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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. 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.

  5. 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.

  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. A Chinese minority script recognition method based on wavelet feature and multinomial naive Bayes

    NASA Astrophysics Data System (ADS)

    Guo, Hai; Zhao, Jing-ying

    2009-07-01

    The existing Chinese Minorities OCR system is mainly oriented in the "literacy" level, the script recognition has not attracted the attention it deserves, and the area of recognizing the kinds of Chinese minority scripts is still in a blank. This paper presents a method of recognizing the kinds of Chinese minority scripts based on wavelet analysis and Multinomial Naive Bayes. The method of recognizing the kinds of Chinese minority scripts based on wavelet analysis and Multinomial Naive Bayes is presented which adopts wavelet decomposition that obtains feature descriptor of wavelet energy and wavelet energy distribution proportion. Combined with the texture feature of Chinese minority scripts, radially classification in Multinomial Naive Bayes. Among Chinese, English and Chinese minority scripts such as Tibetan, Tai Lue, Naxi Pictographs, Uighur, Tai Le, Yi, the experimental results show the recognition rate is up to 90%.

  8. 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.…

  9. 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…

  10. Fuzzy Naive Bayesian model for medical diagnostic decision support.

    PubMed

    Wagholikar, Kavishwar B; Vijayraghavan, Sundararajan; Deshpande, Ashok W

    2009-01-01

    This work relates to the development of computational algorithms to provide decision support to physicians. The authors propose a Fuzzy Naive Bayesian (FNB) model for medical diagnosis, which extends the Fuzzy Bayesian approach proposed by Okuda. A physician's interview based method is described to define a orthogonal fuzzy symptom information system, required to apply the model. For the purpose of elaboration and elicitation of characteristics, the algorithm is applied to a simple simulated dataset, and compared with conventional Naive Bayes (NB) approach. As a preliminary evaluation of FNB in real world scenario, the comparison is repeated on a real fuzzy dataset of 81 patients diagnosed with infectious diseases. The case study on simulated dataset elucidates that FNB can be optimal over NB for diagnosing patients with imprecise-fuzzy information, on account of the following characteristics - 1) it can model the information that, values of some attributes are semantically closer than values of other attributes, and 2) it offers a mechanism to temper exaggerations in patient information. Although the algorithm requires precise training data, its utility for fuzzy training data is argued for. This is supported by the case study on infectious disease dataset, which indicates optimality of FNB over NB for the infectious disease domain. Further case studies on large datasets are required to establish utility of FNB.

  11. 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

  12. 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.

  13. A naive Bayes algorithm for tissue origin diagnosis (TOD-Bayes) of synchronous multifocal tumors in the hepatobiliary and pancreatic system.

    PubMed

    Jiang, Weiqin; Shen, Yifei; Ding, Yongfeng; Ye, Chuyu; Zheng, Yi; Zhao, Peng; Liu, Lulu; Tong, Zhou; Zhou, Linfu; Sun, Shuo; Zhang, Xingchen; Teng, Lisong; Timko, Michael P; Fan, Longjiang; Fang, Weijia

    2017-09-16

    Synchronous multifocal tumors are common in the hepatobiliary and pancreatic system but because of similarities in their histological features, oncologists have difficulty in identifying their precise tissue clonal origin through routine histopathological methods. To address this problem and assist in more precise diagnosis, we developed a computational approach for tissue origin diagnosis based on naive Bayes algorithm (TOD-Bayes) using ubiquitous RNA-Seq data. Massive tissue-specific RNA-Seq data sets were first obtained from The Cancer Genome Atlas (TCGA) and ∼1,000 feature genes were used to train and validate the TOD-Bayes algorithm. The accuracy of the model was > 95% based on 10-fold cross validation by the data from TCGA. A total of 18 clinical cancer samples (including 6 negative controls) with definitive tissue origin were subsequently used for external validation and 17 of the 18 samples were classified correctly in our study (94.4%). Furthermore, we included as cases studies seven tumor samples, taken from two individuals who suffered from synchronous multifocal tumors across tissues, where the efforts to make a definitive primary cancer diagnosis by traditional diagnostic methods had failed. Using our TOD-Bayes analysis, the two clinical test cases were successfully diagnosed as pancreatic cancer (PC) and cholangiocarcinoma (CC), respectively, in agreement with their clinical outcomes. Based on our findings, we believe that the TOD-Bayes algorithm is a powerful novel methodology to accurately identify the tissue origin of synchronous multifocal tumors of unknown primary cancers using RNA-Seq data and an important step towards more precision-based medicine in cancer diagnosis and treatment. This article is protected by copyright. All rights reserved. © 2017 UICC.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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 %.

  1. 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. © 2014 Cognitive Science Society, Inc.

  2. THz identification and Bayes modeling

    NASA Astrophysics Data System (ADS)

    Sokolnikov, Andre

    2017-05-01

    THz Identification is a developing technology. Sensing in the THz range potentially gives opportunity for short range radar sensing because THz waves can better penetrate through obscured atmosphere, such as fog, than visible light. The lower scattering of THz as opposed to the visible light results also in significantly better imaging than in IR spectrum. A much higher contrast can be achieved in medical trans-illumination applications than with X-rays or visible light. The same THz radiation qualities produce better tomographical images from hard surfaces, e.g. ceramics. This effect comes from the delay in time of reflected THz pulses detection. For special or commercial applications alike, the industrial quality control of defects is facilitated with a lower cost. The effectiveness of THz wave measurements is increased with computational methods. One of them is Bayes modeling. Examples of this kind of mathematical modeling are considered.

  3. 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

  4. Wood identification of Dalbergia nigra (CITES Appendix I) using quantitative wood anatomy, principal components analysis and naive Bayes classification.

    PubMed

    Gasson, Peter; Miller, Regis; Stekel, Dov J; Whinder, Frances; Zieminska, Kasia

    2010-01-01

    Dalbergia nigra is one of the most valuable timber species of its genus, having been traded for over 300 years. Due to over-exploitation it is facing extinction and trade has been banned under CITES Appendix I since 1992. Current methods, primarily comparative wood anatomy, are inadequate for conclusive species identification. This study aims to find a set of anatomical characters that distinguish the wood of D. nigra from other commercially important species of Dalbergia from Latin America. Qualitative and quantitative wood anatomy, principal components analysis and naïve Bayes classification were conducted on 43 specimens of Dalbergia, eight D. nigra and 35 from six other Latin American species. Dalbergia cearensis and D. miscolobium can be distinguished from D. nigra on the basis of vessel frequency for the former, and ray frequency for the latter. Principal components analysis was unable to provide any further basis for separating the species. Naïve Bayes classification using the four characters: minimum vessel diameter; frequency of solitary vessels; mean ray width; and frequency of axially fused rays, classified all eight D. nigra correctly with no false negatives, but there was a false positive rate of 36.36 %. Wood anatomy alone cannot distinguish D. nigra from all other commercially important Dalbergia species likely to be encountered by customs officials, but can be used to reduce the number of specimens that would need further study.

  5. 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

  6. 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

  7. 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.

  8. [An accurate approach to hyperspectral mineral identification based on naive bayesian classification model].

    PubMed

    He, Jin-Xin; Chen, Sheng-Bo; Wang, Yang; Wu, Yan-Fan

    2014-02-01

    The spectral absorption features are very similar between some minerals, especially hydrothermal alteration minerals related to mineralization, and they are also influenced by other factors such as spectral mixture. As a result, many of the spectral identification approaches for the minerals with similar spectral absorption features are prone to confusion and misjudgment. Therefore, to solve the phenomenon of "same mineral has different spectrums, and same spectrum belongs to different minerals", this paper proposes an accurate approach to hyperspectral mineral identification based on naive bayesian classification model. By testing and analyzing muscovite and kaolinite, the two typical alteration minerals, and comparing this approach with spectral angle matching, binary encoding and spectral feature fitting, the three popular spectral identification approaches, the results show that this approach can make more obvious differences among different minerals having similar spectrums, and has higher classification accuracy, since it is based on the position of absorption feature, absorption depth and the slope of continuum.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Two modeling strategies for empirical Bayes estimation.

    PubMed

    Efron, Bradley

    2014-05-01

    Empirical Bayes methods use the data from parallel experiments, for instance observations Xk ~ (Θ k , 1) for k = 1, 2, …, N, to estimate the conditional distributions Θ k |Xk . There are two main estimation strategies: modeling on the θ space, called "g-modeling" here, and modeling on the×space, called "f-modeling." The two approaches are de- scribed and compared. A series of computational formulas are developed to assess their frequentist accuracy. Several examples, both contrived and genuine, show the strengths and limitations of the two strategies.

  14. Two modeling strategies for empirical Bayes estimation

    PubMed Central

    Efron, Bradley

    2014-01-01

    Empirical Bayes methods use the data from parallel experiments, for instance observations Xk ~ 𝒩 (Θk, 1) for k = 1, 2, …, N, to estimate the conditional distributions Θk|Xk. There are two main estimation strategies: modeling on the θ space, called “g-modeling” here, and modeling on the×space, called “f-modeling.” The two approaches are de- scribed and compared. A series of computational formulas are developed to assess their frequentist accuracy. Several examples, both contrived and genuine, show the strengths and limitations of the two strategies. PMID:25324592

  15. Default Bayes Factors for Model Selection in Regression

    ERIC Educational Resources Information Center

    Rouder, Jeffrey N.; Morey, Richard D.

    2012-01-01

    In this article, we present a Bayes factor solution for inference in multiple regression. Bayes factors are principled measures of the relative evidence from data for various models or positions, including models that embed null hypotheses. In this regard, they may be used to state positive evidence for a lack of an effect, which is not possible…

  16. 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.

  17. 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.

  18. 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

  19. 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...

  20. 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...

  1. 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.

  2. 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...

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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…

  10. 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

  11. Energy response model of the Daya Bay experiment

    NASA Astrophysics Data System (ADS)

    Viaux, Nicolás; Daya Bay Collaboration

    2017-09-01

    The Daya Bay reactor neutrino experiment has made the most precise measurement of neutrino oscillation parameter sin2 2θ 13 as well as the first direct measurement of effective mass-squared difference |Δ {m}ee2| through the analyses of reactor antineutrino rate and spectral shape. Precise measurements of reactor antineutrino spectrum require an accurate understanding of the detector energy response. We developed an energy response model of the antineutrino detector using various in-situ calibrations and external measurements. The poster will present details of the energy response model that is used in the latest results from the Daya Bay experiment.

  12. 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.

  13. 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.

  14. 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.

  15. Modeling the impact of bay breeze circulations on nitrogen deposition

    NASA Astrophysics Data System (ADS)

    Loughner, C. P.; Tzortziou, M.; Pickering, K. E.; Duffy, M.; Satam, C.

    2012-12-01

    Atmospheric gases and aerosols are deposited into watersheds and estuarine waters contributing to water quality degradation and affecting estuarine and coastal biogeochemical processes. Pollution that is deposited onto land can be transported into storm drains, groundwater, streams, and rivers where it is eventually transported into near-shore waters. Air quality models, which simulate the chemical transformation, atmospheric transport, and deposition of pollutants onto land and surface waters, can play an integral role in forecasting water quality, preparing water quality regulations and providing information on the sources of nutrients and pollutants for advanced estuarine biogeochemical models. Previous studies have found that Chesapeake Bay breezes cause localized areas of high air pollution concentrations and that model simulations with horizontal resolutions coarser than about 5 km are not able to capture bay breeze circulations. Here, we investigate the importance of capturing bay breeze circulations with high resolution model simulations (horizontal resolution of 1.33 km) to accurately simulate the spatial and temporal variability of nitrogen deposition into the Chesapeake Bay watershed. Nitrogen deposition into the watershed from air quality model simulations are compared with observed wet deposition and estimated dry deposition rates from the National Acid Deposition Program (NADP) and the Clean Air Status and Trends Network (CASTNET), respectively. The model simulation is conducted for the months of June and July 2011. Two concurrent air and water quality field campaigns, DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) and GeoCAPE-CBODAQ (Geostationary Coastal and Air Pollution Events-Chesapeake Bay Oceanographic Campaign with DISCOVER-AQ), were conducted in July 2011, and data obtained from these field experiments are used to evaluate the model simulations.

  16. 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.

  17. 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.

  18. Naive time-reversal odd phenomena in semi-inclusive deep-inelastic scattering from light-cone constituent quark models

    SciTech Connect

    Barbara Pasquini, Peter Schweitzer

    2011-06-01

    We present results for leading-twist azimuthal asymmetries in semi-inclusive lepton-nucleon deep-inelastic scattering due to naively time-reversal odd transverse-momentum dependent parton distribution functions from the light-cone constituent quark model. We carefully discuss the range of applicability of the model, especially with regard to positivity constraints and evolution effects. We find good agreement with available experimental data from COMPASS and HERMES, and present predictions to be tested in forthcoming experiments at Jefferson Lab.

  19. Bayes Factor Covariance Testing in Item Response Models.

    PubMed

    Fox, Jean-Paul; Mulder, Joris; Sinharay, Sandip

    2017-08-29

    Two marginal one-parameter item response theory models are introduced, by integrating out the latent variable or random item parameter. It is shown that both marginal response models are multivariate (probit) models with a compound symmetry covariance structure. Several common hypotheses concerning the underlying covariance structure are evaluated using (fractional) Bayes factor tests. The support for a unidimensional factor (i.e., assumption of local independence) and differential item functioning are evaluated by testing the covariance components. The posterior distribution of common covariance components is obtained in closed form by transforming latent responses with an orthogonal (Helmert) matrix. This posterior distribution is defined as a shifted-inverse-gamma, thereby introducing a default prior and a balanced prior distribution. Based on that, an MCMC algorithm is described to estimate all model parameters and to compute (fractional) Bayes factor tests. Simulation studies are used to show that the (fractional) Bayes factor tests have good properties for testing the underlying covariance structure of binary response data. The method is illustrated with two real data studies.

  20. 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.…

  1. 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.…

  2. 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

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

    USGS Publications Warehouse

    Aretxabaleta, Alfredo; Ganju, Neil K.; 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.

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

    NASA Astrophysics Data System (ADS)

    Aretxabaleta, Alfredo L.; Ganju, Neil K.; Butman, Bradford; Signell, Richard P.

    2017-04-01

    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.

  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. Response of the Chesapeake Bay water quality model to loading scenarios (a report of the modeling Subcommittee, Chesapeake Bay Program Office, Annapolis, MD). Technology transfer report

    SciTech Connect

    Thomann, R.V.; Collier, J.R.; Butt, A.; Casman, E.; Linker, L.C.

    1994-01-01

    A modeling framework was constructed for the Chesapeake Bay system to provide a credible basis to assist the decision-making process and to further the understanding of Bay water quality processes and the sensitivity of such processes to external nutrient loading. The modeling structure consists of a Watershed Model to generate nutrient loads from the Bay sub-basins; a three-dimensional, time variable hydrodynamic model; and a three-dimensional, time variable model of water quality coupled to a model of sediment chemistry. Extensive calibration analyses of the entire modeling structure was conducted using data collected primarily during a three year period from 1984-1986. The Chesapeake Bay Program Modeling Subcommittee completed its initial review of the Chesapeake Bay Water Quality Model (CBWQM) calibration in May 1991 and concluded the model could provide useful information to the Bay community, especially with respect to dissolved oxygen problems in the deep water of the main Bay. Final calibration of the CBWQM was completed in January 1992.

  7. 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.

  8. 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.

  9. 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.

  10. Modeling the Residence Time of Mobile Bay in Alabama

    NASA Astrophysics Data System (ADS)

    Han, M. M.; Park, K.

    2016-02-01

    The Three-dimensional Hydrodynamic-Eutrophication Model/Environmental Fluid Dynamics Code (HEM3D/EFDC) was used to calculate the residence time of Mobile Bay in Alabama using Eulerian passive tracer method. Mobile Bay is about 50 km long and 20 km wide, so it can be divided into several sections which may have different residence times. Three typical boundary conditions that affect residence time are tide, river discharge, and wind. Mobile Bay is located in the northern Gulf of Mexico and is a micro-tidal region. Two most important tidal components here are K1 and O1, and the maximum tidal range of tropic (spring) tide is less than 0.6 m. There is a difference between the simulation results with and without tidal condition (K1+O1) even though the tidal range is relatively smaller than that in macro-tidal regions. Also the minimum, mean, and maximum of daily mean river discharge for 38 years (1976-2013) in Mobile and Tensaw River are 80.7 m3/s, 1700.8 m3/s, and 14186.7 m3/s respectively, and there are daily, monthly, seasonal, and annual variations. The residence time can be largely affected by the river discharge because of its large deviation. Even though the dominant wind here is southerly in the spring and summer and is northerly in the fall and winter, the wind speed and direction change over time. Continuous winds from similar directions can reduce and increase the residence time such as the southerly, southwesterly, northerly, and northeasterly winds in alignment with the direction of the inlet and outlet of Mobile Bay. Also the short term changes of wind direction and speed can affect it complicatedly. Therefore, the simulations with the combinations of three boundary conditions allow us to understand the water circulation in Mobile Bay well and to predict the residence time when some accidents happen such as contaminations by factories, sewage plants, ships and oil spills.

  11. 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

  12. 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...

  13. Study of the hydrodynamical processes in the Boka Kotorska Bay with a finite element model

    NASA Astrophysics Data System (ADS)

    Bellafiore, Debora; Guarnieri, Antonio; Grilli, Federica; Penna, Pierluigi; Bortoluzzi, Giovanni; Giglio, Federico; Pinardi, Nadia

    2011-09-01

    Boka Kotorska Bay, located in the southeastern Adriatic Sea along the Montenegro coastline, is a complex morphological structure, consisting of three embayments. They are connected and interact with the sea through narrow straits and the bay can be considered one of the main freshwater inputs into the southern Adriatic Sea. In the framework of the ADRICOSM-STAR project, a hydrodynamical model of this region provided results that are compared with CTD data and hydrodynamic scenarios are discussed for the bay. A finite element coastal model nested in a finite difference model that runs on the Adriatic Sea has been used to reproduce the complex morphology of the bay. Hydrodynamic modeling allows studying the main characteristics of this bay, identifying it as a Region of Freshwater Influence (ROFI). The freshwater input coming from the numerous sources present in the bays can strongly modify temperature, salinity and current patterns. The computation of the buoyancy ratio of the thermal and haline buoyancy flux showed that the Kotor and Morinj Bays experience a major effect of surface heating in summer, while the rest of the bay seems to be mostly affected by freshwater influence from precipitation and river discharge. An average estuarine situation is seen, presenting a surface outflow and a bottom inflow of water. Specific hydrodynamic processes can be detected in the channels that connect the different sub-basins of the Boka Kotorska Bay. Moreover, the computation of the Kelvin number in correspondence of the internal straits suggests classifying the Kotor and Morinj Bays differently from the outermost areas. The innermost Kotor and Morinj Bays, generally exchange little water with the sea and they have high values of residence times. However, their fresh water springs and rivers have the highest discharges that can change abruptly the picture with increase of the total water exchange between the bay and the sea.

  14. Bayesian model reduction and empirical Bayes for group (DCM) studies.

    PubMed

    Friston, Karl J; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E; van Wijk, Bernadette C M; Ziegler, Gabriel; Zeidman, Peter

    2016-03-01

    This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level - e.g., dynamic causal models - and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Bayesian model reduction and empirical Bayes for group (DCM) studies

    PubMed Central

    Friston, Karl J.; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E.; van Wijk, Bernadette C.M.; Ziegler, Gabriel; Zeidman, Peter

    2016-01-01

    This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level – e.g., dynamic causal models – and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. PMID:26569570

  16. Naive coadaptive cortical control.

    PubMed

    Gage, Gregory J; Ludwig, Kip A; Otto, Kevin J; Ionides, Edward L; Kipke, Daryl R

    2005-06-01

    The ability to control a prosthetic device directly from the neocortex has been demonstrated in rats, monkeys and humans. Here we investigate whether neural control can be accomplished in situations where (1) subjects have not received prior motor training to control the device (naive user) and (2) the neural encoding of movement parameters in the cortex is unknown to the prosthetic device (naive controller). By adopting a decoding strategy that identifies and focuses on units whose firing rate properties are best suited for control, we show that naive subjects mutually adapt to learn control of a neural prosthetic system. Six untrained Long-Evans rats, implanted with silicon micro-electrodes in the motor cortex, learned cortical control of an auditory device without prior motor characterization of the recorded neural ensemble. Single- and multi-unit activities were decoded using a Kalman filter to represent an audio "cursor" (90 ms tone pips ranging from 250 Hz to 16 kHz) which subjects controlled to match a given target frequency. After each trial, a novel adaptive algorithm trained the decoding filter based on correlations of the firing patterns with expected cursor movement. Each behavioral session consisted of 100 trials and began with randomized decoding weights. Within 7 +/- 1.4 (mean +/- SD) sessions, all subjects were able to significantly score above chance (P < 0.05, randomization method) in a fixed target paradigm. Training lasted 24 sessions in which both the behavioral performance and signal to noise ratio of the peri-event histograms increased significantly (P < 0.01, ANOVA). Two rats continued training on a more complex task using a bilateral, two-target control paradigm. Both subjects were able to significantly discriminate the target tones (P < 0.05, Z-test), while one subject demonstrated control above chance (P < 0.05, Z-test) after 12 sessions and continued improvement with many sessions achieving over 90% correct targets. Dynamic analysis of

  17. 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.

  18. 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.

  19. 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...

  20. 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...

  1. Confirmatory Latent Class Analysis: Model Selection Using Bayes Factors and (Pseudo) Likelihood Ratio Statistics.

    ERIC Educational Resources Information Center

    Hoijtink, Herbert

    2001-01-01

    Discusses , in the context of confirmatory latent class analysis, model selection using Bayes factors and (pseudo) likelihood ratio statistics. Uses a small simulation study to show that in this context, Bayes factors and the pseudo likelihood ratio statistics have the best properties. (SLD)

  2. 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...

  3. 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...

  4. 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

  5. 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…

  6. HABITAT ASSESSMENT MODELS FOR BAY SCALLOP, ARGOPECTEN IRRADIANS

    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...

  7. 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

  8. 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.

  9. 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.

  10. Bay Scallop Habitat Suitability Models: Predictions over Space and Time

    EPA Science Inventory

    A survey of Lagoon Pond, Martha’s Vineyard, MA, USA was conducted in September 2005 to determine the combination of habitat factors most highly correlated with bay scallop (Argopecten irradians) abundance.

  11. Chesapeake Bay ecosystem modeling program. Technical synthesis report 1993-94

    SciTech Connect

    Brandt, S.B.; Boynton, W.R.; Kemp, W.M.; Wetzel, R.; Bartleson, R.

    1995-03-01

    ;Contents: Ecosystem models for management; Ecosystem regession models; Patuxent River Sav-Littoral Ecosystem Process Model; Lower Chesapeake Bay Polyhaline Sav Model; Emergent Intertidal Marsh Process Model; Plankton-Benthos Ecosystem Process Model; Fish Bioenergetics Models; Linking Water Quality with Fish Habitat; Data Visualization; Publications and Scientific Presentations Resulting From This Research.

  12. 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

  13. 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

  14. Structural equation modelling of viral tropism reveals its impact on achieving viral suppression within 6 months in treatment-naive HIV-1-infected patients after combination antiretroviral therapy.

    PubMed

    Mengoli, Carlo; Andreis, Samantha; Scaggiante, Renzo; Cruciani, Mario; Bosco, Oliviero; Ferretto, Roberto; Leoni, Davide; Maffongelli, Gaetano; Basso, Monica; Torti, Carlo; Sarmati, Loredana; Andreoni, Massimo; Palù, Giorgio; Parisi, Saverio Giuseppe

    2017-01-01

    To evaluate the role of pre-treatment co-receptor tropism of plasma HIV on the achievement of viral suppression (plasma HIV RNA 1.69 log10 copies/mL) at the sixth month of combination antiretroviral therapy (cART) in a cohort of naive patients using, for the first time in this context, a path analysis (PA) approach. Adult patients with chronic infection by subtype B HIV-1 were consecutively enrolled from the start of first-line cART (T0). Genotypic analysis of viral tropism was performed on plasma and interpreted using the bioinformatic tool Geno2pheno, with a false positive rate of 10%. A Bayesian network starting from the viro-immunological data at T0 and at the sixth month of treatment (T1) was set up and this model was evaluated using a PA approach. A total of 262 patients (22.1% bearing an X4 virus) were included; 178 subjects (67.9%) achieved viral suppression. A significant positive indirect effect of bearing X4 virus in plasma at T0 on log10 HIV RNA at T1 was detected (P = 0.009), the magnitude of this effect was, however, over 10-fold lower than the direct effect of log10 HIV RNA at T0 on log10 HIV RNA at T1 (P = 0.000). Moreover, a significant positive indirect effect of bearing an X4 virus on log10 HIV RNA at T0 (P = 0.003) was apparent. PA overcame the limitations implicit in common multiple regression analysis and showed the possible role of pre-treatment viral tropism at the recommended threshold on the outcome of plasma viraemia in naive patients after 6 months of therapy. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. 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)

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. Modelling residence-time response to freshwater input in Apalachicola Bay, Florida, USA

    NASA Astrophysics Data System (ADS)

    Huang, Wenrui; Spaulding, M.

    2002-10-01

    Residence time of an estuary can be used to estimate the rate of removal of freshwater and pollutants from river inflow. In this study, a calibrated three-dimensional hydrodynamic model was used to determine residence time in response to the change of freshwater input in Apalachicola Bay. The bay is about 40 km long and 7 km wide, with an average 3 m water depth. Through hydrodynamic model simulations, the spatial and temporal salinity and the total freshwater volume in the bay were calculated. Then the freshwater fraction method was used to estimate the residence time. Results indicate that the residence time in Apalachicola Bay typically ranges between 3 and 10 days for the daily freshwater input ranging from 177 m3/s to 4561 m3/s. Regression analysis of model results shows that an exponential regression equation can be used to correlate the estuarine residence time to changes of freshwater input.

  3. 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…

  4. 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…

  5. A cost-effectiveness model to personalize antiviral therapy in naive patients with genotype 1 chronic hepatitis C.

    PubMed

    Iannazzo, Sergio; Colombatto, Piero; Ricco, Gabriele; Oliveri, Filippo; Bonino, Ferruccio; Brunetto, Maurizia R

    2015-03-01

    Rapid virologic response is the best predictor of sustained virologic response with dual therapy in genotype-1 chronic hepatitis C, and its evaluation was proposed to tailor triple therapy in F0-F2 patients. Bio-mathematical modelling of viral dynamics during dual therapy has potentially higher accuracy than rapid virologic in the identification of patients who will eventually achieve sustained response. Study's objective was the cost-effectiveness analysis of a personalized therapy in naïve F0-F2 patients with chronic hepatitis C based on a bio-mathematical model (model-guided strategy) rather than on rapid virologic response (guideline-guided strategy). A deterministic bio-mathematical model of the infected cell dynamics was validated in a cohort of 135 patients treated with dual therapy. A decision-analytic economic model was then developed to compare model-guided and guideline-guided strategies in the Italian setting. The outcomes of the cost-effectiveness analysis with model-guided and guideline-guided strategy were 19.1-19.4 and 18.9-19.3 quality-adjusted-life-years. Total per-patient lifetime costs were €25,200-€26,000 with model-guided strategy and €28,800-€29,900 with guideline-guided strategy. When comparing model-guided with guideline-guided strategy the former resulted more effective and less costly. The adoption of the bio-mathematical predictive criterion has the potential to improve the cost-effectiveness of a personalized therapy for chronic hepatitis C, reserving triple therapy for those patients who really need it. Copyright © 2014 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  6. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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/...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    DTIC Science & Technology

    2016-06-01

    Sandeep, and V. Pant. 2016. Modeling salinity exchanges between the equatorial Indian Ocean and the Bay of Bengal. Oceanography 29(2):92–101, http...Bay of Bengal, models ranging from a 1/12.5° global ocean model to a ¼° regional Indian Ocean model to a 2 km local high-resolution coupled model...are used to simulate salinity exchanges in the Indian Ocean . Global Hybrid Coordinate Ocean Model simulations show a surprisingly large persistent flow

  10. First Step Towards a Coastal Modelling System for South Africa: a St. Helena Bay Case Study

    NASA Astrophysics Data System (ADS)

    Collins, C.; Lamont, T.; Loveday, B. R.; Hermes, J. C.; Veitch, J.; Backeberg, B.

    2016-02-01

    St. Helena Bay, forming part of the southern Benguela ecosystem, is the largest bay on the west coast of South Africa and is a biologically important region for pelagic fish, hake, and rock lobster. To date, only a few infrequent studies have focussed on variations in the bay scale circulation. A monthly ship-based monitoring line, the St. Helena Bay Monitoring Line (SHBML), was initiated in 2000 to determine the seasonal changes in cross-shelf hydrography and biology. Even though there has been an increase in ocean modelling in and around South Africa in recent years, coastal modelling is still in its infancy. The 12-year observational data set in the St. Helena Bay region, the only long-term, cross-shelf, full water column data-set for South Africa, makes this area the perfect natural laboratory for the development of a coastal modelling system. In this study, the climatological mean temperature and salinity from three different ROMS simulations and a HYCOM simulation are evaluated against the in situ observations from the SHBML with the aim of determining the influence of different forcing products, horizontal and vertical resolution as well as vertical coordinate schemes on the vertical structure of the ocean. The model simulations tend to overestimate the temperature and salinity across the shelf, and particularly within St. Helena Bay. Furthermore, the models misrepresent the vertical salinity and temperature structures. Interestingly, below 800m, there is a better agreement between temperature in the models and the in-situ observations. This is the first detailed comparison of modelled and in-situ data for the greater St. Helena Bay area at this scale and the next phase will examine whether the model that is most congruent with the observations resolves the same interannual signals as observed in the in-situ data.

  11. 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…

  12. 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...

  13. 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

  14. 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...

  15. 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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

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

  18. [Application of Bayes Probability Model in Differentiation of Yin and Yang Jaundice Syndromes in Neonates].

    PubMed

    Mu, Chun-sun; Zhang, Ping; Kong, Chun-yan; Li, Yang-ning

    2015-09-01

    To study the application of Bayes probability model in differentiating yin and yang jaundice syndromes in neonates. Totally 107 jaundice neonates who admitted to hospital within 10 days after birth were assigned to two groups according to syndrome differentiation, 68 in the yang jaundice syndrome group and 39 in the yin jaundice syndrome group. Data collected for neonates were factors related to jaundice before, during and after birth. Blood routines, liver and renal functions, and myocardial enzymes were tested on the admission day or the next day. Logistic regression model and Bayes discriminating analysis were used to screen factors important for yin and yang jaundice syndrome differentiation. Finally, Bayes probability model for yin and yang jaundice syndromes was established and assessed. Factors important for yin and yang jaundice syndrome differentiation screened by Logistic regression model and Bayes discriminating analysis included mothers' age, mother with gestational diabetes mellitus (GDM), gestational age, asphyxia, or ABO hemolytic diseases, red blood cell distribution width (RDW-SD), platelet-large cell ratio (P-LCR), serum direct bilirubin (DBIL), alkaline phosphatase (ALP), cholinesterase (CHE). Bayes discriminating analysis was performed by SPSS to obtain Bayes discriminant function coefficient. Bayes discriminant function was established according to discriminant function coefficients. Yang jaundice syndrome: y1= -21. 701 +2. 589 x mother's age + 1. 037 x GDM-17. 175 x asphyxia + 13. 876 x gestational age + 6. 303 x ABO hemolytic disease + 2.116 x RDW-SD + 0. 831 x DBIL + 0. 012 x ALP + 1. 697 x LCR + 0. 001 x CHE; Yin jaundice syndrome: y2= -33. 511 + 2.991 x mother's age + 3.960 x GDM-12. 877 x asphyxia + 11. 848 x gestational age + 1. 820 x ABO hemolytic disease +2. 231 x RDW-SD +0. 999 x DBIL +0. 023 x ALP +1. 916 x LCR +0. 002 x CHE. Bayes discriminant function was hypothesis tested and got Wilks' λ =0. 393 (P =0. 000). So Bayes

  19. Estimating postprandial glucose fluxes using hierarchical Bayes modelling.

    PubMed

    Haidar, Ahmad; Potocka, Elizabeth; Boulet, Benoit; Umpleby, A Margot; Hovorka, Roman

    2012-10-01

    A new stochastic computational method was developed to estimate the endogenous glucose production, the meal-related glucose appearance rate (R(a meal)), and the glucose disposal (R(d)) during the meal tolerance test. A prior probability distribution was adopted which assumes smooth glucose fluxes with individualized smoothness level within the context of a Bayes hierarchical model. The new method was contrasted with the maximum likelihood method using data collected in 18 subjects with type 2 diabetes who ingested a mixed meal containing [U-¹³C]glucose. Primed [6,6-²H₂]glucose was infused in a manner that mimicked the expected endogenous glucose production. The mean endogenous glucose production, R(a meal), and R(d) calculated by the new method and maximum likelihood method were nearly identical. However, the maximum likelihood gave constant, nonphysiological postprandial endogenous glucose production in two subjects whilst the new method gave plausible estimates of endogenous glucose production in all subjects. Additionally, the two methods were compared using a simulated triple-tracer experiment in 12 virtual subjects. The accuracy of the estimates of the endogenous glucose production and R(a meal) profiles was similar [root mean square error (RMSE) 1.0±0.3 vs. 1.4±0.7 μmol/kg/min for EGP and 2.6±1.0 vs. 2.9±0.9 μmol/kg/min for R(a meal); new method vs. maximum likelihood method; P=NS, paired t-test]. The accuracy of R(d) estimates was significantly increased by the new method (RMSE 5.3±1.9 vs. 4.2±1.3; new method vs. ML method; P<0.01, paired t-test). We conclude that the new method increases plausibility of the endogenous glucose production and improves accuracy of glucose disposal compared to the maximum likelihood method. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  20. 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…

  1. 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

  2. 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.

  3. 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.

  4. Models for estimating bayes factors with applications to phylogeny and tests of monophyly.

    PubMed

    Suchard, Marc A; Weiss, Robert E; Sinsheimer, Janet S

    2005-09-01

    Bayes factors comparing two or more competing hypotheses are often estimated by constructing a Markov chain Monte Carlo (MCMC) sampler to explore the joint space of the hypotheses. To obtain efficient Bayes factor estimates, Carlin and Chib (1995, Journal of the Royal Statistical Society, Series B57, 473-484) suggest adjusting the prior odds of the competing hypotheses so that the posterior odds are approximately one, then estimating the Bayes factor by simple division. A byproduct is that one often produces several independent MCMC chains, only one of which is actually used for estimation. We extend this approach to incorporate output from multiple chains by proposing three statistical models. The first assumes independent sampler draws and models the hypothesis indicator function using logistic regression for various choices of the prior odds. The two more complex models relax the independence assumption by allowing for higher-lag dependence within the MCMC output. These models allow us to estimate the uncertainty in our Bayes factor calculation and to fully use several different MCMC chains even when the prior odds of the hypotheses vary from chain to chain. We apply these methods to calculate Bayes factors for tests of monophyly in two phylogenetic examples. The first example explores the relationship of an unknown pathogen to a set of known pathogens. Identification of the unknown's monophyletic relationship may affect antibiotic choice in a clinical setting. The second example focuses on HIV recombination detection. For potential clinical application, these types of analyses must be completed as efficiently as possible.

  5. A three-dimensional water quality model and its application to Jiaozhou Bay, China

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Sun, Ying-lan; Yu, Jing; Yuan, Dao-wei; Zhang, Rui-jin

    2012-12-01

    A three-dimensional coupled physical and water quality model was developed and applied to the Jiaozhou Bay to study water quality involving nutrients, biochemical oxygen demand, dissolved oxygen, and phytoplankton that are closely related to eutrophication process. The physical model is a modified ECOM-si version with inclusion of flooding/draining processes over the intertidal zone. The water quality model is based on WASP5 which quantifies processes governing internal nutrients cycling, dissolved oxygen balance and phytoplankton growth. The model was used to simulate the spatial distribution and the temporal variation of water quality in the Jiaozhou Bay for the period of May 2005 to May 2006. In addition, the effect of reduction of riverine nutrients load was simulated and evaluated. The simulated results show that under the influence of nutrients discharged from river, the concentrations of nutrients and phytoplankton were higher in the northwest and northeast of the bay, and decreased from the inner bay to the outer. Affected by strong tidal mixing, the concentrations of all state variables were vertically homogeneous except in the deeper regions where a small gradient was found. Obvious seasonal variation of phytoplankton biomass was found, which exhibited two peaks in March and July, respectively. The variation of riverine waste loads had remarkable impact on nutrients concentration in coastal areas, but slightly altered the distribution in the center of the bay.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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).

  11. Order-Constrained Bayes Inference for Dichotomous Models of Unidimensional Nonparametric IRT

    ERIC Educational Resources Information Center

    Karabatsos, George; Sheu, Ching-Fan

    2004-01-01

    This study introduces an order-constrained Bayes inference framework useful for analyzing data containing dichotomous scored item responses, under the assumptions of either the monotone homogeneity model or the double monotonicity model of nonparametric item response theory (NIRT). The framework involves the implementation of Gibbs sampling to…

  12. 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.

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

    DTIC Science & Technology

    1985-09-01

    Markovian Queueing Systems: M/M/C 4 3.2 Compartment Models in Pharmacology 4 3.3 Logistic Support for a System Depending Upon Repairable Modules 5 4...congestion at service facilities. in these models , some simple arrival or demand process confronts a given service process often presumed to nave i.i.d...Similarly. inventory control models typically assume that parameters of demano distributions a’e fixed, as do reliability- redundancy studies of

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Environmental capacity of petroleum hydrocarbon pollutants in Jiaozhou Bay, China: Modeling and calculation

    NASA Astrophysics Data System (ADS)

    Li, Keqiang; Su, Ying; Ying, Jun; Wang, Xiulin; Mu, Jinbo

    2013-03-01

    An environmental capacity model for the petroleum hydrocarbon pollutions (PHs) in Jiaozhou Bay is constructed based on field surveys, mesocosm, and parallel laboratory experiments. Simulated results of PHs seasonal successions in 2003 match the field surveys of Jiaozhou Bay resaonably well with a highest value in July. The Monte Carlo analysis confirms that the variation of PHs concentration significantly correlates with the river input. The water body in the bay is reasonably subjected to self-purification processes, such as volatilization to the atmosphere, biodegradation by microorganism, and transport to the Yellow Sea by water exchange. The environmental capacity of PHs in Jiaozhou Bay is 1500 tons per year IF the seawater quality criterion (Grade I/II, 0.05 mgL-1) in the region is to be satisfied. The contribution to self-purification by volatilization, biodegradation, and transport to the Yellow Sea accounts for 48%, 28%, and 23%, respectively, which make these three processes the main ways of PHs purification in Jiaozhou Bay.

  1. 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.

  2. Sediment deposition from Tropical Storm Lee in the upper Chesapeake Bay: field observations and model predictions

    NASA Astrophysics Data System (ADS)

    Palinkas, C. M.; Halka, J. P.; Li, M.; Sanford, L. P.; Cheng, P.

    2012-12-01

    Episodic flood and storm events are important drivers of sediment dynamics in estuarine and marine environments. Event-driven sedimentation has been well-documented by field and modeling studies. Yet, few studies have integrated field observations and modeling results to overcome the limitations inherent in both techniques. A unique opportunity to integrate field observations and model results was provided in late August/early September 2011 with the passage of Hurricane Irene and the remnants of Tropical Storm Lee in the Chesapeake Bay region. These storms differed in their timing, track, and impact on the Bay region - Hurricane Irene was primarily a wind/resuspension event, whereas TS Lee was a hydrological/deposition event, with the second largest discharge of the Susquehanna River on record. Because these two storms occurred within a relatively short period of time, both are potentially represented in the sediment record obtained during rapid-response cruises in September and October 2011. The resulting sediment deposit was recognized in cores using classic flood-sediment signatures (fine grain size, uniform 7Be activity, physical stratification in x-radiographs) and was found to be <4 cm, thickest in the upper Bay. Model runs conducted for TS Lee generally agreed with these estimates. One exception with physical stratification but no 7Be activity appears to be due to extreme wave activity during Hurricane Irene. Integration of observations and modeling in this case greatly improved understanding of the transport and fate of flood sediments in the Chesapeake Bay.

  3. 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

  4. 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.

  5. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. 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

  7. 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...

  8. 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...

  9. Modeling water exchange between Baltimore Harbor and Chesapeake Bay using artificial tracers: seasonal variations.

    PubMed

    Hong, Bo; Panday, Nauth; Shen, Jian; Wang, Harry V; Gong, Wenping; Soehl, Anna

    2010-07-01

    Understanding the dynamics of water exchange between Baltimore Harbor and the Chesapeake Bay is essential when evaluating transport and fate of dissolved substances in both of these systems. Conservative artificial tracers are used in this study to investigate transport processes through a three-dimensional hydrodynamic model (CH3D). The model well reproduced the three-layered circulation pattern in Baltimore Harbor. Several numerical experiments are performed to trace the water mass coming from different sources. The results indicate that both the upper and lower layers of the Harbor are the dominant pathways of transporting dissolved substances from Susquehanna River to the Harbor. Such inward transport is intensified (suppressed) during the high-discharge (low-discharge) period. The upper layer inflow transports water mass with high concentrations of dissolved substances while the inflow from the lower layer transports water mass with low concentrations of dissolved substances. The bottom layer is the dominant pathway for transporting dissolved substances from the lower Bay to the Harbor. Lower river discharge and stronger along-Bay pressure gradient (resulting in stronger landward residual flow in the bottom layer of the Bay) facilitate the bottom intrusion of dissolved substances from lower Bay to the Harbor. Once contaminants are transported into the Harbor, they usually stay for a longer time in the mid-depth of the Harbor than those in other layers due to the three-layer circulation in the Harbor. The time needed for the contaminants being transported out of the Harbor during a typical low-discharge period is about 1 month longer than that needed during a typical high-discharge period. The results, from the environmental perspective, provide new insights for quantitative evaluation on the transport processes of the dissolved biogeochemical substances between Baltimore Harbor and Chesapeake Bay. 2010 Elsevier Ltd. All rights reserved.

  10. 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

  11. Modeling the climatic and subsurface stratigraphy controls on the hydrology of a Carolina Bay wetland in South Carolina, USA

    Treesearch

    Ge Sun; Timothy J. Callahan; Jennifer E. Pyzoha; Carl C. Trettin

    2006-01-01

    Restoring depressional wetlands or geographically isolated wetlands such as cypress swamps and Carolina bays on the Atlantic Coastal Plains requires a clear understanding of the hydrologic processes and water balances. The objectives of this paper are to (1) test a distributed forest hydrology model, FLATWOODS, for a Carolina bay wetland system using seven years of...

  12. Modeling the climatic and subsurface stratigraphy controls on the hydrology of a Carolina bay wetland in South Carolina, USA

    Treesearch

    Ge Sun; Timothy J. Callahan; Jennifer E. Pyzoha; Carl C. Trettin

    2006-01-01

    Restoring depressional wetlands or geographically isolated wetlands such as cypress swamps and Carolina bays on the Atlantic Coastal Plains requires a clear understanding of the hydrologic processes and water balances. The objectives of this paper are to (1) test a distributed forest hydrology model, FLATWOODS, for a Carolina bay wetland system using seven years of...

  13. 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.…

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

    USDA-ARS?s Scientific Manuscript database

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. 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.

  17. 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

  18. 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.

  19. Modeling and Field Study of Coupled Bio-Optical Physical Processes in the Monterey Bay Area.

    NASA Astrophysics Data System (ADS)

    Shulman, I.; Arnone, R.; Teague, W.; Chavez, F.; Schofield, O.; Moline, M.; Penta, B.; Ryan, J.; Gould, R.; Anderson, S.; Jolliff, J. K.; Book, J. W.; Derada, S.; Paduan, J. D.

    2008-12-01

    Scientists from government, academia and non-profit organizations participated in an interdisciplinary field program in the Monterey Bay from during May-June of 2008. The experiment was a collaboration between the NRL project "Bio-Optical Studies of Predictability and Assimilation for the Coastal Environment (BIOSPACE)", Multidisciplinary University Research Initiative (MURI) project "Rapid Environmental Assessment Using an Integrated Coastal Ocean Observation-Modeling System (ESPRESSO)", the Monterey Bay Aquarium Research Institute (MBARI), the NRL project "Unattended Sea-bed Power for In-water Operations", and the U.S. Geological Survey. Objectives of the NRL BIOSPACE and MURI ESPRESSO projects are centered around developing an understanding of coupled bio-optical and physical processes in the coastal zone and improvements of predictability of coastal ocean optical properties on time scales of 1-5 days. MBARI has long-term objectives of monitoring, studying and managing the Monterey Bay ecosystem dynamics and health. The goals for the 2008 field program were to create a synoptic view of the coupled bio- optical physical conditions in the Monterey Bay and to relate satellite observed properties to their subsurface structure. The program was focused on the so-called "upwelling shadow area"(northern part of the bay), where biological processes are enhanced as a result of the slower physical dynamics. The field program deployed a wide range of assets: gliders, AUVs, ScanFish (a ship-towed platform), SEPTR, etc. This deployment was supplemented with intensive station sampling from the R/V Point Sur and satellite ocean color imagery (MODIS, MERIS). The field program was supported by a real-time modeling effort consisting of a hierarchy of different resolution, nested, data assimilating, coupled bio-optical physical models. Development of a pair of cyclonic (in the bay) and anticyclonic (outside of the bay) eddies was observed and predicted by the model during an

  20. 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.

  1. 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.

  2. 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.

  3. Hydrodynamic prevention of eutrophication in the Bay of Brest (France), a modelling approach

    NASA Astrophysics Data System (ADS)

    Le Pape, Olivier; Menesguen, Alain

    1997-08-01

    The Bay of Brest is a semi-enclosed coastal ecosystem where primary production is nutrient-limited, even if huge nutrients loading from tributaries are present. The most striking feature of the bay is the semi-diurnal tidal influence, resulting in large water exchange with the continental shelf. A historical study of the available data has shown the steadiness of this ecosystem during the two last decades in spite of increasing eutrophic conditions. This study has focused on hydrodynamic exchange which is one of the factors supposed to explain the resistance of this ecosystem to eutrophication: this stirring hinders the formation of a persistent upper mixed layer where phytoplankton would be in contact with nutrient-rich brackish waters and available light. Moreover, horizontal tidal currents lead to huge exchanges with the Iroise Sea and, then, to big losses of nutrients and living matter. To study this hydrodynamic influence thoroughly, a physical/biological model of this bay has been developed. This box model, based on the horizontal tidal circulation, has been developed thanks to "ELISE", an ecological modelling software and, then, tuned and validated on two data sets corresponding with the years 1977 and 1993. The model has allowed us to quantify the influence of hydrodynamics, climatic conditions and biological factors on biogeochemical processes in this ecosystem. It contributes to explain the good resistance of the Bay of Brest ecosystem to eutrophic conditions; both the hydrodynamic properties of this bay and the grazing pressure have prevented it from disturbances caused by high nitrogen loading from the watersheds and explain the steadiness of phytoplankton stocks in spite of increased loading. So, these results allow us to say that, even if nitrogen inputs increase continues, phytoplankton stocks will not increase in significant proportions. Nevertheless, changes in the phytoplanktonic populations may occur if such an enrichment continues.

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

    PubMed

    Jacobs, J M; Rhodes, M; Brown, C W; Hood, R R; Leight, A; Long, W; Wood, R

    2014-11-01

    To construct statistical models to predict the presence, abundance and potential virulence of Vibrio vulnificus in surface waters of Chesapeake Bay for implementation in ecological forecasting systems. We evaluated and applied previously published qPCR assays to water samples (n = 1636) collected from Chesapeake Bay from 2007-2010 in conjunction with State water quality monitoring programmes. 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. 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. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

  5. Evaluation of groundwater resources of the Chesapeake Bay Watershed using an integrated hydrologic model

    NASA Astrophysics Data System (ADS)

    Seck, A.; Welty, C.; Maxwell, R. M.

    2013-12-01

    We present results from a distributed integrated hydrologic model of the Chesapeake Bay Watershed using ParFlow-CLM. The model covers an area of 400,000 km2 spanning five physiographic provinces, discretized at a horizontal resolution of 2 km and vertical resolution of 5 m. Synthesis of published hydrogeologic data as well as analysis of well completion reports from state agencies were used to construct a hydrogeologic model framework. The model was run for the period of 2003-2004 using National Land Data Assimilation System (NLDAS) meteorological forcing. Model output captures seasonal and spatial variability in subsurface storage and surface storage, and produces water table depths consistent with the topography, meteorological forcing, and hydrogeological setting. Model results show spatial variability in evaporation fluxes correlated to land cover at higher resolution than either NLDAS outputs or the EPA Chesapeake Bay Watershed Model Phase 5.3. Comparison with USGS streamflow data at selected stream gages shows good agreement in daily discharge timing and fluxes for high and average flows, whereas the model does not perform as well for low flows during summer and dry periods. Analysis of groundwater stores and fluxes showed marked variability across physiographic provinces. Highest groundwater stores were expectedly found in the Coastal Plain, while the Blue Ridge physiographic province had the lowest stores. The Appalachian Plateau was characterized by the highest net recharge rates. The highest discharge rates were found in the Valley and Ridge, Piedmont and Coastal Plain. The construction of this model constitutes a step forward in understanding the groundwater system in the Chesapeake Bay Watershed and its role in solute delivery to the Chesapeake Bay.

  6. A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction

    PubMed Central

    Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Montesinos-López, José Cricelio; Luna-Vázquez, Francisco Javier; Salinas-Ruiz, Josafhat; Herrera-Morales, José R.; Buenrostro-Mariscal, Raymundo

    2017-01-01

    There are Bayesian and non-Bayesian genomic models that take into account G×E interactions. However, the computational cost of implementing Bayesian models is high, and becomes almost impossible when the number of genotypes, environments, and traits is very large, while, in non-Bayesian models, there are often important and unsolved convergence problems. The variational Bayes method is popular in machine learning, and, by approximating the probability distributions through optimization, it tends to be faster than Markov Chain Monte Carlo methods. For this reason, in this paper, we propose a new genomic variational Bayes version of the Bayesian genomic model with G×E using half-t priors on each standard deviation (SD) term to guarantee highly noninformative and posterior inferences that are not sensitive to the choice of hyper-parameters. We show the complete theoretical derivation of the full conditional and the variational posterior distributions, and their implementations. We used eight experimental genomic maize and wheat data sets to illustrate the new proposed variational Bayes approximation, and compared its predictions and implementation time with a standard Bayesian genomic model with G×E. Results indicated that prediction accuracies are slightly higher in the standard Bayesian model with G×E than in its variational counterpart, but, in terms of computation time, the variational Bayes genomic model with G×E is, in general, 10 times faster than the conventional Bayesian genomic model with G×E. For this reason, the proposed model may be a useful tool for researchers who need to predict and select genotypes in several environments. PMID:28391241

  7. A Variational Bayes Genomic-Enabled Prediction Model with Genotype × Environment Interaction.

    PubMed

    Montesinos-López, Osval A; Montesinos-López, Abelardo; Crossa, José; Montesinos-López, José Cricelio; Luna-Vázquez, Francisco Javier; Salinas-Ruiz, Josafhat; Herrera-Morales, José R; Buenrostro-Mariscal, Raymundo

    2017-06-07

    There are Bayesian and non-Bayesian genomic models that take into account G×E interactions. However, the computational cost of implementing Bayesian models is high, and becomes almost impossible when the number of genotypes, environments, and traits is very large, while, in non-Bayesian models, there are often important and unsolved convergence problems. The variational Bayes method is popular in machine learning, and, by approximating the probability distributions through optimization, it tends to be faster than Markov Chain Monte Carlo methods. For this reason, in this paper, we propose a new genomic variational Bayes version of the Bayesian genomic model with G×E using half-t priors on each standard deviation (SD) term to guarantee highly noninformative and posterior inferences that are not sensitive to the choice of hyper-parameters. We show the complete theoretical derivation of the full conditional and the variational posterior distributions, and their implementations. We used eight experimental genomic maize and wheat data sets to illustrate the new proposed variational Bayes approximation, and compared its predictions and implementation time with a standard Bayesian genomic model with G×E. Results indicated that prediction accuracies are slightly higher in the standard Bayesian model with G×E than in its variational counterpart, but, in terms of computation time, the variational Bayes genomic model with G×E is, in general, 10 times faster than the conventional Bayesian genomic model with G×E. For this reason, the proposed model may be a useful tool for researchers who need to predict and select genotypes in several environments. Copyright © 2017 Montesinos-López et al.

  8. A three-dimensional water quality model to evaluate the environmental capacity of nitrogen and phosphorus in Jiaozhou Bay, China.

    PubMed

    Li, Keqiang; Zhang, Li; Li, Yan; Zhang, Longjun; Wang, Xiulin

    2015-02-15

    Jiaozhou Bay has recently suffered from serious problems with pollution and eutrophication. Thus, land-based pollutant load must be reduced through a national control program. In this study, we developed a 3D water quality model to determine the environmental capacity of nitrogen and phosphorus in Jiaozhou Bay. A 3D hydrodynamic model (the estuarine, coastal, and ocean modeling system with sediments) was coupled with a water quality model, which was adapted from the dynamic model of nitrogen and phosphorus for a mesocosm near Jiaozhou Bay. The water quality model is divided into seven components: dissolved inorganic nitrogen, phosphate, phytoplankton, zooplankton, detritus, dissolved organic nitrogen, and dissolved organic phosphorus. Furthermore, it was calibrated based on data collected from Jiaozhou Bay in 2003. The proposed model effectively reproduced the spatiotemporal variability in nutrient concentration, thus suggesting that a reasonable numerical representation of the prototype system must be developed for further evaluation of environmental capacity. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Evaluation of CALPUFF nitrogen deposition modeling in the Chesapeake Bay Watershed Area using NADP data

    SciTech Connect

    Garrison, M.; Mayes, P.; Sherwell, J.

    1998-12-31

    The CALMET/CALPUFF modeling system has been used to estimate nitrogen deposition in an area surrounding Baltimore and the northern portion of the Chesapeake Bay. Comprehensive NO{sub x} emissions inventories and meteorological data bases have been developed to conduct the modeling. This paper discusses the results of an evaluation of predicted nitrogen wet deposition rates compared to measured rates at two NADP/NTN sites in Maryland, Wye and White Rock. Underprediction of wet deposition rates is investigated through the use of sensitivity and diagnostic evaluations of model performance. A suggested change to the calculation of NO{sub x} transformation rates involving an alternative specification of minimum NO{sub x} concentrations was made to CALPUFF and the performance evaluation was re-done. Results of the new evaluation show significantly improved model performance, and therefore the modification is tentatively proposed for use in further applications of CALPUFF to the assessment of nitrogen deposition in the Chesapeake Bay watershed.

  10. 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

  11. Modeling the effect of hypoxia on macrobenthos production in the lower Rappahannock River, Chesapeake Bay, USA.

    PubMed

    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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. Numerical modeling of hydrodynamic changes due to coastal reclamation projects in Xiamen Bay, China

    NASA Astrophysics Data System (ADS)

    Wang, Jia; Hong, Huasheng; Zhou, Lumin; Hu, Jianyu; Jiang, Yuwu

    2013-03-01

    Xiamen Bay in South China has experienced extensive coastal exploitation since the 1950s, resulting in some severe environmental problems. Local authorities now have completed or are implementing many environmental restoration projects. Evaluating the cumulative impact of exploitation and restoration activities on the environment is a complicated multi-disciplinary problem. However, hydrodynamic changes in the bay caused by such coastal projects can be characterized directly and definitively through numerical modeling. This paper assesses the cumulative effect of coastal projects on the hydrodynamic setting using a high-resolution numerical modeling method that makes use of tidal current speeds and the tidal prism as two hydrodynamic indices. Changes in tidal velocity and the characteristics of the tidal prism show that hydrodynamic conditions have declined from 1938 to 2007 in the full-tide area. The tidal current speed and tidal prism have decreased by 40% in the western part of the bay and 20% in the eastern part of the bay. Because of the linear relationship between tidal prism and area, the degraded hydrodynamic conditions are anticipated to be restored to 1972 levels following the completion of current and proposed restoration projects, i.e. 33% and 15% decrease in the hydrodynamic conditions of 1938 for the western and eastern parts of the bay, respectively. The results indicate that hydrodynamic conditions can be restored to some extent with the implementation of a sustainable coastal development plan, although a full reversal of conditions is not possible. To fully assess the environmental changes in a region, more indices, e.g., water quality and ecosystem parameters, should be considered in future evaluations.

  17. Development of a finite volume two-dimensional model and its application in a bay with two inlets: Mobile Bay, Alabama

    NASA Astrophysics Data System (ADS)

    Lee, Jun; Lee, Jungwoo; Yun, Sang-Leen; Oh, Hye-Cheol

    2017-08-01

    The purpose of this study was to develop a two-dimensional shallow water flow model using the finite volume method on a combined unstructured triangular and quadrilateral grid system to simulate coastal, estuarine and river flows. The intercell numerical fluxes were calculated using the classical Osher-Solomon's approximate Riemann solver for the governing conservation laws to be able to handle wetting and drying processes and to capture a tidal bore like phenomenon. The developed model was validated with several benchmark test problems including the two-dimensional dam-break problem. The model results were well agreed with results of other models and experimental results in literature. The unstructured triangular and quadrilateral combined grid system was successfully implemented in the model, thus the developed model would be more flexible when applying in an estuarine system, which includes narrow channels. Then, the model was tested in Mobile Bay, Alabama, USA. The developed model reproduced water surface elevation well as having overall Predictive Skill of 0.98. We found that the primary inlet, Main Pass, only covered 35% of the fresh water exchange while it covered 89% of the total water exchange between the ocean and Mobile Bay. There were also discharge phase difference between MP and the secondary inlet, Pass aux Herons, and this phase difference in flows would act as a critical role in substances' exchange between the eastern Mississippi Sound and the northern Gulf of Mexico through Main Pass and Pass aux Herons in Mobile Bay.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Sediment deposition from tropical storms in the upper Chesapeake Bay: Field observations and model simulations

    NASA Astrophysics Data System (ADS)

    Palinkas, Cindy M.; Halka, Jeffrey P.; Li, Ming; Sanford, Lawrence P.; Cheng, Peng

    2014-09-01

    Episodic flood and storm events are important drivers of sediment dynamics in estuarine and marine environments. Event-driven sedimentation has been well-documented by field and modeling studies, though both techniques have inherent limitations. A unique opportunity to integrate field observations and model results was provided in late August/early September 2011 with the passage of Hurricane Irene and Tropical Storm Lee in the Chesapeake Bay region. Because these two storms occurred within a relatively short period of time, both are potentially represented in the sediment record obtained during rapid-response cruises in September and October 2011. Associated sediment deposits were recognized in cores using classic flood-sediment signatures (fine grain size, uniform 7Be activity, physical stratification in x-radiographs) and were found to be <4 cm, thickest in the upper Bay. A coupled hydrodynamic-sediment transport model is used to simulate the sediment plume and sediment deposition onto the seabed. The predicted deposition thickness for TS Lee is in general agreement with the observational estimates. One exception with physical stratification but no 7Be activity appears to be due to extreme wave activity during Hurricane Irene. Integration of observations and modeling in this case greatly improved understanding of the transport and fate of flood sediments in the Chesapeake Bay.

  4. 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

  5. Modelling the dynamics of palaeo ice-stream retreat in Marguerite Bay, Antarctica

    NASA Astrophysics Data System (ADS)

    Jamieson, S. S.; Vieli, A.; Livingstone, S. J.; Stokes, C. R.; O'Cofaigh, C.; Hillenbrand, C.

    2010-12-01

    The aim is to use numerical models of ice stream behaviour to understand the processes that triggered and controlled the retreat of the Marguerite Bay palaeo ice stream after the Last Glacial Maximum (LGM). This is important because at present a number of marine-based ice streams in Antarctica are rapidly losing mass. Given the consequences of this mass loss for future sea-level rise, it is crucial to improve our understanding and predictive abilities of grounding line retreat of marine-based ice streams. Because contemporary records of grounding line retreat are very short (decades) and may not be representative of behaviour on century or millennial timescales, we focus on the longer-term post-LGM retreat dynamics of the palaeo ice stream as recorded in the marine-geophysical record. Our approach combines numerical modelling with geomorphological mapping in order to understand the processes that triggered and controlled the hypothesized rapid retreat of the Marguerite Bay palaeo ice-stream. Here we describe the numerical model, modelling approach and results of sensitivity testing to understand the behaviour of the Marguerite Bay palaeo ice stream. High-resolution bathymetric data of the Marguerite Bay area has enabled detailed geomorphological mapping and provides a record of grounding line retreat. These mapping data, set into a chronological framework of deglaciation, are used to constrain a 1-dimensional flowline model of the Marguerite palaeo- ice-stream. The numerical model includes basal, lateral and longitudinal stresses and a robust treatment of grounding-line motion through the use of a constantly adjusting spatial grid. We subject the model to a range of external forcing including changes in sea-level, temperature and accumulation in order to reproduce the geomorphological evidence and therefore understand the dynamics of ice stream retreat in this area. We find that slow-downs or re-stabilisations of the grounding line occur in areas of reverse bed

  6. Mean sea-level rise impacts on Santos Bay, Southeastern Brazil--physical modelling study.

    PubMed

    Alfredini, Paolo; Arasaki, Emilia; do Amaral, Rogério Fernando

    2008-09-01

    The greenhouse effect and resulting increase in the Earth's temperature may accelerate the mean sea-level rise. The natural response of bays and estuaries to this rise, such as this case study of Santos Bay (Brazil), will include change in shoreline position, land flooding and wetlands impacts. The main impacts of this scenario were studied in a physical model built in the Coastal and Harbour Division of Hydraulic Laboratory, University of São Paulo, and the main conclusions are presented in this paper. The model reproduces near 1,000 km(2) of the study area, including Santos, São Vicente, Praia Grande, Cubatão, Guarujá and Bertioga cities.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification.

    PubMed

    Respuela, Patricia; Nikolić, Miloš; Tan, Minjia; Frommolt, Peter; Zhao, Yingming; Wysocka, Joanna; Rada-Iglesias, Alvaro

    2016-01-07

    Following implantation, mouse epiblast cells transit from a naive to a primed state in which they are competent for both somatic and primordial germ cell (PGC) specification. Using mouse embryonic stem cells as an in vitro model to study the transcriptional regulatory principles orchestrating peri-implantation development, here we show that the transcription factor Foxd3 is necessary for exit from naive pluripotency and progression to a primed pluripotent state. During this transition, Foxd3 acts as a repressor that dismantles a significant fraction of the naive pluripotency expression program through decommissioning of active enhancers associated with key naive pluripotency and early germline genes. Subsequently, Foxd3 needs to be silenced in primed pluripotent cells to allow re-activation of relevant genes required for proper PGC specification. Our findings therefore uncover a cycle of activation and deactivation of Foxd3 required for exit from naive pluripotency and subsequent PGC specification. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. 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.

  14. 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

  15. Mixed models and empirical bayes estimation for retrospective exposure assessment of dust exposures in Canadian sawmills.

    PubMed

    Friesen, Melissa C; Macnab, Ying C; Marion, Stephen A; Demers, Paul A; Davies, Hugh W; Teschke, Kay

    2006-04-01

    Data on job histories is commonly available from study subjects and worksites, therefore jobs are often used for assigning exposures in historical epidemiological studies. Exposure estimates are often derived by offering jobs as fixed effects in statistical models. An alternative approach would be to offer job as a random effect to obtain empirical Bayes estimates of exposure. This approach is more efficient since it weights exposure estimates according to the within-job and between-job variability and the number of measurements for each job. We assess three models for predicting historical dust exposures of sawmill workers. Models were developed using 407 inhalable dust measurements collected from 58 jobs in four sawmills. The first model incorporated all variables as fixed effects; the second added a random term to account for correlation within workers; and the third offered random terms for worker, job and mill (hierarchical model). Empirical Bayes estimates were used to calculate job-specific exposures from the hierarchical model. The fixed effects and random worker mixed models performed nearly identically because there was low within-worker correlation (r = 0.26). The Bayesian exposure predictions from the hierarchical model were slightly more correlated with the observed mill-job arithmetic means than those from the models where jobs were fixed effects (0.74 versus 0.70). While we observed no large differences in exposure estimates by treating job as a fixed or random effect, treating job as a random effect allowed for job-specific coefficients to be estimated for every job while borrowing strength in the presence of sparse data by assuming that the job means are normally distributed around the group mean. In addition, empirical Bayes job estimates can be used for a posteriori job grouping. The use of this method for retrospective exposure assessment should continue to be examined.

  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. 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.

  18. 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.

  19. 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.

  20. 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

  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. 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.

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

    PubMed Central

    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. PMID:24874082

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Trophic models: What do we learn about Celtic Sea and Bay of Biscay ecosystems?

    NASA Astrophysics Data System (ADS)

    Moullec, Fabien; Gascuel, Didier; Bentorcha, Karim; Guénette, Sylvie; Robert, Marianne

    2017-08-01

    Trophic models are key tools to go beyond the single-species approaches used in stock assessments to adopt a more holistic view and implement the Ecosystem Approach to Fisheries Management (EAFM). This study aims to: (i) analyse the trophic functioning of the Celtic Sea and the Bay of Biscay, (ii) investigate ecosystem changes over the 1980-2013 period and, (iii) explore the response to management measures at the food web scale. Ecopath models were built for each ecosystem for years 1980 and 2013, and Ecosim models were fitted to time series data of biomass and catches. EcoTroph diagnosis showed that in both ecosystems, fishing pressure focuses on high trophic levels (TLs) and, to a lesser extent, on intermediate TLs. However, the interplay between local environmental conditions, species composition and ecosystem functioning could explain the different responses to fisheries management observed between these two contiguous ecosystems. Indeed, over the study period, the ecosystem's exploitation status has improved in the Bay of Biscay but not in the Celtic Sea. This improvement does not seem to be sufficient to achieve the objectives of an EAFM, as high trophic levels were still overexploited in 2013 and simulations conducted with Ecosim in the Bay of Biscay indicate that at current fishing effort the biomass will not be rebuilt by 2030. The ecosystem's response to a reduction in fishing mortality depends on which trophic levels receive protection. Reducing fishing mortality on pelagic fish, instead of on demersal fish, appears more efficient at maximising catch and total biomass and at conserving both top-predator and intermediate TLs. Such advice-oriented trophic models should be used on a regular basis to monitor the health status of marine food webs and analyse the trade-offs between multiple objectives in an ecosystem-based fisheries management context.

  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. 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.

  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. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. Detecting Adverse Drug Events in Discharge Summaries Using Variations on the Simple Bayes Model

    PubMed Central

    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. PMID:14728261

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Naive Physics, Event Perception, Lexical Semantics, and Language Acquisition

    DTIC Science & Technology

    1993-04-01

    AD-A276 799 Technical Report 1456 P Naive Physics, Event Perception, Lexical Semantics, and Language Acquisition DTICS ELFCTE MAR 0 91094D v F...Event Perception, Lexical Semantics, and Language Acquisition by .Jeffrev Mark Siskiiid Accesion For B.A. Computer Science (1979) NTIS CRAM Technion...hypotheses about child language acquisition , these systems use only positive examples to drive their acquisition of a language model. MAIMRA. the

  14. Modeling the clinical assessment of men with suspected obstructed voiding using Bayes' Theorem.

    PubMed

    Caffarel, Jennifer; Griffiths, Clive; Pickard, Robert; Robson, Wendy; Drinnan, Michael

    2008-01-01

    Pressure-flow studies (PFS) are the only reliable way to diagnose bladder outlet obstruction (BOO) in men with lower urinary tract symptoms (LUTS). However, in routine clinical practice, BOO is usually inferred by any of a number of tests (symptoms, flow rate, prostate size...). Bayes' Theorem provides a mathematical method, which may be similar to the process used by clinicians, for combining the results of multiple tests to reach a diagnosis. We have applied Bayes' Theorem to the results of several tests known weakly to predict BOO in men with LUTS to assess if they improve the diagnostic accuracy of a flow rate test which alone is known to predict obstruction moderately well. We applied Bayes' Theorem to data from 50 patients using Q(max) alone and with the inclusion of additional variables (IPSS, PSA, and residual urine), to establish individual probabilities of BOO. The chi-squared statistic (with trend) was used to compare the relative diagnostic values, against the BOO index calculated from the results of subsequent PFS. The diagnostic value of Q(max) alone (chi-squared = 9.2, P = 0.002), was superior than that for the Bayesian model using the combination of tests available (chi-squared = 4.9, P = 0.026). Although in our sample relevant additional tests do not improve the diagnostic power of Q(max) as a predictor of BOO, we believe the Bayesian approach is conceptually suited to modeling clinical decision making but may be better tested for a more clinically relevant outcome such as treatment response. (c) 2008 Wiley-Liss, Inc.

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

    DTIC Science & Technology

    2015-03-01

    Figure 1-3 shows the shoreline change that has occurred at Braddock Bay from 1902 to 2009. The Salmon Creek and Buttonwood Creek (Figure 1-3) connect...result, the bay has lost approximately 135 acres (1.3 BRADDOCK BAY Salmon Creek Wetlands Buttonwood Creek ERDC TR-14-8 8 acre/yr) from 1902...measurements of Buttonwood Creek and Salmon Creek that discharge to Braddock Bay. However, the USGS measures flow rates at several rivers and

  16. Cumberland Sound and Kings Bay Pre-Trident and Basic Trident Channel Hydrodynamic and Sediment Transport Hybrid Modeling. Volume 1. Main Text and Appendixes A, C, and D

    DTIC Science & Technology

    1990-12-01

    through and past Kings Bay changed the phasing relationships north of Kings Bay. Although not an explicit objective of the modeling efforts, tidal effects...changed the tidal phasing rela- tionships (earlier times of arrival) north of Kings Bay. The plan channel condition increased the maintained interior...excellent main channel ebb and flood velocity phase and magnitude agreement with the physical model measurements. Tributary and secondary chan- nels adjacent

  17. 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.

  18. 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.

  19. 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.

  20. 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).

  1. Modelling near field regional uplift patterns in West Greenland/Disko Bay with plane-Earth finite element models.

    NASA Astrophysics Data System (ADS)

    Meldgaard, Asger; Nielsen, Lars; Iaffaldano, Giampiero

    2017-04-01

    Relative sea level data, primarily obtained through isolation basin analysis in western Greenland and on Disko Island, indicates asynchronous rates of uplift during the Early Holocene with larger rates of uplift in southern Disko Bay compared to the northern part of the bay. Similar short-wavelength variations can be inferred from the Holocene marine limit as observations on the north and south side of Disko Island differ by as much as 60 m. While global isostatic adjustment models are needed to account for far field contributions to the relative sea level and for the calculation of accurate ocean functions, they are generally not suited for a detailed analysis of the short-wavelength uplift patterns observed close to present ice margins. This is in part due to the excessive computational cost required for sufficient resolution, and because these models generally ignore regional lateral heterogeneities in mantle and lithosphere rheology. To mitigate this problem, we perform sensitivity tests to investigate the effects of near field loading on a regional plane-Earth finite element model of the lithosphere and mantle of the Disko Bay area, where the global isostatic uplift chronology is well documented. By loading the model area through detailed regional ocean function and ice models, and by including a high resolution topography model of the area, we seek to assess the isostatic rebound generated by surface processes with wavelengths similar to those of the observed rebound signal. We also investigate possible effects of varying lithosphere and mantle rheology, which may play an important role in explaining the rebound signal. We use the abundance of relative sea level curves obtained in the region primarily through isolation basin analysis on Disko Island to constrain the parameters of the Earth model.

  2. A new seamless, high-resolution digital elevation model of the San Francisco Bay-Delta Estuary, California

    USGS Publications Warehouse

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

    2017-06-14

    Climate change, sea-level rise, and human development have contributed to the changing geomorphology of the San Francisco Bay - Delta (Bay-Delta) Estuary system. The need to predict scenarios of change led to the development of a new seamless, high-resolution digital elevation model (DEM) of the Bay – Delta that can be used by modelers attempting to understand potential future changes to the estuary system. This report details the three phases of the creation of this DEM. The first phase took a bathymetric-only DEM created in 2005 by the U.S. Geological Survey (USGS), refined it with additional data, and identified areas that would benefit from new surveys. The second phase began a USGS collaboration with the California Department of Water Resources (DWR) that updated a 2012 DWR seamless bathymetric/topographic DEM of the Bay-Delta with input from the USGS and modifications to fit the specific needs of USGS modelers. The third phase took the work from phase 2 and expanded the coverage area in the north to include the Yolo Bypass up to the Fremont Weir, the Sacramento River up to Knights Landing, and the American River up to the Nimbus Dam, and added back in the elevations for interior islands. The constant evolution of the Bay-Delta will require continuous updates to the DEM of the Delta, and there still are areas with older data that would benefit from modern surveys. As a result, DWR plans to continue updating the DEM.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. An investigation into using the CALMET/CALPUFF modeling system for assessing atmospheric nitrogen deposition in the Chesapeake Bay

    SciTech Connect

    Sherwell, J.; Garrison, M.

    1997-12-31

    The Maryland Department of Natural Resources Power Plant Research Program (PPRP) has a long-standing interest in the water quality of the Chesapeake Bay. A plan has been developed for the ten tributary regions in Maryland that feed into the Chesapeake Bay. Possible reductions in NO{sub x} deposition rates achievable from reductions in airborne NO{sub x} due to Clean Air Act mandates for power plants are of interest in helping to meet the nutrient reduction targets. The Regional Acid Deposition Model (RADM) has been used to estimate NO{sub x} deposition quantities and the extent of the airshed for the Chesapeake Bay. The CALMET/CALPUFF modeling system, recently made available to the public via EPA`s Technology Transfer Network (TTN), is a meteorological and concentration/deposition modeling system that offers a great deal of flexibility for modeling airborne NO{sub x} deposition and for possibly complementing the RADM analyses. A study by PPRP is underway to explore different ways in which the CALMET/CALPUFF modeling system can provide insights into magnitudes, sources, and possible reductions of NO{sub x} deposition to the Bay. The Penn State/NCAR Mesoscale Model (MM4) gridded data set for 1990 has been used for meteorological inputs, and EPA`s 1990 National Emissions Inventory for NO{sub x} has been used to derive source inputs. The CALPUFF analysis is being conducted to provide information in three primary areas: first, detailed deposition estimates for the northern part of the Chesapeake Bay around Baltimore; second, source or source group-specific estimates of deposition in the receptor region for both local and distant sources; and third, time series of deposition patterns throughout the receptor region. This paper reports on the experiences gained in preparing and running the CALMET/CALPUFF system, and on the preliminary results of the analysis of NO{sub x} deposition to the Chesapeake Bay.

  8. Improved method for calibration of exchange flows for a physical transport box model of Tampa Bay, FL USA

    EPA Science Inventory

    Results for both sequential and simultaneous calibration of exchange flows between segments of a 10-box, one-dimensional, well-mixed, bifurcated tidal mixing model for Tampa Bay are reported. Calibrations were conducted for three model options with different mathematical expressi...

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Effect of Linezolid on the 50% Lethal Dose and 50% Protective Dose in Treatment of Infections by Gram-Negative Pathogens in Naive and Immunosuppressed Mice and on the Efficacy of Ciprofloxacin in an Acute Murine Model of Septicemia

    PubMed Central

    Marra, Andrea; Lamb, Lucinda; Medina, Ivette; George, David; Gibson, Glenn; Hardink, Joel; Rugg, Jady; Van Deusen, Jeffrey

    2012-01-01

    Murine models of infection were used to study the effect of linezolid on the virulence of Gram-negative bacteria and to assess potential pharmacodynamic interactions with ciprofloxacin in the treatment of these infections, prompted by observations from a recent clinical trial. Naive and immunosuppressed mice were challenged with Klebsiella pneumoniae 53A1109, K. pneumoniae GC6658, and Pseudomonas aeruginosa UC12120 in acute sepsis and pulmonary infection models, using different serial dilutions of these pathogens (groups of 8 animals each). Linezolid (100 mg/kg/dose) was administered orally at 0.5 and 4.0 h postchallenge in the sepsis model and at 4 h postchallenge followed by 2 days of twice-daily treatment in the pulmonary model. Further, ciprofloxacin alone and in combination with oral linezolid was investigated in the sepsis model. Survival was assessed for 4 and 10 days postchallenge in the systemic and respiratory models, respectively. The data were fitted to a nonlinear regression analysis to determine 50% lethal doses (LD50s) and 50% protective doses (PD50s). A clinically relevant, high-dose regimen of linezolid had no significant effect on LD50 in these models. This lack of effect was independent of immune status. A combination of oral ciprofloxacin with linezolid yielded lower PD50s than oral ciprofloxacin alone (ciprofloxacin in combination, 8.4 to 32.7 mg/kg; oral ciprofloxacin, 39.4 to 88.3 mg/kg). Linezolid did not improve the efficacy of subcutaneous ciprofloxacin (ciprofloxacin in combination, 2.0 to 2.4 mg/kg; subcutaneous ciprofloxacin, 2.0 to 2.8 mg/kg). In conclusion, linezolid does not seem to potentiate infections caused by Gram-negative pathogens or to interact antagonistically with ciprofloxacin. PMID:22710118

  15. 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

  16. 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.

  17. Evaluation of the RAMS model for estimating turbulent fluxes over the Chesapeake Bay

    NASA Astrophysics Data System (ADS)

    McQueen, J. T.; Valigura, R. A.; Stunder, B. J. B.

    This study has examined the ability of a mesoscale model to compute pollutant deposition velocity and surface fluxes over water with the accuracy needed for air pollution studies. The Regional Atmospheric Modeling System (RAMS) was evaluated against buoy data over the Chesapeake Bay. Turbulence and surface layer variables (e.g., surface fluxes, friction velocity) and ultimately deposition velocities were primarily examined against the buoy data for 23 cases in 1994. Sensible heat fluxes and temperatures compared well with observations when the model horizontal resolution was reduced to 5 km or less and the first model level were 12 m. Other turbulent variables compared poorly especially under stable stratifications. Overall, latent heat fluxes and deposition velocities were significantly under predicted even with these finer resolutions. Results degraded when the effects of clouds on short- and long-wave radiation were incorporated. Results were also insensitive to increase in the initial sea surface temperature (SST) over the observed daytime range (1°C), and to the use of an improved roughness length parameterization over water. Errors were much larger during stably stratified conditions, therefore, substantial under prediction of pollutants to the bay would be expected by RAMS during stable periods. However, RAMS would be a reliable predictor of fluxes and deposition velocity during unstable conditions. Further experiments were done to help explain the poor predictions during the daytime for stable conditions. Fluxes over water were strongly sensitive to the soil moisture content of the surrounding land masses for stable atmospheric conditions and improved when geostrophic forcing terms were added to the momentum equations. However, the improved results given with geostrophic forcing were either representative of synoptic forcing or a decoupled layer from the surface that could not be resolved.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics.

    PubMed

    Li, Wai Lok Sibon; Drummond, Alexei J

    2012-02-01

    We describe a procedure for model averaging of relaxed molecular clock models in Bayesian phylogenetics. Our approach allows us to model the distribution of rates of substitution across branches, averaged over a set of models, rather than conditioned on a single model. We implement this procedure and test it on simulated data to show that our method can accurately recover the true underlying distribution of rates. We applied the method to a set of alignments taken from a data set of 12 mammalian species and uncovered evidence that lognormally distributed rates better describe this data set than do exponentially distributed rates. Additionally, our implementation of model averaging permits accurate calculation of the Bayes factor(s) between two or more relaxed molecular clock models. Finally, we introduce a new computational approach for sampling rates of substitution across branches that improves the convergence of our Markov chain Monte Carlo algorithms in this context. Our methods are implemented under the BEAST 1.6 software package, available at http://beast-mcmc.googlecode.com.

  8. Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

    PubMed Central

    Li, Wai Lok Sibon; Drummond, Alexei J.

    2012-01-01

    We describe a procedure for model averaging of relaxed molecular clock models in Bayesian phylogenetics. Our approach allows us to model the distribution of rates of substitution across branches, averaged over a set of models, rather than conditioned on a single model. We implement this procedure and test it on simulated data to show that our method can accurately recover the true underlying distribution of rates. We applied the method to a set of alignments taken from a data set of 12 mammalian species and uncovered evidence that lognormally distributed rates better describe this data set than do exponentially distributed rates. Additionally, our implementation of model averaging permits accurate calculation of the Bayes factor(s) between two or more relaxed molecular clock models. Finally, we introduce a new computational approach for sampling rates of substitution across branches that improves the convergence of our Markov chain Monte Carlo algorithms in this context. Our methods are implemented under the BEAST 1.6 software package, available at http://beast-mcmc.googlecode.com. PMID:21940644

  9. Modelling Tsunami-Induced Sediments Transport in the Bay of Tangier - Morocco

    NASA Astrophysics Data System (ADS)

    Ramalho, M. I.; Omira, R.; Baptista, M. A.; El Moussaoui, S.; Zaghloul, M. N.

    2016-12-01

    The NE Atlantic (NEA) is prone to tsunami impact of tectonic origin. Previous studies and tsunami catalogs report the occurrence of significant events namely the 1 November 1755 and the 28 February 1969. In the NEA, the most impacted areas are the coastal zone of Portugal, Morocco and the Cadiz Gulf in Spain. In this study, we focus on the inland tsunami propagation and the changes in coastal morphology due to sediments transport, erosion, and deposition processes. To do this, we implemented a coupled hydrodynamic and morpho-dynamic numerical code, based on two open sources codes: COMCOT and Xbeach. COMCOT solves the shallow water equations to calculate the tsunami generation, propagation and inundation. The Xbeach solves the advection-diffusion equations to determine the amount of sediments eroded, transported and deposited, taking into account the bed-load and suspended load transport of non-cohesive sediments and suspended load of cohesive sediments. We employ the coupled model for an earthquake-generated tsunami in the Gulf of Cadiz and assess the morphological changes in the Bay of Tangier, Morocco. We simulate different earthquake scenarios and the correspondent tsunami impact using a high-resolution digital terrain model of the Bay of Tangier. Additionally, we use information on the present-day sediment layers characteristics (grain size, type of sediment, thickness, etc.). Our results show that in the case of large tsunami events the Bay of Tangier is vulnerable to tsunami-induced morphological changes. The sediment volume transported by a 1755-like event is circa 35000 m3. Additionally, our results give an insight on the consequences of tsunami impact on the coastal morphology, showing the need to consider erosion/deposition processes as an important component of tsunami hazard assessment. This work is supported by the EU project ASTARTE - Assessment, Strategy And Risk Reduction for Tsunamis in Europe, Grant 603839, 7th FP (ENV.2013, 6.4-3) and the EU

  10. 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…

  11. 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...

  12. A Modeling Study of the San Francisco Bay and Delta Ecosystem in High and Low River Flow Years

    NASA Astrophysics Data System (ADS)

    Liu, Q.; Rao, S. A.; Chai, F.; Dugdale, R. C.; Wilkerson, F. P.; Chao, Y.; Zhang, H.

    2016-02-01

    A coupled physical-biogeochemical model is used to study the nutrient and biomass cycles in the San Francisco Bay and Delta Ecosystem (SFE). With high population density, SFE has important interplay with human population and economics. To assist the ecosystem-based management and ecological risk assessment for the California fisheries and water management, we study the nutrient and biomass cycles in the San Francisco Bay by coupling the Carbon, Silicate, and Nitrogen Ecosystem (CoSiNE) model with an unstructured grid, Semi-Implicit Cross-scale Hydroscience Integrated System Model (SCHISM). The model is constrained by USGS water quality observation for the Sacramento, San Joaquin, Napa rivers and the Coyote Creek sewage plant discharge, and tested successfully by the comparisons with USGS water quality observations. This study examines the bay's response to river forcing by simulating two contrasting years, 2011 (a high river flow year) and 2012 (a low river flow year). In addition, an 11-year simulation from 2004 to 2015 is conducted to investigate the long-term cycle of the bay nutrients and biomass.

  13. 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...

  14. 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.

  15. 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

  16. 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…

  17. 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…

  18. 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

  19. 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

  20. A hydrologic network supporting spatially referenced regression modeling in the Chesapeake Bay Watershed.

    PubMed

    Brakebill, John W; Preston, Stephen 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

  1. 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

  2. Field measurement and modeling of near-bed sediment transport processes with fluid mud layer in Tokyo Bay

    NASA Astrophysics Data System (ADS)

    Nakagawa, Yasuyuki; Nadaoka, Kazuo; Yagi, Hiroshi; Ariji, Ryuichi; Yoneyama, Haruo; Shirai, Kazuhiro

    2012-12-01

    Tokyo Bay is one of the estuaries in Japan with a high population of almost 26 million people in the basin area. One of the major concerns for the environment in this water area is the decreasing ecosystem functions including the deterioration of water and sediment qualities caused by various anthropogenic activities. Since the bottom sediments around almost the entire area of the inner bay consist of fine materials with a high organic content, which cause the deterioration of water quality through processes such as hypoxia, an understanding of the fine sediment dynamics in the Bay is crucial for an environmental assessment of the water area. This paper proposes a model for the key processes of fine sediment dynamics, which reflects field data about muddy bed structures and their dynamics obtained during the monitoring campaign in 2007. One of the specific features of the sediment in the Bay at present is the persistent existence of fluid mud layers (water content over 300 %) with a thickness of around a few decimeters, which might be caused by deposition of abundant organic particles due to eutrophication. The present study shows that diffusion flux model delivers quite reliable results for estimating erosion flux from the top of fluid mud layers after calibrating the model parameter against the time series data of vertical flux measured by an acoustic Doppler velocimeter system. This study also derives analytical solutions, based on the Bingham fluid concept, of advection flux in the fluid mud layer on which external shear stress force is applied.

  3. 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.

  4. 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.

  5. James Bay

    Atmospheric Science Data Center

    2013-04-17

    article title:  First Views of James Bay, Canada     View Larger ... (MISR) on February 24, 2000, show the winter landscape of James Bay, Ontario, Canada from three of the instrument's nine cameras. The ...

  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 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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,...

  12. 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 ...

  13. 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,...

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. Modulation of the activity of moxifloxacin and solithromycin in an in vitro pharmacodynamic model of Streptococcus pneumoniae naive and induced biofilms.

    PubMed

    Vandevelde, Nathalie M; Tulkens, Paul M; Muccioli, Giulio G; Van Bambeke, Françoise

    2015-01-01

    Bacterial biofilms developing in the bronchial tree of patients experiencing acute exacerbations of chronic bronchitis (AECBs) are suggested to cause relapses and recurrences of the disease because the matrix barrier impairs antibiotic access to the offending organisms. We examined whether bronchodilators could modulate pneumococcal biofilm development and antibiotic action using an in vitro model. Streptococcus pneumoniae strains from patients hospitalized for AECBs and two reference strains (ATCC 49619 and R6) were screened for biofilm formation (multi-well plates; 2-11 days of growth). Ipratropium and salbutamol (alone or in combination) were added at concentrations of 1.45 and 7.25 mg/L, respectively (mimicking those in the bronchial tree), and their effects were measured on biofilm formation and modulation of the activity of antibiotics [full antibiotic concentration-dependent effects (pharmacodynamic model)] with a focus on moxifloxacin and solithromycin. Bacterial viability and biomass were measured by the reduction of resazurin and crystal violet staining, respectively. Release of sialic acid (from biofilm) and neuraminidase activity were measured using enzymatic and HPLC-MS detection of sialic acid. All clinical isolates produced biofilms, but with fast disassembly if from patients who had received muscarinic antagonists. Ipratropium caused: (i) reduced biomass formation and faster biofilm disassembly with free sialic acid release; and (ii) a marked improvement of antibiotic activity (bacterial killing and biomass reduction). Salbutamol stimulated neuraminidase activity associated with improved antibiotic killing activity (reversed by zanamivir) but modest biomass reduction. Ipratropium and, to a lesser extent, salbutamol may cooperate with antibiotics for bacterial clearance and disassembly of pneumococcal biofilms. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved

  20. 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.

  1. 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.

  2. 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.

  3. Solar Radiation Measurements at the Chesapeake Bay COVE Site and Comparison With Model

    NASA Astrophysics Data System (ADS)

    Jin, Z.; Charlock, T.; Rutledge, K.

    2001-05-01

    To validate retrievals of flux and albedo in the CERES satellite program, broad-band upwelling and downwelling solar irradiances are measured routinely at the CERES Ocean Validation Experiment (COVE) site 25 km east of the coast of Virginia, near the mouth of the Chesapeake Bay. A full year of observations are compared with simulations from a coupled radiative transfer model. The coupled model treats absorption and scattering by layers of both the atmosphere and the ocean explicitly and consistently, in terms of the inherent optical properties of the air and the sea. Key input parameters for the model include aerosol optical depth, wind speed, and total precipitable water; these are measured at COVE. The modeled total downwelling irradiances, which depend mainly on the atmospheric optical properties, agree well with observations. But the modeled upwelling irradiances (and hence ocean surface albedo), which depend heavily on the the ocean optical properties, are generally less than the observations. The measured upwelling irradiances are strongly influenced by sea state and surface wind, resulting in a seasonal variation of the ocean surface albedo. Candidates to explain the discrepancy of observed and modeled albedo are (1) in-ocean scattering that was not included in the model (i.e., sediments or air bubbles), (2) possible inadequacy of the classical Cox-Munk distribution for the wind speed dependence of sea slopes, and (3) uncertainties in aerosol optical properties. We are presently testing SeaWiFS data as a source for the concentrations of chlorophyl and dissolved organic matter (DOM); and plan to compare the model with available upwelling spectral irradiances and radiances, in addition to the broadband fluxes as described above.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. M9.1 Cascadia Subduction Zone Earthquake Tsunami Inundation Modeling of Sequim Bay and Lopez Island, Washington

    NASA Astrophysics Data System (ADS)

    Lee, C. J.; Cakir, R.; Walsh, T. J.; LeVeque, R. J.; Adams, L. M.; Gonzalez, F. I.

    2016-12-01

    The Strait of Juan de Fuca and adjacent coastal zone are prone to tsunami hazard triggered by a M9+ Cascadia Subduction Zone (CSZ) earthquake. In addition to the numerous tsunami deposits observed on the outer coast, there is geological evidence for nine sandy or muddy tsunami layers deposited in last 2500-year period in a tidal marsh area of Discovery Bay, Northeastern Olympic Peninsula, Washington (Williams et al., 2005, The Holocene, v. 15, no. 1). Thus, it is important to assess the potential tsunami hazard due to a future M9+ CSZ earthquake event that may impact local communities in and near Discovery Bay area . In this study, we conducted tsunami simulations using Clawpack-GeoClaw and the earthquake source scenario M9.1 CSZ, designated as "L1" (Witter et al., 2011, Oregon DOGAMI Special Paper 43). A fine-resolution (1/3 arc-second) NOAA digital elevation model (DEM) was used to provide a high resolution tsunami inundation simulation in Sequim Bay (about 5 miles west of Discovery Bay), Clallam county and Lopez Island, San Juan County. The test gauges, set around major infrastructures and properties, provided estimates of wave height, wave velocity, and wave arrival time. The results will contribute to further improving mitigation planning and emergency response efforts of the counties.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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...

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

    2017-04-01

    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.

  2. Using the regional acid deposition model to determine the nitrogen deposition airshed of the Chesapeake Bay watershed. Book chapter

    SciTech Connect

    Dennis, R.L.

    1995-08-25

    The Regional Acid Deposition Model, RADM, an advanced Eulerian model, is used to develop an estimate of the primary airshed of nitrogen oxide (NOx) emissions that is contributing nitrogen deposition to the Chesapeake Bay watershed. A brief description of RADM together with a summary of the aggregation method used to develop annual average deposition is given. The evaluation background of RADM is summarized. The transport range of the nitrogen affecting deposition, principally the termination product nitric acid, is first established in the model. This range is compared to that determined for sulfur.

  3. A coastal three-dimensional water quality model of nitrogen in Jiaozhou Bay linking field experiments with modelling.

    PubMed

    Lu, Dongliang; Li, Keqiang; Liang, Shengkang; Lin, Guohong; Wang, Xiulin

    2017-01-15

    With anthropogenic changes, the structure and quantity of nitrogen nutrients have changed in coastal ocean, which has dramatically influenced the water quality. Water quality modeling can contribute to the necessary scientific grounding of coastal management. In this paper, some of the dynamic functions and parameters of nitrogen were calibrated based on coastal field experiments covering the dynamic nitrogen processes in Jiaozhou Bay (JZB), including phytoplankton growth, respiration, and mortality; particulate nitrogen degradation; and dissolved organic nitrogen remineralization. The results of the field experiments and box model simulations showed good agreement (RSD=20%±2% and SI=0.77±0.04). A three-dimensional water quality model of nitrogen (3DWQMN) in JZB was improved and the dynamic parameters were updated according to field experiments. The 3DWQMN was validated based on observed data from 2012 to 2013, with good agreement (RSD=27±4%, SI=0.68±0.06, and K=0.48±0.04), which testifies to the model's credibility. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Construction of human naive antibody gene libraries.

    PubMed

    Hust, Michael; Frenzel, André; Meyer, Torsten; Schirrmann, Thomas; Dübel, Stefan

    2012-01-01

    Human antibodies are valuable tools for proteome research and diagnostics. Furthermore, antibodies are a rapidly growing class of therapeutic agents, mainly for inflammation and cancer therapy. The first therapeutic antibodies are of murine origin and were chimerized or humanized. The later-developed antibodies are fully human antibodies. Here, two technologies are competing the hybridoma technology using transgenic mice with human antibody gene loci and antibody phage display. The starting point for the selection of human antibodies against any target is the construction of an antibody phage display gene library.In this review we describe the construction of human naive and immune antibody gene libraries for antibody phage display.

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. 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

  10. Vertical structure of currents in Algeciras Bay (Strait of Gibraltar): implications on oil spill modeling under different typical scenarios

    NASA Astrophysics Data System (ADS)

    Megías Trujillo, Bárbara; Caballero de Frutos, Isabel; López Comi, Laura; Tejedor Alvarez, Begoña.; Izquierdo González, Alfredo; Gonzales Mejías, Carlos Jose; Alvarez Esteban, Óscar; Mañanes Salinas, Rafael; Comerma, Eric

    2010-05-01

    Algeciras Bay constitutes a physical environment of special characteristics, due to its bathymetric configuration and geographical location, at the eastern boundary of the Strait of Gibraltar. Hence, the Bay is subject to the complex hydrodynamics of the Strait of Gibraltar, characterized by a mesotidal, semidiurnal regime and the high density-stratification of the water column due to the presence of the upper Atlantic and the lower Mediterranean (more salty and cold) water layers. In addition, this environment is affected by powerful Easterly and Westerly winds episodes. The intense maritime traffic of oil tankers sailing across the Strait and inside the Bay, together with the presence of an oil refinery at its northern coast, imply high risks of oil spilling inside these waters, and unfortunately it has constituted a matter of usual occurrence through the last decades. The above paragraph clearly manifests the necessity of a detailed knowledge on the Bay's hydrodynamics, and the related system of currents, for a correct management and contingency planning in case of oil spilling in this environment. In order to evaluate the range of affectation of oil spills in the Bay's waters and coasts, the OILMAP oil spill model was used, the currents fields being provided by the three-dimensional, nonlinear, finite-differences, sigma-coordinates, UCA 3D hydrodynamic model. Numerical simulations were carried out for a grid domain extended from the western Strait boundary to the Alboran Sea, having a horizontal spatial resolution of 500 m and 50 sigma-levels in the vertical dimension. The system was forced by the tidal constituents M2 (main semidiurnal) and Z0 (constant or zero-frequency), considering three different typical wind conditions: Easterlies, Westerlies and calm (no wind). The most remarkable results from the numerical 3D simulations of Algeciras Bay's hydrodynamics were: a) the occurrence of opposite tidal currents between the upper Atlantic and lower Mediterranean

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Recommendations for using msBayes to incorporate uncertainty in selecting an abc model prior: a response to oaks et Al.

    PubMed

    Hickerson, Michael J; Stone, Graham N; Lohse, Konrad; Demos, Terrence C; Xie, Xiaoou; Landerer, Cedric; Takebayashi, Naoki

    2014-01-01

    Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that critically undersample nonsimultaneous divergence histories of high likelihood. In a reanalysis of their data on Philippine Island vertebrates, we show how this problem can be circumvented by expanding upon a previously developed procedure that accommodates uncertainty in prior selection using Bayesian model averaging. When these procedures are used, msBayes supports recent divergences without support for synchronous divergence in the Oaks et al. data and we further present a simulation analysis that demonstrates that msBayes can have high power to detect asynchronous divergence under narrower priors for divergence time. Our findings highlight the need for exploration of plausible parameter space and prior sampling efficiency for ABC samplers in high dimensions. We discus potential improvements to msBayes and conclude that when used appropriately with model averaging, msBayes remains an effective and powerful tool. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  18. 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

  19. Specific responsible environmental behavior among boaters on the Chesapeake Bay: a predictive model part II

    Treesearch

    Stuart P. Cottrell; Alan R. Graefe

    1995-01-01

    This paper examines predictors of boater behavior in a specific behavior situation, namely the percentage of raw sewage discharged from recreational vessels in a sanitation pumpout facility on the Chesapeake Bay. Results of a multiple regression analysis show knowledge predicts behavior in specific issue situations. In addition, the more specific the...

  20. 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 ...

  1. 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

  2. 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.

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

    PubMed

    Claggett, Peter R; Jantz, Claire A; Goetz, Scott J; Bisland, Carin

    2004-06-01

    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.

  4. 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.

  5. Naive optics: acting on mirror reflections.

    PubMed

    Hecht, Heiko; Bertamini, Marco; Gamer, Matthias

    2005-10-01

    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 conceptual knowledge. Whereas conceptual errors include the assumption of left-right reversals in mirror images and often blatant extensions of the boundary of mirror space, the perceptual context prevents most such errors. However, a consistent bias to misjudge objects in mirrors too far to the outside is demonstrable in all cases including tasks with real mirrors. The authors present a 2-stage hypothesis consisting of an implicit bias of judging the mirror surface to be turned toward the observer's line of sight followed by a normalization that becomes explicit.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Development of an integrated ecosystem model to determine effectiveness of potential watershed management projects on improving Old Tampa Bay

    Treesearch

    Edward T. Sherwood; Holly Greening; Lizanne Garcia; Kris Kaufman; Tony Janicki; Ray Pribble; Brett Cunningham; Steve Peene; Jim Fitzpatrick; Kellie Dixon; Mike Wessel

    2016-01-01

    The Tampa Bay estuary has undergone a remarkable ecosystem recovery since the 1980s despite continued population growth within the region. However during this time, the Old Tampa Bay (OTB) segment has lagged behind the rest of the Bay’s recovery relative to improvements in overall water quality and seagrass coverage. In 2011, the Tampa Bay Estuary Program, in...

  12. 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

  13. 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. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  14. 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.

  15. 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.

  16. Vertical mixing of high salinity and low salinity in the Bay of Bengal: Results from a coupled high-resolution atmosphere-ocean-wave model.

    NASA Astrophysics Data System (ADS)

    Jensen, T. G.; Wijesekera, H. W.

    2016-02-01

    The Indian Peninsula is a barrier between two distinct water masses in the northern Indian Ocean: The high salinity waters in the Arabian Sea associated with the regional desert climate are separated from the low salinity waters in the moist tropical Bay of Bengal. The two water masses meet in the equatorial band south of Sri Lanka and the boundary between them moves west to east and vice versa as the annual cycle of the Asian monsoon changes from southwest monsoon to northeast monsoon. Vertical mixing in the interior of the Bay of Bengal is required to explain the observed salinity in water masses that leaves the bay. In this work we use a very high resolution fully coupled atmosphere-ocean-wave model, the US Navy's Coupled Ocean-Atmosphere Mesoscale Prediction System (COAMPS). It is applied to the Bay of Bengal region has been run during both Northeast Monsoon (NE) (Dec 2014) and Southwest Monsoon (SW) conditions as part of the Office of Naval Research ASIRI (Air-Sea Interactions in the Northern Indian Ocean) project. Since May 1, 2015, the model has been updated daily to show the 10-m wind speed, currents, sea surface height, sea surface temperature, surface salinity, net surface heat flux into the ocean and significant height and direction of surface waves on a web-site available to ASIRI researchers. We find intrusions of high-salinity water Arabian Sea, that spreads out along isopycnals deeper than 75 m into the Bay of Bengal. The spiciness along isopycnals in the bay shows strong gradients in temperature and salinity in eddies, which indicates that mixing of low salinity water and high salinity water can occur in those regions. We also find that semi-diurnal internal waves generated by tides contribute to the mixing in the Bay of Bengal. We will show model results and observations that emphasize the role of mixing, and the regions where mixing between low and high salinity waters appears to take place.

  17. 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

  18. 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.

  19. 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

  20. Memory T cell–driven differentiation of naive cells impairs adoptive immunotherapy

    PubMed Central

    Klebanoff, Christopher A.; Scott, Christopher D.; Leonardi, Anthony J.; Yamamoto, Tori N.; Cruz, Anthony C.; Ouyang, Claudia; Ramaswamy, Madhu; Roychoudhuri, Rahul; Ji, Yun; Eil, Robert L.; Sukumar, Madhusudhanan; Crompton, Joseph G.; Palmer, Douglas C.; Borman, Zachary A.; Clever, David; Thomas, Stacy K.; Patel, Shashankkumar; Yu, Zhiya; Muranski, Pawel; Liu, Hui; Wang, Ena; Marincola, Francesco M.; Gros, Alena; Gattinoni, Luca; Rosenberg, Steven A.; Siegel, Richard M.; Restifo, Nicholas P.

    2015-01-01

    Adoptive cell transfer (ACT) of purified naive, stem cell memory, and central memory T cell subsets results in superior persistence and antitumor immunity compared with ACT of populations containing more-differentiated effector memory and effector T cells. Despite a clear advantage of the less-differentiated populations, the majority of ACT trials utilize unfractionated T cell subsets. Here, we have challenged the notion that the mere presence of less-differentiated T cells in starting populations used to generate therapeutic T cells is sufficient to convey their desirable attributes. Using both mouse and human cells, we identified a T cell–T cell interaction whereby antigen-experienced subsets directly promote the phenotypic, functional, and metabolic differentiation of naive T cells. This process led to the loss of less-differentiated T cell subsets and resulted in impaired cellular persistence and tumor regression in mouse models following ACT. The T memory–induced conversion of naive T cells was mediated by a nonapoptotic Fas signal, resulting in Akt-driven cellular differentiation. Thus, induction of Fas signaling enhanced T cell differentiation and impaired antitumor immunity, while Fas signaling blockade preserved the antitumor efficacy of naive cells within mixed populations. These findings reveal that T cell subsets can synchronize their differentiation state in a process similar to quorum sensing in unicellular organisms and suggest that disruption of this quorum-like behavior among T cells has potential to enhance T cell–based immunotherapies. PMID:26657860

  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. Molecular Criteria for Defining the Naive Human Pluripotent State.

    PubMed

    Theunissen, Thorold W; Friedli, Marc; He, Yupeng; Planet, Evarist; O'Neil, Ryan C; Markoulaki, Styliani; Pontis, Julien; Wang, Haoyi; Iouranova, Alexandra; Imbeault, Michaël; Duc, Julien; Cohen, Malkiel A; Wert, Katherine J; Castanon, Rosa; Zhang, Zhuzhu; Huang, Yanmei; Nery, Joseph R; Drotar, Jesse; Lungjangwa, Tenzin; Trono, Didier; Ecker, Joseph R; Jaenisch, Rudolf

    2016-10-06

    Recent studies have aimed to convert cultured human pluripotent cells to a naive state, but it remains unclear to what extent the resulting cells recapitulate in vivo naive pluripotency. Here we propose a set of molecular criteria for evaluating the naive human pluripotent state by comparing it to the human embryo. We show that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. We also show that induction of the naive state is accompanied by genome-wide DNA hypomethylation, which is reversible except at imprinted genes, and that the X chromosome status resembles that of the human preimplantation embryo. However, we did not see efficient incorporation of naive human cells into mouse embryos. Overall, the different naive conditions we tested showed varied relationships to human embryonic states based on molecular criteria, providing a backdrop for future analysis of naive human pluripotency. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  4. 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%.

  5. 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.

  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. Higher surface ozone concentrations over the Chesapeake Bay than over the adjacent land: Observations and models from the DISCOVER-AQ and CBODAQ campaigns

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

    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.

  8. 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

  9. Modelling Fluids Associated with Sulfate Veining in Yellowknife Bay, Gale Crater

    NASA Astrophysics Data System (ADS)

    Bridges, J. C.; Schwenzer, S. P.; Berger, G.; Mangold, N.; Wiens, R. C.; Westall, F. W.; Oehler, D. Z.; Leveille, R.; MSL Team

    2013-09-01

    The sedimentary outcrops in Yellowknife Bay, Gale Crater show sulfate veining (Fig. 1). Understanding the fluid chemistry, temperature and pH of the associated fluids is an important part of the aims of Mars Science Laboratory - establishing where conditions were habitable for microbial life. The veins are particularly abundant in the Sheepbed area which contains fine-grained lithified sediments in the lowest part of the exposed Yellowknife stratigraphy. The sulfate identity has been determined from Laser Induced Breakdown Spectroscopy analyses, the latter suggesting Ca sulfate [1]. Visually, the MastCam and Remote Micro-Imager photographs suggest that the veins are near pure sulfate.

  10. 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.

  11. A comparison of acoustic and observed sediment classifications as predictor variables for modelling biotope distributions in Galway Bay, Ireland

    NASA Astrophysics Data System (ADS)

    O'Carroll, Jack P. J.; Kennedy, Robert; Ren, Lei; Nash, Stephen; Hartnett, Michael; Brown, Colin

    2017-10-01

    The INFOMAR (Integrated Mapping For the Sustainable Development of Ireland's Marine Resource) initiative has acoustically mapped and classified a significant proportion of Ireland's Exclusive Economic Zone (EEZ), and is likely to be an important tool in Ireland's efforts to meet the criteria of the MSFD. In this study, open source and relic data were used in combination with new grab survey data to model EUNIS level 4 biotope distributions in Galway Bay, Ireland. The correct prediction rates of two artificial neural networks (ANNs) were compared to assess the effectiveness of acoustic sediment classifications versus sediments that were visually classified by an expert in the field as predictor variables. To test for autocorrelation between predictor variables the RELATE routine with Spearman rank correlation method was used. Optimal models were derived by iteratively removing predictor variables and comparing the correct prediction rates of each model. The models with the highest correct prediction rates were chosen as optimal. The optimal models each used a combination of salinity (binary; 0 = polyhaline and 1 = euhaline), proximity to reef (binary; 0 = within 50 m and 1 = outside 50 m), depth (continuous; metres) and a sediment descriptor (acoustic or observed) as predictor variables. As the status of benthic habitats is required to be assessed under the MSFD the Ecological Status (ES) of the subtidal sediments of Galway Bay was also assessed using the Infaunal Quality Index. The ANN that used observed sediment classes as predictor variables could correctly predict the distribution of biotopes 67% of the time, compared to 63% for the ANN using acoustic sediment classes. Acoustic sediment ANN predictions were affected by local sediment heterogeneity, and the lack of a mixed sediment class. The all-round poor performance of ANNs is likely to be a result of the temporally variable and sparsely distributed data within the study area.

  12. 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.

  13. [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.

  14. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. 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.

  16. Lymphatic endothelial S1P promotes mitochondrial function and survival in naive T cells.

    PubMed

    Mendoza, Alejandra; Fang, Victoria; Chen, Cynthia; Serasinghe, Madhavika; Verma, Akanksha; Muller, James; Chaluvadi, V Sai; Dustin, Michael L; Hla, Timothy; Elemento, Olivier; Chipuk, Jerry E; Schwab, Susan R

    2017-06-01

    Effective adaptive immune responses require a large repertoire of naive T cells that migrate throughout the body, rapidly identifying almost any foreign peptide. Because the production of T cells declines with age, naive T cells must be long-lived. However, it remains unclear how naive T cells survive for years while constantly travelling. The chemoattractant sphingosine 1-phosphate (S1P) guides T cell circulation among secondary lymphoid organs, including spleen, lymph nodes and Peyer's patches, where T cells search for antigens. The concentration of S1P is higher in circulatory fluids than in lymphoid organs, and the S1P1 receptor (S1P1R) directs the exit of T cells from the spleen into blood, and from lymph nodes and Peyer's patches into lymph. Here we show that S1P is essential not only for the circulation of naive T cells, but also for their survival. Using transgenic mouse models, we demonstrate that lymphatic endothelial cells support the survival of T cells by secreting S1P via the transporter SPNS2, that this S1P signals through S1P1R on T cells, and that the requirement for S1P1R is independent of the established role of the receptor in guiding exit from lymph nodes. S1P signalling maintains the mitochondrial content of naive T cells, providing cells with the energy to continue their constant migration. The S1P signalling pathway is being targeted therapeutically to inhibit autoreactive T cell trafficking, and these findings suggest that it may be possible simultaneously to target autoreactive or malignant cell survival.

  17. 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.

  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. 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.

  20. 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

  1. 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

  2. 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

  3. 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

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

    PubMed

    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 modeling

  5. 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.

  6. 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.

  7. 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.

  8. 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...

  9. 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, ...

  10. 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...

  11. A 4DVAR System for the Navy Coastal Ocean Model. Part 1: System Description and Assimilation of Synthetic Observations in Monterey Bay

    DTIC Science & Technology

    2014-06-01

    A 4DVAR System for the Navy Coastal Ocean Model . Part I: System Description and Assimilation of Synthetic Observations in Monterey Bay* HANS NGODOCK...ABSTRACT A 4D variational data assimilation systemwas developed for assimilating ocean observations with the Navy Coastal Ocean Model . It is described in...Navy Coastal Ocean Model (NCOM). NCOM is an opera- tional ocean model (primarily at the Naval Oceano- graphic Office) that has been validated (Martin

  12. 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

  13. 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.

  14. VPAC2 receptor agonist BAY 55-9837 increases SMN protein levels and moderates disease phenotype in severe spinal muscular atrophy mouse models

    PubMed Central

    2014-01-01

    Background Spinal Muscular Atrophy (SMA) is one of the most common inherited causes of infant death and is caused by the loss of functional survival motor neuron (SMN) protein due to mutations or deletion in the SMN1 gene. One of the treatment strategies for SMA is to induce the expression of the protein from the homologous SMN2 gene, a rescuing paralog for SMA. Methods and results Here we demonstrate the promise of pharmacological modulation of SMN2 gene by BAY 55-9837, an agonist of the vasoactive intestinal peptide receptor 2 (VPAC2), a member of G protein coupled receptor family. Treatment with BAY 55-9837 lead to induction of SMN protein levels via activation of MAPK14 or p38 pathway in vitro. Importantly, BAY 55-9837 also ameliorated disease phenotype in severe SMA mouse models. Conclusion Our findings suggest the VPAC2 pathway is a potential SMA therapeutic target. PMID:24405637

  15. 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

  16. Extracellular adenosine regulates naive T cell development and peripheral maintenance

    PubMed Central

    Cekic, Caglar; Sag, Duygu; Day, Yuan-Ji

    2013-01-01

    Adenosine produced as a byproduct of metabolic activity is present in all tissues and produces dose-dependent suppression of TCR signaling. Naive T cell maintenance depends on inhibition of TCR signals by environmental sensors, which are yet to be fully defined. We produced mice with a floxed adenosine A2A receptor (A2AR) gene, Adora2a, and show that either global A2AR deletion or cre-mediated T cell deletion elicits a decline in the number of naive but not memory T cells. A2AR signaling maintains naive T cells in a quiescent state by inhibiting TCR-induced activation of the phosphatidylinositide 3-kinase (PI3K)–AKT pathway, thereby reducing IL-7Rα down-regulation and naive T cell apoptosis. Patterns of IL-7Rα expression on T cells in chimeric mice reconstituted with Adora2a+/+ and Adora2a−/− bone marrow cells suggest that decreased IL-7Rα in naive T cells is a cell-intrinsic consequence of Adora2a deletion. In addition, A2AR expression increases in early thymic T cell development and contributes to progression of double-negative thymic precursors to single-positive thymocytes with increased IL-7Rα expression. Therefore, A2AR signaling regulates T cell development and maintenance to sustain normal numbers of naive T cells in the periphery. PMID:24145516

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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...

  2. Establishing and applying of a coupled individual based model of edible jellyfish(Rhopilema esculentum Kishinouye) releasing in the Liaodong Bay

    NASA Astrophysics Data System (ADS)

    Yin, Liping; Qiao, Fangli

    2017-04-01

    A three-dimensional circulation-surface wave coupled hydrodynamic model coupled with an individual-based jellyfish model was established to investigate the influence of physical process on edible jellyfish releasing stock enhancement in Liaodong Bay. Sensitivity experiments show that the wind intensity and direction have both direct and indirect impacts on the distribution of the jellyfish. When the wind is strong, the surface current in Liaodong Bay has the same direction of the wind. Under the co-effect of the ocean current transport and the surface wind transport, the jellyfish inhabits in the northeast of Liaodong bay, which is consistent with the observation. In the circumstance of weak wind, the circulation is clockwise and the jellyfish will spread around the 5m isobaths following the circulation. Research of the jellyfish distribution shows that the releasing jellyfish will stay in Liaodong bay in its whole life history, hence Liaodong Bay is a quite suitable area for enhancement releasing. The influence of the temperature on releasing region and date is also investigated. The threshold date during 2008 to 2016 is calculated, which is the date when the temperature of water within 10m isobaths in Liaodong Bay rises up to 15oC. In 2010, the threshold date came about one week later while the medusa releasing date remains the same in 2009. As a result, higher fatality rate of medusa caused by the cold water resulted in lower recapture rate in 2010. Therefore, the releasing date and location should be varied according to environmental conditions. The threshold date tends to appear earlier during 2008 to 2016, which suggests an earlier releasing date. In summer, due to the cold water mass intrusion from the south, the releasing date in the north area should be earlier than in the south.

  3. Wetland ecosystem health assessment through integrating remote sensing and inventory data with an assessment model for the Hangzhou Bay, China.

    PubMed

    Sun, Tengteng; Lin, Wenpeng; Chen, Guangsheng; Guo, Pupu; Zeng, Ying

    2016-10-01

    Due to rapid urbanization, industrialization and population growth, wetland area in China has shrunk rapidly and many wetland ecosystems have been reported to degrade during recent decades. Wetland health assessment could raise the public awareness of the wetland condition and guide policy makers to make reasonable and sustainable policies or strategies to protect and restore wetland ecosystems. This study assessed the health levels of wetland ecosystem at the Hangzhou Bay, China using the pressure-state-response (PSR) model through synthesizing remote sensing and statistical data. Ten ecological and social-economic indicators were selected to build the wetland health assessment system. Weights of these indicators and PSR model components as well as the normalized wetland health score were assigned and calculated based on the analytic hierarchy process (AHP) method. We analyzed the spatio-temporal changes in wetland ecosystem health status during the past 20years (1990-2010) from the perspectives of ecosystem pressure, state and response. The results showed that the overall wetland health score was in a fair health level, but displayed large spatial variability in 2010. The wetland health score declined from good health level to fair health level from 1990 to 2000, then restored slightly from 2000 to 2010. Overall, wetland health levels showed a decline from 1990 to 2010 for most administrative units. The temporal change patterns in wetland ecosystem health varied significantly among administrative units. Our results could help to clarify the administrative responsibilities and obligations and provide scientific guides not only for wetland protection but also for restoration and city development planning at the Hangzhou Bay area. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. The initiation and tectonic regimes of the Cenozoic extension in the Bohai Bay Basin, North China revealed by numerical modelling

    NASA Astrophysics Data System (ADS)

    Li, Lu; Qiu, Nansheng

    2017-06-01

    In this study the dynamic aspects of the Cenozoic extension in the Bohai Bay Basin are considered in the context of initial thickness of the crust and lithosphere, tectonic force, strain rate and thermal rheology, which are directly or indirectly estimated from a pure shear extensional model. It is accordingly reasonable to expect that, in the Bohai Bay Basin, the thickness variation could be present prior to the initiation of extension. The extensional deformation is localized by a thickness variation of the crust and lithosphere and the heterogeneity of the initial thickness plays an important role in rifting dynamics. The onset of rifting requires a critical tectonic force (initial tectonic force) to be applied, which then immediately begins to decay gradually. Rifting will only occur when the total effective buoyancy force of the subducting slab reaches a critical level, after a certain amount of subduction taking place. The magnitude of the tectonic force decreases with time in the early phase of rifting, which indicates the weakening due to the increase in geothermal gradient. In order to deform the continental lithosphere within the currently accepted maximum magnitude of the force derived from subducted slab roll-back, the following conditions should be satisfied: (1) the thickness of the continental lithosphere is significantly thin and less than 125 km and (2) the lithosphere has a wet and hot rheology, which provides implications for rheological layering in continental lithosphere. Our results are strongly supported by the ;crème brûlée; model, in which the lower crust and mantle are relatively ductile.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. Atmospheric forcing and marsh dissolved organic matter fluxes: Modeling and observations from a Chesapeake Bay tidal marsh-estuary ecosystem

    NASA Astrophysics Data System (ADS)

    Clark, J. B.; Long, W.; Tzortziou, M.; Neale, P.; Hood, R. R.

    2016-02-01

    Biogeochemical processes on the fringes of estuaries are relatively unconstrained especially in terms of tidal marsh-estuary exchanges and carbon budgets. A three-dimensional biogeochemical simulation can be a valuable tool to augment the observations on these exchanges and can provide insights into the carbon fluxes and organic matter fate. The Finite Volume Community Ocean Model (FVCOM) coupled with CE-QUAL-ICM for water quality is used to simulate the physical and biogeochemical characteristics in the year 2005 for the Kirkpatrick Marsh and Rhode River, a sub-estuary of Chesapeake Bay, MD, USA. The Rhode River hydrodynamic simulation (rhodeFVM) accurately recreates the temperature and salinity in the shallow water sub-estuary and includes a marsh grass drag model that gives realistic marsh water flow. Data analysis from spring 2015 shows a strong negative correlation between marsh creek salinity and DOM fluxes, with wind velocity being an important factor driving large amplitude variation. Model results are consistent with observations revealing sub-tidal variability of marsh creek salinity associated with non-linear interactions between wind velocity and precipitation events. A newly developed three-dimensional marsh DOM model that includes chromophoric DOM provides insights into the spatial and temporal variability of DOM being exported to the estuary.

  18. 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.

  19. Challenges associated with the prediction of tropical storms in the Bay of Bengal when using the WRF model

    NASA Astrophysics Data System (ADS)

    Machineni, N.; Veldore, V.; Mesquita, M. D. S.

    2016-12-01

    Accuracy in predicting tropical cyclones over low lying coastal regions is pivotal for understanding storm tracks and their subsequent impacts. The present study highlights the challenges in predicting the Bay of Bengal (BOB) cyclone "AILA" (during 23rd to 25th May 2009) using the Weather Research and Forecast model, Advanced research core module (WRF-ARW). The model configuration uses a two-way interactive nested domain with 10 km resolution over BOB. Its initial and boundary conditions are driven from the NCEP FNL operational global analysis data at every 6 hours. A total of 74 sensitivity experiments were conducted to test the following factors and levels: a) parametrization schemes: two microphysics and two cumulus physics schemes used to select appropriate combination over study region, b) model domain:including/excluding Himalayas, c) vertical resolution: eight various increasing/decreasing vertical levels have been carried out to evaluate the storm track dependencies on these factors, d) domain size: and increasing (decreasing) the grid points of model domain in east-west direction shows that approximately 50-100 km track difference for every two points. Our results show that, the experiments including the Himalayas provide a better representation of cyclone track and speed. In order to reduce the computational time required to do such tremendous amount of experiment, we hypothesize to use statistical tools of experimental design which can involve all the factors that determine the cyclone tracks. A proper experimental design might provide unbiased results and also we might need less number of experiments.

  20. Challenges associated with the prediction of tropical storms in the Bay of Bengal when using the WRF model

    NASA Astrophysics Data System (ADS)

    Machineni, Nehru; Veldore, Vidyunmala; Mesquita, Michel d. S.

    2017-04-01

    Accuracy in predicting tropical cyclones over low lying coastal regions is pivotal for understanding storm tracks and their subsequent impacts. The present study highlights the challenges in predicting the Bay of Bengal (BOB) cyclone "AILA" (during 23rd to 25th May 2009) using the Weather Research and Forecast model, Advanced research core module (WRF-ARW). The model configuration uses a two-way interactive nested domain with 10 km resolution over BOB. Its initial and boundary conditions are driven from the NCEP FNL operational global analysis data at every 6 hours. A total of 74 sensitivity experiments were conducted to test the following factors and levels: a) parametrization schemes: two microphysics and two cumulus physics schemes used to select appropriate combination over study region, b) model domain:including/excluding Himalayas, c) vertical resolution: eight various increasing/decreasing vertical levels have been carried out to evaluate the storm track dependencies on these factors, d) domain size: and increasing (decreasing) the grid points of model domain in east-west direction shows that approximately 50-100 km track difference for every two points. Our results show that, the experiments including the Himalayas provide a better representation of cyclone track and speed. In order to reduce the computational time required to do such tremendous amount of experiment, we hypothesize to use statistical tools of experimental design which can involve all the factors that determine the cyclone tracks. A proper experimental design might provide unbiased results and also we might need less number of experiments.

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

    PubMed

    Langarizadeh, Mostafa; Moghbeli, Fateme

    2016-10-01

    Naive Bayesian networks (NBNs) are one of the most effective and simplest Bayesian networks for prediction. 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. 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. 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. 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. The method, termed NBNs is proposed and can efficiently construct a prediction model for disease.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Sensitivity of physical parameterizations on prediction of tropical cyclone Nargis over the Bay of Bengal using WRF model

    NASA Astrophysics Data System (ADS)

    Raju, P. V. S.; Potty, Jayaraman; Mohanty, U. C.

    2011-09-01

    Comprehensive sensitivity analyses on physical parameterization schemes of Weather Research Forecast (WRF-ARW core) model have been carried out for the prediction of track and intensity of tropical cyclones by taking the example of cyclone Nargis, which formed over the Bay of Bengal and hit Myanmar on 02 May 2008, causing widespread damages in terms of human and economic losses. The model performances are also evaluated with different initial conditions of 12 h intervals starting from the cyclogenesis to the near landfall time. The initial and boundary conditions for all the model simulations are drawn from the global operational analysis and forecast products of National Center for Environmental Prediction (NCEP-GFS) available for the public at 1° lon/lat resolution. The results of the sensitivity analyses indicate that a combination of non-local parabolic type exchange coefficient PBL scheme of Yonsei University (YSU), deep and shallow convection scheme with mass flux approach for cumulus parameterization (Kain-Fritsch), and NCEP operational cloud microphysics scheme with diagnostic mixed phase processes (Ferrier), predicts better track and intensity as compared against the Joint Typhoon Warning Center (JTWC) estimates. Further, the final choice of the physical parameterization schemes selected from the above sensitivity experiments is used for model integration with different initial conditions. The results reveal that the cyclone track, intensity and time of landfall are well simulated by the model with an average intensity error of about 8 hPa, maximum wind error of 12 m s-1and track error of 77 km. The simulations also show that the landfall time error and intensity error are decreasing with delayed initial condition, suggesting that the model forecast is more dependable when the cyclone approaches the coast. The distribution and intensity of rainfall are also well simulated by the model and comparable with the TRMM estimates.

  15. 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

  16. 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.

  17. 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...

  18. 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...

  19. 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.

  20. SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination.

    PubMed

    Xiao, Shu; Lu, Jia; Sridhar, Bharat; Cao, Xiaoyi; Yu, Pengfei; Zhao, Tianyi; Chen, Chieh-Chun; McDee, Darina; Sloofman, Laura; Wang, Yang; Rivas-Astroza, Marcelo; Telugu, Bhanu Prakash V L; Levasseur, Dana; Zhang, Kang; Liang, Han; Zhao, Jing Crystal; Tanaka, Tetsuya S; Stormo, Gary; Zhong, Sheng

    2017-03-28

    Histone citrullination regulates diverse cellular processes. Here, we report that SMARCAD1 preferentially associates with H3 arginine 26 citrullination (H3R26Cit) peptides present on arrays composed of 384 histone peptides harboring distinct post-transcriptional modifications. Among ten histone modifications assayed by ChIP-seq, H3R26Cit exhibited the most extensive genomewide co-localization with SMARCAD1 binding. Increased Smarcad1 expression correlated with naive pluripotency in pre-implantation embryos. In the presence of LIF, Smarcad1 knockdown (KD) embryonic stem cells lost naive state phenotypes but remained pluripotent, as suggested by morphology, gene expression, histone modifications, alkaline phosphatase activity, energy metabolism, embryoid bodies, teratoma, and chimeras. The majority of H3R26Cit ChIP-seq peaks occupied by SMARCAD1 were associated with increased levels of H3K9me3 in Smarcad1 KD cells. Inhibition of H3Cit induced H3K9me3 at the overlapping regions of H3R26Cit peaks and SMARCAD1 peaks. These data suggest a model in which SMARCAD1 regulates naive pluripotency by interacting with H3R26Cit and suppressing heterochromatin formation. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. Modelling pathogen log10 reduction values achieved by activated sludge treatment using naïve and semi naïve Bayes network models.

    PubMed

    Carvajal, Guido; Roser, David J; Sisson, Scott A; Keegan, Alexandra; Khan, Stuart J

    2015-11-15

    Risk management for wastewater treatment and reuse have led to growing interest in understanding and optimising pathogen reduction during biological treatment processes. However, modelling pathogen reduction is often limited by poor characterization of the relationships between variables and incomplete knowledge of removal mechanisms. The aim of this paper was to assess the applicability of Bayesian belief network models to represent associations between pathogen reduction, and operating conditions and monitoring parameters and predict AS performance. Naïve Bayes and semi-naïve Bayes networks were constructed from an activated sludge dataset including operating and monitoring parameters, and removal efficiencies for two pathogens (native Giardia lamblia and seeded Cryptosporidium parvum) and five native microbial indicators (F-RNA bacteriophage, Clostridium perfringens, Escherichia coli, coliforms and enterococci). First we defined the Bayesian network structures for the tw