that the NCUM-R simulates the position and intensity of TCs more accurately compared to the NCUM-G. A majority of the TC tracks in the NCUM-G diverge more from the IMD track when compared to NCUM-R simulated tracks. It is also clearly noticed that both the models are more skillful in track prediction when initialized at intensity stages greater than "cyclone" category. However, the mean position errors at different forecast hours and landfall errors of TCs are reduced by approximately 31 and 47% in the NCUM-R simulations compared to NCUM-G simulations, respectively. The mean gain in skill of the NCUM-R in cross track (CT) and along track (AT) error is around 29 and 24% over NCUM-G, respectively. The intensity errors are less in the NCUM-R simulations. The mean rainfall skill scores are considerably improved in the NCUM-R simulations in day-1 and day-2 as compared to the NCUM-G simulations. It is noticed that the mean position errors of the TCs are approximately 8% lower when compared against the JTWC tracks than the IMD tracks. However, the intensity errors are higher against the JTWC than that of IMD most likely due to the averaging period of the wind speed.

  6. Spatial Predictive Modeling and Remote Sensing of Land Use Change in the Chesapeake Bay Watershed

    NASA Technical Reports Server (NTRS)

    Goetz, Scott J.; Bockstael, Nancy E.; Jantz, Claire A.

    2005-01-01

    This project was focused on modeling the processes by which increasing demand for developed land uses, brought about by changes in the regional economy and the socio-demographics of the region, are translated into a changing spatial pattern of land use. Our study focused on a portion of the Chesapeake Bay Watershed where the spatial patterns of sprawl represent a set of conditions generally prevalent in much of the U.S. Working in the region permitted us access to (i) a time-series of multi-scale and multi-temporal (including historical) satellite imagery and (ii) an established network of collaborating partners and agencies willing to share resources and to utilize developed techniques and model results. In addition, a unique parcel-level tax assessment database and linked parcel boundary maps exists for two counties in the Maryland portion of this region that made it possible to establish a historical cross-section time-series database of parcel level development decisions. Scenario analyses of future land use dynamics provided critical quantitative insight into the impact of alternative land management and policy decisions. These also have been specifically aimed at addressing growth control policies aimed at curbing exurban (sprawl) development. Our initial technical approach included three components: (i) spatial econometric modeling of the development decision, (ii) remote sensing of suburban change and residential land use density, including comparisons of past change from Landsat analyses and more traditional sources, and (iii) linkages between the two through variable initialization and supplementation of parcel level data. To these we added a fourth component, (iv) cellular automata modeling of urbanization, which proved to be a valuable addition to the project. This project has generated both remote sensing and spatially explicit socio-economic data to estimate and calibrate the parameters for two different types of land use change models and has

  7. Florida Bay salinity and Everglades wetlands hydrology circa 1900 CE: A compilation of paleoecology-based statistical modeling analyses

    USGS Publications Warehouse

    Marshall, F.E.; Wingard, G.L.

    2012-01-01

    The upgraded method of coupled paleosalinity and hydrologic models was applied to the analysis of the circa-1900 CE segments of five estuarine sediment cores collected in Florida Bay. Comparisons of the observed mean stage (water level) data to the paleoecology-based model's averaged output show that the estimated stage in the Everglades wetlands was 0.3 to 1.6 feet higher at different locations. Observed mean flow data compared to the paleoecology-based model output show an estimated flow into Shark River Slough at Tamiami Trail of 401 to 2,539 cubic feet per second (cfs) higher than existing flows, and at Taylor Slough Bridge an estimated flow of 48 to 218 cfs above existing flows. For salinity in Florida Bay, the difference between paleoecology-based and observed mean salinity varies across the bay, from an aggregated average salinity of 14.7 less than existing in the northeastern basin to 1.0 less than existing in the western basin near the transition into the Gulf of Mexico. When the salinity differences are compared by region, the difference between paleoecology-based conditions and existing conditions are spatially consistent.

  8. A modeling study of processes controlling the Bay of Bengal sea surface salinity interannual variability

    NASA Astrophysics Data System (ADS)

    Akhil, V. P.; Lengaigne, M.; Vialard, J.; Durand, F.; Keerthi, M. G.; Chaitanya, A. V. S.; Papa, F.; Gopalakrishna, V. V.; de Boyer Montégut, Clément

    2016-12-01

    Recent observational studies provided preliminary insights on the interannual variability of Bay of Bengal (BoB) Sea Surface Salinity (SSS), but are limited by the poor data coverage. Here, we describe the BoB interannual SSS variability and its driving processes from a regional eddy-permitting ocean general circulation model forced by interannually varying air-sea fluxes and altimeter-derived discharges of major rivers over the past two decades. Simulated interannual SSS variations compare favorably with both in situ and satellite data and are largest in boreal fall in three regions: the northern BoB, the coastal region off east India, and the Andaman Sea. In the northern BoB, these variations are independent from those in other regions and mostly driven by summer-fall Ganga-Brahmaputra runoff interannual variations. In fall, remote forcing from the Indian Ocean Dipole results in anticlockwise anomalous horizontal currents that drive interannual SSS variations of opposite polarity along the east coast of India and in the Southern Andaman Sea. From winter onward, these anomalies are damped by vertical mixing in the northern BoB and along the east coast of India and by horizontal advection in the Southern Andaman Sea. While river runoff fluctuations locally play a strong role near the Ganga-Brahmaputra river mouth, wind-driven interannual current anomalies are responsible for a large fraction of SSS interannual variability in most of the basin.

  9. Modeling bioaccumulation and biotransformation of PAHs and PCBs by benthic macrofauna from lower Chesapeake Bay

    SciTech Connect

    Dickhut, R.M.; Schaffner, L.C.; Lay, P.; Mitra, S.

    1995-12-31

    The bioaccumulation and biotransformation of selected PAHs and PCBs from sediments spiked with radiolabeled compounds were examined in benthic communities from lower chesapeake Bay during summer and winter. Kinetic models were then used to determine the steady-state bioaccumulation factors (BAFs) for the parent compounds in various benthic macrofaunal organisms, as well as the BAFs of aqueous soluble metabolites that tended to accumulate in the animals. BAFs for the parent compounds increased with the octanol-water partition coefficient (K{sub ow}) of the compound up to a log K{sub ow} of approximately 6. However, in contrast to previous studies, the elimination rate constant was the dominant factor controlling the observed nonequilibrium with respect to bioaccumulation of the organic contaminants. Consequently, BAFs for the parent contaminants were related to the physical-chemical factors regulating passive elimination, as well as metabolic transformation of the parent compound. Aqueous soluble metabolite BAFs were directly related to the physical-chemical factors dictating the rate of formation of the conjugated complexes. Overall, body burdens of organic contaminants were higher in the summer relative to winter, as were the aqueous soluble metabolite fractions of contaminants in the animals, possibly indicating that organism activities as well as lipid pools are higher in summer compared to winter. The results indicate that a variety of physical, chemical, and biological factors interact in the ecosystem to dictate bioaccumulation and biotransformation of organic contaminants.

  10. San Francisco Bay-Delta bathymetric/topographic digital elevation model (DEM)

    USGS Publications Warehouse

    Fregoso, Theresa; Wang, Rueen-Fang; Ateljevich, Eli; Jaffe, Bruce E.

    2017-01-01

    bathymetry data collected by the COE and USGS scientists, expanding the DEM to include the northernmost areas of the Sacramento-San Joaquin Delta, and by making use of a two-meter seamless bathymetric/topographic DEM from the USGS EROS Data Center (2013) of the San Francisco Bay region.The resulting 10-meter USGS DEM encompasses the entirety of Suisun Bay, beginning with the Carquinez Strait in the west, east to California Interstate 5, north following the path of the Yolo Bypass and the Sacramento River up to Knights Landing, and the American River northeast to the Nimbus Dam, and south to areas around Tracy. The DEM incorporates the newest available bathymetry data at the time of release, as well as including, at minimum, a 100-meter band of available topography data adjacent to most shorelines. No data areas within the DEM are areas where no elevation data exists, either due to a gap in the land/water interface, or because lidar was collected over standing water that was then cut out of the DEM.Environmental Systems Research Institute, Inc., 2015, Topo to Raster:  http://desktop.arcgis.com/en/desktop/latest/tools/3d-analyst-toolbox/topo-to-raster.htmFoxgrover, A., Smith, R.E., and Jaffe, B.E., 2005, Suisun Bay and Delta Bathymetry: http://sfbay.wr.usgs.gov/sediment/delta/index.htmlUSGS EROS Data Center, 2013, 2 m Coastal National Elevation Dataset: http://topotools.cr.usgs.gov/topobathy_viewer/Wang, R-F., and Ateljevich, E., 2012, A continuous surface elevation map for modeling, chapter 6 in California Department of Water Resources, Methodology for flow and salinity estimates in the Sacramento-San Joaquin Delta and Suisun Marsh, 33rd Annual Progress Report to the StateWater Resources Control Board:  California Department of Water Resources, Bay-Delta Office, Delta Modeling Section, http://baydeltaoffice.water.ca.gov/modeling/deltamodeling/AR2012/Chapter%206_2012_Web.pdf

  11. Modeling bed-load transport of coarse sediments in the Great Bay Estuary, New Hampshire

    NASA Astrophysics Data System (ADS)

    Bilgili, A.; Swift, M. R.; Lynch, D. R.; Ip, J. T. C.

    2003-12-01

    Current, sea level and bed-load transport are investigated in the Lower Piscataqua River section of the Great Bay Estuary, New Hampshire, USA—a well-mixed and geometrically complex system with low freshwater input, having main channel tidal currents ranging between 0.5 and 2 m s -1. Current and sea level forced by the M 2M 4M 6 tides at the estuarine mouth are simulated by a vertically averaged, non-linear, time-stepping finite element model. The hydrodynamic model uses a fixed boundary computational domain and accounts for flooding-drying of tidal flats by making use of a groundwater component. Inertia terms are neglected in comparison with pressure gradient and bottom friction terms, which is consistent with the observed principal dynamic balance for this section of the system. The accuracy of hydrodynamic predictions in the study area is demonstrated by comparison with four tidal elevation stations and two cross-section averaged current measurements. Simulated current is then used to model bed-load transport in the vicinity of a rapidly growing shoal located in the main channel of the lower system. Consisting of coarse sand and gravel, the shoal must be dredged every five to eight years. Two approaches are taken—an Eulerian parametric method in which nodal bed-load flux vectors are averaged over the tidal cycle and a Lagrangian particle tracking approach in which a finite number of sediment particles are released and tracked. Both methods yield pathways and accumulations in agreement with the observed shoal formation and the long-term rate of sediment accumulation in the shoal area.

  12. Vitalistic causality in young children's naive biology.

    PubMed

    Inagaki, Kayoko; Hatano, Giyoo

    2004-08-01

    One of the key issues in conceptual development research concerns what kinds of causal devices young children use to understand the biological world. We review evidence that children predict and interpret biological phenomena, especially human bodily processes, on the basis of 'vitalistic causality'. That is, they assume that vital power or life force taken from food and water makes humans active, prevents them from being taken ill, and enables them to grow. These relationships are also extended readily to other animals and even to plants. Recent experimental results show that a majority of preschoolers tend to choose vitalistic explanations as most plausible. Vitalism, together with other forms of intermediate causality, constitute unique causal devices for naive biology as a core domain of thought.

  13. Formation of summer phytoplankton bloom in the northwestern Bay of Bengal in a coupled physical-ecosystem model

    NASA Astrophysics Data System (ADS)

    Thushara, V.; Vinayachandran, P. N.

    2016-12-01

    The Bay of Bengal (BoB) is considered to be a region of low biological productivity, owing to nutrient limitation, caused by strong salinity stratification induced by the freshwater influx from rivers and precipitation. Satellite and in situ observations, however, reveal the presence of prominent regional blooms in the bay in response to monsoonal forcings. Bloom dynamics of the BoB are presumably determined by freshwater as well as the local and remote effect of winds and remain to be explored in detail. Using a coupled physical-ecosystem model, we have examined the oceanic processes controlling productivity in the northwestern BoB during the summer monsoon. The region exhibits a prominent bloom lasting for a period of about 2 months, supporting major fishing zones along the northeast coast of India. The ecosystem model simulates the spatial and temporal evolution of the surface bloom in good agreement with Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) observations. Vertical distribution of upper ocean physical and biological tracers and a nitrate budget analysis reveal the dominant role of coastal upwelling induced by alongshore winds in triggering the bloom. Horizontal advection plays a secondary role by supplying nutrients from coastal to offshore regions. The bloom decays with the weakening of winds and upwelling by the end of summer monsoon. The simulated bloom in the northwestern bay remains largely unaffected by the freshwater effects, since the peak bloom occurs before the arrival of river plumes.

  14. Fuzzy Naive Bayesian for constructing regulated network with weights.

    PubMed

    Zhou, Xi Y; Tian, Xue W; Lim, Joon S

    2015-01-01

    In the data mining field, classification is a very crucial technology, and the Bayesian classifier has been one of the hotspots in classification research area. However, assumptions of Naive Bayesian and Tree Augmented Naive Bayesian (TAN) are unfair to attribute relations. Therefore, this paper proposes a new algorithm named Fuzzy Naive Bayesian (FNB) using neural network with weighted membership function (NEWFM) to extract regulated relations and weights. Then, we can use regulated relations and weights to construct a regulated network. Finally, we will classify the heart and Haberman datasets by the FNB network to compare with experiments of Naive Bayesian and TAN. The experiment results show that the FNB has a higher classification rate than Naive Bayesian and TAN.

  15. A study case of bioluminescence potential dynamics in the Delaware Bay with observations and modeling

    NASA Astrophysics Data System (ADS)

    Shulman, Igor; Moline, Mark A.; Anderson, Stephanie; Sakalaukus, Peter; Rowley, Clark; Ladner, Sherwin

    2017-03-01

    Results from first observational program of bioluminescence (BL) potential in the Delaware Bay area are presented. During the field program July 30-August 1, 2015, the satellite Visible Infrared Imaging Radiometer Suite (VIIRS) imagery shows the development of the submesoscale filament with elevated chlorophyll-a in the area of interaction of lighter water masses of the Bay outflow with denser upwelled water. We have shown that ageostrophic secondary circulation (ASC) cells contributed to the development of this filament. Analysis of BL potential observations have shown elevated values of BL potential in the area of the submesoscale filament. Analysis of observed temperature, salinity, sigma-t, and BL potential along the stations crossing the Bay mouth have shown a presence of a strong frontal structure separating colder, more saline, denser offshore water from the bay water masses. Over 3 days of sampling, this frontal structure moved onshore to the entrance of the bay, and brought offshore BL plankton communities with higher values of BL potential. We compared two surveys (at the end of July and in the middle of August) of water masses located in the area where the buoyant outflow of the Delaware Coastal Current is turned around and taken to the north up the shelf by upwelling favorable winds. Analysis of observations shows that the survey at the end of July has fresher water masses (due to higher river runoff before and during survey) and higher values of BL potential in comparison to the survey at the middle of August.

  16. Intercomparison of Suspended Sediment Concentration Derived from Models, Measurements and Hyperspectral Imagery in a System of Shallow, Relatively Pristine Coastal Bays: A Preliminary Study

    DTIC Science & Technology

    2013-09-30

    13-10149 LONG-TERM GOALS To improve our capabilities for remotely sensing and modeling water column properties in shallow coastal bays, especially...light attenuation in the bays, and shallow depths (≤1m MLW for tidal flats, with some deeper channels) such that that remotely sensed water -column...suspended sediment concentration and other contributions to water clarity/ turbidity , and their spatial and temporal variability. OBJECTIVES This

  17. Shallow-water System Dynamics in Chesapeake Bay, with Physical-Biological Modeling Application

    NASA Astrophysics Data System (ADS)

    Tian, R.; Wang, P.; Linker, L. C.

    2014-12-01

    Chesapeake Bay is the largest estuary in the United States. The total surface area is 9920 square kilometers of which 7540 square kilometers are shallower than 10 m. These shallow systems provide vital habitats and nursery grounds for numerous species of fish, shellfish, and wildlife. In the Chesapeake the shallow water systems have deteriorated in terms of healthy ecosystem levels and submerged aquatic vegetation (SAV). Restoration of the shallow water systems requires an understanding of their dynamics including wave-current interactions, shoreline erosion, sediment suspension, biological and biogeochemical processes, sediment diagenesis, sediment-water exchange, and diel cycles of temperature, salinity, turbidity, alkalinity, chlorophyll, nutrients, and dissolved oxygen (DO). To this end, an extensive shallow water monitoring program has been implemented in the Chesapeake since 2003. The program includes bi-weekly cruises of nutrient sampling, a continuous monitoring network with electronic sensors collecting data at a 15 minute interval, and a unique data flow survey from moving boats that collect underway observations with a datum frequency of seconds. The data reveal large diel cycles, with chlorophyll varying between a few mg/l to hundreds of mg/l, DO between 0 to 20 mg/l (with saturation from 0 to 250%), turbidity between 0 to 1500 NTUs, and pH from 6.0 to 9.5, which demonstrate the highly dynamic nature in physical and biological process of the shallow water systems . In order to better understand the key mechanisms and processes of these shallow-water systems and to explore the monitoring data, we applied a coupled physical and water quality model to the Chester and Corsica tributaries. The physical model is the Unstructured Finite Volume Coastal Ocean Model (FVCOM) and the water quality model is the Integrated Compartment Model (ICM) which has 36 state variables such as phytoplankton, zooplankton, DO, nutrients, and various organic matter and sediment

  18. Wind-Farm Forecasting Using the HARMONIE Weather Forecast Model and Bayes Model Averaging for Bias Removal.

    NASA Astrophysics Data System (ADS)

    O'Brien, Enda; McKinstry, Alastair; Ralph, Adam

    2015-04-01

    Building on previous work presented at EGU 2013 (http://www.sciencedirect.com/science/article/pii/S1876610213016068 ), more results are available now from a different wind-farm in complex terrain in southwest Ireland. The basic approach is to interpolate wind-speed forecasts from an operational weather forecast model (i.e., HARMONIE in the case of Ireland) to the precise location of each wind-turbine, and then use Bayes Model Averaging (BMA; with statistical information collected from a prior training-period of e.g., 25 days) to remove systematic biases. Bias-corrected wind-speed forecasts (and associated power-generation forecasts) are then provided twice daily (at 5am and 5pm) out to 30 hours, with each forecast validation fed back to BMA for future learning. 30-hr forecasts from the operational Met Éireann HARMONIE model at 2.5km resolution have been validated against turbine SCADA observations since Jan. 2014. An extra high-resolution (0.5km grid-spacing) HARMONIE configuration has been run since Nov. 2014 as an extra member of the forecast "ensemble". A new version of HARMONIE with extra filters designed to stabilize high-resolution configurations has been run since Jan. 2015. Measures of forecast skill and forecast errors will be provided, and the contributions made by the various physical and computational enhancements to HARMONIE will be quantified.

  19. 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

  20. Sources of suspended-sediment flux in streams of the chesapeake bay watershed: A regional application of the sparrow model

    USGS Publications Warehouse

    Brakebill, J.W.; Ator, S.W.; Schwarz, G.E.

    2010-01-01

    We describe the sources and transport of fluvial suspended sediment in nontidal streams of the Chesapeake Bay watershed and vicinity. We applied SPAtially Referenced Regressions on Watershed attributes, which spatially correlates estimated mean annual flux of suspended sediment in nontidal streams with sources of suspended sediment and transport factors. According to our model, urban development generates on average the greatest amount of suspended sediment per unit area (3,928 Mg/km2/year), although agriculture is much more widespread and is the greatest overall source of suspended sediment (57 Mg/km2/year). Factors affecting sediment transport from uplands to streams include mean basin slope, reservoirs, physiography, and soil permeability. On average, 59% of upland suspended sediment generated is temporarily stored along large rivers draining the Coastal Plain or in reservoirs throughout the watershed. Applying erosion and sediment controls from agriculture and urban development in areas of the northern Piedmont close to the upper Bay, where the combined effects of watershed characteristics on sediment transport have the greatest influence may be most helpful in mitigating sedimentation in the bay and its tributaries. Stream restoration efforts addressing floodplain and bank stabilization and incision may be more effective in smaller, headwater streams outside of the Coastal Plain. ?? 2010 American Water Resources Association. No claim to original U.S. government works.

  1. Characterization of the finch embryo supports evolutionary conservation of the naive stage of development in amniotes

    PubMed Central

    Mak, Siu-Shan; Alev, Cantas; Nagai, Hiroki; Wrabel, Anna; Matsuoka, Yoko; Honda, Akira; Sheng, Guojun; Ladher, Raj K

    2015-01-01

    Innate pluripotency of mouse embryos transits from naive to primed state as the inner cell mass differentiates into epiblast. In vitro, their counterparts are embryonic (ESCs) and epiblast stem cells (EpiSCs), respectively. Activation of the FGF signaling cascade results in mouse ESCs differentiating into mEpiSCs, indicative of its requirement in the shift between these states. However, only mouse ESCs correspond to the naive state; ESCs from other mammals and from chick show primed state characteristics. Thus, the significance of the naive state is unclear. In this study, we use zebra finch as a model for comparative ESC studies. The finch blastoderm has mESC-like properties, while chick blastoderm exhibits EpiSC features. In the absence of FGF signaling, finch cells retained expression of pluripotent markers, which were lost in cells from chick or aged finch epiblasts. Our data suggest that the naive state of pluripotency is evolutionarily conserved among amniotes. DOI: http://dx.doi.org/10.7554/eLife.07178.001 PMID:26359635

  2. Results of a modeling workshop concerning economic and environmental trends and concomitant resource management issues in the Mobile Bay area

    USGS Publications Warehouse

    Hamilton, David B.; Andrews, Austin K.; Auble, Gregor T.; Ellison, Richard A.; Johnson, Richard A.; Roelle, James E.; Staley, Michael J.

    1982-01-01

    During the past decade, the southern regions of the U.S. have experienced rapid change which is expected to continue into the foreseeable future. Growth in population, industry, and resource development has been attributed to a variety of advantages such as an abundant and inexpensive labor force, a mild climate, and the availability of energy, water, land, and other natural resources. While this growth has many benefits for the region, it also creates the potential for increased air, water, and solid waste pollution, and modification of natural habitats. A workshop was convened to consider the Mobile Bay area as a site-specific case of growth and its environmental consequences in the southern region. The objectives of the modeling workshop were to: (1) identify major factors of economic development as they relate to growth in the area over the immediate and longer term; (2) identify major environmental and resource management issues associated with this expected growth; and (3) identify and characterize the complex interrelationships among economic and environmental factors. This report summarizes the activities and results of a modeling workshop concerning economic growth and concomitant resource management issues in the Mobile Bay area. The workshop was organized around construction of a simulation model representing the relationships between a series of actions and indicators identified by participants. The workshop model had five major components. An Industry Submodel generated scenarios of growth in several industrial and transportation sectors. A Human Population/Economy Submodel calculated human population and economic variables in response to employment opportunities. A Land Use/Air Quality Submodel tabulated changes in land use, shoreline use, and air quality. A Water Submodel calculated indicators of water quality and quantity for fresh surface water, ground water, and Mobile Bay based on discharge information provided by the Industry and Human

  3. Modelling survival after treatment of intraocular melanoma using artificial neural networks and Bayes theorem.

    PubMed

    Taktak, Azzam F G; Fisher, Anthony C; Damato, Bertil E

    2004-01-07

    This paper describes the development of an artificial intelligence (AI) system for survival prediction from intraocular melanoma. The system used artificial neural networks (ANNs) with five input parameters: coronal and sagittal tumour location, anterior tumour margin, largest basal tumour diameter and the cell type. After excluding records with missing data, 2331 patients were included in the study. These were split randomly into training and test sets. Date censorship was applied to the records to deal with patients who were lost to follow-up and patients who died from general causes. Bayes theorem was then applied to the ANN output to construct survival probability curves. A validation set with 34 patients unseen to both training and test sets was used to compare the AI system with Cox's regression (CR) and Kaplan-Meier (KM) analyses. Results showed large differences in the mean 5 year survival probability figures when the number of records with matching characteristics was small. However, as the number of matches increased to > 100 the system tended to agree with CR and KM. The validation set was also used to compare the system with a clinical expert in predicting time to metastatic death. The rms error was 3.7 years for the system and 4.3 years for the clinical expert for 15 years survival. For < 10 years survival, these figures were 2.7 and 4.2, respectively. We concluded that the AI system can match if not better the clinical expert's prediction. There were significant differences with CR and KM analyses when the number of records was small, but it was not known which model is more accurate.

  4. Interannual variability of upper ocean stratification in Bay of Bengal: observational and modeling aspects

    NASA Astrophysics Data System (ADS)

    Fousiya, T. S.; Parekh, Anant; Gnanaseelan, C.

    2016-10-01

    The annual cycle and interannual variability of stratification in Bay of Bengal (BoB) are studied using both observations and Global Ocean Data Assimilation System (GODAS) analysis during 2003-2012. Annual cycle of stratification and sea surface temperature (SST) evolve coherently, highlighting its role on modulating air-sea interaction over this climatologically important region. Spatial distribution of stratification shows strong seasonality in ARGO observations, whereas it is highly underestimated in GODAS with highest discrepancies during fall and spring. The annual cycle of sea surface salinity (SSS) in GODAS is out of phase with observations implying potential feedbacks. During La Niña years, SSS drop in fall and winter and are lesser than those reported during El Niño years. All these features are misrepresented in GODAS. As stratification modulates air-sea interaction over BoB especially during El Niño and La Niña years, such misrepresentation of ocean stratification may lead to unrealistic thermocline-SST coupling in the models. The mean stratification and its interannual variability in GODAS are weaker than observed even though interannual variability in freshwater flux (P-E) is higher in GODAS. Detailed analysis of GODAS with in situ observations reveals that upper ocean current shear (vertical) is overestimated in GODAS, leading to unrealistically strong mixing which is primarily responsible for the deeper penetration of surface warm and freshwater resulting weaker stratification. As GODAS is used to initialize the ocean component of the coupled forecasting system for seasonal prediction of Asian monsoon, proper representation of stratification is essential. This study advocates the need of accurate representation of upper ocean salinity in GODAS for improved stratification. We speculate that improved stratification and mixing in the BoB improve summer monsoon forecast.

  5. Influence of water allocation and freshwater inflow on oyster production: a hydrodynamic-oyster population model for Galveston Bay, Texas, USA.

    PubMed

    Powell, Eric N; Klinck, John M; Hofmann, Eileen E; McManus, Margaret A

    2003-01-01

    A hydrodynamic-oyster population model was developed to assess the effect of changes in freshwater inflow on oyster populations in Galveston Bay, Texas, USA. The population model includes the effects of environmental conditions, predators, and the oyster parasite, Perkinsus marinus, on oyster populations. The hydrodynamic model includes the effects of wind stress, river runoff, tides, and oceanic exchange on the circulation of the bay. Simulations were run for low, mean, and high freshwater inflow conditions under the present (1993) hydrology and predicted hydrologies for 2024 and 2049 that include both changes in total freshwater inflow and diversions of freshwater from one primary drainage basin to another. Freshwater diversion to supply the Houston metropolitan area is predicted to negatively impact oyster production in Galveston Bay. Fecundity and larval survivorship both decline. Mortality from Perkinsus marinus increases, but to a lesser extent. A larger negative impact in 2049 relative to 2024 originates from the larger drop in fecundity under that hydrology. Changes in recruitment and mortality, resulting in lowered oyster abundance, occur because the bay volume available for mixing freshwater input from the San Jacinto and Buffalo Bayou drainage basins that drain metropolitan Houston is small in comparison to the volume of Trinity Bay that presently receives the bulk of the bay's freshwater inflow. A smaller volume for mixing results in salinities that decline more rapidly and to a greater extent under conditions of high freshwater discharge.Thus, the decline in oyster abundance results from a disequilibrium between geography and salinity brought about by freshwater diversion. Although the bay hydrology shifts, available hard substrate does not. The simulations stress the fact that it is not just the well-appreciated reduction in freshwater inflow that can result in decreased oyster production. Changing the location of freshwater inflow can also

  6. 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.

  7. A SIMPLE MODEL FOR FORECASTING THE EFFECTS OF NITROGEN LOADS ON CHESAPEAKE BAY HYPOXIA

    EPA Science Inventory

    The causes and consequences of oxygen depletion in Chesapeake Bay have been the focus of research, assessment, and policy action over the past several decades. An ongoing scientific re-evaluation of what nutrients load reductions are necessary to meet the water quality goals is ...

  8. A physical model for strain accumulation in the San Francisco Bay Region

    USGS Publications Warehouse

    Pollitz, F.F.; Nyst, M.

    2005-01-01

    Strain accumulation in tectonically active regions is generally a superposition of the effects of background tectonic loading, steady-state dislocation processes, such as creep, and transient deformation. In the San Francisco Bay region (SFBR), the most uncertain of these processes is transient deformation, which arises primarily in association with large earthquakes. As such, it depends upon the history of faulting and the rheology of the crust and mantle, which together determine the pattern of longer term (decade-scale) post-seismic response to earthquakes. We utilize a set of 102 GPS velocity vectors in the SFBR in order to characterize the strain rate field and construct a physical model of its present deformation. We first perform an inversion for the continuous velocity gradient field from the discrete GPS velocity field, from which both tensor strain rate and rotation rate may be extracted. The present strain rate pattern is well described as a nearly uniform shear strain rate oriented approximately N34??W (140 nanostrain yr-1) plus a N56??E uniaxial compression rate averaging 20 nanostrain yr-1 across the shear zone. We fit the velocity and strain rate fields to a model of time-dependent deformation within a 135-kin-wide, arcuate shear zone bounded by strong Pacific Plate and Sierra Nevada block lithosphere to the SW and NE, respectively. Driving forces are purely lateral, consisting of shear zone deformation imposed by the relative motions between the thick Pacific Plate and Sierra Nevada block lithospheres. Assuming a depth-dependent viscoelastic structure within the shear zone, we account for the effects of steady creep on faults and viscoelastic relaxation following the 1906 San Francisco and 1989 Loma Prieta earthquakes, subject to constant velocity boundary conditions on the edges of the shear zone. Fault creep is realized by evaluating dislocations on the creeping portions of faults in the fluid limit of the viscoelastic model. A priori plate

  9. Evaluation of effects of changes in canal management and precipitation patterns on salinity in Biscayne Bay, Florida, using an integrated surface-water/groundwater model

    USGS Publications Warehouse

    Lohmann, Melinda A.; Swain, Eric D.; Wang, John D.; Dixon, Joann

    2012-01-01

    Biscayne National Park, located in Biscayne Bay in southeast Florida, is one of the largest marine parks in the country and sustains a large natural marine fishery where numerous threatened and endangered species reproduce. In recent years, the bay has experienced hypersaline conditions (salinity greater than 35 practical salinity units) of increasing magnitude and duration. Hypersalinity events were particularly pronounced during April to August 2004 in nearshore areas along the southern and middle parts of the bay. Prolonged hypersaline conditions can cause degradation of water quality and permanent damage to, or loss of, brackish nursery habitats for multiple species of fish and crustaceans as well as damage to certain types of seagrasses that are not tolerant of extreme changes in salinity. To evaluate the factors that contribute to hypersalinity events and to test the effects of possible changes in precipitation patterns and canal flows into Biscayne Bay on salinity in the bay, the U.S. Geological Survey constructed a coupled surface-water/groundwater numerical flow model. The model is designed to account for freshwater flows into Biscayne Bay through the canal system, leakage of salty bay water into the underlying Biscayne aquifer, discharge of fresh and salty groundwater from the Biscayne aquifer into the bay, direct effects of precipitation on bay salinity, indirect effects of precipitation on recharge to the Biscayne aquifer, direct effects of evapotranspiration (ET) on bay salinity, indirect effects of ET on recharge to the Biscayne aquifer, and maintenance of mass balance of both water and solute. The model was constructed using the Flow and Transport in a Linked Overland/Aquifer Density Dependent System (FTLOADDS) simulator, version 3.3, which couples the two-dimensional, surface-water flow and solute-transport simulator SWIFT2D with the density-dependent, groundwater flow an solute-transport simulator SEAWAT. The model was calibrated by a trial

  10. 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.

  11. Performance of WRF-ARW model in real-time prediction of Bay of Bengal cyclone `Phailin'

    NASA Astrophysics Data System (ADS)

    Mandal, M.; Singh, K. S.; Balaji, M.; Mohapatra, M.

    2016-05-01

    This study examines the performance of the Advanced Research core of Weather Research and Forecasting (ARW-WRF) model in prediction of the Bay of Bengal cyclone `Phailin'. The two-way interactive double-nested model at 27 and 9-km resolutions customized at Indian Institute of Technology Kharagpur (IITKGP) is used to predict the storm on real-time basis and five predictions are made with five different initial conditions. The initial and boundary conditions for the model are derived from the Global Forecasting System (GFS) analysis and forecast respectively. The track of storm is well predicted in all the five forecasts. In particular, the forecast with less initial positional error led to more accurate track and landfall prediction. It is observed that the predicted peak intensity and translation speed of the storm depends strongly on initial intensity error, vertical wind shear and vertical distribution of maximum potential vorticity. The trend of intensification and dissipation of the storm is well predicted by the model in terms of central sea level pressure (CSLP). The intensity in terms of maximum surface wind (MSW) is under-predicted by the model and it is suggested that the MSW estimated from predicted pressure drop may be used as prediction guideline. The storm intensified rapidly during its passage over the high Tropical Cyclone Heat Potential zone and is reasonably well predicted by the model. Though the magnitude of the precipitation is not well predicted, distribution of precipitation is fairly well predicted by the model. The track and intensity of the storm predicted by the customized WRF-ARW is better than that of other NWP models. The landfall (time and position) is also better predicted by the model compared to other NWP models if initialized at cyclonic storm stage. The results indicate that the customized model have good potential for real-time prediction of Bay of Bengal cyclones and encourage further investigation with larger number of cyclones.

  12. 78 FR 14007 - Special Conditions: Embraer S.A., Model EMB-550 Airplanes; Electrical/Electronic Equipment Bay...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-04

    ..., specifically distributed electrical and electronic equipment bays in pressurized areas of the airplane. Older... manual procedure. In distributed electrical/electronic bay installations it is not as straightforward... incorporate the following novel or unusual design features: Distributed electrical and electronic...

  13. Risk of erectile dysfunction in transfusion-naive thalassemia men: a nationwide population-based retrospective cohort study.

    PubMed

    Chen, Yu-Guang; Lin, Te-Yu; Lin, Cheng-Li; Dai, Ming-Shen; Ho, Ching-Liang; Kao, Chia-Hung

    2015-04-01

    Based on the mechanism of pathophysiology, thalassemia major or transfusion-dependent thalassemia patients may have an increased risk of developing organic erectile dysfunction resulting from hypogonadism. However, there have been few studies investigating the association between erectile dysfunction and transfusion-naive thalassemia populations. We constructed a population-based cohort study to elucidate the association between transfusion-naive thalassemia populations and organic erectile dysfunction. This nationwide population-based cohort study involved analyzing data from 1998 to 2010 obtained from the Taiwanese National Health Insurance Research Database, with a follow-up period extending to the end of 2011. We identified men with transfusion-naive thalassemia and selected a comparison cohort that was frequency-matched with these according to age, and year of diagnosis thalassemia at a ratio of 1 thalassemia man to 4 control men. We analyzed the risks for transfusion-naive thalassemia men and organic erectile dysfunction by using Cox proportional hazards regression models. In this study, 588 transfusion-naive thalassemia men and 2337 controls were included. Total 12 patients were identified within the thalassaemia group and 10 within the control group. The overall risks for developing organic erectile dysfunction were 4.56-fold in patients with transfusion-naive thalassemia men compared with the comparison cohort after we adjusted for age and comorbidities. Our long-term cohort study results showed that in transfusion-naive thalassemia men, there was a higher risk for the development of organic erectile dysfunction, particularly in those patients with comorbidities.

  14. Characteristics of cyclone generated gravity waves observed using assimilated WRF model simulations over Bay of Bengal

    NASA Astrophysics Data System (ADS)

    Hima Bindu, H.; Venkat Ratnam, M.; Yesubabu, V.; Narayana Rao, T.; Kesarkar, Amit; Naidu, C. V.

    2016-11-01

    Characteristics of gravity waves (GWs) generated due to tropical cyclone (TC) Phailin (2013) that occurred over Bay of Bengal are investigated using the Weather Research and Forecast (WRF) model simulations from its depression stage to weakening stage (10-14 October 2013). Two types of numerical experiments are conducted with and without assimilating conventional and satellite observations using the 3-Dimentional Variational (3DVAR) technique. The results show that the experiment without assimilating any observations (control) has produced a large difference in terms of track and intensity with observed best track estimates of IMD. Similar features are noticed also in winds, reflectivity and independent GPS Radio Occultation (temperature) and radiosonde (temperature and winds) profiles. The experiment with assimilation significantly reduced the observed differences in all the above mentioned parameters. A close match of the assimilated outputs with observations prompted us to use it to identify the TC generated GW characteristics. GW perturbation components are extracted from the three day mean (4-7 October 2013) calm background atmosphere prior to the formation of depression. When compared to the control run, assimilated outputs show a clear increase in all the gravity wave parameters except the amplitudes where control run wave amplitudes are found to be stronger than the assimilated outputs. Fast Fourier transform (FFT) analysis in the time domain revealed dominance of GWs with periods of 2-4 h. Band pass filtered vertical velocity perturbations for these periods showed clear downward phase propagation (0.05-0.07 ms- 1) in the upper troposphere and lower stratosphere (UTLS) at different latitude/longitude positions away from the centre of the TC revealing an upward energy propagation of generated GWs. Interestingly, an increase in GW activity during the landfall of the TC is found. FFT in the vertical domain revealed vertical wavelengths ranging from 3 to 8 km

  15. Hydrodynamic modeling and analysis of sea-level rise impacts on salinity for oyster growth in Apalachicola Bay, Florida

    NASA Astrophysics Data System (ADS)

    Huang, Wenrui; Hagen, Scott; Bacopoulos, Peter; Wang, Dingbao

    2015-04-01

    In this study, a previously calibrated hydrodynamic model was applied to investigate the impacts of sea level rise on salinity variations and oyster growth in Apalachicola Bay. With available observed data (winds, tides, and river flow), a case study has been conducted for the period of June 10-July 9, 2005. In addition, sea level rise impacts under a range of river flow conditions have also been examined, which include minimum monthly flow, average monthly flow, and maximum monthly flow based on the flow data from 1977 to 2013. Referring to the case study conditions under the existing sea level, model simulations were conducted to examine salinity changes in the bay in response to the sea level rise scenarios of 0.31 m, 0.5 m and 1.0 m. SLR-induced saline water intrusion mainly enters the estuary from the large opening in the east boundary. Based on the optimal salinity range for oyster growth (20-25 at Cat Point and 17-26 at Dry Bar) in Apalachicola Bay, SLR impacts were evaluated based on the model predicted salinity at Dry Bay and Cat Point. Results indicate that sea level rise results in stronger impacts on Cat Point than Dry Bar. Under the flow conditions of average monthly flow and the observed daily flow during June 10-July 9, mean salinity at Dry Bar varies within 21-24 in the optimal salinity range under 0.31 m and 0.5 m SLR conditions; and further increase above 26.0 when SLR is equal to 1.0 m. Under the conditions of average monthly flow and the observed daily flow during June 10-July 9, the mean salinity at Cat Point is within the optimal range under existing sea level, and increases above the maximum optimal salinity of 27 under the SLR scenarios of 0.31 m, 0.5 m, and 1.0 m, respectively. Extreme low and high flow conditions have also been investigated to examine the combined effects of flow and SLR. At the same sea level rise conditions, salinity under minimum flow is much higher than those under average flow, while salinity under maximum flow is

  16. Mapping the route from naive pluripotency to lineage specification

    PubMed Central

    Kalkan, Tüzer; Smith, Austin

    2014-01-01

    In the mouse blastocyst, epiblast cells are newly formed shortly before implantation. They possess a unique developmental plasticity, termed naive pluripotency. For development to proceed, this naive state must be subsumed by multi-lineage differentiation within 72 h following implantation. In vitro differentiation of naive embryonic stem cells (ESCs) cultured in controlled conditions provides a tractable system to dissect and understand the process of exit from naive pluripotency and entry into lineage specification. Exploitation of this system in recent large-scale RNAi and mutagenesis screens has uncovered multiple new factors and modules that drive or facilitate progression out of the naive state. Notably, these studies show that the transcription factor network that governs the naive state is rapidly dismantled prior to upregulation of lineage specification markers, creating an intermediate state that we term formative pluripotency. Here, we summarize these findings and propose a road map for state transitions in ESC differentiation that reflects the orderly dynamics of epiblast progression in the embryo. PMID:25349449

  17. 77 FR 75071 - Special Conditions: Embraer S.A., Model EMB-550 Airplanes; Electrical/Electronic Equipment Bay...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-19

    ... features, specifically distributed electrical and electronic equipment bays in pressurized areas of the... straightforward airplane flight manual procedure. In distributed electrical/electronic bay installations it is not...-550 airplane has distributed electrical and electronic equipment bays that were not envisioned at...

  18. A numerical model simulation of the regional air pollution meteorology of the greater Chesapeake Bay area - Summer day case study

    NASA Technical Reports Server (NTRS)

    Segal, M.; Pielke, R. A.; Mcnider, R. T.; Mcdougal, D. S.

    1982-01-01

    The mesoscale numerical model of the University of Virginia (UVMM), has been applied to the greater Chesapeake Bay area in order to provide a detailed description of the air pollution meteorology during a typical summer day. This model provides state of the art simulations for land-sea thermally induced circulations. The model-predicted results agree favorably with available observed data. The effects of synoptic flow and sea breeze coupling on air pollution meteorological characteristics in this region, are demonstrated by a spatial and temporal presentation of various model predicted fields. A transport analysis based on predicted wind velocities indicated possible recirculation of pollutants back onto the Atlantic coast due to the sea breeze circulation.

  19. Combined SEM/AVS and attenuation of concentration models for the assessment of bioavailability and mobility of metals in sediments of Sepetiba Bay (SE Brazil).

    PubMed

    Ribeiro, Andreza Portella; Figueiredo, Ana Maria Graciano; dos Santos, José Osman; Dantas, Elizabeth; Cotrim, Marycel Elena Barboza; Figueira, Rubens Cesar Lopes; Silva Filho, Emmanoel V; Wasserman, Julio Cesar

    2013-03-15

    This study proposes a new methodology to study contamination, bioavailability and mobility of metals (Cd, Cu, Ni, Pb, and Zn) using chemical and geostatistics approaches in marine sediments of Sepetiba Bay (SE Brazil). The chemical model of SEM (simultaneously extracted metals)/AVS (acid volatile sulfides) ratio uses a technique of cold acid extraction of metals to evaluate their bioavailability, and the geostatistical model of attenuation of concentrations estimates the mobility of metals. By coupling the two it was observed that Sepetiba Port, the urban area of Sepetiba and the riverine discharges may constitute potential sources of metals to Sepetiba Bay. The metals are concentrated in the NE area of the bay, where they tend to have their lowest mobility, as shown by the attenuation model, and are not bioavailable, as they tend to associate with sulfide and organic matter originated in the mangrove forests of nearby Guaratiba area.

  20. A coupled modelling system for the Irish Sea and Liverpool Bay with application to coastal flood forecasting and beyond

    NASA Astrophysics Data System (ADS)

    Wolf, J.; Bricheno, L. R.; Brown, J. E.; Bolaños, R.

    2012-04-01

    The POLCOMS-WAM coupled wave and hydrodynamic model has been implemented at 1.8km resolution for the Irish Sea and 180m in a nested model of Liverpool Bay. It can be forced with output from the UK Met Office Unified Model. This allows the use of Smith and Banke (1975) and Charnock (1955) formulations for the wind-stress. The former gives an underestimate of the wind-stress, requiring enhanced winds for accurate surge hindcasts. While the latter gives good results for the Irish Sea and Liverpool Bay, with different values of the Charnock coefficient, it also allows the inclusion of a coupled wave stress into the wind-stress (Brown and Wolf, 2009). New results have been obtained by using wind and pressures from the WRF atmospheric model, allowing further development of air-sea coupling. The coupled model also includes bottom friction and the Doppler shift of the waves by the depth-averaged current), as well as advanced coupling procedures: use of the 3D current in the wave physics and calculation of radiation stress and Stokes' drift (Brown et al., 2011). During storm conditions it is found that the radiation stress is the most important term in this shallow water application. However, WAM runs in near real time, making this model only practical for research purposes. The model system has been used to hindcast tides, surges and waves in Liverpool Bay. Data are readily available from the Liverpool Bay Coastal Observatory to quantify the importance of each coupled term with the aim of producing the most accurate model setup for coastal forecasting. A storm event, 18th January 2007, has been hindcast to investigate extreme tide-surge-wave condition both offshore and inshore. During storm events, wave setup in shallow regions can contribute significantly to the total water elevation. The application of a 2D method to calculate radiation stress in a 3D hydrodynamic model is thoroughly examined by comparison with observations and a 3D model (Mellor, 2003). The results show

  1. Environmental consequences of a power plant shut-down: a three-dimensional water quality model of Dublin Bay.

    PubMed

    Bedri, Zeinab; Bruen, Michael; Dowley, Aodh; Masterson, Bartholomew

    2013-06-15

    A hydro-environmental model is used to investigate the effect of cessation of thermal discharges from a power plant on the bathing water quality of Dublin Bay. Before closing down, cooling water from the plant was mixed with sewage effluent prior to its discharge, creating a warmer, less-saline buoyant pollutant plume that adversely affects the water quality of Dublin Bay. The model, calibrated to data from the period prior to the power-plant shut-down (Scenario1), assessed the water quality following its shut-down under two scenarios; (i) Scenario2: continued abstraction of water to dilute sewage effluents before discharge, and (ii) Scnenario3: sewage effluents are discharged directly into the Estuary. Comparison between scenarios was based on distribution of Escherichia coli (E. coli), a main bathing quality indicator. Scenarios1 and 2, showed almost similar E. coli distribution patterns while Scenario3 displayed significantly higher E. coli concentrations due to the increased stratification caused by the lack of prior dilution.

  2. Numerical study of coastal hydrodynamics using a coupled model for Hudhud cyclone in the Bay of Bengal

    NASA Astrophysics Data System (ADS)

    Murty, P. L. N.; Bhaskaran, Prasad K.; Gayathri, R.; Sahoo, Bishnupriya; Srinivasa Kumar, T.; SubbaReddy, B.

    2016-12-01

    The past decade has witnessed an increased intensity of cyclones in the Bay of Bengal region. With higher winds spread over a larger area, the associated risk and coastal vulnerability have increased with wider destructive potential from high waves, storm surges, and associated coastal inundation. The very severe cyclones that made landfall over the Bay of Bengal in the past decade had strong winds in their outer cores, unlike those cyclones that made landfall in previous years. The original parametric wind formulation performs well for more compact cyclones, but at a radial distance far away from the cyclone centre, the winds are under-estimated. Hence, there is a need to revisit and modify this formula for practical applications, and this study attempts to provide a better representation of the overall radial distance in the wind field envelope. The study postulates a 3/5-power law fitted to the original wind formulae, which provides a reasonably good estimate for the surface wind field. The recent very severe cyclones that developed over the Bay of Bengal provided an excellent test-bed to verify this hypothesis, which is supported by validation from six in-situ buoys. The modified wind formula used with a coupled hydrodynamic model (ADCIRC + SWAN) simulated the storm surge and wave characteristics associated with a recent very severe cyclonic storm 'Hudhud' that made landfall in Andhra, located on the east coast of India in 2014. The study also investigated the dependence of coastal geomorphic features and beach slope on the variability of wave-induced setup. Computed significant wave height and storm surge show an excellent match with wave-rider buoy and tide gauge observations.

  3. Investigation of Wave Energy Converter Effects on Near-shore Wave Fields: Model Generation Validation and Evaluation - Kaneohe Bay HI.

    SciTech Connect

    Roberts, Jesse D.; Chang, Grace; Jones, Craig

    2014-09-01

    The numerical model, SWAN (Simulating WAves Nearshore) , was used to simulate wave conditions in Kaneohe Bay, HI in order to determine the effects of wave energy converter ( WEC ) devices on the propagation of waves into shore. A nested SWAN model was validated then used to evaluate a range of initial wave conditions: significant wave heights (H s ) , peak periods (T p ) , and mean wave directions ( MWD) . Differences between wave height s in the presence and absence of WEC device s were assessed at locations in shore of the WEC array. The maximum decrease in wave height due to the WEC s was predicted to be approximately 6% at 5 m and 10 m water depths. Th is occurred for model initiation parameters of H s = 3 m (for 5 m water depth) or 4 m (10 m water depth) , T p = 10 s, and MWD = 330deg . Subsequently, bottom orbital velocities were found to decrease by about 6%.

  4. Post-stratification sampling in small area estimation (SAE) model for unemployment rate estimation by Bayes approach

    NASA Astrophysics Data System (ADS)

    Hanike, Yusrianti; Sadik, Kusman; Kurnia, Anang

    2016-02-01

    This research implemented unemployment rate in Indonesia that based on Poisson distribution. It would be estimated by modified the post-stratification and Small Area Estimation (SAE) model. Post-stratification was one of technique sampling that stratified after collected survey data. It's used when the survey data didn't serve for estimating the interest area. Interest area here was the education of unemployment which separated in seven category. The data was obtained by Labour Employment National survey (Sakernas) that's collected by company survey in Indonesia, BPS, Statistic Indonesia. This company served the national survey that gave too small sample for level district. Model of SAE was one of alternative to solved it. According the problem above, we combined this post-stratification sampling and SAE model. This research gave two main model of post-stratification sampling. Model I defined the category of education was the dummy variable and model II defined the category of education was the area random effect. Two model has problem wasn't complied by Poisson assumption. Using Poisson-Gamma model, model I has over dispersion problem was 1.23 solved to 0.91 chi square/df and model II has under dispersion problem was 0.35 solved to 0.94 chi square/df. Empirical Bayes was applied to estimate the proportion of every category education of unemployment. Using Bayesian Information Criteria (BIC), Model I has smaller mean square error (MSE) than model II.

  5. Higher Surface Ozone Concentrations Over the Chesapeake Bay than Over the Adjacent Land: Observations and Models from the DISCOVER-AQ and CBODAQ Campaigns

    NASA Technical Reports Server (NTRS)

    Goldberg, Daniel L.; Loughner, Christopher P.; Tzortziou, Maria; Stehr, Jeffrey W.; Pickering, Kenneth E.; Marufu, Lackson T.; Dickerson, Russell R.

    2013-01-01

    Air quality models, such as the Community Multiscale Air Quality (CMAQ) model, indicate decidedly higher ozone near the surface of large interior water bodies, such as the Great Lakes and Chesapeake Bay. In order to test the validity of the model output, we performed surface measurements of ozone (O3) and total reactive nitrogen (NOy) on the 26-m Delaware II NOAA Small Research Vessel experimental (SRVx), deployed in the Chesapeake Bay for 10 daytime cruises in July 2011 as part of NASA's GEO-CAPE CBODAQ oceanographic field campaign in conjunction with NASA's DISCOVER-AQ air quality field campaign. During this 10-day period, the EPA O3 regulatory standard of 75 ppbv averaged over an 8-h period was exceeded four times over water while ground stations in the area only exceeded the standard at most twice. This suggests that on days when the Baltimore/Washington region is in compliance with the EPA standard, air quality over the Chesapeake Bay might exceed the EPA standard. Ozone observations over the bay during the afternoon were consistently 10-20% higher than the closest upwind ground sites during the 10-day campaign; this pattern persisted during good and poor air quality days. A lower boundary layer, reduced cloud cover, slower dry deposition rates, and other lesser mechanisms, contribute to the local maximum of ozone over the Chesapeake Bay. Observations from this campaign were compared to a CMAQ simulation at 1.33 km resolution. The model is able to predict the regional maximum of ozone over the Chesapeake Bay accurately, but NOy concentrations are significantly overestimated. Explanations for the overestimation of NOy in the model simulations are also explored

  6. 2D soil and engineering-seismic bedrock modeling of eastern part of Izmir inner bay/Turkey

    NASA Astrophysics Data System (ADS)

    Pamuk, Eren; Akgün, Mustafa; Özdağ, Özkan Cevdet; Gönenç, Tolga

    2017-02-01

    Soil-bedrock models are used as a base when the earthquake-soil common behaviour is defined. Moreover, the medium which is defined as bedrock is classified as engineering and seismic bedrock in itself. In these descriptions, S-wave velocity is (Vs) used as a base. The mediums are called soil where the Vs is < 760 m/s, the bigger ones are called bedrock as well. Additionally, the parts are called engineering bedrock where the Vs is between 3000 m/s and 760 m/s, the parts where are bigger than 3000 m/s called seismic bedrock. The interfacial's horizontal topography where is between engineering and seismic bedrock is effective on earthquake's effect changing on the soil surface. That's why, 2D soil-bedrock models must be used to estimate the earthquake effect that could occur on the soil surface. In this research, surface wave methods and microgravity method were used for occuring the 2D soil-bedrock models in the east of İzmir bay. In the first stage, velocity values were obtained by the studies using surface wave methods. Then, density values were calculated from these velocity values by the help of the empiric relations. 2D soil-bedrock models were occurred based upon both Vs and changing of density by using these density values in microgravity model. When evaluating the models, it was determined that the soil is 300-400 m thickness and composed of more than one layers in parts where are especially closer to the bay. Moreover, it was observed that the soil thickness changes in the direction of N-S. In the study area, geologically, it should be thought the engineering bedrock is composed of Bornova melange and seismic bedrock unit is composed of Menderes massif. Also, according to the geophysical results, Neogene limestone and andesite units at between 200 and 400 m depth show that engineering bedrock characteristic.

  7. Investigation of the spreading and dilution of domestic waste water inputs into a tidal bay using the finite-volume model FVCOM

    NASA Astrophysics Data System (ADS)

    Lettmann, Karsten; Wolff, Jörg-Olaf; Liebezeit, Gerd; Meier, Georg

    2010-05-01

    The 'Jade Bay' is a tidal bay located in the western part of the German Wadden Sea, southern North-Sea coast. During particularly heavy rain falls, rain water mixed with domestic waste water is discharged into the bay due to the limited capacities of the waste water treatment plant of the city of Wilhelmshaven. As the discharge point is located only a few hundred meters from a public bathing beach it is important to know spreading and dilution of the waste waters by tidal and wind-driven mixing. To model the behaviour of the waste water plumes, the unstructured mesh finite-volume model FVCOM (Chen and al., 2003) is used, which allows to cover the large area of the Jade and the nearby North Sea with a relatively high resolution near the point of discharge and a coarser resolution at the outer edges of the study side. We adapted the included sediment module of FVCOM to handle the sedimentation, decay and evolution in the bottom sediments of the discharged waste water particles, especially with respect to bacteria. Furthermore, alternative discharge points located in the interior of the Jade bay were tested, which might be more suited for a faster dilution and a smaller residence time of the waste water particles in the tidal bay.

  8. Mobile Bay turbidity study

    NASA Technical Reports Server (NTRS)

    Crozier, G. F.; Schroeder, W. W.

    1978-01-01

    The termination of studies carried on for almost three years in the Mobile Bay area and adjacent continental shelf are reported. The initial results concentrating on the shelf and lower bay were presented in the interim report. The continued scope of work was designed to attempt a refinement of the mathematical model, assess the effectiveness of optical measurement of suspended particulate material and disseminate the acquired information. The optical characteristics of particulate solutions are affected by density gradients within the medium, density of the suspended particles, particle size, particle shape, particle quality, albedo, and the angle of refracted light. Several of these are discussed in detail.

  9. Joint inversion of seismic traveltime and gravity data: A synthetic study using geologically realistic models from the Voisey's Bay deposit

    NASA Astrophysics Data System (ADS)

    Carter-McAuslan, A.; Lelièvre, P. G.; Farquharson, C.

    2012-12-01

    Seismic methods provide high resolving potential for use in mineral exploration. Unfortunately, complicated hard-rock geology can make seismic data processing and interpretation difficult. It may help to overcome these difficulties by jointly inverting seismic tomography data with gravity data. We investigated the viability of deterministic minimum-structure style joint inversion of seismic traveltime and gravity data for the delineation of geological targets from the Voisey's Bay sulfide deposit in Labrador, Canada. These tests also assessed the potential of employing borehole gravity. A number of synthetic Earth models were created based on the geology of the Eastern Deeps zone of the Voisey's Bay deposit. These models were built on triangular (2D) and tetrahedral (3D) unstructured meshes, allowing for efficient generation of complicated, realistic geological structures. 2D models were based on conceptualized models of the Eastern Deeps. A detailed 3D model was built using information from extensive drilling. Single property and joint inversions were performed with seismic traveltimes and both ground-based and borehole gravity. There is a known relationship between seismic velocity and density for both silicate rocks and sulphide minerals for our study area; this lithological relationship was used to design an appropriate coupling strategy in the joint inversions. Joint inversions were able to successfully locate a buried high contrast target with a variety of survey designs. Experimentation with noise levels, mesh design, and various inversion parameters has lead to a better understanding of how to practically apply joint inversion of traveltimes and gravity data to this and similar exploration problems.

  10. [Ecological carrying capacity of Chinese shrimp stock enhancement in Laizhou Bay of East China based on Ecopath model].

    PubMed

    Lin, Qun; Li, Xian-sen; Li, Zhong-yi; Jin, Xian-shi

    2013-04-01

    Stock enhancement is an important way of fishery resources conservation, which can increase the high quality fishery resources and improve the fish population structure. The study of ecological carrying capacity is the premise for the scientific implementation of stock enhancement. Based on the survey data of the fishery resources and ecological environment in Laizhou Bay from 2009 to 2010, an Ecopath mass-balance model of the Laizhou Bay ecosystem consisted of 26 functional groups was constructed, and applied to analyze the overall characteristics of the ecosystem, the trophic interrelationships, and the keystone species, and to calculate the ecological carrying capacity of Chinese shrimp enhancement. As for the overall characteristics of the ecosystem, the total primary production/total respiration (TPP/TR) was 1. 53, total primary production/total biomass (TPP/B) was 24.54, Finn' s cycling index was lower (0.07), surplus production was higher (434. 41 t km-2 a-1 ), and system connectance index was lower (0. 29), indicating that this ecosystem was at an early development stage. The analysis on the keystone species showed that Chinese shrimp was not a keystone species of this ecosystem. At present, the biomass of Chinese shrimp in the ecosystem was 0. 1143 t km-2, with a greater potential of continued enhancement. It did not exceed the ecological carrying capacity of 2. 9489 t km-2 when the biomass of the Chinese shrimp was increased by 25. 8 times.

  11. Modeling Tidal Stream Energy Extraction and its Effects on Transport Processes in a Tidal Channel and Bay System Using a Three-dimensional Coastal Ocean Model

    SciTech Connect

    Yang, Zhaoqing; Wang, Taiping; Copping, Andrea E.

    2013-02-28

    This paper presents a numerical modeling study for simulating in-stream tidal energy extraction and assessing its effects on the hydrodynamics and transport processes in a tidal channel and bay system connecting to coastal ocean. A marine and hydrokinetic (MHK) module was implemented in a three-dimensional (3-D) coastal ocean model using the momentum sink approach. The MHK model was validated with the analytical solutions for tidal channels under one-dimensional (1-D) conditions. Model simulations were further carried out to compare the momentum sink approach with the quadratic bottom friction approach. The effects of 3-D simulations on the vertical velocity profile, maximum extractable energy, and volume flux reduction across the channel were investigated through a series of numerical experiments. 3-D model results indicate that the volume flux reduction at the maximum extractable power predicted by the 1-D analytical model or two-dimensional (2-D) depth-averaged numerical model may be overestimated. Maximum extractable energy strongly depends on the turbine hub height in the water column, and which reaches a maximum when turbine hub height is located at mid-water depth. Far-field effects of tidal turbines on the flushing time of the tidal bay were also investigated. Model results demonstrate that tidal energy extraction has a greater effect on the flushing time than volume flux reduction, which could negatively affect the biogeochemical processes in estuarine and coastal waters that support primary productivity and higher forms of marine life.

  12. Full Bayes Poisson gamma, Poisson lognormal, and zero inflated random effects models: Comparing the precision of crash frequency estimates.

    PubMed

    Aguero-Valverde, Jonathan

    2013-01-01

    In recent years, complex statistical modeling approaches have being proposed to handle the unobserved heterogeneity and the excess of zeros frequently found in crash data, including random effects and zero inflated models. This research compares random effects, zero inflated, and zero inflated random effects models using a full Bayes hierarchical approach. The models are compared not just in terms of goodness-of-fit measures but also in terms of precision of posterior crash frequency estimates since the precision of these estimates is vital for ranking of sites for engineering improvement. Fixed-over-time random effects models are also compared to independent-over-time random effects models. For the crash dataset being analyzed, it was found that once the random effects are included in the zero inflated models, the probability of being in the zero state is drastically reduced, and the zero inflated models degenerate to their non zero inflated counterparts. Also by fixing the random effects over time the fit of the models and the precision of the crash frequency estimates are significantly increased. It was found that the rankings of the fixed-over-time random effects models are very consistent among them. In addition, the results show that by fixing the random effects over time, the standard errors of the crash frequency estimates are significantly reduced for the majority of the segments on the top of the ranking.

  13. Automated detection of circulating tumor cells with naive Bayesian classifiers.

    PubMed

    Svensson, Carl-Magnus; Krusekopf, Solveigh; Lücke, Jörg; Thilo Figge, Marc

    2014-06-01

    Personalized medicine is a modern healthcare approach where information on each person's unique clinical constitution is exploited to realize early disease intervention based on more informed medical decisions. The application of diagnostic tools in combination with measurement evaluation that can be performed in a reliable and automated fashion plays a key role in this context. As the progression of various cancer diseases and the effectiveness of their treatments are related to a varying number of tumor cells that circulate in blood, the determination of their extremely low numbers by liquid biopsy is a decisive prognostic marker. To detect and enumerate circulating tumor cells (CTCs) in a reliable and automated fashion, we apply methods from machine learning using a naive Bayesian classifier (NBC) based on a probabilistic generative mixture model. Cells are collected with a functionalized medical wire and are stained for fluorescence microscopy so that their color signature can be used for classification through the construction of Red-Green-Blue (RGB) color histograms. Exploiting the information on the fluorescence signature of CTCs by the NBC does not only allow going beyond previous approaches but also provides a method of unsupervised learning that is required for unlabeled training data. A quantitative comparison with a state-of-the-art support vector machine, which requires labeled data, demonstrates the competitiveness of the NBC method.

  14. Light controls cerebral blood flow in naive animals

    PubMed Central

    Rungta, Ravi L; Osmanski, Bruno-Félix; Boido, Davide; Tanter, Mickael; Charpak, Serge

    2017-01-01

    Optogenetics is increasingly used to map brain activation using techniques that rely on functional hyperaemia, such as opto-fMRI. Here we test whether light stimulation protocols similar to those commonly used in opto-fMRI or to study neurovascular coupling modulate blood flow in mice that do not express light sensitive proteins. Combining two-photon laser scanning microscopy and ultrafast functional ultrasound imaging, we report that in the naive mouse brain, light per se causes a calcium decrease in arteriolar smooth muscle cells, leading to pronounced vasodilation, without excitation of neurons and astrocytes. This photodilation is reversible, reproducible and energy-dependent, appearing at about 0.5 mJ. These results impose careful consideration on the use of photo-activation in studies involving blood flow regulation, as well as in studies requiring prolonged and repetitive stimulations to correct cellular defects in pathological models. They also suggest that light could be used to locally increase blood flow in a controlled fashion. PMID:28139643

  15. Applying Naive Bayesian Networks to Disease Prediction: a Systematic Review

    PubMed Central

    Langarizadeh, Mostafa; Moghbeli, Fateme

    2016-01-01

    Introduction: Naive Bayesian networks (NBNs) are one of the most effective and simplest Bayesian networks for prediction. Objective: This paper aims to review published evidence about the application of NBNs in predicting disease and it tries to show NBNs as the fundamental algorithm for the best performance in comparison with other algorithms. Methods: PubMed was electronically checked for articles published between 2005 and 2015. For characterizing eligible articles, a comprehensive electronic searching method was conducted. Inclusion criteria were determined based on NBN and its effects on disease prediction. A total of 99 articles were found. After excluding the duplicates (n= 5), the titles and abstracts of 94 articles were skimmed according to the inclusion criteria. Finally, 38 articles remained. They were reviewed in full text and 15 articles were excluded. Eventually, 23 articles were selected which met our eligibility criteria and were included in this study. Result: In this article, the use of NBN in predicting diseases was described. Finally, the results were reported in terms of Accuracy, Sensitivity, Specificity and Area under ROC curve (AUC). The last column in Table 2 shows the differences between NBNs and other algorithms. Discussion: This systematic review (23 studies, 53,725 patients) indicates that predicting diseases based on a NBN had the best performance in most diseases in comparison with the other algorithms. Finally in most cases NBN works better than other algorithms based on the reported accuracy. Conclusion: The method, termed NBNs is proposed and can efficiently construct a prediction model for disease. PMID:28077895

  16. The South Carolina Coastal Erosion Study: Numerical modeling of circulation and sediment transport in Long Bay, SC

    NASA Astrophysics Data System (ADS)

    Warner, J. C.; Sullivan, C.; Voulgaris, G.; Work, P.; Haas, K.; Hanes, D. M.

    2004-12-01

    Long Bay, South Carolina, is a heavily populated coastal region that supports a large tourism industry. Sand resources are important for both recreation and coastal habitat. Earlier geological framework studies have identified a large sand deposit oblique to the shoreline, oriented clockwise in the offshore direction. This sand feature is ~ 10 km long, 2 km wide, and in excess of 3m thick, possibly providing a source for beach nourishment material. Objectives of this study are to describe the physical processes that control the transport of sediment in Long Bay, specifically off the coast of Myrtle Beach, South Carolina. Specifically we seek to 1) measure and model the oceanographic circulation in the region, 2) identify the processes that maintain the presence of the offshore sand feature, 3) quantify the control that the shoal exerts on the nearshore through changes in wave energy propagation, and 4) identify consequences of removal of the offshore sand feature. Both observational and numerical experiments are used to study the oceanographic circulation and transport of sediment. The observational study is described in an accompanying poster and consists of eight sites that measured tides, surface waves, currents, salinity, temperature, suspended sediment concentrations, and bed forms from October 2003 to April 2004. Numerical modeling for circulation and sediment transport in the study region uses a new version of ROMS (v2.1) that now includes transport of multiple grain sizes, coupling of sediment transport to wave bottom boundary layer models, and evolution of the bottom morphology. The SWAN model is used to compute wave propagation. Results indicate that currents in the study area are strongly influenced by both tidal motion and wind driven setup / setdown. The presence of the offshore sand feature alters the residual flows in the region. Sediment transport is more significant during periods of sustained strong winds that generate local waves. Wind direction

  17. Predicting spatial and temporal distribution of Indo-Pacific lionfish (Pterois volitans) in Biscayne Bay through habitat suitability modeling

    USGS Publications Warehouse

    Bernal, Nicholas A.; DeAngelis, Donald L.; Schofield, Pamela J.; Sullivan Sealey, Kathleen

    2014-01-01

    Invasive species may exhibit higher levels of growth and reproduction when environmental conditions are most suitable, and thus their effects on native fauna may be intensified. Understanding potential impacts of these species, especially in the nascent stages of a biological invasion, requires critical information concerning spatial and temporal distributions of habitat suitability. Using empirically supported environmental variables (e.g., temperature, salinity, dissolved oxygen, rugosity, and benthic substrate), our models predicted habitat suitability for the invasive lionfish (Pterois volitans) in Biscayne Bay, Florida. The use of Geographic Information Systems (GIS) as a platform for the modeling process allowed us to quantify correlations between temporal (seasonal) fluctuations in the above variables and the spatial distribution of five discrete habitat quality classes, whose ranges are supported by statistical deviations from the apparent best conditions described in prior studies. Analysis of the resulting models revealed little fluctuation in spatial extent of the five habitat classes on a monthly basis. Class 5, which represented the area with environmental variables closest to the best conditions for lionfish, occupied approximately one-third of Biscayne Bay, with subsequent habitats declining in area. A key finding from this study was that habitat suitability increased eastward from the coastline, where higher quality habitats were adjacent to the Atlantic Ocean and displayed marine levels of ambient water quality. Corroboration of the models with sightings from the USGS-NAS database appeared to support our findings by nesting 79 % of values within habitat class 5; however, field testing (i.e., lionfish surveys) is necessary to confirm the relationship between habitat classes and lionfish distribution.

  18. Use of multivariate calibration models based on UV-Vis spectra for seawater quality monitoring in Tianjin Bohai Bay, China.

    PubMed

    Liu, Xianhua; Wang, Lili

    2015-01-01

    A series of ultraviolet-visible (UV-Vis) spectra from seawater samples collected from sites along the coastline of Tianjin Bohai Bay in China were subjected to multivariate partial least squares (PLS) regression analysis. Calibration models were developed for monitoring chemical oxygen demand (COD) and concentrations of total organic carbon (TOC). Three different PLS models were developed using the spectra from raw samples (Model-1), diluted samples (Model-2), and diluted and raw samples combined (Model-3). Experimental results showed that: (i) possible nonlinearities in the signal concentration relationships were well accounted for by the multivariate PLS model; (ii) the predicted values of COD and TOC fit the analytical values well; the high correlation coefficients and small root mean squared error of cross-validation (RMSECV) showed that this method can be used for seawater quality monitoring; and (iii) compared with Model-1 and Model-2, Model-3 had the highest coefficient of determination (R2) and the lowest number of latent variables. This latter finding suggests that only large data sets that include data representing different combinations of conditions (i.e., various seawater matrices) will produce stable site-specific regressions. The results of this study illustrate the effectiveness of the proposed method and its potential for use as a seawater quality monitoring technique.

  19. Modeling magnetic fields from a DC power cable buried beneath San Francisco Bay based on empirical measurements

    SciTech Connect

    Kavet, Robert; Wyman, Megan T.; Klimley, A. Peter; Carretero, Luis

    2016-02-25

    Here, the Trans Bay Cable (TBC) is a ±200-kilovolt (kV), 400 MW 85-km long High Voltage Direct Current (DC) buried transmission line linking Pittsburg, CA with San Francisco, CA (SF) beneath the San Francisco Estuary. The TBC runs parallel to the migratory route of various marine species, including green sturgeon, Chinook salmon, and steelhead trout. In July and August 2014, an extensive series of magnetic field measurements were taken using a pair of submerged Geometrics magnetometers towed behind a survey vessel in four locations in the San Francisco estuary along profiles that cross the cable’s path; these included the San Francisco-Oakland Bay Bridge (BB), the Richmond-San Rafael Bridge (RSR), the Benicia- Martinez Bridge (Ben) and an area in San Pablo Bay (SP) in which a bridge is not present. In this paper, we apply basic formulas that ideally describe the magnetic field from a DC cable summed vectorially with the background geomagnetic field (in the absence of other sources that would perturb the ambient field) to derive characteristics of the cable that are otherwise not immediately observable. Magnetic field profiles from measurements taken along 170 survey lines were inspected visually for evidence of a distinct pattern representing the presence of the cable. Many profiles were dominated by field distortions unrelated to the cable caused by bridge structures or other submerged objects, and the cable’s contribution to the field was not detectable. BB, with 40 of the survey lines, did not yield usable data for these reasons. The unrelated anomalies could be up to 100 times greater than those from the cable. In total, discernible magnetic field profiles measured from 76 survey lines were regressed against the equations, representing eight days of measurement. The modeled field anomalies due to the cable (the difference between the maximum and minimum field along the survey line at the cable crossing) were virtually identical to the measured values. The

  20. Modeling Magnetic Fields from a DC Power Cable Buried Beneath San Francisco Bay Based on Empirical Measurements

    PubMed Central

    Kavet, Robert; Wyman, Megan T.; Klimley, A. Peter

    2016-01-01

    The Trans Bay Cable (TBC) is a ±200-kilovolt (kV), 400 MW 85-km long High Voltage Direct Current (DC) buried transmission line linking Pittsburg, CA with San Francisco, CA (SF) beneath the San Francisco Estuary. The TBC runs parallel to the migratory route of various marine species, including green sturgeon, Chinook salmon, and steelhead trout. In July and August 2014, an extensive series of magnetic field measurements were taken using a pair of submerged Geometrics magnetometers towed behind a survey vessel in four locations in the San Francisco estuary along profiles that cross the cable’s path; these included the San Francisco-Oakland Bay Bridge (BB), the Richmond-San Rafael Bridge (RSR), the Benicia-Martinez Bridge (Ben) and an area in San Pablo Bay (SP) in which a bridge is not present. In this paper, we apply basic formulas that ideally describe the magnetic field from a DC cable summed vectorially with the background geomagnetic field (in the absence of other sources that would perturb the ambient field) to derive characteristics of the cable that are otherwise not immediately observable. Magnetic field profiles from measurements taken along 170 survey lines were inspected visually for evidence of a distinct pattern representing the presence of the cable. Many profiles were dominated by field distortions unrelated to the cable caused by bridge structures or other submerged objects, and the cable’s contribution to the field was not detectable. BB, with 40 of the survey lines, did not yield usable data for these reasons. The unrelated anomalies could be up to 100 times greater than those from the cable. In total, discernible magnetic field profiles measured from 76 survey lines were regressed against the equations, representing eight days of measurement. The modeled field anomalies due to the cable (the difference between the maximum and minimum field along the survey line at the cable crossing) were virtually identical to the measured values. The

  1. Modeling magnetic fields from a DC power cable buried beneath San Francisco Bay based on empirical measurements

    DOE PAGES

    Kavet, Robert; Wyman, Megan T.; Klimley, A. Peter; ...

    2016-02-25

    Here, the Trans Bay Cable (TBC) is a ±200-kilovolt (kV), 400 MW 85-km long High Voltage Direct Current (DC) buried transmission line linking Pittsburg, CA with San Francisco, CA (SF) beneath the San Francisco Estuary. The TBC runs parallel to the migratory route of various marine species, including green sturgeon, Chinook salmon, and steelhead trout. In July and August 2014, an extensive series of magnetic field measurements were taken using a pair of submerged Geometrics magnetometers towed behind a survey vessel in four locations in the San Francisco estuary along profiles that cross the cable’s path; these included the Sanmore » Francisco-Oakland Bay Bridge (BB), the Richmond-San Rafael Bridge (RSR), the Benicia- Martinez Bridge (Ben) and an area in San Pablo Bay (SP) in which a bridge is not present. In this paper, we apply basic formulas that ideally describe the magnetic field from a DC cable summed vectorially with the background geomagnetic field (in the absence of other sources that would perturb the ambient field) to derive characteristics of the cable that are otherwise not immediately observable. Magnetic field profiles from measurements taken along 170 survey lines were inspected visually for evidence of a distinct pattern representing the presence of the cable. Many profiles were dominated by field distortions unrelated to the cable caused by bridge structures or other submerged objects, and the cable’s contribution to the field was not detectable. BB, with 40 of the survey lines, did not yield usable data for these reasons. The unrelated anomalies could be up to 100 times greater than those from the cable. In total, discernible magnetic field profiles measured from 76 survey lines were regressed against the equations, representing eight days of measurement. The modeled field anomalies due to the cable (the difference between the maximum and minimum field along the survey line at the cable crossing) were virtually identical to the measured

  2. Integration of bed characteristics, geochemical tracers, current measurements, and numerical modeling for assessing the provenance of beach sand in the San Francisco Bay Coastal System

    USGS Publications Warehouse

    Barnard, Patrick L.; Foxgrover, Amy; Elias, Edwin P.L.; Erikson, Li H.; Hein, James; McGann, Mary; Mizell, Kira; Rosenbauer, Robert J.; Swarzenski, Peter W.; Takesue, Renee K.; Wong, Florence L.; Woodrow, Don

    2013-01-01

    Over 150 million m3 of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach-sized sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.

  3. Risk assessment of TBT in the Japanese short-neck clam ( Ruditapes philippinarum) of Tokyo Bay using a chemical fate model

    NASA Astrophysics Data System (ADS)

    Horiguchi, Fumio; Nakata, Kisaburo; Ito, Naganori; Okawa, Ken

    2006-12-01

    A risk assessment of Tributyltin (TBT) in Tokyo Bay was conducted using the Margin of Exposure (MOE) method at the species level using the Japanese short-neck clam, Ruditapes philippinarum. The assessment endpoint was defined to protect R. philippinarum in Tokyo Bay from TBT (growth effects). A No Observed Effect Concentration (NOEC) for this species with respect to growth reduction induced by TBT was estimated from experimental results published in the scientific literature. Sources of TBT in this study were assumed to be commercial vessels in harbors and navigation routes. Concentrations of TBT in Tokyo Bay were estimated using a three-dimensional hydrodynamic model, an ecosystem model and a chemical fate model. MOEs for this species were estimated for the years 1990, 2000, and 2007. Estimated MOEs for R. philippinarum for 1990, 2000, and 2007 were approximately 1-3, 10, and 100, respectively, indicating a declining temporal trend in the probability of adverse growth effects. A simplified software package called RAMTB was developed by incorporating the chemical fate model and the databases of seasonal flow fields and distributions of organic substances (phytoplankton and detritus) in Tokyo Bay, simulated by the hydrodynamic and ecological model, respectively.

  4. Numerical modeling of the effects of Hurricane Sandy and potential future hurricanes on spatial patterns of salt marsh morphology in Jamaica Bay, New York City

    USGS Publications Warehouse

    Wang, Hongqing; Chen, Qin; Hu, Kelin; Snedden, Gregg A.; Hartig, Ellen K.; Couvillion, Brady R.; Johnson, Cody L.; Orton, Philip M.

    2017-03-29

    The salt marshes of Jamaica Bay, managed by the New York City Department of Parks & Recreation and the Gateway National Recreation Area of the National Park Service, serve as a recreational outlet for New York City residents, mitigate flooding, and provide habitat for critical wildlife species. Hurricanes and extra-tropical storms have been recognized as one of the critical drivers of coastal wetland morphology due to their effects on hydrodynamics and sediment transport, deposition, and erosion processes. However, the magnitude and mechanisms of hurricane effects on sediment dynamics and associated coastal wetland morphology in the northeastern United States are poorly understood. In this study, the depth-averaged version of the Delft3D modeling suite, integrated with field measurements, was utilized to examine the effects of Hurricane Sandy and future potential hurricanes on salt marsh morphology in Jamaica Bay, New York City. Hurricane Sandy-induced wind, waves, storm surge, water circulation, sediment transport, deposition, and erosion were simulated by using the modeling system in which vegetation effects on flow resistance, surge reduction, wave attenuation, and sedimentation were also incorporated. Observed marsh elevation change and accretion from a rod surface elevation table and feldspar marker horizons and cesium-137- and lead-210-derived long-term accretion rates were used to calibrate and validate the wind-waves-surge-sediment transport-morphology coupled model.The model results (storm surge, waves, and marsh deposition and erosion) agreed well with field measurements. The validated modeling system was then used to detect salt marsh morphological change due to Hurricane Sandy across the entire Jamaica Bay over the short-term (for example, 4 days and 1 year) and long-term (for example, 5 and 10 years). Because Hurricanes Sandy (2012) and Irene (2011) were two large and destructive tropical cyclones which hit the northeast coast, the validated coupled

  5. Cenozoic lithospheric evolution of the Bohai Bay Basin, eastern North China Craton: Constraint from tectono-thermal modeling

    NASA Astrophysics Data System (ADS)

    Liu, Qiongying; He, Lijuan; Huang, Fang; Zhang, Linyou

    2016-01-01

    It is well established that the lithosphere beneath the eastern North China Craton (NCC) had been thinned before the Cenozoic. A 2D multi-phase extension model, in which the initial crustal and lithospheric thicknesses are variable, is presented to reconstruct the initial thicknesses of the crust and lithosphere in the early Cenozoic and to further investigate the lithospheric evolution beneath the eastern NCC through the Cenozoic. We conduct thermal modeling along three profiles from east to west in the Bohai Bay Basin, which is the center of the lithospheric destruction and thinning of the NCC. Using multiple constraints, such as tectonic subsidence, the present-day heat flow and the Moho depth, we determine the initial crustal and lithospheric thicknesses of the Bohai Bay Basin before the Cenozoic rift to be 33-36 km and 80-105 km, respectively. The model results show that the most rapid lithospheric thinning during the Cenozoic occurred in the middle Eocene for most depressions, and the thinning activity ceased at the end of the Oligocene, reaching a minimum lithospheric thickness of 53-74 km, followed by a thermal relaxation phase. Combined with previous studies, we infer that the lithosphere beneath the eastern NCC experienced two stages of alternating thinning and thickening: notable thinning in the Early Cretaceous and Paleogene, and thickening in the Late Cretaceous and late Cenozoic. We believe that thermo-chemical erosion, together with extension, was probably the major mechanism of the significant lithospheric removal during the Mesozoic, whereas the Cenozoic lithospheric thinning was mainly dominated by tectonic extension in the eastern NCC; lithospheric thickening was generally a result of thermal cooling.

  6. A SIMPLIFIED MODELING OF FLUSHING AND RESIDENCE TIME IN 42 EMBAYMENTS IN NEW ENGLAND, USA, WITH SPECIAL ATTENTION TO GRENWICH BAY, RHODE ISLAND

    EPA Science Inventory

    A simplified protocol has been developed to meet the need for modeling hydrodynamics and transport in large numbers of embayments quickly and reliably. The procedure is illustrated with 42 embayments in southern New England, USA, giving special attention to Greenwich Bay, RI. The...

  7. Narragansett Bay

    EPA Science Inventory

    Narragansett Bay, situated on the eastern side of Rhode Island, comprises about 15% of the State’s total area. Ninety-five percent of the Bay’s surface area is in Rhode Island with the remainder in southeastern Massachusetts; 60% of the Bay’s watershed is in Massachusetts. At the...

  8. James Bay

    Atmospheric Science Data Center

    2013-04-17

    article title:  First Light over James Bay     View Larger Image MISR "First light", 16:40 UTC, 24 February 2000 . This is the first image of Earth's ... the line of flight. At the top of the image, the dark-to-light transition captures the opening of the MISR cover. Progressing southward, ...

  9. Wave modelling as a proxy for seagrass ecological modelling: Comparing fetch and process-based predictions for a bay and reef lagoon

    NASA Astrophysics Data System (ADS)

    Callaghan, David P.; Leon, Javier X.; Saunders, Megan I.

    2015-02-01

    The distribution, abundance, behaviour, and morphology of marine species is affected by spatial variability in the wave environment. Maps of wave metrics (e.g. significant wave height Hs, peak energy wave period Tp, and benthic wave orbital velocity URMS) are therefore useful for predictive ecological models of marine species and ecosystems. A number of techniques are available to generate maps of wave metrics, with varying levels of complexity in terms of input data requirements, operator knowledge, and computation time. Relatively simple "fetch-based" models are generated using geographic information system (GIS) layers of bathymetry and dominant wind speed and direction. More complex, but computationally expensive, "process-based" models are generated using numerical models such as the Simulating Waves Nearshore (SWAN) model. We generated maps of wave metrics based on both fetch-based and process-based models and asked whether predictive performance in models of benthic marine habitats differed. Predictive models of seagrass distribution for Moreton Bay, Southeast Queensland, and Lizard Island, Great Barrier Reef, Australia, were generated using maps based on each type of wave model. For Lizard Island, performance of the process-based wave maps was significantly better for describing the presence of seagrass, based on Hs, Tp, and URMS. Conversely, for the predictive model of seagrass in Moreton Bay, based on benthic light availability and Hs, there was no difference in performance using the maps of the different wave metrics. For predictive models where wave metrics are the dominant factor determining ecological processes it is recommended that process-based models be used. Our results suggest that for models where wave metrics provide secondarily useful information, either fetch- or process-based models may be equally useful.

  10. Attenuation of morphine tolerance by minocycline and pentoxifylline in naive and neuropathic mice.

    PubMed

    Mika, Joanna; Wawrzczak-Bargiela, Agnieszka; Osikowicz, Maria; Makuch, Wioletta; Przewlocka, Barbara

    2009-01-01

    We have previously demonstrated that glial inhibitors reduce the development of allodynia and hyperalgesia, potentiating the effect of a single morphine dose in a neuropathic pain model. This study explores the effects of two glial activation inhibitors, minocycline and pentoxifylline, on the development of tolerance to morphine in naive and chronic constriction injury (CCI)-exposed mice. Administration of morphine to naive (20 mg/kg; i.p.) and CCI-exposed mice (40 mg/kg; i.p.) twice daily resulted in tolerance to its anti-nociceptive effect after 6 days. Injections of morphine were combined with minocycline (30 mg/kg, i.p.) or pentoxifylline (20 mg/kg, i.p.) administered as two preemptive doses before first morphine administration in naive or pre-injury in CCI-exposed mice, and repeated twice daily 30 min before each morphine administration. With treatment, development of morphine tolerance was delayed by 5 days (from 6 to 11 days), as measured by the tail-flick test in naive and by tail-flick, von Frey, and cold plate tests in CCI-exposed mice. Western blot analysis of CD11b/c and GFAP protein demonstrated that minocycline and pentoxifylline, at doses delaying development of tolerance to morphine analgesia, significantly diminished the morphine-induced increase in CD11b/c protein level. We found that repeated systemic administration of glial inhibitors significantly delays development of morphine tolerance by attenuating the level of this microglial marker under normal and neuropathic pain conditions. Our results support the idea that targeting microglial activation during morphine therapy/treatment is a novel and clinically promising method for enhancing morphine's analgesic effects, especially in neuropathic pain.

  11. Experiment design for nonparametric models based on minimizing Bayes Risk: application to voriconazole[Formula: see text].

    PubMed

    Bayard, David S; Neely, Michael

    2017-04-01

    An experimental design approach is presented for individualized therapy in the special case where the prior information is specified by a nonparametric (NP) population model. Here, a NP model refers to a discrete probability model characterized by a finite set of support points and their associated weights. An important question arises as to how to best design experiments for this type of model. Many experimental design methods are based on Fisher information or other approaches originally developed for parametric models. While such approaches have been used with some success across various applications, it is interesting to note that they largely fail to address the fundamentally discrete nature of the NP model. Specifically, the problem of identifying an individual from a NP prior is more naturally treated as a problem of classification, i.e., to find a support point that best matches the patient's behavior. This paper studies the discrete nature of the NP experiment design problem from a classification point of view. Several new insights are provided including the use of Bayes Risk as an information measure, and new alternative methods for experiment design. One particular method, denoted as MMopt (multiple-model optimal), will be examined in detail and shown to require minimal computation while having distinct advantages compared to existing approaches. Several simulated examples, including a case study involving oral voriconazole in children, are given to demonstrate the usefulness of MMopt in pharmacokinetics applications.

  12. Air-water gas exchange of mercury in the Bay Saint François wetlands: Observation and model parameterization

    NASA Astrophysics Data System (ADS)

    Zhang, Hong H.; Poissant, Laurier; Xu, Xiaohong; Pilote, Martin; Beauvais, Conrad; Amyot, Marc; Garcia, Edenise; Laroulandie, Jerome

    2006-09-01

    Total gaseous mercury (TGM) air-water flux measurements were taken using a dynamic flux chamber (DFC) coupled with a gaseous mercury (Hg) analyzer at the Bay St. François (BSF) wetlands (Quebec, Canada) in summer 2003. The measured TGM fluxes over water exhibited a consistent diurnal pattern, with maximum emissions during daytime and minimum fluxes occurring at night. Pearson correlation analysis showed that solar radiation was the most influential environmental parameter in TGM air-water exchange. Significant correlations were also found between TGM fluxes and 1 hour time-lagged water temperature, indicating the enhancement of fluxes by bacterial activities or chemical reactions. The concentrations of dissolved gaseous mercury (DGM) in water were measured during the 2003 sampling period and indicated that DGM was always supersaturated, which implied that the water body acted primarily as a source of mercury to the atmosphere. Several empirical models of mercury air-water gas exchange were developed and evaluated. Compared to the published models, these proposed models were capable of producing good results, leading to a better agreement between the measured and modeled fluxes (improvements by 48-98%). Among these empirical models, the ones linking TGM fluxes with net radiation were superior because of their strong predictive capability. Two preferred models were selected for air-water TGM flux estimation from Lake St. Pierre's surrounding wetlands. These two models yield a mean emission of 0.19-0.24 kg mercury during May-September each year from 1999 to 2003.

  13. Using Hyperspectral Remote Sensing Models to Determine Phytoplankton Density in the Coastal Waters of Long Bay, South Carolina

    NASA Astrophysics Data System (ADS)

    Harrington, J. E.; Ali, K.

    2013-12-01

    as an index for the estimation of phytoplankton density. Efficiency of the algorithms were evaluated through a least squares regression and residual analysis. Results show that for prediction models of chlorophyll a concentrations, the Oc4v4 by Reilly et al (2000), two -band blue-green empirical algorithm yielded coefficients of determination as high as 0.64 with RMSE=0.29μg/l for an aggregated dataset (n=62, P<0.05). The NIR-red -based two-band algorithm by Dekker et al. (1993) and Gitelson et al. (2000) gave the best chlorophyll a prediction model, with R2 =0.79, RMSE=0.19μg/l. The results illustrate the potential of remote sensing in accounting for the chlorophyll a variability in the turbid waters of Long Bay, SC.

  14. Prescription of Opioids for Opioid-Naive Medical Inpatients

    PubMed Central

    Lail, Sharan; Sequeira, Kelly; Lieu, Jenny; Dhalla, Irfan A

    2014-01-01

    Background: Harms associated with prescription opioids are a major and increasing public health concern. Prescribing of opioids for inpatients may contribute to the problem, especially if primary care practitioners continue opioid therapy that is initiated in hospital. Objectives: To describe the extent and nature of opioid prescribing for opioid-naive patients (i.e., no use of opioids within 2 weeks before admission) on an internal medicine unit. Methods: This single-centre study involved chart review for opioid-naive patients admitted to the internal medicine unit of a large academic health sciences centre in Toronto, Ontario. Over 12 weeks, patients were prospectively identified for the study, and charts were later reviewed to characterize opioid use during the hospital stay and upon discharge. The primary outcomes were the proportions of opioid-naive patients for whom opioids were prescribed in hospital and upon discharge. Data on serious adverse events related to opioid use (e.g., need for naloxone or occurrence of falls) were also collected through chart review. Results: From July 4 to September 22, 2011, a total of 721 patients were admitted to the study unit, of whom 381 (53%) were classified as opioid-naive. Opioids were prescribed for 82 (22%) of these opioid-naive patients while they were in hospital. Among the opioid-naive patients, there were a total of 247 opioid prescriptions, with hydromorphone (110 prescriptions) and morphine (92 prescriptions) being the drugs most commonly prescribed. For 23 (28%) of the patients with a prescription for opioids in hospital (6% of all opioid-naive patients), an opioid was also prescribed upon discharge. The indication for opioids was documented in 16 (70%) of the 23 discharge prescriptions. No adverse events or deaths related to opioid use were identified during the hospital stays. Conclusions: Among opioid-naive patients admitted to the internal medicine unit, opioids were prescribed for about 1 in 5 patients, and

  15. Using Remotely Sensed Data and Watershed and Hydrodynamic Models to Evaluate the Effects of Land Cover Land Use Change on Aquatic Ecosystems in Mobile Bay, AL

    NASA Technical Reports Server (NTRS)

    Al-Hamdan, Mohammad; Estes, Maurice G., Jr.; Judd, Chaeli; Woodruff, Dana; Ellis, Jean; Quattrochi, Dale; Watson, Brian; Rodriquez, Hugo; Johnson, Hoyt

    2012-01-01

    Alabama coastal systems have been subjected to increasing pressure from a variety of activities including urban and rural development, shoreline modifications, industrial activities, and dredging of shipping and navigation channels. The impacts on coastal ecosystems are often observed through the use of indicator species. One such indicator species for aquatic ecosystem health is submerged aquatic vegetation (SAV). Watershed and hydrodynamic modeling has been performed to evaluate the impact of land cover land use (LCLU) change in the two counties surrounding Mobile Bay (Mobile and Baldwin) on SAV stressors and controlling factors (temperature, salinity, and sediment) in the Mobile Bay estuary. Watershed modeling using the Loading Simulation Package in C++ (LSPC) was performed for all watersheds contiguous to Mobile Bay for LCLU scenarios in 1948, 1992, 2001, and 2030. Remotely sensed Landsat-derived National Land Cover Data (NLCD) were used in the 1992 and 2001 simulations after having been reclassified to a common classification scheme. The Prescott Spatial Growth Model was used to project the 2030 LCLU scenario based on current trends. The LSPC model simulations provided output on changes in flow, temperature, and sediment for 22 discharge points into the estuary. These results were inputted in the Environmental Fluid Dynamics Computer Code (EFDC) hydrodynamic model to generate data on changes in temperature, salinity, and sediment on a grid throughout Mobile Bay and adjacent estuaries. The changes in the aquatic ecosystem were used to perform an ecological analysis to evaluate the impact on SAV habitat suitability. This is the key product benefiting the Mobile Bay coastal environmental managers that integrates the influences of temperature, salinity, and sediment due to LCLU driven flow changes with the restoration potential of SAVs. Data products and results are being integrated into NOAA s EcoWatch and Gulf of Mexico Data Atlas online systems for

  16. Using Remotely Sensed Data and Hydrologic Models to Evaluate the Effects of Climate Change on Shallow Aquatic Ecosystems in the Mobile Bay, AL Estuary

    NASA Technical Reports Server (NTRS)

    Estes, M. G.; Al-Hamdan, M. Z.; Thom, R.; Judd, C.; Woodruff, D.; Ellis, J. T.; Quattrochi, D.; Swann, R.

    2012-01-01

    Coastal systems in the northern Gulf of Mexico, including the Mobile Bay, AL estuary, are subject to increasing pressure from a variety of activities including climate change. Climate changes have a direct effect on the discharge of rivers that drain into Mobile Bay and adjacent coastal water bodies. The outflows change water quality (temperature, salinity, and sediment concentrations) in the shallow aquatic areas and affect ecosystem functioning. Mobile Bay is a vital ecosystem that provides habitat for many species of fauna and flora. Historically, submerged aquatic vegetation (SAV) and seagrasses were found in this area of the northern Gulf of Mexico; however the extent of vegetation has significantly decreased over the last 60 years. The objectives of this research are to determine: how climate changes affect runoff and water quality in the estuary and how these changes will affect habitat suitability for SAV and seagrasses. Our approach is to use watershed and hydrodynamic modeling to evaluate the impact of climate change on shallow water aquatic ecosystems in Mobile Bay and adjacent coastal areas. Remotely sensed Landsat data were used for current land cover land use (LCLU) model input and the data provided by Intergovernmental Panel on Climate Change (IPCC) of the future changes in temperature, precipitation, and sea level rise were used to create the climate scenarios for the 2025 and 2050 model simulations. Project results are being shared with Gulf coast stakeholders through the Gulf of Mexico Data Atlas to benefit coastal policy and climate change adaptation strategies.

  17. Using Remotely Sensed Data and Hydrologic Models to Evaluate the Effects of Climate Change on Shallow Aquatic Ecosystems in the Mobile Bay, AL Estuary

    NASA Astrophysics Data System (ADS)

    Estes, M. G.; Al-Hamdan, M. Z.; Thom, R.; Judd, C.; Ellis, J.; Woodruff, D.; Quattrochi, D.; Rose, K.; Swann, R.

    2012-12-01

    Coastal systems in the northern Gulf of Mexico, including the Mobile Bay, AL estuary, are subject to increasing pressure from a variety of activities including climate change. Climate changes have a direct effect on the discharge of rivers that drain into Mobile Bay and adjacent coastal water bodies. The outflows change water quality (temperature, salinity, and sediment concentrations) in the shallow aquatic areas and affect ecosystem functioning. Mobile Bay is a vital ecosystem that provides habitat for many species of fauna and flora. Historically, submerged aquatic vegetation (SAV) and seagrasses were found in this area of the northern Gulf of Mexico; however the extent of vegetation has significantly decreased over the last 60 years. The objectives of this research are to determine: how climate changes affect runoff and water quality in the estuary and how these changes will affect habitat suitability for SAV and seagrasses. Our approach is to use watershed and hydrodynamic modeling to evaluate the impact of climate change on shallow water aquatic ecosystems in Mobile Bay and adjacent coastal areas. Remotely sensed Landsat data were used for current land cover land use (LCLU) model input and the data provided by Intergovernmental Panel on Climate Change (IPCC) of the future changes in temperature, precipitation, and sea level rise were used to create the climate scenarios for the 2025 and 2050 model simulations. Project results are being shared with Gulf coast stakeholders through the Gulf of Mexico Data Atlas to benefit coastal policy and climate change adaptation strategies.

  18. Using Remotely Sensed Data and Watershed and Hydrodynamic Models to Evaluate the Effects of Land Cover Land Use Change on Aquatic Ecosystems in Mobile Bay, AL

    NASA Technical Reports Server (NTRS)

    Al-Hamdan, Mohammad Z.; Estes, Maurice G., Jr.; Judd, Chaeli; Thom, Ron; Woodruff, Dana; Ellis, Jean T.; Quattrochi, Dale; Watson, Brian; Rodriquez, Hugo; Johnson, Hoyt

    2012-01-01

    Alabama coastal systems have been subjected to increasing pressure from a variety of activities including urban and rural development, shoreline modifications, industrial activities, and dredging of shipping and navigation channels. The impacts on coastal ecosystems are often observed through the use of indicator species. One such indicator species for aquatic ecosystem health is submerged aquatic vegetation (SAV). Watershed and hydrodynamic modeling has been performed to evaluate the impact of land cover land use (LCLU) change in the two counties surrounding Mobile Bay (Mobile and Baldwin) on SAV stressors and controlling factors (temperature, salinity, and sediment) in the Mobile Bay estuary. Watershed modeling using the Loading Simulation Package in C++ (LSPC) was performed for all watersheds contiguous to Mobile Bay for LCLU scenarios in 1948, 1992, 2001, and 2030. Remotely sensed Landsat-derived National Land Cover Data (NLCD) were used in the 1992 and 2001 simulations after having been reclassified to a common classification scheme. The Prescott Spatial Growth Model was used to project the 2030 LCLU scenario based on current trends. The LSPC model simulations provided output on changes in flow, temperature, and sediment for 22 discharge points into the estuary. These results were inputted in the Environmental Fluid Dynamics Computer Code (EFDC) hydrodynamic model to generate data on changes in temperature, salinity, and sediment on a grid throughout Mobile Bay and adjacent estuaries. The changes in the aquatic ecosystem were used to perform an ecological analysis to evaluate the impact on SAV habitat suitability. This is the key product benefiting the Mobile Bay coastal environmental managers that integrates the influences of temperature, salinity, and sediment due to LCLU driven flow changes with the restoration potential of SAVs. Data products and results are being integrated into NOAA s EcoWatch and Gulf of Mexico Data Atlas online systems for

  19. Assessing development pressure in the Chesapeake Bay watershed: An evaluation of two land-use change models

    USGS Publications Warehouse

    Claggett, P.R.; Jantz, C.A.; Goetz, S.J.; Bisland, C.

    2004-01-01

    Natural resource lands in the Chesapeake Bay watershed are increasingly susceptible to conversion into developed land uses, particularly as the demand for residential development grows. We assessed development pressure in the Baltimore-Washington, DC region, one of the major urban and suburban centers in the watershed. We explored the utility of two modeling approaches for forecasting future development trends and patterns by comparing results from a cellular automata model, SLEUTH (slope, land use, excluded land, urban extent, transportation), and a supply/demand/allocation model, the Western Futures Model. SLEUTH can be classified as a land-cover change model and produces projections on the basis of historic trends of changes in the extent and patterns of developed land and future land protection scenarios. The Western Futures Model derives forecasts from historic trends in housing units, a U.S. Census variable, and exogenously supplied future population projections. Each approach has strengths and weaknesses, and combining the two has advantages and limitations. ?? 2004 Kluwer Academic Publishers.

  20. Three dimensional numerical modeling of Hydrodynamics and sediment transport in the Mississippi River Diversion at West Bay

    NASA Astrophysics Data System (ADS)

    Sadid, K. M.; Meselhe, E. A.; Roth, B.; Allison, M. A.

    2013-12-01

    The coastal wetlands of Louisiana have been experiencing high rates of land subsidence and erosion for decades. Anthropogenic alterations to the hydrology and geology, powerful hurricanes, and relative sea level rise have caused major coastal land loss in Louisiana. After years of research and discussions, the use of sediment diversions from the Mississippi River to adjacent embayment areas were proposed and further authorized as a solution for land building. To this end, the West Bay diversion (WBD) was constructed in 2003 to restore approximately 9,831 acres of wetlands in the West Bay area under the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA). The WBD is located along the right-descending bank of the Mississippi River south of Venice, LA near River Mile (RM) 4.7. The initial size of the channel post-construction was designed to convey 20,000 cubic feet per second (cfs), and over time it was anticipated to support a maximum of 50,000 cfs. This sediment diversion provides an opportunity to examine and analyze the impact of such diversion on the morphology of the river channel, and the retention characteristics and rate of delta growth in the receiving basin. Additionally, the WBD serve as analogue to fully validate morphologic models that could consequently be used to model proposed land building sediment diversions in the Lower Mississippi River. In this study a three-dimensional numerical model is developed for the WBD which includes the main channel of the Mississippi River as well as the receiving basin. The model is being calibrated and validated for hydrodynamics and morphology using detailed field observations. Since 2003 regular monitoring has taken place as per the CWPPRA project guidelines. This includes bathymetric surveys of the receiving basin from 2002 (pre-construction), 2003, 2006, and 2009. A recent monitoring survey has been completed and will be available in the near future. In addition to this monitoring data, the U

  1. An individual-based modeling approach to spawning-potential per-recruit models: An application to blue crab (Callinectes sapidus) in Chesapeake Bay

    USGS Publications Warehouse

    Bunnell, D.B.; Miller, T.J.

    2005-01-01

    An individual-based modeling approach to estimate biological reference points for blue crabs (Callinectes sapidus) in Chesapeake Bay offered several advantages over conventional models: (i) known individual variation in size and growth rate could be incorporated, (ii) the underlying discontinuous growth pattern could be simulated, and (iii) the complexity of the fishery, where vulnerability is based on size, shell status (e.g., soft, hard), maturity, and sex could be accommodated. Across a range of natural mortality (M) scenarios (0.375-1.2??year-1), we determined the exploitation fraction (??) and fishing mortality (F) that protected 20% of the spawning potential of an unfished population, the current target. As M increased, ??20% and F-20% decreased. Assuming that M = 0.9??year-1, our models estimated ??20% = 0.45, which is greater than field-based estimates of ?? in 64% of the years since 1990. Hence, the commercial fishery has likely contributed to the recent population decline in Chesapeake Bay. Comparisons of our results with conventional per-recruit approaches indicated that incorporating the complexity of the fishery was the most important advantage in our individual-based modeling approach. ?? 2005 NRC.

  2. Simple model of dissolved oxygen consumption in a bay within high organic loading: an applied remediation tool.

    PubMed

    Ahumada, Ramón; Vargas, José; Pagliero, Liliana

    2006-07-01

    San Vicente Bay is a coastal shallow embayment in Central Chile with multiple uses, one of which is receiving wastewater from industrial fisheries, steel mill effluents, and domestic sewage. A simulation model was developed and applied to dissolved oxygen consumption by organic residues released into this embayment. Three compartments were established as function of: depth, circulation and outfall location. The model compartments had different volumes, and their oxygen saturation value was used as baseline. The parameters: (a) BOD5 of the industrial and urban effluents, (b) oxygen demand by organic sediments, (c) respiration, (d) photosynthesis and (e) re-aeration were included in the model. Iteration results of the model showed severe alterations in Compartment 1, with a decrease of 65% in the oxygen below saturation. Compartment 2 showed a small decline (10%) and compartment 3 did not show apparent changes in oxygen values. Measures recommended for remediation were to decrease the BOD5 loading by 30% in the affected sector. Iteration of the model for 200 h following recommendations derived from the preceding results produced an increase in saturation of 60% (5 ml O2 L(-1)), which suggested an improvement of the environmental conditions.

  3. Bayes factors and multimodel inference

    USGS Publications Warehouse

    Link, W.A.; Barker, R.J.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    Multimodel inference has two main themes: model selection, and model averaging. Model averaging is a means of making inference conditional on a model set, rather than on a selected model, allowing formal recognition of the uncertainty associated with model choice. The Bayesian paradigm provides a natural framework for model averaging, and provides a context for evaluation of the commonly used AIC weights. We review Bayesian multimodel inference, noting the importance of Bayes factors. Noting the sensitivity of Bayes factors to the choice of priors on parameters, we define and propose nonpreferential priors as offering a reasonable standard for objective multimodel inference.

  4. Modeling the marine magnetic field of Bahía de Banderas, Mexico, confirms the half-graben structure of the bay

    NASA Astrophysics Data System (ADS)

    Alvarez, Román; López-Loera, Héctor; Arzate, Jorge

    2010-06-01

    An existing aeromagnetic survey flown on the central, western portion of Mexico did not include an important tectonic structure: Bahía de Banderas. The bay has an extension of approximately 1400 km 2 and is located within the Puerto Vallarta batholith, a granitic structure of Cretaceous origin. We report here the additional gathering of 5523 magnetic values on the bay, in order to complement the existing land aeromagnetic information; this allowed modeling the structure of the bay from the magnetic viewpoint. A late Miocene age has been proposed for the bay making it roughly contemporaneous with the first stages of separation of Baja California from mainland Mexico. Initially proposed as a graben, it was subsequently shown that its structure actually corresponds to a half-graben of the fault growth type, with reverse drag geometry; it appears to have been developed in response to an extensional process in the ˜ N-S direction. Valle de Banderas neighbors the bay constituting its eastern land continuation; it has also been proposed as a graben and it is also likely the result of an extensional process. However, it seems to be a structure more recently formed, probably around 5 Ma. The different time origin of the bay and of the valley is strengthened by the different alignment of the valley axis, where Ameca River flows and discharges into the bay, of around 30° from the trace of Banderas fault. The magnetic responses of the valley, aeromagnetic and terrestrial, support the existence of an extensional process. Upward and downward continuations of the magnetic fields show that Sierra de Vallejo and Sierra de Zapotán, to the NW of the valley, are deeply rooted structures and their magnetic responses are similar to those obtained in the Puerto Vallarta batholith; these characteristics support a common origin for them. Three magnetic profiles trending NNW are modeled across Bahía de Banderas. The models identify the structure as a half-graben with a listric main

  5. Monitoring and modeling conditions for regional shallow landslide initiation in the San Francisco Bay area, California

    NASA Astrophysics Data System (ADS)

    Collins, B. D.; Stock, J. D.; Godt, J. W.

    2012-12-01

    Intense winter storms in the San Francisco Bay area (SFBA) of California often trigger widespread landsliding, including debris flows that originate as shallow (<3 m) landslides. The strongest storms result in the loss of lives and millions of dollars in damage. Whereas precipitation-based rainfall intensity-duration landslide initiation thresholds are available for the SFBA, antecedent soil moisture conditions also play a major role in determining the likelihood for landslide generation from a given storm. Previous research has demonstrated that antecedent triggering conditions can be obtained using pre-storm precipitation thresholds (e.g., 250-400 mm of seasonal pre-storm rainfall). However, these types of thresholds do not account for the often cyclic pattern of wetting and drying that can occur early in the winter storm season (i.e. October - December), and which may skew the applicability of precipitation-only based thresholds. To account for these cyclic and constantly evolving soil moisture conditions, we have pursued methods to measure soil moisture directly and integrate these measurements into predictive analyses. During the past three years, the USGS installed a series of four subsurface hydrology monitoring stations in shallow landslide-prone locations of the SFBA to establish a soil-moisture-based antecedent threshold. In addition to soil moisture sensors, the monitoring stations are each equipped with piezometers to record positive pore water pressure that is likely required for shallow landslide initiation and a rain gauge to compare storm intensities with existing precipitation-based thresholds. Each monitoring station is located on a natural, grassy hillslope typically composed of silty sands, underlain by sandstone, sloping at approximately 30°, and with a depth to bedrock of approximately 1 meter - conditions typical of debris flow generation in the SFBA. Our observations reveal that various locations respond differently to seasonal

  6. Tampa Bay as a model estuary for examining the impact of human activities on biogeochemical processes: an introduction

    USGS Publications Warehouse

    Swarzenski, Peter W.; Baskaran, Mark; Henderson, Carl S.; Yates, Kim

    2007-01-01

    Tampa Bay is a shallow, Y-shaped coastal embayment that is located along the center of the Florida Platform – an expansive accumulation of Cretaceous–Tertiary shallow-water carbonates and evaporites that were periodically exposed during glacio–eustatic sea level fluctuations. As a consequence, extensive karstification likely had a controlling impact on the geologic evolution of Tampa Bay. Despite its large aerial size (∼ 1000 km2), Tampa Bay is relatively shallow (mean depth = 4 m) and its watershed (6700 km2) is among the smallest in the Gulf of Mexico. About 85% of all freshwater inflow (mean = 63 m3 s-1) to the bay is carried by four principal tributaries (Orlando et al., 1993). Groundwater makes up an important component of baseflow of these coastal streams and may also be important in delivering nutrients and other constituents to the bay proper by submarine groundwater discharge.

  7. Three Naive Questions: Addressed to the Modern Educational Optimism

    ERIC Educational Resources Information Center

    Krstic, Predrag

    2016-01-01

    This paper aims to question anew the popular and supposedly self-evident affirmation of education, in its modern incarnation as in its historical notion. The "naive" questions suggest that we have recently taken for granted that education ought to be for the masses, that it ought to be upbringing, and that it is better than ignorance.…

  8. Theory-Driven Science and Naive Empiricism in Counseling Psychology.

    ERIC Educational Resources Information Center

    Strong, Stanley R.

    1991-01-01

    Asserts that counseling psychologists' aversion to theory-driven science and their enthusiasm for naive empiricism impede scientific progress. Identifies "received view" of science as theory-driven science, points out symptoms and consequences of the failure to apply this view, and argues that greater scientific progress will result from moving…

  9. Naive vs. Sophisticated Methods of Forecasting Public Library Circulations.

    ERIC Educational Resources Information Center

    Brooks, Terrence A.

    1984-01-01

    Two sophisticated--autoregressive integrated moving average (ARIMA), straight-line regression--and two naive--simple average, monthly average--forecasting techniques were used to forecast monthly circulation totals of 34 public libraries. Comparisons of forecasts and actual totals revealed that ARIMA and monthly average methods had smallest mean…

  10. Thinking Process of Naive Problem Solvers to Solve Mathematical Problems

    ERIC Educational Resources Information Center

    Mairing, Jackson Pasini

    2017-01-01

    Solving problems is not only a goal of mathematical learning. Students acquire ways of thinking, habits of persistence and curiosity, and confidence in unfamiliar situations by learning to solve problems. In fact, there were students who had difficulty in solving problems. The students were naive problem solvers. This research aimed to describe…

  11. A Workshop for High School Students on Naive Set Theory

    ERIC Educational Resources Information Center

    Wegner, Sven-Ake

    2014-01-01

    In this article we present the prototype of a workshop on naive set theory designed for high school students in or around the seventh year of primary education. Our concept is based on two events which the author organized in 2006 and 2010 for students of elementary school and high school, respectively. The article also includes a practice report…

  12. Children's Conceptions of Mental Illness: A Naive Theory Approach

    ERIC Educational Resources Information Center

    Fox, Claudine; Buchanan-Barrow, Eithne; Barrett, Martyn

    2010-01-01

    This paper reports two studies that investigated children's conceptions of mental illness using a naive theory approach, drawing upon a conceptual framework for analysing illness representations which distinguishes between the identity, causes, consequences, curability, and timeline of an illness. The studies utilized semi-structured interviewing…

  13. Simultaneous learning and filtering without delusions: a Bayes-optimal combination of Predictive Inference and Adaptive Filtering.

    PubMed

    Kneissler, Jan; Drugowitsch, Jan; Friston, Karl; Butz, Martin V

    2015-01-01

    Predictive coding appears to be one of the fundamental working principles of brain processing. Amongst other aspects, brains often predict the sensory consequences of their own actions. Predictive coding resembles Kalman filtering, where incoming sensory information is filtered to produce prediction errors for subsequent adaptation and learning. However, to generate prediction errors given motor commands, a suitable temporal forward model is required to generate predictions. While in engineering applications, it is usually assumed that this forward model is known, the brain has to learn it. When filtering sensory input and learning from the residual signal in parallel, a fundamental problem arises: the system can enter a delusional loop when filtering the sensory information using an overly trusted forward model. In this case, learning stalls before accurate convergence because uncertainty about the forward model is not properly accommodated. We present a Bayes-optimal solution to this generic and pernicious problem for the case of linear forward models, which we call Predictive Inference and Adaptive Filtering (PIAF). PIAF filters incoming sensory information and learns the forward model simultaneously. We show that PIAF is formally related to Kalman filtering and to the Recursive Least Squares linear approximation method, but combines these procedures in a Bayes optimal fashion. Numerical evaluations confirm that the delusional loop is precluded and that the learning of the forward model is more than 10-times faster when compared to a naive combination of Kalman filtering and Recursive Least Squares.

  14. Drivers of circulation in a fringing coral reef embayment: A wave-flow coupled numerical modeling study of Hanalei Bay, Hawaii

    NASA Astrophysics Data System (ADS)

    Hoeke, Ron K.; Storlazzi, Curt D.; Ridd, Peter V.

    2013-04-01

    A coupled wave-circulation numerical model of Hanalei Bay, Hawaii, was constructed to investigate controls on nearshore hydrodynamics and overall circulation of a bathymetrically-complex coral reef embayment that is exposed to large waves and river floods several times per annum. The model was calibrated using in situ data representative of the two conditions that dominate the region's wave climate: one associated with local trade winds and associated trade-wind waves, and the other with distant-source episodic large swells. The model results were improved by including spatially-varying hydrodynamic bed roughness and making the semi-empirical wave-breaking parameter dependent on incident wave steepness and reef slope. During trade-wind conditions, circulation was primarily wind-driven and volume flux-based flushing times of the bay were on the order of 35 h. Under the episodic swell conditions, circulation were dominated by wave-driven flows and flushing times decreased to as little as 2 h. The vigorous hydrodynamics that occur during the upper 10% most energetic swell conditions indicate that only a few (0-10) events each year are likely capable of exporting significant volumes of sediment from the bay. Like many fringing reef areas backed by steep-sided watersheds on tropical and sub-tropical high islands worldwide, Hanalei Bay receives high episodic fluvial sediment load during a similarly low number of flood events. These similarly episodic but decoupled processes of sediment delivery and removal identified here suggest that the water quality and sedimentary environment of Hanalei Bay and similar linked watershed-reef systems are sensitive to changes in annual storm frequency and intensity.

  15. A numerical modeling analysis of the phytoplankton and nutrients dynamics for Todos Santos Bay and northwestern Baja California

    NASA Astrophysics Data System (ADS)

    Cruz Rico, J. E., Sr.; Rivas, D.

    2015-12-01

    A tridimensional physical-biological numerical model is implemented for the Todos Santos Bay and the northwest of Baja California to investigate the mechanics and ecological processes associated with the regional plankton dynamics. An NPZD (Nitrate, Phytoplankton, Zooplankton, and Detritus) ecosystem simple model is used to describe the distribution and evolution of the lower trophic levels in the area of study. The model adequately reproduces the spatial distribution of the concentration of chlorophyll for the different seasons of the year. In general, the distribution of the subsurface chlorophyll maximum (SCM) depends primarily on the seasonal circulation patterns, the total solar irradiance, and the vertical flux of nutrients. Interannual variability shows two extreme years in the analyzed period: 2006 and 2007. Year 2006 was an anomalous warm year, with a weak upwelling activity and low chlorophyll concentrations compared to year 2011. These anomalies are related to the activity of the Pacific Decadal Oscillation, the El Niño+3, and the regional Outgoing Longwave Radiation. Thus, in spite of the simplicity of the NPZD model, both temporal and spatial patterns of distribution of chlorophyll and nutrients are generally reproduced.

  16. Nitrogen transfers off Walvis Bay: a 3-D coupled physical/biogeochemical modeling approach in the Namibian upwelling system

    NASA Astrophysics Data System (ADS)

    Gutknecht, E.; Dadou, I.; Marchesiello, P.; Cambon, G.; Le Vu, B.; Sudre, J.; Garçon, V.; Machu, E.; Rixen, T.; Kock, A.; Flohr, A.; Paulmier, A.; Lavik, G.

    2013-06-01

    Eastern boundary upwelling systems (EBUS) are regions of high primary production often associated with oxygen minimum zones (OMZs). They represent key regions for the oceanic nitrogen (N) cycle. By exporting organic matter (OM) and nutrients produced in the coastal region to the open ocean, EBUS can play an important role in sustaining primary production in subtropical gyres. However, losses of fixed inorganic N through denitrification and anammox processes take place in oxygen depleted environments such as EBUS, and can potentially mitigate the role of these regions as a source of N to the open ocean. EBUS can also represent a considerable source of nitrous oxide (N2O) to the atmosphere, affecting the atmospheric budget of N2O. In this paper a 3-D coupled physical/biogeochemical model (ROMS/BioEBUS) is used to investigate the N budget in the Namibian upwelling system. The main processes linked to EBUS and associated OMZs are taken into account. The study focuses on the northern part of the Benguela upwelling system (BUS), especially the Walvis Bay area (between 22° S and 24° S) where the OMZ is well developed. Fluxes of N off the Walvis Bay area are estimated in order to understand and quantify (1) the total N offshore export from the upwelling area, representing a possible N source that sustains primary production in the South Atlantic subtropical gyre; (2) export production and subsequent losses of fixed N via denitrification and anammox under suboxic conditions (O2 < 25 mmol O2 m-3); and (3) the N2O emission to the atmosphere in the upwelling area. In the mixed layer, the total N offshore export is estimated as 8.5 ± 3.9 × 1010 mol N yr-1 at 10° E off the Walvis Bay area, with a mesoscale contribution of 20%. Extrapolated to the whole BUS, the coastal N source for the subtropical gyre corresponds to 0.1 ± 0.04 mol N m-2 yr-1. This N flux represents a major source of N for the gyre compared with other N sources, and contributes 28% of the new primary

  17. Galveston Bay

    USGS Publications Warehouse

    Handley, Lawrence R.; Spear, Kathryn A.; Eleonor Taylor,; Thatcher, Cindy

    2011-01-01

    The Galveston Bay estuary is located on the upper Texas Gulf coast (Lester and Gonzalez, 2002). It is composed of four major sub-bays—Galveston, Trinity, East, and West Bays. It is Texas’ largest estuary on the Gulf Coast with a total area of 155,399 hectares (384,000 acres) and 1,885 km (1,171 miles) of shoreline (Burgan and Engle, 2006). The volume of the bay has increased over the past 50 years due to subsidence, dredging, and sea level rise. Outside of ship channels, the maximum depth is only 3.7 m (12 ft), with the average depth ranging from 1.2 m (4 ft) to 2.4 m (8 ft)— even shallower in areas with widespread oyster reefs (Lester and Gonzalez, 2002). The tidal range is less than 0.9 m (3 ft), but water levels and circulation are highly influenced by wind. The estuary was formed in a drowned river delta, and its bayous were once channels of the Brazos and Trinity Rivers. Today, the watersheds surrounding the Trinity and San Jacinto Rivers, along with many other smaller bayous, feed into the bay. The entire Galveston Bay watershed is 85,470 km2 (33,000 miles2 ) large (Figure 1). Galveston Island, a 5,000 year old sand bar that lies at the western edge of the bay’s opening into the Gulf of Mexico, impedes the freshwater flow of the Trinity and San Jacinto Rivers into the Gulf, the majority of which comes from the Trinity. The Bolivar Peninsula lies at the eastern edge of the bay’s opening into the Gulf. Water flows into the Gulf at Bolivar Roads, 1 U.S. Geological Survey National Wetlands Research Center, 700 Cajundome Blvd., Lafayette, LA 70506 2 Harte Research Institute for Gulf of Mexico Studies, Texas A&M University - Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, Texas 78412 2 Galveston Pass, between Galveston Island and Bolivar Peninsula, and at San Luis Pass, between the western side of Galveston Island and Follets Island.

  18. An ecological model of the artificial ecosystem (northern Hangzhou Bay, China): analysis of ecosystem structure and fishing impacts

    NASA Astrophysics Data System (ADS)

    Chen, Zuozhi; Xu, Shannan; He, Peimin

    2011-06-01

    The artificial ecosystem is a large-scale enclosure in northern Hangzhou Bay, China. Using the Ecopath with Ecosim software, a trophic structure model is constructed for 2006-2007 to characterize the food web structure, functioning, and describing the ecosystem impacts of fishing. Input information for the model were gathered from published and unpublished reports and from our own estimates during the period 2006-2007. Pedigree work and simple sensitivity analysis were carried out to evaluate the quality and the uncertainty of the model. Results show that the food web in the enclosed sea area was dominated by a detritus pathway. The trophic levels of the groups varied from 1.00 for primary producers and detritus to 3.90 for piscivorous fish in the artificial system. Using network analysis, the system network was mapped into a linear food chain, and five discrete trophic levels were found with a mean transfer efficiency of 9.8% from detritus, 9.4% from primary producer within the ecosystem. The geometric mean of the trophic transfer efficiencies was 9.5%. Detritus contributed 57% of the total energy flux, and the other 43% came from primary producers. The ecosystem maturity indices-TPP/TR (total primary production/total respiration), FCI (Finn cycling index), A (ascendancy) and TB/TDET were 2.672, 25%, 31.5%, and 0.013, respectively, showing that the artificial system is at developmental stage according to Odum's theory of ecosystem development. The `Keystoneness' result indicates that herbivorous zooplankton was identified as keystone species in this system. Furthermore, a simple dynamical simulation was preformed for varying fishing mortality over 10 years. The biomass of most fish groups has a small increase when the fishing mortality at current level. Increasing fishing mortality by twofold resulted in a marked decrease in biomass of piscivorous fish accompanied by an increase in that of other fish groups, notable zooplanktivorous fish. Generally, this study

  19. Multilevel Empirical Bayes Modeling for Improved Estimation of Toxicant Formulations to Suppress Parasitic Sea Lamprey in the Upper Great Lakes

    USGS Publications Warehouse

    Hatfield, L.A.; Gutreuter, S.; Boogaard, M.A.; Carlin, B.P.

    2011-01-01

    Estimation of extreme quantal-response statistics, such as the concentration required to kill 99.9% of test subjects (LC99.9), remains a challenge in the presence of multiple covariates and complex study designs. Accurate and precise estimates of the LC99.9 for mixtures of toxicants are critical to ongoing control of a parasitic invasive species, the sea lamprey, in the Laurentian Great Lakes of North America. The toxicity of those chemicals is affected by local and temporal variations in water chemistry, which must be incorporated into the modeling. We develop multilevel empirical Bayes models for data from multiple laboratory studies. Our approach yields more accurate and precise estimation of the LC99.9 compared to alternative models considered. This study demonstrates that properly incorporating hierarchical structure in laboratory data yields better estimates of LC99.9 stream treatment values that are critical to larvae control in the field. In addition, out-of-sample prediction of the results of in situ tests reveals the presence of a latent seasonal effect not manifest in the laboratory studies, suggesting avenues for future study and illustrating the importance of dual consideration of both experimental and observational data. ?? 2011, The International Biometric Society.

  20. NASA-modified precipitation products to improve USEPA nonpoint source water quality modeling for the Chesapeake Bay.

    PubMed

    Nigro, Joseph; Toll, David; Partington, Ed; Ni-Meister, Wenge; Lee, Shihyan; Gutierrez-Magness, Angelica; Engman, Ted; Arsenault, Kristi

    2010-01-01

    The USEPA has estimated that over 20,000 water bodies within the United States do not meet water quality standards. One of the regulations in the Clean Water Act of 1972 requires states to monitor the total maximum daily load, or the amount of pollution that can be carried by a water body before it is determined to be "polluted," for any watershed in the United States (Copeland, 2005). In response to this mandate, the USEPA developed Better Assessment Science Integrating Nonpoint Sources (BASINS) as a decision support tool for assessing pollution and to guide the decision-making process for improving water quality. One of the models in BASINS, the Hydrological Simulation Program-Fortran (HSPF), computes continuous streamflow rates and pollutant concentration at each basin outlet. By design, precipitation and other meteorological data from weather stations serve as standard model input. In practice, these stations may be unable to capture the spatial heterogeneity of precipitation events, especially if they are few and far between. An attempt was made to resolve this issue by substituting station data with NASA-modified/NOAA precipitation data. Using these data within HSPF, streamflow was calculated for seven watersheds in the Chesapeake Bay Basin during low flow periods, convective storm periods, and annual flows. In almost every case, the modeling performance of HSPF increased when using the NASA-modified precipitation data, resulting in better streamflow statistics and, potentially, in improved water quality assessment.

  1. Multilevel empirical bayes modeling for improved estimation of toxicant formulations to suppress parasitic sea lamprey in the upper great lakes.

    PubMed

    Hatfield, Laura A; Gutreuter, Steve; Boogaard, Michael A; Carlin, Bradley P

    2011-09-01

    Estimation of extreme quantal-response statistics, such as the concentration required to kill 99.9% of test subjects (LC99.9), remains a challenge in the presence of multiple covariates and complex study designs. Accurate and precise estimates of the LC99.9 for mixtures of toxicants are critical to ongoing control of a parasitic invasive species, the sea lamprey, in the Laurentian Great Lakes of North America. The toxicity of those chemicals is affected by local and temporal variations in water chemistry, which must be incorporated into the modeling. We develop multilevel empirical Bayes models for data from multiple laboratory studies. Our approach yields more accurate and precise estimation of the LC99.9 compared to alternative models considered. This study demonstrates that properly incorporating hierarchical structure in laboratory data yields better estimates of LC99.9 stream treatment values that are critical to larvae control in the field. In addition, out-of-sample prediction of the results of in situ tests reveals the presence of a latent seasonal effect not manifest in the laboratory studies, suggesting avenues for future study and illustrating the importance of dual consideration of both experimental and observational data.

  2. Multi-Model Validation in the Chesapeake Bay Region in June 2010

    DTIC Science & Technology

    2013-05-31

    current predictions from three coastal hydrodynamic models and document the resource and operational requirements for each modeling system . The...current predictions on three coastal hydrodynamic models and 3) document the resource and operational requirements for each modeling system . Three...requirements including hardware, personnel, training and operations for each modeling system . This paper is organized as follows: Section Two describes model

  3. Multi-Model Validation in the Chesapeake Bay Region During Frontier Sentinel 2010

    DTIC Science & Technology

    2012-09-28

    hydrodynamic models and document the resource and operational requirements for each modeling system . The ADvanced CIRCulation Model (ADCIRC), the Navy...including hardware, personnel, training and operations for each modeling system . This report is organized as follows: Section Two describes model ...Resource issues and requirements for the modeling systems are discussed in Section Five. Conclusions are summarized in Section Six

  4. Application of a Hidden Bayes Naive Multiclass Classifier in Network Intrusion Detection

    ERIC Educational Resources Information Center

    Koc, Levent

    2013-01-01

    With increasing Internet connectivity and traffic volume, recent intrusion incidents have reemphasized the importance of network intrusion detection systems for combating increasingly sophisticated network attacks. Techniques such as pattern recognition and the data mining of network events are often used by intrusion detection systems to classify…

  5. A Naive Bayes Approach for Converging Learning Objects with Open Educational Resources

    ERIC Educational Resources Information Center

    Sabitha, A. Sai; Mehrotra, Deepti; Bansal, Abhay; Sharma, B. K.

    2016-01-01

    Open educational resources (OER) are digitised material freely available to the students and self learners. Many institutions had initiated in incorporating these OERs in their higher educational system, to improve the quality of teaching and learning. These resources promote individualised study, collaborative learning. If they are coupled with…

  6. Levels of 137Cs in muddy sediments on the seabed in the Bay of Cadiz (Spain). Part II. Model of vertical migration of (137)Cs.

    PubMed

    Ligero, R A; Barrera, M; Casas-Ruiz, M

    2005-01-01

    This second part of the study reports the development of a model to describe the vertical migration of the artificial radioisotope (137)Cs in the sediment column on the seabed of the Bay of Cadiz. The application of the model provides an overall picture of the process of sedimentation in the Inner Bay of Cadiz. The spatial distribution of the rate of sedimentation enables us to study the sources of sediments and the means by which the sediments have been transported. A method has been derived from the rate of sedimentation to perform the dating of the layers of sediment. The model describes the behaviour of (137)Cs in the area under study, taking into account the time of residence in the zones that are the source of accumulation, the origin of the sedimentary material, together with the diffusion of the radionuclide in the sediment of the seabed.

  7. Role of naive-derived T memory stem cells in T-cell reconstitution following allogeneic transplantation

    PubMed Central

    Roberto, Alessandra; Castagna, Luca; Zanon, Veronica; Bramanti, Stefania; Crocchiolo, Roberto; McLaren, James E.; Gandolfi, Sara; Tentorio, Paolo; Sarina, Barbara; Timofeeva, Inna; Santoro, Armando; Carlo-Stella, Carmelo; Bruno, Benedetto; Carniti, Cristiana; Corradini, Paolo; Gostick, Emma; Ladell, Kristin; Price, David A.; Roederer, Mario; Mavilio, Domenico

    2015-01-01

    Early T-cell reconstitution following allogeneic transplantation depends on the persistence and function of T cells that are adoptively transferred with the graft. Posttransplant cyclophosphamide (pt-Cy) effectively prevents alloreactive responses from unmanipulated grafts, but its effect on subsequent immune reconstitution remains undetermined. Here, we show that T memory stem cells (TSCM), which demonstrated superior reconstitution capacity in preclinical models, are the most abundant circulating T-cell population in the early days following haploidentical transplantation combined with pt-Cy and precede the expansion of effector cells. Transferred naive, but not TSCM or conventional memory cells preferentially survive cyclophosphamide, thus suggesting that posttransplant TSCM originate from naive precursors. Moreover, donor naive T cells specific for exogenous and self/tumor antigens persist in the host and contribute to peripheral reconstitution by differentiating into effectors. Similarly, pathogen-specific memory T cells generate detectable recall responses, but only in the presence of the cognate antigen. We thus define the cellular basis of T-cell reconstitution following pt-Cy at the antigen-specific level and propose to explore naive-derived TSCM in the clinical setting to overcome immunodeficiency. These trials were registered at www.clinicaltrials.gov as #NCT02049424 and #NCT02049580. PMID:25742699

  8. Numerical modeling of tides in the Great Bay Estuarine System: dynamical balance and spring-neap residual modulation

    NASA Astrophysics Data System (ADS)

    McLaughlin, J. W.; Bilgili, A.; Lynch, D. R.

    2003-05-01

    The Great Bay Estuarine System, in New Hampshire, USA, has been the focus area for an attempt to develop a robust finite element method model for estuarine hydrodynamics. Past studies used a nonlinear, time stepping, kinematic model with limited success (Ip et al. Advances in fluid mechanics III, WIT, Southampton (2000) 569; Bilgili et al. J. Geophys. Res. - Oceans 107 (2002); Ertürk et al. Estuar. Coast. Shelf Sci. 47 (1998) 119). We add dynamic physics (that is, local accelerations) for deep-water areas and keep kinematic physics (that is, without local and advective accelerations), with the inclusion of a porous medium beneath the open channel, for shallow and dewatering areas. The choice of which physics set to apply is made on an elemental depth dependent basis. The addition of the local acceleration terms for deep-water areas is seen to greatly improve accuracy in matching of tidal phasing over previous studies. Simulations involving M 2/M 4/M 6 tidal constituents result in strong agreement to observed data from the 1975 Great Bay field program (Swift & Brown, Estuar. Coast. Shelf Sci. 17 (1983) 297), in terms of both tidal heights and cross-section averaged velocities. Comparisons with 10 tidal elevation observation stations and four cross-section averaged current transects show good agreement, displaying average normalized root mean square misfit values of 0.08 and 0.25, respectively. Study of the simulated momentum balance shows the size of the contributions from acceleration terms to be on the order of a third the size of the contributions from the pressure gradient and bottom stress terms. Although relatively small, they are observed to peak at the crucial time of tidal reversal. Application of the model for long-term simulation using an M 2/N 2/S 2 forcing shows the ability to realistically capture the spring-neap cycle. The tidally rectified flow is generally described as a constant spatial pattern with overall amplitude modulation following the

  9. Reactive transport model of the formation of oxide-type Ni-laterite profiles (Punta Gorda, Moa Bay, Cuba)

    NASA Astrophysics Data System (ADS)

    Domènech, Cristina; Galí, Salvador; Villanova-de-Benavent, Cristina; Soler, Josep M.; Proenza, Joaquín A.

    2017-01-01

    Oxide-type Ni-laterite deposits are characterized by a dominant limonite zone with goethite as the economically most important Ni ore mineral and a thin zone of hydrous Mg silicate-rich saprolite beneath the magnesium discontinuity. Fe, less soluble, is mainly retained forming goethite, while Ni is redeposited at greater depth in a Fe(III) and Ni-rich serpentine (serpentine II) or in goethite, where it adsorbs or substitutes for Fe in the mineral structure. Here, a 1D reactive transport model, using CrunchFlow, of Punta Gorda oxide-type Ni-laterite deposit (Moa Bay, Cuba) formation is presented. The model reproduces the formation of the different laterite horizons in the profile from an initial, partially serpentinized peridotite, in 106 years, validating the conceptual model of the formation of this kind of deposits in which a narrow saprolite horizon rich in Ni-bearing serpentine is formed above peridotite parent rock and a thick limonite horizon is formed over saprolite. Results also confirm that sorption of Ni onto goethite can explain the weight percent of Ni found in the Moa goethite. Sensitivity analyses accounting for the effect of key parameters (composition, dissolution rate, carbonate concentration, quartz precipitation) on the model results are also presented. It is found that aqueous carbonate concentration and quartz precipitation significantly affects the laterization process rate, while the effect of the composition of secondary serpentine or of mineral dissolution rates is minor. The results of this reactive transport modeling have proven useful to validate the conceptual models derived from field observations.

  10. Spatial Statistical Network Models for Stream and River Temperature in the Chesapeake Bay Watershed, USA

    EPA Science Inventory

    Regional temperature models are needed for characterizing and mapping stream thermal regimes, establishing reference conditions, predicting future impacts and identifying critical thermal refugia. Spatial statistical models have been developed to improve regression modeling techn...

  11. The Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1996-04-01

    The authors are developing a computer application, called the Bayes Inference Engine, to provide the means to make inferences about models of physical reality within a Bayesian framework. The construction of complex nonlinear models is achieved by a fully object-oriented design. The models are represented by a data-flow diagram that may be manipulated by the analyst through a graphical programming environment. Maximum a posteriori solutions are achieved using a general, gradient-based optimization algorithm. The application incorporates a new technique of estimating and visualizing the uncertainties in specific aspects of the model.

  12. Probabilistic ecological risk assessment of DDTs in the Bohai Bay based on a food web bioaccumulation model.

    PubMed

    Wang, Bin; Yu, Gang; Huang, Jun; Wang, Tai; Hu, Hongying

    2011-01-01

    The fugacity-based food web model was developed to simulate the bioaccumulation of dichloro-diphenyl-trichloroethanes (DDTs) in the aquatic ecosystem in the Bohai Bay. The internal exposure levels (IELs) of DDTs in various organism categories were calculated. Monte Carlo-based uncertainty analysis was performed to get the of IEL distributions of DDTs in organisms. Probabilistic ecological risk assessment (ERA) was performed based on IEL distributions and internal species sensitivity distributions (SSDs). The results show that fugacities and bioaccumulation factors (BAFs) generally increased with increasing trophic level in the food web. Octanol-water partition coefficient (K(ow)), DDT levels in water and the lipid contents had the greatest influences on IELs in the organism bodies. The ecological risks of DDTs were relatively high. The risk order was p,p'-DDT>p,p'-DDE>p,p'-DDD. At an internal hazard quotient (HQ(int)) criterion of 1/5, the risk probabilities were 0.10 (0.055-0.17), 0.079 (0.045-0.13) and 0.053 (0.028-0.092) for p,p'-DDT, p,p'-DDE and p,p'-DDD, respectively. The results from ERA based on the internal exposure approximated those based on external exposure. The food web model is a feasible method to predict the extent of bioaccumulation and IELs of hydrophobic organic pollutants in organisms as a step to evaluate their risk posed on aquatic ecosystems.

  13. Watershed and Hydrodynamic Modeling for Evaluating the Impact of Land Use Change on Submerged Aquatic Vegetation and Seagrasses in Mobile Bay

    NASA Technical Reports Server (NTRS)

    Estes, Maurice G.; Al-Hamdan, Mohammed; Thom, Ron; Quattrochi, Dale; Woodruff, Dana; Judd, Chaeli; Ellism Jean; Watson, Brian; Rodriguez, Hugo; Johnson, Hoyt

    2009-01-01

    There is a continued need to understand how human activities along the northern Gulf of Mexico coast are impacting the natural ecosystems. The gulf coast is experiencing rapid population growth and associated land cover/land use change. Mobile Bay, AL is a designated pilot region of the Gulf of Mexico Alliance (GOMA) and is the focus area of many current NASA and NOAA studies, for example. This is a critical region, both ecologically and economically to the entire United States because it has the fourth largest freshwater inflow in the continental USA, is a vital nursery habitat for commercially and recreational important fisheries, and houses a working waterfront and port that is expanding. Watershed and hydrodynamic modeling has been performed for Mobile Bay to evaluate the impact of land use change in Mobile and Baldwin counties on the aquatic ecosystem. Watershed modeling using the Loading Simulation Package in C++ (LSPC) was performed for all watersheds contiguous to Mobile Bay for land use Scenarios in 1948, 1992, 2001, and 2030. The Prescott Spatial Growth Model was used to project the 2030 land use scenario based on observed trends. All land use scenarios were developed to a common land classification system developed by merging the 1992 and 2001 National Land Cover Data (NLCD). The LSPC model output provides changes in flow, temperature, sediments and general water quality for 22 discharge points into the Bay. These results were inputted in the Environmental Fluid Dynamics Computer Code (EFDC) hydrodynamic model to generate data on changes in temperature, salinity, and sediment concentrations on a grid with four vertical profiles throughout the Bay s aquatic ecosystems. The models were calibrated using in-situ data collected at sampling stations in and around Mobile bay. This phase of the project has focused on sediment modeling because of its significant influence on light attenuation which is a critical factor in the health of submerged aquatic

  14. A Model for the Formation of the Chesapeake Bay Impact Crater as Revealed by Drilling and Numerical Simulation

    NASA Astrophysics Data System (ADS)

    Collins, G. S.; Kenkmann, T.; Wünnemann, K.; Wittmann, A.; Reimold, W. U.; Melosh, H. J.

    The combination of numerical simulation results and petrographic analysis of drill core from the recent ICDP-USGS drilling project provides new insight into the formation of the Chesapeake Bay impact crater.

  15. Quantitative Models Describing Past and Current Nutrient Fluxes and Associated Ecosystem Level Responses in the Narragansett Bay Ecosystem

    EPA Science Inventory

    Multiple drivers, including nutrient loading and climate change, affect the Narragansett Bay ecosystem in Rhode Island/Massachusetts, USA. Managers are interested in understanding the timing and magnitude of these effects, and ecosystem responses to restoration actions. To provid...

  16. Probabilistic seismic hazard in the San Francisco Bay area based on a simplified viscoelastic cycle model of fault interactions

    USGS Publications Warehouse

    Pollitz, F.F.; Schwartz, D.P.

    2008-01-01

    We construct a viscoelastic cycle model of plate boundary deformation that includes the effect of time-dependent interseismic strain accumulation, coseismic strain release, and viscoelastic relaxation of the substrate beneath the seismogenic crust. For a given fault system, time-averaged stress changes at any point (not on a fault) are constrained to zero; that is, kinematic consistency is enforced for the fault system. The dates of last rupture, mean recurrence times, and the slip distributions of the (assumed) repeating ruptures are key inputs into the viscoelastic cycle model. This simple formulation allows construction of stress evolution at all points in the plate boundary zone for purposes of probabilistic seismic hazard analysis (PSHA). Stress evolution is combined with a Coulomb failure stress threshold at representative points on the fault segments to estimate the times of their respective future ruptures. In our PSHA we consider uncertainties in a four-dimensional parameter space: the rupture peridocities, slip distributions, time of last earthquake (for prehistoric ruptures) and Coulomb failure stress thresholds. We apply this methodology to the San Francisco Bay region using a recently determined fault chronology of area faults. Assuming single-segment rupture scenarios, we find that fature rupture probabilities of area faults in the coming decades are the highest for the southern Hayward, Rodgers Creek, and northern Calaveras faults. This conclusion is qualitatively similar to that of Working Group on California Earthquake Probabilities, but the probabilities derived here are significantly higher. Given that fault rupture probabilities are highly model-dependent, no single model should be used to assess to time-dependent rupture probabilities. We suggest that several models, including the present one, be used in a comprehensive PSHA methodology, as was done by Working Group on California Earthquake Probabilities.

  17. Inverse modeling of surface-water discharge to achieve restoration salinity performance measures in Florida Bay, Florida

    USGS Publications Warehouse

    Swain, E.D.; James, D.E.

    2008-01-01

    The use of numerical modeling to evaluate regional water-management practices involves the simulation of various alternative water-delivery scenarios, which typically are designed intuitively rather than analytically. These scenario simulations are used to analyze how specific water-management practices affect factors such as water levels, flows, and salinities. In lieu of testing a variety of scenario simulations in a trial-and-error manner, an optimization technique may be used to more precisely and directly define good water-management alternatives. A numerical model application in the coastal regions of Florida Bay and Everglades National Park (ENP), representing the surface- and ground-water hydrology for the region, is a good example of a tool used to evaluate restoration scenarios. The Southern Inland and Coastal System (SICS) model simulates this area with a two-dimensional hydrodynamic surface-water model and a three-dimensional ground-water model, linked to represent the interaction of the two systems with salinity transport. This coastal wetland environment is of great interest in restoration efforts, and the SICS model is used to analyze the effects of alternative water-management scenarios. The SICS model is run within an inverse modeling program called UCODE. In this application, UCODE adjusts the regulated inflows to ENP while SICS is run iteratively. UCODE creates parameters that define inflow within an allowable range for the SICS model based on SICS model output statistics, with the objective of matching user-defined target salinities that meet ecosystem restoration criteria. Preliminary results obtained using two different parameterization methods illustrate the ability of the model to achieve the goals of adjusting the range and reducing the variance of salinity values in the target area. The salinity variance in the primary zone of interest was reduced from an original value of 0.509 psu2 to values 0.418 psu2 and 0.342 psu2 using different

  18. Simulation of nutrient and sediment concentrations and loads in the Delaware inland bays watershed: Extension of the hydrologic and water-quality model to ungaged segments

    USGS Publications Warehouse

    Gutierrez-Magness, Angelica L.

    2006-01-01

    Rapid population increases, agriculture, and industrial practices have been identified as important sources of excessive nutrients and sediments in the Delaware Inland Bays watershed. The amount and effect of excessive nutrients and sediments in the Inland Bays watershed have been well documented by the Delaware Geological Survey, the Delaware Department of Natural Resources and Environmental Control, the U.S. Environmental Protection Agency's National Estuary Program, the Delaware Center for Inland Bays, the University of Delaware, and other agencies. This documentation and data previously were used to develop a hydrologic and water-quality model of the Delaware Inland Bays watershed to simulate nutrients and sediment concentrations and loads, and to calibrate the model by comparing concentrations and streamflow data at six stations in the watershed over a limited period of time (October 1998 through April 2000). Although the model predictions of nutrient and sediment concentrations for the calibrated segments were fairly accurate, the predictions for the 28 ungaged segments located near tidal areas, where stream data were not available, were above the range of values measured in the area. The cooperative study established in 2000 by the Delaware Department of Natural Resources and Environmental Control, the Delaware Geological Survey, and the U.S. Geological Survey was extended to evaluate the model predictions in ungaged segments and to ensure that the model, developed as a planning and management tool, could accurately predict nutrient and sediment concentrations within the measured range of values in the area. The evaluation of the predictions was limited to the period of calibration (1999) of the 2003 model. To develop estimates on ungaged watersheds, parameter values from calibrated segments are transferred to the ungaged segments; however, accurate predictions are unlikely where parameter transference is subject to error. The unexpected nutrient and

  19. Children's naive theories of intelligence influence their metacognitive judgments.

    PubMed

    Miele, David B; Son, Lisa K; Metcalfe, Janet

    2013-01-01

    Recent studies have shown that the metacognitive judgments adults infer from their experiences of encoding effort vary in accordance with their naive theories of intelligence. To determine whether this finding extends to elementary schoolchildren, a study was conducted in which 27 third graders (M(age) = 8.27) and 24 fifth graders (M(age) = 10.39) read texts presented in easy- or difficult-to-encode fonts. The more children in both grades viewed intelligence as fixed, the less likely they were to interpret effortful or difficult encoding as a sign of increasing mastery and the more likely they were to report lower levels of comprehension as their perceived effort increased. This suggests that children may use naive theories of intelligence to make motivationally relevant inferences earlier than previously thought.

  20. Upper oceanic response to tropical cyclone Phailin in the Bay of Bengal using a coupled atmosphere-ocean model

    NASA Astrophysics Data System (ADS)

    Prakash, Kumar Ravi; Pant, Vimlesh

    2017-01-01

    A numerical simulation of very severe cyclonic storm `Phailin', which originated in southeastern Bay of Bengal (BoB) and propagated northwestward during 10-15 October 2013, was carried out using a coupled atmosphere-ocean model. A Model Coupling Toolkit (MCT) was used to make exchanges of fluxes consistent between the atmospheric model `Weather Research and Forecasting' (WRF) and ocean circulation model `Regional Ocean Modelling System' (ROMS) components of the `Coupled Ocean-Atmosphere-Wave-Sediment Transport' (COAWST) modelling system. The track and intensity of tropical cyclone (TC) Phailin simulated by the WRF component of the coupled model agrees well with the best-track estimates reported by the India Meteorological Department (IMD). Ocean model component (ROMS) was configured over the BoB domain; it utilized the wind stress and net surface heat fluxes from the WRF model to investigate upper oceanic response to the passage of TC Phailin. The coupled model shows pronounced sea surface cooling (2-2.5 °C) and an increase in sea surface salinity (SSS) (2-3 psu) after 06 GMT on 12 October 2013 over the northwestern BoB. Signature of this surface cooling was also observed in satellite data and buoy measurements. The oceanic mixed layer heat budget analysis reveals relative roles of different oceanic processes in controlling the mixed layer temperature over the region of observed cooling. The heat budget highlighted major contributions from horizontal advection and vertical entrainment processes in governing the mixed layer cooling (up to -0.1 °C h-1) and, thereby, reduction in sea surface temperature (SST) in the northwestern BoB during 11-12 October 2013. During the post-cyclone period, the net heat flux at surface regained its diurnal variations with a noontime peak that provided a warming tendency up to 0.05 °C h-1 in the mixed layer. Clear signatures of TC-induced upwelling are seen in vertical velocity (about 2.5 × 10-3 m s-1), rise in isotherms and

  1. Modeling of turbulent dissipation and its validation in periodically stratified region in the Liverpool Bay and in the North Sea

    NASA Astrophysics Data System (ADS)

    Sasmal, Kaushik; Maity, Subhendu; Warrior, Hari V.

    2015-07-01

    The present work explores the applicability of an alternative eddy viscosity formulation in numerical models dealing with the dynamics of the coastal ocean. The formulation is based on the Reynolds stress anisotropy-anisotropy being an important tool for capturing turbulent mixing. Initially idealized entrainment scenarios are evaluated that are typical for shelf seas viz. entrainment in linearly stratified and two-layer fluids caused by surface wind stress or barotropic pressure gradient-driven bottom stress. An attempt is made to simulate the realistic semi-diurnal cycle of turbulent dissipation in Liverpool Bay Region of Freshwater Inflow (ROFI) in the Irish Sea characterized by strong horizontal gradients and interactions with tidal flow. Turbulent dissipation cycles with a 25-h period using free-falling light yo-yo (FLY) dissipation profiler exhibits a strong asymmetry between ebb and flood. The above dynamics involving tidal straining during the ebb and mixing during the flood has been simulated using k- and the alternative formulated turbulence scheme in a one-dimensional (1-D) dynamic model. The model is forced with observed tidal flow and horizontal gradients of temperature and salinity. Simulated dissipation cycles show good agreement with observation. The present work also involves a comparison of dissipation rate measurements in northern North Sea using the abovementioned turbulence schemes—the measurements being taken using free-falling shear probes and CTD (conductivity, temperature, and depth) sensors. The main forcing provided for the upper and bottom boundary layers are atmospheric forcing and tides, respectively. To compare the observations and model results, quantitative error measurements have also been studied which reveal the applicability of the alternative turbulence scheme.

  2. A Lagrangian Physical-Biological Model to Study Water Parcels Associated with Algal Blooms from Southern California Bight to Todos Santos Bay.

    NASA Astrophysics Data System (ADS)

    Vivas Téllez, I. E.; Rivas, D.

    2015-12-01

    Lagrangian ocean circulation and biological dynamics are numerically studied in Todos Santos Bay during the spring of 2007. This period is particularly interesting after an intense toxic algal bloom occurred in April 2007 in this area, which was associated with the wind-driven upwelling in the region. High resolution, numerical model simulations were carried out to study dynamical features along of the Southern California Bight (SCB), the coast of the northern Baja California (BC), and the interior of Todos Santos Bay (TSB). These simulations are used in a three-dimensional Lagrangian (particle tracking) analysis which provides information about the origin and distribution of the waters present in the Bay during the occurrence of the toxic bloom. After the selection of trajectories of particles showing coherent patterns, a Nitrate-Phytoplankton-Zooplankton-Detritus (NPZD) lower trophic model is implemented to study the influence of the environmental conditions that occur during the particle advection, solving the NPZD equations at every time-varying position of the advected particles. The model is also modified for phytoplankton growth as a function of the environmental temperature to somehow emulate the life cycle of Pseudo-nitzschia. The analysis of the trajectories shows that particles mainly come from two regions: from the north, in the southern portion of SCB and from regions west of the TSB. Knowing the regional circulation patterns and their phytoplankton dynamics can help to understand and even predict the origin and destination of the harmful algal blooms that occur in TSB and its surroundings.

  3. Autoantibodies in biological agent naive patients with psoriatic arthritis

    PubMed Central

    Johnson, S; Schentag, C; Gladman, D

    2005-01-01

    Objective: To investigate the prevalence of autoantibodies in biological agent naive patients with psoriatic arthritis (PsA). Methods: 94 consecutive, prospectively collected, biological agent naive patients with PsA at the University of Toronto PsA clinic underwent clinical and laboratory assessment. Disease activity was assessed by the number of actively inflamed joints, and the Psoriasis Activity and Severity Index (PASI) score. Antinuclear antibodies (ANA), rheumatoid factor (RF), double stranded DNA (dsDNA), Ro, La, Smith, and RNP were tested. Descriptive statistics and non-parametric tests were used to analyse the data. Results: 44/94 (47%) patients with PsA were ANA positive (⩾1/40); 13/94 (14%) had a clinically significant titre of ⩾1/80. Three per cent had dsDNA antibodies, 2% had RF and anti-Ro antibodies, 1% had anti-RNP antibodies, and none had anti-La or anti-Smith antibodies. Conclusions: The background prevalence of ANA ⩾1/80 in patients with PsA was 14%, with very few patients having specific lupus antibodies. This should serve as a baseline figure for the frequency of autoantibodies in biological agent naive patients with PsA for studies of the use of anti-TNFα agents. PMID:15834057

  4. Mixing heights and surface fluxes over Galveston Bay and the Gulf of Mexico: Implications for modeling of pollution episodes

    NASA Astrophysics Data System (ADS)

    Angevine, W. M.; Tucker, S. C.; Fairall, C.; Bariteau, L.; Wolfe, D.; Zagar, M.; Brewer, A.

    2007-12-01

    During the 2006 Texas Air Quality Study, boundary layer measurements were made by in-situ instruments, lidars, and rawinsondes on the NOAA RV Ronald H. Brown as well as by radar wind profilers on land. Brown also carried instruments to measure surface heat and momentum fluxes. This presentation will emphasize measurements made in Galveston Bay and in the Gulf of Mexico near the Houston area. Details of boundary layer depth and turbulence intensity over these waters have not been well known previously, but are quite important to the understanding of high ozone episodes in Houston. One somewhat surprising result is that the boundary layer over water was almost always slightly unstable, with positive surface heat flux. Mixing depths were moderate, although mixing was generally weak compared to that over land. Boundary layer heights over the water were substantially shallower than daytime heights over land. Experiments in modeling ozone episodes with WRF at 1.5-km grid spacing will be shown and compared with the measurements.

  5. Application of the Pearl model to analyze fecal coliform data from conditionally approved shellfish harvest areas in seven Texas bays.

    PubMed

    Conte, F S; Ahmadi, A

    2014-09-01

    The U.S. National Shellfish Sanitation Program (NSSP) 14/43 standard states that conditionally approved shellfish growing areas must be closed for harvest when the geometric mean of fecal coliform concentration exceeds the NSSP limit of 14 most probable number (MPN)/100 mL, or the estimated 90th percentile of fecal coliform concentrations exceeds 43 MPN/100 mL for a five-tube test. The authors hypothesized that the NSSP 14/43 standard is not sufficient to protect the public from risks from consumption of biologically contaminated shellfish and the standard should be modified to 8/26 MPN/100 mL. To verify this hypothesis, the authors analyzed fecal coliform data from conditionally approved shellfish harvest areas of seven Texas bays using the Pearl sanitation model. Results showed that the shellfish closure rules mandated by the Texas Department of State Health Services actually enforced the "Pearl" limits of 8/26 MPN/100 mL, and not the NSSP limit of 14/43 MPN/100 mL.

  6. Using twelve years of USGS refraction lines to calibrate the Brocher and others (1997) 3D velocity model of the Bay Area

    USGS Publications Warehouse

    Boatwright, John; Blair, Luke; Catchings, Rufus; Goldman, Mark; Perosi, Fabio; Steedman, Clare

    2004-01-01

    Campbell (1983) demonstrated that site amplification correlates with depths to the 1.0, 1.5, and 2.5 km/s S-wave velocity horizons. To estimate these depths for the Bay Area stations in the PEER/NGA database, we compare the depths to the 3.2 and 4.4 km/s P-wave velocities in the Brocher and others (1997) 3D velocity model with the depths to these horizons determined from 6 refraction lines shot in the Bay Area from 1991 to 2003. These refraction lines range from two recent 20 km lines that extend from Los Gatos to downtown San Jose, and from downtown San Jose into Alum Rock Park, to two older 200 km lines than run axially from Hollister up the San Francisco Peninsula to Inverness and from Hollister up the East Bay across San Pablo Bay to Santa Rosa. Comparison of these cross-sections with the Brocher and others (1997) model indicates that the 1.5 km/s S-wave horizon, which we correlate with the 3.2 km/s P-wave horizon, is the most reliable horizon that can be extracted from the Brocher and others (1997) velocity model. We determine simple adjustments to bring the Brocher and others (1997) 3.2 and 4.4 km/s P-wave horizons into an average agreement with the refraction results. Then we apply these adjustments to estimate depths to the 1.5 and 2.5 km/s S-wave horizons beneath the strong motion stations in the PEER/NGA database.

  7. Using NASA and Earth Science Products to Improve EPA Non-point Source Water Quality Modeling for the Chesapeake Bay

    NASA Astrophysics Data System (ADS)

    Toll, D.; Engman, T.; Edward, P.; Magness, A.; Townsend, P.; N-Meister, W.; Nigro, J.; Lee, S.

    2007-12-01

    The Environmental Protection Agency (EPA) estimates that over 20,000 bodies of water throughout the country do not meet water quality standards. Nonpoint sources -- pollution from urban, agricultural, and forest land that is transported by runoff -- typically cause 90 percent of impairments. EPA has developed the BASINS (Better Assessment Science Integrating Point and Nonpoint Sources) modeling system for performing numerous water quality studies. The key to this suite of models is the Hydrological Simulation Program - Fortran (HSPF), which calculates daily stream flow rates and the corresponding pollutant concentrations at the watershed outlet. EPA has partnered with NASA to use high spatial and temporal hydrological variables (e.g., precipitation, evaporation, etc.) from the NASA Land Information System (LIS) and land cover/vegetative indices derived from primarily MODIS and Landsat satellite data non-point source water quality for the Chesapeake Bay Basin. For the precipitation and evaporation data, EPA-based BASINS-HSPF streamflow runs were conducted on seven study watersheds in the Chesapeake Bay Basin. Sets of runs using precipitation from default weather stations, the NASA LIS 1/8th degree precipitation, NOAA Stage IV precipitation, NASA LIS Noah land surface model evapotranspiration datasets were conducted for each watershed. The output statistics summarized reveal that for 74% of the runs, the NASA LIS 1/8th degree and Stage IV precipitation-based runs performed better than when using only the default EPA precipitation station data. In addition, an automatic calibration method ('PEST') and Noah land surface model evapotranspiration (ET) being further incorporated. The empirical ability of generalized spectral indices and land cover derived from Landsat and MODIS was tested for predicting stream water nitrogen export from predominately forested watersheds undergoing disturbance. The disturbance index, a summary index that is easily computed from Landsat

  8. NASA-Modified Precipitation Products to Improve EPA Nonpoint Source Water Quality Modeling for the Chesapeake Bay

    NASA Technical Reports Server (NTRS)

    Nigro, Joseph; Toll, David; Partington, Ed; Ni-Meister, Wenge; Lee, Shihyan; Gutierrez-Magness, Angelica; Engman, Ted; Arsenault, Kristi

    2010-01-01

    The Environmental Protection Agency (EPA) has estimated that over 20,000 water bodies within the United States do not meet water quality standards. Ninety percent of the impairments are typically caused by nonpoint sources. One of the regulations in the Clean Water Act of 1972 requires States to monitor the Total Maximum Daily Load (TMDL), or the amount of pollution that can be carried by a water body before it is determined to be "polluted", for any watershed in the U.S.. In response to this mandate, the EPA developed Better Assessment Science Integrating Nonpoint Sources (BASINS) as a Decision Support Tool (DST) for assessing pollution and to guide the decision making process for improving water quality. One of the models in BASINS, the Hydrological Simulation Program -- Fortran (HSPF), computes daily stream flow rates and pollutant concentration at each basin outlet. By design, precipitation and other meteorological data from weather stations serve as standard model input. In practice, these stations may be unable to capture the spatial heterogeneity of precipitation events especially if they are few and far between. An attempt was made to resolve this issue by substituting station data with NASA modified/NOAA precipitation data. Using these data within HSPF, stream flow was calculated for seven watersheds in the Chesapeake Bay Basin during low flow periods, convective storm periods, and annual flows. In almost every case, the modeling performance of HSPF increased when using the NASA-modified precipitation data, resulting in better stream flow statistics and, ultimately, in improved water quality assessment.

  9. Bioturbation depths, rates and processes in Massachusetts Bay sediments inferred from modeling of 210Pb and 239 + 240Pu profiles

    USGS Publications Warehouse

    Crusius, John; Bothner, Michael H.; Sommerfield, Christopher K.

    2004-01-01

    Profiles of 210Pb and 239 + Pu from sediment cores collected throughout Massachusetts Bay (water depths of 36-192 m) are interpreted with the aid of a numerical sediment-mixing model to infer bioturbation depths, rates and processes. The nuclide data suggest extensive bioturbation to depths of 25-35 cm. Roughly half the cores have 210Pb and 239 + 240Pu profiles that decrease monotonically from the surface and are consistent with biodiffusive mixing. Bioturbation rates are reasonably well constrained by these profiles and vary from ~0.7 to ~40 cm2 yr-1. As a result of this extensive reworking, however, sediment ages cannot be accurately determined from these radionuclides and only upper limits on sedimentation rates (of ~0.3 cm yr-1) can be inferred. The other half of the radionuclide profiles are characterized by subsurface maxima in each nuclide, which cannot be reproduced by biodiffusive mixing models. A numerical model is used to demonstrate that mixing caused by organisms that feed at the sediment surface and defecate below the surface can cause the subsurface maxima, as suggested by previous work. The deep penetration depths of excess 210Pb and 239 + 240Pu suggest either that the organisms release material over a range of >15 cm depth or that biodiffusive mixing mediated by other organisms is occurring at depth. Additional constraints from surficial sediment 234Th data suggest that in this half of the cores, the vast majority of the present-day flux of recent, nuclide-bearing material to these core sites is transported over a timescale of a month or more to a depth of a few centimeters below the sediment surface. As a consequence of the complex mixing processes, surface sediments include material spanning a range of ages and will not accurately record recent changes in contaminant deposition.

  10. Sediment transport patterns in the San Francisco Bay Coastal System from cross-validation of bedform asymmetry and modeled residual flux

    USGS Publications Warehouse

    Barnard, Patrick L.; Erikson, Li H.; Elias, Edwin P.L.; Dartnell, Peter; Barnard, P.L.; Jaffee, B.E.; Schoellhamer, D.H.

    2013-01-01

    The morphology of ~ 45,000 bedforms from 13 multibeam bathymetry surveys was used as a proxy for identifying net bedload sediment transport directions and pathways throughout the San Francisco Bay estuary and adjacent outer coast. The spatially-averaged shape asymmetry of the bedforms reveals distinct pathways of ebb and flood transport. Additionally, the region-wide, ebb-oriented asymmetry of 5% suggests net seaward-directed transport within the estuarine-coastal system, with significant seaward asymmetry at the mouth of San Francisco Bay (11%), through the northern reaches of the Bay (7–8%), and among the largest bedforms (21% for λ > 50 m). This general indication for the net transport of sand to the open coast strongly suggests that anthropogenic removal of sediment from the estuary, particularly along clearly defined seaward transport pathways, will limit the supply of sand to chronically eroding, open-coast beaches. The bedform asymmetry measurements significantly agree (up to ~ 76%) with modeled annual residual transport directions derived from a hydrodynamically-calibrated numerical model, and the orientation of adjacent, flow-sculpted seafloor features such as mega-flute structures, providing a comprehensive validation of the technique. The methods described in this paper to determine well-defined, cross-validated sediment transport pathways can be applied to estuarine-coastal systems globally where bedforms are present. The results can inform and improve regional sediment management practices to more efficiently utilize often limited sediment resources and mitigate current and future sediment supply-related impacts.

  11. Sediment transport patterns in the San Francisco Bay Coastal System from cross-validation of bedform asymmetry and modeled residual flux

    USGS Publications Warehouse

    Barnard, Patrick L.; Erikson, Li H.; Elias, Edwin P.L.; Dartnell, Peter

    2013-01-01

    The morphology of ~ 45,000 bedforms from 13 multibeam bathymetry surveys was used as a proxy for identifying net bedload sediment transport directions and pathways throughout the San Francisco Bay estuary and adjacent outer coast. The spatially-averaged shape asymmetry of the bedforms reveals distinct pathways of ebb and flood transport. Additionally, the region-wide, ebb-oriented asymmetry of 5% suggests net seaward-directed transport within the estuarine-coastal system, with significant seaward asymmetry at the mouth of San Francisco Bay (11%), through the northern reaches of the Bay (7-8%), and among the largest bedforms (21% for λ > 50 m). This general indication for the net transport of sand to the open coast strongly suggests that anthropogenic removal of sediment from the estuary, particularly along clearly defined seaward transport pathways, will limit the supply of sand to chronically eroding, open-coast beaches. The bedform asymmetry measurements significantly agree (up to ~ 76%) with modeled annual residual transport directions derived from a hydrodynamically-calibrated numerical model, and the orientation of adjacent, flow-sculpted seafloor features such as mega-flute structures, providing a comprehensive validation of the technique. The methods described in this paper to determine well-defined, cross-validated sediment transport pathways can be applied to estuarine-coastal systems globally where bedforms are present. The results can inform and improve regional sediment management practices to more efficiently utilize often limited sediment resources and mitigate current and future sediment supply-related impacts.

  12. Physical-Biological-Optics Model Development and Simulation for the Pacific Ocean and Monterey Bay, California

    DTIC Science & Technology

    2011-04-01

    advanced ROMS-CoSiNE-Optics model in a full three-dimensional environment. We collaborate with Dr. Curt Mobley at Sequoia Scientific to implement...projects. Besides working closely with the modeling group at the NRL and their BioSpace project, we are collaborating with Dr. Curtis Mobley of Sequoia

  13. Tidal Prism Modeling of Phytoplankton and Nitrogen Concentrations in Narragansett Bay and its Sub-Embayments

    EPA Science Inventory

    A tidal prism model was developed to calculate temporal changes in the spatially averaged concentration of three state variables: phytoplankton, dissolved inorganic nitrogen, and detritus. Our main objective was to develop a model to help us understand the causes of phytoplankton...

  14. Endospore abundance and D:L-amino acid modeling of bacterial turnover in holocene marine sediment (Aarhus Bay)

    NASA Astrophysics Data System (ADS)

    Langerhuus, Alice T.; Røy, Hans; Lever, Mark A.; Morono, Yuki; Inagaki, Fumio; Jørgensen, Bo B.; Lomstein, Bente Aa.

    2012-12-01

    In order to study bacterial activity, and turnover times of bacterial necromass and biomass in marine sediment, two stations from the Aarhus Bay, Denmark were analyzed. Sediment cores were up to 11 m deep and covered a timescale from the present to ˜11,000 years ago. Sediment was analyzed for total hydrolysable amino acids (THAA), total hydrolysable amino sugars, the bacterial endospore marker dipicolinic acid (DPA), and amino acid enantiomers (L- and D-form) of aspartic acid. Turnover times of bacterial necromass and vegetative cells, as well as carbon oxidation rates were estimated by use of the D:L-amino acid racemization model. Diagenetic indicators were applied to evaluate the diagenetic state of the sedimentary organic matter. The contribution of amino acids to total organic carbon, and the ratio between the amino acids aspartic acid and glutamic acid, and their respective non protein degradation products, β-alanine and γ-amino butyric acid, all indicated increasing degradation state of the organic matter with sediment depth and age. Quantification of DPA showed that endospores were abundant, and increased with depth relative to vegetative cells. Most of the amino acids (97%) could be ascribed to microbial necromass, i.e. the remains of dead bacterial cells. Model estimates showed that the turnover times of microbial necromass were in the range of 0.5-1 × 105 years, while turnover times of vegetative cells were in the range of tens to hundreds of years. The turnover time of the TOC pool increased with depth in the sediment, indicating that the TOC pool became progressively more refractory and unavailable to microorganisms with depth and age of the organic matter.

  15. Spatial and Temporal Variations of Wind Energy in Long Bay of the Carolinas: Numeric Modeling Estimates for the Year 2009-2010

    NASA Astrophysics Data System (ADS)

    Xu, K.; Pietrafesa, L. J.; Gayes, P. T.; Peng, M.; Ma, Y.; Tarpley, D.; Gregorek, K.; Mynhier, L.

    2010-12-01

    In Long Bay of the Carolinas, wind energy varies greatly in space and time. Natural variations of winds make it challenging to select the best location of wind farms. The Palmetto Wind Research Project is designed to physically measure and numerically model the variations of wind field within Long Bay. Particular focus is on resolving the gradient of the cross-shore wind profile and the areas where the most energetic winds 100 m above sea surface can be found closest to the coast. As a modeling part of this collaborative Project, a three-dimensional Weather Research and Forecasting (WRF) model (Version 3.2) was used to investigate the variability of wind field in this area. A 12-month simulation was focused on the period of July 2009 to June 2010. Model initial and boundary conditions were from the final analysis dataset (1 degree resolution, every 6 hours) of National Centers for Environmental Prediction (NCEP). Three model domains and twenty-seven vertical grid layers were used. The parent domain (3-km resolution) covered the entire land-sea boundary of Long Bay from Cape Fear, NC to Cape Romain, SC, and two high-resolution (1-km) domains were one-way nested in the parent domain offshore of North Myrtle Beach and Winyah Bay mouth, respectively. Another atmosphere-ocean coupled model also was used to study the air-sea interaction in this area, and the differences between the results from the coupled model and these from WRF alone were relatively small under fare-weather conditions. Under storm conditions, however, the coupled model produced better wind field. Wind speeds at 3m, 10m and 100m above the surface were calculated from the pressure-based three-dimensional WRF grids. The 12-month WRF modeling results were validated by six observational buoys deployed (at 3 m elevation) by this Project as well as three nearby metrological stations (at 10 m elevation) maintained by National Data Buoy Center (NDBC). Modeling results indicate that wind energy increases

  16. Turning the tide: Saving the Chesapeake Bay

    SciTech Connect

    Horton, T.; Eichbaum, W.

    1991-07-01

    The Chesapeake Bay is one of the most productive and important ecosystems on earth, and as such is a model for other estuaries facing the demands of commerce, tourism, transportation, recreation, and other uses. This book presents a comprehensive look at two decades of efforts to save the bay, outlining which methods have worked and which have not.

  17. Modeling Benthic Sediment Processes to Predict Water Quality and Ecology in Narragansett Bay

    EPA Science Inventory

    The benthic sediment acts as a huge reservoir of particulate and dissolved material (within interstitial water) which can contribute to loading of contaminants and nutrients to the water column. A benthic sediment model is presented in this report to predict spatial and temporal ...

  18. Data Report for Calibration of a Bio-Optical Model for Narragansett Bay

    EPA Science Inventory

    Bio-optical models describe the quality and quantity of the light field at various depths in the water column. The absorption and scattering of light within the water column are wavelength dependent. The behavior of light also varies depending on the specific dissolved and partic...

  19. Spatial Statistical Network Models for Stream and River Temperatures in the Chesapeake Bay Watershed

    EPA Science Inventory

    Numerous metrics have been proposed to describe stream/river thermal regimes, and researchers are still struggling with the need to describe thermal regimes in a parsimonious fashion. Regional temperature models are needed for characterizing and mapping current stream thermal re...

  20. Rheumatoid Arthritis Naive T Cells Share Hypermethylation Sites With Synoviocytes

    PubMed Central

    Rhead, Brooke; Holingue, Calliope; Cole, Michael; Shao, Xiaorong; Quach, Hong L.; Quach, Diana; Shah, Khooshbu; Sinclair, Elizabeth; Graf, John; Link, Thomas; Harrison, Ruby; Rahmani, Elior; Halperin, Eran; Wang, Wei; Firestein, Gary S.; Barcellos, Lisa F.

    2017-01-01

    Objective To determine whether differentially methylated CpGs in synovium‐derived fibroblast‐like synoviocytes (FLS) of patients with rheumatoid arthritis (RA) were also differentially methylated in RA peripheral blood (PB) samples. Methods For this study, 371 genome‐wide DNA methylation profiles were measured using Illumina HumanMethylation450 BeadChips in PB samples from 63 patients with RA and 31 unaffected control subjects, specifically in the cell subsets of CD14+ monocytes, CD19+ B cells, CD4+ memory T cells, and CD4+ naive T cells. Results Of 5,532 hypermethylated FLS candidate CpGs, 1,056 were hypermethylated in CD4+ naive T cells from RA PB compared to control PB. In analyses of a second set of CpG candidates based on single‐nucleotide polymorphisms from a genome‐wide association study of RA, 1 significantly hypermethylated CpG in CD4+ memory T cells and 18 significant CpGs (6 hypomethylated, 12 hypermethylated) in CD4+ naive T cells were found. A prediction score based on the hypermethylated FLS candidates had an area under the curve of 0.73 for association with RA case status, which compared favorably to the association of RA with the HLA–DRB1 shared epitope risk allele and with a validated RA genetic risk score. Conclusion FLS‐representative DNA methylation signatures derived from the PB may prove to be valuable biomarkers for the risk of RA or for disease status. PMID:27723282

  1. Nonparametric Bayes approach for a semi-mechanistic pharmacokinetic and pharmacodynamic model

    NASA Astrophysics Data System (ADS)

    Dong, Yan

    Both frequentist and Bayesian approaches have been used to characterize population pharmacokinetics and pharmacodynamics(PK/PD) models. These methods focus on estimating the population parameters and assessing the association between the characteristics of PK/PD and the subject covariates. In this work, we propose a Dirichlet process mixture model to classify the patients based on their individualized pharmacokinetic and pharmacodynamic profiles. Then we can predict the new patients' dose-response curves given their concentration-time profiles. Additionally, we implement a modern Markov Chain Monte Carlo algorithm for sampling inference of parameters. The detailed sampling procedures as well as the results are discussed in a simulation data and a real data example. We also evaluate an approximate solution of a system of nonlinear differential equations from Euler's method and compare the results with a general numerical solver, ode from R package, deSolve.

  2. Physical-Biological-Optics Model Development and Simulation for the Pacific Ocean and Monterey Bay, California

    DTIC Science & Technology

    2012-09-30

    contains color images. 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT SAR 18. NUMBER OF PAGES 10 19a...including the color dissolved organic carbon (CDOC) in the modified CoSiNE model to mimic color dissolved organic matter (CDOM) dynamics in the ocean...distribution of underwater light field that can substantially affect phytoplankton photosynthesis and shortwave radiation near the surface. To

  3. Management of fluid mud in estuaries, bays, and lakes. II: Measurement, modeling, and management

    USGS Publications Warehouse

    McAnally, W.H.; Teeter, A.; Schoellhamer, D.; Friedrichs, C.; Hamilton, D.; Hayter, E.; Shrestha, P.; Rodriguez, H.; Sheremet, A.; Kirby, R.

    2007-01-01

    Techniques for measurement, modeling, and management of fluid mud are available, but research is needed to improve them. Fluid mud can be difficult to detect, measure, or sample, which has led to new instruments and new ways of using existing instruments. Multifrequency acoustic fathometers sense neither density nor viscosity and are, therefore, unreliable in measuring fluid mud. Nuclear density probes, towed sleds, seismic, and drop probes equipped with density meters offer the potential for accurate measurements. Numerical modeling of fluid mud requires solving governing equations for flow velocity, density, pressure, salinity, water surface, plus sediment submodels. A number of such models exist in one-, two-, and three-dimensional form, but they rely on empirical relationships that require substantial site-specific validation to observations. Management of fluid mud techniques can be classified as those that accomplish: Source control, formation control, and removal. Nautical depth, a fourth category, defines the channel bottom as a specific fluid mud density or alternative parameter as safe for navigation. Source control includes watershed management measures to keep fine sediment out of waterways and in-water measures such as structures and traps. Formation control methods include streamlined channels and structures plus other measures to reduce flocculation and structures that train currents. Removal methods include the traditional dredging and transport of dredged material plus agitation that contributes to formation control and/or nautical depth. Conditioning of fluid mud by dredging and aerating offers the possibility of improved navigability. Two examples-the Atchafalaya Bar Channel and Savannah Harbor-illustrate the use of measurements and management of fluid mud. ?? 2007 ASCE.

  4. Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery.

    PubMed

    Artalejo, J R; Gómez-Corral, A; López-García, M; Molina-París, C

    2017-02-01

    The population of naive T cells in the periphery is best described by determining both its T cell receptor diversity, or number of clonotypes, and the sizes of its clonal subsets. In this paper, we make use of a previously introduced mathematical model of naive T cell homeostasis, to study the fate and potential of naive T cell clonotypes in the periphery. This is achieved by the introduction of several new stochastic descriptors for a given naive T cell clonotype, such as its maximum clonal size, the time to reach this maximum, the number of proliferation events required to reach this maximum, the rate of contraction of the clonotype during its way to extinction, as well as the time to a given number of proliferation events. Our results show that two fates can be identified for the dynamics of the clonotype: extinction in the short-term if the clonotype experiences too hostile a peripheral environment, or establishment in the periphery in the long-term. In this second case the probability mass function for the maximum clonal size is bimodal, with one mode near one and the other mode far away from it. Our model also indicates that the fate of a recent thymic emigrant (RTE) during its journey in the periphery has a clear stochastic component, where the probability of extinction cannot be neglected, even in a friendly but competitive environment. On the other hand, a greater deterministic behaviour can be expected in the potential size of the clonotype seeded by the RTE in the long-term, once it escapes extinction.

  5. Risk assessment of butyltins based on a fugacity-based food web bioaccumulation model in the Jincheng Bay mariculture area: I. Model development.

    PubMed

    Hu, Yanbing; Gong, Xianghong; Xu, Yingjiang; Song, Xiukai; Liu, Huihui; Deng, Xuxiu; Ru, Shaoguo

    2014-08-01

    A fugacity-based model was developed to simulate the bioaccumulation of butyltins in the food web of the Jincheng Bay mariculture area. The predicted biological tissue residues of tributyltin (TBT), dibutyltin (DBT), and monobutyltin (MBT) were 0.04-17.09, 0.14-53.54, and 0.27-108.77 ng-Sn g(-1), respectively, and the predicted values in six mollusca agreed well with the measured ones. The lipid-normalized concentrations did not significantly increase across trophic levels, indicating no biomagnification across aquatic food webs. These results were highly consistent with those observed both in the laboratory and field, which had been reported in numerous references. The explanation, from calculating their flux equilibrium in the food web, was that butyltins were primarily taken in via respiration from the water column by marine organisms. The sensitivities of the model parameters were analyzed, revealing that the hydrophobicity of butyltins played the dominant role in their bioaccumulation phenomena. The verified model predictions of the biotic tissue concentrations of the butyltins could be readily applied to perform internal ecological risk and human health risk assessments in this area.

  6. Bathymetry and digital elevation models of Coyote Creek and Alviso Slough, South San Francisco Bay, California

    USGS Publications Warehouse

    Foxgrover, Amy C.; Finlayson, David P.; Jaffe, Bruce E.; Fregoso, Theresa A.

    2011-01-01

    The bathymetry surveys were conducted using the state-of-the-art research vessel R/V Parke Snavely outfitted with an interferometric sidescan sonar for swath mapping in extremely shallow water. We provide high-resolution bathymetric data collected by the USGS. For the 2010 baseline survey we have merged the bathymetry with aerial lidar data that were collected for the USGS during the same time period to create a seamless, high-resolution digital elevation model (DEM) of the study area. The series of bathymetry datasets are provided at 1 m resolution and the 2010 bathymetric/topographic DEM at 2 m resolution. The data are formatted as both X, Y, Z text files and ESRI Arc ASCII files that are accompanied by FGDC compliant metadata.

  7. Urban Greening Bay Area

    EPA Pesticide Factsheets

    Information about the San Francisco Bay Water Quality Project (SFBWQP) Urban Greening Bay Area, a large-scale effort to re-envision urban landscapes to include green infrastructure (GI) making communities more livable and reducing stormwater runoff.

  8. Chesapeake Bay TMDL Document

    EPA Pesticide Factsheets

    This page provides the Total Maximum Daily Load (TMDL) report for the Chesapeake Bay. It includes the executive summary, main report, and appendices. The Chesapeake Bay TMDL was established by U.S. EPA Region 3 on December 29, 2010

  9. Chesapeake Bay TMDL

    EPA Pesticide Factsheets

    In 2010 EPA established the Chesapeake Bay TMDL, a comprehensive pollution diet with accountability measures to restore clean water in the bay and local waters. It set limits for nutrients and sediment to meet water quality standards across the watershed

  10. Exploration models for Tertiary lacustrine carbonates, Liaodong Bay, People's Republic of China

    SciTech Connect

    Lomando, A.J. )

    1996-01-01

    Lacustrine carbonates are a significant reservoir target in the basins of eastern China. Difficulty in seismically imaging this play type generates the need for accurate exploration models to define geometries for lead and prospect identification. Rifted and karsted Cambro-Ordovician carbonates form the base of the section which is overlain by thick Tertiary lacustrine deposits. Two types of lacustrine carbonate plays have been identified. Carbonate alluvial fans developed from the erosion of Cambro-Ordovician dolomites and limestones in places along the flanks of tilted fault block ridges. During lake formation and expansion, these fans formed small shelves along the lake margins which became the sites of active carbonate production and winnowing. This play type forms discontinuous trends of lacustrine shoreline skeletal grainstones which mimic the underlying fan geometries. A second play type was identified in the JZ-20/JZ-9 trend. Stacked, shoaling upward cycles of skeletal grainstones occur on the gentle ramp sides of tilted fault blocks. In contrast, a different style of lake margin accumulation occurs on the bounding fault side of these blocks. Blocks with single major bounding faults have narrow shelves prohibiting accumulation of carbonate, whereas structures with sets of subsidiary faults form perched platforms ideal for the accumulation of thick lacustrine carbonate sections. Both of these play types have good modern analogues from the Great Salt Lake in Utah and the East African Rift System.

  11. Exploration models for Tertiary lacustrine carbonates, Liaodong Bay, People`s Republic of China

    SciTech Connect

    Lomando, A.J.

    1996-12-31

    Lacustrine carbonates are a significant reservoir target in the basins of eastern China. Difficulty in seismically imaging this play type generates the need for accurate exploration models to define geometries for lead and prospect identification. Rifted and karsted Cambro-Ordovician carbonates form the base of the section which is overlain by thick Tertiary lacustrine deposits. Two types of lacustrine carbonate plays have been identified. Carbonate alluvial fans developed from the erosion of Cambro-Ordovician dolomites and limestones in places along the flanks of tilted fault block ridges. During lake formation and expansion, these fans formed small shelves along the lake margins which became the sites of active carbonate production and winnowing. This play type forms discontinuous trends of lacustrine shoreline skeletal grainstones which mimic the underlying fan geometries. A second play type was identified in the JZ-20/JZ-9 trend. Stacked, shoaling upward cycles of skeletal grainstones occur on the gentle ramp sides of tilted fault blocks. In contrast, a different style of lake margin accumulation occurs on the bounding fault side of these blocks. Blocks with single major bounding faults have narrow shelves prohibiting accumulation of carbonate, whereas structures with sets of subsidiary faults form perched platforms ideal for the accumulation of thick lacustrine carbonate sections. Both of these play types have good modern analogues from the Great Salt Lake in Utah and the East African Rift System.

  12. [Naive objectivism in the assessment of behavioral disorders].

    PubMed

    Schmid, P

    1977-01-01

    Naive objectivism is a widespread attitude in human and social science research, although it disregards important principles of the theory of cognition. In the history of philosophy two naive approaches to the understanding of the world were continually disputed; 1. rationalism which purports unlimited cognitive power of the human mind, 2. a kind of empiricism which denies subjective elements in the process of cognition. Today the overestimation of human understanding is reflected in a dogmatic adherence to specific professional or idealogically biased doctrines and in the dubious ideal of a purely empirical science with its limited applicability to mankind. The exaggerated expectations regarding the inherent lawfulness of the empirical research field is demonstrated by excessive data collection and by the useless attempt to define behavioral disorders as deviation from the statistical norm. However, behavior disorders can only be understood, if the totality of being human is considered. They are to be seen as failing attempts to give and to maintain a meaning to life.

  13. Evaluating Tidal Marsh Sustainability in the Face of Sea-Level Rise: A Hybrid Modeling Approach Applied to San Francisco Bay

    PubMed Central

    Stralberg, Diana; Brennan, Matthew; Callaway, John C.; Wood, Julian K.; Schile, Lisa M.; Jongsomjit, Dennis; Kelly, Maggi; Parker, V. Thomas; Crooks, Stephen

    2011-01-01

    Background Tidal marshes will be threatened by increasing rates of sea-level rise (SLR) over the next century. Managers seek guidance on whether existing and restored marshes will be resilient under a range of potential future conditions, and on prioritizing marsh restoration and conservation activities. Methodology Building upon established models, we developed a hybrid approach that involves a mechanistic treatment of marsh accretion dynamics and incorporates spatial variation at a scale relevant for conservation and restoration decision-making. We applied this model to San Francisco Bay, using best-available elevation data and estimates of sediment supply and organic matter accumulation developed for 15 Bay subregions. Accretion models were run over 100 years for 70 combinations of starting elevation, mineral sediment, organic matter, and SLR assumptions. Results were applied spatially to evaluate eight Bay-wide climate change scenarios. Principal Findings Model results indicated that under a high rate of SLR (1.65 m/century), short-term restoration of diked subtidal baylands to mid marsh elevations (−0.2 m MHHW) could be achieved over the next century with sediment concentrations greater than 200 mg/L. However, suspended sediment concentrations greater than 300 mg/L would be required for 100-year mid marsh sustainability (i.e., no elevation loss). Organic matter accumulation had minimal impacts on this threshold. Bay-wide projections of marsh habitat area varied substantially, depending primarily on SLR and sediment assumptions. Across all scenarios, however, the model projected a shift in the mix of intertidal habitats, with a loss of high marsh and gains in low marsh and mudflats. Conclusions/Significance Results suggest a bleak prognosis for long-term natural tidal marsh sustainability under a high-SLR scenario. To minimize marsh loss, we recommend conserving adjacent uplands for marsh migration, redistributing dredged sediment to raise elevations, and

  14. South San Francisco Bay, California

    USGS Publications Warehouse

    Dartnell, Peter; Gibbons, Helen

    2007-01-01

    View eastward. Elevations in mapped area color coded: purple (approx 15 m below sea level) to red-orange (approx 90 m above sea level). South San Francisco Bay is very shallow, with a mean water depth of 2.7 m (8.9 ft). Trapezoidal depression near San Mateo Bridge is where sediment has been extracted for use in cement production and as bay fill. Land from USGS digital orthophotographs (DOQs) overlaid on USGS digital elevation models (DEMs). Distance across bottom of image approx 11 km (7 mi); vertical exaggeration 1.5X.

  15. Observed and modeled patterns of circulation in a semi-enclosed bay: Ria de Vigo (NW Iberia)

    NASA Astrophysics Data System (ADS)

    Pilczynski, Krzysztof; Dubert, Jesus; Nolasco, Rita; Barton, Des; Souto Torres, Carlos

    2016-04-01

    The Ría de Vigo, as a semi-enclosed bay, belonging to the area so-called Rias Baixas, located at the northern tip of the Iberian coastal upwelling system. The circulation of the Ria de Vigo, being one of the major areas of mussels production, has become the subject of intensive research. The Ria de Vigo behaves as a partially-mixed estuary with a two-layered residual circulation, and is influenced by water exchange with the surrounding ocean. During northerly (upwelling favorable) winds, water enters into the Ria through the northern mouth and leaves through the surface layer of the southern mouth, in a double layer circulation at this mouth. Nearly opposed situation occours during downwelling favourable wind periods. Numerical models have become useful tools to study the hydrology and circulation of the Ria de Vigo. In this research we used the ROMS - AGRIF model. The implementation of several nested domains to increase the spatial resolution (up to 150m resolution) allowed solving the interactions between Ria de Vigo and surrounding coastal ocean in a realistic way. We have obtained a detailed description of the circulation with good agreement between observational data (ADCP moorings at both mouths, and weekly hydrological cruises) and predicted currents, salinity and temperature fields. Two new patterns of circulation in the Ria are revealed by our research: -In particular conditions associated with northerly wind relaxation, there are two-layer circulation occurs in both mouths of the Ria, consisting of outflow and inflow though the surface and bottom layers. This situation happens in the absence of stratification during winter. -Also during winter, one-layer circulation in the southern mouth of the Ria (typically there are two layers) can occur during long periods of persistent and strong upwelling-favourable wind. Our research has provided a detailed study of the circulation and hydrology of the Ria de Vigo, explaining specifically different mechanisms of

  16. Naive Probability: Model-based Estimates of Unique Events

    DTIC Science & Technology

    2014-05-04

    will end the shortage of replacement organs in the next 15 years? 3 the Supreme Court rules on the constitutionality of gay marriage in the next 5...La Mont, K., Lipton, J., Dehaene, S., Kanwisher, N., & Spelke, E.S. (2006). Nonsymbolic arithmetic in adults and young children . Cognition, 98, 199...years? that a gay person will be elected as president in the next 50 years? 4 Greece will make a full economic recovery in the next 10 years

  17. Targeted Help for Spoken Dialogue Systems: Intelligent Feedback Improves Naive Users' Performance

    NASA Technical Reports Server (NTRS)

    Hockey, Beth Ann; Lemon, Oliver; Campana, Ellen; Hiatt, Laura; Aist, Gregory; Hieronymous, Jim; Gruenstein, Alexander; Dowding, John

    2003-01-01

    We present experimental evidence that providing naive users of a spoken dialogue system with immediate help messages related to their out-of-coverage utterances improves their success in using the system. A grammar-based recognizer and a Statistical Language Model (SLM) recognizer are run simultaneously. If the grammar-based recognizer suceeds, the less accurate SLM recognizer hypothesis is not used. When the grammar-based recognizer fails and the SLM recognizer produces a recognition hypothesis, this result is used by the Targeted Help agent to give the user feed-back on what was recognized, a diagnosis of what was problematic about the utterance, and a related in-coverage example. The in-coverage example is intended to encourage alignment between user inputs and the language model of the system. We report on controlled experiments on a spoken dialogue system for command and control of a simulated robotic helicopter.

  18. Integrating Entropy-Based Naïve Bayes and GIS for Spatial Evaluation of Flood Hazard.

    PubMed

    Liu, Rui; Chen, Yun; Wu, Jianping; Gao, Lei; Barrett, Damian; Xu, Tingbao; Li, Xiaojuan; Li, Linyi; Huang, Chang; Yu, Jia

    2016-09-24

    Regional flood risk caused by intensive rainfall under extreme climate conditions has increasingly attracted global attention. Mapping and evaluation of flood hazard are vital parts in flood risk assessment. This study develops an integrated framework for estimating spatial likelihood of flood hazard by coupling weighted naïve Bayes (WNB), geographic information system, and remote sensing. The north part of Fitzroy River Basin in Queensland, Australia, was selected as a case study site. The environmental indices, including extreme rainfall, evapotranspiration, net-water index, soil water retention, elevation, slope, drainage proximity, and density, were generated from spatial data representing climate, soil, vegetation, hydrology, and topography. These indices were weighted using the statistics-based entropy method. The weighted indices were input into the WNB-based model to delineate a regional flood risk map that indicates the likelihood of flood occurrence. The resultant map was validated by the maximum inundation extent extracted from moderate resolution imaging spectroradiometer (MODIS) imagery. The evaluation results, including mapping and evaluation of the distribution of flood hazard, are helpful in guiding flood inundation disaster responses for the region. The novel approach presented consists of weighted grid data, image-based sampling and validation, cell-by-cell probability inferring and spatial mapping. It is superior to an existing spatial naive Bayes (NB) method for regional flood hazard assessment. It can also be extended to other likelihood-related environmental hazard studies.

  19. A preclinical evaluation of the PI3K alpha/delta dominant inhibitor BAY 80-6946 in HER2-positive breast cancer models with acquired resistance to the HER2-targeted therapies trastuzumab and lapatinib.

    PubMed

    Elster, N; Cremona, M; Morgan, C; Toomey, S; Carr, A; O'Grady, A; Hennessy, B T; Eustace, A J

    2015-01-01

    The PI3K pathway is a key mechanism of trastuzumab resistance, but early attempts to indirectly target this pathway with mTOR inhibitors have had limited success. We present the results of a preclinical study of the selective alpha/delta isoform dominant PI3K inhibitor BAY 80-6946 tested alone and in combination with HER2-targeted therapies in HER2-positive cell lines, including models with acquired resistance to trastuzumab and/or lapatinib. A panel of HER2-positive breast cancer cells were profiled for their mutational status using Sequenom MassARRAY, PTEN status by Western blot, and anti-proliferative response to BAY 80-6946 alone and in combination with the HER2-targeted therapies trastuzumab, lapatinib and afatinib. Reverse phase protein array was used to determine the effect of BAY 80-6946 on expression and phosphorylation of 68 proteins including members of the PI3K and MAPK pathways. The Boyden chamber method was used to determine if BAY 80-6946 affected cellular invasion and migration. BAY 80-6946 has anti-proliferative and anti-invasive effects when used alone in our panel of cell lines (IC50s 3.9-29.4 nM). BAY 80-6946 inhibited PI3K signalling and was effective in cells regardless of their PI3K, P53 or PTEN status. The combination of HER2-targeted therapies and BAY 80-6946 inhibited growth more effectively than either therapy used alone (with clear synergism in many cases), and can restore sensitivity to trastuzumab and lapatinib in cells with acquired resistance to either trastuzumab and/or lapatinib. The addition of BAY 80-6946 to HER2-targeted therapy could represent an improved treatment strategy for patients with refractory metastatic HER2-positive breast cancer, and should be considered for clinical trial evaluation.

  20. Development of hydroacoustical techniques for the monitoring and classification of benthic habitats in Puck Bay: Modeling of acoustic waves scattering by seagrass

    NASA Astrophysics Data System (ADS)

    Raczkowska, A.; Gorska, N.

    2012-12-01

    Puck Bay is an area of high species biodiversity belonging to the Coastal Landscape Park of Baltic Sea Protected Areas (BSPA) and is also included in the list of the World Wide Fund for Nature (WWF) and covered by the protection program "Natura 2000". The underwater meadows of the Puck Bay are important for Europe's natural habitats due to their role in enhancing the productivity of marine ecosystems and providing shelter and optimal feeding conditions for many marine organisms. One of the dominant species comprising the underwater meadows of the Southern Baltic Sea is the seagrass Zostera marina. The spatial extent of underwater seagrass meadows is altered by pollution and eutrophication; therefore, to properly manage the area one must monitor its ecological state. Remote acoustic methods are useful tools for the monitoring of benthic habitats in many marine areas because they are non-invasive and allow researchers to obtain data from a large area in a short period of time. Currently there is a need to apply these methods in the Baltic Sea. Here we present an analysis of the mechanism of scattering of acoustic waves on seagrass in the Southern Baltic Sea based on the numerical modeling of acoustic wave scattering by the biological tissues of plants. The study was conducted by adapting a model developed on the basis of DWBA (Distorted Wave Born Approximation) developed by Stanton and Chu (2005) for fluid-like objects, including the characteristics of the Southern Baltic seagrass. Input data for the model, including the morphometry of seagrass leaves, their angle of inclination and the density plant cover, was obtained through the analysis of biological materials collected in the Puck Bay in the framework of a research project financed by the Polish Government (Development of hydroacoustic methods for studies of underwater meadows of Puck Bay, 6P04E 051 20). On the basis of the developed model, we have analyzed the dependence of the target strength of a single

  1. Gradient Analysis and Classification of Carolina Bay Vegetation: A Framework for Bay Wetlands Conservation and Restoration

    SciTech Connect

    Diane De Steven,Ph.D.; Maureen Tone,PhD.

    1997-10-01

    This report address four project objectives: (1) Gradient model of Carolina bay vegetation on the SRS--The authors use ordination analyses to identify environmental and landscape factors that are correlated with vegetation composition. Significant factors can provide a framework for site-based conservation of existing diversity, and they may also be useful site predictors for potential vegetation in bay restorations. (2) Regional analysis of Carolina bay vegetation diversity--They expand the ordination analyses to assess the degree to which SRS bays encompass the range of vegetation diversity found in the regional landscape of South Carolina's western Upper Coastal Plain. Such comparisons can indicate floristic status relative to regional potentials and identify missing species or community elements that might be re-introduced or restored. (3) Classification of vegetation communities in Upper Coastal Plain bays--They use cluster analysis to identify plant community-types at the regional scale, and explore how this classification may be functional with respect to significant environmental and landscape factors. An environmentally-based classification at the whole-bay level can provide a system of templates for managing bays as individual units and for restoring bays to desired plant communities. (4) Qualitative model for bay vegetation dynamics--They analyze present-day vegetation in relation to historic land uses and disturbances. The distinctive history of SRS bays provides the possibility of assessing pathways of post-disturbance succession. They attempt to develop a coarse-scale model of vegetation shifts in response to changing site factors; such qualitative models can provide a basis for suggesting management interventions that may be needed to maintain desired vegetation in protected or restored bays.

  2. Tampa Bay Integrated Science Pilot Study: Baseline mapping, land surface dynamics and predictive modeling, and hazards vulnerability studies

    USGS Publications Warehouse

    Crane, Michael; Yates, Kimberly; Clark, Robert; Gesch, Dean; Hess, Kurt; Koehmstedt, John; Milbert, Dennis; Parker, Bruce; Sechrist, Dan; Tilley, Janet; Wilson, Robert

    2001-01-01

    Tampa Bay and its environs have experienced phenomenal urban growth and significant changes in land cover and land-use practices over the past 50 years. This trend is expected to continue, with the impact of human activity broadening geographically and intensifying throughout the region.One of the immediate impacts of urban growth is the creation of additional impervious surfaces, which in turn, generate increased urban runoff that contributes to higher levels of nutrient loading in water bodies throughout the area.To better understand these and other anthropogenic affects on the ecology of the natural environment of the region, this component of the Tampa Bay Pilot Study took a broad basin-wide view. This regional view was intended to provide geographic and temporal context for the smaller intensely studied sample field site locations within the estuarine environment.

  3. Sources, fate, and transport of nitrogen and phosphorus in the Chesapeake Bay watershed-An empirical model

    USGS Publications Warehouse

    Ator, Scott W.; Brakebill, John W.; Blomquist, Joel D.

    2011-01-01

    Nutrient fate and transport through the Chesapeake Bay watershed to the bay reflect the diferent physical and chemical properties of nitrogen and phosphorus compounds. Groundwater is an important pathway for nitrogen transport (as nitrate), and TN flux is greatest in areas with greater groundwater flow and in areas of the Piedmont underlain by carbonate rocks. TN flux decreases with increasing vegetative growth (likely indicative of plant uptake) and soil available water capacity (likely indicative of reducing conditions). Phosphorus transport to streams, conversely, is greatest in areas most likely to generate overland runoff and related erosion, including those with less permeable and more erodible soils and greater precipitation. Phosphorus transport also is greater in the Coastal Plain than in other areas, possibly due to saturation of soils with historical phosphorus applications. Both nitrogen and phosphorus are lost within watershed impoundments (lakes, ponds, or reservoirs), and nitrogen is also lost significantly along flowing reaches, particularly in small streams and in larger streams in warmer areas.

  4. Naive Theory of Biology: The Pre-School Child's Explanation of Death

    ERIC Educational Resources Information Center

    Vlok, Milandre; de Witt, Marike W.

    2012-01-01

    This article explains the naive theory of biology that the pre-school child uses to explain the cause of death. The empirical investigation showed that the young participants do use a naive theory of biology to explain function and do make reference to "vitalistic causality" in explaining organ function. Furthermore, most of these…

  5. Children and Adolescents' Understandings of Family Resemblance: A Study of Naive Inheritance Concepts

    ERIC Educational Resources Information Center

    Williams, Joanne M.

    2012-01-01

    This paper aims to provide developmental data on two connected naive inheritance concepts and to explore the coherence of children's naive biology knowledge. Two tasks examined children and adolescents' (4, 7, 10, and 14 years) conceptions of phenotypic resemblance across kin (in physical characteristics, disabilities, and personality traits). The…

  6. The Persistence of "Solid" and "Liquid" Naive Conceptions: A Reaction Time Study

    ERIC Educational Resources Information Center

    Babai, Reuven; Amsterdamer, Anat

    2008-01-01

    The study explores whether the naive concepts of "solid" and "liquid" persist in adolescence. Accuracy of responses and reaction times where measured while 41 ninth graders classified different solids (rigid, non-rigid and powders) and different liquids (runny, dense) into solid or liquid. The results show that these naive conceptions affect…

  7. What Fits into a Mirror: Naive Beliefs about the Field of View

    ERIC Educational Resources Information Center

    Bianchi, Ivana; Savardi, Ugo

    2012-01-01

    Research on naive physics and naive optics have shown that people hold surprising beliefs about everyday phenomena that are in contrast with what they see. In this article, we investigated what adults expect to be the field of view of a mirror from various viewpoints. The studies presented here confirm that humans have difficulty dealing with the…

  8. The influence of naive causal theories on lay concepts of mental illness.

    PubMed

    Kim, Nancy S; Ahn, Woo-Kyoung

    2002-01-01

    Two experiments, incorporating both real-life (Experiment 1) and artificial (Experiment 2) stimuli, demonstrated that lay concepts of mental disorders can be reliably predicted from subjects' naive causal theories about those disorders. Symptoms that are deeper causes (X, where X causes Y, which causes Z) are more important in lay concepts than intermediate causes (Y), which in turn are more important than terminal effects (Z). In addition, symptoms that cause or are caused by other symptoms are more important in lay concepts than symptoms not participating in any causal relationships. Implications of these results for current models of categorization and for research on lay theories of mental disorders are discussed, and future directions for research are suggested.

  9. Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass

    PubMed Central

    Guo, Ge; von Meyenn, Ferdinand; Santos, Fatima; Chen, Yaoyao; Reik, Wolf; Bertone, Paul; Smith, Austin; Nichols, Jennifer

    2016-01-01

    Summary Conventional generation of stem cells from human blastocysts produces a developmentally advanced, or primed, stage of pluripotency. In vitro resetting to a more naive phenotype has been reported. However, whether the reset culture conditions of selective kinase inhibition can enable capture of naive epiblast cells directly from the embryo has not been determined. Here, we show that in these specific conditions individual inner cell mass cells grow into colonies that may then be expanded over multiple passages while retaining a diploid karyotype and naive properties. The cells express hallmark naive pluripotency factors and additionally display features of mitochondrial respiration, global gene expression, and genome-wide hypomethylation distinct from primed cells. They transition through primed pluripotency into somatic lineage differentiation. Collectively these attributes suggest classification as human naive embryonic stem cells. Human counterparts of canonical mouse embryonic stem cells would argue for conservation in the phased progression of pluripotency in mammals. PMID:26947977

  10. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

    PubMed Central

    DeKosky, Brandon J.; Lungu, Oana I.; Park, Daechan; Johnson, Erik L.; Charab, Wissam; Chrysostomou, Constantine; Kuroda, Daisuke; Ellington, Andrew D.; Ippolito, Gregory C.; Gray, Jeffrey J.; Georgiou, George

    2016-01-01

    Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19+CD20+CD27− IgM-naive B cells, >120,000 antibody clusters from CD19+CD20+CD27+ antigen–experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ–Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease. PMID:27114511

  11. Statistical modeling of interannual shoreline change driven by North Atlantic climate variability spanning 2000-2014 in the Bay of Biscay

    NASA Astrophysics Data System (ADS)

    Robinet, A.; Castelle, B.; Idier, D.; Le Cozannet, G.; Déqué, M.; Charles, E.

    2016-12-01

    Modeling studies addressing daily to interannual coastal evolution typically relate shoreline change with waves, currents and sediment transport through complex processes and feedbacks. For wave-dominated environments, the main driver (waves) is controlled by the regional atmospheric circulation. Here a simple weather regime-driven shoreline model is developed for a 15-year shoreline dataset (2000-2014) collected at Truc Vert beach, Bay of Biscay, SW France. In all, 16 weather regimes (four per season) are considered. The centroids and occurrences are computed using the ERA-40 and ERA-Interim reanalyses, applying k-means and EOF methods to the anomalies of the 500-hPa geopotential height over the North Atlantic Basin. The weather regime-driven shoreline model explains 70% of the observed interannual shoreline variability. The application of a proven wave-driven equilibrium shoreline model to the same period shows that both models have similar skills at the interannual scale. Relation between the weather regimes and the wave climate in the Bay of Biscay is investigated and the primary weather regimes impacting shoreline change are identified. For instance, the winter zonal regime characterized by a strengthening of the pressure gradient between the Iceland low and the Azores high is associated with high-energy wave conditions and is found to drive an increase in the shoreline erosion rate. The study demonstrates the predictability of interannual shoreline change from a limited number of weather regimes, which opens new perspectives for shoreline change modeling and encourages long-term shoreline monitoring programs.

  12. Low-Dose Pharmacokinetics and Oral Bioavailability of Dichloroacetate in Naive and GST-zeta Depleted Rats

    SciTech Connect

    Saghir, Shakil A.; Schultz, Irv R. )

    2002-01-01

    Pharmacokinetics of dichloroacetate (DCA) in naive and glutathione-S-transferase-zeta (GSTzeta) depleted rats was studied at doses approaching human daily exposure levels. In vitro metabolism of DCA by rat and human liver cytosol was also compared. Jugular vein cannulated male Fischer-344 rats were administered (i.v or gavage) with graded doses of DCA ranging from 0.05-20 mg/kg and time-course blood samples collected from the cannula. GSTzeta was depleted by exposing rats to DCA (0.2 g/L DCA) in drinking water for 7 days. Elimination of DCA by naive rats was so rapid that only the 1-20 mg/kg i.v. and 5 and 20 mg/kg gavage doses provided plasma concentrations above the method detection limit. GSTzeta depletion slowed DCA elimination from plasma allowing kinetic analysis of doses as low as 0.05 mg/kg. DCA elimination was strongly dose-dependent in the naive rats with total body clearance declining with increasing dose. In the GSTzeta depleted rats, the pharmacokinetics became line ar at doses No.1 mg/kg. All oral doses were rapidly absorbed without any lag time. At higher oral doses (?5 mg/kg in GSTzeta depleted and?20 mg/kg in naive), secondary peaks in the plasma concentration appeared long after the completion of the initial absorption phase. Virtually all the dose was eliminated through metabolic clearance; the rate of urinary elimination of DCA was < 1 ml h-1kg-1. A maximum of 1.0?0.3% dose was recovered in urine within 24 h in the GSTzeta depleted rats dosed i.v. with 20 mg/kg. The rate of in vitro metabolism of DCA by human cytosol was statistically similar to the GSTzeta depleted rats (p > 0.3), which supported the use of GSTzeta depleted rats as a model for assessing kinetics of DCA in humans. Oral bioavailability of DCA was 0-13% in naive and 14-75% in GSTzeta depleted rats. Oral bioavailability of DCA to humans through consumption of drinking water was predicted to be a maximum of 0.05%.

  13. A Quantum Bayes Net Approach to Causal Reasoning

    NASA Astrophysics Data System (ADS)

    Trueblood, Jennifer S.; Mistry, Percy K.; Pothos, Emmanuel M.

    When individuals have little knowledge about a causal system and must make causal inferences based on vague and imperfect information, their judgments often deviate from the normative prescription of classical probability. Previously, many researchers have dealt with violations of normative rules by elaborating causal Bayesian networks through the inclusion of hidden variables. While these models often provide good accounts of data, the addition of hidden variables is often post hoc, included when a Bayes net fails to capture data. Further, Bayes nets with multiple hidden variables are often difficult to test. Rather than elaborating a Bayes net with hidden variables, we generalize the probabilistic rules of these models. The basic idea is that any classic Bayes net can be generalized to a quantum Bayes net by replacing the probabilities in the classic model with probability amplitudes in the quantum model. We discuss several predictions of quantum Bayes nets for human causal reasoning.

  14. Chesapeake Bay Low Freshwater Inflow Study. Appendix B. Plan Formulation. Appendix C. Hydrology. Appendix D. Hydraulic Model Test.

    DTIC Science & Technology

    1984-09-01

    estuaries. The circulation of small sub-estuaries (Gunpowder, Bush, Back, Magothy , Severn) do not follow the classic two-layered pattern exhibited in...The larger rivers on the Upper Western Shore include the Severn, Magothy , Patapsco, Middle, Back, Gunpowder and Bush Rivers. The flat, low discharge...01 17 4, 12 LC-02-01 22 4, 12, 21 Magothy River MA-0 1-01 21 L4, 12, 18 MA-02-01 18 4, 15 Mob jack Bay 1 1 MB-0l1-02 20 0, 20 MB-01-03 20 0, 20 MB- 03

  15. A review of 20 years of naive tests of significance for high-dimensional mean vectors and covariance matrices

    NASA Astrophysics Data System (ADS)

    Hu, Jiang; Bai, ZhiDong

    2016-12-01

    In this paper, we will introduce the so called naive tests and give a brief review on the newly development. Naive testing methods are easy to understand and performs robust especially when the dimension is large. In this paper, we mainly focus on reviewing some naive testing methods for the mean vectors and covariance matrices of high dimensional populations and believe this naive test idea can be wildly used in many other testing problems.

  16. Development of Land Segmentation, Stream-Reach Network, and Watersheds in Support of Hydrological Simulation Program-Fortran (HSPF) Modeling, Chesapeake Bay Watershed, and Adjacent Parts of Maryland, Delaware, and Virginia

    USGS Publications Warehouse

    Martucci, Sarah K.; Krstolic, Jennifer L.; Raffensperger, Jeff P.; Hopkins, Katherine J.

    2006-01-01

    The U.S. Geological Survey, U.S. Environmental Protection Agency Chesapeake Bay Program Office, Interstate Commission on the Potomac River Basin, Maryland Department of the Environment, Virginia Department of Conservation and Recreation, Virginia Department of Environmental Quality, and the University of Maryland Center for Environmental Science are collaborating on the Chesapeake Bay Regional Watershed Model, using Hydrological Simulation Program - FORTRAN to simulate streamflow and concentrations and loads of nutrients and sediment to Chesapeake Bay. The model will be used to provide information for resource managers. In order to establish a framework for model simulation, digital spatial datasets were created defining the discretization of the model region (including the Chesapeake Bay watershed, as well as the adjacent parts of Maryland, Delaware, and Virginia outside the watershed) into land segments, a stream-reach network, and associated watersheds. Land segmentation was based on county boundaries represented by a 1:100,000-scale digital dataset. Fifty of the 254 counties and incorporated cities in the model region were divided on the basis of physiography and topography, producing a total of 309 land segments. The stream-reach network for the Chesapeake Bay watershed part of the model region was based on the U.S. Geological Survey Chesapeake Bay SPARROW (SPAtially Referenced Regressions On Watershed attributes) model stream-reach network. Because that network was created only for the Chesapeake Bay watershed, the rest of the model region uses a 1:500,000-scale stream-reach network. Streams with mean annual streamflow of less than 100 cubic feet per second were excluded based on attributes from the dataset. Additional changes were made to enhance the data and to allow for inclusion of stream reaches with monitoring data that were not part of the original network. Thirty-meter-resolution Digital Elevation Model data were used to delineate watersheds for each

  17. Risk assessment of butyltins based on a fugacity-based food web bioaccumulation model in the Jincheng Bay mariculture area: II. Risk assessment.

    PubMed

    Hu, Yanbing; Song, Xiukai; Gong, Xianghong; Xu, Yingjiang; Liu, Huihui; Deng, Xuxiu; Ru, Shaoguo

    2014-08-01

    A fugacity-based food web bioaccumulation model was constructed, and the biotic concentrations of butyltins in the food web of the Jincheng Bay mariculture area were estimated accordingly, using the water and sediment concentrations described in the accompanying paper (Part I). This paper presents an ecological risk assessment (ERA) and a human health risk assessment (HHRA) of the butyltins, based on the estimated tissue residues in the marine life in this area. The results showed that the ecological risk probability was greater than 0.05. At this level, management control is critical since sensitive marine species would be profoundly endangered by butyltin contamination. Few if any detrimental effects, however, would be generated for humans from exposure to butyltins through seafood consumption. The fugacity-based model can refine the ERA and HHRA of pollutants in marine areas, provide a basis for protecting marine ecology and the security of fishery products, and thus help determine the feasibility of a proposed aquaculture project.

  18. A New Trait-Based Auto-Emergent Model for Zooplankton and Confrontation with Size-Structured Observations from the Bay of Biscay

    NASA Astrophysics Data System (ADS)

    Vandromme, Pieter; Sourisseau, Marc; Huret, Martin

    2013-04-01

    Zooplankton plays a significant role in marine ecosystems bridging the gap between primary producers and top consumers and interacting with the particle flux through complex dynamics. Scarcity of data and complexity of observing zooplankton make it difficult to integrate it in biogeochemical models where it is most often formulated in a simpler manner, i.e. classic box models with usually two compartments (micro and meso/macro zooplankton). Recent advances in automatic sizing, counting and identification allow better estimates of the dynamics and distribution of zooplankton, notably through the measurement of its size structure, and for zooplankton size matter. Most zooplankton physiological rates as well as predator:prey interactions can be significantly relied to individuals size through allometric relations. Such size-dependency was used in recent models. Yet, these models were neither confronted to observations nor integrated in 3D biogeochemical models. Here we propose a newly developed model of zooplankton dynamics based on size-dependent allometric relations but which allows various diet types regardless of the size. A size and a degree of herbivory is randomly drawn for each zooplankton species generated within the model (up to 400 here, limited by actual computational costs). By generating random degree of herbivory zooplankton species of same size could have various diet (from herbivore to carnivore). Other parameters leading to various reproductive strategies or vertical migration could also be drawn randomly (not tested here). The zooplankton model is coupled to the 3D biogeochemical model MARS3D on a test case representing a simplified view of the Bay of Biscay (i.e., continental shelf, estuary, tides). The model shows auto-emergent properties with the selection of size/diet most adapted to local conditions (here offshore vs. coastal, estuary…). Then, patterns of the modeled size-structure of the zooplankton are confronted to the ones observed during

  19. Tampa Bay: Chapter N

    USGS Publications Warehouse

    Handley, Larry; Spear, Kathryn; Cross, Lindsay; Baumstark, René; Moyer, Ryan; Thatcher, Cindy

    2013-01-01

    Tampa Bay is Florida’s largest open-water estuary and encompasses an area of approximately 1036 km2 (400 mi2) (Burgan and Engle, 2006; TBNEP, 2006). The Bay’s watershed drains 5,698 km2 (2,200 mi2) of land and includes freshwater from the Hillsborough River to the north east, the Alafia and Little Manatee rivers to the east, and the Manatee River to the south (Figure 1). Freshwater inflow also enters the bay from the Lake Tarpon Canal, from small tidal tributaries, and from watershed runoff. Outflow travels from the upper bay segments (Hillsborough Bay and Old Tampa Bay) into Middle and Lower Tampa Bay. Southwestern portions of the water shed flow through Boca Ciega Bay into the Intracoastal Waterway and through the Southwest Channel and Passage Key Inlet into the Gulf of Mexico. The average depth in most of Tampa Bay is only 3.4 m (11 ft); however, 129 km (80 mi) of shipping channels with a maximum depth of 13.1 m (43 ft) have been dredged over time and are regularly maintained. These channels help to support the three ports within the bay, as well as commercial and recreational boat traffic.

  20. Circulation in a bay influenced by flooding of a river discharging outside the bay

    NASA Astrophysics Data System (ADS)

    Kakehi, Shigeho; Takagi, Takamasa; Okabe, Katsuaki; Takayanagi, Kazufumi

    2017-03-01

    To investigate the influence of a river discharging outside a bay on circulation in the bay, we carried out current and salinity measurements from mooring systems and hydrographic observations in Matsushima Bay, Japan, and off the Naruse River, which discharges outside the bay. Previously, enhancement of horizontal circulation in the bay induced by increased freshwater input from the Naruse River was reported to have degraded the seedling yield of wild Pacific oysters in the bay, but the freshwater inflow from the river was not directly measured. Our hydrographic observations in Katsugigaura Strait, approximately 3 km southwest of the Naruse River mouth, detected freshwater derived from the river. The mooring data revealed that freshwater discharged by the river flowed into Matsushima Bay via the strait and that the freshwater transport increased when the river was in flood. The inflow through straits other than Katsugigaura was estimated by a box model analysis to be 26-145 m3 s-1 under normal river discharge conditions, and it decreased to 6 m3 s-1 during flood conditions. During flood events, the salt and water budgets in the bay were maintained by the horizontal circulation: inflow occurred mainly via Katsugigaura Strait, and outflow was mainly via other straits.

  1. Extreme weather events influence dispersal of naive northern fur seals.

    PubMed

    Lea, Mary-Anne; Johnson, Devin; Ream, Rolf; Sterling, Jeremy; Melin, Sharon; Gelatt, Tom

    2009-04-23

    Since 1975, northern fur seal (Callorhinus ursinus) numbers at the Pribilof Islands (PI) in the Bering Sea have declined rapidly for unknown reasons. Migratory dispersal and habitat choice may affect first-year survivorship, thereby contributing to this decline. We compared migratory behaviour of 166 naive pups during 2 years from islands with disparate population trends (increasing: Bogoslof and San Miguel Islands; declining: PI), hypothesizing that climatic conditions at weaning may differentially affect dispersal and survival. Atmospheric conditions (Bering Sea) in autumn 2005-2006 were anomalously cold, while 2006-2007 was considerably warmer and less stormy. In 2005, pups departed earlier at all sites, and the majority of PI pups (68-85%) departed within 1 day of Arctic storms and dispersed quickly, travelling southwards through the Aleutian Islands. Tailwinds enabled faster rates of travel than headwinds, a trend not previously shown for marine mammals. Weather effects were less pronounced at Bogoslof Island (approx. 400 km further south), and, at San Miguel Island, (California) departures were more gradual, and only influenced by wind and air pressure in 2005. We suggest that increasingly variable climatic conditions at weaning, particularly timing, frequency and intensity of autumnal storms in the Bering Sea, may alter timing, direction of dispersal and potentially survival of pups.

  2. A Modeling Study of In-stream Tidal Energy Extraction and Its Potential Environmental Impacts in a Tidal Channel and Bay System

    NASA Astrophysics Data System (ADS)

    Wang, T.; Yang, Z.; Copping, A. E.

    2012-12-01

    In recent years, there has been growing interest in harnessing in-stream tidal energy in response to concerns of increasing energy demand and to mitigate climate change impacts. While efforts have been made to assess and map available tidal energy resources using numerical models, little attention has been paid directly quantifying the associated potential environmental impacts as part of tidal energy generation. This paper presents the development of a tidal turbine module within a three-dimensional (3-D) unstructured grid coastal ocean model. The model is used to investigate in-stream tidal energy extraction and associated impacts on estuarine hydrodynamic and biological processes in a stratified estuarine system. A series of numerical experiments with varying numbers and configurations of turbines were carried out to assess the changes in the hydrodynamics and biological processes in the tidal channel and bay system due to tidal energy extraction. Model results show the maximum extractable energy depends strongly on the turbine hub height, and that the effects of energy extraction on the flow fields vary vertically. Preliminary model results also indicate that extraction of tidal energy increases vertical mixing and decreases flushing rate in the estuary. As one of the early modeling efforts aimed directly at examining the impacts of tidal energy extraction on estuarine circulation and biological processes, this study demonstrates that numerical models can serve as a very useful tool for this purpose. However, careful efforts are warranted to address system-specific environmental issues in real world, complex estuarine systems.

  3. CD4/CD8 ratio and CD8 counts predict CD4 response in HIV-1-infected drug naive and in patients on cART

    PubMed Central

    Sauter, Rafael; Huang, Ruizhu; Ledergerber, Bruno; Battegay, Manuel; Bernasconi, Enos; Cavassini, Matthias; Furrer, Hansjakob; Hoffmann, Matthias; Rougemont, Mathieu; Günthard, Huldrych F; Held, Leonhard

    2016-01-01

    Abstract Plasma HIV viral load is related to declining CD4 lymphocytes. The extent to which CD8 cells, in addition to RNA viral load, predict the depletion of CD4 cells is not well characterized so far. We examine if CD8 cell count is a prognostic factor for CD4 cell counts during an HIV infection. A longitudinal analysis is conducted using data from the Swiss HIV cohort study collected between January 2000 and October 2014. Linear mixed regression models were applied to observations from HIV-1-infected treatment naive patients (NAIVE) and cART-treated patients to predict the short-term evolution of CD4 cell counts. For each subgroup, it was quantified to which extent CD8 cell counts or CD4/CD8 ratios are prognostic factors for disease progression. In both subgroups, 2500 NAIVE and 8902 cART patients, past CD4 cells are positively (P < 0.0001) and past viral load is negatively (P < 0.0001) associated with the outcome. Including additionally past CD8 cell counts improves the fit significantly (P < 0.0001) and increases the marginal explained variation 31.7% to 40.7% for the NAIVE and from 44.1% to 50.7% for the cART group. The past CD4/CD8 ratio (instead of the past CD8 level) is positively associated with the outcome, increasing the explained variation further to 41.8% for NAIVE and 51.9% for cART. PMID:27759638

  4. Simulations of Cyclone Sidr in the Bay of Bengal with a High-Resolution Model: Sensitivity to Large-Scale Boundary Forcing

    NASA Technical Reports Server (NTRS)

    Kumar, Anil; Done, James; Dudhia, Jimy; Niyogi, Dev

    2011-01-01

    The predictability of Cyclone Sidr in the Bay of Bengal was explored in terms of track and intensity using the Advanced Research Hurricane Weather Research Forecast (AHW) model. This constitutes the first application of the AHW over an area that lies outside the region of the North Atlantic for which this model was developed and tested. Several experiments were conducted to understand the possible contributing factors that affected Sidr s intensity and track simulation by varying the initial start time and domain size. Results show that Sidr s track was strongly controlled by the synoptic flow at the 500-hPa level, seen especially due to the strong mid-latitude westerly over north-central India. A 96-h forecast produced westerly winds over north-central India at the 500-hPa level that were notably weaker; this likely caused the modeled cyclone track to drift from the observed actual track. Reducing the model domain size reduced model error in the synoptic-scale winds at 500 hPa and produced an improved cyclone track. Specifically, the cyclone track appeared to be sensitive to the upstream synoptic flow, and was, therefore, sensitive to the location of the western boundary of the domain. However, cyclone intensity remained largely unaffected by this synoptic wind error at the 500-hPa level. Comparison of the high resolution, moving nested domain with a single coarser resolution domain showed little difference in tracks, but resulted in significantly different intensities. Experiments on the domain size with regard to the total precipitation simulated by the model showed that precipitation patterns and 10-m surface winds were also different. This was mainly due to the mid-latitude westerly flow across the west side of the model domain. The analysis also suggested that the total precipitation pattern and track was unchanged when the domain was extended toward the east, north, and south. Furthermore, this highlights our conclusion that Sidr was influenced from the west

  5. CASCO BAY PLAN

    EPA Science Inventory

    Casco Bay lies at the heart of Maine's most populated area. The health of its waters, wetlands, and wildlife depend in large part on the activities of the quarter-million residents who live in its watershed. Less than 30 years ago, portions of Casco Bay were off-limits to recr...

  6. Bay Mills' Bold Approach

    ERIC Educational Resources Information Center

    Freedman, Eric

    2011-01-01

    It's a long, long way from Bay Mills Community College, near the shores of frigid Lake Superior, to Detroit. But distance, time and demographics aside, the school and the city are united by Bay Mills' status as the nation's only tribally controlled college that authorizes quasi-public schools, known officially as public school academies. And it's…

  7. A model of the effects of land-based, human activities on the health of coral reefs in the Great Barrier Reef and in Fouha Bay, Guam, Micronesia

    NASA Astrophysics Data System (ADS)

    Wolanski, Eric; Richmond, Robert H.; McCook, Laurence

    2004-05-01

    A model is proposed to explain coral and algal abundance on coastal coral reefs as a function of spike-like natural disturbances from tropical cyclones and turbid river floods, followed by long recovery periods where the rate of reef recovery depends on ambient water and substratum quality. The model includes competition for space between corals and algae, coral recruitment and reef connectivity. The model is applied to a 400-km stretch of Australia's Great Barrier Reef and to the 200-m-long reef tract at Fouha Bay, in Guam, Micronesia. For these two sites and at these two scales, the model appears successful at reproducing the observed distribution of algae and coral. For both sites, it is suggested that the reefs have been degraded by human activities on land and that they will recover provided remedial measures are implemented on land to restore the water and substrate conditions. We suggest ways to improve the model and to use the model to guide future ecological research and management efforts on coastal coral reefs.

  8. An assessment of the trophic structure of the Bay of Biscay continental shelf food web: Comparing estimates derived from an ecosystem model and isotopic data

    NASA Astrophysics Data System (ADS)

    Lassalle, G.; Chouvelon, T.; Bustamante, P.; Niquil, N.

    2014-01-01

    Comparing outputs of ecosystem models with estimates derived from experimental and observational approaches is important in creating valuable feedback for model construction, analyses and validation. Stable isotopes and mass-balanced trophic models are well-known and widely used as approximations to describe the structure of food webs, but their consistency has not been properly established as attempts to compare these methods remain scarce. Model construction is a data-consuming step, meaning independent sets for validation are rare. Trophic linkages in the French continental shelf of the Bay of Biscay food webs were recently investigated using both methodologies. Trophic levels for mono-specific compartments representing small pelagic fish and marine mammals and multi-species functional groups corresponding to demersal fish and cephalopods, derived from modelling, were compared with trophic levels calculated from independent carbon and nitrogen isotope ratios. Estimates of the trophic niche width of those species, or groups of species, were compared between these two approaches as well. A significant and close-to-one positive (rSpearman2 = 0.72 , n = 16, p < 0.0001) correlation was found between trophic levels estimated by Ecopath modelling and those derived from isotopic signatures. Differences between estimates were particularly low for mono-specific compartments. No clear relationship existed between indices of trophic niche width derived from both methods. Given the wide recognition of trophic levels as a useful concept in ecosystem-based fisheries management, propositions were made to further combine these two approaches.

  9. The Chesapeake Bay impact structure

    USGS Publications Warehouse

    Powars, David S.; Edwards, Lucy E.; Gohn, Gregory S.; Horton, Jr., J. Wright

    2015-10-28

    About 35 million years ago, during late Eocene time, a 2-mile-wide asteroid or comet smashed into Earth in what is now the lower Chesapeake Bay in Virginia. The oceanic impact vaporized, melted, fractured, and (or) displaced the target rocks and sediments and sent billions of tons of water, sediments, and rocks into the air. Glassy particles of solidified melt rock rained down as far away as Texas and the Caribbean. Models suggest that even up to 50 miles away the velocity of the intensely hot air blast was greater than 1,500 miles per hour, and ground shaking was equivalent to an earthquake greater than magnitude 8.0 on the Richter scale. Large tsunamis affected most of the North Atlantic basin. The Chesapeake Bay impact structure is among the 20 largest known impact structures on Earth.

  10. A STAGE-BASED POPULATION MODEL FOR BAY SCALLOPS (ARGOPECTEN IRRADIANS) AND IMPLICATIONS FOR POPULATION-LEVEL EFFECTS OF HABITAT ATLERATION.

    EPA Science Inventory

    Bay scallops (Argopecten irradians) inhabit shallow subtidal habitats along the Atlantic coast of the United States and require settlement substrates, such as submerged aquatic vegetation (SAV), for their early juvenile stages. The short lifespan of bay scallops (1-2 yr) coupled...

  11. Do naive juvenile seabirds forage differently from adults?

    PubMed

    Riotte-Lambert, Louise; Weimerskirch, Henri

    2013-10-07

    Foraging skills of young individuals are assumed to be inferior to those of adults. The reduced efficiency of naive individuals may be the primary cause of the high juvenile mortality and explain the deferment of maturity in long-lived species. However, the study of juvenile and immature foraging behaviour has been limited so far. We used satellite telemetry to compare the foraging movements of juveniles, immatures and breeding adult wandering albatrosses Diomedea exulans, a species where foraging success is positively influenced by the distance covered daily. We showed that juveniles are able to use favourable winds as soon as the first month of independence, but cover shorter distances daily and spend more time sitting on water than adults during the first two months after fledging. These reduced movement capacities do not seem to be the cause of higher juvenile mortality. Moreover, juveniles almost never restrict their movement to specific areas, as adults and immatures frequently do over shelf edges or oceanic zones, which suggest that the location of appropriate areas is learned through experience. Immatures and adults have equivalent movement capacities, but when they are central place foragers, i.e. when adults breed or immatures come to the colony to display and pair, immatures make shorter trips than adults. The long duration of immaturity in this species seems to be related to a long period of learning to integrate the foraging constraints associated with reproduction and central place foraging. Our results indicate that foraging behaviour of young albatrosses is partly innate and partly learned progressively over immaturity. The first months of learning appear critical in terms of survival, whereas the long period of immaturity is necessary for young birds to attain the skills necessary for efficient breeding without fitness costs.

  12. Do naive juvenile seabirds forage differently from adults?

    PubMed Central

    Riotte-Lambert, Louise; Weimerskirch, Henri

    2013-01-01

    Foraging skills of young individuals are assumed to be inferior to those of adults. The reduced efficiency of naive individuals may be the primary cause of the high juvenile mortality and explain the deferment of maturity in long-lived species. However, the study of juvenile and immature foraging behaviour has been limited so far. We used satellite telemetry to compare the foraging movements of juveniles, immatures and breeding adult wandering albatrosses Diomedea exulans, a species where foraging success is positively influenced by the distance covered daily. We showed that juveniles are able to use favourable winds as soon as the first month of independence, but cover shorter distances daily and spend more time sitting on water than adults during the first two months after fledging. These reduced movement capacities do not seem to be the cause of higher juvenile mortality. Moreover, juveniles almost never restrict their movement to specific areas, as adults and immatures frequently do over shelf edges or oceanic zones, which suggest that the location of appropriate areas is learned through experience. Immatures and adults have equivalent movement capacities, but when they are central place foragers, i.e. when adults breed or immatures come to the colony to display and pair, immatures make shorter trips than adults. The long duration of immaturity in this species seems to be related to a long period of learning to integrate the foraging constraints associated with reproduction and central place foraging. Our results indicate that foraging behaviour of young albatrosses is partly innate and partly learned progressively over immaturity. The first months of learning appear critical in terms of survival, whereas the long period of immaturity is necessary for young birds to attain the skills necessary for efficient breeding without fitness costs. PMID:23926153

  13. Control of a Free-Surface Barotropic Model of the Bay of Biscay by Assimilation of Sealevel Data in Presence of Atmospheric Forcings

    NASA Astrophysics Data System (ADS)

    Lamouroux, J.; De Mey, P.; Lyard, F.; Jeansou, E.

    2006-07-01

    The purpose of this study is to assimilate satellite altimetry and tide-gauge data in the barotropic, free-surface, finite element model MOG2D, covering the Bay of Biscay and nested in a North East Atlantic domain. In a first step, we explore the error sub-space of the model in presence of forcing uncertainties, and especially in presence of high frequency atmospheric forcing errors. This is done by an ensemble modelling approach (Monte-Car lo) in which the atmospheric fields are perturbed in a multivariate way: by generating an a priori ensemble of perturbed atmospheric forcing fields (10-meter wind and surface pressure from ARPEGE the meteorological model), and computing the corresponding a posteriori ensemble of model states, one can approximate the forecast errors of the model by ensemble spread statistics. These statistics are shown to be neither homogeneous over the domain, nor stationary, since they are very dependent on the meteorological forcing. Then, the forecast covariance matrix is modelled through forecast error Ensemble EOFs. These statistics, in form of 3D multivariate EOFs (Sea Level Anomaly, barotropic velocities, surface pressure and wind-stress components), are used in a reduced-order sequential scheme, SEQUOIA, set up in an Optimal Interpolation configuration with the MANTA kernel developed at LEGOS/POC (De Mey, 2005), to constrain the model forecast in the framework of twin experiments. In a reference experiment, the data assimilation system is calibrated and sensitivity tests are conducted. The system provides significant error reduction for all state vector variables, but appears to be sensitive to configuration parameters: particularly, one need to constrain atmospheric forcing fields to achieve an efficient control of the model errors. Finally, the capability of realistic observing networks to reduce the model errors are compared. Frequent and regularly spaced observations, such as tide-gauges (SLA) or HF radars and buoys (velocity

  14. Bayesian network modelling of upper gastrointestinal bleeding

    NASA Astrophysics Data System (ADS)

    Aisha, Nazziwa; Shohaimi, Shamarina; Adam, Mohd Bakri

    2013-09-01

    Bayesian networks are graphical probabilistic models that represent causal and other relationships between domain variables. In the context of medical decision making, these models have been explored to help in medical diagnosis and prognosis. In this paper, we discuss the Bayesian network formalism in building medical support systems and we learn a tree augmented naive Bayes Network (TAN) from gastrointestinal bleeding data. The accuracy of the TAN in classifying the source of gastrointestinal bleeding into upper or lower source is obtained. The TAN achieves a high classification accuracy of 86% and an area under curve of 92%. A sensitivity analysis of the model shows relatively high levels of entropy reduction for color of the stool, history of gastrointestinal bleeding, consistency and the ratio of blood urea nitrogen to creatinine. The TAN facilitates the identification of the source of GIB and requires further validation.

  15. Relevance popularity: A term event model based feature selection scheme for text classification.

    PubMed

    Feng, Guozhong; An, Baiguo; Yang, Fengqin; Wang, Han; Zhang, Libiao

    2017-01-01

    Feature selection is a practical approach for improving the performance of text classification methods by optimizing the feature subsets input to classifiers. In traditional feature selection methods such as information gain and chi-square, the number of documents that contain a particular term (i.e. the document frequency) is often used. However, the frequency of a given term appearing in each document has not been fully investigated, even though it is a promising feature to produce accurate classifications. In this paper, we propose a new feature selection scheme based on a term event Multinomial naive Bayes probabilistic model. According to the model assumptions, the matching score function, which is based on the prediction probability ratio, can be factorized. Finally, we derive a feature selection measurement for each term after replacing inner parameters by their estimators. On a benchmark English text datasets (20 Newsgroups) and a Chinese text dataset (MPH-20), our numerical experiment results obtained from using two widely used text classifiers (naive Bayes and support vector machine) demonstrate that our method outperformed the representative feature selection methods.

  16. Iterative modeling of hydrogen in multiple subsurface layers with MSL/DAN exit traverse data from Yellowknife Bay, Gale crater, Mars

    NASA Astrophysics Data System (ADS)

    Moersch, J.; Hardgrove, C. J.; Tate, C.; Litvak, M.; Mitrofanov, I. G.; Behar, A.; Boynton, W. V.; DeFlores, L.; Fedosov, F.; Harshman, K.; Golovin, D.; Jun, I.; Kozyrev, A.; Kuzmin, R.; Lisov, D.; Malakhov, A.; Milliken, R.; Mischna, M. A.; Mokrousov, M.; Nikiforov, S.; Sanin, A.; Shvetsov, V.; Tretyakov, V.; Vostrukhin, A.

    2013-12-01

    The active mode of the Dynamic Albedo of Neutrons (DAN) experiment on MSL uses a pulsed neutron generator and detectors to determine the abundance and vertical distribution of hydrogen in the top ~60 cm of the Martian subsurface, with a horizontal sensing 'footprint' of about 1 m. As of this writing, the most ambitious measurement campaign to make use of DAN took place as Curiosity was exiting the region known as Yellowknife Bay (YB), where the Yellowknife Bay formation is exposed and comprised, in ascending order, of the Sheepbed, Gillespie lake, Point Lake and Shaler members. In a ~20-m traverse dedicated to the DAN experiment, active measurements were made every 0.75 to 1 m. This traverse crossed three contacts between: the lower and upper subunits of the clay-rich Sheepbed member, the Sheepbed member and the Gillespie Lake member, and and internal boundary within the Gillespie member. Other supporting observations were acquired in concert with the DAN measurements, including images showing the thicknesses of the strata and engineering telemetry showing the rover's vertical position as it ascended along the traverse. Most previous analyses of DAN active data have consisted of a statistical comparison between the actual measurements and three candidate models of the subsurface: a single homogeneous layer with fixed density but variable H and Cl content, a single homogeneous layer with fixed Cl content but variable H content and density, and a two layer model with fixed density and Cl content but variable H content in the two layers, and a variable depth of the interface between the two layers. Here, we start with the same analysis approach for the first measurements along the DAN YB exit traverse, acquired over the lower Sheepbed member. However, for subsequent points, our modeling approach is different in that it makes use of known layer thicknesses and the assumption of horizontal layering (which is supported by the geometry of the contact around YB). For

  17. Aging promotes acquisition of naive-like CD8+ memory T cell traits and enhanced functionalities.

    PubMed

    Eberlein, Jens; Davenport, Bennett; Nguyen, Tom; Victorino, Francisco; Haist, Kelsey; Jhun, Kevin; Karimpour-Fard, Anis; Hunter, Lawrence; Kedl, Ross; Clambey, Eric T; Homann, Dirk

    2016-10-03

    Protective T cell memory is an acquired trait that is contingent upon the preservation of its constituents and therefore vulnerable to the potentially deleterious effects of organismal aging. Here, however, we have found that long-term T cell memory in a natural murine host-pathogen system can substantially improve over time. Comprehensive molecular, phenotypic, and functional profiling of aging antiviral CD8+ memory T cells (CD8+ TM) revealed a pervasive remodeling process that promotes the gradual acquisition of distinct molecular signatures, of increasingly homogeneous phenotypes, and of diversified functionalities that combine to confer a CD8+ TM-autonomous capacity for enhanced recall responses and immune protection. Notably, the process of CD8+ TM aging is characterized by a progressive harmonization of memory and naive T cell traits, is broadly amenable to experimental acceleration or retardation, and serves as a constitutional component for the "rebound model" of memory T cell maturation. By casting CD8+ TM populations within the temporal framework of their slowly evolving properties, this model establishes a simple ontogenetic perspective on the principal organization of CD8+ T cell memory that may directly inform the development of improved diagnostic, prophylactic, and therapeutic modalities.

  18. An age-structured population model for horseshoe crabs in the Delaware Bay area to assess harvest and egg availability for shorebirds

    USGS Publications Warehouse

    Sweka, J.A.; Smith, D.R.; Millard, M.J.

    2007-01-01

    The objective of this simulation study was to create an age-structured population model for horseshoe crabs (Limulus polyphenols) in the Delaware Bay region using best available estimates of age-specific mortality and recent harvest levels. Density dependence was incorporated using a spatial model relating egg mortality with abundance of spawning females. Combinations of annual female harvest (0, 50, 100, and 200 thousand), timing of female harvest (before or after spawning), and three levels of density-dependent egg mortality were simulated. The probability of the population increasing was high (> 80%) with low and medium egg mortality and harvest less than 200 thousand females per year. Under the high egg mortality case, the probability of the population increasing was < 50% regardless of harvest. Harvest occurring after spawning increased the probability of population growth. The number of eggs available to shorebirds was highest when egg mortality was lowest and female abundance was at its highest levels. Although harvest and egg mortality influenced population growth and food availability to shorebirds, sensitivity and elasticity analyses showed that early-life stage mortality, age 0 mortality in particular, was the most important parameter for population growth. Our modeling results indicate areas where further research is needed and suggest effective management will involve a combination of harvest management and actions to increase early juvenile survival. ?? 2007 Estuarine Research Federation.

  19. Multilevel eEmpirical Bayes modeling for improved estimation of toxicant formulations tosuppress parasitic sea lamprey in the Upper Great Lakes

    USGS Publications Warehouse

    Hatfield, Laura A.; Gutreuter, Steve; Boogaard, Michael A.; Carlin, Bradley P.

    2011-01-01

    Estimation of extreme quantal-response statistics, such as the concentration required to kill 99.9% of test subjects (LC99.9), remains a challenge in the presence of multiple covariates and complex study designs. Accurate and precise estimates of the LC99.9 for mixtures of toxicants are critical to ongoing control of a parasitic invasive species, the sea lamprey, in the Laurentian Great Lakes of North America. The toxicity of those chemicals is affected by local and temporal variations in water chemistry, which must be incorporated into the modeling. We develop multilevel empirical Bayes models for data from multiple laboratory studies. Our approach yields more accurate and precise estimation of the LC99.9 compared to alternative models considered. This study demonstrates that properly incorporating hierarchical structure in laboratory data yields better estimates of LC99.9 stream treatment values that are critical to larvae control in the field. In addition, out-of-sample prediction of the results of in situ tests reveals the presence of a latent seasonal effect not manifest in the laboratory studies, suggesting avenues for future study and illustrating the importance of dual consideration of both experimental and observational data.

  20. Spatial distribution of hydrocarbon reservoirs in the West Korea Bay Basin in the northern part of the Yellow Sea, estimated by 3-D gravity forward modelling

    NASA Astrophysics Data System (ADS)

    Choi, Sungchan; Ryu, In-Chang; Götze, H.-J.; Chae, Y.

    2017-01-01

    Although an amount of hydrocarbon has been discovered in the West Korea Bay Basin (WKBB), located in the North Korean offshore area, geophysical investigations associated with these hydrocarbon reservoirs are not permitted because of the current geopolitical situation. Interpretation of satellite-derived potential field data can be alternatively used to image the 3-D density distribution in the sedimentary basin associated with hydrocarbon deposits. We interpreted the TRIDENT satellite-derived gravity field data to provide detailed insights into the spatial distribution of sedimentary density structures in the WKBB. We used 3-D forward density modelling for the interpretation that incorporated constraints from existing geological and geophysical information. The gravity data interpretation and the 3-D forward modelling showed that there are two modelled areas in the central subbasin that are characterized by very low density structures, with a maximum density of about 2000 kg m-3, indicating some type of hydrocarbon reservoir. One of the anticipated hydrocarbon reservoirs is located in the southern part of the central subbasin with a volume of about 250 km3 at a depth of about 3000 m in the Cretaceous/Jurassic layer. The other hydrocarbon reservoir should exist in the northern part of the central subbasin, with an average volume of about 300 km3 at a depth of about 2500 m.

  1. Spatial distribution of Hydrocarbon Reservoirs in the West Korea Bay Basin in the northern part of the Yellow Sea, estimated by 3D gravity forward modeling

    NASA Astrophysics Data System (ADS)

    Choi, Sungchan; Ryu, In-Chang; Götze, H.-J.; Chae, Y.

    2016-10-01

    Although an amount of hydrocarbon has been discovered in the West Korea Bay Basin (WKBB), located in the North Korean offshore area, geophysical investigations associated with these hydrocarbon reservoirs are not permitted because of the current geopolitical situation. Interpretation of satellite- derived potential field data can be alternatively used to image the three-dimensional (3D) density distribution in the sedimentary basin associated with hydrocarbon deposits. We interpreted the TRIDENT satellite-derived gravity field data to provide detailed insights into the spatial distribution of sedimentary density structures in the WKBB. We used 3D forward density modeling for the interpretation that incorporated constraints from existing geological and geophysical information. The gravity data interpretation and the 3D forward modeling showed that there are two modeled areas in the central subbasin that are characterized by very low density structures, with a maximum density of about 2000 kg/m3, indicating some type of hydrocarbon reservoir. One of the anticipated hydrocarbon reservoirs is located in the southern part of the central subbasin with a volume of about 250 km3 at a depth of about 3000 m in the Cretaceous/Jurassic layer. The other hydrocarbon reservoir should exist in the northern part of the central subbasin, with an average volume of about 300 km3 at a depth of about 2500 m.

  2. Operational protocol for the sighting and tracking of Portuguese man-of-war in the southeastern Bay of Biscay: Observations and modeling

    NASA Astrophysics Data System (ADS)

    Ferrer, L.; Zaldua-Mendizabal, N.; Del Campo, A.; Franco, J.; Mader, J.; Cotano, U.; Fraile, I.; Rubio, A.; Uriarte, Ad.; Caballero, A.

    2015-03-01

    This paper describes the operational protocol established in the southeastern Bay of Biscay (study area) for the sighting and tracking of Portuguese man-of-war. This action protocol combines sightings of Portuguese man-of-war at sea with hourly surface currents and winds obtained with the Regional Ocean Modeling System (ROMS) and the Weather Research and Forecasting model (WRF), respectively. These data are used in the Sediment, Oil spill and Fish Tracking model (SOFT) to estimate the drift of Portuguese man-of-war. Here we provide information on sightings of Portuguese man-of-war in the study area and show the most relevant results of the SOFT calibration obtained using trajectories from eight satellite pop-up tags for fish tracking. These tags have similar characteristics (such as weight and density) to the Portuguese man-of-war that reach the study area. In 2012 and 2013, there were a total of 48 sightings of Portuguese man-of-war, most of them located in the Zarautz beach area (Basque Country coast). The SOFT calibration shows that the tag drift is mainly controlled by the wind. With winds from the southern and western sectors (third quadrant), SOFT is able to reproduce the tag drift using surface current velocities estimated as ~1.8% of the WRF wind velocities. The SOFT simulations carried out using the ROMS current velocities (with or without the WRF wind velocities) do not improve the results.

  3. A modeling study of tidal energy extraction and the associated impact on tidal circulation in a multi-inlet bay system of Puget Sound

    DOE PAGES

    Wang, Taiping; Yang, Zhaoqing

    2017-03-25

    Previously, a major focus of tidal energy studies in Puget Sound were the deep channels such as Admiralty Inlet that have a larger power potential. Our paper focuses on the possibility of extracting tidal energy from minor tidal channels of Puget Sound by using a hydrodynamic model to quantify the power potential and the associated impact on tidal circulation. The study site is a multi-inlet bay system connected by two narrow inlets, Agate Pass and Rich Passage, to the Main Basin of Puget Sound. A three-dimensional hydrodynamic model was applied to the study site and validated for tidal elevations andmore » currents. Here, we examined three energy extraction scenarios in which turbines were deployed in each of the two passages and concurrently in both. Extracted power rates and associated changes in tidal elevation, current, tidal flux, and residence time were examined. Maximum instantaneous power rates reached 250 kW, 1550 kW, and 1800 kW, respectively, for the three energy extraction scenarios. Model results suggest that with the level of energy extraction in the three energy extraction scenarios, the impact on tidal circulation is very small. It is worth investigating the feasibility of harnessing tidal energy from minor tidal channels of Puget Sound.« less

  4. Differential T cell receptor-mediated signaling in naive and memory CD4 T cells.

    PubMed

    Farber, D L; Acuto, O; Bottomly, K

    1997-08-01

    Naive and memory CD4 T cells differ in cell surface phenotype, function, activation requirements, and modes of regulation. To investigate the molecular bases for the dichotomies between naive and memory CD4 T cells and to understand how the T cell receptor (TCR) directs diverse functional outcomes, we investigated proximal signaling events triggered through the TCR/CD3 complex in naive and memory CD4 T cell subsets isolated on the basis of CD45 isoform expression. Naive CD4 T cells signal through TCR/CD3 similar to unseparated CD4 T cells, producing multiple tyrosine-phosphorylated protein species overall and phosphorylating the T cell-specific ZAP-70 tyrosine kinase which is recruited to the CD3zeta subunit of the TCR. Memory CD4 T cells, however, exhibit a unique pattern of signaling through TCR/CD3. Following stimulation through TCR/CD3, memory CD4 T cells produce fewer species of tyrosine-phosphorylated substrates and fail to phosphorylate ZAP-70, yet unphosphorylated ZAP-70 can associate with the TCR/CD3 complex. Moreover, a 26/28-kDa phosphorylated doublet is associated with CD3zeta in resting and activated memory but not in naive CD4 T cells. Despite these differences in the phosphorylation of ZAP-70 and CD3-associated proteins, the ZAP-70-related kinase, p72syk, exhibits similar phosphorylation in naive and memory T cell subsets, suggesting that this kinase could function in place of ZAP-70 in memory CD4 T cells. These results indicate that proximal signals are differentially coupled to the TCR in naive versus memory CD4 T cells, potentially leading to distinct downstream signaling events and ultimately to the diverse functions elicited by these two CD4 T cell subsets.

  5. Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals

    PubMed Central

    Winand, Raf; Theys, Kristof; Eusébio, Mónica; Aerts, Jan; Camacho, Ricardo J.; Gomes, Perpetua; Suchard, Marc A.; Vandamme, Anne-Mieke; Abecasis, Ana B.

    2015-01-01

    Objectives: Surveillance drug resistance mutations (SDRMs) in drug-naive patients are typically used to survey HIV-1-transmitted drug resistance (TDR). We test here how SDRMs in patients failing treatment, the original source of TDR, contribute to assessing TDR, transmissibility and transmission source of SDRMs. Design: This is a retrospective observational study analyzing a Portuguese cohort of HIV-1-infected patients. Methods: The prevalence of SDRMs to protease inhibitors, nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs) in drug-naive and treatment-failing patients was measured for 3554 HIV-1 subtype B patients. Transmission ratio (prevalence in drug-naive/prevalence in treatment-failing patients), average viral load and robust linear regression with outlier detection (prevalence in drug-naive versus in treatment-failing patients) were analyzed and used to interpret transmissibility. Results: Prevalence of SDRMs in drug-naive and treatment-failing patients were linearly correlated, but some SDRMs were classified as outliers – above (PRO: D30N, N88D/S, L90 M, RT: G190A/S/E) or below (RT: M184I/V) expectations. The normalized regression slope was 0.073 for protease inhibitors, 0.084 for NRTIs and 0.116 for NNRTIs. Differences between SDRMs transmission ratios were not associated with differences in viral loads. Conclusion: The significant linear correlation between prevalence of SDRMs in drug-naive and in treatment-failing patients indicates that the prevalence in treatment-failing patients can be useful to predict levels of TDR. The slope is a cohort-dependent estimate of rate of TDR per drug class and outlier detection reveals comparative persistence of SDRMs. Outlier SDRMs with higher transmissibility are more persistent and more likely to have been acquired from drug-naive patients. Those with lower transmissibility have faster reversion dynamics after transmission and are associated with

  6. Subsurface lacustrine storm-seiche depositional model in the Eocene Lijin Sag of the Bohai Bay Basin, East China

    NASA Astrophysics Data System (ADS)

    Wang, Junhui; Jiang, Zaixing; Zhang, Yuanfu

    2015-10-01

    Recent progress in facies analysis helps to discriminate storm-induced deposits based on interpretation of sedimentary records of combination of oscillatory and unidirectional flows. Located in the southeastern corner of the Bohai Bay Basin in East China, the Lijin Sag is a NE-SW trending Cenozoic half-graben basin. Part of its Eocene deposits (Bindong deposits), which are deposited far away from a contemporary shoreline, consists of thin bedded fine-sandstones and siltstones, interlayed with dark-gray mudstones. New data from drilling wells permit an interpretation of the sedimentary facies. Based on seismic data, well log data, core data and thin-section analyses, storm-dominated deposits were recognized. Petrologic analysis shows that these deposits mainly consist of fine sand- to silt-sized lithic arkose. Detailed sedimentological analyses on lithofacies were conducted to address flowtypes dominant during their geneses. The beds are normal graded and contain Bouma-like sequences. The typical and complete sedimentary sequence consists of fining-upwards successions from an erosive base, followed by gravity flow-induced massive or faint laminated bed or soft sediment deformation structures and unidirectional-combined-oscillatory flow induced beddings, which are attributed to storm wave and seiche processes. From proximal to distal in plane, the Bindong storm deposits exhibit different lithofacies associations and sedimentary processes, i.e., the proximal facies is coarser and dominated by gravity flows, unidirectional flows and combined flows, and formed under strong hydrodynamic conditions; the transitional facies is formed under full range of flow regimes exhibiting a complete Bouma-like sequence; while the distal facies is dominated by gravity flows and pure unidirectional flows without influence of waves. During the deposition period of the Bindong deposits, the paleo-environmental characteristics, such as paleogeographic position, paleoclimate, provenance

  7. Differential susceptibility of naive and differentiated PC-12 cells to methylglyoxal-induced apoptosis: influence of cellular redox.

    PubMed

    Okouchi, Masahiro; Okayama, Naotsuka; Aw, Tak Yee

    2005-01-01

    Neuropathologies have been associated with neuronal de-differentiation and oxidative susceptibility. To address whether cellular states determines their oxidative vulnerability, we have challenged naive (undifferentiated) and nerve growth factor-induced differentiated pheochromocytoma (PC12) with methylglyoxal (MG), a model of carbonyl stress. MG dose-dependently induced greater apoptosis (24 h) in naive (nPC12) than differentiated (dPC12) cells. This enhanced nPC12 susceptibility was correlated with a high basal oxidized cellular glutathione-to-glutathione disulfide (GSH/GSSG) redox and an MG-induced GSH-to-Disulfide (GSSG plus protein-bound SSG) imbalance. The loss of redox balance occurred at 30 min post-MG exposure, and was prevented by N-acetylcysteine (NAC) that was unrelated to de novo GSH synthesis. NAC was ineffective when added at 1h post-MG, consistent with an early window of redox signaling. This redox shift was kinetically linked to decreased BcL-2, increased Bax, and release of mitochondrial cytochrome c which preceded caspase-9 and -3 activation and poly ADP-ribose polymerase (PARP) cleavage (1-2 h), consistent with mitochondrial apoptotic signaling. The blockade of apoptosis by cyclosporine A supported an involvement of the mitochondrial permeability transition pore. The enhanced vulnerability of nPC12 cells to MG and its relationship to cellular redox shifts will have important implications for understanding differential oxidative vulnerability in various cell types and their transition states.

  8. Relative consistency and subjects' "theories" in domains such as naive physics: common research difficulties illustrated by Cooke and Breedin.

    PubMed

    Ranney, M

    1994-07-01

    While augmenting the literature with data that further exhibit context-specific responding to qualitative motion problems, Cooke and Breedin (1994) exhibit common theoretical and methodological difficulties that undermine their conclusions. Herein, these flaws are explicated and contrasted with features of studies that avoid the pitfalls of (1) theoretical vagueness, (2) overly coarse data aggregation, (3) nondiagnostic, errorful assessment items, and (4) imprecise measures of the variety of (mis/)conceptions (e.g., of "impetus," or inertia). The difficulties call into question Cooke and Breedin's claims that impetus ideas play minor roles in performance and that "naive theories" of motion are largely constructed on line. Because such confusion often arises from the polysemy of "theory," some empirical criteria for "theoryness" are discussed, including subjects' conceptual, temporal, and coherence-based consistencies (regarding researchers' models and isomorphs). While naive physics may be idiosyncratic, baroque, context-driven, and apparently inconsistent, it might (additionally) be based upon fairly a priori, systematic, and temporally stable information.

  9. Telomere elongation and naive pluripotent stem cells achieved from telomerase haplo-insufficient cells by somatic cell nuclear transfer.

    PubMed

    Sung, Li-Ying; Chang, Wei-Fang; Zhang, Qian; Liu, Chia-Chia; Liou, Jun-Yang; Chang, Chia-Chun; Ou-Yang, Huan; Guo, Renpeng; Fu, Haifeng; Cheng, Winston T K; Ding, Shih-Torng; Chen, Chuan-Mu; Okuka, Maja; Keefe, David L; Chen, Y Eugene; Liu, Lin; Xu, Jie

    2014-12-11

    Haplo-insufficiency of telomerase genes in humans leads to telomere syndromes such as dyskeratosis congenital and idiopathic pulmonary fibrosis. Generation of pluripotent stem cells from telomerase haplo-insufficient donor cells would provide unique opportunities toward the realization of patient-specific stem cell therapies. Recently, pluripotent human embryonic stem cells (ntESCs) have been efficiently achieved by somatic cell nuclear transfer (SCNT). We tested the hypothesis that SCNT could effectively elongate shortening telomeres of telomerase haplo-insufficient cells in the ntESCs with relevant mouse models. Indeed, telomeres of telomerase haplo-insufficient (Terc(+/-)) mouse cells are elongated in ntESCs. Moreover, ntESCs derived from Terc(+/-) cells exhibit naive pluripotency as evidenced by generation of Terc(+/-) ntESC clone pups by tetraploid embryo complementation, the most stringent test of naive pluripotency. These data suggest that SCNT could offer a powerful tool to reprogram telomeres and to discover the factors for robust restoration of telomeres and pluripotency of telomerase haplo-insufficient somatic cells.

  10. An Empirical Bayes Approach to Spatial Analysis

    NASA Technical Reports Server (NTRS)

    Morris, C. N.; Kostal, H.

    1983-01-01

    Multi-channel LANDSAT data are collected in several passes over agricultural areas during the growing season. How empirical Bayes modeling can be used to develop crop identification and discrimination techniques that account for spatial correlation in such data is considered. The approach models the unobservable parameters and the data separately, hoping to take advantage of the fact that the bulk of spatial correlation lies in the parameter process. The problem is then framed in terms of estimating posterior probabilities of crop types for each spatial area. Some empirical Bayes spatial estimation methods are used to estimate the logits of these probabilities.

  11. Lessons Learned from the Bay Region Atmospheric Chemistry Experiment (BRACE) and Implications for Nitrogen Management of Tampa Bay

    EPA Science Inventory

    Results from air quality modeling and field measurements made as part of the Bay Region Atmospheric Chemistry Experiment (BRACE) along with related scientific literature were reviewed to provide an improved estimate of atmospheric reactive nitrogen (N) deposition to Tampa Bay, to...

  12. A conditional approach for modelling patient readmissions to hospital using a mixture of Coxian phase-type distributions incorporating Bayes' theorem.

    PubMed

    Gordon, Andrew S; Marshall, Adele H; Cairns, Karen J

    2016-09-20

    The number of elderly patients requiring hospitalisation in Europe is rising. With a greater proportion of elderly people in the population comes a greater demand for health services and, in particular, hospital care. Thus, with a growing number of elderly patients requiring hospitalisation competing with non-elderly patients for a fixed (and in some cases, decreasing) number of hospital beds, this results in much longer waiting times for patients, often with a less satisfactory hospital experience. However, if a better understanding of the recurring nature of elderly patient movements between the community and hospital can be developed, then it may be possible for alternative provisions of care in the community to be put in place and thus prevent readmission to hospital. The research in this paper aims to model the multiple patient transitions between hospital and community by utilising a mixture of conditional Coxian phase-type distributions that incorporates Bayes' theorem. For the purpose of demonstration, the results of a simulation study are presented and the model is applied to hospital readmission data from the Lombardy region of Italy. Copyright © 2016 John Wiley & Sons, Ltd.

  13. Multivariate and Naive Bayes Text Classification Approach to Cost Growth Risk in Department of Defense Acquisition Programs

    DTIC Science & Technology

    2013-03-01

    verification 0.009308 0.00746 wbs 0.05849 0.040364 weeks 0.001595 0.002441 wheel 0.000248 0.000168 winglet 0.000139 3.26E-06 wire 0.001407 0.003107...0.057981 weekend 0.000448 0.000166 weeks 0.001955 0.003482 west 0.000516 0.000224 winglet 0.000109 4.48E-06 worked 0.004398 0.004669 wrong

  14. Tameness and stress physiology in a predator-naive island species confronted with novel predation threat.

    PubMed

    Rödl, Thomas; Berger, Silke; Romero, L Michael; Wikelski, Martin

    2007-02-22

    Tame behaviour, i.e. low wariness, in terrestrial island species is often attributed to low predation pressure. However, we know little about its physiological control and its flexibility in the face of predator introductions. Marine iguanas (Amblyrhynchus cristatus) on the Galapagos Islands are a good model to study the physiological correlates of low wariness. They have lived virtually without predation for 5-15 Myr until some populations were first confronted with feral cats and dogs some 150 years ago. We tested whether and to what extent marine iguanas can adjust their behaviour and endocrine stress response to novel predation threats. Here, we show that a corticosterone stress response to experimental chasing is absent in naive animals, but is quickly restored with experience. Initially, low wariness also increases with experience, but remains an order of magnitude too low to allow successful escape from introduced predators. Our data suggest that the ability of marine iguanas to cope with predator introductions is limited by narrow reaction norms for behavioural wariness rather than by constraints in the underlying physiological stress system. In general, we predict that island endemics show flexible physiological stress responses but are restricted by narrow behavioural plasticity.

  15. Tameness and stress physiology in a predator-naive island species confronted with novel predation threat

    PubMed Central

    Rödl, Thomas; Berger, Silke; Michael Romero, L; Wikelski, Martin

    2006-01-01

    Tame behaviour, i.e. low wariness, in terrestrial island species is often attributed to low predation pressure. However, we know little about its physiological control and its flexibility in the face of predator introductions. Marine iguanas (Amblyrhynchus cristatus) on the Galápagos Islands are a good model to study the physiological correlates of low wariness. They have lived virtually without predation for 5–15 Myr until some populations were first confronted with feral cats and dogs some 150 years ago. We tested whether and to what extent marine iguanas can adjust their behaviour and endocrine stress response to novel predation threats. Here, we show that a corticosterone stress response to experimental chasing is absent in naive animals, but is quickly restored with experience. Initially, low wariness also increases with experience, but remains an order of magnitude too low to allow successful escape from introduced predators. Our data suggest that the ability of marine iguanas to cope with predator introductions is limited by narrow reaction norms for behavioural wariness rather than by constraints in the underlying physiological stress system. In general, we predict that island endemics show flexible physiological stress responses but are restricted by narrow behavioural plasticity. PMID:17476779

  16. Aging promotes acquisition of naive-like CD8+ memory T cell traits and enhanced functionalities

    PubMed Central

    Davenport, Bennett; Nguyen, Tom; Victorino, Francisco; Haist, Kelsey; Jhun, Kevin; Karimpour-Fard, Anis; Hunter, Lawrence; Kedl, Ross; Clambey, Eric T.

    2016-01-01

    Protective T cell memory is an acquired trait that is contingent upon the preservation of its constituents and therefore vulnerable to the potentially deleterious effects of organismal aging. Here, however, we have found that long-term T cell memory in a natural murine host-pathogen system can substantially improve over time. Comprehensive molecular, phenotypic, and functional profiling of aging antiviral CD8+ memory T cells (CD8+ TM) revealed a pervasive remodeling process that promotes the gradual acquisition of distinct molecular signatures, of increasingly homogeneous phenotypes, and of diversified functionalities that combine to confer a CD8+ TM–autonomous capacity for enhanced recall responses and immune protection. Notably, the process of CD8+ TM aging is characterized by a progressive harmonization of memory and naive T cell traits, is broadly amenable to experimental acceleration or retardation, and serves as a constitutional component for the “rebound model” of memory T cell maturation. By casting CD8+ TM populations within the temporal framework of their slowly evolving properties, this model establishes a simple ontogenetic perspective on the principal organization of CD8+ T cell memory that may directly inform the development of improved diagnostic, prophylactic, and therapeutic modalities. PMID:27617858

  17. Bim/Bcl-2 balance is critical for maintaining naive and memory T cell homeostasis

    PubMed Central

    Wojciechowski, Sara; Tripathi, Pulak; Bourdeau, Tristan; Acero, Luis; Grimes, H. Leighton; Katz, Jonathan D.; Finkelman, Fred D.; Hildeman, David A.

    2007-01-01

    We examined the role of the antiapoptotic molecule Bcl-2 in combating the proapoptotic molecule Bim in control of naive and memory T cell homeostasis using Bcl-2−/− mice that were additionally deficient in one or both alleles of Bim. Naive T cells were significantly decreased in Bim+/−Bcl-2−/− mice, but were largely restored in Bim−/−Bcl-2−/− mice. Similarly, a synthetic Bcl-2 inhibitor killed wild-type, but not Bim−/−, T cells. Further, T cells from Bim+/−Bcl-2−/− mice died rapidly ex vivo and were refractory to cytokine-driven survival in vitro. In vivo, naive CD8+ T cells required Bcl-2 to combat Bim to maintain peripheral survival, whereas naive CD4+ T cells did not. In contrast, Bim+/−Bcl-2−/− mice generated relatively normal numbers of memory T cells after lymphocytic choriomeningitis virus infection. Accumulation of memory T cells in Bim+/−Bcl-2−/− mice was likely caused by their increased proliferative renewal because of the lymphopenic environment of the mice. Collectively, these data demonstrate a critical role for a balance between Bim and Bcl-2 in controlling homeostasis of naive and memory T cells. PMID:17591857

  18. Bim/Bcl-2 balance is critical for maintaining naive and memory T cell homeostasis.

    PubMed

    Wojciechowski, Sara; Tripathi, Pulak; Bourdeau, Tristan; Acero, Luis; Grimes, H Leighton; Katz, Jonathan D; Finkelman, Fred D; Hildeman, David A

    2007-07-09

    We examined the role of the antiapoptotic molecule Bcl-2 in combating the proapoptotic molecule Bim in control of naive and memory T cell homeostasis using Bcl-2(-/-) mice that were additionally deficient in one or both alleles of Bim. Naive T cells were significantly decreased in Bim(+/-)Bcl-2(-/-) mice, but were largely restored in Bim(-/-)Bcl-2(-/-) mice. Similarly, a synthetic Bcl-2 inhibitor killed wild-type, but not Bim(-/-), T cells. Further, T cells from Bim(+/-)Bcl-2(-/-) mice died rapidly ex vivo and were refractory to cytokine-driven survival in vitro. In vivo, naive CD8(+) T cells required Bcl-2 to combat Bim to maintain peripheral survival, whereas naive CD4(+) T cells did not. In contrast, Bim(+/-)Bcl-2(-/-) mice generated relatively normal numbers of memory T cells after lymphocytic choriomeningitis virus infection. Accumulation of memory T cells in Bim(+/-)Bcl-2(-/-) mice was likely caused by their increased proliferative renewal because of the lymphopenic environment of the mice. Collectively, these data demonstrate a critical role for a balance between Bim and Bcl-2 in controlling homeostasis of naive and memory T cells.

  19. Pertussis toxin activates adult and neonatal naive human CD4+ T lymphocytes.

    PubMed

    Tonon, Sandrine; Badran, Bassam; Benghiat, Fleur Samantha; Goriely, Stanislas; Flamand, Véronique; Willard-Gallo, Karen; Willems, Fabienne; Goldman, Michel; De Wit, Dominique

    2006-07-01

    Pertussis toxin (PTX) is known to be mitogenic for T lymphocytes, but its direct action on naive human T cells has not been specified. Herein, we show that PTX induces the proliferation of purified adult CD45RA(+)CD4(+) T cells independently of its ADP-ribosyltransferase activity. PTX directly induces TNF-alpha and IL-2 mRNA expression, modulates the level of several cell surface receptors and induces Forkhead box p3 (Foxp3) protein accumulation in naive CD4(+) T cells. Addition of autologous dendritic cells was found to be required for the production of high levels of IFN-gamma by PTX-stimulated naive T cells. These effects of PTX occurred in conjunction with activation of NF-kappaB and NFAT transcription factors. Overall, responses of neonatal CD4(+) T cells to PTX were similar to those of adult CD45RA(+)CD4(+) naive T cells except for their blunted CD40 ligand up-regulation. We suggest that the adjuvant properties of PTX during primary cell-mediated immune responses involve a direct action on naive T lymphocytes in addition to activation of antigen-presenting cells.

  20. Module bay with directed flow

    DOEpatents

    Torczynski, John R.

    2001-02-27

    A module bay requires less cleanroom airflow. A shaped gas inlet passage can allow cleanroom air into the module bay with flow velocity preferentially directed toward contaminant rich portions of a processing module in the module bay. Preferential gas flow direction can more efficiently purge contaminants from appropriate portions of the module bay, allowing a reduced cleanroom air flow rate for contaminant removal. A shelf extending from an air inlet slit in one wall of a module bay can direct air flowing therethrough toward contaminant-rich portions of the module bay, such as a junction between a lid and base of a processing module.

  1. 33 CFR 100.124 - Maggie Fischer Memorial Great South Bay Cross Bay Swim, Great South Bay, New York.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... South Bay Cross Bay Swim, Great South Bay, New York. 100.124 Section 100.124 Navigation and Navigable... NAVIGABLE WATERS § 100.124 Maggie Fischer Memorial Great South Bay Cross Bay Swim, Great South Bay, New York... swimmer or safety craft on the swim event race course bounded by the following points: Starting Point...

  2. 75 FR 29891 - Special Local Regulation; Maggie Fischer Memorial Great South Bay Cross Bay Swim, Great South Bay...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-28

    ... South Bay Cross Bay Swim, Great South Bay, NY AGENCY: Coast Guard, DHS. ACTION: Final rule. SUMMARY: The... Fischer Memorial Great South Bay Cross Bay Swim. This special local regulation is necessary to protect... Swim, Great South Bay, NY, in the Federal Register (74 FR 32428). We did not receive any comments...

  3. 33 CFR 100.124 - Maggie Fischer Memorial Great South Bay Cross Bay Swim, Great South Bay, New York.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... South Bay Cross Bay Swim, Great South Bay, New York. 100.124 Section 100.124 Navigation and Navigable... NAVIGABLE WATERS § 100.124 Maggie Fischer Memorial Great South Bay Cross Bay Swim, Great South Bay, New York... swimmer or safety craft on the swim event race course bounded by the following points: Starting Point...

  4. Box Model of a Series of Salt Ponds, as Applied to the Alviso Salt Pond Complex, South San Francisco Bay, California

    USGS Publications Warehouse

    Lionberger, Megan A.; Schoellhamer, David H.; Shellenbarger, Gregory; Orlando, James L.; Ganju, Neil K.

    2007-01-01

    This report documents the development and application of a box model to simulate water level, salinity, and temperature of the Alviso Salt Pond Complex in South San Francisco Bay. These ponds were purchased for restoration in 2003 and currently are managed by the U.S. Fish and Wildlife Service to maintain existing wildlife habitat and prevent a build up of salt during the development of a long-term restoration plan. The model was developed for the purpose of aiding pond managers during the current interim management period to achieve these goals. A previously developed box model of a salt pond, SPOOM, which calculates daily pond volume and salinity, was reconfigured to simulate multiple connected ponds and a temperature subroutine was added. The updated model simulates rainfall, evaporation, water flowing between the ponds and the adjacent tidal slough network, and water flowing from one pond to the next by gravity and pumps. Theoretical and measured relations between discharge and corresponding differences in water level are used to simulate most flows between ponds and between ponds and sloughs. The principle of conservation of mass is used to calculate daily pond volume and salinity. The model configuration includes management actions specified in the Interim Stewardship Plan for the ponds. The temperature subroutine calculates hourly net heat transfer to or from a pond resulting in a rise or drop in pond temperature and daily average, minimum, and maximum pond temperatures are recorded. Simulated temperature was compared with hourly measured data from pond 3 of the Napa?Sonoma Salt Pond Complex and monthly measured data from pond A14 of the Alviso Salt-Pond Complex. Comparison showed good agreement of measured and simulated pond temperature on the daily and monthly time scales.

  5. Moxifloxacin (BAY12-8039), a New 8-Methoxyquinolone, Is Active in a Mouse Model of Tuberculosis

    PubMed Central

    Miyazaki, Eishi; Miyazaki, Miki; Chen, Jong Min; Chaisson, Richard E.; Bishai, William R.

    1999-01-01

    Moxifloxacin (BAY12-8039) is a new 8-methoxyquinolone shown to be active against Mycobacterium tuberculosis in vitro. We tested moxifloxacin for activity in mice against M. tuberculosis CSU93, a highly virulent, recently isolated clinical strain. The MIC of moxifloxacin for the CSU93 strain was 0.25 μg/ml. The serum moxifloxacin concentration after oral administration in mice peaked within 0.25 h, reaching 7.8 μg/ml with doses of 100 mg/kg of body weight; the maximum concentration and the analysis of the area under the concentration-time curve revealed dose dependency. When mice were infected with a sublethal inoculum of mycobacteria and then treated with moxifloxacin at 100 mg/kg per day for 8 weeks, the log10 CFU counts in the organs of treated mice were significantly lower than those for the control group (0.6 ± 0.2 versus 5.6 ± 0.3 in the lungs and 1.5 ± 0.7 versus 4.9 ± 0.5 in the spleens, respectively; P < 0.001 in both organs). The effectiveness of moxifloxacin monotherapy was comparable to that seen in mice receiving isoniazid alone. Combination therapy with moxifloxacin plus isoniazid was superior to that with moxifloxacin or with isoniazid alone in reducing bacillary counts in the organs studied. Using a sensitive broth-passage subculture method, we demonstrated that 8 weeks of treatment with moxifloxacin (100 mg/kg per day) or with moxifloxacin plus isoniazid (100 mg/kg and 25 mg/kg, respectively, per day) sterilized the lungs in seven of eight and in eight of eight mice, respectively. Among surviving bacilli isolated from animals infected with a high-titer inoculum and treated for 7 weeks with low-dose moxifloxacin (20 mg/kg per day), breakthrough resistance to moxifloxacin was not observed. These results indicate that moxifloxacin is highly effective in reducing M. tuberculosis infection in mice and has activity comparable to that of isoniazid. Combination therapy with moxifloxacin and isoniazid was highly effective, suggesting that moxifloxacin

  6. Magnetic fabrics of drumlins of the Green Bay Lobe: Implications for the bed-deformation model of drumlin formation

    NASA Astrophysics Data System (ADS)

    Vreeland, Nicholas Paul

    According to some theories, subglacial deformation of sediment is the process of sediment transport most responsible for drumlin formation. If so, strain indicators in the sediment should yield deformation patterns that are systematically related to drumlin morphology. Clast fabrics have been used most commonly to make inferences about strain patterns in drumlins but with a wide range of sometimes divergent interpretations. These divergent interpretations reflect, in part, a lack of experimental control on the relationship between the state of strain and resulting fabrics. Herein, fabrics determined from the anisotropy of magnetic susceptibility (AMS) of till within selected drumlins of the Green Bay Lobe are used to study the role of bed deformation in drumlin formation. AMS fabrics are a proxy for fabrics formed by non-equant, silt-sized, magnetite grains. Unlike past fabric studies of drumlins, laboratory deformation experiments conducted with this till provide a quantitative foundation for inferring strain magnitude, shearing direction, and shear-plane orientations from fabrics determined from principal directions of magnetic susceptibility (k1, k2, and k3). Intact till samples were collected from transects in seven drumlins in Dane, Dodge, Jefferson, Waupaca, and Waushara counties of south-central Wisconsin, by both exploiting five existing outcrops and collecting 42 89 mm-diameter cores and sub-sampling them. Overall, ˜2800 samples were collected for AMS analysis, and 112 AMS fabrics were computed. Much of the till sampled (84% of fabrics) has k1 fabric strengths weaker than the lower 95% confidence limit for till (S1< 0.82) sheared to moderate strains (˜10), suggesting the till has been deformed but to strains too small to indicate that bed deformation was the principal till transport mechanism. Three of five drumlins studied have k1 fabric orientations that are not symmetrically disposed about the local flow direction indicated by drumlins. Rather, these

  7. Influence of net freshwater supply on salinity in Florida Bay

    USGS Publications Warehouse

    Nuttle, W.K.; Fourqurean, J.W.; Cosby, B.J.; Zieman, J.C.; Robblee, M.B.

    2000-01-01

    An annual water budget for Florida Bay, the large, seasonally hypersaline estuary in the Everglades National Park, was constructed using physically based models and long-term (31 years) data on salinity, hydrology, and climate. Effects of seasonal and interannual variations of the net freshwater supply (runoff plus rainfall minus evaporation) on salinity variation within the bay were also examined. Particular attention was paid to the effects of runoff, which are the focus of ambitious plans to restore and conserve the Florida Bay ecosystem. From 1965 to 1995 the annual runoff from the Everglades into the bay was less than one tenth of the annual direct rainfall onto the bay, while estimated annual evaporation slightly exceeded annual rainfall. The average net freshwater supply to the bay over a year was thus approximately zero, and interannual variations in salinity appeared to be affected primarily by interannual fluctuations in rainfall. At the annual scale, runoff apparently had little effect on the bay as a whole during this period. On a seasonal basis, variations in rainfall, evaporation, and runoff were not in phase, and the net freshwater supply to the bay varied between positive and negative values, contributing to a strong seasonal pattern in salinity, especially in regions of the bay relatively isolated from exchanges with the Gulf of Mexico and Atlantic Ocean. Changes in runoff could have a greater effect on salinity in the bay if the seasonal patterns of rainfall and evaporation and the timing of the runoff are considered. One model was also used to simulate spatial and temporal patterns of salinity responses expected to result from changes in net freshwater supply. Simulations in which runoff was increased by a factor of 2 (but with no change in spatial pattern) indicated that increased runoff will lower salinity values in eastern Florida Bay, increase the variability of salinity in the South Region, but have little effect on salinity in the Central

  8. The Persistence of Solid and Liquid Naive Conceptions: A Reaction Time Study

    NASA Astrophysics Data System (ADS)

    Babai, Reuven; Amsterdamer, Anat

    2008-12-01

    The study explores whether the naive concepts of solid and liquid persist in adolescence. Accuracy of responses and reaction times where measured while 41 ninth graders classified different solids (rigid, non-rigid and powders) and different liquids (runny, dense) into solid or liquid. The results show that these naive conceptions affect adolescences' classifications in terms of both accuracy and reaction time. The rate of correct classifications of non-rigid solids and powders was significantly lower than of rigid solids. Lower rate of success was also found for classification of dense liquids compared with runny liquids. In addition, the reaction time results of correct classifications for non-rigid solids and powders were longer than those for rigid solids and, likewise, reaction times for dense liquids were longer than for runny ones. These results suggest that reasoning processes associated with correct classification of objects that are not consistent with the naive conceptions are more demanding.

  9. Estimation of the maximum allowable loading amount of COD in Luoyuan Bay by a 3-D COD transport and transformation model

    NASA Astrophysics Data System (ADS)

    Wu, Jialin; Li, Keqiang; Shi, Xiaoyong; Liang, Shengkang; Han, Xiurong; Ma, Qimin; Wang, Xiulin

    2014-08-01

    The rapid economic and social developments in the Luoyuan and Lianjiang counties of Fujian Province, China, raise certain environment and ecosystem issues. The unusual phytoplankton bloom and eutrophication, for example, have increased in severity in Luoyuan Bay (LB). The constant increase of nutrient loads has largely caused the environmental degradation in LB. Several countermeasures have been implemented to solve these environmental problems. The most effective of these strategies is the reduction of pollutant loadings into the sea in accordance with total pollutant load control (TPLC) plans. A combined three-dimensional hydrodynamic transport-transformation model was constructed to estimate the marine environmental capacity of chemical oxygen demand (COD). The allowed maximum loadings for each discharge unit in LB were calculated with applicable simulation results. The simulation results indicated that the environmental capacity of COD is approximately 11×104 t year-1 when the water quality complies with the marine functional zoning standards for LB. A pollutant reduction scheme to diminish the present levels of mariculture- and domestic-based COD loadings is based on the estimated marine COD environmental capacity. The obtained values imply that the LB waters could comply with the targeted water quality criteria. To meet the revised marine functional zoning standards, discharge loadings from discharge units 1 and 11 should be reduced to 996 and 3236 t year-1, respectively.

  10. The geochemistry model of the surface sediment determined by using ED-XRF technique: a case study of the Boka Kotorska bay, Adriatic Sea.

    PubMed

    Tanaskovski, Bojan; Jović, Mihajlo; Miličić, Ljiljana; Pezo, Lato; Mandić, Milica; Stanković, Slavka

    2016-06-01

    The spatial distribution of major oxides (Na2O, K2O, SiO2, Al2O3, Fe2O3, CaO, MgO, MnO, TiO2, P2O5) and numerous elements (Cr, Co, Ni, Cu, Zn, As, Se, Pb, Sn, Sb, Ba, Sr, Br, Rb, Zr, Mo, Cs, Y, V, Ga, La, U, Th, Nb, W, Sc, Ge, Gd, Yb, Hf, and Ce) was determined by using energy dispersive X-ray fluorescence spectrometry on the basis of previously measured organic matter and carbonates. The optimal measuring variables for the investigated oxides and elements were determined by using five standard reference materials. The carbonated sediment type can be determined on the basis of the highest Sr, Sc, La, Nb, Hf, and Yb concentrations followed with the lowest concentrations of the remaining elements and the negative Ce anomaly. The complexity of the obtained data was also examined by principal component analysis (PCA) and cluster analysis (CA) in the identifying geochemical composition of the surface sediment. Boka Kotorska bay's geographical position, orographical configuration, and hydrographic characteristics influence the geochemistry model of the surface sediment, quite different from the open sea.

  11. Modeling environmental bias and computing velocity field from data of Terra Nova Bay GPS network in Antarctica by means of a quasi-observation processing approach

    USGS Publications Warehouse

    Casula, Giuseppe; Dubbini, Marco; Galeandro, Angelo

    2007-01-01

    A semi-permanent GPS network of about 30 vertices has been installed at Terra Nova Bay (TNB) near Ross Sea in Antarctica. A permanent GPS station TNB1 based on an Ashtech Z-XII dual frequency P-code GPS receiver with ASH700936D_M Choke Ring Antenna has been mounted on a reinforced concrete pillar built on bedrock since October 1998 and has recorded continuously up to the present. The semi-permanent network has been routinely surveyed every summer