Sample records for java dom parsers

  1. Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

    PubMed

    Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart

    2011-08-05

    The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.

  2. Parser Combinators: a Practical Application for Generating Parsers for NMR Data

    PubMed Central

    Fenwick, Matthew; Weatherby, Gerard; Ellis, Heidi JC; Gryk, Michael R.

    2013-01-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a technique for acquiring protein data at atomic resolution and determining the three-dimensional structure of large protein molecules. A typical structure determination process results in the deposition of a large data sets to the BMRB (Bio-Magnetic Resonance Data Bank). This data is stored and shared in a file format called NMR-Star. This format is syntactically and semantically complex making it challenging to parse. Nevertheless, parsing these files is crucial to applying the vast amounts of biological information stored in NMR-Star files, allowing researchers to harness the results of previous studies to direct and validate future work. One powerful approach for parsing files is to apply a Backus-Naur Form (BNF) grammar, which is a high-level model of a file format. Translation of the grammatical model to an executable parser may be automatically accomplished. This paper will show how we applied a model BNF grammar of the NMR-Star format to create a free, open-source parser, using a method that originated in the functional programming world known as “parser combinators”. This paper demonstrates the effectiveness of a principled approach to file specification and parsing. This paper also builds upon our previous work [1], in that 1) it applies concepts from Functional Programming (which is relevant even though the implementation language, Java, is more mainstream than Functional Programming), and 2) all work and accomplishments from this project will be made available under standard open source licenses to provide the community with the opportunity to learn from our techniques and methods. PMID:24352525

  3. MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

    PubMed

    Yang, Chunguang G; Granite, Stephen J; Van Eyk, Jennifer E; Winslow, Raimond L

    2006-11-01

    Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

  4. "gnparser": a powerful parser for scientific names based on Parsing Expression Grammar.

    PubMed

    Mozzherin, Dmitry Y; Myltsev, Alexander A; Patterson, David J

    2017-05-26

    Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role. We refer to this as 'parsing' the name. Parsing categorizes name's elements into those that are stable and those that are prone to change. Names are matched first by combining them according to their stable elements. Matches are then refined by examining their varying elements. This two stage process dramatically improves the number and quality of matches. It is especially useful for the automatic data exchange within the context of "Big Data" in biology. We introduce Global Names Parser (gnparser). It is a Java tool written in Scala language (a language for Java Virtual Machine) to parse scientific names. It is based on a Parsing Expression Grammar. The parser can be applied to scientific names of any complexity. It assigns a semantic meaning (such as genus name, species epithet, rank, year of publication, authorship, annotations, etc.) to all elements of a name. It is able to work with nested structures as in the names of hybrids. gnparser performs with ≈99% accuracy and processes 30 million name-strings/hour per CPU thread. The gnparser library is compatible with Scala, Java, R, Jython, and JRuby. The parser can be used as a command line application, as a socket server, a web-app or as a RESTful HTTP-service. It is released under an Open source MIT license. Global Names Parser (gnparser) is a fast, high precision tool for biodiversity informaticians and biologists working with large numbers of scientific names. It can replace expensive and error

  5. COD::CIF::Parser: an error-correcting CIF parser for the Perl language.

    PubMed

    Merkys, Andrius; Vaitkus, Antanas; Butkus, Justas; Okulič-Kazarinas, Mykolas; Kairys, Visvaldas; Gražulis, Saulius

    2016-02-01

    A syntax-correcting CIF parser, COD::CIF::Parser , is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser , the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.

  6. Syntactic dependency parsers for biomedical-NLP.

    PubMed

    Cohen, Raphael; Elhadad, Michael

    2012-01-01

    Syntactic parsers have made a leap in accuracy and speed in recent years. The high order structural information provided by dependency parsers is useful for a variety of NLP applications. We present a biomedical model for the EasyFirst parser, a fast and accurate parser for creating Stanford Dependencies. We evaluate the models trained in the biomedical domains of EasyFirst and Clear-Parser in a number of task oriented metrics. Both parsers provide stat of the art speed and accuracy in the Genia of over 89%. We show that Clear-Parser excels at tasks relating to negation identification while EasyFirst excels at tasks relating to Named Entities and is more robust to changes in domain.

  7. jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

    PubMed

    Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2012-03-01

    We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. jmzML, an open-source Java API for mzML, the PSI standard for MS data.

    PubMed

    Côté, Richard G; Reisinger, Florian; Martens, Lennart

    2010-04-01

    We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

  9. Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features

    PubMed Central

    Zhang, Yaoyun; Jiang, Min; Wang, Jingqi; Xu, Hua

    2016-01-01

    Semantic role labeling (SRL), which extracts shallow semantic relation representation from different surface textual forms of free text sentences, is important for understanding clinical narratives. Since semantic roles are formed by syntactic constituents in the sentence, an effective parser, as well as an effective syntactic feature set are essential to build a practical SRL system. Our study initiates a formal evaluation and comparison of SRL performance on a clinical text corpus MiPACQ, using three state-of-the-art parsers, the Stanford parser, the Berkeley parser, and the Charniak parser. First, the original parsers trained on the open domain syntactic corpus Penn Treebank were employed. Next, those parsers were retrained on the clinical Treebank of MiPACQ for further comparison. Additionally, state-of-the-art syntactic features from open domain SRL were also examined for clinical text. Experimental results showed that retraining the parsers on clinical Treebank improved the performance significantly, with an optimal F1 measure of 71.41% achieved by the Berkeley parser. PMID:28269926

  10. Tactical Applications (TACAPPS) JavaScript Framework Investigation

    DTIC Science & Technology

    2017-02-01

    frameworks explored were Angular JavaScript (AngularJS), jQuery UI, Meteor, Ember, React JavaScript (ReactJS) and Web Components. The team evaluated the...10 Issues and Risks 11 Web Components 11 Benefits 13 Issues and Risks 13 Conclusions 14 Bibliography 15 Distribution List 19...3 Basic Flux flow 10 4 Shadow DOM tree hierarchy 12 5 Web Components browser support 13 UNCLASSIFIED Approved for

  11. Parsing clinical text: how good are the state-of-the-art parsers?

    PubMed

    Jiang, Min; Huang, Yang; Fan, Jung-wei; Tang, Buzhou; Denny, Josh; Xu, Hua

    2015-01-01

    Parsing, which generates a syntactic structure of a sentence (a parse tree), is a critical component of natural language processing (NLP) research in any domain including medicine. Although parsers developed in the general English domain, such as the Stanford parser, have been applied to clinical text, there are no formal evaluations and comparisons of their performance in the medical domain. In this study, we investigated the performance of three state-of-the-art parsers: the Stanford parser, the Bikel parser, and the Charniak parser, using following two datasets: (1) A Treebank containing 1,100 sentences that were randomly selected from progress notes used in the 2010 i2b2 NLP challenge and manually annotated according to a Penn Treebank based guideline; and (2) the MiPACQ Treebank, which is developed based on pathology notes and clinical notes, containing 13,091 sentences. We conducted three experiments on both datasets. First, we measured the performance of the three state-of-the-art parsers on the clinical Treebanks with their default settings. Then we re-trained the parsers using the clinical Treebanks and evaluated their performance using the 10-fold cross validation method. Finally we re-trained the parsers by combining the clinical Treebanks with the Penn Treebank. Our results showed that the original parsers achieved lower performance in clinical text (Bracketing F-measure in the range of 66.6%-70.3%) compared to general English text. After retraining on the clinical Treebank, all parsers achieved better performance, with the best performance from the Stanford parser that reached the highest Bracketing F-measure of 73.68% on progress notes and 83.72% on the MiPACQ corpus using 10-fold cross validation. When the combined clinical Treebanks and Penn Treebank was used, of the three parsers, the Charniak parser achieved the highest Bracketing F-measure of 73.53% on progress notes and the Stanford parser reached the highest F-measure of 84.15% on the Mi

  12. Parsing clinical text: how good are the state-of-the-art parsers?

    PubMed Central

    2015-01-01

    Background Parsing, which generates a syntactic structure of a sentence (a parse tree), is a critical component of natural language processing (NLP) research in any domain including medicine. Although parsers developed in the general English domain, such as the Stanford parser, have been applied to clinical text, there are no formal evaluations and comparisons of their performance in the medical domain. Methods In this study, we investigated the performance of three state-of-the-art parsers: the Stanford parser, the Bikel parser, and the Charniak parser, using following two datasets: (1) A Treebank containing 1,100 sentences that were randomly selected from progress notes used in the 2010 i2b2 NLP challenge and manually annotated according to a Penn Treebank based guideline; and (2) the MiPACQ Treebank, which is developed based on pathology notes and clinical notes, containing 13,091 sentences. We conducted three experiments on both datasets. First, we measured the performance of the three state-of-the-art parsers on the clinical Treebanks with their default settings. Then we re-trained the parsers using the clinical Treebanks and evaluated their performance using the 10-fold cross validation method. Finally we re-trained the parsers by combining the clinical Treebanks with the Penn Treebank. Results Our results showed that the original parsers achieved lower performance in clinical text (Bracketing F-measure in the range of 66.6%-70.3%) compared to general English text. After retraining on the clinical Treebank, all parsers achieved better performance, with the best performance from the Stanford parser that reached the highest Bracketing F-measure of 73.68% on progress notes and 83.72% on the MiPACQ corpus using 10-fold cross validation. When the combined clinical Treebanks and Penn Treebank was used, of the three parsers, the Charniak parser achieved the highest Bracketing F-measure of 73.53% on progress notes and the Stanford parser reached the highest F

  13. Benchmarking natural-language parsers for biological applications using dependency graphs.

    PubMed

    Clegg, Andrew B; Shepherd, Adrian J

    2007-01-25

    Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance is difficult because differences in linguistic convention can falsely appear to be errors. We present a method for evaluating their accuracy using an intermediate representation based on dependency graphs, in which the semantic relationships important in most information extraction tasks are closer to the surface. We also demonstrate how this method can be easily tailored to various application-driven criteria. Using the GENIA corpus as a gold standard, we tested four open-source parsers which have been used in bioinformatics projects. We first present overall performance measures, and test the two leading tools, the Charniak-Lease and Bikel parsers, on subtasks tailored to reflect the requirements of a system for extracting gene expression relationships. These two tools clearly outperform the other parsers in the evaluation, and achieve accuracy levels comparable to or exceeding native dependency parsers on similar tasks in previous biological evaluations. Evaluating using dependency graphs allows parsers to be tested easily on criteria chosen according to the semantics of particular biological applications, drawing attention to important mistakes and soaking up many insignificant differences that would otherwise be reported as errors. Generating high-accuracy dependency graphs from the output of phrase-structure parsers also provides access to the more detailed syntax trees that are used in several natural-language processing techniques.

  14. Benchmarking natural-language parsers for biological applications using dependency graphs

    PubMed Central

    Clegg, Andrew B; Shepherd, Adrian J

    2007-01-01

    Background Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance is difficult because differences in linguistic convention can falsely appear to be errors. We present a method for evaluating their accuracy using an intermediate representation based on dependency graphs, in which the semantic relationships important in most information extraction tasks are closer to the surface. We also demonstrate how this method can be easily tailored to various application-driven criteria. Results Using the GENIA corpus as a gold standard, we tested four open-source parsers which have been used in bioinformatics projects. We first present overall performance measures, and test the two leading tools, the Charniak-Lease and Bikel parsers, on subtasks tailored to reflect the requirements of a system for extracting gene expression relationships. These two tools clearly outperform the other parsers in the evaluation, and achieve accuracy levels comparable to or exceeding native dependency parsers on similar tasks in previous biological evaluations. Conclusion Evaluating using dependency graphs allows parsers to be tested easily on criteria chosen according to the semantics of particular biological applications, drawing attention to important mistakes and soaking up many insignificant differences that would otherwise be reported as errors. Generating high-accuracy dependency graphs from the output of phrase-structure parsers also provides access to the more detailed syntax trees that are used in several natural-language processing techniques. PMID:17254351

  15. The parser generator as a general purpose tool

    NASA Technical Reports Server (NTRS)

    Noonan, R. E.; Collins, W. R.

    1985-01-01

    The parser generator has proven to be an extremely useful, general purpose tool. It can be used effectively by programmers having only a knowledge of grammars and no training at all in the theory of formal parsing. Some of the application areas for which a table-driven parser can be used include interactive, query languages, menu systems, translators, and programming support tools. Each of these is illustrated by an example grammar.

  16. Storing files in a parallel computing system based on user-specified parser function

    DOEpatents

    Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Manzanares, Adam; Torres, Aaron

    2014-10-21

    Techniques are provided for storing files in a parallel computing system based on a user-specified parser function. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a parser from the distributed application for processing the plurality of files prior to storage; and storing one or more of the plurality of files in one or more storage nodes of the parallel computing system based on the processing by the parser. The plurality of files comprise one or more of a plurality of complete files and a plurality of sub-files. The parser can optionally store only those files that satisfy one or more semantic requirements of the parser. The parser can also extract metadata from one or more of the files and the extracted metadata can be stored with one or more of the plurality of files and used for searching for files.

  17. PDB file parser and structure class implemented in Python.

    PubMed

    Hamelryck, Thomas; Manderick, Bernard

    2003-11-22

    The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

  18. Policy-Based Management Natural Language Parser

    NASA Technical Reports Server (NTRS)

    James, Mark

    2009-01-01

    The Policy-Based Management Natural Language Parser (PBEM) is a rules-based approach to enterprise management that can be used to automate certain management tasks. This parser simplifies the management of a given endeavor by establishing policies to deal with situations that are likely to occur. Policies are operating rules that can be referred to as a means of maintaining order, security, consistency, or other ways of successfully furthering a goal or mission. PBEM provides a way of managing configuration of network elements, applications, and processes via a set of high-level rules or business policies rather than managing individual elements, thus switching the control to a higher level. This software allows unique management rules (or commands) to be specified and applied to a cross-section of the Global Information Grid (GIG). This software embodies a parser that is capable of recognizing and understanding conversational English. Because all possible dialect variants cannot be anticipated, a unique capability was developed that parses passed on conversation intent rather than the exact way the words are used. This software can increase productivity by enabling a user to converse with the system in conversational English to define network policies. PBEM can be used in both manned and unmanned science-gathering programs. Because policy statements can be domain-independent, this software can be applied equally to a wide variety of applications.

  19. Processing of ICARTT Data Files Using Fuzzy Matching and Parser Combinators

    NASA Technical Reports Server (NTRS)

    Rutherford, Matthew T.; Typanski, Nathan D.; Wang, Dali; Chen, Gao

    2014-01-01

    In this paper, the task of parsing and matching inconsistent, poorly formed text data through the use of parser combinators and fuzzy matching is discussed. An object-oriented implementation of the parser combinator technique is used to allow for a relatively simple interface for adapting base parsers. For matching tasks, a fuzzy matching algorithm with Levenshtein distance calculations is implemented to match string pair, which are otherwise difficult to match due to the aforementioned irregularities and errors in one or both pair members. Used in concert, the two techniques allow parsing and matching operations to be performed which had previously only been done manually.

  20. Designing a Constraint Based Parser for Sanskrit

    NASA Astrophysics Data System (ADS)

    Kulkarni, Amba; Pokar, Sheetal; Shukl, Devanand

    Verbal understanding (śā bdabodha) of any utterance requires the knowledge of how words in that utterance are related to each other. Such knowledge is usually available in the form of cognition of grammatical relations. Generative grammars describe how a language codes these relations. Thus the knowledge of what information various grammatical relations convey is available from the generation point of view and not the analysis point of view. In order to develop a parser based on any grammar one should then know precisely the semantic content of the grammatical relations expressed in a language string, the clues for extracting these relations and finally whether these relations are expressed explicitly or implicitly. Based on the design principles that emerge from this knowledge, we model the parser as finding a directed Tree, given a graph with nodes representing the words and edges representing the possible relations between them. Further, we also use the Mīmā ṃsā constraint of ākā ṅkṣā (expectancy) to rule out non-solutions and sannidhi (proximity) to prioritize the solutions. We have implemented a parser based on these principles and its performance was found to be satisfactory giving us a confidence to extend its functionality to handle the complex sentences.

  1. A Protocol for Annotating Parser Differences. Research Report. ETS RR-16-02

    ERIC Educational Resources Information Center

    Bruno, James V.; Cahill, Aoife; Gyawali, Binod

    2016-01-01

    We present an annotation scheme for classifying differences in the outputs of syntactic constituency parsers when a gold standard is unavailable or undesired, as in the case of texts written by nonnative speakers of English. We discuss its automated implementation and the results of a case study that uses the scheme to choose a parser best suited…

  2. JBioWH: an open-source Java framework for bioinformatics data integration

    PubMed Central

    Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

    2013-01-01

    The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

  3. JBioWH: an open-source Java framework for bioinformatics data integration.

    PubMed

    Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

    2013-01-01

    The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

  4. Linking Parser Development to Acquisition of Syntactic Knowledge

    ERIC Educational Resources Information Center

    Omaki, Akira; Lidz, Jeffrey

    2015-01-01

    Traditionally, acquisition of syntactic knowledge and the development of sentence comprehension behaviors have been treated as separate disciplines. This article reviews a growing body of work on the development of incremental sentence comprehension mechanisms and discusses how a better understanding of the developing parser can shed light on two…

  5. GazeParser: an open-source and multiplatform library for low-cost eye tracking and analysis.

    PubMed

    Sogo, Hiroyuki

    2013-09-01

    Eye movement analysis is an effective method for research on visual perception and cognition. However, recordings of eye movements present practical difficulties related to the cost of the recording devices and the programming of device controls for use in experiments. GazeParser is an open-source library for low-cost eye tracking and data analysis; it consists of a video-based eyetracker and libraries for data recording and analysis. The libraries are written in Python and can be used in conjunction with PsychoPy and VisionEgg experimental control libraries. Three eye movement experiments are reported on performance tests of GazeParser. These showed that the means and standard deviations for errors in sampling intervals were less than 1 ms. Spatial accuracy ranged from 0.7° to 1.2°, depending on participant. In gap/overlap tasks and antisaccade tasks, the latency and amplitude of the saccades detected by GazeParser agreed with those detected by a commercial eyetracker. These results showed that the GazeParser demonstrates adequate performance for use in psychological experiments.

  6. Towards automated processing of clinical Finnish: sublanguage analysis and a rule-based parser.

    PubMed

    Laippala, Veronika; Ginter, Filip; Pyysalo, Sampo; Salakoski, Tapio

    2009-12-01

    In this paper, we present steps taken towards more efficient automated processing of clinical Finnish, focusing on daily nursing notes in a Finnish Intensive Care Unit (ICU). First, we analyze ICU Finnish as a sublanguage, identifying its specific features facilitating, for example, the development of a specialized syntactic analyser. The identified features include frequent omission of finite verbs, limitations in allowed syntactic structures, and domain-specific vocabulary. Second, we develop a formal grammar and a parser for ICU Finnish, thus providing better tools for the development of further applications in the clinical domain. The grammar is implemented in the LKB system in a typed feature structure formalism. The lexicon is automatically generated based on the output of the FinTWOL morphological analyzer adapted to the clinical domain. As an additional experiment, we study the effect of using Finnish constraint grammar to reduce the size of the lexicon. The parser construction thus makes efficient use of existing resources for Finnish. The grammar currently covers 76.6% of ICU Finnish sentences, producing highly accurate best-parse analyzes with F-score of 91.1%. We find that building a parser for the highly specialized domain sublanguage is not only feasible, but also surprisingly efficient, given an existing morphological analyzer with broad vocabulary coverage. The resulting parser enables a deeper analysis of the text than was previously possible.

  7. The parser doesn't ignore intransitivity, after all

    PubMed Central

    Staub, Adrian

    2015-01-01

    Several previous studies (Adams, Clifton, & Mitchell, 1998; Mitchell, 1987; van Gompel & Pickering, 2001) have explored the question of whether the parser initially analyzes a noun phrase that follows an intransitive verb as the verb's direct object. Three eyetracking experiments examined this issue in more detail. Experiment 1 strongly replicated the finding (van Gompel & Pickering, 2001) that readers experience difficulty on this noun phrase in normal reading, and found that this difficulty occurs even with a class of intransitive verbs for which a direct object is categorically prohibited. Experiment 2, however, demonstrated that this effect is not due to syntactic misanalysis, but is instead due to disruption that occurs when a comma is absent at a subordinate clause/main clause boundary. Exploring a different construction, Experiment 3 replicated the finding (Pickering & Traxler, 2003; Traxler & Pickering, 1996) that when a noun phrase “filler” is an implausible direct object for an optionally transitive relative clause verb, processing difficulty results; however, there was no evidence for such difficulty when the relative clause verb was strictly intransitive. Taken together, the three experiments undermine the support for the claim that the parser initially ignores a verb's subcategorization restrictions. PMID:17470005

  8. Software Development Of XML Parser Based On Algebraic Tools

    NASA Astrophysics Data System (ADS)

    Georgiev, Bozhidar; Georgieva, Adriana

    2011-12-01

    In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

  9. Vulnerabilities in Bytecode Removed by Analysis, Nuanced Confinement and Diversification (VIBRANCE)

    DTIC Science & Technology

    2015-06-01

    VIBRANCE tool starts with a vulnerable Java application and automatically hardens it against SQL injection, OS command injection, file path traversal...7 2.2 Java Front End...7 2.2.2 Java Byte Code Parser

  10. ImageParser: a tool for finite element generation from three-dimensional medical images

    PubMed Central

    Yin, HM; Sun, LZ; Wang, G; Yamada, T; Wang, J; Vannier, MW

    2004-01-01

    Background The finite element method (FEM) is a powerful mathematical tool to simulate and visualize the mechanical deformation of tissues and organs during medical examinations or interventions. It is yet a challenge to build up an FEM mesh directly from a volumetric image partially because the regions (or structures) of interest (ROIs) may be irregular and fuzzy. Methods A software package, ImageParser, is developed to generate an FEM mesh from 3-D tomographic medical images. This software uses a semi-automatic method to detect ROIs from the context of image including neighboring tissues and organs, completes segmentation of different tissues, and meshes the organ into elements. Results The ImageParser is shown to build up an FEM model for simulating the mechanical responses of the breast based on 3-D CT images. The breast is compressed by two plate paddles under an overall displacement as large as 20% of the initial distance between the paddles. The strain and tangential Young's modulus distributions are specified for the biomechanical analysis of breast tissues. Conclusion The ImageParser can successfully exact the geometry of ROIs from a complex medical image and generate the FEM mesh with customer-defined segmentation information. PMID:15461787

  11. Adding a Medical Lexicon to an English Parser

    PubMed Central

    Szolovits, Peter

    2003-01-01

    We present a heuristic method to map lexical (syntactic) information from one lexicon to another, and apply the technique to augment the lexicon of the Link Grammar Parser with an enormous medical vocabulary drawn from the Specialist lexicon developed by the National Library of Medicine. This paper presents and justifies the mapping method and addresses technical problems that have to be overcome. It illustrates the utility of the method with respect to a large corpus of emergency department notes. PMID:14728251

  12. Transformations of DOM in forested catchments: the pathways of DOM from litter and soil to river export

    NASA Astrophysics Data System (ADS)

    Lajtha, K.; Yano, Y.; Crow, S.; Kaushal, S.

    2006-12-01

    Although the quality and quantity of DOM ultimately derives from plant detritus and soils in watersheds, three is substantial alteration of DOM as it passes from litter through the terrestrial landscape. As DOM is generated from plant and microbial detritus and processing, different fractions may be lost via respiration, form quasi-stable soil organic matter, or be temporarily sorbed to soil minerals. We followed the fate of DOC and DON from forested plots with experimentally altered detritus loads to determine the relative roles of original plant litter chemistry and soil transformations. Our study site was the DIRT (Detrital Input and Removal Treatment) plots at the H.J. Andrews Experimental Forest in Oregon, where treatments include detrital additions (wood vs. needle litter), litter exclusion, and root exclusions. Fractionation of detritus leachate solutions demonstrated significant differences in DOC chemistry from different detrital sources. Root leachates produced high quantities of hydrophilic neutral DOC, a fraction rich in labile sugars and polysaccharides; young wood extracts produced higher quantities of weak hydrophobic acids and hydrophobic neutrals (longer chain hydrocarbons); older wood had lower quantities of most labile constituents but was rich in strong hydrophobic acids. Although laboratory extracts of different litter types showed differences in DOM chemistry, soil solutions collected just below the forest floor from the differing detrital treatments were remarkably uniform and poor in labile constituents, suggesting microbial equalization of DOM leachate in the field. DOM quality and concentrations changed significantly with passage through soil profiles. DOC concentrations decreased through the soil profile in all plots to a greater degree than did dissolved organic nitrogen (DON), most likely due to preferential sorption of high C:N hydrophobic dissolved organic matter (DOM) in upper horizons. Percent hydrophobic DOM decreased significantly

  13. Tracking the evolution of stream DOM source during storm events using end member mixing analysis based on DOM quality

    NASA Astrophysics Data System (ADS)

    Yang, Liyang; Chang, Soon-Woong; Shin, Hyun-Sang; Hur, Jin

    2015-04-01

    The source of river dissolved organic matter (DOM) during storm events has not been well constrained, which is critical in determining the quality and reactivity of DOM. This study assessed temporal changes in the contributions of four end members (weeds, leaf litter, soil, and groundwater), which exist in a small forested watershed (the Ehwa Brook, South Korea), to the stream DOM during two storm events, using end member mixing analysis (EMMA) based on spectroscopic properties of DOM. The instantaneous export fluxes of dissolved organic carbon (DOC), chromophoric DOM (CDOM), and fluorescent components were all enhanced during peak flows. The DOC concentration increased with the flow rate, while CDOM and humic-like fluorescent components were diluted around the peak flows. Leaf litter was dominant for the DOM source in event 2 with a higher rainfall, although there were temporal variations in the contributions of the four end members to the stream DOM for both events. The contribution of leaf litter peaked while that of deeper soils decreased to minima at peak flows. Our results demonstrated that EMMA based on DOM properties could be used to trace the DOM source, which is of fundamental importance for understanding the factors responsible for river DOM dynamics during storm events.

  14. Parsley: a Command-Line Parser for Astronomical Applications

    NASA Astrophysics Data System (ADS)

    Deich, William

    Parsley is a sophisticated keyword + value parser, packaged as a library of routines that offers an easy method for providing command-line arguments to programs. It makes it easy for the user to enter values, and it makes it easy for the programmer to collect and validate the user's entries. Parsley is tuned for astronomical applications: for example, dates entered in Julian, Modified Julian, calendar, or several other formats are all recognized without special effort by the user or by the programmer; angles can be entered using decimal degrees or dd:mm:ss; time-like intervals as decimal hours, hh:mm:ss, or a variety of other units. Vectors of data are accepted as readily as scalars.

  15. Java, Indonesia

    NASA Image and Video Library

    1996-01-20

    STS072-737-012 (11-20 Jan. 1996) --- The astronauts photographed this view of Java, an Indonesian island. Java lies between the Java Sea at top and the Indian Ocean at bottom (north is located at top center). A line of volcanoes on the southern edge of the island, trending from central to eastern areas, is highlighted by a ring of clouds. Off the southern coast of Java is the Java Trench where the Australian plate, to the south, is diving under the Eurasia plate to the north. According to anthropologists, Java has one of the highest populations in Indonesia because the soil is enriched by volcanic ash. Merapi volcano, at left edge, second volcano to the right, rises to 9,550 feet and erupts frequently. Madura Island, partially obscured by clouds, can be seen on the upper eastern end of Java.

  16. GBParsy: a GenBank flatfile parser library with high speed.

    PubMed

    Lee, Tae-Ho; Kim, Yeon-Ki; Nahm, Baek Hie

    2008-07-25

    GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory. We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5-100x faster than current parsers in benchmark tests. GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.

  17. Dom34 Links Translation to Protein O-mannosylation.

    PubMed

    van Wijlick, Lasse; Geissen, René; Hilbig, Jessica S; Lagadec, Quentin; Cantero, Pilar D; Pfeifer, Eugen; Juchimiuk, Mateusz; Kluge, Sven; Wickert, Stephan; Alepuz, Paula; Ernst, Joachim F

    2016-10-01

    In eukaryotes, Dom34 upregulates translation by securing levels of activatable ribosomal subunits. We found that in the yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans, Dom34 interacts genetically with Pmt1, a major isoform of protein O-mannosyltransferase. In C. albicans, lack of Dom34 exacerbated defective phenotypes of pmt1 mutants, while they were ameliorated by Dom34 overproduction that enhanced Pmt1 protein but not PMT1 transcript levels. Translational effects of Dom34 required the 5'-UTR of the PMT1 transcript, which bound recombinant Dom34 directly at a CA/AC-rich sequence and regulated in vitro translation. Polysomal profiling revealed that Dom34 stimulates general translation moderately, but that it is especially required for translation of transcripts encoding Pmt isoforms 1, 4 and 6. Because defective protein N- or O-glycosylation upregulates transcription of PMT genes, it appears that Dom34-mediated specific translational upregulation of the PMT transcripts optimizes cellular responses to glycostress. Its translational function as an RNA binding protein acting at the 5'-UTR of specific transcripts adds another facet to the known ribosome-releasing functions of Dom34 at the 3'-UTR of transcripts.

  18. Dom34 Links Translation to Protein O-mannosylation

    PubMed Central

    van Wijlick, Lasse; Geissen, René; Hilbig, Jessica S.; Lagadec, Quentin; Cantero, Pilar D.; Juchimiuk, Mateusz; Kluge, Sven; Wickert, Stephan; Alepuz, Paula; Ernst, Joachim F.

    2016-01-01

    In eukaryotes, Dom34 upregulates translation by securing levels of activatable ribosomal subunits. We found that in the yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans, Dom34 interacts genetically with Pmt1, a major isoform of protein O-mannosyltransferase. In C. albicans, lack of Dom34 exacerbated defective phenotypes of pmt1 mutants, while they were ameliorated by Dom34 overproduction that enhanced Pmt1 protein but not PMT1 transcript levels. Translational effects of Dom34 required the 5′-UTR of the PMT1 transcript, which bound recombinant Dom34 directly at a CA/AC-rich sequence and regulated in vitro translation. Polysomal profiling revealed that Dom34 stimulates general translation moderately, but that it is especially required for translation of transcripts encoding Pmt isoforms 1, 4 and 6. Because defective protein N- or O-glycosylation upregulates transcription of PMT genes, it appears that Dom34-mediated specific translational upregulation of the PMT transcripts optimizes cellular responses to glycostress. Its translational function as an RNA binding protein acting at the 5′-UTR of specific transcripts adds another facet to the known ribosome-releasing functions of Dom34 at the 3′-UTR of transcripts. PMID:27768707

  19. Disambiguating the species of biomedical named entities using natural language parsers

    PubMed Central

    Wang, Xinglong; Tsujii, Jun'ichi; Ananiadou, Sophia

    2010-01-01

    Motivation: Text mining technologies have been shown to reduce the laborious work involved in organizing the vast amount of information hidden in the literature. One challenge in text mining is linking ambiguous word forms to unambiguous biological concepts. This article reports on a comprehensive study on resolving the ambiguity in mentions of biomedical named entities with respect to model organisms and presents an array of approaches, with focus on methods utilizing natural language parsers. Results: We build a corpus for organism disambiguation where every occurrence of protein/gene entity is manually tagged with a species ID, and evaluate a number of methods on it. Promising results are obtained by training a machine learning model on syntactic parse trees, which is then used to decide whether an entity belongs to the model organism denoted by a neighbouring species-indicating word (e.g. yeast). The parser-based approaches are also compared with a supervised classification method and results indicate that the former are a more favorable choice when domain portability is of concern. The best overall performance is obtained by combining the strengths of syntactic features and supervised classification. Availability: The corpus and demo are available at http://www.nactem.ac.uk/deca_details/start.cgi, and the software is freely available as U-Compare components (Kano et al., 2009): NaCTeM Species Word Detector and NaCTeM Species Disambiguator. U-Compare is available at http://-compare.org/ Contact: xinglong.wang@manchester.ac.uk PMID:20053840

  20. Adsorptive fractionation of dissolved organic matter (DOM) by carbon nanotubes.

    PubMed

    Engel, Maya; Chefetz, Benny

    2015-02-01

    Dissolved organic matter (DOM) and carbon nanotubes are introduced into aquatic environments. Thus, it is important to elucidate whether their interaction affects DOM amount and composition. In this study, the composition of DOM, before and after interactions with single-walled carbon nanotubes (SWCNTs), was measured and the adsorption affinity of the individual structural fractions of DOM to SWCNTs was investigated. Adsorption of DOM to SWCNTs was dominated by the hydrophobic acid fraction, resulting in relative enhancement of the hydrophilic character of non-adsorbed DOM. The preferential adsorption of the HoA fraction was concentration-dependent, increasing with increasing concentration. Adsorption affinities of bulk DOM calculated as the normalized sum of affinities of the individual structural fractions were similar to the measured affinities, suggesting that the structural fractions of DOM act as independent adsorbates. The altered DOM composition may affect the nature and reactivity of DOM in aquatic environments polluted with carbon nanotubes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Dissolved organic matter (DOM) in pore water of Arctic Ocean sediments: linking DOM molecular composition with microbial community structure

    NASA Astrophysics Data System (ADS)

    Rossel, P. E.; Bienhold, C.; Boetius, A.; Dittmar, T.

    2016-02-01

    Marine organic matter (OM) that sinks from surface waters to the seafloor is the energy and carbon source for benthic communities. These communities produce dissolved organic matter (DOM) in the process of remineralization, enriching the sediment porewater with fresh DOM compounds. In the Arctic Ocean, primary production is limited by nutrients and light and is thus strongly influenced by sea ice cover. Ice cover is expected to further decrease due to global warming, which may have important consequences for primary production and the quantity and quality of OM exported to the seafloor. This study focused on: 1) the molecular composition of the DOM in sediment pore waters of the deep Eurasian Arctic basins, 2) whether there is any relation between Arctic Ocean ice cover and DOM composition and 3) whether the DOM composition correlates with microbial community structure. Molecular data, obtained via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry, were statistically correlated with environmental parameters. The productive ice margin stations showed higher abundances of molecular formulae of peptides, unsaturated aliphatics and saturated fatty acids. This molecular trend is indicative of fresh OM and phytodetritus deposition, compared to the northernmost, ice-covered stations which had stronger aromatic signals. Benthic bacterial community structure, as assessed with the fingerprinting method ARISA, was significantly correlated with DOM molecular composition. Further analyses using Illumina next-generation sequencing will enable the taxonomic identification of specific bacterial groups and their interdependence with DOM compounds. This study contributes to the understanding of the coupling between Arctic Ocean productivity and its depositional regime, and provides first insights into potential links between microbial community structure and DOM molecular composition in Arctic sediments

  2. Tracing the origin of dissolved organic matter (DOM) in subterranean estuaries using colored DOM and amino acids

    NASA Astrophysics Data System (ADS)

    Kim, T.; Kwon, E.; Kim, G.

    2011-12-01

    In order to determine the origin of dissolved organic matter (DOM) in the subterranean estuary (STE), the mixing zone of fresh terrestrial groundwater and recirculating seawater in a coastal permeable aquifer, we conducted water sampling from two STEs with different geological settings: (1) Jeju Island beaches (Hwasun and Samyang), which are composed of volcanic rocks and sandy sediments, and (2) Hampyeong beach, which is located in a large intertidal, sandy flat zone. The distributions of salinity, total hydrolysable amino acids (THAA), dissolved organic carbon (DOC), and colored DOM (CDOM) were measured for groundwater samples in these STEs. In the Hwasun STE, the humic-like peak decreases with increasing salinity, whereas the protein-like peak does not show a clear relationship with salinity. In contrast, in the Samyang STE, both humic-like peak and protein-like peak increase with increasing salinity. These contrasting results indicate that DOM in the Hwasun STE originates mainly from terrestrial inputs, while that in the Samyang STE originates mainly from biological and/or microbial activities. In the Hampyeong STE, we observed good correlations among the biodegradation index, alanine D/L ratios, THAA concentrations, DOC, and CDOM index (both humic-like and protein-like). Together with their geographical distribution patterns, these correlations indicate that DOM in the Hampyeong STE is mainly derived from marine sediments in the course of seawater recirculation. Our study shows that CDOM and amino acids are excellent tracers of DOM in the STE where DOM is derived from diverse sources.

  3. Illuminating the dark side of DOM: A bottom up approach to understanding the structure and composition of DOM.

    NASA Astrophysics Data System (ADS)

    Zito, P.; Tarr, M. A.; Spencer, R. G.; Podgorski, D. C.

    2017-12-01

    Dissolved organic matter (DOM) is one of the most complex natural mixtures on Earth. It is generally comprised of hydrocarbons incorporating a diverse subset of oxygen-containing functional groups along with a small amount of nitrogen, sulfur and phosphorous heteroatoms all of which make it very difficult to chromatographically separate. The only way to directly characterize and quantify these structural and compositional changes is by separating the DOM continuum into defined bins of structure and chemistry. In this study, we take an alternate bottom-up approach that utilizes petroleum to work toward identifying the molecular structures of DOM. Although petroleum is the most structurally diverse mixture in nature, it is almost exclusively comprised of hydrocarbons with only trace quantities of heteroatoms, including oxygen. Here, crude oil was chromatographically separated into bins based on the number of aromatic rings to be used as a starting carbon source. Photochemically produced DOM from these aromatic ring bins provides unique opportunities to gain insight in the compositional controls associated with transport, processing and fate of DOM in natural systems. Here, we present EEMs data from individual ring fractions that were subjected to 24 hours of sunlight to use as a model to fingerprint specific aromatic regions in the DOM fraction. Results illustrate that the 1-, 2-, 3-, 4- and 5- ring fractions exhibit a wide range of structurally dependent excitation and emission spectra. A well-known red-shift in the emission and excitation occurs as the number of rings increase. In order to understand changes in the elemental composition of the data, ultra high-resolution mass spectrometry was used to obtain molecular level information. Together, these data will provide a tool to help understand the relationship of the composition and structure of DOM released into the environment in terms of aromaticity. It is well known that aromaticity is an important indicator

  4. Formation of nanocolloidal metacinnabar in mercury-DOM-sulfide systems

    USGS Publications Warehouse

    Gerbig, Chase A.; Kim, Christopher S.; Stegemeier, John P.; Ryan, Joseph N.; Aiken, George R.

    2011-01-01

    Direct determination of mercury (Hg) speciation in sulfide-containing environments is confounded by low mercury concentrations and poor analytical sensitivity. Here we report the results of experiments designed to assess mercury speciation at environmentally relevant ratios of mercury to dissolved organic matter (DOM) (i.e., <4 nmol Hg (mg DOM)−1) by combining solid phase extraction using C18 resin with extended X-ray absorption fine structure (EXAFS) spectroscopy. Aqueous Hg(II) and a DOM isolate were equilibrated in the presence and absence of 100 μM total sulfide. In the absence of sulfide, mercury adsorption to the resin increased as the Hg:DOM ratio decreased and as the strength of Hg-DOM binding increased. EXAFS analysis indicated that in the absence of sulfide, mercury bonds with an average of 2.4 ± 0.2 sulfur atoms with a bond length typical of mercury-organic thiol ligands (2.35 Å). In the presence of sulfide, mercury showed greater affinity for the C18 resin, and its chromatographic behavior was independent of Hg:DOM ratio. EXAFS analysis showed mercury–sulfur bonds with a longer interatomic distance (2.51–2.53 Å) similar to the mercury–sulfur bond distance in metacinnabar (2.53 Å) regardless of the Hg:DOM ratio. For all samples containing sulfide, the sulfur coordination number was below the ideal four-coordinate structure of metacinnabar. At a low Hg:DOM ratio where strong binding DOM sites may control mercury speciation (1.9 nmol mg–1) mercury was coordinated by 2.3 ± 0.2 sulfur atoms, and the coordination number rose with increasing Hg:DOM ratio. The less-than-ideal coordination numbers indicate metacinnabar-like species on the nanometer scale, and the positive correlation between Hg:DOM ratio and sulfur coordination number suggests progressively increasing particle size or crystalline order with increasing abundance of mercury with respect to DOM. In DOM-containing sulfidic systems nanocolloidal metacinnabar-like species may form

  5. Performance evaluation of continuity of care records (CCRs): parsing models in a mobile health management system.

    PubMed

    Chen, Hung-Ming; Liou, Yong-Zan

    2014-10-01

    In a mobile health management system, mobile devices act as the application hosting devices for personal health records (PHRs) and the healthcare servers construct to exchange and analyze PHRs. One of the most popular PHR standards is continuity of care record (CCR). The CCR is expressed in XML formats. However, parsing is an expensive operation that can degrade XML processing performance. Hence, the objective of this study was to identify different operational and performance characteristics for those CCR parsing models including the XML DOM parser, the SAX parser, the PULL parser, and the JSON parser with regard to JSON data converted from XML-based CCR. Thus, developers can make sensible choices for their target PHR applications to parse CCRs when using mobile devices or servers with different system resources. Furthermore, the simulation experiments of four case studies are conducted to compare the parsing performance on Android mobile devices and the server with large quantities of CCR data.

  6. Java Application Shell: A Framework for Piecing Together Java Applications

    NASA Technical Reports Server (NTRS)

    Miller, Philip; Powers, Edward I. (Technical Monitor)

    2001-01-01

    This session describes the architecture of Java Application Shell (JAS), a Swing-based framework for developing interactive Java applications. Java Application Shell is being developed by Commerce One, Inc. for NASA Goddard Space Flight Center Code 588. The purpose of JAS is to provide a framework for the development of Java applications, providing features that enable the development process to be more efficient, consistent and flexible. Fundamentally, JAS is based upon an architecture where an application is considered a collection of 'plugins'. In turn, a plug-in is a collection of Swing actions defined using XML and packaged in a jar file. Plug-ins may be local to the host platform or remotely-accessible through HTTP. Local and remote plugins are automatically discovered by JAS upon application startup; plugins may also be loaded dynamically without having to re-start the application. Using Extensible Markup Language (XML) to define actions, as opposed to hardcoding them in application logic, allows easier customization of application-specific operations by separating application logic from presentation. Through XML, a developer defines an action that may appear on any number of menus, toolbars, and buttons. Actions maintain and propagate enable/disable states and specify icons, tool-tips, titles, etc. Furthermore, JAS allows actions to be implemented using various scripting languages through the use of IBM's Bean Scripting Framework. Scripted action implementation is seamless to the end-user. In addition to action implementation, scripts may be used for application and unit-level testing. In the case of application-level testing, JAS has hooks to assist a script in simulating end-user input. JAS also provides property and user preference management, JavaHelp, Undo/Redo, Multi-Document Interface, Single-Document Interface, printing, and logging. Finally, Jini technology has also been included into the framework by means of a Jini services browser and the

  7. Understanding microbial/DOM interactions using fluorescence and flow cytometry

    NASA Astrophysics Data System (ADS)

    Fox, Bethany; Rushworth, Cathy; Attridge, John; Anesio, Alexandre; Cox, Tim; Reynolds, Darren

    2015-04-01

    The transformation and movement of dissolved organic carbon (DOC) within freshwater aquatic systems is an important factor in the global cycling of carbon. DOC within aquatic systems is known to underpin the microbial food web and therefore plays an essential role in supporting and maintaining the aquatic ecosystem. Despite this the interactions between bacteria and dissolved organic matter (DOM) are not well understood, although the literature indicates that the microbial processing of bioavailable DOM is essential during the production of autochthonous, labile, DOM. DOM can be broadly characterised by its fluorescing properties and Coble et al. (2014) define terrestrially derived DOM as exhibiting "peak C" fluorescence, whilst labile microbially derived DOM is defined as showing "peak T" fluorescence. Our work explores the microbial/DOM interactions by analysing aquatic samples using fluorescence excitation and emission matrices (EEMs) in conjunction with microbial consumption of dissolved oxygen. Environmental and synthetic water samples were subjected to fluorescence characterisation using both fluorescence spectroscopy and in situ fluorescence sensors (Chelsea Technologies Group Ltd.). PARAFAC analysis and peak picking were performed on EEMs and compared with flow cytometry data, used to quantify bacterial numbers present within samples. Synthetic samples were created using glucose, glutamic acid, nutrient-rich water and a standard bacterial seed. Synthetic samples were provided with terrestrially derived DOM via the addition of an aliquot of environmental water. Using a closed system approach, samples were incubated over time (up to a maximum of 20 days) and analysed at pre-defined intervals. The main focus of our work is to improve our understanding of microbial/DOM interactions and how these interactions affect both the DOM characteristics and microbial food web in freshwater aquatic systems. The information gained, in relation to the origin, microbial

  8. Why dissolved organic matter (DOM) enhances photodegradation of methylmercury

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

    Qian, Yun; Yin, Xiangping Lisa; Brooks, Scott C

    2014-01-01

    Methylmercury (MeHg) is known to degrade photochemically, but it remains unclear what roles naturally dissolved organic matter (DOM) and complexing organic ligands play in MeHg photodegradation. Here we investigate the rates and mechanisms of MeHg photodegradation using DOM samples with varying oxidation states and origins as well as organic ligands with known molecular structures. All DOM and organic ligands increased MeHg photodegradation under solar irradiation, but the first-order rate constants varied depending on the oxidation state of DOM and the type and concentration of the ligands. Compounds containing both thiols and aromatics (e.g., thiosalicylate and reduced DOM) increased MeHg degradationmore » rates far greater than those containing only aromatic or thiol functional groups (e.g., salicylate or glutathione). Our results suggest that, among other factors, the synergistic effects of thiolate and aromatic moieties in DOM greatly enhance MeHg photodegradation.« less

  9. Effects of dissolved organic matter (DOM) sources and nature of solid extraction sorbent on recoverable DOM composition: Implication into potential lability of different compound groups.

    PubMed

    Chen, Meilian; Kim, Sunghwan; Park, Jae-Eun; Kim, Hyun Sik; Hur, Jin

    2016-07-01

    Noting the source-dependent properties of dissolved organic matter (DOM), this study explored the recoverable compounds by solid phase extraction (SPE) of two common sorbents (C18 and PPL) eluted with methanol solvent for contrasting DOM sources via fluorescence excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Fresh algae and leaf litter extracts DOM, one riverine DOM, and one upstream lacustrine DOM were selected for the comparison. C18 sorbent was generally found to extract more diverse molecular formula, relatively higher molecular weight, and more heteroatomic DOM compounds within the studied mass range than PPL sorbent except for the leaf litter extract. Even with the same sorbent, the main molecular features of the two end member DOM were distributed on different sides of the axes of a multivariate ordination, indicating the source-dependent characteristics of the recoverable compounds by the sorbents. In addition, further examination of the molecular formula uniquely present in the two end members and the upstream lake DOM suggested that proteinaceous, tannin-like, and heteroatomic DOM constituents might be potential compound groups which are labile and easily degraded during their mobilization into downstream watershed. This study provides new insights into the sorbent selectivity of DOM from diverse sources and potential lability of various compound groups.

  10. Model Checking Real Time Java Using Java PathFinder

    NASA Technical Reports Server (NTRS)

    Lindstrom, Gary; Mehlitz, Peter C.; Visser, Willem

    2005-01-01

    The Real Time Specification for Java (RTSJ) is an augmentation of Java for real time applications of various degrees of hardness. The central features of RTSJ are real time threads; user defined schedulers; asynchronous events, handlers, and control transfers; a priority inheritance based default scheduler; non-heap memory areas such as immortal and scoped, and non-heap real time threads whose execution is not impeded by garbage collection. The Robust Software Systems group at NASA Ames Research Center has JAVA PATHFINDER (JPF) under development, a Java model checker. JPF at its core is a state exploring JVM which can examine alternative paths in a Java program (e.g., via backtracking) by trying all nondeterministic choices, including thread scheduling order. This paper describes our implementation of an RTSJ profile (subset) in JPF, including requirements, design decisions, and current implementation status. Two examples are analyzed: jobs on a multiprogramming operating system, and a complex resource contention example involving autonomous vehicles crossing an intersection. The utility of JPF in finding logic and timing errors is illustrated, and the remaining challenges in supporting all of RTSJ are assessed.

  11. Operationalizing Dynamic Ocean Management (DOM): Understanding the Incentive Structure, Policy and Regulatory Context for DOM in Practice

    NASA Astrophysics Data System (ADS)

    Lewison, R. L.; Saumweber, W. J.; Erickson, A.; Martone, R. G.

    2016-12-01

    Dynamic ocean management, or management that uses near real-time data to guide the spatial distribution of commercial activities, is an emerging approach to balance ocean resource use and conservation. Employing a wide range of data types, dynamic ocean management in a fisheries context can be used to meet multiple objectives - managing target quota, bycatch reduction, and reducing interactions with species of conservation concern. There is a growing list of DOM applications currently in practice in fisheries around the world, yet the approach is new enough that both fishers and fisheries managers are unclear how DOM can be applied to their fishery. Here, we use the experience from dynamic ocean management applications that are currently in practice to address the commonly asked question "How can dynamic management approaches be implemented in a traditionally managed fishery?". Combining knowledge from the DOM participants with a review of regulatory frameworks and incentive structures, stakeholder participation, and technological requirements of DOM in practice, we identify ingredients that have supported successful implementation of this new management approach.

  12. A statistic-thermodynamic model for the DOM degradation in the estuary

    NASA Astrophysics Data System (ADS)

    Zheng, Quanan; Chen, Qin; Zhao, Haihong; Shi, Jiuxin; Cao, Yong; Wang, Dan

    2008-03-01

    This study aims to clarify the role of dissolved salts playing in the degradation process of terrestrial dissolved organic matter (DOM) at a scale of molecular movement. The molecular thermal movement is perpetual motion. In a multi-molecular system, this random motion also causes collision between the molecules. Seawater is a multi-molecular system consisting from water, salt, and terrestrial DOM molecules. This study attributes the DOM degradation in the estuary to the inelastic collision of DOM molecule with charged salt ions. From statistic-thermodynamic theories of molecular collision, the DOM degradation model and the DOM distribution model are derived. The models are validated by the field observations and satellite data. Thus, we conclude that the inelastic collision between the terrestrial DOM molecules and dissolved salt ions in seawater is a decisive dynamic mechanism for rapid loss of terrestrial DOM.

  13. ACPYPE - AnteChamber PYthon Parser interfacE.

    PubMed

    Sousa da Silva, Alan W; Vranken, Wim F

    2012-07-23

    ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein-ligand complexes from the PDB. ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

  14. Biogeochemical and Optical Analysis of Coastal DOM for Satellite Retrieval of Terrigenous DOM in the U.S. Middle Atlantic Bight

    NASA Technical Reports Server (NTRS)

    Mannino, A.; Dyda, R. Y.; Hernes, P. J.; Hooker, Stan; Hyde, Kim; Novak, Mike

    2012-01-01

    Estuaries and coastal ocean waters experience a high degree of variability in the composition and concentration of particulate and dissolved organic matter (DOM) as a consequence of riverine/estuarine fluxes of terrigenous DOM, sediments, detritus and nutrients into coastal waters and associated phytoplankton blooms. Our approach integrates biogeochemical measurements (elemental content, molecular analyses), optical properties (absorption) and remote sensing to examine terrestrial DOM contributions into the U.S. Middle Atlantic Bight (MAB). We measured lignin phenol composition, DOC and CDOM absorption within the Chesapeake and Delaware Bay mouths, plumes and adjacent coastal ocean waters to derive empirical relationships between CDOM and biogeochemical measurements for satellite remote sensing application. Lignin ranged from 0.03 to 6.6 ug/L between estuarine and outer shelf waters. Our results demonstrate that satellite-derived CDOM is useful as a tracer of terrigenous DOM in the coastal ocean

  15. Monitoring Java Programs with Java PathExplorer

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Rosu, Grigore; Clancy, Daniel (Technical Monitor)

    2001-01-01

    We present recent work on the development Java PathExplorer (JPAX), a tool for monitoring the execution of Java programs. JPAX can be used during program testing to gain increased information about program executions, and can potentially furthermore be applied during operation to survey safety critical systems. The tool facilitates automated instrumentation of a program's late code which will then omit events to an observer during its execution. The observer checks the events against user provided high level requirement specifications, for example temporal logic formulae, and against lower level error detection procedures, for example concurrency related such as deadlock and data race algorithms. High level requirement specifications together with their underlying logics are defined in the Maude rewriting logic, and then can either be directly checked using the Maude rewriting engine, or be first translated to efficient data structures and then checked in Java.

  16. Model Checking JAVA Programs Using Java Pathfinder

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Pressburger, Thomas

    2000-01-01

    This paper describes a translator called JAVA PATHFINDER from JAVA to PROMELA, the "programming language" of the SPIN model checker. The purpose is to establish a framework for verification and debugging of JAVA programs based on model checking. This work should be seen in a broader attempt to make formal methods applicable "in the loop" of programming within NASA's areas such as space, aviation, and robotics. Our main goal is to create automated formal methods such that programmers themselves can apply these in their daily work (in the loop) without the need for specialists to manually reformulate a program into a different notation in order to analyze the program. This work is a continuation of an effort to formally verify, using SPIN, a multi-threaded operating system programmed in Lisp for the Deep-Space 1 spacecraft, and of previous work in applying existing model checkers and theorem provers to real applications.

  17. Effective Cyber Situation Awareness (CSA) Assessment and Training

    DTIC Science & Technology

    2013-11-01

    activity/scenario. y. Save Wireshark Captures. z. Save SNORT logs. aa. Save MySQL databases. 4. After the completion of the scenario, the reversion...line or from custom Java code. • Cisco ASA Parser: Builds normalized vendor-neutral firewall rule specifications from Cisco ASA and PIX firewall...The Service tool lets analysts build Cauldron models from either the command line or from custom Java code. Functionally, it corresponds to the

  18. How Reservoirs Alter DOM Amount and Composition: Sources, Sinks, and Transformations

    NASA Astrophysics Data System (ADS)

    Kraus, T. E.; Bergamaschi, B. A.; Hernes, P. J.; Doctor, D. H.; Kendall, C.; Losee, R. F.; Downing, B. D.

    2011-12-01

    Reservoirs are critical components of many water supply systems as they allow the storage of water when supply exceeds demand. However, during water storage biogeochemical processes can alter both the amount and composition of dissolved organic matter (DOM), which can in turn affect water quality. While the balance between production and loss determines whether a reservoir is a net sink or source of DOM, changes in chemical composition are also relevant as they affect DOM reactivity (e.g. persistence in the environment, removability during coagulation treatment, and potential to form toxic compounds during drinking water treatment). The composition of the DOM pool also provides information about the DOM sources and processing, which can inform reservoir management. We examined the concentration and composition of DOM in San Luis Reservoir (SLR), a large off-stream impoundment of the California State Water Project. We used an array of DOM chemical tracers including dissolved organic carbon (DOC) concentration, optical properties, isotopic composition, lignin phenol content, and structural groupings determined by 13C NMR. There were periods when the reservoir was i) a net source of DOM due to the predominance of algal production (summer), ii) a net sink due to the predominance of degradation (fall/winter), and iii) balanced between production and consumption (spring). Despite only moderate variation in bulk DOC concentration (3.0-3.6 mg C/L), substantial changes in DOM composition indicated that terrestrial-derived material entering the reservoir was being degraded and replaced by aquatic-derived DOM produced within the reservoir. Results suggest reservoirs have the potential to reduce DOM amount and reactivity via degradative processes, however, these benefits can be decreased or even negated by the production of algal-derived DOM.

  19. The Unification Space implemented as a localist neural net: predictions and error-tolerance in a constraint-based parser.

    PubMed

    Vosse, Theo; Kempen, Gerard

    2009-12-01

    We introduce a novel computer implementation of the Unification-Space parser (Vosse and Kempen in Cognition 75:105-143, 2000) in the form of a localist neural network whose dynamics is based on interactive activation and inhibition. The wiring of the network is determined by Performance Grammar (Kempen and Harbusch in Verb constructions in German and Dutch. Benjamins, Amsterdam, 2003), a lexicalist formalism with feature unification as binding operation. While the network is processing input word strings incrementally, the evolving shape of parse trees is represented in the form of changing patterns of activation in nodes that code for syntactic properties of words and phrases, and for the grammatical functions they fulfill. The system is capable, at least qualitatively and rudimentarily, of simulating several important dynamic aspects of human syntactic parsing, including garden-path phenomena and reanalysis, effects of complexity (various types of clause embeddings), fault-tolerance in case of unification failures and unknown words, and predictive parsing (expectation-based analysis, surprisal effects). English is the target language of the parser described.

  20. Analysis of variables affecting unemployment rate and detecting for cluster in West Java, Central Java, and East Java in 2012

    NASA Astrophysics Data System (ADS)

    Samuel, Putra A.; Widyaningsih, Yekti; Lestari, Dian

    2016-02-01

    The objective of this study is modeling the Unemployment Rate (UR) in West Java, Central Java, and East Java, with rate of disease, infant mortality rate, educational level, population size, proportion of married people, and GDRP as the explanatory variables. Spatial factors are also considered in the modeling since the closer the distance, the higher the correlation. This study uses the secondary data from BPS (Badan Pusat Statistik). The data will be analyzed using Moran I test, to obtain the information about spatial dependence, and using Spatial Autoregressive modeling to obtain the information, which variables are significant affecting UR and how great the influence of the spatial factors. The result is, variables proportion of married people, rate of disease, and population size are related significantly to UR. In all three regions, the Hotspot of unemployed will also be detected districts/cities using Spatial Scan Statistics Method. The results are 22 districts/cities as a regional group with the highest unemployed (Most likely cluster) in the study area; 2 districts/cities as a regional group with the highest unemployed in West Java; 1 district/city as a regional groups with the highest unemployed in Central Java; 15 districts/cities as a regional group with the highest unemployed in East Java.

  1. Further insight into the roles of the chemical composition of dissolved organic matter (DOM) on ultrafiltration membranes as revealed by multiple advanced DOM characterization tools.

    PubMed

    Ly, Quang Viet; Hur, Jin

    2018-06-01

    This study assessed the relative contributions of different constitutes in dissolved organic matter (DOM) with two different sources (i.e., urban river and effluent) to membrane fouling on three types of ultrafiltration (UF) membranes via excitation emission matrix - parallel factor analysis (EEM-PARAFAC), size exclusion chromatography (SEC), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Two polyethersulfone membranes with different pore sizes and one regenerated cellulose membrane were used as representative hydrophobic (HPO) and hydrophilic (HPI) UF membranes, respectively. Although size exclusion effect was found to be the most prevailing rejection mechanism, the behaviors of individual fluorescent components (one tryptophan-like, one microbial-humic-like, and terrestrial humic-like) and different size fractions upon the UF filtration revealed that chemical interactions (e.g., hydrophobic interactions and hydrogen bonding) between DOM and membrane might play important roles in UF membrane fouling, especially for small sized DOM molecules. Based on the molecular level composition determined by FT-ICR-MS, the CHOS formula group showed a greater removal tendency toward the HPO membrane, while the CHONS group was prone to be removed by the HPI membrane. The changes in the overall molecular composition of DOM upon UF filtration were highly dependent on the sources of DOM. The molecules of more acidic nature tended to remain in the permeate of effluent DOM, while the river DOM was shifted into more nitrogen-enriched composition after filtration. Regardless of the DOM sources, the HPO membrane with a smaller pore size led to the most pronounced changes in the molecular composition of DOM. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Java Programming Language

    NASA Technical Reports Server (NTRS)

    Shaykhian, Gholam Ali

    2007-01-01

    The Java seminar covers the fundamentals of Java programming language. No prior programming experience is required for participation in the seminar. The first part of the seminar covers introductory concepts in Java programming including data types (integer, character, ..), operators, functions and constants, casts, input, output, control flow, scope, conditional statements, and arrays. Furthermore, introduction to Object-Oriented programming in Java, relationships between classes, using packages, constructors, private data and methods, final instance fields, static fields and methods, and overloading are explained. The second part of the seminar covers extending classes, inheritance hierarchies, polymorphism, dynamic binding, abstract classes, protected access. The seminar conclude by introducing interfaces, properties of interfaces, interfaces and abstract classes, interfaces and cailbacks, basics of event handling, user interface components with swing, applet basics, converting applications to applets, the applet HTML tags and attributes, exceptions and debugging.

  3. Modeling Effects of Lability on Microbial Uptake of DOM in River Reaches

    NASA Astrophysics Data System (ADS)

    Li, A.; Drummond, J. D.; Bowen, J. C.; Cory, R. M.; Kaplan, L.; Packman, A. I.

    2017-12-01

    Rivers are hotspots for biological degradation of dissolved organic matter (DOM), contributing to 1.8 petagrams of carbon emissions per year. DOM represents approximately 60% of the total mass of organic carbon transported within river networks, fueling stream ecosystem metabolism. Not all DOM is biodegradable, biodegradation rates vary based on lability, and lability decreases with reaction time. Fluorescent fractions of DOM (FDOM) are often used as proxies of DOM lability. Humic-like FDOM, previously considered recalcitrant and thought to contribute minimally to the biodegradable DOM pools, has recently been shown to contribute more than 50% to DOM uptake in bioreactor columns colonized by bacteria in stream water. Protein-like FDOM, a proxy for the biodegradable DOM pool, also contributes to the recalcitrant DOM pool in bioreactors. However, the contribution of different lability pools to DOM uptake at the reach scale remains elusive. Here we combine local-scale results from a bioreactor study and measures of stream geomorphology parameters to model reach-scale DOM uptake in White Clay Creek, a Pennsylvania piedmont stream with an intact, forested riparian zone and inputs from upland agriculture. Steady state modeling of a point-source, continuous injection of FDOM shows that humic-like FDOM contributes up to 80% of the total removal of FDOM at the reach scale, suggesting its importance to in-stream DOM uptake. Tryptophan-like FDOM, a protein-like FDOM, contributes to 80% of the remaining fraction of FDOM at the reach scale that incorporates longer timescales of transport and retention. This is consistent with recent local-scale findings that the lability of tryptophan-like FDOM decreases substantially with reaction time in bioreactors, such that it becomes much more recalcitrant as it travels downstream. Steady state modeling of a distributed source, continuous injection of FDOM shows that contributing sources distribute differently along the river reach for

  4. The power and limits of a rule-based morpho-semantic parser.

    PubMed Central

    Baud, R. H.; Rassinoux, A. M.; Ruch, P.; Lovis, C.; Scherrer, J. R.

    1999-01-01

    The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors. PMID:10566313

  5. The power and limits of a rule-based morpho-semantic parser.

    PubMed

    Baud, R H; Rassinoux, A M; Ruch, P; Lovis, C; Scherrer, J R

    1999-01-01

    The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors.

  6. What Do We Know about DOM Chemical Composition Based on Its Optical Properties?

    NASA Astrophysics Data System (ADS)

    Aiken, G.

    2016-02-01

    Dissolved organic matter (DOM) optical measurements (UV-Vis light absorbance and fluorescence) provide useful information related to DOM composition and reactivity, and can serve as proxies for DOM concentration and the concentrations of some metals, such as mercury. While these measurements are useful for a range of objectives, they only measure aromatic molecules that absorb UV-Vis light and a smaller subset of these molecules that fluoresce. They provide no information about the substantial fraction of DOM that is non-chromophoric. Based on chromatographic fractionation on XAD resins, DOM optical properties measured on whole water samples strongly correlate with both the concentration and composition of the hydrophobic acid (HPOA) fraction of the DOM. In this presentation the results of DOM optical measurements, DOM fractionation analyses, and 13C-nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (FTICR_MS) of HPOA fractions obtained from a wide range a natural waters will be presented to examine the relationships between DOM optical properties and DOM chemical composition. The HPOA fractions within and between rivers exhibit a wide range of optical behaviors reflective of sources and transformations compared to other DOM fractions. While, 13C-NMR and FTICR-MS analyses generally show greater relative concentrations of aromatic molecules for those samples with strong optical signals, they also indicate that the HPOA fractions are mostly composed of a large number of non-chromophoric molecules, such as carbohydrates carboxyl-rich alicyclic molecules (CRAM), and other aliphatic molecules, all of which have implications regarding DOM reactivity, biolability, sources, and age. The utility and short-comings of employing optical data for assessing sources and transformations of DOM in natural waters will be examined using case studies involving organic matter in the Yukon River Basin and riverine export of DOM to the Gulf of Maine.

  7. Characterising Event-Based DOM Inputs to an Urban Watershed

    NASA Astrophysics Data System (ADS)

    Croghan, D.; Bradley, C.; Hannah, D. M.; Van Loon, A.; Sadler, J. P.

    2017-12-01

    Dissolved Organic Matter (DOM) composition in urban streams is dominated by terrestrial inputs after rainfall events. Urban streams have particularly strong terrestrial-riverine connections due to direct input from terrestrial drainage systems. Event driven DOM inputs can have substantial adverse effects on water quality. Despite this, DOM from important catchment sources such as road drains and Combined Sewage Overflows (CSO's) remains poorly characterised within urban watersheds. We studied DOM sources within an urbanised, headwater watershed in Birmingham, UK. Samples from terrestrial sources (roads, roofs and a CSO), were collected manually after the onset of rainfall events of varying magnitude, and again within 24-hrs of the event ending. Terrestrial samples were analysed for fluorescence, absorbance and Dissolved Organic Carbon (DOC) concentration. Fluorescence and absorbance indices were calculated, and Parallel Factor Analysis (PARAFAC) was undertaken to aid sample characterization. Substantial differences in fluorescence, absorbance, and DOC were observed between source types. PARAFAC-derived components linked to organic pollutants were generally highest within road derived samples, whilst humic-like components tended to be highest within roof samples. Samples taken from the CSO generally contained low fluorescence, however this likely represents a dilution effect. Variation within source groups was particularly high, and local land use seemed to be the driving factor for road and roof drain DOM character and DOC quantity. Furthermore, high variation in fluorescence, absorbance and DOC was apparent between all sources depending on event type. Drier antecedent conditions in particular were linked to greater presence of terrestrially-derived components and higher DOC content. Our study indicates that high variations in DOM character occur between source types, and over small spatial scales. Road drains located on main roads appear to contain the poorest

  8. Wet-dry cycles impact DOM retention in subsurface soils

    NASA Astrophysics Data System (ADS)

    Olshansky, Yaniv; Root, Robert A.; Chorover, Jon

    2018-02-01

    Transport and reactivity of carbon in the critical zone are highly controlled by reactions of dissolved organic matter (DOM) with subsurface soils, including adsorption, transformation and exchange. These reactions are dependent on frequent wet-dry cycles common to the unsaturated zone, particularly in semi-arid regions. To test for an effect of wet-dry cycles on DOM interaction and stabilization in subsoils, samples were collected from subsurface (Bw) horizons of an Entisol and an Alfisol from the Catalina-Jemez Critical Zone Observatory and sequentially reacted (four batch steps) with DOM extracted from the corresponding soil litter layers. Between each reaction step, soils either were allowed to air dry (wet-dry treatment) before introduction of the following DOM solution or were maintained under constant wetness (continually wet treatment). Microbial degradation was the dominant mechanism of DOM loss from solution for the Entisol subsoil, which had higher initial organic C content, whereas sorptive retention predominated in the lower C Alfisol subsoil. For a given soil, bulk dissolved organic C losses from solution were similar across treatments. However, a combination of Fourier transform infrared (FTIR) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopic analyses revealed that wet-dry treatments enhanced the interactions between carboxyl functional groups and soil particle surfaces. Scanning transmission X-ray microscopy (STXM) data suggested that cation bridging by Ca2+ was the primary mechanism for carboxyl association with soil surfaces. STXM data also showed that spatial fractionation of adsorbed OM on soil organo-mineral surfaces was diminished relative to what might be inferred from previously published observations pertaining to DOM fractionation on reaction with specimen mineral phases. This study provides direct evidence of the role of wet-dry cycles in affecting sorption reactions of DOM to a complex soil matrix. In

  9. Pain-evoked trunk muscle activity changes during fatigue and DOMS.

    PubMed

    Larsen, L H; Hirata, R P; Graven-Nielsen, T

    2017-05-01

    Muscle pain may reorganize trunk muscle activity but interactions with exercise-related muscle fatigue and delayed onset muscle soreness (DOMS) is to be clarified. In 19 healthy participants, the trunk muscle activity during 20 multi-directional unpredictable surface perturbations were recorded after bilateral isotonic saline injections (control) and during unilateral and bilateral hypertonic saline-induced low back pain (LBP) in conditions of back muscle fatigue (Day-1) and DOMS (Day-2). Pain intensity and distribution were assessed by visual analogue scale (VAS) scores and pain drawings. The degree of fatigue and DOMS were assessed by Likert scale scores. Root-mean-square electromyographic (RMS-EMG) signals were recorded post-perturbation from six bilateral trunk muscles and the difference from baseline conditions (Delta-RMS-EMG) was extracted and averaged across abdominal and back muscles. In DOMS, peak VAS scores were higher during bilateral control and bilateral saline-induced pain than fatigue (p < 0.001) and during bilateral compared with unilateral pain (p < 0.001). The saline-induced pain areas were larger during DOMS than fatigue (p < 0.01). In response to surface perturbations during fatigue and DOMS, the back muscle Delta-RMS-EMG increased during bilateral compared with unilateral pain and control injections (p < 0.001) and decreased during unilateral pain compared with control injections (p < 0.04). In DOMS compared with fatigue, the post-perturbation Delta-RMS-EMG in back muscles was higher during bilateral pain and lower during unilateral pain (p < 0.001). The abdominal Delta-RMS-EMG was not significantly affected. Facilitated and attenuated back muscle responses to surface perturbations in bilateral and unilateral LBP, respectively, was more expressed during exercise-induced back muscle soreness compared with fatigue. Back muscle activity decreased during unilateral and increased during bilateral pain after unpredictable surface

  10. Implementation of NAS Parallel Benchmarks in Java

    NASA Technical Reports Server (NTRS)

    Frumkin, Michael; Schultz, Matthew; Jin, Hao-Qiang; Yan, Jerry

    2000-01-01

    A number of features make Java an attractive but a debatable choice for High Performance Computing (HPC). In order to gauge the applicability of Java to the Computational Fluid Dynamics (CFD) we have implemented NAS Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would move Java closer to Fortran in the competition for CFD applications.

  11. Understanding and Capturing People’s Mobile App Privacy Preferences

    DTIC Science & Technology

    2013-10-28

    The entire apps’ metadata takes up about 500MB of storage space when stored in a MySQL database and all the binary files take approximately 300GB of...functionality that can de- compile Dalvik bytecodes to Java source code faster than other de-compilers. Given the scale of the app analysis we planned on... java libraries, such as parser, sql connectors, etc Targeted Ads 137 admob, adwhirl, greystripe… Provided by mobile behavioral ads company to

  12. Volcanoes, Central Java, Indonesia

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The island of Java (8.0S, 112.0E), perhaps better than any other, illustrates the volcanic origin of Pacific Island groups. Seen in this single view are at least a dozen once active volcano craters. Alignment of the craters even defines the linear fault line of Java as well as the other some 1500 islands of the Indonesian Archipelago. Deep blue water of the Indian Ocean to the south contrasts to the sediment laden waters of the Java Sea to the north.

  13. Volcanoes, Central Java, Indonesia

    NASA Image and Video Library

    1992-08-08

    The island of Java (8.0S, 112.0E), perhaps better than any other, illustrates the volcanic origin of Pacific Island groups. Seen in this single view are at least a dozen once active volcano craters. Alignment of the craters even defines the linear fault line of Java as well as the other some 1500 islands of the Indonesian Archipelago. Deep blue water of the Indian Ocean to the south contrasts to the sediment laden waters of the Java Sea to the north.

  14. Java PathFinder: A Translator From Java to Promela

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus

    1999-01-01

    JAVA PATHFINDER, JPF, is a prototype translator from JAVA to PROMELA, the modeling language of the SPIN model checker. JPF is a product of a major effort by the Automated Software Engineering group at NASA Ames to make model checking technology part of the software process. Experience has shown that severe bugs can be found in final code using this technique, and that automated translation from a programming language to a modeling language like PROMELA can help reducing the effort required.

  15. Behavioral characterization of 2-O-desmethyl and 5-O-desmethyl metabolites of the phenylethylamine hallucinogen DOM.

    PubMed

    Eckler, J R; Chang-Fong, J; Rabin, R A; Smith, C; Teitler, M; Glennon, R A; Winter, J C

    2003-07-01

    The present investigation was undertaken to test the hypothesis that known metabolites of the phenylethylamine hallucinogen 1-(2,5-dimethoxy-4-methylphenyl)-2-aminopropane (DOM) are pharmacologically active. This hypothesis was tested by evaluating the ability of racemic DOM metabolites 2-O-desmethyl DOM (2-DM-DOM) and 5-O-desmethyl DOM (5-DM-DOM) to substitute for the stimulus properties of (+)lysergic acid diethylamide (LSD). The data indicate that both metabolites are active in LSD-trained subjects and are significantly inhibited by the selective 5-HT(2A) receptor antagonist M100907. Full generalization of LSD to both 2-DM-DOM and 5-DM-DOM occurred, and 5-DM-DOM was slightly more potent than 2-DM-DOM. Similarly, 5-DM-DOM had a slightly higher affinity than 2-DM-DOM for both 5-HT(2A) and 5-HT(2C) receptors. Additionally, it was of interest to determine if the formation of active metabolite(s) resulted in a temporal delay associated with maximal stimulus effects of DOM. We postulated that if metabolite formation resulted in the aforementioned delay, direct administration of the metabolites might result in maximally stable stimulus effects at an earlier pretreatment time. This hypothesis was tested by evaluating (1) the time point at which DOM produces the greatest degree of LSD-appropriate responding, (2) the involvement of 5-HT(2A) receptor in the stimulus effects of DOM at various pretreatment times by administration of M100907 and (3) the ability of 2-DM-DOM and 5-DM-DOM to substitute for the stimulus properties of LSD using either 15- or 75-min pretreatment time. The data indicate that (a) the DOM stimulus produces the greatest degree of LSD-appropriate responding at the 75-min time point in comparison with earlier pretreatment times and (b) the stimulus effects of DOM are differentially antagonized by M100907 and this effect is a function of DOM pretreatment time prior to testing. Both 2-DM-DOM and 5-DM-DOM were found to be most active, at all doses tested

  16. GSTARI model of BPR assets in West Java, Central Java, and East Java

    NASA Astrophysics Data System (ADS)

    Susanti, Susi; Sulistijowati Handajani, Sri; Indriati, Diari

    2018-05-01

    Bank Perkreditan Rakyat (BPR) is a financial institution in Indonesia dealing with Micro, Small, and Medium Enterprises (MSMEs). Though limited to MSMEs, the development of the BPR industry continues to increase. West Java, Central Java, and East Java have high BPR asset development are suspected to be interconnected because of their economic activities as a neighboring provincies. BPR assets are nonstationary time series data that follow the uptrend pattern. Therefore, the suitable model with the data is generalized space time autoregressive integrated (GSTARI) which considers the spatial and time interrelationships. GSTARI model used spatial order 1 and the autoregressive order is obtained of optimal lag which has the smallest value of Akaike information criterion corrected. The correlation test results showed that the location used in this study had a close relationship. Based on the results of model identification, the best model obtained is GSTAR(31)-I(1). The parameter estimation used the ordinary least squares with the selection of significant variables used the stepwise method and the normalization cross correlation weighting. The residual model fulfilled the assumption of white noise and normal multivariate, so the model was appropriate. The average RMSE and MAPE values of the model were 498.75 and 2.48%.

  17. Implementation of the NAS Parallel Benchmarks in Java

    NASA Technical Reports Server (NTRS)

    Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan (Technical Monitor)

    2002-01-01

    Several features make Java an attractive choice for High Performance Computing (HPC). In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for CFD applications.

  18. APINetworks Java. A Java approach to the efficient treatment of large-scale complex networks

    NASA Astrophysics Data System (ADS)

    Muñoz-Caro, Camelia; Niño, Alfonso; Reyes, Sebastián; Castillo, Miriam

    2016-10-01

    We present a new version of the core structural package of our Application Programming Interface, APINetworks, for the treatment of complex networks in arbitrary computational environments. The new version is written in Java and presents several advantages over the previous C++ version: the portability of the Java code, the easiness of object-oriented design implementations, and the simplicity of memory management. In addition, some additional data structures are introduced for storing the sets of nodes and edges. Also, by resorting to the different garbage collectors currently available in the JVM the Java version is much more efficient than the C++ one with respect to memory management. In particular, the G1 collector is the most efficient one because of the parallel execution of G1 and the Java application. Using G1, APINetworks Java outperforms the C++ version and the well-known NetworkX and JGraphT packages in the building and BFS traversal of linear and complete networks. The better memory management of the present version allows for the modeling of much larger networks.

  19. Model Checker for Java Programs

    NASA Technical Reports Server (NTRS)

    Visser, Willem

    2007-01-01

    Java Pathfinder (JPF) is a verification and testing environment for Java that integrates model checking, program analysis, and testing. JPF consists of a custom-made Java Virtual Machine (JVM) that interprets bytecode, combined with a search interface to allow the complete behavior of a Java program to be analyzed, including interleavings of concurrent programs. JPF is implemented in Java, and its architecture is highly modular to support rapid prototyping of new features. JPF is an explicit-state model checker, because it enumerates all visited states and, therefore, suffers from the state-explosion problem inherent in analyzing large programs. It is suited to analyzing programs less than 10kLOC, but has been successfully applied to finding errors in concurrent programs up to 100kLOC. When an error is found, a trace from the initial state to the error is produced to guide the debugging. JPF works at the bytecode level, meaning that all of Java can be model-checked. By default, the software checks for all runtime errors (uncaught exceptions), assertions violations (supports Java s assert), and deadlocks. JPF uses garbage collection and symmetry reductions of the heap during model checking to reduce state-explosion, as well as dynamic partial order reductions to lower the number of interleavings analyzed. JPF is capable of symbolic execution of Java programs, including symbolic execution of complex data such as linked lists and trees. JPF is extensible as it allows for the creation of listeners that can subscribe to events during searches. The creation of dedicated code to be executed in place of regular classes is supported and allows users to easily handle native calls and to improve the efficiency of the analysis.

  20. Molecular characterization of dissolved organic matter (DOM): a critical review.

    PubMed

    Nebbioso, Antonio; Piccolo, Alessandro

    2013-01-01

    Advances in water chemistry in the last decade have improved our knowledge about the genesis, composition, and structure of dissolved organic matter, and its effect on the environment. Improvements in analytical technology, for example Fourier-transform ion cyclotron (FT-ICR) mass spectrometry (MS), homo and hetero-correlated multidimensional nuclear magnetic resonance (NMR) spectroscopy, and excitation emission matrix fluorimetry (EEMF) with parallel factor (PARAFAC) analysis for UV-fluorescence spectroscopy have resulted in these advances. Improved purification methods, for example ultrafiltration and reverse osmosis, have enabled facile desalting and concentration of freshly collected DOM samples, thereby complementing the analytical process. Although its molecular weight (MW) remains undefined, DOM is described as a complex mixture of low-MW substances and larger-MW biomolecules, for example proteins, polysaccharides, and exocellular macromolecules. There is a general consensus that marine DOM originates from terrestrial and marine sources. A combination of diagenetic and microbial processes contributes to its origin, resulting in refractory organic matter which acts as carbon sink in the ocean. Ocean DOM is derived partially from humified products of plants decay dissolved in fresh water and transported to the ocean, and partially from proteinaceous and polysaccharide material from phytoplankton metabolism, which undergoes in-situ microbial processes, becoming refractory. Some of the DOM interacts with radiation and is, therefore, defined as chromophoric DOM (CDOM). CDOM is classified as terrestrial, marine, anthropogenic, or mixed, depending on its origin. Terrestrial CDOM reaches the oceans via estuaries, whereas autochthonous CDOM is formed in sea water by microbial activity; anthropogenic CDOM is a result of human activity. CDOM also affects the quality of water, by shielding it from solar radiation, and constitutes a carbon sink pool. Evidence in support

  1. Dissolved Organic Matter (DOM) Export from Watersheds to Coastal Oceans

    NASA Astrophysics Data System (ADS)

    Chen, R. F.; Gardner, G. B.; Peri, F.

    2016-02-01

    Dissolved organic matter (DOM) from terrestrial plants and soils is transported by surface waters and groundwaters to coastal ocean waters. Along the way, photochemical and biological degradation can remove DOM, and in situ processes such as phytoplankton leaching and sediment sources can add to the DOM in the river water. Wetlands, especially coastal wetlands can add significant amounts of DOM that is carried by rivers and is exported through estuaries to coastal systems. We will present observational data from a variety of coastal systems (San Francisco Bay, Boston Harbor, Chesapeake Bay, Hudson River, the Mississippi River, and a small salt marsh in the Gulf of Mexico). High resolution measurements of chromophoric dissolved organic matter (CDOM) can be correlated with dissolved organic carbon (DOC) so can be used to estimate DOC in specific systems and seasons. Gradients in CDOM/DOC combined with water fluxes can be used to estimate DOC fluxes from a variety of coastal watersheds to coastal systems. Influences of land use, system size, residence time, DOM quality, and photochemical and biological degradation will be discussed. The significance of coastal wetlands in the land-to-ocean export of DOC will be emphasized.

  2. Java: An Explosion on the Internet.

    ERIC Educational Resources Information Center

    Read, Tim; Hall, Hazel

    Summer 1995 saw the release, with considerable media attention, of draft versions of Sun Microsystems' Java computer programming language and the HotJava browser. Java has been heralded as the latest "killer" technology in the Internet explosion. Sun Microsystems and numerous companies including Microsoft, IBM, and Netscape have agreed…

  3. JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Globus, Al; Langhirt, Eric; Livny, Miron; Ramamurthy, Ravishankar; Soloman, Marvin; Traugott, Steve

    2000-01-01

    A genetic algorithm code, JavaGenes, was written in Java and used to evolve pharmaceutical drug molecules and digital circuits. JavaGenes was run under the Condor cycle-scavenging batch system managing 100-170 desktop SGI workstations. Genetic algorithms mimic biological evolution by evolving solutions to problems using crossover and mutation. While most genetic algorithms evolve strings or trees, JavaGenes evolves graphs representing (currently) molecules and circuits. Java was chosen as the implementation language because the genetic algorithm requires random splitting and recombining of graphs, a complex data structure manipulation with ample opportunities for memory leaks, loose pointers, out-of-bound indices, and other hard to find bugs. Java garbage-collection memory management, lack of pointer arithmetic, and array-bounds index checking prevents these bugs from occurring, substantially reducing development time. While a run-time performance penalty must be paid, the only unacceptable performance we encountered was using standard Java serialization to checkpoint and restart the code. This was fixed by a two-day implementation of custom checkpointing. JavaGenes is minimally integrated with Condor; in other words, JavaGenes must do its own checkpointing and I/O redirection. A prototype Java-aware version of Condor was developed using standard Java serialization for checkpointing. For the prototype to be useful, standard Java serialization must be significantly optimized. JavaGenes is approximately 8700 lines of code and a few thousand JavaGenes jobs have been run. Most jobs ran for a few days. Results include proof that genetic algorithms can evolve directed and undirected graphs, development of a novel crossover operator for graphs, a paper in the journal Nanotechnology, and another paper in preparation.

  4. Java PathFinder User Guide

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus

    1999-01-01

    The JAVA PATHFINDER, JPF, is a translator from a subset of JAVA 1.0 to PROMELA, the programming language of the SPIN model checker. The purpose of JPF is to establish a framework for verification and debugging of JAVA programming based on model checking. The main goal is to automate program verification such that a programmer can apply it in the daily work without the need for a specialist to manually reformulate a program into a different notation in order to analyze the program. The system is especially suited for analyzing multi-threaded JAVA applications, where normal testing usually falls short. The system can find deadlocks and violations of boolean assertions stated by the programmer in a special assertion language. This document explains how to Use JPF.

  5. Light limitation plays a central role in regulating DOM reactions in temperate watersheds

    NASA Astrophysics Data System (ADS)

    Yoon, B.; Hosen, J. D.; Kyzivat, E.; Fair, J. H.; Weber, L.; Aho, K. S.; Stubbins, A.; Lowenthal, R. S.; Raymond, P. A.

    2017-12-01

    Biological uptake and photochemical oxidation determine how much dissolved organic matter (DOM) can be removed and exported from inland waters. It is thus critical to understand the control on the biological and photochemical oxidation of DOM, and identify potential synergy between these two DOM removal processes. Yet, the variability of biological and photochemical lability, and the prevalence of priming effects between the two removal mechanisms are poorly understood at larger spatiotemporal scale. To address this knowledge gap, we analyzed the lability of 900 samples collected throughout the Connecticut River across two years (n = 510 for biolability, n=394 for photolability). Furthermore, we measured the effect of photochemical priming for biological removal and of biological priming for photochemical removal (n= 151, n=146, respectively). Our results show that photolability is on average 5 times greater than biolability, and that the mass of photolabile DOM can be predicted from UV absorbance at 254 nm. Photochemical DOM removal also led to additional "unlocking" of previously bio-recalcitrant DOM in 80% of the samples, and increased the biological lability by threefold on average. Scaling further, we extrapolate our model to estimate that the DOM fluxes leaving the Connecticut River and the Mississippi River are 49% and 45% photolabile, respectively. The significant photoreactivity observed across the samples and the subsequent increase in biolability demonstrate that sunlight is a more potent agent of DOM removal than the biological reactions. Yet, the photolability of DOM fluxes leaving the Connecticut River and Mississippi River indicates that the full photo-oxidation potential is not achieved due to light limitation.

  6. Effects of molecular size fraction of DOM on photodegradation of aqueous methylmercury.

    PubMed

    Kim, Moon-Kyung; Won, A-Young; Zoh, Kyung-Duk

    2017-05-01

    This study investigated the photodegradation kinetics of MeHg in the presence of various size fractions of dissolved organic matter (DOM) with MW < 3.5 kDa, 3.5 < MW < 10 kDa, and MW > 10 kDa. The DOM fraction with MW < 3.5 kDa was most effective in MeHg photodegradation. Increasing UV intensity resulted in the increase of photodegradation rate of the MeHg in all size of DOM fractions. Higher rates of MeHg degradation was observed at higher pH. For the portion of MW < 3.5 kDa, the photodegradation rate of MeHg increased with increasing DOM concentration, indicating that radicals such as singlet oxygen ( 1 O 2 ) radicals can be effectively produced by DOM. At higher portion of MW > 3.5 kDa, the inhibition of MeHg degradation was observed due to the effect of DOM photo-attenuation. Our result indicates that radical mediated reaction is the main mechanism of photodegradation of MeHg especially in the presence of MW < 3.5 kDa. Our results imply that the smaller molecular weight fraction (MW < 3.5 kDa) of DOM mainly increased the photodegradation rate of MeHg. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Photochemical reactivities of dissolved organic matter (DOM) in a sub-alpine lake revealed by EEM-PARAFAC: An insight into the fate of allochthonous DOM in alpine lakes affected by climate change.

    PubMed

    Du, Yingxun; Zhang, Yuanyuan; Chen, Feizhou; Chang, Yuguang; Liu, Zhengwen

    2016-10-15

    Due to climate change, tree line advance is occurring in many alpine regions. Within the next 50 to 100years, alpine lake catchments are expected to develop increased vegetation cover similar to that of sub-alpine lake catchments which currently exist below the tree line. Such changes in vegetation could trigger increased allochthonous DOM inputs to alpine lakes. To understand the fate of allochthonous DOM in alpine lakes impacted by climate change, the photochemical reactivity of DOM in sub-alpine Lake Tiancai (located 200m below the tree line) was investigated by excitation emission matrix fluorescence combined with parallel factor analysis (EEM-PARAFAC) and UV-Vis spectra analysis. With photo-exposure, a decrease in apparent DOM molecular weight was observed and 32% DOM was photomineralized to CO2. Interestingly, the aromaticity of DOM increased after photodegradation, as evidenced by increases in both the specific UV absorbance at 254nm (SUVA254) and the humification index (HIX). Five EEM-PARAFAC components were identified, including four terrestrially-derived substances (C1, C2, C3 and C4; allochthonous) and one tryptophan-like substance (C5; autochthonous). Generally, allochthonous DOM represented by C2 and C3 exhibited greater photoreactivity than autochthonous DOM represented by C5. C4 was identified as a possible photoproduct with relatively high aromaticity and photorefractive tendencies and contributed to the observed increase in SUVA254 and HIX. UV light facilitated the photodegradation of DOM and had the greatest effect on the removal of C3. This study provides information on the transformation of EEM-PARAFAC components in a sub-alpine lake, which is important in understanding the fate of increased allochthonous DOM inputs to alpine lakes impacted by climate change. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Java simulations of embedded control systems.

    PubMed

    Farias, Gonzalo; Cervin, Anton; Arzén, Karl-Erik; Dormido, Sebastián; Esquembre, Francisco

    2010-01-01

    This paper introduces a new Open Source Java library suited for the simulation of embedded control systems. The library is based on the ideas and architecture of TrueTime, a toolbox of Matlab devoted to this topic, and allows Java programmers to simulate the performance of control processes which run in a real time environment. Such simulations can improve considerably the learning and design of multitasking real-time systems. The choice of Java increases considerably the usability of our library, because many educators program already in this language. But also because the library can be easily used by Easy Java Simulations (EJS), a popular modeling and authoring tool that is increasingly used in the field of Control Education. EJS allows instructors, students, and researchers with less programming capabilities to create advanced interactive simulations in Java. The paper describes the ideas, implementation, and sample use of the new library both for pure Java programmers and for EJS users. The JTT library and some examples are online available on http://lab.dia.uned.es/jtt.

  9. Java Simulations of Embedded Control Systems

    PubMed Central

    Farias, Gonzalo; Cervin, Anton; Årzén, Karl-Erik; Dormido, Sebastián; Esquembre, Francisco

    2010-01-01

    This paper introduces a new Open Source Java library suited for the simulation of embedded control systems. The library is based on the ideas and architecture of TrueTime, a toolbox of Matlab devoted to this topic, and allows Java programmers to simulate the performance of control processes which run in a real time environment. Such simulations can improve considerably the learning and design of multitasking real-time systems. The choice of Java increases considerably the usability of our library, because many educators program already in this language. But also because the library can be easily used by Easy Java Simulations (EJS), a popular modeling and authoring tool that is increasingly used in the field of Control Education. EJS allows instructors, students, and researchers with less programming capabilities to create advanced interactive simulations in Java. The paper describes the ideas, implementation, and sample use of the new library both for pure Java programmers and for EJS users. The JTT library and some examples are online available on http://lab.dia.uned.es/jtt. PMID:22163674

  10. Temporal Changes in Photochemically Labile DOM and Implications for Carbon Budgets in Peatland Aquatic Systems

    NASA Astrophysics Data System (ADS)

    Pickard, A.

    2015-12-01

    Aquatic systems in peatland catchments are subject to high loading of dissolved organic matter (DOM) from surrounding terrestrial environments. However the significance of photochemical transformation of DOM in peatland carbon budgets remains poorly constrained. In this study UV irradiation experiments were conducted on water samples collected over one year from two contrasting systems in Scotland: a stream draining a peatland with high levels of DOM and a reservoir draining a peat catchment with low levels of DOM. Further samples were collected from the high DOM system during two storm events. After experimental exposure, optical and chemical analyses were employed to determine photochemical lability of the DOM pool. At both sites irradiation-induced decreases in dissolved organic carbon (DOC) as a percentage of the total carbon pool were greatest in winter, suggesting that DOM was depleted in photo-reactive molecules in summer. Seasonal variability in DOC was high at the stream site and was positively correlated with CO₂ and CO photoproduction (r2 = 0.81 and 0.83, respectively; p<0.05). Lignin phenol analyses indicate considerable contribution of peat to the DOM pool at the stream site, particularly during summer. Whilst DOC concentrations did not vary greatly during storm events, UV-Vis absorbance indicators did, signifying changing DOM source material from activation of different hydrological pathways. The most photo-reactive DOM occurred 5-10 hours after peak discharge, suggesting that storms replenish photochemically labile DOM in headwater streams. Conservative estimates using data from this study suggest that up to 7% of the DOM pool of peatland streams can be lost (primarily as CO₂ and CO) upon exposure to 8 hours of environmentally representative UV irradiation. Further investigation in field campaigns under natural UV exposure are underway to assess the importance of photodegradation of DOM as a loss pathway of carbon based gases from aquatic systems.

  11. Effect of dissolved organic matter source and character on microbial Hg methylation in Hg–S–DOM solutions

    USGS Publications Warehouse

    Graham, Andrew M.; Aiken, George R.; Gilmour, Cynthia

    2013-01-01

    Dissolved organic matter (DOM) is a key component of fate and transport models for most metals, including mercury (Hg). Utilizing a suite of diverse DOM isolates, we demonstrated that DOM character, in addition to concentration, influences inorganic Hg (Hg(II)i) bioavailability to Hg-methylating bacteria. Using a model Hg-methylating bacterium, Desulfovibrio desulfuricansND132, we evaluated Hg-DOM-sulfide bioavailability in washed-cell assays at environmentally relevant Hg/DOM ratios (∼1–8 ng Hg/mg C) and sulfide concentrations (1–1000 μM). All tested DOM isolates significantly enhanced Hg methylation above DOM-free controls (from ∼2 to >20-fold for 20 mg C/L DOM solutions), but high molecular weight/highly aromatic DOM isolates and/or those with high sulfur content were particularly effective at enhancing Hg methylation. Because these experiments were conducted under conditions of predicted supersaturation with respect to metacinnabar (β-HgS(s)), we attribute the DOM-dependent enhancement of Hg(II)i bioavailability to steric and specific chemical (e.g., DOM thiols) inhibition of β-HgS(s) growth and aggregation by DOM. Experiments examining the role of DOM across a wide sulfide gradient revealed that DOM only enhances Hg methylation under fairly low sulfide conditions (≲30 μM), conditions that favor HgS nanoparticle/cluster formation relative to dissolved HgS species.

  12. Bringing Interactivity to the Web: The JAVA Solution.

    ERIC Educational Resources Information Center

    Knee, Richard H.; Cafolla, Ralph

    Java is an object-oriented programming language of the Internet. It's popularity lies in its ability to create interactive Web sites across platforms. The most common Java programs are applications and applets, which adhere to a set of conventions that lets them run within a Java-compatible browser. Java is becoming an essential subject matter and…

  13. THE INFLUENCE OF DOM CHARACTER ON OZONE DECOMPOSITION RATES AND RCT

    EPA Science Inventory

    The effects of DOM character on ozonation of natural waters and solutions of DOM isolates were investigated. Batch kinetic investigations measured O3 decomposition rate constants and Rct values. Rct describes the ratio of ?OH concentration to O3 concentration, and thus provides...

  14. Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon

    PubMed Central

    Huang, Yang; Lowe, Henry J.; Klein, Dan; Cucina, Russell J.

    2005-01-01

    Objective: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS® Specialist Lexicon to improve noun phrase identification within clinical radiology documents. Design: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)® Clinical Document Architecture (CDA)–compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. Results: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. Conclusion: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain. PMID:15684131

  15. Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

    PubMed

    Huang, Yang; Lowe, Henry J; Klein, Dan; Cucina, Russell J

    2005-01-01

    The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

  16. The effect of source material in determining the photoreactivity of DOM in peatland aquatic systems

    NASA Astrophysics Data System (ADS)

    Pickard, Amy; Heal, Kate; McLeod, Andy; Dinsmore, Kerry

    2016-04-01

    Aquatic systems draining peatlands receive a high loading of dissolved organic matter (DOM) from surrounding terrestrial environments. However the fate of aquatic DOM remains poorly constrained, in part due to lack of knowledge regarding the photoreactivity of DOM and how this changes as a function of variability in source material. In this study water samples were collected monthly for a 13-month period from two contrasting aquatic systems in Scotland: a stream draining a peatland with high DOM concentrations (33.3 ± 14.2 mg DOC L-1) and a reservoir draining a peat catchment with low DOM concentrations (4.16 ± 0.91 mg DOC L-1). Controlled UV irradiation laboratory experiments were conducted on samples filtered to 0.2 μm in order to assess the photoreactivity of the DOM, measured as the unit mass of DOC lost upon irradiation. Experiments took place over 8h in temperature controlled conditions, with unirradiated samples used as controls. After exposure, a range of analytical techniques were used to characterise the DOM to yield information about its source material and to determine how this was related to the observed photoreactivity. Lignin phenol analyses indicate considerable contribution of Sphagnum to DOM at the stream site, particularly during summer, as demonstrated by high P-hydroxy/Vanillyl phenol ratios (P/V). Low P/V ratios were correlated with increased photoreactivity, (Pearson's: -0.410; p = 0.15, n = 13), suggesting that DOM from woody lignin sources within the catchment was more photolabile. Photoreactivity was also negatively correlated with Fluorescence Index (FI) values (Pearson's: -0.555; p = 0.055, n = 13), where low FI values are understood to indicate greater contribution of terrestrially derived material to aquatic DOM. Excitation-emission matrices (EEMs) indicate that DOM at the stream site was primarily comprised of a humic-like peak (Ex/Em = 340, 380/460 nm). However, there was also contribution from a protein-like peak (Ex/Em = 290

  17. Optical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation

    USGS Publications Warehouse

    Hansen, Angela; Kraus, Tamara; Pellerin, Brian; Fleck, Jacob; Downing, Bryan D.; Bergamaschi, Brian

    2016-01-01

    Advances in spectroscopic techniques have led to an increase in the use of optical properties (absorbance and fluorescence) to assess dissolved organic matter (DOM) composition and infer sources and processing. However, little information is available to assess the impact of biological and photolytic processing on the optical properties of original DOM source materials. We measured changes in commonly used optical properties and indices in DOM leached from peat soil, plants, and algae following biological and photochemical degradation to determine whether they provide unique signatures that can be linked to original DOM source. Changes in individual optical parameters varied by source material and process, with biodegradation and photodegradation often causing values to shift in opposite directions. Although values for different source materials overlapped at the end of the 111-day lab experiment, multivariate statistical analyses showed that unique optical signatures could be linked to original DOM source material even after degradation, with 17 optical properties determined by discriminant analysis to be significant (p<0.05) in distinguishing between DOM source and environmental processing. These results demonstrate that inferring the source material from optical properties is possible when parameters are evaluated in combination even after extensive biological and photochemical alteration.

  18. After the flood: consistency in DOM response to the 2010/2011 Australian floods

    NASA Astrophysics Data System (ADS)

    Shutova, Y.; Baker, A.; Bridgeman, J.; Henderson, R.

    2014-12-01

    The 2010/2011 floods in Eastern Australia were one of the worst on record, causing more than one billion AUD of damages and killing 35 people. This field campaign, monitoring raw water DOM concentration and character on three contrasting rivers across the region captured the late recession curve (October 2011- September 2012). DOM was characterized using fluorescence excitation-emission matrix (EEM) spectra with PARAFAC analysis; δ 13C-DOC; and molecular size using liquid chromatography with organic carbon, UV254 and nitrogen detection (LC-OCD) to identify DOC fractions: biopolymers, humic substance (HS), building blocks (BB), low molecular weight acids, and low molecular weight neutrals. Despite the difference in catchment and climatic zones, similar trends were observed in all three rivers, where DOC concentrations gradually decreased in river streams over a year from 8-11 mgCL-1 to 3-4 mgCL-1, followed by similar changes of HS, BB and fluorescent terrestrially delivered DOM components (C1-C3). In Allyn and Patterson rivers the proportion of HS, fluorescent terrestrially delivered DOM components (C1, C2) in DOC have decreased, in contrast to Logan River, where the ratio of HS/DOC was highly variable and showed no particular trends. The proportion of other DOC components remained almost the same. Molecular weight of the HS declined from 700 gmol-1 to 610 gmol-1 in all sites. δ 13C-DOC increased during monitoring, this could be linked to general decrease of DOM proportion delivered from C4 type plants after the flood. Overall, although DOC concentration decreased over the year post flood at all sites, most importantly the composition of DOM changed, with major changes occurring in proportion of humic-like and fluorescent terrestrially delivered DOM. Therefore it is important to monitor DOM character to be able to assess the impact of climate change and extreme weather events on the DOM transport and transformation.

  19. Geothermal and volcanism in west Java

    NASA Astrophysics Data System (ADS)

    Setiawan, I.; Indarto, S.; Sudarsono; Fauzi I, A.; Yuliyanti, A.; Lintjewas, L.; Alkausar, A.; Jakah

    2018-02-01

    Indonesian active volcanoes extend from Sumatra, Jawa, Bali, Lombok, Flores, North Sulawesi, and Halmahera. The volcanic arc hosts 276 volcanoes with 29 GWe of geothermal resources. Considering a wide distribution of geothermal potency, geothermal research is very important to be carried out especially to tackle high energy demand in Indonesia as an alternative energy sources aside from fossil fuel. Geothermal potency associated with volcanoes-hosted in West Java can be found in the West Java segment of Sunda Arc that is parallel with the subduction. The subduction of Indo-Australian oceanic plate beneath the Eurasian continental plate results in various volcanic products in a wide range of geochemical and mineralogical characteristics. The geochemical and mineralogical characteristics of volcanic and magmatic rocks associated with geothermal systems are ill-defined. Comprehensive study of geochemical signatures, mineralogical properties, and isotopes analysis might lead to the understanding of how large geothermal fields are found in West Java compared to ones in Central and East Java. The result can also provoke some valuable impacts on Java tectonic evolution and can suggest the key information for geothermal exploration enhancement.

  20. A DOM Odyssey: The Tale of Molecular Transformations in an Aquifer near Bemidji, MN

    NASA Astrophysics Data System (ADS)

    Podgorski, D. C.; Zito, P.; Smith, D. F.; Cao, X.; Schmidt-Rohr, K.; Wagner, S.; Stubbins, A.; Aiken, G.; Cozzarelli, I.; Bekins, B. A.; Spencer, R. G.

    2017-12-01

    Analytical methods including fluorescence spectroscopy, NMR spectroscopy, and ultrahigh resolution mass spectrometry have significantly advanced the understanding of compositional controls on dissolved organic matter (DOM) processing and fate. Yet, we still heavily rely on extrapolation of chemical changes identified at the edges of the compositional continuum (i.e., endmembers) to assess DOM reactivity and stability. While extrapolation of chemical transformations is useful for determining relative changes in DOM composition, a comprehensive understanding of the underlying core structures and composition is required to develop advanced biogeochemical models. Studying DOM from natural systems is complicated by many variables associated with an open system including input from multiple sources, simultaneous photo-alteration and microbial processing, and obtaining samples that cover high spatial and temporal resolution. A 38-year biodegradation study at the National Crude Oil Spill Research site near Bemidji, MN provides a unique opportunity to monitor DOM in a relatively closed system. An extensively characterized 1 m thick oil body is confined to a 25 x 75 m2 area at the water table in the aquifer. Oxidized metabolites partition from the oil into the underlying aquifer increase the DOC concentration to > 100 ppm from < 2 ppm up-gradient from the oil body. This newly produced DOM is comprised of aliphatic compounds with high H/C, low O/C and blue-shifted fluorescence, similar in composition to permafrost- and algal-derived DOM. The aliphatic DOM is transported laterally from the oil pool by groundwater, creating a plume that ultimately discharges into the Unnamed Lake 325 m downgradient. More than 10 years later and hundreds of meters downgradient from the oil body, the DOC concentration has decreased to 3-5 ppm and the DOM is compositionally non-distinct. Microbes have left behind degradation products and selectively preserved compounds that exhibit red

  1. Cadmium accumulation in zebrafish (Danio rerio) eggs is modulated by dissolved organic matter (DOM).

    PubMed

    Burnison, B Kent; Meinelt, Thomas; Playle, Richard; Pietrock, Michael; Wienke, Andreas; Steinberg, Christian E W

    2006-08-23

    Experiments were conducted to investigate factors influencing the accumulation of cadmium (Cd(2+)) into zebrafish (Danio rerio) eggs. The accumulation of (109)Cd was affected by: (1) concentration, (2) time, (3) presence of dissolved organic material (DOM), (4) different origin of DOM and (5) different parts of fish eggs. Over a 5-h exposure, zebrafish eggs showed a steady increase in Cd-accumulation. DOM-concentrations over 15ppm carbon (C) decreased Cd-uptake significantly. Both samples of DOM, brown water marsh (LM) and a eutrophic pond (SP), at 16.9ppmC, reduced the Cd-accumulation in the chorion, perivitelline liquid and the embryo. Cd was mainly accumulated in the egg's outer shell chorion (61%) and only small amounts passed through the chorion into the perivitelline liquid (38%) and embryo (1%). In the presence of LM-DOM, the accumulation of Cd into the egg components was decreased by 43% (chorion), 52% (perivitelline liquid) and 52% (embryo), respectively, compared with the control group. Similarly, the presence of SP-DOM reduced the Cd-accumulation by 29% (chorion), 61% (perivitelline liquid) and 60% (embryo), respectively, compared with the controls. DOM-concentration should be taken into consideration when determining ecotoxicological effects of Cd on fish populations.

  2. Accountable Information Flow for Java-Based Web Applications

    DTIC Science & Technology

    2010-01-01

    runtime library Swift server runtime Java servlet framework HTTP Web server Web browser Figure 2: The Swift architecture introduced an open-ended...On the server, the Java application code links against Swift’s server-side run-time library, which in turn sits on top of the standard Java servlet ...AFRL-RI-RS-TR-2010-9 Final Technical Report January 2010 ACCOUNTABLE INFORMATION FLOW FOR JAVA -BASED WEB APPLICATIONS

  3. JAVA PathFinder

    NASA Technical Reports Server (NTRS)

    Mehhtz, Peter

    2005-01-01

    JPF is an explicit state software model checker for Java bytecode. Today, JPF is a swiss army knife for all sort of runtime based verification purposes. This basically means JPF is a Java virtual machine that executes your program not just once (like a normal VM), but theoretically in all possible ways, checking for property violations like deadlocks or unhandled exceptions along all potential execution paths. If it finds an error, JPF reports the whole execution that leads to it. Unlike a normal debugger, JPF keeps track of every step how it got to the defect.

  4. Spatial pattern of dissolved organic matter (DOM) along a stream drainage in a forested, Piedmont catchment

    NASA Astrophysics Data System (ADS)

    Inamdar, S. P.; Singh, S.

    2013-12-01

    Understanding how dissolved organic matter (DOM) varies spatially in catchments and the processes and mechanisms that regulate this variation is critical for developing accurate and reliable models of DOM. We determined the concentrations and composition of DOM at multiple locations along a stream drainage network in a 79 ha forested, Piedmont, watershed in Maryland, USA. DOM concentrations and composition was compared for five stream locations during baseflow (drainage areas - 0.62, 3.5, 4.5, 12 and 79 ha) and three locations (3.5, 12, 79 ha) for storm flow. Sampling was conducted by manual grab samples and automated ISCO samplers. DOM composition was characterized using a suite of spectrofluorometric indices which included - HIX, a254, and FI. A site-specific PARAFAC model was also developed for DOM fluorescence to determine the humic-, fulvic-, and protein-like DOM constituents. Hydrologic flow paths during baseflow and stormflow were characterized for all stream locations using an end-member mixing model (EMMA). DOM varied notably across the sampled positions for baseflow and stormflow. During baseflow, mean DOC concentrations for the sampled locations ranged between 0.99-3.1 mg/L whereas for stormflow the range was 5.22-8.11 mg/L. Not surprisingly, DOM was more humic and aromatic during stormflow versus baseflow. The 3.5 ha stream drainage location that contained a large wetland yielded the highest DOC concentration as well as the most humic and aromatic DOM, during both, baseflow and stormflow. In contrast, a headwater stream location (0.62 ha) that received runoff from a groundwater seep registered the highest mean value for % protein-like DOM (30%) and the lowest index for aromaticity (mean a254 = 6.52) during baseflow. During stormflow, the mean % protein-like DOM was highest at the largest 79 ha drainage location (mean = 11.8%) and this site also registered the lowest mean value for a254 (46.3). Stream drainage locations that received a larger proportion

  5. Hydrological changes of DOM composition and biodegradability of rivers in temperate monsoon climates

    NASA Astrophysics Data System (ADS)

    Shin, Yera; Lee, Eun-Ju; Jeon, Young-Joon; Hur, Jin; Oh, Neung-Hwan

    2016-09-01

    The spatial and hydrological dynamics of dissolved organic matter (DOM) composition and biodegradability were investigated for the five largest rivers in the Republic of Korea (South Korea) during the years 2012-2013 using incubation experiments and spectroscopic measurements, which included parallel factor analysis (PARAFAC). The lower reaches of the five rivers were selected as windows showing the integrated effects of basin biogeochemistry of different land use under Asian monsoon climates, providing an insight on consistency of DOM dynamics across multiple sites which could be difficult to obtain from a study on an individual river. The mean dissolved organic carbon (DOC) concentrations of the five rivers were relatively low, ranging from 1.4 to 3.4 mg L-1, due to the high slope and low percentage of wetland cover in the basin. Terrestrial humic- and fulvic-like components were dominant in all the rivers except for one, where protein-like compounds were up to ∼80%. However, terrestrial components became dominant in all five of the rivers after high precipitation during the summer monsoon season, indicating the strong role of hydrology on riverine DOM compositions for the basins under Asian monsoon climates. Considering that 64% of South Korea is forested, our results suggest that the forests could be a large source of riverine DOM, elevating the DOM loads during monsoon rainfall. Although more DOM was degraded when DOM input increased, regardless of its sources, the percent biodegradability was reduced with increased proportions of terrestrially derived aromatic compounds. The shift in DOM quality towards higher percentages of aromatic terrestrial compounds may alter the balance of the carbon cycle of coastal ecosystems by changing microbial metabolic processes if climate extremes such as heavy storms and typhoons become more frequent due to climate change.

  6. High-Performance Java Codes for Computational Fluid Dynamics

    NASA Technical Reports Server (NTRS)

    Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

    2001-01-01

    The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

  7. Performance and Scalability of the NAS Parallel Benchmarks in Java

    NASA Technical Reports Server (NTRS)

    Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan A. (Technical Monitor)

    2002-01-01

    Several features make Java an attractive choice for scientific applications. In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for scientific applications.

  8. Molecular characteristics of continuously released DOM during one year of root and leaf litter decomposition

    NASA Astrophysics Data System (ADS)

    Altmann, Jens; Jansen, Boris; Kalbitz, Karsten; Filley, Timothy

    2013-04-01

    Dissolved organic matter (DOM) is one of the most dynamic carbon pools linking the terrestrial with the aquatic carbon cycle. Besides the insecure contribution of terrestrial DOM to the greenhouse effect, DOM also plays an important role for the mobility and availability of heavy metals and organic pollutants in soils. These processes depend very much on the molecular characteristics of the DOM. Surprisingly the processes that determine the molecular composition of DOM are only poorly understood. DOM can originate from various sources, which influence its molecular composition. It has been recognized that DOM formation is not a static process and DOM characteristics vary not only between different carbon sources. However, molecular characteristics of DOM extracts have scarcely been studied continuously over a longer period of time. Due to constant molecular changes of the parent litter material or soil organic matter during microbial degradation, we assumed that also the molecular characteristics of litter derived DOM varies at different stages during root and needle decomposition. For this study we analyzed the chemical composition of root and leaf samples of 6 temperate tree species during one year of litter decomposition in a laboratory incubation. During this long-term experiment we measured continuously carbon and nitrogen contents of the water extracts and the remaining residues, C mineralization rates, and the chemical composition of water extracts and residues by Curie-point pyrolysis mass spectrometry with TMAH We focused on the following questions: (I) How mobile are molecules derived from plant polymers like tannin, lignin, suberin and cutin? (II) How does the composition of root and leaf derived DOM change over time in dependence on the stage of decomposition and species? Litter derived DOM was generally dominated by aromatic compounds. Substituded fatty acids as typically cutin or suberin derived were not detected in the water extracts. Fresh leaf and

  9. Aps and Tep Chemical Characterization: Link Between The Dom and Pom Pools

    NASA Astrophysics Data System (ADS)

    Gogou, A.; Repeta, D. J.

    The ocean inventory of dissolved organic carbon (DOC) is approximately 750 GT, comprising one of the Earth's largest carbon reservoirs on Earth. Despite its potential significance, the mechanisms that lead to DOM production and to spatial and temporal variations of DOM concentration in the world ocean are poorly understood. Chemical characterization studies show that up to 50% of HMW DOM is a structurally well-defined class of acylated polysaccharides (APS), which exhibits novel molecular-level characteris tics. Although APS synthesis occurs in the euphotic zone, a large fraction of the marine inventory of APS (appr. 10-30 GT C), resides in the deep ocean, and is approximately equal in mass to the total marine inventory of particulate organic carbon. While radiocarbon dating of deep sea DOC yields very old apparent ages (4000-6000 ybp), radiocarbon measurements made by our group on individual APS sugars shows that APS in the deep ocean has a radiocarbon value of +56 per mil, equivalent to surface water POC and DIC. This is the first clear evidence for the presence of "young" DOC in the deep ocean. One mechanism that could be important for the rapid removal of APS from surface seawater is physical removal by macroaggregates. To investigate the significance of this mechanism, we studied the chemical composition of surface-active POM (TEP) produced naturally on surface waters and in laboratory experiments, after bubbling of HMW DOM isolated from algal cultures. 1H-NMR spectral properties and molecular-level distribution of neutral sugars in natural and artificially produced TEP closely resembled those observed for cultured and oceanic HMW DOM, while they are significantly different from those of suspended particulate matter in the ocean (Gogou and Repeta, 2000). The results of these experiments provide evidence that POM with similar chemical characteristics to HMW DOM can be produced from algal-derived DOM in the surface ocean.

  10. Contrasting effects of photochemical and microbial degradation on Cu(II) binding with fluorescent DOM from different origins.

    PubMed

    Xu, Huacheng; Guan, Dong-Xing; Zou, Li; Lin, Hui; Guo, Laodong

    2018-08-01

    Effects of photochemical and microbial degradation on variations in composition and molecular-size of dissolved organic matter (DOM) from different sources (algal and soil) and the subsequent influence on Cu(II) binding were investigated using UV-Vis, fluorescence excitation-emission matrices coupled with parallel factor analysis, flow field-flow fractionation (FlFFF), and metal titration. The degradation processes resulted in an initial rapid decline in the bulk dissolved organic carbon and chromophoric and fluorescent DOM components, followed by a small or little decrease. Specifically, photochemical reaction decreased the aromaticity, humification and apparent molecular weights of all DOM samples, whereas a reverse trend was observed during microbial degradation. The FlFFF fractograms revealed that coagulation of both protein- and humic-like DOM induced an increase in molecular weights for algal-DOM, while the molecular weight enhancement for allochthonous soil samples was mainly attributed to the self-assembly of humic-like components. The Cu(II) binding capacity of algal-derived humic-like and fulvic-like DOM consistently increased during photo- and bio-degradation, while the soil-derived DOM exhibited a slight decline in Cu(II) binding capacity during photo-degradation but a substantial increase during microbial degradation, indicating source- and degradation-dependent metal binding heterogeneities. Pearson correlation analysis demonstrated that the Cu(II) binding potential was mostly related with aromaticity and molecular size for allochthonous soil-derived DOM, but was regulated by both DOM properties and specific degradation processes for autochthonous algal-derived DOM. This study highlighted the coupling role of inherent DOM properties and external environmental processes in regulating metal binding, and provided new insights into metal-DOM interactions and the behavior and fate of DOM-bound metals in aquatic environments. Copyright © 2018 Elsevier Ltd

  11. High frequency monitoring revels new insights into baseflow DOM processing

    NASA Astrophysics Data System (ADS)

    Khamis, K.; Bradley, C.; Blaen, P.; Krause, S.; Hannah, D. M.

    2017-12-01

    Dissolved organic matter (DOM) is important for myriad biogeochemical processes in river ecosystems. Currently, however, we have limited knowledge of DOM dynamics under low flow conditions as most previous studies have focused largely on storm event dynamics. Field deployable fluorescence technology offers new opportunities to explore diurnal DOM dynamics at finer time-steps and for longer periods than previously possible, thus providing new insights into in-stream DOM processing. In this study, we collected hourly fluorescence data (Spring - Fall) and a suite of hydro-climatological variables from two contrasting UK headwater watersheds: the urban Bourn Brook, Birmingham (52° 26' N, 1° 55' W) and agricultural Mill Haft, Shropshire (52° 48' N, 2° 14' W). We hypothesised that diurnal dynamics in humic-like fluorescence (Peak C; Ex. 365 nm / Em. 490 nm) would be driven by photo-oxidation processes; while tryptophan-like fluorescence (Peak T; Ex. 285 nm / Em. 345 nm) would respond to diurnal biomass production cycles. Wavelet analysis identified significant diurnal variations in Peak C for both the Bourn Brook and Mill Haft, with the strongest signal in early summer. While the amplitude was broadly similar between sites, peak timing and consistency differed, the Bourn Brook displayed peaks in the early morning (04:00 ± 2.2 h) and Mill Haft in early evening (19:00 ± 6.6 h). Cross wavelet analysis identified strong coherence with SW radiation for the urban stream but stronger relationships with discharge for the agricultural system. Hence, results from the Bourn Brook support our hypothesis regarding Peak C photo-oxidation processes but for Mill Haft, discharge (DOM dilution) appeared to be the key control. Contrary to our hypothesis, no strong diurnal pattern was identified for Peak T for either system. From this, we infer that the low levels of Peak T produced were rapidly taken up by bacteria and/or that productivity in these systems was low. Future work on in

  12. The ENSDF Java Package

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

    Sonzogni, A.A.

    2005-05-24

    A package of computer codes has been developed to process and display nuclear structure and decay data stored in the ENSDF (Evaluated Nuclear Structure Data File) library. The codes were written in an object-oriented fashion using the java language. This allows for an easy implementation across multiple platforms as well as deployment on web pages. The structure of the different java classes that make up the package is discussed as well as several different implementations.

  13. [The Influence of Runoff Pollution to DOM Features in an Urban Wastewater Treatment Plant].

    PubMed

    He, Li; Ji, Fang-ying; Lai, Ming-sheng; Xu, Xuan; Zhou, Wei-wei; Mao, Bo-lin; Yang, Ming-jia

    2015-03-01

    Combined with wastewater treatment process, the sewage in sunny and rainy day was collected from a wastewater treatment plant in Chongqing. Three-dimensional fluorescence spectra was used to investigate the characteristic fluorescence of dissolved organic matter (DOM). DOM dissolved organic carbon (DOC), chemical oxygen demand (COD), fluorescence index (ƒ450/500) and fluorescence intensity ratio γ (A, C) of fulvic acid in ultraviolet and visible region were used to analyze the impact of rain runoff pollution on sewage DOM. According to the experimental data, the DOM fluorescence fingerprints of this wastewater treatment plant were quite different from typical municipal sewage, and the main component was tryptophan with low excitation wavelength (Peak S), then the tryptophan with long wavelength excitation (Peak T) followed. A2/O process had an approximative degradation of the protein-like both in sunny day and rainy day, but had a better degradation of fulvic-like, DOC and COD in rainy day than that in sunny day. Morever, the fluorescence peaks got red-shifted after the biological treatment. The differences of DOM fluorescence fingerprint between sunny and rainy day were significant, the fluorescence center of UV fulvic (Peak A) in rainy day getting blue-shifted obviously, shifting from 240 - 248/390 - 440 to 240 - 250/370 - 400 nm. Although the DOM types in sunny and rainy day were the same, the source of fulvic got more complex by runoff and the component ratio of DOM also changed. Compared with the sunny day, the proportion of Peak S in DOM dereased by 10%, and the proportion of Peak A increased by 7% in rainy day.

  14. JavaGenes Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

    2007-01-01

    JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

  15. East Java Maritime Connectivity and Its Regional Development Support

    NASA Astrophysics Data System (ADS)

    Purboyo, H.; Ibad, M. Z.

    2017-07-01

    The study presents an evolution of maritime connectivity index of East Java which is associated with accessibility and mobility index of regions in East Java. The findings show that East Java increased connectivity more than three times from 1996 to 2011. Initially, the East Java is importer but then become exporter to national territory. For accessibility, the inland regions of East Java in general is higher than the coastal areas. And for mobility, inland regions initially have a small index, but in subsequent years its index is greater than the coastal areas.

  16. Removal of triazine-based pollutants from water by carbon nanotubes: Impact of dissolved organic matter (DOM) and solution chemistry.

    PubMed

    Engel, Maya; Chefetz, Benny

    2016-12-01

    Adsorption of organic pollutants by carbon nanotubes (CNTs) in the environment or removal of pollutants during water purification require deep understanding of the impacts of the presence of dissolved organic matter (DOM). DOM is an integral part of environmental systems and plays a key role affecting the behavior of organic pollutants. In this study, the effects of solution chemistry (pH and ionic strength) and the presence of DOM on the removal of atrazine and lamotrigine by single-walled CNTs (SWCNTs) was investigated. The solubility of atrazine slightly decreased (∼5%) in the presence of DOM, whereas that of lamotrigine was significantly enhanced (by up to ∼70%). Simultaneous introduction of DOM and pollutant resulted in suppression of removal of both atrazine and lamotrigine, which was attributed to DOM-pollutant competition or blockage of adsorption sites by DOM. However the decrease in removal of lamotrigine was also a result of its complexation with DOM. Pre-introduction of DOM significantly reduced pollutant adsorption by the SWCNTs, whereas introduction of DOM after the pollutant resulted in the release of adsorbed atrazine and lamotrigine from the SWCNTs. These data imply that DOM exhibits higher affinity for the adsorption sites than the triazine-based pollutants. In the absence of DOM atrazine was a more effective competitor than lamotrigine for adsorption sites in SWCNTs. However, competition between pollutants in the presence of DOM revealed lamotrigine as the better competitor. Our findings help unravel the complex DOM-organic pollutant-CNT system and will aid in CNT-implementation in water-purification technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Visualization Software for VisIT Java Client

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

    Billings, Jay Jay; Smith, Robert W

    The VisIT Java Client (JVC) library is a lightweight thin client that is designed and written purely in the native language of Java (the Python & JavaScript versions of the library use the same concept) and communicates with any new unmodified standalone version of VisIT, a high performance computing parallel visualization toolkit, over traditional or web sockets and dynamically determines capabilities of the running VisIT instance whether local or remote.

  18. A Java Applet for Illustrating Internet Error Control

    ERIC Educational Resources Information Center

    Holliday, Mark A.

    2004-01-01

    This paper discusses the author's experiences developing a Java applet that illustrates how error control is implemented in the Transmission Control Protocol (TCP). One section discusses the concepts which the TCP error control Java applet is intended to convey, while the nature of the Java applet is covered in another section. The author…

  19. The composition and character of DOM from an upland peat catchment - sources, roles and fate

    NASA Astrophysics Data System (ADS)

    Worrall, F.; Moody, C.; Clay, G.; Boothroyd, I.; Burt, T. P.

    2017-12-01

    The fluvial fluxes of dissolved organic carbon (DOC) from peatlands form an important part of that ecosystem's carbon cycle, contributing approximately 35% of the overall peatland carbon budget. The source, role and fate of this component of the carbon cycle was explored for a peat covered catchment in the north east of England with dissolved organic matter (DOM) being sampled from both a first-order peat-hosted stream and soil water at two depths within the peat profile. All DOM samples were analysed within the context of analysing the particulate organic matter (POM) from the catchment; the peat profile; and biomass. All samples were analysed using: elemental analysis (C, H, N, O, P and S); bomb calorimetry; thermogravimetric analysis (TGA); 13C solid state NMR; and S isotopes. Furthermore, the degradation of fresh DOC was examined over periods of 70 hours every month for 23 months. The analysis has shown that: DOM is highly oxidised compared to all other organic in the ecosystem and DOM did not exist until [C]/[O] < 1.44. The DOM was dominantly the product of lignin breakdown and not the processing of proteins or carbohydrates, i.e. it was not an intermediate of oxidation to CO2. DOM could only be sourced from high in the peat profile at most above 41 cm depth. Thermodynamic inhibition shows that only DOM from the surface layers could be reactive in the catotelmic layers of the peat. There was a significant role for the composition of the DOM in controlling degradation with degradation rates significantly increasing with the proportion of aldehyde and carboxylic acid functional groups but decreasing with the proportion of N-alkyl functional groups. The study meant that is was possible to consider the behaviour of DOM in terms of its thermodynamic properties (DH, DS & DG) for both formation and reaction.

  20. Spatial Variations of DOM Compositions in the River with Multi-functional Weir

    NASA Astrophysics Data System (ADS)

    Yoon, S. M.; Choi, J. H.

    2017-12-01

    With the global trend to construct artificial impoundments over the last decades, there was a Large River Restoration Project conducted in South Korea from 2010 to 2011. The project included enlargement of river channel capacity and construction of multi-functional weirs, which can alter the hydrological flow of the river and cause spatial variations of water quality indicators, especially DOM (Dissolved Organic Matter) compositions. In order to analyze the spatial variations of organic matter, water samples were collected longitudinally (5 points upstream from the weir), horizontally (left, center, right at each point) and vertically (1m interval at each point). The specific UV-visible absorbance (SUVA) and fluorescence excitation-emission matrices (EEMs) have been used as rapid and non-destructive analytical methods for DOM compositions. In addition, parallel factor analysis (PARAFAC) has adopted for extracting a set of representative fluorescence components from EEMs. It was assumed that autochthonous DOM would be dominant near the weir due to the stagnation of hydrological flow. However, the results showed that the values of fluorescence index (FI) were 1.29-1.47, less than 2, indicating DOM of allochthonous origin dominated in the water near the weir. PARAFAC analysis also showed the peak at 450 nm of emission and < 250 nm of excitation which represented the humic substances group with terrestrial origins. There was no significant difference in the values of Biological index (BIX), however, values of humification index (HIX) spatially increased toward the weir. From the results of the water sample analysis, the river with multi-functional weir is influenced by the allochthonous DOM instead of autochthonous DOM and seems to accumulate humic substances near the weir.

  1. jFuzz: A Concolic Whitebox Fuzzer for Java

    NASA Technical Reports Server (NTRS)

    Jayaraman, Karthick; Harvison, David; Ganesh, Vijay; Kiezun, Adam

    2009-01-01

    We present jFuzz, a automatic testing tool for Java programs. jFuzz is a concolic whitebox fuzzer, built on the NASA Java PathFinder, an explicit-state Java model checker, and a framework for developing reliability and analysis tools for Java. Starting from a seed input, jFuzz automatically and systematically generates inputs that exercise new program paths. jFuzz uses a combination of concrete and symbolic execution, and constraint solving. Time spent on solving constraints can be significant. We implemented several well-known optimizations and name-independent caching, which aggressively normalizes the constraints to reduce the number of calls to the constraint solver. We present preliminary results due to the optimizations, and demonstrate the effectiveness of jFuzz in creating good test inputs. The source code of jFuzz is available as part of the NASA Java PathFinder. jFuzz is intended to be a research testbed for investigating new testing and analysis techniques based on concrete and symbolic execution. The source code of jFuzz is available as part of the NASA Java PathFinder.

  2. The openEHR Java reference implementation project.

    PubMed

    Chen, Rong; Klein, Gunnar

    2007-01-01

    The openEHR foundation has developed an innovative design for interoperable and future-proof Electronic Health Record (EHR) systems based on a dual model approach with a stable reference information model complemented by archetypes for specific clinical purposes.A team from Sweden has implemented all the stable specifications in the Java programming language and donated the source code to the openEHR foundation. It was adopted as the openEHR Java Reference Implementation in March 2005 and released under open source licenses. This encourages early EHR implementation projects around the world and a number of groups have already started to use this code. The early Java implementation experience has also led to the publication of the openEHR Java Implementation Technology Specification. A number of design changes to the specifications and important minor corrections have been directly initiated by the implementation project over the last two years. The Java Implementation has been important for the validation and improvement of the openEHR design specifications and provides building blocks for future EHR systems.

  3. Interactions between copper(II) and DOM in the urban stormwater runoff: modeling and characterizations.

    PubMed

    Zhao, Chen; Wang, Chong-Chen; Li, Jun-Qi; Wang, Peng; Ou, Jia-Qi; Cui, Jing-Rui

    2018-01-01

    Dissolved organic matter (DOM) can strongly interact with both organic and inorganic contaminants to influence their transportation, transformation, bioavailability, toxicity and even their ultimate fate. Within this work, DOM was extracted from urban stormwater runoff samples collected from a regular sampling site of a typical residential area in Beijing, China. Copper(II) ions were selected as model to investigate the interactions between DOM and typical heavy metals. Both ultraviolet (UV) absorbance and fluorescence titration methods were introduced to determine the complex capacities (C L ) and conditional stability constants (log K M ) of bonding between DOM and copper (II) ions, which revealed that the values of C L were 85.62 and 87.23 μmol mg -1 and the log K M values were 5.37 and 5.48, respectively. The results suggested the successful complexation between DOM and copper(II) ions. Furthermore, morphology of the DOM binding to copper(II) ions was confirmed by both energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS), which can facilitate to clarify the corresponding mechanism. The Cu 2p 3/2 peak at 933.7 eV and the characteristic shake-up peaks of Cu-O were found in the XPS spectra, implying that copper(II) ions might coordinate with hydroxyl (aliphatic or phenolic) or carboxyl groups. With these profitable results, it can be concluded that DOM in urban stormwater runoff has a strong binding affinity with copper(II) ions, which may further lead to potentially significant influence on their migration and transformation.

  4. New Web Server - the Java Version of Tempest - Produced

    NASA Technical Reports Server (NTRS)

    York, David W.; Ponyik, Joseph G.

    2000-01-01

    A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

  5. [Absorption and fluorescence characteristics of dissolved organic matter (DOM) in rainwater and sources analysis in summer and winter season].

    PubMed

    Liang, Jian; Jiang, Tao; WeiI, Shi-Qiang; Lu, Song; Yan, Jin-Long; Wang, Qi-Lei; Gao, Jie

    2015-03-01

    This study aimed at evaluating the variability of the optical properties including UV-Vis and fluorescence characteristics of dissolved organic matter (DOM) from rainwater in summer and winter seasons. UV-Vis and fluorescence spectroscopy, together with Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model and fire events map, were conducted to characterize DOM and investigate its sources and contributions. The results showed that as compared with aquatic and soil DOM, rainwater DOM showed similar spectral characteristics, suggesting DOM in precipitation was also an important contributor to DOM pool in terrestrial and aquatic systems. The concentrations of DOC in rainwater were 0.88-12.80 mg x L(-1), and the CDOM concentrations were 3.17-21.11 mg x L(-1). Differences of DOM samples between summer and winter were significant (P < 0.05). In comparison to summer, DOM samples in winter had lower molecular weight and aromaticity, and also lower humification. Input of DOM in winter was predominantly derived from local and short-distance distances, while non-special scattering sources were identified as the main contributors in summer. Although absorption and fluorescence spectroscopy could be used to identify DOM composition and sources, there were obvious differences in spectra and sources analysis between rainwater DOM and the others from other sources. Thus, the classic differentiation method by "allochthonous (terrigenous) and autochthonous (authigenic)" is possibly too simple and arbitrary for characterization of DOM in rainwater.

  6. Modelling the interactions between DOM and bacteria in marine ecosystems: state of the art and future prospective

    NASA Astrophysics Data System (ADS)

    polimene, Luca

    2014-05-01

    Marine dissolved organic matter (DOM) is the main source of carbon, nutrients and energy for marine prokaryotes, the most abundant life form in the oceans. Only a fraction of assimilated DOM is used by prokaryotes to synthesise new biomass (particulate organic matter, POM), while the rest is used for respiration or is excreted back into the environment as recalcitrant DOM (RDOM). The relative proportions of assimilated DOM that is distributed either to POM, respiration or RDOM is not constant but highly variable depending on the environmental conditions (e.g. nutrient availability, quality/quantity of DOM, temperature). This metabolic plasticity allows bacteria to shape the biogeochemistry of the surrounding waters by modulating three key carbon/energy fluxes fundamental for the functioning of the marine ecosystem: i) the transition from DOM to POM, ii) the remineralisation of carbon and nutrients, and iii) the transformation of labile DOM into recalcitrant DOM. The explicit representation of these processes (and their relative efficiency) in marine ecosystem models is a crucial (and challenging) issue which cannot be overlooked if we want to properly simulate marine biogeochemical cycles under present and climate changing conditions. This talk will provide an overview of how state of the art marine ecosystem models represent the interactions between DOM and bacteria, highlighting strengths and limits of the approaches currently used. A summary of future developments along with issues still open on the topic will also be presented and discussed.

  7. DOM in recharge waters of the Santa Ana River Basin

    USGS Publications Warehouse

    Leenheer, J.A.; Aiken, G.R.; Woodside, G.; O'Connor-Patel, K.

    2007-01-01

    The urban Santa Ana River in California is the primary source of recharge water for Orange County's groundwater basin, which provides water to more than two million residents. This study was undertaken to determine the unidentified portion of dissolved organic matter (DOM) in various natural surface and reclaimed waters of the Santa Ana River Basin and to assess the potential health risk of this material. The most abundant organic contaminants were anionic detergent degradation products (constituting about 12% of the DOM), which have no known adverse health effects. In addition, high percentages of dissolved colloids from bacterial cell walls were found during storm flows; these colloids foul membranes used in water treatment. Although no significant health risks were ascribed to the newly characterized DOM, the authors note that even the small amounts of humic substances deposited during storm flow periods were responsible for significant increases in disinfection by_product formation potential in these waters.

  8. Release and microbial degradation of dissolved organic matter (DOM) from the macroalgae Ulva prolifera.

    PubMed

    Zhang, Tao; Wang, Xuchen

    2017-12-15

    Release and microbial degradation of dissolved organic matter (DOM) and chromophoric dissolved organic matter (CDOM) from the macroalgae Ulva prolifera were studied in laboratory incubation experiments. The release of DOM and CDOM from Ulva prolifera was a rapid process, and hydrolysis played an important role in the initial leaching of the organic compounds from the algae. Bacterial activity enhanced the release of DOM and CDOM during degradation of the algae and utilization of the released organic compounds. It is calculated that 43±2% of the C and 63±3% of the N from Ulva prolifera's biomass were released during the 20-day incubation, and 65±3% of the released C and 87±4% of the released N were utilized by bacteria. In comparison, only 18±1% of the algae's C and 17±1% of its N were released when bacterial activities were inhibited. The fluorescence characteristics of the CDOM indicate that protein-like DOM was the major organic component released from Ulva prolifera that was highly labile and biodegradable. Bacteria played an important role in regulating the chemical composition and fluorescence characteristics of the DOM. Our study suggests that the release of DOM from Ulva prolifera provides not only major sources of organic C and N, but also important food sources to microbial communities in coastal waters. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. DOM composition and transformation in boreal forest soils: The effects of temperature and organic-horizon decomposition state

    USGS Publications Warehouse

    O’Donnell, Jonathan A.; Aiken, George R.; Butler, Kenna D.; Guillemette, Francois; Podgorski, David C.; Spencer, Robert G. M.

    2016-01-01

    The boreal region stores large amounts of organic carbon (C) in organic-soil horizons, which are vulnerable to destabilization via warming and disturbance. Decomposition of soil organic matter (SOM) contributes to the production and turnover of dissolved organic matter (DOM). While temperature is a primary control on rates of SOM and DOM cycling, little is known about temperature effects on DOM composition in soil leachate. Here we conducted a 30 day incubation to examine the effects of temperature (20 versus 5°C) and SOM decomposition state (moss versus fibric versus amorphous horizons) on DOM composition in organic soils of interior Alaska. We characterized DOM using bulk dissolved organic C (DOC) concentration, chemical fractionation, optical properties, and ultrahigh-resolution mass spectrometry. We observed an increase in DOC concentration and DOM aromaticity in the 20°C treatment compared to the 5°C treatment. Leachate from fibric horizons had higher DOC concentration than shallow moss or deep amorphous horizons. We also observed chemical shifts in DOM leachate over time, including increases in hydrophobic organic acids, polyphenols, and condensed aromatics and decreases in low-molecular weight hydrophilic compounds and aliphatics. We compared ultrahigh-resolution mass spectrometry and optical data and observed strong correlations between polyphenols, condensed aromatics, SUVA254, and humic-like fluorescence intensities. These findings suggest that biolabile DOM was preferentially mineralized, and the magnitude of this transformation was determined by kinetics (i.e., temperature) and substrate quality (i.e., soil horizon). With future warming, our findings indicate that organic soils may release higher concentrations of aromatic DOM to aquatic ecosystems.

  10. Spatial patterns of DOC concentration and DOM optical properties in a Brazilian tropical river-wetland system

    NASA Astrophysics Data System (ADS)

    Dalmagro, Higo J.; Johnson, Mark S.; de Musis, Carlo R.; Lathuillière, Michael J.; Graesser, Jordan; Pinto-Júnior, Osvaldo B.; Couto, Eduardo G.

    2017-08-01

    The Cerrado (savanna) and Pantanal (wetland) biomes of Central Western Brazil have experienced significant development activity in recent decades, including extensive land cover conversion from natural ecosystems to agriculture and urban expansion. The Cuiabá River transects the Cerrado biome prior to inundating large areas of the Pantanal, creating one of the largest biodiversity hot spots in the world. We measured dissolved organic carbon (DOC) and the optical absorbance and fluorescence properties of dissolved organic matter (DOM) from 40 sampling locations spanning Cerrado and Pantanal biomes during wet and dry seasons. In the upper, more agricultural region of the basin, DOC concentrations were highest in the rainy season with more aromatic and humified DOM. In contrast, DOC concentrations and DOM optical properties were more uniform for the more urbanized middle region of the basin between wet and dry seasons, as well as across sample locations. In the lower region of the basin, wet season connectivity between the river and the Pantanal floodplain led to high DOC concentrations, a fourfold increase in humification index (HIX) (an indicator of DOM humification), and a 50% reduction in the spectral slope (SR). Basin-wide, wet season values for SR, HIX, and FI (fluorescence index) indicated an increasing representation of terrestrially derived DOM that was more humified. Parallel factor analysis identified two terrestrially derived components (C1 and C2) representing 77% of total fluorescing DOM (fDOM). A third, protein-like fDOM component increased markedly during the wet season within the more urban-impacted region.

  11. High Resolution Seamless Dom Generation Over CHANG'E-5 Landing Area Using Lroc Nac Images

    NASA Astrophysics Data System (ADS)

    Di, K.; Jia, M.; Xin, X.; Liu, B.; Liu, Z.; Peng, M.; Yue, Z.

    2018-04-01

    Chang'e-5, China's first sample return lunar mission, will be launched in 2019, and the planned landing area is near Mons Rümker in Oceanus Procellarum. High-resolution and high-precision mapping of the landing area is of great importance for supporting scientific analysis and safe landing. This paper proposes a systematic method for large area seamless digital orthophoto map (DOM) generation, and presents the mapping result of Chang'e-5 landing area using over 700 LROC NAC images. The developed method mainly consists of two stages of data processing: stage 1 includes subarea block adjustment with rational function model (RFM) and seamless subarea DOM generation; stage 2 includes whole area adjustment through registration of the subarea DOMs with thin plate spline model and seamless DOM mosaicking. The resultant seamless DOM coves a large area (20° longitude × 4° latitude) and is tied to the widely used reference DEM - SLDEM2015. As a result, the RMS errors of the tie points are all around half pixel in image space, indicating a high internal precision; the RMS errors of the control points are about one grid cell size of SLDEM2015, indicating that the resultant DOM is tied to SLDEM2015 well.

  12. Muria Volcano, Island of Java, Indonesia

    NASA Technical Reports Server (NTRS)

    1991-01-01

    This view of the north coast of central Java, Indonesia centers on the currently inactive Muria Volcano (6.5S, 111.0E). Muria is 5,330 ft. tall and lies just north of Java's main volcanic belt which runs east - west down the spine of the island attesting to the volcanic origin of the more than 1,500 Indonesian Islands.

  13. Size distribution of absorbing and fluorescing DOM in Beaufort Sea, Canada Basin

    NASA Astrophysics Data System (ADS)

    Gao, Zhiyuan; Guéguen, Céline

    2017-03-01

    The molecular weight (MW) of dissolved organic matter (DOM) is considered as an important factor affecting the bioavailability of organic matter and associated chemical species. Colored DOM (CDOM) MW distribution was determined, for the first time, in the Beaufort Sea (Canada Basin) by asymmetrical flow field-flow fractionation (AF4) coupled with online diode array ultra violet-visible photometer and offline fluorescence detectors. The apparent MW ranged from 1.07 to 1.45 kDa, congruent with previous studies using high performance size exclusion chromatography and tangential flow filtration. Interestingly, a minimum in MW was associated with the Pacific Summer Waters (PSW), while higher MW was associated with the Pacific Winter Waters (PWW). The Arctic Intermediate Waters (AIW) did not show any significant change in MW and fluorescence intensities distribution between stations, suggesting homogeneous DOM composition in deep waters. Three fluorescence components including two humic-like components and one protein-like component were PARAFAC-validated. With the increase of MW, protein-like fluorescence component became more dominant while the majority remained as marine/microbially derived humic-like components. Overall, it is concluded that water mass origin influenced DOM MW distribution in the Arctic Ocean.

  14. Urbanization and agriculture increase exports and differentially alter elemental stoichiometry of dissolved organic matter (DOM) from tropical catchments.

    PubMed

    Gücker, Björn; Silva, Ricky C S; Graeber, Daniel; Monteiro, José A F; Boëchat, Iola G

    2016-04-15

    Many tropical biomes are threatened by rapid land-use change, but its catchment-wide biogeochemical effects are poorly understood. The few previous studies on DOM in tropical catchments suggest that deforestation and subsequent land use increase stream water dissolved organic carbon (DOC) concentrations, but consistent effects on DOM elemental stoichiometry have not yet been reported. Here, we studied stream water DOC concentrations, catchment DOC exports, and DOM elemental stoichiometry in 20 tropical catchments at the Cerrado-Atlantic rainforest transition, dominated by natural vegetation, pasture, intensive agriculture, and urban land cover. Streams draining pasture could be distinguished from those draining natural catchments by their lower DOC concentrations, with lower DOM C:N and C:P ratios. Catchments with intensive agriculture had higher DOC exports and lower DOM C:P ratios than natural catchments. Finally, with the highest DOC concentrations and exports, as well as the highest DOM C:P and N:P ratios, but the lowest C:N ratios among all land-use types, urbanized catchments had the strongest effects on catchment DOM. Thus, urbanization may have alleviated N limitation of heterotrophic DOM decomposition, but increased P limitation. Land use-especially urbanization-also affected the seasonality of catchment biogeochemistry. While natural catchments exhibited high DOC exports and concentrations, with high DOM C:P ratios in the rainy season only, urbanized catchments had high values in these variables throughout the year. Our results suggest that urbanization and pastoral land use exerted the strongest impacts on DOM biogeochemistry in the investigated tropical catchments and should thus be important targets for management and mitigation efforts. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Enhancing SAMOS Data Access in DOMS via a Neo4j Property Graph Database.

    NASA Astrophysics Data System (ADS)

    Stallard, A. P.; Smith, S. R.; Elya, J. L.

    2016-12-01

    The Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative provides routine access to high-quality marine meteorological and near-surface oceanographic observations from research vessels. The Distributed Oceanographic Match-Up Service (DOMS) under development is a centralized service that allows researchers to easily match in situ and satellite oceanographic data from distributed sources to facilitate satellite calibration, validation, and retrieval algorithm development. The service currently uses Apache Solr as a backend search engine on each node in the distributed network. While Solr is a high-performance solution that facilitates creation and maintenance of indexed data, it is limited in the sense that its schema is fixed. The property graph model escapes this limitation by creating relationships between data objects. The authors will present the development of the SAMOS Neo4j property graph database including new search possibilities that take advantage of the property graph model, performance comparisons with Apache Solr, and a vision for graph databases as a storage tool for oceanographic data. The integration of the SAMOS Neo4j graph into DOMS will also be described. Currently, Neo4j contains spatial and temporal records from SAMOS which are modeled into a time tree and r-tree using Graph Aware and Spatial plugin tools for Neo4j. These extensions provide callable Java procedures within CYPHER (Neo4j's query language) that generate in-graph structures. Once generated, these structures can be queried using procedures from these libraries, or directly via CYPHER statements. Neo4j excels at performing relationship and path-based queries, which challenge relational-SQL databases because they require memory intensive joins due to the limitation of their design. Consider a user who wants to find records over several years, but only for specific months. If a traditional database only stores timestamps, this type of query would be complex

  16. FPV: fast protein visualization using Java 3D.

    PubMed

    Can, Tolga; Wang, Yujun; Wang, Yuan-Fang; Su, Jianwen

    2003-05-22

    Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/

  17. Java and its future in biomedical computing.

    PubMed Central

    Rodgers, R P

    1996-01-01

    Java, a new object-oriented computing language related to C++, is receiving considerable attention due to its use in creating network-sharable, platform-independent software modules (known as "applets") that can be used with the World Wide Web. The Web has rapidly become the most commonly used information-retrieval tool associated with the global computer network known as the Internet, and Java has the potential to further accelerate the Web's application to medical problems. Java's potentially wide acceptance due to its Web association and its own technical merits also suggests that it may become a popular language for non-Web-based, object-oriented computing. PMID:8880677

  18. Highly Sensitive and Selective Ethanol Sensor Fabricated with In-Doped 3DOM ZnO.

    PubMed

    Wang, Zhihua; Tian, Ziwei; Han, Dongmei; Gu, Fubo

    2016-03-02

    ZnO is an important n-type semiconductor sensing material. Currently, much attention has been attracted to finding an effective method to prepare ZnO nanomaterials with high sensing sensitivity and excellent selectivity. A three-dimensionally ordered macroporous (3DOM) ZnO nanostructure with a large surface area is beneficial to gas and electron transfer, which can enhance the gas sensitivity of ZnO. Indium (In) doping is an effective way to improve the sensing properties of ZnO. In this paper, In-doped 3DOM ZnO with enhanced sensitivity and selectivity has been synthesized by using a colloidal crystal templating method. The 3DOM ZnO with 5 at. % of In-doping exhibits the highest sensitivity (∼88) to 100 ppm ethanol at 250 °C, which is approximately 3 times higher than that of pure 3DOM ZnO. The huge improvement to the sensitivity to ethanol was attributed to the increase in the surface area and the electron carrier concentration. The doping by In introduces more electrons into the matrix, which is helpful for increasing the amount of adsorbed oxygen, leading to high sensitivity. The In-doped 3DOM ZnO is a promising material for a new type of ethanol sensor.

  19. Using Java for distributed computing in the Gaia satellite data processing

    NASA Astrophysics Data System (ADS)

    O'Mullane, William; Luri, Xavier; Parsons, Paul; Lammers, Uwe; Hoar, John; Hernandez, Jose

    2011-10-01

    In recent years Java has matured to a stable easy-to-use language with the flexibility of an interpreter (for reflection etc.) but the performance and type checking of a compiled language. When we started using Java for astronomical applications around 1999 they were the first of their kind in astronomy. Now a great deal of astronomy software is written in Java as are many business applications. We discuss the current environment and trends concerning the language and present an actual example of scientific use of Java for high-performance distributed computing: ESA's mission Gaia. The Gaia scanning satellite will perform a galactic census of about 1,000 million objects in our galaxy. The Gaia community has chosen to write its processing software in Java. We explore the manifold reasons for choosing Java for this large science collaboration. Gaia processing is numerically complex but highly distributable, some parts being embarrassingly parallel. We describe the Gaia processing architecture and its realisation in Java. We delve into the astrometric solution which is the most advanced and most complex part of the processing. The Gaia simulator is also written in Java and is the most mature code in the system. This has been successfully running since about 2005 on the supercomputer "Marenostrum" in Barcelona. We relate experiences of using Java on a large shared machine. Finally we discuss Java, including some of its problems, for scientific computing.

  20. Late Holocene carbon and nitrogen input into the Java Sea recorded in sediment cores off rivers from Java and Kalimantan

    NASA Astrophysics Data System (ADS)

    Herbeck, Lucia; Kwiatkowski, Cornelia; Mohtadi, Mahyar; Jennerjahn, Tim

    2014-05-01

    Beginning a few thousand years ago, global climate and environmental change have become more and more affected by human activities. Hence, quantifying the 'human component' becomes increasingly important in order to predict future developments. Indonesia and the surrounding oceans are key in this respect, because it is in the region (i) that receives the highest inputs of water, sediment and associated dissolved and particulate substances and (ii) that suffers from anthropogenically modified landscapes and coastal zones. As opposing the global trend, land-based human activities have increased the sediment input into the ocean from Indonesia since pre-human times. Nevertheless, there are strong gradients in land use/cover and resulting river fluxes within Indonesia as, for example, between Java and Kalimantan. Major goal of this study is to identify the contribution of human activities in river catchments (i.e. land use/cover change, hydrological alterations) to gradients in carbon and nitrogen deposition in sediments of the Java Sea between densely populated Java and sparsely populated Kalimantan during the Late Holocene. We hypothesized that the riverine input of C and N increased during the late Holocene and increased more off Java than off Kalimantan. Sediment cores (80 to 130 cm long) off major river mouths from Java (2 cores off Bengawan Solo) and Kalimantan (1 core off Pembuang, 1 core off Jelai) were dated and analysed for Corg, Ntot, carbonate and stable isotope composition (δ13Corg, δ15N) in 3 cm intervals. Sedimentation rates off the Kalimantan rivers with 0.05-0.11 cm yr-1 were higher than off the Bengawan Solo, the largest river catchment on Java (<0.04 cm yr-1). Ntot contents in all sediment cores were low with ~0.07% and varied little over time. A higher Corg content, molar C/N ratio and variability over the past 5000 years in all parameters in the core closer to the river mouth off the Bengawan Solo than the one further offshore indicates that

  1. Implementation of BT, SP, LU, and FT of NAS Parallel Benchmarks in Java

    NASA Technical Reports Server (NTRS)

    Schultz, Matthew; Frumkin, Michael; Jin, Hao-Qiang; Yan, Jerry

    2000-01-01

    A number of Java features make it an attractive but a debatable choice for High Performance Computing. We have implemented benchmarks working on single structured grid BT,SP,LU and FT in Java. The performance and scalability of the Java code shows that a significant improvement in Java compiler technology and in Java thread implementation are necessary for Java to compete with Fortran in HPC applications.

  2. Distributed nuclear medicine applications using World Wide Web and Java technology.

    PubMed

    Knoll, P; Höll, K; Mirzaei, S; Koriska, K; Köhn, H

    2000-01-01

    At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT).

  3. An Extraction Method of an Informative DOM Node from a Web Page by Using Layout Information

    NASA Astrophysics Data System (ADS)

    Tsuruta, Masanobu; Masuyama, Shigeru

    We propose an informative DOM node extraction method from a Web page for preprocessing of Web content mining. Our proposed method LM uses layout data of DOM nodes generated by a generic Web browser, and the learning set consists of hundreds of Web pages and the annotations of informative DOM nodes of those Web pages. Our method does not require large scale crawling of the whole Web site to which the target Web page belongs. We design LM so that it uses the information of the learning set more efficiently in comparison to the existing method that uses the same learning set. By experiments, we evaluate the methods obtained by combining one that consists of the method for extracting the informative DOM node both the proposed method and the existing methods, and the existing noise elimination methods: Heur removes advertisements and link-lists by some heuristics and CE removes the DOM nodes existing in the Web pages in the same Web site to which the target Web page belongs. Experimental results show that 1) LM outperforms other methods for extracting the informative DOM node, 2) the combination method (LM, {CE(10), Heur}) based on LM (precision: 0.755, recall: 0.826, F-measure: 0.746) outperforms other combination methods.

  4. Revealing Sources and Distribution Changes of Dissolved Organic Matter (DOM) in Pore Water of Sediment from the Yangtze Estuary

    PubMed Central

    Wang, Ying; Zhang, Di; Shen, Zhenyao; Feng, Chenghong; Chen, Jing

    2013-01-01

    Dissolved organic matter (DOM) in sediment pore waters from Yangtze estuary of China based on abundance, UV absorbance, molecular weight distribution and fluorescence were investigated using a combination of various parameters of DOM as well as 3D fluorescence excitation emission matrix spectra (F-EEMS) with the parallel factor and principal component analysis (PARAFAC-PCA). The results indicated that DOM in pore water of Yangtze estuary was very variable which mainly composed of low aromaticity and molecular weight materials. Three humic-like substances (C1, C2, C4) and one protein-like substance (C3) were identified by PARAFAC model. C1, C2 and C4 exhibited same trends and were very similar. The separation of samples on both axes of the PCA showed the difference in DOM properties. C1, C2 and C4 concurrently showed higher positive factor 1 loadings, while C3 showed highly positive factor 2 loadings. The PCA analysis showed a combination contribution of microbial DOM signal and terrestrial DOM signal in the Yangtze estuary. Higher and more variable DOM abundance, aromaticity and molecular weight of surface sediment pore water DOM can be found in the southern nearshore than the other regions primarily due to the influence of frequent and intensive human activities and tributaries inflow in this area. The DOM abundance, aromaticity, molecular weight and fluorescence intensity in core of different depth were relative constant and increased gradually with depth. DOM in core was mainly composed of humic-like material, which was due to higher release of the sedimentary organic material into the porewater during early diagenesis. PMID:24155904

  5. JPARSS: A Java Parallel Network Package for Grid Computing

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

    Chen, Jie; Akers, Walter; Chen, Ying

    2002-03-01

    The emergence of high speed wide area networks makes grid computinga reality. However grid applications that need reliable data transfer still have difficulties to achieve optimal TCP performance due to network tuning of TCP window size to improve bandwidth and to reduce latency on a high speed wide area network. This paper presents a Java package called JPARSS (Java Parallel Secure Stream (Socket)) that divides data into partitions that are sent over several parallel Java streams simultaneously and allows Java or Web applications to achieve optimal TCP performance in a grid environment without the necessity of tuning TCP window size.more » This package enables single sign-on, certificate delegation and secure or plain-text data transfer using several security components based on X.509 certificate and SSL. Several experiments will be presented to show that using Java parallelstreams is more effective than tuning TCP window size. In addition a simple architecture using Web services« less

  6. Instrumentation of Java Bytecode for Runtime Analysis

    NASA Technical Reports Server (NTRS)

    Goldberg, Allen; Haveland, Klaus

    2003-01-01

    This paper describes JSpy, a system for high-level instrumentation of Java bytecode and its use with JPaX, OUT system for runtime analysis of Java programs. JPaX monitors the execution of temporal logic formulas and performs predicative analysis of deadlocks and data races. JSpy s input is an instrumentation specification, which consists of a collection of rules, where a rule is a predicate/action pair The predicate is a conjunction of syntactic constraints on a Java statement, and the action is a description of logging information to be inserted in the bytecode corresponding to the statement. JSpy is built using JTrek an instrumentation package at a lower level of abstraction.

  7. Spatial and temporal variations in DOM composition in ecosystems: The importance of long-term monitoring of optical properties

    Treesearch

    R. Jaffe; D. McKnight; N. Maie; R. Cory; W. H. McDowell; J.L. Campbell

    2008-01-01

    Source, transformation, and preservation mechanisms of dissolved organic matter (DOM) remain elemental questions in contemporary marine and aquatic sciences and represent a missing link in models of global elemental cycles. Although the chemical character of DOM is central to its fate in the global carbon cycle, DOM characterizations in long-term ecological research...

  8. Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon.

    PubMed

    Qiu, Qingyan; Wu, Lanfang; Ouyang, Zhu; Li, Binbin; Xu, Yanyan

    2016-03-01

    Soil organic carbon (SOC) mineralization is important for the regulation of the global climate and soil fertility. Decomposition of SOC may be significantly affected by the supply of plant-derived labile carbon (C). To investigate the impact of plant-derived dissolved organic matter (DOM) and urea (N) additions on the decomposition of native SOC as well as to elucidate the underlying mechanisms of priming effects (PEs), a batch of incubation experiments was conducted for 250 days by application of (13)C-labeled plant-derived DOM and urea to soils. The direction of PE induced by the addition of DOM was different from the addition of N, i.e. it switched from negative to positive in DOM-amended soils, whereas in the N-treated soil it switched from positive to negative. Adding DOM alone was favorable for soil C sequestration (59 ± 5 mg C per kg soil), whereas adding N alone or together with DOM accelerated the decomposition of native SOC, causing net C losses (-62 ± 4 and -34 ± 31 mg C per kg soil, respectively). These findings indicate that N addition and its interaction with DOM are not favorable for soil C sequestration. Adding DOM alone increased the level of dissolved organic carbon (DOC), but it did not increase the level of soil mineral N. Changes in the ratio of microbial biomass carbon (MBC) to microbial biomass nitrogen (MBN) and microbial metabolic quotient (qCO2) after the addition of DOM and N suggest that a possible shift in the microbial community composition may occur in the present study. Adding DOM with or without N increased the activities of β-glucosidase and urease. Changes in the direction and magnitude of PE were closely related to changes in soil C and N availability. Soil C and N availability might influence the PE through affecting the microbial biomass and extracellular enzyme activity as well as causing a possible shift in the microbial community composition.

  9. Analysing Submarine Groundwater Discharge (SGD)-borne Dissolved Organic Matter (DOM) in a karstic aquifer, Co. Galway, Ireland.

    NASA Astrophysics Data System (ADS)

    Kelly, Tara; Rocha, Carlos

    2014-05-01

    Submarine Groundwater Discharge (SGD) constitutes an "invisible" link between land and sea, transporting allochthonous and autochthonous dissolved organic matter (DOM), nutrients and metals to the ocean via the subterranean estuary. The latter acts as a powerful bioreactor where groundwater, in transit from land to sea, mixes with seawater leading to active modulation of both DOM content and chemical makeup of SGD. DOM in freshwater systems is a key component of the global carbon cycle. Climate change may hence increase the concentration of allochthonous carbon entering the oceans as terrestrial DOC is released from soils at higher temperatures, and transported via SGD. Presently, little is known about the effects of SGD-borne DOM on coastal carbon cycling. SGD therefore represents a dynamic reservoir and analysis is critical to forecast future environmental management programmes, both on a local and global scale. Labile DOM plays a crucial role in microbial remineralisation processes, and as it breaks down it contributes to the groundwater nutrient pool. Locally, this could add to eutrophication. However, if refractory carbon is present, it will be recalcitrant to mineralisation in transit and at the subterranean estuary. This putative additional input will thus imply the contribution of SGD to oceanic carbon storage. This study is focused on Kinvara Bay (Galway, western Ireland), the focal point for waters discharging from the Gort-Kinvara karstic aquifer. This aquifer represents the ideal study location for evaluation of SGD contribution to the coastal DOM pool, as SGD is focused in the bay, surface drainage is very limited, and groundwater travels across a large catchment area with a short residence time, minimising DOM modification in transit. DOM samples collected in the field have been analysed using Three-Dimensional Excitation Emission Matrix Fluorescence (3D-EEMF) and High Temperature Catalytic Oxidation. PARAFAC is subsequently used as a tool to

  10. Real-time Java for flight applications: an update

    NASA Technical Reports Server (NTRS)

    Dvorak, D.

    2003-01-01

    The RTSJ is a specification for supporting real-time execution in the Java programming language. The specification has been shaped by several guiding principles, particularly: predictable execution as the first priority in all tradeoffs, no syntactic extensions to Java, and backward compatibility.

  11. 'invisible' DOM in hourly-resolved headwater river records from Northern Amazonia

    NASA Astrophysics Data System (ADS)

    Pereira, R.; Bovolo, C.; Spencer, R. G.; Hernes, P. J.; Tipping, E.; Vieth-Hillebrand, A.; Chappell, N.; Lewis-Franklin, A.; Parkin, G.; Wagner, T.

    2012-12-01

    , whereas high levels in DOC are not explained by humic substances. Size exclusion chromatography confirms that the DOM pool is divided into two main fractions, humic substances and 'invisible' DOM, or 'iDOM'. The latter group includes non UV-absorbing organic compounds of mono- and oligosaccharides, alcohols, aldehydes, ketones and amino sugars. Our new records from Guyana show that whilst lignin phenols are present and closely track the UV absorbance (R2 = 0.97), it is iDOM that dominates the total DOC pool at peak concentrations (up to 84%). Notably, iDOM is still found in the main Burro Burro River (20-40%), indicating that iDOM has some potential to survive transport downstream. The results suggest that DOC could be significantly underestimated in tropical systems due to the observed decoupling of DOC, water colour (CDOM) and river flux related to large amounts of iDOM entering the river during rainstorm events and wet seasons. Furthermore, given that headwaters represent roughly 50-85% of the total area of tropical river catchments, it is likely that iDOM is a significant component of the terrestrial carbon and nutrient cycles. It is therefore necessary to conduct further field studies that will produce high resolution (temporal and spatial) geochemical records from a large number of tropical systems to better quantify the role of tropical inland waters in carbon and nutrient cycling.

  12. Investigating the effect of hardness cations on coagulation: The aspect of neutralisation through Al(III)-dissolved organic matter (DOM) binding.

    PubMed

    Zhou, Yuxuan; Yan, Mingquan; Liu, Ruiping; Wang, Dongsheng; Qu, Jiuhui

    2017-05-15

    Hardness cations are ubiquitous and abundant in source water, while the effect of hardness on the performance of coagulation for dissolved organic matter (DOM) removal in water treatment remains unclear due to the limitation of methods that can characterise the subtle interactions between DOM, coagulant and hardness cations. This work quantified the competition between coagulant Al 3+ and hardness cations to bind onto DOM using absorbance spectroscopy acquired at different Al 3+ concentrations in the absence and presence of Ca 2+ or Mg 2+ . The results indicate that, in the presence of either Mg 2+ or Ca 2+ , an increasing depression of the binding of Al 3+ -DOM could be observed in the differential spectra of DOM with the increasing of Mg 2+ or Ca 2+ at a level of 10, 100 and 1000 μM, with the observation being more significant at higher pH from 6.5 to 8.5. The results of zeta potentials of DOM indicate that the competition of hardness cations results in the negative DOM being less efficiently neutralised by Al 3+ . This study demonstrates that the removal of DOM by coagulation would significantly deteriorate with the presence of hardness cations, which would compete with coagulant Al 3+ to neutralise the unsaturated sites in DOM. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Characterization of spectral responses of dissolved organic matter (DOM) for atrazine binding during the sorption process onto black soil.

    PubMed

    Wang, Yifan; Zhang, Xinyuan; Zhang, Xing; Meng, Qingjuan; Gao, Fengjie; Zhang, Ying

    2017-08-01

    This study was aim to investigate the interaction between soil-derived dissolved organic matter (DOM) and atrazine as a kind of pesticides during the sorption process onto black soil. According to the experimental data, the adsorption capacity of Soil + DOM, Soil and DOM were 41.80, 31.45 and 9.35 mg kg -1 , separately, which indicated that DOM significantly enhanced the adsorption efficiency of atrazine by soil. Data implied that the pseudo-second-order kinetic equation could well explain the adsorption process. The adsorption isotherms (R 2  > 0.99) had a satisfactory fit in both Langmuir and Freundlich models. Three-dimensional excitation-emission matrix (3D-EEM), synchronous fluorescence, two-dimensional correlation spectroscopy (2D-COS) and Fourier transform infrared spectroscopy (FT-IR) were selected to analyze the interaction between DOM and atrazine. 3D-EEM showed that humic acid-like substances were the main component of DOM. The fluorescence of DOM samples were gradually quenched with the increased of atrazine concentrations. Synchronous fluorescence spectra showed that static fluorescence quenching was the main quenching process. 2D-COS indicated that the order of the spectral changes were as following: 336 nm > 282 nm. Furthermore, the fluorescence quenching of humic-like fraction occurred earlier than that of protein-like fraction under atrazine surroundings. FT-IR spectra indicated that main compositions of soil DOM include proteins, polysaccharides and humic substances. The findings of this study are significant to reveal DOM played an important role in the environmental fate of pesticides during sorption process onto black soil and also provide more useful information for understanding the interaction between DOM and pesticides by using spectral responses. Copyright © 2017. Published by Elsevier Ltd.

  14. Sawja: Static Analysis Workshop for Java

    NASA Astrophysics Data System (ADS)

    Hubert, Laurent; Barré, Nicolas; Besson, Frédéric; Demange, Delphine; Jensen, Thomas; Monfort, Vincent; Pichardie, David; Turpin, Tiphaine

    Static analysis is a powerful technique for automatic verification of programs but raises major engineering challenges when developing a full-fledged analyzer for a realistic language such as Java. Efficiency and precision of such a tool rely partly on low level components which only depend on the syntactic structure of the language and therefore should not be redesigned for each implementation of a new static analysis. This paper describes the Sawja library: a static analysis workshop fully compliant with Java 6 which provides OCaml modules for efficiently manipulating Java bytecode programs. We present the main features of the library, including i) efficient functional data-structures for representing a program with implicit sharing and lazy parsing, ii) an intermediate stack-less representation, and iii) fast computation and manipulation of complete programs. We provide experimental evaluations of the different features with respect to time, memory and precision.

  15. Visualizing DOM super-spectrum covariance in vanKrevelen space

    NASA Astrophysics Data System (ADS)

    Fatland, D. R.; Kalawe, J.; Stubbins, A.; Spencer, R. G.; Sleighter, R. L.; Abdulla, H. A.; Dittmar, T.

    2011-12-01

    We investigate the fate of terrigenous organic matter, DOM exported to the coastal marine environ. Many methods (fluor., FT-ICR-MS, NMR, 13C, lignin, etc) help characterize this DOM. We define a 'super spectrum' as amalgamation of analyses to a data stack and we search for physically significant patterns therein beginning with covariance across 31 samples from six circum-Arctic rivers: The Ob, Kolyma, Mackenzie, Yukon, Lena, and Yenisey sampled five times throughout the year. A vanKrevelen diagram is convenient to view distributions of molecules provided by Fourier Transform Ion Cyclotron Resonance Mass Spectometry (FT-ICR-MS). We augment this distribution space in the vertical dimension, for example to show peak height, molecular mass, principle component weighting or covariance. We use Worldwide Telescope, a virtual globe with strong data support from Microsoft Research to explore covariance results along 3+ dimensions (adding brightness, color and a parameter slide). The results show interesting covariance e.g. between molecules and PARAFAC peaks, a step towards fluorophore and cohort identification in the terrigenous DOM spectrum. Given the geoscience explosion in data volume and data complexity we feel these results should survive beyond the end point of a journal article. We are building a cloud-based Library on the Microsoft Azure platform to support this and subsequent analyses to enable data and methods to carry over and benefit other research groups and objectives.

  16. Seeing the light: Applications of in situ optical measurements for understanding DOM dynamics in river systems (Invited)

    NASA Astrophysics Data System (ADS)

    Pellerin, B. A.; Bergamaschi, B. A.; Downing, B. D.; Saraceno, J.; Fleck, J.; Shanley, J. B.; Aiken, G.; Boss, E.; Fujii, R.

    2009-12-01

    A critical challenge for understanding the sources, character and cycling of dissolved organic matter (DOM) is making measurements at the time scales in which changes occur in aquatic systems. Traditional approaches for data collection (daily to monthly discrete sampling) are often limited by analytical and field costs, site access and logistical challenges, particularly for long-term sampling at a large number of sites. The ability to make optical measurements of DOM in situ has been known for more than 50 years, but much of the work on in situ DOM absorbance and fluorescence using commercially-available instruments has taken place in the last few years. Here we present several recent examples that highlight the application of in situ measurements for understanding DOM dynamics in riverine systems at intervals of minutes to hours. Examples illustrate the utility of in situ optical sensors for studies of DOM over short-duration events of days to weeks (diurnal cycles, tidal cycles, storm events and snowmelt periods) as well as longer-term continuous monitoring for months to years. We also highlight the application of in situ optical DOM measurements as proxies for constituents that are significantly more difficult and expensive to measure at high frequencies (e.g. methylmercury, trihalomethanes). Relatively simple DOM absorbance and fluorescence measurements made in situ could be incorporated into short and long-term ecological research and monitoring programs, resulting in advanced understanding of organic matter sources, character and cycling in riverine systems.

  17. The Effects of Biodegradation and Photodegradation on DOM Optical Properties: Controlled Laboratory Study Using Plant, Soil and Algal Leachates

    NASA Astrophysics Data System (ADS)

    Hansen, A. M.; Kraus, T. E. C.; Pellerin, B. A.; Fleck, J.

    2014-12-01

    Many studies use optical properties to infer dissolved organic matter (DOM) composition and origin; however, there are few controlled studies which examine the effects of environmental processing on different DOM sources. Our goal was to better understand the roles DOM plays in wetland environments of the Sacramento-San Joaquin Delta. Therefore, five endmember sources of DOM from this region were selected for use in this study: peat soil (euic, thermic Typic Medisaprists); three aquatic macrophytes (white rice (Oryza sativa); tule (Schoenoplectus acutus); cattail (Typha spp.)); and one diatom (Thalassiosira weissflogii). We measured DOM concentrations (mg C/L) and optical properties (absorbance and fluorescence) of these sources following biological and photochemical degradation over a three month period. DOM concentration decreased by over 90% in plant and algal leachates following 3 months of biodegradation, while photoexposure had negligible effects. The fluorescence index (FI), humic index (HI), specific UV absorbance at 254 nm (SUVA), and carbon-normalized fluorescence of Peaks C and A increased with biodegradation, whereas Peak T decreased. Photoexposure resulted in a decrease of the FI, HI and SUVA values. Our results emphasize the need to better understand how environmental processing affects DOM properties in aquatic environments; the frequently opposing effects of biodegradation and photodegradation, which occur simultaneously in nature, make it challenging to decipher the original DOM source without considering multiple parameters. This dataset can help us better identify which optical properties, either individual or in combination, can provide insight into how biogeochemical processes affect DOM in aquatic environments.

  18. ULTRA: Universal Grammar as a Universal Parser

    PubMed Central

    Medeiros, David P.

    2018-01-01

    A central concern of generative grammar is the relationship between hierarchy and word order, traditionally understood as two dimensions of a single syntactic representation. A related concern is directionality in the grammar. Traditional approaches posit process-neutral grammars, embodying knowledge of language, put to use with infinite facility both for production and comprehension. This has crystallized in the view of Merge as the central property of syntax, perhaps its only novel feature. A growing number of approaches explore grammars with different directionalities, often with more direct connections to performance mechanisms. This paper describes a novel model of universal grammar as a one-directional, universal parser. Mismatch between word order and interpretation order is pervasive in comprehension; in the present model, word order is language-particular and interpretation order (i.e., hierarchy) is universal. These orders are not two dimensions of a unified abstract object (e.g., precedence and dominance in a single tree); rather, both are temporal sequences, and UG is an invariant real-time procedure (based on Knuth's stack-sorting algorithm) transforming word order into hierarchical order. This shift in perspective has several desirable consequences. It collapses linearization, displacement, and composition into a single performance process. The architecture provides a novel source of brackets (labeled unambiguously and without search), which are understood not as part-whole constituency relations, but as storage and retrieval routines in parsing. It also explains why neutral word order within single syntactic cycles avoids 213-like permutations. The model identifies cycles as extended projections of lexical heads, grounding the notion of phase. This is achieved with a universal processor, dispensing with parameters. The empirical focus is word order in noun phrases. This domain provides some of the clearest evidence for 213-avoidance as a cross

  19. The r-Java 2.0 code: nuclear physics

    NASA Astrophysics Data System (ADS)

    Kostka, M.; Koning, N.; Shand, Z.; Ouyed, R.; Jaikumar, P.

    2014-08-01

    Aims: We present r-Java 2.0, a nucleosynthesis code for open use that performs r-process calculations, along with a suite of other analysis tools. Methods: Equipped with a straightforward graphical user interface, r-Java 2.0 is capable of simulating nuclear statistical equilibrium (NSE), calculating r-process abundances for a wide range of input parameters and astrophysical environments, computing the mass fragmentation from neutron-induced fission and studying individual nucleosynthesis processes. Results: In this paper we discuss enhancements to this version of r-Java, especially the ability to solve the full reaction network. The sophisticated fission methodology incorporated in r-Java 2.0 that includes three fission channels (beta-delayed, neutron-induced, and spontaneous fission), along with computation of the mass fragmentation, is compared to the upper limit on mass fission approximation. The effects of including beta-delayed neutron emission on r-process yield is studied. The role of Coulomb interactions in NSE abundances is shown to be significant, supporting previous findings. A comparative analysis was undertaken during the development of r-Java 2.0 whereby we reproduced the results found in the literature from three other r-process codes. This code is capable of simulating the physical environment of the high-entropy wind around a proto-neutron star, the ejecta from a neutron star merger, or the relativistic ejecta from a quark nova. Likewise the users of r-Java 2.0 are given the freedom to define a custom environment. This software provides a platform for comparing proposed r-process sites.

  20. Factorial analysis of the trihalomethane formation in the reaction of colloidal, hydrophobic, and transphilic fractions of DOM with free chlorine.

    PubMed

    Platikanov, Stefan; Tauler, Roma; Rodrigues, Pedro M S M; Antunes, Maria Cristina G; Pereira, Dilson; Esteves da Silva, Joaquim C G

    2010-09-01

    This study focuses on the factors that affect trihalomethane (THMs) formation when dissolved organic matter (DOM) fractions (colloidal, hydrophobic, and transphilic fractions) in aqueous solutions were disinfected with chlorine. DOM fractions were isolated and fractionated from filtered lake water and were characterized by elemental analysis. The investigation involved a screening Placket-Burman factorial analysis design of five factors (DOM concentration, chlorine dose, temperature, pH, and bromide concentration) and a Box-Behnken design for a detailed assessment of the three most important factor effects (DOM concentration, chlorine dose, and temperature). The results showed that colloidal fraction has a relatively low contribution to THM formation; transphilic fraction was responsible for about 50% of the chloroform generation, and the hydrophobic fraction was the most important to the brominated THM formation. When colloidal and hydrophobic fraction solutions were disinfected, the most significant factors were the following: higher DOM fraction concentration led to higher THM concentration, an increase of pH corresponded to higher concentration levels of chloroform and reduced bromoform, higher levels of chlorine dose and temperature produced a rise in the total THM formation, especially of the chlorinated THMs; higher bromide concentration generates higher concentrations of brominated THMs. Moreover, linear models were implemented and response surface plots were obtained for the four THM concentrations and their total sum in the disinfection solution as a function of the DOM concentration, chlorine dose, and temperature. Overall, results indicated that THM formation models were very complex due to individual factor effects and significant interactions among the factors. In order to reduce the concentration of THMs in drinking water, DOM concentrations must be reduced in the water prior to the disinfection. Fractionation of DOM, together with an elemental

  1. Prototyping Faithful Execution in a Java virtual machine.

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

    Tarman, Thomas David; Campbell, Philip LaRoche; Pierson, Lyndon George

    2003-09-01

    This report presents the implementation of a stateless scheme for Faithful Execution, the design for which is presented in a companion report, ''Principles of Faithful Execution in the Implementation of Trusted Objects'' (SAND 2003-2328). We added a simple cryptographic capability to an already simplified class loader and its associated Java Virtual Machine (JVM) to provide a byte-level implementation of Faithful Execution. The extended class loader and JVM we refer to collectively as the Sandia Faithfully Executing Java architecture (or JavaFE for short). This prototype is intended to enable exploration of more sophisticated techniques which we intend to implement in hardware.

  2. The Urban Watershed as a Transformer of DOM Chemistry

    NASA Astrophysics Data System (ADS)

    Gabor, R. S.; Smith, R. M.; Follstad Shah, J.; Kelso, J. E.; Baker, M. A.; Brooks, P. D.

    2017-12-01

    Growing urban systems stress watersheds, resulting in water quality impacts downstream. Urban stresses can include nutrient runoff from fertilizer, effluent from wastewater treatment plants, and changes in hydrologic routing. Synoptic surveys were performed at two rivers in Salt Lake City, Utah to identify how urbanization drives dissolved organic matter (DOM) chemistry. Red Butte Creek, a small third order stream, flows from a protected mountain environment directly into a highly urbanized mountain area. The organic matter chemistry, as measured by fluorescence, changed dynamics in the urban system, with organic matter demonstrating greater aromaticity and different seasonal patterns than observed in the canyon. Several kilometers downstream of the start of urbanization, the C:N ratio of the organic matter changes from 12.5 to 17.7, at a location where the stream is fed by urban-impacted groundwater, suggesting that subsurface DOC is utilized for microbial respiration in denitrification of urban nitrate inputs. This also corresponds with a shift in the chemistry of the DOM, as measured by fluorescence. Red Butte Creek terminates at the Jordan River, which flows from a highly eutrophic lake and is fed by seven tributaries and five wastewater treatment plants before ending at the Great Salt Lake. The Jordan River is heavily contaminated, with low dissolved oxygen and high nutrient content. The fluorescence index (FI) of DOM in the Jordan River indicates a dominant microbial contribution to the fluorescent organic material, particularly in areas where the dissolved oxygen is low, with the FI becoming less microbial as the DO sag lessens. This corresponds to increasing fluorescence signal in the protein-like area of the fluorescence excitation-emission matrices. Additionally, effluent from four wastewater treatment plants, each with different technologies, had distinct organic matter fluorescence, corresponding with differences in the nitrogen and microbial dynamics

  3. Creating Web-Based Scientific Applications Using Java Servlets

    NASA Technical Reports Server (NTRS)

    Palmer, Grant; Arnold, James O. (Technical Monitor)

    2001-01-01

    There are many advantages to developing web-based scientific applications. Any number of people can access the application concurrently. The application can be accessed from a remote location. The application becomes essentially platform-independent because it can be run from any machine that has internet access and can run a web browser. Maintenance and upgrades to the application are simplified since only one copy of the application exists in a centralized location. This paper details the creation of web-based applications using Java servlets. Java is a powerful, versatile programming language that is well suited to developing web-based programs. A Java servlet provides the interface between the central server and the remote client machines. The servlet accepts input data from the client, runs the application on the server, and sends the output back to the client machine. The type of servlet that supports the HTTP protocol will be discussed in depth. Among the topics the paper will discuss are how to write an http servlet, how the servlet can run applications written in Java and other languages, and how to set up a Java web server. The entire process will be demonstrated by building a web-based application to compute stagnation point heat transfer.

  4. HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

    ERIC Educational Resources Information Center

    Machovec, George S., Ed.

    1995-01-01

    Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

  5. Modeling rates of DOC degradation using DOM composition and hydroclimatic variables

    NASA Astrophysics Data System (ADS)

    Moody, C. S.; Worrall, F.

    2017-05-01

    The fluvial fluxes of dissolved organic carbon (DOC) from peatlands form an important part of that ecosystem's carbon cycle, contributing approximately 35% of the overall peatland carbon budget. The in-stream processes acting on the DOC, such as photodegradation and biodegradation, can lead to DOC loss and thus contribute CO2 to the atmosphere. The aim of this study was to understand what controls the rates of DOC degradation. Water samples from a headwater, peat-covered catchment, were collected over a 23 month period and analyzed for the DOC degradation rate and dissolved organic matter (DOM) composition in the context of hydroclimatic monitoring. Measures of DOM composition included 13C solid-state nuclear magnetic resonance spectroscopy, bomb calorimetry, and elemental analysis. Regression analysis showed that there was a significant role for the composition of the DOM in controlling degradation with degradation rates significantly increasing with the proportion of aldehyde and carboxylic acid functional groups but decreasing with the proportion of N-alkyl functional groups. The highest rates of DOC degradation occurred when aldehyde functionality was at its greatest and this occurred on the recession limb of storm hydrographs. Including this knowledge into models of fluvial carbon fate for an 818 km2 catchment gave an annual average DOC removal rate of 67% and 50% for total organic carbon, slightly lower than previously predicted. The compositional controls suggest that DOM is primarily being used as a ready energy source to the aquatic ecosystem rather than as a nutrient source.

  6. MzJava: An open source library for mass spectrometry data processing.

    PubMed

    Horlacher, Oliver; Nikitin, Frederic; Alocci, Davide; Mariethoz, Julien; Müller, Markus; Lisacek, Frederique

    2015-11-03

    Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library's API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Petrographic and major elements results as indicator of the geothermal potential in Java

    NASA Astrophysics Data System (ADS)

    Indarto, S.; Setiawan, I.; Kausar, A.; Permana, dan H.

    2018-02-01

    Geothermal manifestations existed in West Java (Cilayu, Papandayan Mountain, Telagabodas, Karaha, Tampomas Mountain), Central Java (Slamet Mountain, Dieng) and East Java (Argopuro Mountain) show a difference in their mineral and geochemical compositions. The petrographic analysis of volcanic rocks from Garut (West Java) are basalt, andesite basaltic and andesite. However, based on SiO2 vs K2O value, those volcanic rocks have wide ranges of fractionated magma resulting basalt - basaltic andesite to dacitic in composition rather than those of Slamet Mountain, Dieng, and Argopuro Mountain areas which have a narrower range of fractionation magma resulting andesite basaltic and andesite in compositions. The volcanic rocks from Garut show tholeiitic affinity and calc-alkaline affinity. The geothermal potential of Java is assumed to be related to the magma fractionation level. Geothermal potential of West Java (Garut) is higher than that of Central Java (Slamet Mountain, Dieng) and East Java (Argopuro Mountain).

  8. Almost stochastic dominance for poverty level in Central Java Province

    NASA Astrophysics Data System (ADS)

    Slamet, Isnandar; Agus Wibowo, Aryanto; Roswitha, Mania

    2017-12-01

    The criteria for the domination of the distribution function has been used in the investment issues, momentum, agricultural production, and so on. One criteria of domination is stochastic dominance (SD). When this criteria is applied to the dominating area that has smaller value than the dominated area, then almost stochastic dominance (ASD) can be used. It this research, we apply the ASD criteria on data of expenditure per capita based on districts/cities in Central Java. Furthermore, we determine which year the expenditure per capita in the period 2009-2013 is the most dominating to know the level of poverty in Central Java. From the discussion, it can be concluded that the expenditure per capita in Central Java in 2013 dominates expenditure per capita in Central Java in 2009-2012. In other words, the level of poverty in Central Java in 2013 is lower than in 2009-2012.

  9. Java for flight software

    NASA Technical Reports Server (NTRS)

    Benowitz, E. G.; Niessner, A. F.

    2003-01-01

    We have successfully demonstrated a portion of the spacecraft attitude control and fault protection, running on a standard Java platform, and are currently in the process of taking advantage of the features provided by the RTSJ.

  10. JavaScript: Data Visualizations

    EPA Pesticide Factsheets

    D3 is a JavaScript library that, in a manner similar to jQuery library, allows direct inspection and manipulation of the Document Object Model, but is intended for the primary purpose of data visualization.

  11. Java Performance for Scientific Applications on LLNL Computer Systems

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

    Kapfer, C; Wissink, A

    2002-05-10

    Languages in use for high performance computing at the laboratory--Fortran (f77 and f90), C, and C++--have many years of development behind them and are generally considered the fastest available. However, Fortran and C do not readily extend to object-oriented programming models, limiting their capability for very complex simulation software. C++ facilitates object-oriented programming but is a very complex and error-prone language. Java offers a number of capabilities that these other languages do not. For instance it implements cleaner (i.e., easier to use and less prone to errors) object-oriented models than C++. It also offers networking and security as part ofmore » the language standard, and cross-platform executables that make it architecture neutral, to name a few. These features have made Java very popular for industrial computing applications. The aim of this paper is to explain the trade-offs in using Java for large-scale scientific applications at LLNL. Despite its advantages, the computational science community has been reluctant to write large-scale computationally intensive applications in Java due to concerns over its poor performance. However, considerable progress has been made over the last several years. The Java Grande Forum [1] has been promoting the use of Java for large-scale computing. Members have introduced efficient array libraries, developed fast just-in-time (JIT) compilers, and built links to existing packages used in high performance parallel computing.« less

  12. Development of a Web-Based Distributed Interactive Simulation (DIS) Environment Using JavaScript

    DTIC Science & Technology

    2014-09-01

    scripting that let users change or interact with web content depending on user input, which is in contrast with server-side scripts such as PHP, Java and...transfer, DIS usually broadcasts or multicasts its PDUs based on UDP socket. 3. JavaScript JavaScript is the scripting language of the web, and all...IDE) for developing desktop, mobile and web applications with JAVA , C++, HTML5, JavaScript and more. b. Framework The DIS implementation of

  13. An efficient framework for Java data processing systems in HPC environments

    NASA Astrophysics Data System (ADS)

    Fries, Aidan; Castañeda, Javier; Isasi, Yago; Taboada, Guillermo L.; Portell de Mora, Jordi; Sirvent, Raül

    2011-11-01

    Java is a commonly used programming language, although its use in High Performance Computing (HPC) remains relatively low. One of the reasons is a lack of libraries offering specific HPC functions to Java applications. In this paper we present a Java-based framework, called DpcbTools, designed to provide a set of functions that fill this gap. It includes a set of efficient data communication functions based on message-passing, thus providing, when a low latency network such as Myrinet is available, higher throughputs and lower latencies than standard solutions used by Java. DpcbTools also includes routines for the launching, monitoring and management of Java applications on several computing nodes by making use of JMX to communicate with remote Java VMs. The Gaia Data Processing and Analysis Consortium (DPAC) is a real case where scientific data from the ESA Gaia astrometric satellite will be entirely processed using Java. In this paper we describe the main elements of DPAC and its usage of the DpcbTools framework. We also assess the usefulness and performance of DpcbTools through its performance evaluation and the analysis of its impact on some DPAC systems deployed in the MareNostrum supercomputer (Barcelona Supercomputing Center).

  14. JSME: a free molecule editor in JavaScript.

    PubMed

    Bienfait, Bruno; Ertl, Peter

    2013-01-01

    A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

  15. Characterization of DOM adsorption of CNTs by using excitation-emission matrix fluorescence spectroscopy and multiway analysis.

    PubMed

    Peng, Mingguo; Li, Huajie; Li, Dongdong; Du, Erdeng; Li, Zhihong

    2017-06-01

    Carbon nanotubes (CNTs) were utilized to adsorb DOM in micro-polluted water. The characteristics of DOM adsorption on CNTs were investigated based on UV 254 , TOC, and fluorescence spectrum measurements. Based on PARAFAC (parallel factor) analysis, four fluorescent components were extracted, including one protein-like component (C4) and three humic acid-like components (C1, C2, and C3). The adsorption isotherms, kinetics, and thermodynamics of DOM adsorption on CNTs were further investigated. A Freundlich isotherm model fit the adsorption data well with high values of correlation. As a type of macro-porous and meso-porous adsorbent, CNTs preferably adsorb humic acid-like substances rather than protein-like substances. The increasing temperature will speed up the adsorption process. The self-organizing map (SOM) analysis further explains the fluorescent properties of water samples. The results provide a new insight into the adsorption behaviour of DOM fluorescent components on CNTs.

  16. Dynamic Learning Objects to Teach Java Programming Language

    ERIC Educational Resources Information Center

    Narasimhamurthy, Uma; Al Shawkani, Khuloud

    2010-01-01

    This article describes a model for teaching Java Programming Language through Dynamic Learning Objects. The design of the learning objects was based on effective learning design principles to help students learn the complex topic of Java Programming. Visualization was also used to facilitate the learning of the concepts. (Contains 1 figure and 2…

  17. Java: A New Brew for Educators, Administrators and Students.

    ERIC Educational Resources Information Center

    Gordon, Barbara

    1996-01-01

    Java is an object-oriented programming language developed by Sun Microsystems; its benefits include platform independence, security, and interactivity. Within the college community, Java is being used in programming courses, collaborative technology research projects, computer graphics instruction, and distance education. (AEF)

  18. FastScript3D - A Companion to Java 3D

    NASA Technical Reports Server (NTRS)

    Koenig, Patti

    2005-01-01

    FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

  19. Enhancing Web applications in radiology with Java: estimating MR imaging relaxation times.

    PubMed

    Dagher, A P; Fitzpatrick, M; Flanders, A E; Eng, J

    1998-01-01

    Java is a relatively new programming language that has been used to develop a World Wide Web-based tool for estimating magnetic resonance (MR) imaging relaxation times, thereby demonstrating how Java may be used for Web-based radiology applications beyond improving the user interface of teaching files. A standard processing algorithm coded with Java is downloaded along with the hypertext markup language (HTML) document. The user (client) selects the desired pulse sequence and inputs data obtained from a region of interest on the MR images. The algorithm is used to modify selected MR imaging parameters in an equation that models the phenomenon being evaluated. MR imaging relaxation times are estimated, and confidence intervals and a P value expressing the accuracy of the final results are calculated. Design features such as simplicity, object-oriented programming, and security restrictions allow Java to expand the capabilities of HTML by offering a more versatile user interface that includes dynamic annotations and graphics. Java also allows the client to perform more sophisticated information processing and computation than is usually associated with Web applications. Java is likely to become a standard programming option, and the development of stand-alone Java applications may become more common as Java is integrated into future versions of computer operating systems.

  20. Conversion of the agent-oriented domain-specific language ALAS into JavaScript

    NASA Astrophysics Data System (ADS)

    Sredojević, Dejan; Vidaković, Milan; Okanović, Dušan; Mitrović, Dejan; Ivanović, Mirjana

    2016-06-01

    This paper shows generation of JavaScript code from code written in agent-oriented domain-specific language ALAS. ALAS is an agent-oriented domain-specific language for writing software agents that are executed within XJAF middleware. Since the agents can be executed on various platforms, they must be converted into a language of the target platform. We also try to utilize existing tools and technologies to make the whole conversion process as simple as possible, as well as faster and more efficient. We use the Xtext framework that is compatible with Java to implement ALAS infrastructure - editor and code generator. Since Xtext supports Java, generation of Java code from ALAS code is straightforward. To generate a JavaScript code that will be executed within the target JavaScript XJAF implementation, Google Web Toolkit (GWT) is used.

  1. Characterizing Dissolved Organic Matter (DOM) Isolated From Specific Allochthonous and Autochthonous Sources in a North-Temperate Stream Ecosystem

    NASA Astrophysics Data System (ADS)

    Wong, J. C.; Williams, D.

    2009-05-01

    Detrital energy in temperate headwater streams is mainly derived from the annual input of leaf litter from the surrounding landscape. Presumably, its decomposition and other sources of autochthonous organic matter will change dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) quality. To investigate this, DOM was leached from two allochthonous sources: white birch (Betula papyrifera) and white cedar (Thuja occidentalis); and one autochthonous source, streambed biofilm, for a period of 7 days on 3 separate occasions in fall 2007. As a second treatment, microorganisms from the water column were filtered out. Deciduous leaf litter was responsible for high, short-term increases to DOC concentrations whereas the amounts leached from conifer needles were relatively constant in each month. Using UV spectroscopy, changes to DOM characteristics like aromaticity, spectral slopes, and molecular weight were mainly determined by source and indicated a preferential use of the labile DOM pool by the microorganisms. Excitation-emission matrices (EEMs) collected using fluorescence spectroscopy suggested that cedar litter was an important source of protein-like fluorescence and that the nature of the fluorescing DOM components changed in the presence of microorganisms. This study demonstrates that simultaneous examination of DOC concentrations and DOM quality will allow a better understanding of the carbon dynamics that connect terrestrial with aquatic ecosystems.

  2. Abundance and Bulk Composition of DOM in the Lower Mississippi and Pearl Rivers (USA)

    NASA Astrophysics Data System (ADS)

    Duan, S.; Bianchi, T. S.; Shiller, A. M.; Dria, K.; Hatcher, P. G.

    2005-05-01

    Here we report on temporal changes in the composition of dissolved organic carbon (DOC) and nitrogen (DON) collected in the tidal freshwater region of the lower Mississippi and Pearl Rivers (MR and PR) (USA). Bulk stable carbon isotopes and 13C nuclear magnetic resonance (NMR) spectrometry were used to examine the composition of high molecular weight (< 0.2 µm > 1 kDa) dissolved organic matter (HMW DOM). Monthly water samples were collected at one station in each river from August 2001 to July 2003. Surveys of spatial variability (225 km downstream in the MR and from Jackson to Stennis Space Center in the PR) in total DOC and DON were also conducted in both rivers in June 2003. Higher total DOC (336 to 1156 uM), DON (9.3 to 59.5 uM), % HMW DOM (25 to 47 %), ultraviolet (UV) absorption (0.13 to 0.70 /m), and more depleted delta-15N (0.76 to 2.16 per mil) delta-13C (-25.1 to -28.0 permil) were observed in the PR than in the lower MR (223 to 380 uM, 6.1 to 13.4 uM, 16 to 38 %, 0.08 to 0.17 /m, 0.76 to 2.16 permil, -25.7 to -27.1 permil, respectively). 13C-NMR spectra revealed that alkyl and carbohydrate carbons were dominant in HMW DOC in both rivers. However, a significantly lower percentage of aromatic C (13.2 to 16.6 %) and higher carboxyl C (17.1 to 25.8 %) were observed in the lower MR than in the PR (16.9 to 21.3 % and 12.3 to 20.9 %). Total DOC, DON, HMW DOM, and percent aromaticity of HMW DOM were higher in the PR during local flooding events, and lower during low discharge, indicating a coupling between local carbon inputs (soil and wetlands) and regional precipitation events in the PR. Conversely, seasonal variability of total DOC, DON, and HMW DOM in the lower MR was controlled by spatial variability of an integrative signal from watershed inputs and in-situ production from upriver sources, resulting in a more phytoplankton-derived 13C-NMR signature of HMW DOM. Spatially, very little change occurred in total DOC (259 to 282 uM) and DON (8.85 to 13.3 u

  3. Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying.

    PubMed

    Zhang, Junya; Cai, Xing; Qi, Lu; Shao, Chunyan; Lin, Yang; Zhang, Jin; Zhang, Yuanli; Shen, Peihong; Wei, Yuansong

    2015-09-01

    Sludge bio-drying in which sludge is dried by means of the heat generated by the aerobic degradation of its own organic substances has been widely used for sludge treatment. A better understanding of the evolution of dissolved organic matter (DOM) and its degradation drivers during sludge bio-drying could facilitate its control. Aeration is one of the key factors that affect sludge bio-drying performance. In this study, two aeration strategies (pile I-the optimized and pile II-the current) were established to investigate their impacts on the evolution of DOM and the microbial community in a full-scale sludge bio-drying plant. A higher pile temperature in pile I caused pile I to enter the DOM and microbiology stable stage approximately2 days earlier than pile II. The degradation of easily degradable components in the DOM primarily occurred in the thermophilic phase; after that degradation, the DOM components changed a little. Along with the evolution of the DOM, its main degradation driver, the microbial community, changed considerably. Phyla Firmicutes and Proteobacteria were dominant in the thermophilic stage, and genus Ureibacillus, which was the primary thermophilic bacteria, was closely associated with the degradation of the DOM. In the mesophilic stage, the microbial community changed significantly at first and subsequently stabilized, and the genus Parapedobacter, which belongs to Bacteriodetes, became dominant. This study elucidates the interplay between the DOM and microbial community during sludge bio-drying.

  4. Modular VO oriented Java EE service deployer

    NASA Astrophysics Data System (ADS)

    Molinaro, Marco; Cepparo, Francesco; De Marco, Marco; Knapic, Cristina; Apollo, Pietro; Smareglia, Riccardo

    2014-07-01

    The International Virtual Observatory Alliance (IVOA) has produced many standards and recommendations whose aim is to generate an architecture that starts from astrophysical resources, in a general sense, and ends up in deployed consumable services (that are themselves astrophysical resources). Focusing on the Data Access Layer (DAL) system architecture, that these standards define, in the last years a web based application has been developed and maintained at INAF-OATs IA2 (Italian National institute for Astrophysics - Astronomical Observatory of Trieste, Italian center of Astronomical Archives) to try to deploy and manage multiple VO (Virtual Observatory) services in a uniform way: VO-Dance. However a set of criticalities have arisen since when the VO-Dance idea has been produced, plus some major changes underwent and are undergoing at the IVOA DAL layer (and related standards): this urged IA2 to identify a new solution for its own service layer. Keeping on the basic ideas from VO-Dance (simple service configuration, service instantiation at call time and modularity) while switching to different software technologies (e.g. dismissing Java Reflection in favour of Enterprise Java Bean, EJB, based solution), the new solution has been sketched out and tested for feasibility. Here we present the results originating from this test study. The main constraints for this new project come from various fields. A better homogenized solution rising from IVOA DAL standards: for example the new DALI (Data Access Layer Interface) specification that acts as a common interface system for previous and oncoming access protocols. The need for a modular system where each component is based upon a single VO specification allowing services to rely on common capabilities instead of homogenizing them inside service components directly. The search for a scalable system that takes advantage from distributed systems. The constraints find answer in the adopted solutions hereafter sketched. The

  5. Java for flight software

    NASA Technical Reports Server (NTRS)

    Benowitz, E.; Niessner, A.

    2003-01-01

    This work involves developing representative mission-critical spacecraft software using the Real-Time Specification for Java (RTSJ). This work currently leverages actual flight software used in the design of actual flight software in the NASA's Deep Space 1 (DSI), which flew in 1998.

  6. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  7. The concept of geothermal exploration in west Java based on geophysical data

    NASA Astrophysics Data System (ADS)

    Gaffar, Eddy Z.

    2018-02-01

    Indonesia has the largest geothermal prospects in the world and most of them are concentrated in Java and Sumatera. The ones on Sumatra island are generally controlled by Sumatra Fault, either the main fault or the second and the third order fault. Geothermal in Java is still influenced by the subduction of oceanic plates from the south of Java island that forms the southern mountains extending from West Java to East Java. From a geophysical point of view, there is still no clue or concept that accelerates the process of geothermal exploration. The concept is that geothermal is located around the volcano (referred to the volcano as a host) and around the fault (fault as a host). There is another method from remote sensing analysis that often shows circular feature. In a study conducted by LIPI, we proposed a new concept for geothermal exploration which is from gravity analysis using Bouguer anomaly data from Java Island, which also show circular feature. The feature is supposed to be an "ancient crater" or a hidden caldera. Therefore, with this hypothesis, LIPI Geophysics team will try to prove whether this symptom can help accelerate the process of geothermal exploration on the island of West Java. Geophysical methods might simplify the exploration of geothermal prospect in West Java. Around the small circular feature, there are some large geothermal prospect areas such as Guntur, Kamojang, Drajat, Papandayan, Karaha Bodas, Patuha. The concept proposed by our team will try be applied to explore geothermal in Java Island for future work.

  8. Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean.

    PubMed

    Goldberg, S J; Nelson, C E; Viviani, D A; Shulse, C N; Church, M J

    2017-09-01

    Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. A Telemetry Browser Built with Java Components

    NASA Astrophysics Data System (ADS)

    Poupart, E.

    In the context of CNES balloon scientific campaigns and telemetry survey field, a generic telemetry processing product, called TelemetryBrowser in the following, was developed reusing COTS, Java Components for most of them. Connection between those components relies on a software architecture based on parameter producers and parameter consumers. The first one transmit parameter values to the second one which has registered to it. All of those producers and consumers can be spread over the network thanks to Corba, and over every kind of workstation thanks to Java. This gives a very powerful mean to adapt to constraints like network bandwidth, or workstations processing or memory. It's also very useful to display and correlate at the same time information coming from multiple and various sources. An important point of this architecture is that the coupling between parameter producers and parameter consumers is reduced to the minimum and that transmission of information on the network is made asynchronously. So, if a parameter consumer goes down or runs slowly, there is no consequence on the other consumers, because producers don't wait for their consumers to finish their data processing before sending it to other consumers. An other interesting point is that parameter producers, also called TelemetryServers in the following are generated nearly automatically starting from a telemetry description using Flavori component. Keywords Java components, Corba, distributed application, OpenORBii, software reuse, COTS, Internet, Flavor. i Flavor (Formal Language for Audio-Visual Object Representation) is an object-oriented media representation language being developed at Columbia University. It is designed as an extension of Java and C++ and simplifies the development of applications that involve a significant media processing component (encoding, decoding, editing, manipulation, etc.) by providing bitstream representation semantics. (flavor.sourceforge.net) ii Open

  10. Influence of solar radiation on DOM release from resuspended Florida Bay sediments

    NASA Astrophysics Data System (ADS)

    Shank, G. C.; Evans, A.; Jaffé, R.; Yamashita, Y.

    2009-12-01

    This study investigated dissolved organic matter (DOM) release from resuspended Florida Bay sediments under dark and sunlit conditions. Much of Florida Bay (located between Everglades and Florida Keys) is very shallow (< 2 m) so sediment resuspension events have the potential to substantially impact the concentration and composition of DOM in the water column. For our study, sediments were collected at several sites across Florida Bay and ranged from 3-11 percent organic carbon (by weight). Sediments were resuspended in oligotrophic seawater for 48 hours in 1 L quartz flasks in the dark and under simulated solar radiation (SunTest XLS+) at concentrations of 100 mg L-1 and 1 g L-1 (wet weight). Final solutions were analyzed for DOC, chromophoric dissolved organic matter (CDOM), and Excitation Emission Matrix (EEM) fluorescence. Results showed little to no DOC increases in the resuspensions performed under dark conditions, but substantial release of DOM in irradiated resuspensions, especially at high sediment concentrations where DOC increases ranged from 100-500%. The sediments also released substantial quantities of CDOM to solution under irradiated conditions. The magnitude of DOC increases in irradiated resuspensions were well-correlated with the amount of particulate organic carbon (POC) added. Data from EEM-PARAFAC analyses suggests the photochemically produced DOM was comprised of desorbed humic material with a smaller fraction from microbial mediated processes. Our study provides evidence that sediment resuspension episodes in shallow sunlit waters such as Florida Bay have the potential to provide an important source of organic carbon to overlying waters.

  11. Scientific Programming Using Java: A Remote Sensing Example

    NASA Technical Reports Server (NTRS)

    Prados, Don; Mohamed, Mohamed A.; Johnson, Michael; Cao, Changyong; Gasser, Jerry

    1999-01-01

    This paper presents results of a project to port remote sensing code from the C programming language to Java. The advantages and disadvantages of using Java versus C as a scientific programming language in remote sensing applications are discussed. Remote sensing applications deal with voluminous data that require effective memory management, such as buffering operations, when processed. Some of these applications also implement complex computational algorithms, such as Fast Fourier Transformation analysis, that are very performance intensive. Factors considered include performance, precision, complexity, rapidity of development, ease of code reuse, ease of maintenance, memory management, and platform independence. Performance of radiometric calibration code written in Java for the graphical user interface and of using C for the domain model are also presented.

  12. Short-term degradation of terrestrial DOM in the coastal ocean: Implications for nutrient subsidies and marine microbial community structure

    NASA Astrophysics Data System (ADS)

    Oliver, A. A.; Tank, S. E.; Kellogg, C.

    2015-12-01

    The export of riverine dissolved organic matter (DOM) to the coastal ocean provides an important link between terrestrial and aquatic ecosystems. The coastal temperate rainforests of British Columbia contain extensive freshwater networks that export significant amounts of water and DOM to the ocean, representing significant cross-system hydrologic and biogeochemical linkages. To better understand the importance of these linkages and implications for ecosystem structure and function, we used an experimental approach to investigate the role of microbial and photodegradation transformations of DOM exported from small coastal catchments to the marine environment. At two time periods (August 2014, March 2015), stream water from the outlets of two coastal watersheds was filtered (<0.2 μm), and treated with microbial inoculums from across a salinity gradient (i.e., freshwater, estuarine, and marine). Treatments were incubated in the ocean under light and dark conditions for 8 days. At 0, 3 and 8 days, samples were analyzed for DOC, TDN, DIN, and DON. Changes in DOM composition were determined with optical characterization techniques such as absorbance (SUVA, S, Sr) and fluorescence (EEM). Microbial community response was measured using cell counts and DNA/RNA amplicon sequencing to determine changes in bacterial abundance and community composition. General patterns indicated that microbial communities from the high salinity treatment (i.e. most marine) were the most effective at utilizing freshwater DOM, especially under light conditions. In some treatments, DOM appeared as a potential source of inorganic nitrogen with corresponding shifts in microbial community composition. Incubations using inoculum from low and mid salinity levels demonstrated smaller changes, indicating that DOM exported from these streams may not be extensively utilized until exposed to higher salinity environments further from stream outlets. These results suggest a role for terrestrial sourced-DOM

  13. Experience in the application of Java Technologies in telemedicine

    PubMed Central

    Fedyukin, IV; Reviakin, YG; Orlov, OI; Doarn, CR; Harnett, BM; Merrell, RC

    2002-01-01

    Java language has been demonstrated to be an effective tool in supporting medical image viewing in Russia. This evaluation was completed by obtaining a maximum of 20 images, depending on the client's computer workstation from one patient using a commercially available computer tomography (CT) scanner. The images were compared against standard CT images that were viewed at the site of capture. There was no appreciable difference. The client side is a lightweight component that provides an intuitive interface for end users. Each image is loaded in its own thread and the user can begin work after the first image has been loaded. This feature is especially useful on slow connection speed, 9.6 Kbps for example. The server side, which is implemented by the Java Servlet Engine works more effective than common gateway interface (CGI) programs do. Advantages of the Java Technology place this program on the next level of application development. This paper presents a unique application of Java in telemedicine. PMID:12459045

  14. Experience in the application of Java Technologies in telemedicine.

    PubMed

    Fedyukin, IV; Reviakin, YG; Orlov, OI; Doarn, CR; Harnett, BM; Merrell, RC

    2002-09-17

    Java language has been demonstrated to be an effective tool in supporting medical image viewing in Russia. This evaluation was completed by obtaining a maximum of 20 images, depending on the client's computer workstation from one patient using a commercially available computer tomography (CT) scanner. The images were compared against standard CT images that were viewed at the site of capture. There was no appreciable difference. The client side is a lightweight component that provides an intuitive interface for end users. Each image is loaded in its own thread and the user can begin work after the first image has been loaded. This feature is especially useful on slow connection speed, 9.6 Kbps for example. The server side, which is implemented by the Java Servlet Engine works more effective than common gateway interface (CGI) programs do. Advantages of the Java Technology place this program on the next level of application development. This paper presents a unique application of Java in telemedicine.

  15. Dissolved Organic Matter (DOM) From Different Composts: Comparative Study Of Properties And Allelochemical Effects On Horticultural Plants

    NASA Astrophysics Data System (ADS)

    Traversa, A.; Loffredo, E.; Gattullo, C. E.; Senesi, N.

    2009-04-01

    Dissolved organic matter (DOM) from compost has a major role in numerous chemical and biological processes occurring in the bulk substrate or compost amended soil, and can exert allelochemical effects on plant germination and growth. The objectives of this study were: (i) to investigate comparatively the main properties of three DOM fractions isolated from a green compost (DOMGC), a mixed compost (DOMMC) and a green coffee compost (DOMGCC), and (ii) to evaluate their allelochemical effects on the germination and early growth of two horticultural plants of worldwide interest such as tomato and lettuce. The DOM was extracted from each compost with distilled water (1/10 w/v) under mechanical shaking for 15 min. The suspension was then centrifuged at 6000 rpm for 15 min and filtered sequentially through filters with decreasing particle size retention (from 11 to 0.45 μm). Each DOM sample was characterized by means of pH, electrical conductivity, total organic carbon (TOC), E4/E6 ratio, fluorescence and FT IR spectroscopies and HPLC analysis. Comparative evaluation of the three DOM samples indicated the occurrence of significant differences among them. In particular, the pH value was similar and close to neutrality for DOMMC and DOMGC, whereas it resulted alkaline (pH 8.3) for DOMGCC. The EC values were also similar (about 3.2 mS/cm) for DOMMC and DOMGC and almost half value for DOMGCC. The TOC content, the E4/E6 ratio, the ɛ280 value and the humification index followed the same order: DOMGCC>DOMMC>DOMGC. The fluorescence analysis of the three DOM samples showed the presence of a common fluorophore unit associated to simple aromatic units such as phenolic-like, hydroxy-substituted benzoic and cinnamic acid derivatives. The peak wavelengths observed in the fluorescence emission, excitation and synchronous scan spectra of DOMGCC were generally higher than those of the two other DOM samples, which can be ascribed to a more extended aromatic system of the former. The FT

  16. Petroleum systems of the Northwest Java Province, Java and offshore southeast Sumatra, Indonesia

    USGS Publications Warehouse

    Bishop, Michele G.

    2000-01-01

    Mature, synrift lacustrine shales of Eocene to Oligocene age and mature, late-rift coals and coaly shales of Oligocene to Miocene age are source rocks for oil and gas in two important petroleum systems of the onshore and offshore areas of the Northwest Java Basin. Biogenic gas and carbonate-sourced gas have also been identified. These hydrocarbons are trapped primarily in anticlines and fault blocks involving sandstone and carbonate reservoirs. These source rocks and reservoir rocks were deposited in a complex of Tertiary rift basins formed from single or multiple half-grabens on the south edge of the Sunda Shelf plate. The overall transgressive succession was punctuated by clastic input from the exposed Sunda Shelf and marine transgressions from the south. The Northwest Java province may contain more than 2 billion barrels of oil equivalent in addition to the 10 billion barrels of oil equivalent already identified.

  17. Infrastructure for Rapid Development of Java GUI Programs

    NASA Technical Reports Server (NTRS)

    Jones, Jeremy; Hostetter, Carl F.; Wheeler, Philip

    2006-01-01

    The Java Application Shell (JAS) is a software framework that accelerates the development of Java graphical-user-interface (GUI) application programs by enabling the reuse of common, proven GUI elements, as distinguished from writing custom code for GUI elements. JAS is a software infrastructure upon which Java interactive application programs and graphical user interfaces (GUIs) for those programs can be built as sets of plug-ins. JAS provides an application- programming interface that is extensible by application-specific plugins that describe and encapsulate both specifications of a GUI and application-specific functionality tied to the specified GUI elements. The desired GUI elements are specified in Extensible Markup Language (XML) descriptions instead of in compiled code. JAS reads and interprets these descriptions, then creates and configures a corresponding GUI from a standard set of generic, reusable GUI elements. These elements are then attached (again, according to the XML descriptions) to application-specific compiled code and scripts. An application program constructed by use of JAS as its core can be extended by writing new plug-ins and replacing existing plug-ins. Thus, JAS solves many problems that Java programmers generally solve anew for each project, thereby reducing development and testing time.

  18. A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

    NASA Technical Reports Server (NTRS)

    Reed, John A.; Afjeh, Abdollah A.

    1997-01-01

    This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

  19. Toxic metals (Ni2+, Pb2+, Hg2+) binding affinity of dissolved organic matter (DOM) derived from different ages municipal landfill leachate

    NASA Astrophysics Data System (ADS)

    Rikta, S. Y.; Tareq, Shafi M.; Uddin, M. Khabir

    2018-03-01

    Solid waste production is rapidly increasing in Bangladesh and landfill leachate is the consequence of the decomposition of this waste. These leachates contain heavy metals and significant amount of dissolved organic matter (DOM). DOM is known to have considerable role in heavy metals speciation. Hence, it is important to characterize DOM/leachate and evaluate toxic metals binding affinity of DOM. The objectives of this study were to characterize the DOM in landfill leachate through physico-chemical and optical analyses and to investigate the toxic metals (Ni2+, Pb2+ and Hg2+) binding affinity of three different ages (fresh sample L-1, young sample L-2 and mature sample L-3) DOM samples. Results suggested that leachate is a potential pollutant which contained very high organic pollutant load. Conditional stability constant (Log K) and percentages of fluorophores that correspond to metal binding (% f) values indicated that young DOM sample (L-2) had the highest binding affinity to all the three metals ions. In general, DOM samples showed the following order affinity to the metal ions; Ni2+ binding affinity: L-2 > L-3 > L-1, Pb2+ binding affinity: L-2 > L-3 > L-1 and Hg2+ binding affinity: L-2 > L-1 > L-3.

  20. Sequence alignment visualization in HTML5 without Java.

    PubMed

    Gille, Christoph; Birgit, Weyand; Gille, Andreas

    2014-01-01

    Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary. Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons. Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software. Under GPL at: http://www.bioinformatics.org/strap/toHTML/.

  1. Unraveling signatures of biogeochemical processes and the depositional setting in the molecular composition of pore water DOM across different marine environments

    NASA Astrophysics Data System (ADS)

    Schmidt, Frauke; Koch, Boris P.; Goldhammer, Tobias; Elvert, Marcus; Witt, Matthias; Lin, Yu-Shih; Wendt, Jenny; Zabel, Matthias; Heuer, Verena B.; Hinrichs, Kai-Uwe

    2017-06-01

    Dissolved organic matter (DOM) in marine sediment pore waters derives largely from decomposition of particulate organic matter and its composition is influenced by various biogeochemical and oceanographic processes in yet undetermined ways. Here, we determine the molecular inventory of pore water DOM in marine sediments of contrasting depositional regimes with ultrahigh-resolution mass spectrometry and complementary bulk chemical analyses in order to elucidate the factors that shape DOM composition. Our sample sets from the Mediterranean, Marmara and Black Seas covered different sediment depths, ages and a range of marine environments with different (i) organic matter sources, (ii) balances of organic matter production and preservation, and (iii) geochemical conditions in sediment and water column including anoxic, sulfidic and hypersaline conditions. Pore water DOM had a higher molecular formula richness than overlying water with up to 11,295 vs. 2114 different molecular formulas in the mass range of 299-600 Da and covered a broader range of element ratios (H/C = 0.35-2.19, O/C = 0.03-1.19 vs. H/C = 0.56-2.13, O/C = 0.15-1.14). Formula richness was independent of concentrations of DOC and TOC. Near-surface pore water DOM was more similar to water column DOM than to deep pore water DOM from the same core with respect to formula richness and the molecular composition, suggesting exchange at the sediment-water interface. The DOM composition in the deeper sediments was controlled by organic matter source, selective decomposition of specific DOM fractions and early diagenetic molecule transformations. Compounds in pelagic sediment pore waters were predominantly highly unsaturated and N-bearing formulas, whereas oxygen-rich CHO-formulas and aromatic compounds were more abundant in pore water DOM from terrigenous sediments. The increase of S-bearing molecular formulas in the water column and pore waters of the Black Sea and the Mediterranean Discovery Basin was

  2. WaveJava: Wavelet-based network computing

    NASA Astrophysics Data System (ADS)

    Ma, Kun; Jiao, Licheng; Shi, Zhuoer

    1997-04-01

    Wavelet is a powerful theory, but its successful application still needs suitable programming tools. Java is a simple, object-oriented, distributed, interpreted, robust, secure, architecture-neutral, portable, high-performance, multi- threaded, dynamic language. This paper addresses the design and development of a cross-platform software environment for experimenting and applying wavelet theory. WaveJava, a wavelet class library designed by the object-orient programming, is developed to take advantage of the wavelets features, such as multi-resolution analysis and parallel processing in the networking computing. A new application architecture is designed for the net-wide distributed client-server environment. The data are transmitted with multi-resolution packets. At the distributed sites around the net, these data packets are done the matching or recognition processing in parallel. The results are fed back to determine the next operation. So, the more robust results can be arrived quickly. The WaveJava is easy to use and expand for special application. This paper gives a solution for the distributed fingerprint information processing system. It also fits for some other net-base multimedia information processing, such as network library, remote teaching and filmless picture archiving and communications.

  3. First geodetic measurement of convergence across the Java Trench

    NASA Technical Reports Server (NTRS)

    Tregoning, P.; Brunner, F. K.; Bock, Y.; Puntodewo, S. S. O.; Mccraffrey, R.; Genrich, J. F.; Calais, E.; Rais, J.; Subarya, C.

    1994-01-01

    Convergence across the Java Trench has been estimated for the first time, from annual Global Positioning System (GPS) measurements commencing in 1989. The directions of motion of Christmas and Cocos Island are within 1 deg of that predicted by the No-Net Rotation (NNR) NUVEL-1 plate motion model for the Australian plate although their rates are 25% and 37% less than predcited, respectively. The motion of West Java differs significantly from the NNR NUVEL-1 prediction for the Eurasian plate with a 1 deg difference in direction and a 40% increase in rate. We infer that either West Java moves with a distinct Southeast Asian plate or this region experiences plate margin deformation. The convergence of Christmas Island with respect to West Java is 67 +/- mm/yr in a direction N11 deg E +/- 4 deg which is orthogonal to the trench. The magnitude of convergence agrees well with rescaled NUVEL-1 relative plate model which predicts a value of 71 mm/yr between Australia and Eurasia. The direction of motion matches the direction inferred from earthquake slip vectors at the trench but may be more northerly than the N20 deg E +/- 3 deg predicted by NUVEL-1. On June 2, 1994, almost a year after the last GPS survey, an M(sub W) = 7.5 earthquake with slip vector direction N5 deg occurred south of central Java.

  4. Urbanization in Central Java and Yogyakarta.

    PubMed

    Soehartadji

    1980-06-01

    The author examines urbanization in the provinces of Central Java and Yogyakarta, Indonesia. Changes in the number and definition of rural and urban areas and in the proportion of the population living in these areas between 1930 and 1971 are analyzed. Causes of urbanization are then discussed, with attention to income levels, push and pull factors, and trade and communication. The study reveals that the rate of urbanization is comparatively low because economic conditions in the cities and towns of Central Java and Yogyakarta are less favorable than in the urban areas of other provinces, with the result that migrants tend to choose destinations in these other provinces.

  5. Developmental Process Model for the Java Intelligent Tutoring System

    ERIC Educational Resources Information Center

    Sykes, Edward

    2007-01-01

    The Java Intelligent Tutoring System (JITS) was designed and developed to support the growing trend of Java programming around the world. JITS is an advanced web-based personalized tutoring system that is unique in several ways. Most programming Intelligent Tutoring Systems require the teacher to author problems with corresponding solutions. JITS,…

  6. DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.

    PubMed

    Wang, Tianmin; Mori, Hiroshi; Zhang, Chong; Kurokawa, Ken; Xing, Xin-Hui; Yamada, Takuji

    2015-03-21

    Computational predictions of catalytic function are vital for in-depth understanding of enzymes. Because several novel approaches performing better than the common BLAST tool are rarely applied in research, we hypothesized that there is a large gap between the number of known annotated enzymes and the actual number in the protein universe, which significantly limits our ability to extract additional biologically relevant functional information from the available sequencing data. To reliably expand the enzyme space, we developed DomSign, a highly accurate domain signature-based enzyme functional prediction tool to assign Enzyme Commission (EC) digits. DomSign is a top-down prediction engine that yields results comparable, or superior, to those from many benchmark EC number prediction tools, including BLASTP, when a homolog with an identity >30% is not available in the database. Performance tests showed that DomSign is a highly reliable enzyme EC number annotation tool. After multiple tests, the accuracy is thought to be greater than 90%. Thus, DomSign can be applied to large-scale datasets, with the goal of expanding the enzyme space with high fidelity. Using DomSign, we successfully increased the percentage of EC-tagged enzymes from 12% to 30% in UniProt-TrEMBL. In the Kyoto Encyclopedia of Genes and Genomes bacterial database, the percentage of EC-tagged enzymes for each bacterial genome could be increased from 26.0% to 33.2% on average. Metagenomic mining was also efficient, as exemplified by the application of DomSign to the Human Microbiome Project dataset, recovering nearly one million new EC-labeled enzymes. Our results offer preliminarily confirmation of the existence of the hypothesized huge number of "hidden enzymes" in the protein universe, the identification of which could substantially further our understanding of the metabolisms of diverse organisms and also facilitate bioengineering by providing a richer enzyme resource. Furthermore, our results

  7. Modelling of THM formation potential and DOM removal based on drinking water catchment characteristics.

    PubMed

    Awad, John; Fisk, Claire A; Cox, Jim W; Anderson, Sharolyn J; van Leeuwen, John

    2018-09-01

    Catchment properties influence the character and concentration of dissolved organic matter (DOM). Surface and subsurface runoff from discrete catchments were collected and DOM was measured and assessed in terms of its treatability by Enhanced Coagulation and potential for disinfection by-product (trihalomethane, THMFP) formation potential. Models were developed of [1] DOM character [i.e. SUVA and SpCoL] and concentration (measured as dissolved organic carbon), [2] treatability of DOM by coagulation/flocculation processes and [3] specific THMFP based on the catchment features including: (a) surface and sub-surface soil texture (% clay: 5-25%), (b) topography (% slope: 5-15%) and (c) vegetation cover [i.e. high photosynthetic vegetation, low photosynthetic vegetation and bare soil] extracted from RapidEye satellite imagery using spectral mixture analysis. From these models, a catchment management decision support tool was designed for application by catchment managers to support decision-making of land-use and expected water quality related to water resources for drinking water supply. Data sets used for models developing presented in this paper have been published in Research Data Australia (RDA) under the title of "Impacts of catchment properties on DOM and nutrients in waters from drinking water catchments". 1 These data sets are available in open access and published in June 2017. A catchment management decision support model (CMDSM) tool was developed. Macros created using Visual Basic for Applications in Excel 2010. Excel 2010 or higher is required to open the CMDSM tool. The tool is provided by the University of South Australia (UniSA) and is not currently available on-line so please contact the corresponding author for access or further information. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

  8. Survival of Acetate in Biodegraded Stream Water DOM: New Insights Based on NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Whitty, S.; Waggoner, D. C.; Bowen, J. C.; Cory, R. M.; Kaplan, L.; Hatcher, P.

    2017-12-01

    DOM is a complex chemical mixture of high- (HMW) and low-molecular-weight (LMW) organic molecules that serve as the primary energy sources for heterotrophic bacteria in freshwater environments. However, there are still large uncertainties on the composition of DOM that is labile and thus rapidly metabolized. The current thinking is that labile DOM is primarily composed of monosaccharides, amino acids, and other LMW organic acids such as formic, acetic, or propionic among others, although some humic substances also are biologically labile. To test the contribution of LMW organic acids to the labile fraction of DOM, freshwater samples were collected from five streams within the Rio Tempisquito watershed in Costa Rica and subjected to differing degrees of biodegradation using a series of plug-flow bioreactors with residence times ranging from 0.5-150 min. Varying the residence times of bioreactors allows for separation and identification of labile from less labile to more recalcitrant DOM. The stream water fed into the bioreactors had DOC concentrations that ranged from 0.7-1.2 ppm C and the GF/F-filtered stream water as well as the bioreactor effluents were analyzed directly without pre-treatment using proton nuclear magnetic resonance spectroscopy (1H NMR). Small molecules dominated the 1H NMR spectra with the greatest changes, as a function of bioreactor residence time, in the carbohydrate, terminal methyl, and long-chain methylene structures. In contrast, acetate remained relatively constant after 150 min of bioreactor residence time, thus raising the question of why this inherently labile volatile fatty acid was not consumed by stream microbes colonizing bioreactors that otherwise metabolized approximately 35% of the total dissolved organic carbon present in the stream water. We suggest that acetate may resist biodegradation because it is complexed strongly with inorganic cations.

  9. The genesis and exodus of vascular plant DOM from an oak woodland landscape

    NASA Astrophysics Data System (ADS)

    Hernes, Peter J.; Spencer, Robert G. M.; Dyda, Rachael Y.; O'Geen, Anthony T.; Dahlgren, Randy A.

    2017-02-01

    Evaluating the collective impact of small source inputs to larger rivers is a constant challenge in riverine biogeochemistry. In this study, we investigated the generation of dissolved organic matter (DOM) in a small oak woodland catchment in the foothills of northern California, the subsequent transformation in lignin biomarkers and chromophoric DOM (CDOM) parameters during transport through the landscape to an exporting stream, and finally the overall compositional impact on the larger receiving stream and river. Our study included a natural leaching experiment in which precipitation passing through oak, pine, and grass litter and duff samples was collected after each of a series of storms. Also included were soil trench samples to capture subsurface flow, stream samples along with point-source reservoir inputs, and samples of canopy throughfall, stemflow, and gopher hole (bypass) flow. The litter/duff leaching study demonstrated changing DOM fractionation patterns throughout the season, as evidenced by changing lignin compositions in the leachates with each successive storm. This adds a necessary seasonal component to interpreting lignin compositions in streams, as the source signatures are constantly changing. Released DOM from leaching was modified extensively during transit through the subsurface to the stream, with preferential increases in aromaticity as evidenced by increases in carbon-normalized absorbance at 254 nm, yet preferential decreases in lignin phenols, as evidence by carbon-normalized lignin yields in the headwater stream that was less than half that of the litter/duff leachates. Our extensive number of lignin measurements for source materials reveals a much more complex perspective on using lignin as a source indicator, as many riverine values for syringyl:vanillyl and cinnamyl:vanillyl ratios that have previously been interpreted as degraded lignin signatures are also possible as unmodified source signatures. Finally, this study demonstrated

  10. The characteristics of dissolved organic matter (DOM) in storm sewer sediments and the binding interaction with Cu(II) in four typical regions in Beijing, China.

    PubMed

    Zhang, Ziyang; Li, Kun; Zhang, Xiaoran; Li, Haiyan

    2017-07-01

    In this work, dissolved organic matter (DOM) was extracted from storm sewer sediments collected in four typical regions (residential, campus, traffic and business regions) in Beijing, China. The basic characteristics of DOM were analyzed by UV-visible spectroscopy (UV-Vis), excitation-emission matrix Fluorescence Spectroscopy and Fourier Transform Infrared Spectroscopy. Furthermore, the complexation between DOM and Cu(II) were investigated. The results showed that there were large amount of aromatic structure in the DOM extracted from storm sewer sediments. The microbial activities had also made a contribution to the DOM in storm sewer sediments. The composition of DOM influenced the complexing capacity of Cu(II) greatly, which may be attributed to the protein-like and humic-like substances in storm sewer sediments. This study demonstrated valuable information on the structure present in the DOM of storm sewer sediments and provided new insight for exploring the relationship between DOM and co-existing heavy metals in storm sewer sediments.

  11. JavaScript: Convenient Interactivity for the Class Web Page.

    ERIC Educational Resources Information Center

    Gray, Patricia

    This paper shows how JavaScript can be used within HTML pages to add interactive review sessions and quizzes incorporating graphics and sound files. JavaScript has the advantage of providing basic interactive functions without the use of separate software applications and players. Because it can be part of a standard HTML page, it is…

  12. Temporal Dynamics in the Concentration, Flux, and Optical Properties of Tree-derived Dissolved Organic Matter (Tree-DOM) in an Epiphyte-laden Oak-cedar Forest.

    NASA Astrophysics Data System (ADS)

    Whitetree, A.; Van Stan, J. T., II; Wagner, S.; Guillemette, F.; Lewis, J.; Silva, L.; Stubbins, A.

    2017-12-01

    Studies on the fate and transport of dissolved organic matter (DOM) along the rainfall-to-discharge flow pathway typically begin in streams or soils, neglecting the initial enrichment of rainfall with DOM during contact with plant canopies. However, rain water can gather significant amounts of tree-derived DOM (tree-DOM) when it drains from the canopy, as throughfall, and down the stem, as stemflow. We examined the temporal variability of event-scale tree-DOM concentrations, yield, and optical (light absorbance and fluorescence) characteristics from an epiphyte-laden Quercus virginiana-Juniperus virginiana forest on Skidaway Island, Savannah, Georgia (USA). All tree-DOM fluxes were highly enriched compared to rainfall and epiphytes further increased concentrations. Stemflow DOC concentrations were greater than throughfall across study species, yet larger throughfall water yields produced greater DOC yields versus stemflow. Tree-DOM optical characteristics indicate it is aromatic-rich with FDOM dominated by humic-like fluorescence, containing 10-20% protein-like (tryptophan-like) fluorescence. Storm size was the only storm condition that strongly correlated with tree-DOM concentration and flux; however, throughfall and stemflow optical characteristics varied little across a wide range of storm conditions (from low magnitude events to intense tropical storms). Annual tree-DOM yields from the study forest (0.8-46 g-C m-2 yr-1) compared well to other yields along the rainfall-to- discharge flow pathway, exceeding DOM yields from some river watersheds.

  13. Testing the application of Teflon/quartz soil solution samplers for DOM sampling in the Critical Zone: Field and laboratory approaches

    NASA Astrophysics Data System (ADS)

    Dolan, E. M.; Perdrial, J. N.; Vazquez, A.; Hernández, S.; Chorover, J.

    2010-12-01

    Elizabeth Dolan1,2, Julia Perdrial3, Angélica Vázquez-Ortega3, Selene Hernández-Ruiz3, Jon Chorover3 1Deptartment of Soil, Environmental, and Atmospheric Science, University of Missouri. 2Biosphere 2, University of Arizona. 3Deptartment of Soil, Water, and Environmental Science, University of Arizona. Abstract: The behavior of dissolved organic matter (DOM) in soil is important to many biogeochemical processes. Extraction methods to obtain DOM from the unsaturated zone remain a current focus of research as different methods can influence the type and concentration of DOM obtained. Thus, the present comparison study involves three methods for soil solution sampling to assess their impact on DOM quantity and quality: 1) aqueous soil extracts, 2) solution yielded from laboratory installed suction cup samplers and 3) solutions from field installed suction cup samplers. All samples were analyzed for dissolved organic carbon and total nitrogen concentrations. Moreover, DOM quality was analyzed using fluorescence, UV-Vis and FTIR spectroscopies. Results indicate higher DOC values for laboratory extracted DOM: 20 mg/L for aqueous soil extracts and 31 mg/L for lab installed samplers compared to 12 mg/L for field installed samplers. Large variations in C/N ratios were also observed ranging from 1.5 in laboratory extracted DOM to 11 in field samples. Fluorescence excitation-emission matrices of DOM solutions obtained for the laboratory extraction methods showed higher intensities in regions typical for fulvic and humic acid-like materials relative to those extracted in the field. Similarly, the molar absorptivity calculated from DOC concentration normalization of UV-Vis absorbance of the laboratory-derived solutions was significantly higher as well, indicating greater aromaticity. The observed differences can be attributed to soil disturbance associated with obtaining laboratory derived solution samples. Our results indicate that laboratory extraction methods are not

  14. The 17 July 2006 Tsunami earthquake in West Java, Indonesia

    USGS Publications Warehouse

    Mori, J.; Mooney, W.D.; Afnimar,; Kurniawan, S.; Anaya, A.I.; Widiyantoro, S.

    2007-01-01

    A tsunami earthquake (Mw = 7.7) occurred south of Java on 17 July 2006. The event produced relatively low levels of high-frequency radiation, and local felt reports indicated only weak shaking in Java. There was no ground motion damage from the earthquake, but there was extensive damage and loss of life from the tsunami along 250 km of the southern coasts of West Java and Central Java. An inspection of the area a few days after the earthquake showed extensive damage to wooden and unreinforced masonry buildings that were located within several hundred meters of the coast. Since there was no tsunami warning system in place, efforts to escape the large waves depended on how people reacted to the earthquake shaking, which was only weakly felt in the coastal areas. This experience emphasizes the need for adequate tsunami warning systems for the Indian Ocean region.

  15. Jannovar: a java library for exome annotation.

    PubMed

    Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

    2014-05-01

    Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

  16. Molecular characterization of phytoplankton dissolved organic matter (DOM) and sulfur components using high resolution Orbitrap mass spectrometry.

    PubMed

    Mangal, Vaughn; Stock, Naomi L; Guéguen, Celine

    2016-03-01

    Orbitrap high resolution mass spectrometry (HRMS) with electrospray ionization in both positive and negative polarity was conducted on Suwannee River fulvic acid (SRFA), Pony Lake fulvic acid (PLFA) standards, and dissolved organic matter (DOM) released by freshwater phytoplankton (Scenedesmus obliquus, Euglena mutabilis, and Euglena gracilis). Three-dimensional van Krevelen diagrams expressing various oxygenation states of sulfur molecules and abundance plots of sulfur-containing species were constructed. Orbitrap HRMS analysis of SRFA found a high density of peaks in the lignin region (77 %) and low density of protein material (6.53 %), whereas for PLFA, 25 % of the total peaks were lignin related compared to 56 % of peaks in protein regions, comparable with other HRMS studies. Phytoplankton-derived DOM of S. obliquus, E. mutabilis, and E. gracilis was dominated by protein molecules at respective percentages of 36, 46, and 49 %, and is consistent with previous experiments examining phytoplankton-derived DOM composition. The normalized percentage of SO-containing compounds was determined among the three phytoplankton to be 56 % for Scenedesmus, 54 % for E. mutabilis, and 47 % for E. gracilis, suggesting variation between sulfur content in phytoplankton-derived DOM and differences in metal binding capacities. These results suggest the level of resolution by Orbitrap mass spectrometry is sufficient for preliminary characterization of phytoplankton DOM at an affordable cost relative to other HRMS techniques.

  17. Dynamics of dissolved organic matter (DOM) in a typical inland lake of the Three Gorges Reservoir area: Fluorescent properties and their implications for dissolved mercury species.

    PubMed

    Jiang, Tao; Chen, Xueshuang; Wang, Dingyong; Liang, Jian; Bai, Weiyang; Zhang, Cheng; Wang, Qilei; Wei, Shiqiang

    2018-01-15

    Dissolved organic matter (DOM) plays an important environmental and ecological role in inland aquatic systems, including lakes. In this study, using fluorescence analysis, we investigated the seasonal dynamics of DOM characteristics in Changshou Lake, which is a typical inland lake in the Three Gorges Reservoir (TGR) area. We also discuss the environmental implications of DOM for mercury (Hg) dynamics. Based on the origins of two end-members, the variations in DOM observed in this study in Changshou Lake suggest that hydrological processes (e.g., terrestrial inputs resulting from runoff and humic-like component residences) and biological activities (e.g., microbial and algae growth) are the two main principal components controlling the seasonal dynamics of DOM characteristics. Furthermore, the dynamics of dissolved Hg co-varied with variations in DOM properties, rather than with dissolved organic carbon (DOC) concentrations. This indicates that the previously reported simple correlations between DOC and Hg were not comprehensive and may lead to misunderstanding the interactions between DOM and Hg. Therefore, we recommend that when using DOM-Hg correlations to evaluate the role of DOM in the environmental fate of Hg, especially in field investigations of the spatial and temporal distribution of Hg, the properties of DOM must be taken into account. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

    PubMed Central

    Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

    2009-01-01

    We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

  19. Evolution of the Generic Lock System at Jefferson Lab

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

    Brian Bevins; Yves Roblin

    2003-10-13

    The Generic Lock system is a software framework that allows highly flexible feedback control of large distributed systems. It allows system operators to implement new feedback loops between arbitrary process variables quickly and with no disturbance to the underlying control system. Several different types of feedback loops are provided and more are being added. This paper describes the further evolution of the system since it was first presented at ICALEPCS 2001 and reports on two years of successful use in accelerator operations. The framework has been enhanced in several key ways. Multiple-input, multiple-output (MIMO) lock types have been added formore » accelerator orbit and energy stabilization. The general purpose Proportional-Integral-Derivative (PID) locks can now be tuned automatically. The generic lock server now makes use of the Proxy IOC (PIOC) developed at Jefferson Lab to allow the locks to be monitored from any EPICS Channel Access aware client. (Previously clients had to be Cdev aware.) The dependency on the Qt XML parser has been replaced with the freely available Xerces DOM parser from the Apache project.« less

  20. Paintbrush of Discovery: Using Java Applets to Enhance Mathematics Education

    ERIC Educational Resources Information Center

    Eason, Ray; Heath, Garrett

    2004-01-01

    This article addresses the enhancement of the learning environment by using Java applets in the mathematics classroom. Currently, the first year mathematics program at the United States Military Academy involves one semester of modeling with discrete dynamical systems (DDS). Several faculty members from the Academy have integrated Java applets…

  1. JSBML: a flexible Java library for working with SBML.

    PubMed

    Dräger, Andreas; Rodriguez, Nicolas; Dumousseau, Marine; Dörr, Alexander; Wrzodek, Clemens; Le Novère, Nicolas; Zell, Andreas; Hucka, Michael

    2011-08-01

    The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.

  2. Toward understanding the role of individual fluorescent components in DOM-metal binding.

    PubMed

    Wu, Jun; Zhang, Hua; Yao, Qi-Sheng; Shao, Li-Ming; He, Pin-Jing

    2012-05-15

    Knowledge on the function of individual fractions in dissolved organic matter (DOM) is essential for understanding the impact of DOM on metal speciation and migration. Herein, fluorescence excitation-emission matrix quenching and parallel factor (PARAFAC) analysis were adopted for bulk DOM and chemically isolated fractions from landfill leachate, i.e., humic acids (HA), fulvic acids and hydrophilic (HyI) fraction, to elucidate the role of individual fluorescent components in metal binding (Cu(II) and Cd(II)). Three components were identified by PARAFAC model, including one humic substance (HS)-like, one protein-like and one component highly correlated with the HyI fraction. Among them, the HS-like and protein-like components were responsible for Cu(II) binding, while the protein-like component was the only fraction involved in Cd(II) complexation. It was further identified that the slight quenching effect of HA fraction by Cd(II) was induced by the presence of proteinaceous materials in HA. Fluorescent substances in the HyI fraction of landfill leachate did not play as important a role as HS did. Therefore, it was suggested that the potential risk of aged leachate (more humified) as a carrier of heavy metal should not be overlooked. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Structural and electronic engineering of 3DOM WO3 by alkali metal doping for improved NO2 sensing performance

    NASA Astrophysics Data System (ADS)

    Wang, Zhihua; Fan, Xiaoxiao; Han, Dongmei; Gu, Fubo

    2016-05-01

    Novel alkali metal doped 3DOM WO3 materials were prepared using a simple colloidal crystal template method. Raman, XRD, SEM, TEM, XPS, PL, Hall and UV-Vis techniques were used to characterize the structural and electronic properties of all the products, while the corresponding sensing performances targeting ppb level NO2 were determined at different working temperatures. For the overall goal of structural and electronic engineering, the co-effect of structural and electronic properties on the improved NO2 sensing performance of alkali metal doped 3DOM WO3 was studied. The test results showed that the gas sensing properties of 3DOM WO3/Li improved the most, with the fast response-recovery time and excellent selectivity. More importantly, the response of 3DOM WO3/Li to 500 ppb NO2 was up to 55 at room temperature (25 °C). The especially high response to ppb level NO2 at room temperature (25 °C) in this work has a very important practical significance. The best sensing performance of 3DOM WO3/Li could be ascribed to the most structure defects and the highest carrier mobility. And the possible gas sensing mechanism based on the model of the depletion layer was proposed to demonstrate that both structural and electronic properties are responsible for the NO2 sensing behavior.Novel alkali metal doped 3DOM WO3 materials were prepared using a simple colloidal crystal template method. Raman, XRD, SEM, TEM, XPS, PL, Hall and UV-Vis techniques were used to characterize the structural and electronic properties of all the products, while the corresponding sensing performances targeting ppb level NO2 were determined at different working temperatures. For the overall goal of structural and electronic engineering, the co-effect of structural and electronic properties on the improved NO2 sensing performance of alkali metal doped 3DOM WO3 was studied. The test results showed that the gas sensing properties of 3DOM WO3/Li improved the most, with the fast response-recovery time and

  4. Effect of dissolved organic matter (DOM) of contrasting origins on Cu and Pb speciation and toxicity to Paracentrotus lividus larvae.

    PubMed

    Sánchez-Marín, Paula; Santos-Echeandía, Juan; Nieto-Cid, Mar; Alvarez-Salgado, Xosé Antón; Beiras, Ricardo

    2010-01-31

    Water samples of contrasting origin, including natural seawater, two sediment elutriates and sewage-influenced seawater, were collected and obtained to examine the effect of the dissolved organic matter (DOM) present on metal bioavailability. The carbon content (DOC) and the optical properties (absorbance and fluorescence) of the coloured DOM fraction (CDOM) of these materials were determined. Cu and Pb complexation properties were measured by anodic stripping voltammetry (ASV) and the effect of DOM on Cu and Pb bioavailability was studied by means of the Paracentrotus lividus embryo-larval bioassay. Sediment elutriates and sewage-influenced water (1) were enriched 1.4-1.7 times in DOC; (2) absorbed and reemitted more light; and (3) presented higher Cu complexation capacities (L(Cu)) than the natural seawater used for their preparation. L(Cu) varied from 0.08 microM in natural seawater to 0.3 and 0.5 microM in sediment elutriates and sewage-influenced water, respectively. Differences in DOC, CDOM and Cu complexation capacities were reflected in Cu toxicity. DOM enriched samples presented a Cu EC(50) of 0.64 microM, significantly higher than the Cu EC(50) of natural and artificial seawater, which was 0.38 microM. The protecting effect of DOM on Cu toxicity greatly disappeared when the samples were irradiated with high intensity UV-light. Cu toxicity could be successfully predicted considering ASV-labile Cu concentrations in the samples. Pb complexation by DOM was only detected in the DOM-enriched samples and caused little effect on Pb EC(50). This effect was contrary for both elutriates: one elutriate reduced Pb toxicity in comparison with the control artificial seawater, while the other increased it. UV irradiation of the samples caused a marked increase in Pb toxicity, which correlated with the remaining DOC concentration. DOM parameters were related to Cu speciation and toxicity: good correlations were found between DOC and Cu EC(50), while L(Cu) correlated

  5. Java Mission Evaluation Workstation System

    NASA Technical Reports Server (NTRS)

    Pettinger, Ross; Watlington, Tim; Ryley, Richard; Harbour, Jeff

    2006-01-01

    The Java Mission Evaluation Workstation System (JMEWS) is a collection of applications designed to retrieve, display, and analyze both real-time and recorded telemetry data. This software is currently being used by both the Space Shuttle Program (SSP) and the International Space Station (ISS) program. JMEWS was written in the Java programming language to satisfy the requirement of platform independence. An object-oriented design was used to satisfy additional requirements and to make the software easily extendable. By virtue of its platform independence, JMEWS can be used on the UNIX workstations in the Mission Control Center (MCC) and on office computers. JMEWS includes an interactive editor that allows users to easily develop displays that meet their specific needs. The displays can be developed and modified while viewing data. By simply selecting a data source, the user can view real-time, recorded, or test data.

  6. A Java application for tissue section image analysis.

    PubMed

    Kamalov, R; Guillaud, M; Haskins, D; Harrison, A; Kemp, R; Chiu, D; Follen, M; MacAulay, C

    2005-02-01

    The medical industry has taken advantage of Java and Java technologies over the past few years, in large part due to the language's platform-independence and object-oriented structure. As such, Java provides powerful and effective tools for developing tissue section analysis software. The background and execution of this development are discussed in this publication. Object-oriented structure allows for the creation of "Slide", "Unit", and "Cell" objects to simulate the corresponding real-world objects. Different functions may then be created to perform various tasks on these objects, thus facilitating the development of the software package as a whole. At the current time, substantial parts of the initially planned functionality have been implemented. Getafics 1.0 is fully operational and currently supports a variety of research projects; however, there are certain features of the software that currently introduce unnecessary complexity and inefficiency. In the future, we hope to include features that obviate these problems.

  7. Sedimentary deposits study of the 2006 Java tsunami, in Pangandaran, West Java (preliminary result)

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

    Maemunah, Imun, E-mail: imun-m2001@yahoo.com; Institute Technology of Bandung; Suparka, Emmy, E-mail: emmy@gc.itb.ac.id

    The 2006 Java Earthquake (Mw 7.2) has generated a tsunami that reached Pangandaran coastal plain with 9.7 m above sea level height of wave. In 2014 we examined the tsunami deposit exposed in shallow trenches along a∼300 m at 5 transect from shoreline to inland on Karapyak and Madasari, Pangandaran. We documented stratigraphically and sedimentologically, the characteristics of Java Tsunami deposit on Karapyak and Madasari and compared both sediments. In local farmland a moderately-sorted, brown soil is buried by a poorly-sorted, grey, medium-grained sand-sheet. The tsunami deposit was distinguished from the underlying soil by a pronounced increase in grain size that becomesmore » finner upwards and landwards. Decreasing concentration of coarse size particles with distance toward inland are in agreement with grain size analysis. The thickest tsunami deposit is about 25 cm found at 84 m from shoreline in Madasari and about 15 cm found at 80 m from shoreline in Karapyak. The thickness of tsunami deposits in some transect become thinner landward but in some other transect lack a consistent suggested strongly affected by local topography. Tsunami deposits at Karapyak and Madasari show many similarities. Both deposits consist of coarse sand that sharply overlies a finer sandy soil. The presence mud drapes and other sedimentary structure like graded bedding, massive beds, mud clasts in many locations shows a dynamics process of tsunami waves. The imbrication coarse and shell fragments of the 2006 Java, tsunami deposits also provide information about the curent direction, allowing us to distinguish run up deposits from backwash deposits.« less

  8. Fluorescence fingerprints and Cu2+-complexing ability of individual molecular size fractions in soil- and waste-borne DOM.

    PubMed

    Knoth de Zarruk, K; Scholer, G; Dudal, Y

    2007-09-01

    Land spreading of organic materials introduces large amounts of dissolved organic matter (DOM) into the soil. DOM has the ability to form stable complexes with heavy metals and can facilitate their transport towards the groundwater. The effects on soil processes are difficult to assess, because different DOM components might react differently towards metal ions. The objective of this study was to investigate the fluorescence signature and the Cu2+-binding capacity of individual molecular size fractions of DOM from various sources. DOM extracted from leaf compost, chicken manure, sugar cane vinasse and a fulvic hypercalcaric cambisol was fractionated by the means of dialysis into four molecular size classes: MW<500, 50012000-14000 Da. Vinasse and leaf compost contained around 80% and 70%, respectively, of the total organic carbon in the fractions with low molecular weight (MW<3500 Da); in chicken manure and soil these fractions accounted for 40% and 50% only. Fluorescence was highest in the fraction MW>12000 Da for leaf compost, chicken manure and soil. The opposite result was obtained for vinasse, where the fractions with low molecular weight showed highest fluorescence intensities, distinguishing it from all other samples. Vinasse showed the greatest ability to bind Cu2+ with a resulting complex concentration of 6.31mgl(-1) while in contact with an excess of Cu2+. Leaf compost, soil and chicken manure followed with 2.69, 1.12, and 0.85mgl(-1), respectively. Within vinasse, the fraction MW<500 Da was able to form the most DOM-Cu complexes, indicating the importance of low molecular weight fractions in metal binding.

  9. Absence of plague in certain mammals from Java and Kalimantan (Borneo).

    PubMed

    Van Peenen, P F; Joseph, S W; Cavanaugh, D C; Williams, J E; Luyster, L F; Saroso, J S

    1976-09-01

    Antibodies against plague were lacking in 237 wild mammal sera from Java and 103 from Kalimantan. Wild mammal spleens, 114 from Java and 18 from Kalimantan were negative for plague bacilli. A variety of mammalian species and areas was examined.

  10. Symbolic PathFinder: Symbolic Execution of Java Bytecode

    NASA Technical Reports Server (NTRS)

    Pasareanu, Corina S.; Rungta, Neha

    2010-01-01

    Symbolic Pathfinder (SPF) combines symbolic execution with model checking and constraint solving for automated test case generation and error detection in Java programs with unspecified inputs. In this tool, programs are executed on symbolic inputs representing multiple concrete inputs. Values of variables are represented as constraints generated from the analysis of Java bytecode. The constraints are solved using off-the shelf solvers to generate test inputs guaranteed to achieve complex coverage criteria. SPF has been used successfully at NASA, in academia, and in industry.

  11. A Visual Editor in Java for View

    NASA Technical Reports Server (NTRS)

    Stansifer, Ryan

    2000-01-01

    In this project we continued the development of a visual editor in the Java programming language to create screens on which to display real-time data. The data comes from the numerous systems monitoring the operation of the space shuttle while on the ground and in space, and from the many tests of subsystems. The data can be displayed on any computer platform running a Java-enabled World Wide Web (WWW) browser and connected to the Internet. Previously a special-purpose program bad been written to display data on emulations of character-based display screens used for many years at NASA. The goal now is to display bit-mapped screens created by a visual editor. We report here on the visual editor that creates the display screens. This project continues the work we bad done previously. Previously we had followed the design of the 'beanbox,' a prototype visual editor created by Sun Microsystems. We abandoned this approach and implemented a prototype using a more direct approach. In addition, our prototype is based on newly released Java 2 graphical user interface (GUI) libraries. The result has been a visually more appealing appearance and a more robust application.

  12. Modelling of cayenne production in Central Java using ARIMA-GARCH

    NASA Astrophysics Data System (ADS)

    Tarno; Sudarno; Ispriyanti, Dwi; Suparti

    2018-05-01

    Some regencies/cities in Central Java Province are known as producers of horticultural crops in Indonesia, for example, Brebes which is the largest area of shallot producer in Central Java, while the others, such as Cilacap and Wonosobo are the areas of cayenne commodities production. Currently, cayenne is a strategic commodity and it has broad impact to Indonesian economic development. Modelling the cayenne production is necessary to predict about the commodity to meet the need for society. The needs fulfillment of society will affect stability of the concerned commodity price. Based on the reality, the decreasing of cayenne production will cause the increasing of society’s basic needs price, and finally it will affect the inflation level at that area. This research focused on autoregressive integrated moving average (ARIMA) modelling by considering the effect of autoregressive conditional heteroscedasticity (ARCH) to study about cayenne production in Central Java. The result of empirical study of ARIMA-GARCH modelling for cayenne production in Central Java from January 2003 to November 2015 is ARIMA([1,3],0,0)-GARCH(1,0) as the best model.

  13. Implications of the Java language on computer-based patient records.

    PubMed

    Pollard, D; Kucharz, E; Hammond, W E

    1996-01-01

    The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

  14. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

    PubMed Central

    Martin, Andrew C. R.

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

  15. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    PubMed

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

  16. The effect of dissolved organic matter (DOM) on sodium transport and nitrogenous waste excretion of the freshwater cladoceran (Daphnia magna) at circumneutral and low pH.

    PubMed

    Al-Reasi, Hassan A; Yusuf, Usman; Smith, D Scott; Wood, Chris M

    2013-11-01

    Dissolved organic matter (DOM), a heterogeneous substance found in all natural waters, has many documented abiotic roles, but recently, several possible direct influences of DOM on organism physiology have been reported. However, most studies have been carried out with a limited number of natural DOM isolates or were restricted to the use of commercial or artificial humic substances. We therefore employed three previously characterized, chemically-distinct natural DOMs, as well as a commercially available humic acid (Aldrich, AHA), at circumneutral (7-8) and acidic pH (~5), to examine DOM effects on whole-body Na(+) concentration, unidirectional influx and efflux rates of Na(+), and ammonia and urea excretion rates in Daphnia magna. Whole-body Na(+) concentration, Na(+) influx, and Na(+) efflux rates were all unaffected regardless of pH, suggesting no influence of the various natural DOMs on active uptake and passive diffusion of Na(+) in this organism. Ammonia and urea excretion rates were both increased by low pH. Ammonia excretion rates were reduced at circumneutral pH by the most highly colored, allochthonous DOM, and at low pH by all three natural DOMs, as well as by the commercial AHA. Urea excretion rates were not influenced by the presence of the various DOMs in circumneutral solutions, but were attenuated by the presence of two allochthonous DOM sources (isolated from Bannister Lake and Luther Marsh) at acidic pH. The observed reductions may be attributed partially to the higher buffering capacities of natural DOM sources, as well as their ability to interact with biological membranes as estimated by a new measure calculated from their acid-base titration characteristics, the Proton Binding Index (PBI). © 2013.

  17. [Three dimensional fluorescent characteristics of soil dissolved organic matter (DOM) in Jiaozhou Bay coastal wetlands, China].

    PubMed

    Zi, Yuan Yuan; Kong, Fan Long; Xi, Min; Li, Yue; Yang, Ling

    2016-12-01

    In order to elucidate the structure characteristics of soil dissolved organic matter (DOM) and analyze the sources in Jiaozhou Bay coastal wetlands, four typical types of wetlands around Jiaozhou Bay were chosen, including Spartina anglica wetland, the barren wetland, Suaeda glauca wetland and Phragmites australis wetland. The soil samples were collected in January 2014. The contents of soil DOM were determined and the spectral analysis was made by three-dimensional fluorescent technology. The results showed that the contents of soil dissolved organic carbon (DOC) in four types of wetlands all decreased with the increasing soil depth, and S. anglica wetland ranked the first in the contents of soil DOC, followed by the barren wetland, S. glauca wetland and P. australis wetland. Five fluorescence peaks including B, T, A, D and C were found in the three-dimensional fluorescence spectrum (3DEEMs), indicating tyrosine-like, tryptophan-like, phenol-like, soluble microbial byproduct-like and humic acid-like- substances, respectively. Fluorescence integration (FRI) was applied in the qualitative analysis of five components. The results showed that tryptophan-like, phenol-like and tyrosine-like substances ranked in top three in content, followed by soluble microbial byproduct-like and humic acid-like substances which were not significantly different. Pearson correlation analysis demonstrated that a positive correlation existed between any two of the five components of DOM, and they were all positively related to DOC content. In addition, there existed different correlations between the five components of DOM and total phosphorus (TP), available phosphorus (AP) and total nitrogen (TN). The soil DOM in the four types of wetlands was mainly produced by biotic interactions, and the degree of humification was relatively low.

  18. Mechanistic consideration of the photochemical transformation of domoic acid (algal toxin) in DOM-Rich brackish water.

    PubMed

    Jin, Hangxing; Lian, Lushi; Zhou, Huaxi; Yan, Shuwen; Song, Weihua

    2018-06-14

    Domoic acid (DA) is a neurotoxin generated by several diatom species in harmful algae blooms (HABs). We report the photo-induced transformation products (TPs) and degradation mechanisms of DA in dissolved organic matter (DOM)-rich freshwater and brackish water. High-resolution quadrupole time-of-flight mass spectrometry (QTOF-MS) and the multivariate statistical strategy orthogonal partial least-squares discriminant analysis (OPLS-DA) identified 36 and 23 potential TPs in DOM-rich freshwater and brackish water, respectively. The main reactive sites of DA are the conjugated double bond and proline ring. Isomerization is the predominant transformation pathway induced by excited-state triplet DOM ( 3 DOM ∗ ). The second-order rate constant of the isomerization reaction was measured as (3.8 ± 0.2) × 10 8  M -1  s -1 . The inverse correlation between the dissolved oxygen (DO) concentration and the rate of photo-induced DA isomerization was revealed. Furthermore, under halide-present conditions, halide radicals are mainly responsible for the differentiation of products by quenching hydroxyl radicals and generating unique organic peroxide products. Our results indicated that halide radicals could be important in the photochemical transformation of organic contaminants in high saline environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. A Geostationary Earth Orbit Satellite Model Using Easy Java Simulation

    ERIC Educational Resources Information Center

    Wee, Loo Kang; Goh, Giam Hwee

    2013-01-01

    We develop an Easy Java Simulation (EJS) model for students to visualize geostationary orbits near Earth, modelled using a Java 3D implementation of the EJS 3D library. The simplified physics model is described and simulated using a simple constant angular velocity equation. We discuss four computer model design ideas: (1) a simple and realistic…

  20. Multimedia consultation session recording and playback using Java-based browser in global PACS

    NASA Astrophysics Data System (ADS)

    Martinez, Ralph; Shah, Pinkesh J.; Yu, Yuan-Pin

    1998-07-01

    The current version of the Global PACS software system uses a Java-based implementation of the Remote Consultation and Diagnosis (RCD) system. The Java RCD includes a multimedia consultation session between physicians that includes text, static image, image annotation, and audio data. The JAVA RCD allows 2-4 physicians to collaborate on a patient case. It allows physicians to join the session via WWW Java-enabled browsers or stand alone RCD application. The RCD system includes a distributed database archive system for archiving and retrieving patient and session data. The RCD system can be used for store and forward scenarios, case reviews, and interactive RCD multimedia sessions. The RCD system operates over the Internet, telephone lines, or in a private Intranet. A multimedia consultation session can be recorded, and then played back at a later time for review, comments, and education. A session can be played back using Java-enabled WWW browsers on any operating system platform. The JAVA RCD system shows that a case diagnosis can be captured digitally and played back with the original real-time temporal relationships between data streams. In this paper, we describe design and implementation of the RCD session playback.

  1. The state of the Java universe

    ScienceCinema

    Gosling, James

    2018-05-22

    Speaker Bio: James Gosling received a B.Sc. in computer science from the University of Calgary, Canada in 1977. He received a Ph.D. in computer science from Carnegie-Mellon University in 1983. The title of his thesis was The Algebraic Manipulation of Constraints. He has built satellite data acquisition systems, a multiprocessor version of UNIX®, several compilers, mail systems, and window managers. He has also built a WYSIWYG text editor, a constraint-based drawing editor, and a text editor called Emacs, for UNIX systems. At Sun his early activity was as lead engineer of the NeWS window system. He did the original design of the Java programming language and implemented its original compiler and virtual machine. He has recently been a contributor to the Real-Time Specification for Java.

  2. Developing a java android application of KMV-Merton default rate model

    NASA Astrophysics Data System (ADS)

    Yusof, Norliza Muhamad; Anuar, Aini Hayati; Isa, Norsyaheeda Natasha; Zulkafli, Sharifah Nursyuhada Syed; Sapini, Muhamad Luqman

    2017-11-01

    This paper presents a developed java android application for KMV-Merton model in predicting the defaut rate of a firm. Predicting default rate is essential in the risk management area as default risk can be immediately transmitted from one entity to another entity. This is the reason default risk is known as a global risk. Although there are several efforts, instruments and methods used to manage the risk, it is said to be insufficient. To the best of our knowledge, there has been limited innovation in developing the default risk mathematical model into a mobile application. Therefore, through this study, default risk is predicted quantitatively using the KMV-Merton model. The KMV-Merton model has been integrated in the form of java program using the Android Studio Software. The developed java android application is tested by predicting the levels of default risk of the three different rated companies. It is found that the levels of default risk are equivalent to the ratings of the respective companies. This shows that the default rate predicted by the KMV-Merton model using the developed java android application can be a significant tool to the risk mangement field. The developed java android application grants users an alternative to predict level of default risk within less procedure.

  3. Development of a Long-Range Gliding Underwater Vehicle Utilizing Java Sun SPOT Technology

    DTIC Science & Technology

    2008-09-01

    release; distribution is unlimited DEVELOPMENT OF A LONG-RANGE GLIDING UNMANNED UNDERWATER VEHICLE UTILIZING JAVA SUN SPOT TECHNOLOGY by...TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE: Development of a Long-Range Gliding Underwater Vehicle Utilizing Java Sun SPOT...vehicle. Further work is needed to demonstrate the efficiency and effectiveness of this design. 15. NUMBER OF PAGES 117 14. SUBJECT TERMS Java

  4. Influence of DOM components, salinity, pH, nitrate, and bicarbonate on the indirect photodegradation of acetaminophen in simulated coastal waters.

    PubMed

    Bai, Ying; Cui, Zhengguo; Su, Rongguo; Qu, Keming

    2018-04-18

    The indirect photodegradation behaviors of acetaminophen (APAP) were investigated in the presence of four kinds of dissolved organic matter (DOM) and were also assessed in the presence of seawater components and conditions such as salinity, pH, nitrate and bicarbonate. The results showed three important findings: firstly, in the indirect photolysis of APAP, the contributions of 3 DOM*, ·OH and 1 O 2 were >85.0%, 2.3-9.9% and 0.8-2.6% at pH 8.0. Secondly, DOM was divided into four terrestrial humic-like components by Excitation-emission matrix spectroscopy (EEMs) combined with parallel factor analysis (PARAFAC). This study showed a good linearity between DOM fluorescence components and the indirect photodegradation of APAP (R 2  = 0.92) and the differences in photodegradation rates of APAP among various DOM solutions were due to the diverse compositions of DOM. Finally, salinity was an important factor influencing the removal of APAP, and the APAP photodegradation rate constants increased from (3.33 ± 0.07) × 10 -5 s -1 to (1.25 ± 0.05) × 10 -4 s -1 with increasing salinity. The increased pseudo-first-order rate constants for photolysis of APAP with increasing salinity, pH and nitrate were attributed to the enhanced generation of reactive intermediates (RI) and easier reactions between RI and APAP. The increased APAP removal rate constant with increasing bicarbonate was likely ascribed to the yield of ∙CO 3 - . This is the first report of the roles of DOM components and salinity on the indirect photolysis of APAP. These findings would be essential to predict the photochemical fate of APAP and would also allow for a better understanding of the environmental fate of other phenolic contaminants. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Towards Crustal Structure of Java Island (Sunda Arc) from Ambient Seismic Noise Tomography

    NASA Astrophysics Data System (ADS)

    Widiyantoro, Sri; Zulhan, Zulfakriza; Martha, Agustya; Saygin, Erdinc; Cummins, Phil

    2015-04-01

    In our previous studies, P- and S-wave velocity structures beneath the Sunda Arc were successfully imaged using a global data set and a nested regional-global tomographic method was employed. To obtain more detailed P- and S-wave velocity structures beneath Java, in the central part of the Sunda Arc, we then used local data sets, i.e. newline from the MErapi AMphibious EXperiment (MERAMEX) and the Meteorological, Climatological and Geophysical Agency (MCGA), as well as employed a double-difference technique for tomographic imaging. The results of the imaging show e.g. that P- and S-wave velocities are significantly reduced in the uppermost mantle beneath central Java. In order to obtain detailed crustal structure information beneath Java, the Ambient Noise Tomography (ANT) method was used. The application of this method to the MERAMEX data has produced a good crustal model beneath central Java. We continue our experiment to image crustal structure of eastern Java. We have used seismic waveform data recorded by 22 MCGA stationary seismographic stations and 25 portable seismographs installed for 2 to 8 weeks. The data were processed to obtain waveforms of cross-correlated noise between pairs of seismographic stations. Our preliminary results presented here indicate that the Kendeng zone, an area of low gravity anomaly, is associated with a low velocity zone. On the other hand, the southern mountain range, which has a high gravity anomaly, is related to a high velocity anomaly (as shown by our tomographic images). In future work we will install more seismographic stations in eastern Java as well as in western Java to conduct ANT imaging for the whole of Java Island. The expected result combined with the mantle velocity models resulting from our body wave tomography will allow for accurate location of earthquake hypocenters and determination of regional tectonic structures. Both of these are valuable for understanding seismic hazard in Java, the most densely populated

  6. JAVA CLASSES FOR NONPROCEDURAL VARIOGRAM MONITORING. JOURNAL OF COMPUTERS AND GEOSCIENCE

    EPA Science Inventory

    NRMRL-ADA-00229 Faulkner*, B.P. Java Classes for Nonprocedural Variogram Monitoring. Journal of Computers and Geosciences ( Elsevier Science, Ltd.) 28:387-397 (2002). EPA/600/J-02/235. A set of Java classes was written for variogram modeling to support research for US EPA's Reg...

  7. PrismTech Data Distribution Service Java API Evaluation

    NASA Technical Reports Server (NTRS)

    Riggs, Cortney

    2008-01-01

    My internship duties with Launch Control Systems required me to start performance testing of an Object Management Group's (OMG) Data Distribution Service (DDS) specification implementation by PrismTech Limited through the Java programming language application programming interface (API). DDS is a networking middleware for Real-Time Data Distribution. The performance testing involves latency, redundant publishers, extended duration, redundant failover, and read performance. Time constraints allowed only for a data throughput test. I have designed the testing applications to perform all performance tests when time is allowed. Performance evaluation data such as megabits per second and central processing unit (CPU) time consumption were not easily attainable through the Java programming language; they required new methods and classes created in the test applications. Evaluation of this product showed the rate that data can be sent across the network. Performance rates are better on Linux platforms than AIX and Sun platforms. Compared to previous C++ programming language API, the performance evaluation also shows the language differences for the implementation. The Java API of the DDS has a lower throughput performance than the C++ API.

  8. Java PathExplorer: A Runtime Verification Tool

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Rosu, Grigore; Clancy, Daniel (Technical Monitor)

    2001-01-01

    We describe recent work on designing an environment called Java PathExplorer for monitoring the execution of Java programs. This environment facilitates the testing of execution traces against high level specifications, including temporal logic formulae. In addition, it contains algorithms for detecting classical error patterns in concurrent programs, such as deadlocks and data races. An initial prototype of the tool has been applied to the executive module of the planetary Rover K9, developed at NASA Ames. In this paper we describe the background and motivation for the development of this tool, including comments on how it relates to formal methods tools as well as to traditional testing, and we then present the tool itself.

  9. Export of pre-aged, labile DOM from a central California coastal upwelling system: Insights from D/L amino acids and Δ14C signatures

    NASA Astrophysics Data System (ADS)

    Walker, B. D.; Shen, Y.; Benner, R. H.; Druffel, E. R. M.

    2014-12-01

    Coastal upwelling zones are among the most productive regions in the world and play a major role in global carbon and nitrogen cycles. Recent research suggests that a substantial fraction of newly fixed organic matter is exported offshore in the form of dissolved organic matter (DOM). However, to date only a few studies have examined DOM composition in the context of production and export from upwelling systems. The ultimate fate and geochemical impact of coastal DOM exported to offshore and mesopelagic ecosystems also remains largely unknown. Between 2007-2009 we conducted a high-resolution biogeochemical time series at the Granite Canyon Marine Pollution Studies Lab in part to evaluate the seasonal production and export of DOM from the Central CA coast. Our previous work demonstrated substantial, albeit disparate, seasonal production of dissolved organic carbon and nitrogen (DOC, DON) - with high DON (and low C:N ratios) produced during upwelling and high DOC produced during summer/fall water column stratification (Walker and McCarthy, 2012). Here we present new total dissolved D/L amino acid (TDAA) and UV-oxidizable DOC radiocarbon (Δ14C) data with the goal of determining the relative sources (heterotrophic vs. autotrophic), bioavailability, microbial processing and 14C-ages of C-rich vs. N-rich DOM exported from this upwelling system. Our results suggest that C-rich DOM produced during water column stratification carries a large microbial signature (i.e. high D/L AA ratios and non-protein AA abundance), whereas N-rich DOM produced during upwelling appears to be fresh, autotrophic DOM (i.e. lowest D/L AA ratios and highest TDAA abundance). DOM Δ14C signatures also did not approximate in situ dissolved inorganic carbon (DIC), and instead were far more negative and highly correlated to water mass density. Together our results indicate a previously unrecognized source of highly labile yet pre-aged DOM potentially impacting offshore and mesopelagic ecosystems.

  10. The effect of freezing and drying on leaching of DOM from above ground vascular plant material from the Alaskan Arctic

    NASA Astrophysics Data System (ADS)

    Khosh, M. S.; McClelland, J. W.

    2014-12-01

    Our understanding of the seasonal dynamics of fluvial dissolved organic matter (DOM) concentrations and fluxes in Arctic catchments has increased substantially during recent years, especially during the spring, which historically has been an under-sampled time period. While a number of studies have observed peaks in both DOM concentrations and fluxes during the spring snowmelt, our knowledge of the mechanisms that control these observations are still lacking. During the initial snowmelt period, frozen ground and the snow matrix act to constrain melt-water to the soil surface. We hypothesize that restriction of flow during this time facilitates leaching of DOM from senescent above ground vegetation and detritus contributing to the high DOM concentrations observed during the spring melt. This study focuses on the effect of freezing and drying on the leaching of dissolved organic carbon and nitrogen (DOC and DON) from above ground vascular plant material. Specifically, we examined the treatment effects of freezing, drying, and freeze-drying on three genera of common Alaskan Arctic vascular plants; Eriophorum (spp.), Carex (spp.), and Salix (spp.). Frozen and freeze-dried plant material released more DOC over the experimental 96 hour leaching period compared to plant material that was only dried. Qualitatively, these patterns were similar among the different plant types, while quantitatively Salix leached more DOC than either Eriophorum or Carex in all treatments. Similar patterns were also seen for DON between the different treatments and among the different plant types. Compositionally, DOM that was leached from frozen and freeze-dried material had higher C:N ratios than material that was only dried. Comparatively, DOM leached from Salix had much higher C:N ratios than either Eriophorum or Carex. During the first 24 hours of leaching, C:N ratios tended to increase followed by a subsequent leveling or decrease, suggesting that the composition of leached DOM varied

  11. Review of subduction and its association with geothermal system in Sumatera-Java

    NASA Astrophysics Data System (ADS)

    Ladiba, A. F.; Putriyana, L.; Sibarani, B. br.; Soekarno, H.

    2017-12-01

    Java and Sumatera have the largest geothermal resources in Indonesia, in which mostly are spatially associated with volcanoes of subduction zones. However, those volcanoes are not distributed in a regular pattern due to the difference of subduction position. Subduction position in java is relatively more perpendicular to the trench than in Sumatera. In addition, Java has a concentration of large productive geothermal field with vapour dominated system in the western part of Java, which may be caused by the various subduction dip along the island. In order to understand the relationship between the subduction process and geothermal system in the subduction zone volcanoes, we examined several kinematic parameters of subduction that potentially relevant to the formation of geothermal system in overriding plate such as slab dip, subduction rate, and direction of subduction. Data and information regarding tectonic setting of Sumatera and Java and productive geothermal field in Sumatera and Java have been collected and evaluated. In conclusion, there are three condition that caused the geothermal fluid to be more likely being in vapour phase, which are: the subduction is in an orthogonal position, the slab dip is high, and rate of subduction is high. Although there are plenty researches of subduction zone volcanoes, only a few of them present information about its formation and implication to the geothermal system. The result of this study may be used as reference in exploration of geothermal field in mutual geologic environment.

  12. [Radiology information system using HTML, JavaScript, and Web server].

    PubMed

    Sone, M; Sasaki, M; Oikawa, H; Yoshioka, K; Ehara, S; Tamakawa, Y

    1997-12-01

    We have developed a radiology information system using intranet techniques, including hypertext markup language, JavaScript, and Web server. JavaScript made it possible to develop an easy-to-use application, as well as to reduce network traffic and load on the server. The system we have developed is inexpensive and flexible, and its development and maintenance are much easier than with the previous system.

  13. STS-108 Crew Interviews: Dom Gorie

    NASA Technical Reports Server (NTRS)

    2001-01-01

    STS-108 Commander Dom Gorie is seen during a prelaunch interview. He answers questions about the mission's goals and significance, explaining the meaning of 'utilization flight 1' (UF-1) as opposed to an 'assembly flight'. He gives details on the payload (Starshine Satellite, Avian Development Facility, and Rafaello Multipurpose Logistics Module (MPLM)), his role in the rendezvous, docking, and undocking of the Endeavour Orbiter to the International Space Station (ISS), how he will participate in the unloading and reloading of the MPLM, and the way in which the old and new resident crews of ISS will exchanged. Gorie ends with his thoughts on the short-term and long-term future of the International Space Station.

  14. Study on Design and Implementation of JAVA Programming Procedural Assessment Standard

    ERIC Educational Resources Information Center

    Tingting, Xu; Hua, Ma; Xiujuan, Wang; Jing, Wang

    2015-01-01

    The traditional JAVA course examination is just a list of questions from which we cannot know students' skills of programming. According to the eight abilities in curriculum objectives, we designed an assessment standard of JAVA programming course that is based on employment orientation and apply it to practical teaching to check the teaching…

  15. EOL-1, the Homolog of the Mammalian Dom3Z, Regulates Olfactory Learning in C. elegans

    PubMed Central

    Shen, Yu; Zhang, Jiangwen; Calarco, John A.

    2014-01-01

    Learning is an essential function of the nervous system. However, our understanding of molecular underpinnings of learning remains incomplete. Here, we characterize a conserved protein EOL-1 that regulates olfactory learning in Caenorhabditis elegans. A recessive allele of eol-1 (enhanced olfactory learning) learns better to adjust its olfactory preference for bacteria foods and eol-1 acts in the URX sensory neurons to regulate learning. The mammalian homolog of EOL-1, Dom3Z, which regulates quality control of pre-mRNAs, can substitute the function of EOL-1 in learning regulation, demonstrating functional conservation between these homologs. Mutating the residues of Dom3Z that are critical for its enzymatic activity, and the equivalent residues in EOL-1, abolishes the function of these proteins in learning. Together, our results provide insights into the function of EOL-1/Dom3Z and suggest that its activity in pre-mRNA quality control is involved in neural plasticity. PMID:25274815

  16. Wedge geometry, frictional properties and interseismic coupling of the Java megathrust

    NASA Astrophysics Data System (ADS)

    Koulali, Achraf; McClusky, Simon; Cummins, Phil; Tregoning, Paul

    2018-06-01

    The mechanical interaction between rocks at fault zones is a key element for understanding how earthquakes nucleate and propagate. Therefore, estimating frictional properties along fault planes allows us to infer the degree of elastic strain accumulation throughout the seismic cycle. The Java subduction zone is an active plate boundary where high seismic activity has long been documented. However, very little is known about the seismogenic processes of the megathrust, especially its shallowest portion where onshore geodetic networks are insensitive to recover the pattern of elastic strain. Here, we use the geometry of the offshore accretionary prism to infer frictional properties along the Java subduction zone, using Coulomb critical taper theory. We show that large portions of the inner wedge in the eastern part of the Java subduction megathrust are in a critical state, where the wedge is on the verge of failure everywhere. We identify four clusters with an internal coefficient of friction μint of ∼ 0.8 and hydrostatic pore pressure within the wedge. The average effective coefficient of friction ranges between 0.3 and 0.4, reflecting a strong décollement. Our results also show that the aftershock sequence of the 1994 Mw 7.9 earthquake halted adjacent to a critical segment of the wedge, suggesting that critical taper wedge areas in the eastern Java subduction interface may behave as a permanent barrier to large earthquake rupture. In contrast, in western Java topographic slope and slab dip profiles suggest that the wedge is mechanically stable, i.e deformation is restricted to sliding along the décollement, and likely to coincide with a seismogenic portion of the megathrust. We discuss the seismic hazard implications and highlight the importance of considering the segmentation of the Java subduction zone when assessing the seismic hazard of this region.

  17. Collaborative Scheduling Using JMS in a Mixed Java and .NET Environment

    NASA Technical Reports Server (NTRS)

    Wang, Yeou-Fang; Wax, Allan; Lam, Ray; Baldwin, John; Borden, Chet

    2006-01-01

    A viewgraph presentation to demonstrate collaborative scheduling using Java Message Service (JMS) in a mixed Java and .Net environment is given. The topics include: 1) NASA Deep Space Network scheduling; 2) Collaborative scheduling concept; 3) Distributed computing environment; 4) Platform concerns in a distributed environment; 5) Messaging and data synchronization; and 6) The prototype.

  18. The kinematics of crustal deformation in Java from GPS observations: Implications for fault slip partitioning

    NASA Astrophysics Data System (ADS)

    Koulali, A.; McClusky, S.; Susilo, S.; Leonard, Y.; Cummins, P.; Tregoning, P.; Meilano, I.; Efendi, J.; Wijanarto, A. B.

    2017-01-01

    Our understanding of seismic risk in Java has been focused primarily on the subduction zone, where the seismic records during the last century have shown the occurrence of a number of tsunami earthquakes. However, the potential of the existence of active crustal structures within the island of Java itself is less well known. Historical archives show the occurrence of several devastating earthquake ruptures north of the volcanic arc in west Java during the 18th and the 19th centuries, suggesting the existence of active faults that need to be identified in order to guide seismic hazard assessment. Here we use geodetic constraints from the Global Positioning System (GPS) to quantify the present day crustal deformation in Java. The GPS velocities reveal a homogeneous counterclockwise rotation of the Java Block independent of Sunda Block, consistent with a NE-SW convergence between the Australian Plate and southeast Asia. Continuous GPS observations show a time-dependent change in the linear rate of surface motion in west Java, which we interpret as an ongoing long-term post-seismic deformation following the 2006 Mw 7.7 Java earthquake. We use an elastic block model in combination with a viscoelastic model to correct for this post-seismic transient and derive the long-term inter-seismic velocity, which we interpret as a combination of tectonic block motions and crustal faults strain related deformation. There is a north-south gradient in the resulting velocity field with a decrease in the magnitude towards the North across the Kendeng Thrust in the east and the Baribis Thrust in the west. We suggest that the Baribis Thrust is active and accommodating a slow relative motion between Java and the Sunda Block at about 5 ± 0.2 mm /yr. We propose a kinematic model of convergence of the Australian Plate and the Sunda Block, involving a slip partitioning between the Java Trench and a left-lateral structure extending E-W along Java with most of the convergence being

  19. SPV: a JavaScript Signaling Pathway Visualizer.

    PubMed

    Calderone, Alberto; Cesareni, Gianni

    2018-03-24

    The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.

  20. JAVA CLASSES FOR NONPROCEDURAL VARIOGRAM MONITORING

    EPA Science Inventory

    A set of Java classes was written for variogram modeling to support research for US EPA's Regional Vulnerability Assessment Program (ReVA). The modeling objectives of this research program are to use conceptual programming tools for numerical analysis for regional risk assessm...

  1. BioLayout(Java): versatile network visualisation of structural and functional relationships.

    PubMed

    Goldovsky, Leon; Cases, Ildefonso; Enright, Anton J; Ouzounis, Christos A

    2005-01-01

    Visualisation of biological networks is becoming a common task for the analysis of high-throughput data. These networks correspond to a wide variety of biological relationships, such as sequence similarity, metabolic pathways, gene regulatory cascades and protein interactions. We present a general approach for the representation and analysis of networks of variable type, size and complexity. The application is based on the original BioLayout program (C-language implementation of the Fruchterman-Rheingold layout algorithm), entirely re-written in Java to guarantee portability across platforms. BioLayout(Java) provides broader functionality, various analysis techniques, extensions for better visualisation and a new user interface. Examples of analysis of biological networks using BioLayout(Java) are presented.

  2. Prevalence of antibodies to Japanese encephalitis virus among pigs in Bali and East Java, Indonesia, 2008.

    PubMed

    Yamanaka, Atsushi; Mulyatno, Kris Cahyo; Susilowati, Helen; Hendrianto, Eryk; Utsumi, Takako; Amin, Mochamad; Lusida, Maria Inge; Soegijanto, Soegeng; Konishi, Eiji

    2010-01-01

    Japanese encephalitis virus (JEV) is a fatal disease in Asia. Pigs are considered to be the effective amplifying host for JEV in the peridomestic environment. Bali Island and Java Island in Indonesia provide a model to assess the effect of pigs on JEV transmission, since the pig density is nearly 100-fold higher in Bali than Java, while the geographic and climatologic environments are equivalent in these areas. We surveyed antibodies to JEV among 123 pigs in Mengwi (Bali) and 96 pigs in Tulungagung (East Java) in 2008 by the hemagglutination-inhibition (HAI) test. Overall prevalences were 49% in Bali and 6% in Java, with a significant difference between them (P < 0.001). Monthly infection rates estimated from age-dependent antibody prevalences were 11% in Bali and 2% in Java. In addition, 2-mercaptoethanol-sensitive antibodies were found only from Bali samples. Further, the average HAI antibody titer obtained from positive samples was significantly higher in Bali (1:52) than Java (1:10; P < 0.001). These results indicated that JEV transmission in nature is more active in Bali than East Java.

  3. Application of UV-visible absorption spectroscopy combined with two-dimensional correlation for insight into DOM fractions from native halophyte soils in a larger estuarine delta.

    PubMed

    Wei, Huaibin; Yu, Huibin; Pan, Hongwei; Gao, Hongjie

    2018-05-01

    UV-visible absorption spectroscopy combined with principal component analysis (PCA) and two-dimensional correlation (2D correlation) is used to trace components of dissolved organic matter (DOM) extracted from soils in a larger estuarine delta and to investigate spatial variations of DOM fractions. Soil samples of different depths were collected from native halophyte soils along a saline gradient, i.e., Suaeda salsa Comm. (SSC), Chenopodium album Comm. (CAC), Phragmites australis Comm. (PAC), and Artemisia selengensis Comm. (ASC). Molecular weights of DOM within the SSC soil profile were the lowest, followed by the CAC, PAC, and ASC soil profiles. Humification degree of DOM within the ASC soil profile was the highest, followed by the PAC, SSC, and CAC soil profiles. DOM within the soil profiles mainly contained phenolic, carboxylic, microbial products, and aromatic and alkyl groups through the PCA, which presented the significant differentiation among the four native halophyte soil profiles. The 2D UV correlation spectra of DOM within the SSC soil profile indicated that the variations of the phenolic groups were the largest, followed by the carboxylic groups, microbial products, and humified organic materials according to the band changing order of 285 → 365 → 425 → 520 nm. The 2D UV correlation spectra of DOM within the CAC soil profiles determined that the decreasing order of the variations was phenolic groups > carboxylic groups > microbial products according the band changing order of 285 → 365 → 425 nm. The 2D UV correlation spectra of DOM within the PAC soil profile proved that the variations of the phenolic groups were larger than those of the carboxylic groups according to the band changing order of 285 → 365 nm. The 2D UV correlation spectra of DOM within the ASC soil profile demonstrated that the variations of the phenolic groups were larger than those of the other DOM fractions according to the broad cross-peak at

  4. Parallel programming with Easy Java Simulations

    NASA Astrophysics Data System (ADS)

    Esquembre, F.; Christian, W.; Belloni, M.

    2018-01-01

    Nearly all of today's processors are multicore, and ideally programming and algorithm development utilizing the entire processor should be introduced early in the computational physics curriculum. Parallel programming is often not introduced because it requires a new programming environment and uses constructs that are unfamiliar to many teachers. We describe how we decrease the barrier to parallel programming by using a java-based programming environment to treat problems in the usual undergraduate curriculum. We use the easy java simulations programming and authoring tool to create the program's graphical user interface together with objects based on those developed by Kaminsky [Building Parallel Programs (Course Technology, Boston, 2010)] to handle common parallel programming tasks. Shared-memory parallel implementations of physics problems, such as time evolution of the Schrödinger equation, are available as source code and as ready-to-run programs from the AAPT-ComPADRE digital library.

  5. [FTIR and 13C NMR Analysis of Dissolved Organic Matter (DOM) in the Treatment Process of Tannery Wastewater].

    PubMed

    Fan, Chun-hui; Zhang, Ying-chao; Tang, Ze-heng; Wang, Jia-hong

    2015-05-01

    Nowadays, the wastewater quantity discharged yearly from tannery industry is around 0. 2 billion t in China. The contaminants of tannery wastewater include macromolecular organic matters, such as grease, fur scraps and collagen, and the alkaline wastewater appears to be of high content of salt and COD. The quality of tannery wastewater is monitored strictly among all kinds of industry wastewater. In the treatment process of tannery wastewater, the quality of inlet and outlet water is generally analyzed. In fact, the transformation behavior of contaminants should be additionally checked to optimize the treatment conditions. Dissolved organic matter (DOM) is commonly existed in water-bodies and helpful to understand the physicochemical characteristics, while the related work should be further studied on tannery wastewater. The approaches of elemental analysis, thermal gravimetric analysis (TG), Fourier infrared spectroscopy (FTIR) and 13C nuclear magnetic resonance (13C NMR) were used to reveal the characteristics of DOM in the treatment process of tannery wastewater. The results showed the carbon content of DOM samples increased gradually, atomic ratios of H/C increased firstly and then decreased, indicating the organic matters were decomposed into chain structures firstly, finally forming the component hard to degraded. The pyrolysis process of DOM mainly proceeded in the regions of 110~530 °C (aliphatic compound, protein, etc. ) and 530~800 °C (aromatic ring, single bond of C-C, etc. ). The functional groups of DOM included -OH, -NH2, C=O and so on, and the aromatic substances were detected, shown from FTIR figures, in the later period of the reaction, caused by the metabolism effect of micro-organism. The content of alkoxy-C increased to the maximum in the second biochemical pond, and the minimum content of aromatic-C appeared in the second biochemical pond, suggesting the transformation behavior of carbon functional groups. The investigation on DOM in tannery

  6. Tsunami Disaster Risk Assessment and Prevention in West Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Deng, H.; Harris, R. A.; Horns, D. M.; Yulianto, E.; Bunds, M. P.; Prasetyadi, C.; Emmett, C.; Hall, S.

    2016-12-01

    Java Island, Indonesia is the most populated area and one of the most tectonically active coastal nations on Earth. This island is the volcanic arc and accretionary wedge of the subduction zone of the Sunda and the Australia plate, where the Java Trench is located. However, the Java Trench hasn't had a mega or giant earthquake for at least 430 years according to historical records. Up to 30 m of slip may have accumulated on the subduction zone interface during this time, which is enough to produce a Mw 9.0 earthquake and large tsunami. One of the largest seismic gaps along the Sunda Arc is a 640 km section of the coast of west Java. The largest population center in this region is Pelabuhan Ratu, with is partially built on ridge and swale coastal plain topography. Candidate tsunami deposits were found in swales that may indicate inundation up to 1 km inland. Numerical modeling of various possible tsunami scenarios indicate that the configuration of the coastline may amplify a tsunami and cause high run-up in the most populated areas or the coast. Also, data from questionnaire surveys administered in Pelabuhan Ratu show a lack of awareness about how tsunamis threaten these communities and plans of action.

  7. Data mining for clustering naming of the village at Java Island

    NASA Astrophysics Data System (ADS)

    Setiawan Abdullah, Atje; Nurani Ruchjana, Budi; Hidayat, Akik; Akmal; Setiana, Deni

    2017-10-01

    Clustering of query based data mining to identify the meaning of the naming of the village in Java island, done by exploring the database village with three categories namely: prefix in the naming of the village, syllables contained in the naming of the village, and full word naming of the village which is actually used. While syllables contained in the naming of the village are classified by the behaviour of the culture and character of each province that describes the business, feelings, circumstances, places, nature, respect, plants, fruits, and animals. Sources of data used for the clustering of the naming of the village on the island of Java was obtained from Geospatial Information Agency (BIG) in the form of a complete village name data with the coordinates in six provinces in Java, which is arranged in a hierarchy of provinces, districts / cities, districts and villages. The research method using KDD (Knowledge Discovery in Database) through the process of preprocessing, data mining and postprocessing to obtain knowledge. In this study, data mining applications to facilitate the search query based on the name of the village, using Java software. While the contours of a map is processed using ArcGIS software. The results of the research can give recommendations to stakeholders such as the Department of Tourism to describe the meaning of the classification of naming the village according to the character in each province at Java island.

  8. Enhanced catalytic performance for methane combustion of 3DOM CoFe2O4 by co-loading MnOx and Pd-Pt alloy nanoparticles

    NASA Astrophysics Data System (ADS)

    Li, Xiangyu; Liu, Yuxi; Deng, Jiguang; Xie, Shaohua; Zhao, Xingtian; Zhang, Yang; Zhang, Kunfeng; Arandiyan, Hamidreza; Guo, Guangsheng; Dai, Hongxing

    2017-05-01

    Three-dimensionally ordered macroporous (3DOM) CoFe2O4, zMnOx/3DOM CoFe2O4 (z = 4.99-12.30 wt%), and yPd-Pt/6.70 wt% MnOx/3DOM CoFe2O4 (y = 0.44-1.81 wt%; Pd/Pt molar ratio = 2.1-2.2) have been prepared using the polymethyl methacrylate microspheres-templating, incipient wetness impregnation, and bubble-assisted polyvinyl alcohol-protected reduction strategies, respectively. All of the samples were characterized by means of various techniques. Catalytic performance of the samples was measured for methane combustion. It is shown that the as-prepared samples exhibited a high-quality 3DOM structure (103 ± 20 nm in pore size) and a surface area of 19-28 m2/g, and the noble metal or alloy nanoparticles (NPs) with a size of 2.2-3.0 nm were uniformly dispersed on the macropore wall surface of 3DOM CoFe2O4. The loading of MnOx on CoFe2O4 gave rise to a slight increase in activity, however, the dispersion of Pd-Pt NPs on 6.70MnOx/3DOM CoFe2O4 significantly enhanced the catalytic performance, with the 1.81Pd2.1Pt/6.70MnOx/3DOM CoFe2O4 sample showing the highest activity (T10% = 255 °C, T50% = 301 °C, and T90% = 372 °C at a space velocity of 20,000 mL/(g h)). We believe that the excellent catalytic activity of 1.81Pd2.1Pt/6.70MnOx/3DOM CoFe2O4 was related to its well-dispersed Pd-Pt alloy NPs, high adsorbed oxygen species concentration, good low-temperature reducibility, and strong interaction between MnOx or Pd-Pt NPs and 3DOM CoFe2O4.

  9. Studies of the DOM aqueous extracts from coastal marine sediments

    NASA Astrophysics Data System (ADS)

    Sakellariadou, F.

    2012-04-01

    Dissolved organic matter (DOM) represents a major exchangeable organic pool playing an outstanding role in the ocean carbon cycle. It has a complex chemical structure made up of a wide range of organic molecules. The composition of DOM depends on the sources proximity and the exposure to any sort of degradation mechanism. The coloured (or chromophoric) dissolved organic matter (CDOM), representing the optically active fraction of DOM, consists of aromatic rings able to absorb light in the visible and UV regions (Kirk, 1994) and fluorophoric molecules that emit light. The main fluorophoric moieties of CDOM are humic material with a blue fluorescence and protein material with an ultraviolet (UV) fluorescence (Mopper and Schultz, 1993). Dissolved organic matter interacts with pollutants either by enhancing their bioavailability or by influencing their transportation to the soluble phase. In addition, DOM affects the remineralisation of carbon and its preservation in marine sediments. Referring to its origin, it can be terrestrial, freshwater or marine one. Fluorescence spectroscopy is a technique widely applied for the identification and characterization of organic matter, being fast, simple, non-destructive and sensitive. In addition, the fluorescence analysis for the physico-chemical characterization of organic matter requires a small amount of aqueous sample at a low concentration, in comparison with the large sample volumes needed for conventional techniques. At the present study coastal sediment samples were collected from Messiniakos gulf in the south western Peloponnese in South Greece. Messiniakos gulf has a seabed dominated by very abrupt inclinations reaching depths of more than 1000m. All samples, according to their grain size, are classified as fine clayey silt. Dissolved organic matter was extracted under gentle extraction conditions (4 mM CaCl2 solution). The various classes of organic components present at the DOM aqueous extracts were characterised by

  10. Developing Interactive Educational Engineering Software for the World Wide Web with Java.

    ERIC Educational Resources Information Center

    Reed, John A.; Afjeh, Abdollah A.

    1998-01-01

    Illustrates the design and implementation of a Java applet for use in educational propulsion engineering curricula. The Java Gas Turbine Simulator applet provides an interactive graphical environment which allows the rapid, efficient construction and analysis of arbitrary gas turbine systems. The simulator can be easily accessed from the World…

  11. Annual risks of tuberculous infection in East Nusa Tenggara and Central Java Provinces, Indonesia.

    PubMed

    Bachtiar, A; Miko, T Y; Machmud, R; Besral, B; Yudarini, P; Mehta, F; Chadha, V K; Basri, C; Loprang, F; Jitendra, R

    2009-01-01

    East Nusa Tenggara (NTT) and Central Java Provinces, Indonesia. To estimate the average annual risk of tuberculous infection (ARTI) among school children aged 6-9 years in each province. Children attending Classes 1-4 in 65 schools in NTT and 79 in Central Java, selected by two-stage sampling, were intradermally administered 2 tuberculin units of purified protein derivative RT23 with Tween 80 on the mid-volar aspect of the left forearm. The maximum transverse diameter of induration was measured 72 h later. The analysis was carried out among 5479 satisfactorily test-read children in NTT and 6943 in Central Java. One hundred and fifty-five new sputum smear-positive pulmonary tuberculosis (PTB) cases (78 in NTT and 77 in Central Java) were also tuberculin tested. Based on the frequency distribution of reaction sizes among the children and PTB cases, the prevalence of infection was estimated by the mirror-image method using the modes of tuberculous reactions at 15 and 17 mm. Using the 15 mm mode, ARTI was estimated at 1% in NTT and 0.9% in Central Java. Using the 17 mm mode, ARTI was estimated at 0.5% in NTT and 0.4% in Central Java. Transmission of tuberculous infection may be further reduced by intensification of tuberculosis control efforts.

  12. Java 3D Interactive Visualization for Astrophysics

    NASA Astrophysics Data System (ADS)

    Chae, K.; Edirisinghe, D.; Lingerfelt, E. J.; Guidry, M. W.

    2003-05-01

    We are developing a series of interactive 3D visualization tools that employ the Java 3D API. We have applied this approach initially to a simple 3-dimensional galaxy collision model (restricted 3-body approximation), with quite satisfactory results. Running either as an applet under Web browser control, or as a Java standalone application, this program permits real-time zooming, panning, and 3-dimensional rotation of the galaxy collision simulation under user mouse and keyboard control. We shall also discuss applications of this technology to 3-dimensional visualization for other problems of astrophysical interest such as neutron star mergers and the time evolution of element/energy production networks in X-ray bursts. *Managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.

  13. Characteristic and Behavior of Rainfall Induced Landslides in Java Island, Indonesia : an Overview

    NASA Astrophysics Data System (ADS)

    Christanto, N.; Hadmoko, D. S.; Westen, C. J.; Lavigne, F.; Sartohadi, J.; Setiawan, M. A.

    2009-04-01

    Landslides are important natural hazards occurring on mountainous area situated in the wet tropical climate like in Java, Indonesia. As a central of economic and government activity, Java become the most populated island in Indonesia and is increasing every year. This condition create population more vulnerable to hazard. Java is populated by 120 million inhabitants or equivalent with 60% of Indonesian population in only 6,9% of the total surface of Indonesia. Due to its geological setting, its topographical characteristics, and its climatic characteristics, Java is the most exposed regions to landslide hazard and closely related to several factors: (1) located on a subduction zone, 60% of Java is mountainous, with volcano-tectonic mountain chains and 36 active volcanoes out of the 129 in Indonesia, and these volcanic materials are intensively weathered (2) Java is under a humid tropical climate associated with heavy rainfall during the rainy season from October to April. On top of these "natural" conditions, the human activity is an additional factor of landslide occurrence, driven by a high demographic density The purpose of this paper was to collect and analyze spatial and temporal data concerning landslide hazard for the period 1981-2007 and to evaluate and analyze the characteristic and the behavior of landslide in Java. The results provides a new insight into our understanding of landslide hazard and characteristic in the humid tropics, and a basis for predicting future landslides and assessing related hazards at a regional scale. An overview of characteristic and behavior of landslides in Java is given. The result of this work would be valuable for decision makers and communities in the frame of future landslide risk reduction programs. Landslide inventory data was collected from internal database at the different institutions. The result is then georefenced. The temporal changes of landslide activities was done by examining the changes in number and

  14. Lisp as an Alternative to Java

    NASA Technical Reports Server (NTRS)

    Gat, E.

    2000-01-01

    In a recent study, Prechelt compared the relative performance of Java and C++ in terms of execution time and memory utilization. Unlike many benchmark studies, Prechelt compared mulitple implementations of the same task by multiple programmers in order to control for the effects of difference in programmer skill.

  15. EOL-1, the homolog of the mammalian Dom3Z, regulates olfactory learning in C. elegans.

    PubMed

    Shen, Yu; Zhang, Jiangwen; Calarco, John A; Zhang, Yun

    2014-10-01

    Learning is an essential function of the nervous system. However, our understanding of molecular underpinnings of learning remains incomplete. Here, we characterize a conserved protein EOL-1 that regulates olfactory learning in Caenorhabditis elegans. A recessive allele of eol-1 (enhanced olfactory learning) learns better to adjust its olfactory preference for bacteria foods and eol-1 acts in the URX sensory neurons to regulate learning. The mammalian homolog of EOL-1, Dom3Z, which regulates quality control of pre-mRNAs, can substitute the function of EOL-1 in learning regulation, demonstrating functional conservation between these homologs. Mutating the residues of Dom3Z that are critical for its enzymatic activity, and the equivalent residues in EOL-1, abolishes the function of these proteins in learning. Together, our results provide insights into the function of EOL-1/Dom3Z and suggest that its activity in pre-mRNA quality control is involved in neural plasticity. Copyright © 2014 the authors 0270-6474/14/3413364-07$15.00/0.

  16. Distributed Object Technology with CORBA and Java: Key Concepts and Implications.

    DTIC Science & Technology

    1997-06-01

    commercial use should be addressed to the SEI Licensing Agent. NO WARRANTY THIS CARNEGIE MELLON UNIVERSITY AND SOFTWARE ENGINEERING INSTITUTE MATERIAL...retrieval. This power is not derived from the language per se, but from the architecture-neutral approach used by Java. The Java Virtual Machine...pattern that is focused on performance considerations, the PCo archi- tecture also uses CORBA interface definition language (IDL) to model the

  17. Interface Generation and Compositional Verification in JavaPathfinder

    NASA Technical Reports Server (NTRS)

    Giannakopoulou, Dimitra; Pasareanu, Corina

    2009-01-01

    We present a novel algorithm for interface generation of software components. Given a component, our algorithm uses learning techniques to compute a permissive interface representing legal usage of the component. Unlike our previous work, this algorithm does not require knowledge about the component s environment. Furthermore, in contrast to other related approaches, our algorithm computes permissive interfaces even in the presence of non-determinism in the component. Our algorithm is implemented in the JavaPathfinder model checking framework for UML statechart components. We have also added support for automated assume-guarantee style compositional verification in JavaPathfinder, using component interfaces. We report on the application of the presented approach to the generation of interfaces for flight software components.

  18. Server-Side JavaScript Debugging: Viewing the Contents of an Object

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

    Hampton, J.; Simons, R.

    1999-04-21

    JavaScript allows the definition and use of large, complex objects. Unlike some other object-oriented languages, it also allows run-time modifications not only of the values of object components, but also of the very structure of the object itself. This feature is powerful and sometimes very convenient, but it can be difficult to keep track of the object's structure and values throughout program execution. What's needed is a simple way to view the current state of an object at any point during execution. There is a debug function that is included in the Netscape server-side JavaScript environment. The function outputs themore » value(s) of the expression given as the argument to the function in the JavaScript Application Manager's debug window [SSJS].« less

  19. Neogene subduction beneath Java, Indonesia: Slab tearing and changes in magmatism

    NASA Astrophysics Data System (ADS)

    Cottam, Michael; Hall, Robert; Cross, Lanu; Clements, Benjamin; Spakman, Wim

    2010-05-01

    Java is a Neogene calc-alkaline volcanic island arc formed by the northwards subduction of the Indo-Australian Plate beneath Sundaland, the continental core of SE Asia. The island has a complex history of volcanism and displays unusual subduction characteristics. These characteristics are consistent with the subduction of a hole in the down going slab that was formed by the arrival of a buoyant oceanic plateau at the trench. Subduction beneath Java began in the Eocene. However, the position and character of the calc-alkaline arc has changed over time. An older Paleogene arc ceased activity in the Early Miocene. Volcanic activity resumed in the Late Miocene producing a younger arc to the north of the older arc, and continues to the present day. An episode of Late Miocene thrusting at about 7 Ma is observed throughout Java and appears to be linked to northward movement of the arc. Arc rocks display typical calc-alkaline characteristics and reflect melting of the mantle wedge and subducted sediments associated with high fluid fluxes. Between West Java and Bali the present arc-trench gap is unusually wide at about 300 km. Seismicity identifies subducted Indian Ocean lithosphere that dips north at about 20° between the trench and the arc and then dips more steeply at about 60-70° from 100 to 600 km depth. In East Java there is gap in seismicity between about 250 and 500 km. Seismic tomography shows that this gap is not an aseismic section of the subduction zone but a hole in the slab. East Java is also unusual in the presence of K-rich volcanoes, now inactive, to the north of the calc-alkaline volcanoes of the active arc. In contrast to the calc-alkaline volcanism of the main arc, these K-rich melts imply lower fluid fluxes and a different mantle source. We suggest that all these observations can be explained by the tearing of the subducting slab when a buoyant oceanic plateau arrived at the trench south of East Java at about 8 Ma. With the slab unable to subduct

  20. JVM: Java Visual Mapping tool for next generation sequencing read.

    PubMed

    Yang, Ye; Liu, Juan

    2015-01-01

    We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

  1. JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.

    PubMed

    Feng, Guangjie; Burton, Nick; Hill, Bill; Davidson, Duncan; Kerwin, Janet; Scott, Mark; Lindsay, Susan; Baldock, Richard

    2005-03-09

    Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.

  2. Imaging of upper crustal structure beneath East Java-Bali, Indonesia with ambient noise tomography

    NASA Astrophysics Data System (ADS)

    Martha, Agustya Adi; Cummins, Phil; Saygin, Erdinc; Sri Widiyantoro; Masturyono

    2017-12-01

    The complex geological structures in East Java and Bali provide important opportunities for natural resource exploitation, but also harbor perils associated with natural disasters. Such a condition makes the East Java region an important area for exploration of the subsurface seismic wave velocity structure, especially in its upper crust. We employed the ambient noise tomography method to image the upper crustal structure under this study area. We used seismic data recorded at 24 seismographs of BMKG spread over East Java and Bali. In addition, we installed 28 portable seismographs in East Java from April 2013 to January 2014 for 2-8 weeks, and we installed an additional 28 seismographs simultaneously throughout East Java from August 2015 to April 2016. We constructed inter-station Rayleigh wave Green's functions through cross-correlations of the vertical component of seismic noise recordings at 1500 pairs of stations. We used the Neighborhood Algorithm to construct depth profiles of shear wave velocity (Vs). The main result obtained from this study is the thickness of sediment cover. East Java's southern mountain zone is dominated by higher Vs, the Kendeng basin in the center is dominated by very low Vs, and the Rembang zone (to the North of Kendeng zone) is associated with medium Vs. The existence of structures with oil and gas potential in the Kendeng and Rembang zones can be identified by low Vs.

  3. Internet Patient Records: new techniques

    PubMed Central

    Moehrs, Sascha; Anedda, Paolo; Tuveri, Massimiliano; Zanetti, Gianluigi

    2001-01-01

    Background The ease by which the Internet is able to distribute information to geographically-distant users on a wide variety of computers makes it an obvious candidate for a technological solution for electronic patient record systems. Indeed, second-generation Internet technologies such as the ones described in this article - XML (eXtensible Markup Language), XSL (eXtensible Style Language), DOM (Document Object Model), CSS (Cascading Style Sheet), JavaScript, and JavaBeans - may significantly reduce the complexity of the development of distributed healthcare systems. Objective The demonstration of an experimental Electronic Patient Record (EPR) system built from those technologies that can support viewing of medical imaging exams and graphically-rich clinical reporting tools, while conforming to the newly emerging XML standard for digital documents. In particular, we aim to promote rapid prototyping of new reports by clinical specialists. Methods We have built a prototype EPR client, InfoDOM, that runs in both the popular web browsers. In this second version it receives each EPR as an XML record served via the secure SSL (Secure Socket Layer) protocol. JavaBean software components manipulate the XML to store it and then to transform it into a variety of useful clinical views. First a web page summary for the patient is produced. From that web page other JavaBeans can be launched. In particular, we have developed a medical imaging exam Viewer and a clinical Reporter bean parameterized appropriately for the particular patient and exam in question. Both present particular views of the XML data. The Viewer reads image sequences from a patient-specified network URL on a PACS (Picture Archiving and Communications System) server and presents them in a user-controllable animated sequence, while the Reporter provides a configurable anatomical map of the site of the pathology, from which individual "reportlets" can be launched. The specification of these reportlets is

  4. Classification of java tea (Orthosiphon aristatus) quality using FTIR spectroscopy and chemometrics

    NASA Astrophysics Data System (ADS)

    Heryanto, R.; Pradono, D. I.; Marlina, E.; Darusman, L. K.

    2017-05-01

    Java tea (Orthosiphon aristatus) is a plant that widely used as a medicinal herb in Indonesia. Its quality is varying depends on various factors, such as cultivating area, climate and harvesting time. This study aimed to investigate the effectiveness of FTIR spectroscopy coupled with chemometrics for discriminating the quality of java tea from different cultivating area. FTIR spectra of ethanolic extracts were collected from five different regions of origin of java tea. Prior to chemometrics evaluation, spectra were pre-processed by using baselining, normalization and derivatization. Principal Components Analysis (PCA) was used to reduce the spectra to two PCs, which explained 73% of the total variance. Score plot of two PCs showed groupings of the samples according to their regions of origin. Furthermore, Partial Least Squares-Discriminant Analysis (PLSDA) was applied to the pre-processed data. The approach produced an external validation success rate of 100%. This study shows that FTIR analysis and chemometrics has discriminatory power to classify java tea based on its quality related to the region of origin.

  5. X3DOM as Carrier of the Virtual Heritage

    NASA Astrophysics Data System (ADS)

    Jung, Y.; Behr, J.; Graf, H.

    2011-09-01

    Virtual Museums (VM) are a new model of communication that aims at creating a personalized, immersive, and interactive way to enhance our understanding of the world around us. The term "VM" is a short-cut that comprehends various types of digital creations. One of the carriers for the communication of the virtual heritage at future internet level as de-facto standard is browser front-ends presenting the content and assets of museums. A major driving technology for the documentation and presentation of heritage driven media is real-time 3D content, thus imposing new strategies for a web inclusion. 3D content must become a first class web media that can be created, modified, and shared in the same way as text, images, audio and video are handled on the web right now. A new integration model based on a DOM integration into the web browsers' architecture opens up new possibilities for declarative 3 D content on the web and paves the way for new application scenarios for the virtual heritage at future internet level. With special regards to the X3DOM project as enabling technology for declarative 3D in HTML, this paper describes application scenarios and analyses its technological requirements for an efficient presentation and manipulation of virtual heritage assets on the web.

  6. West Java Snack Mapping based on Snack Types, Main Ingredients, and Processing Techniques

    NASA Astrophysics Data System (ADS)

    Nurani, A. S.; Subekti, S.; Ana

    2016-04-01

    The research was motivated by lack of literature on archipelago snack especially from West Java. It aims to explore the snack types, the processing techniques, and the main ingredients by planning a learning material on archipelago cake especially from West Java. The research methods used are descriptive observations and interviews. The samples were randomly chosen from all regions in West Java. The findings show the identification of traditional snack from West java including: 1. snack types which are similar in all regions as research sample namely: opak, rangginang, nagasari, aliagrem, cuhcur, keripik, semprong, wajit, dodol, kecimpring, combro, tape ketan, and surabi. The typical snack types involve burayot (Garut), simping kaum (Purwakarta), surabi hejo (Karawang), papais cisaat (Subang), Papais moyong, opak bakar (Kuningan), opak oded, ranggesing (Sumedang), gapit, tapel (Cirebon), gulampo, kue aci (Tasikmalaya), wajit cililin, gurilem (West Bandung), and borondong (Bandung District); 2. various processing techniques namely: steaming, boiling, frying, caramelizing, baking, grilling, roaster, sugaring; 3. various main ingredients namely rice, local glutinous rice, rice flour, glutinous rice flour, starch, wheat flour, hunkue flour, cassava, sweet potato, banana, nuts, and corn; 4. snack classification in West Java namely (1) traditional snack, (2) creation-snack, (3) modification-snack, (4) outside influence-snack.

  7. Increased xanthine oxidase-related ROS production and TRPV1 synthesis preceding DOMS post-eccentric exercise in rats.

    PubMed

    Retamoso, Leandro T; Silveira, Mauro E P; Lima, Frederico D; Busanello, Guilherme L; Bresciani, Guilherme; Ribeiro, Leandro R; Chagas, Pietro M; Nogueira, Cristina W; Braga, Ana Claudia M; Furian, Ana Flávia; Oliveira, Mauro S; Fighera, Michele R; Royes, Luiz Fernando F

    2016-05-01

    It is well-known that unaccustomed exercise, especially eccentric exercise, is associated to delayed onset muscle soreness (DOMS). Whether DOMS is associated with reactive oxygen species (ROS) and the transient receptor potential vanilloid 1 (TRPV1) is still an open question. Thus, the aim of this study was to investigate the association between TRPV1 and xanthine oxidase-related ROS production in muscle and DOMS after a bout of eccentric exercise. Male Wistar rats performed a downhill running exercise on a treadmill at a -16° tilt and a constant speed for 90min (5min/bout separated by 2min of rest). Mechanical allodynia and grip force tests were performed before and 1, 3, 6, 9, 12, 24, 48 and 72h after the downhill running. Biochemical assays probing oxidative stress, purine degradation, xanthine oxidase activity, Ca(2+) ATPase activity and TRPV1 protein content were performed in gastrocnemius muscle at 12, 24, and 48h after the downhill running. Our statistical analysis showed an increase in mechanical allodynia and a loss of strength after the downhill running. Similarly, an increase in carbonyl, xanthine oxidase activity, uric acid levels and TRPV1 immunoreactivity were found 12h post-exercise. On the other hand, Ca(2+) ATPase activity decreased in all analyzed times. Our results suggest that a possible relationship between xanthine oxidase-related ROS and TRPV1 may exist during the events preceding eccentric exercise-related DOMS. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. How Architecture-Driven Modernization Is Changing the Game in Information System Modernization

    DTIC Science & Technology

    2010-04-01

    Health Administration MUMPS  to Java 300K 4 mo. State of OR Employee Retirement System COBOL to C# .Net 250K 4 mo. Civilian State of WA Off. of Super of...Jovial, Mumps , A MagnaX, Natural, B PVL, P owerBuilder, A SQL, Vax Basic, s V B 6, + Others E revolution, inc. C, Target System "To Be" C#, C...successfully completed in 4 months • Created a new JANUSTM MUMPS parser TM , Implementation • Final “To-Be” Documentation • JANUS rules engine

  9. JSXGraph--Dynamic Mathematics with JavaScript

    ERIC Educational Resources Information Center

    Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

    2010-01-01

    Since Java applets seem to be on the retreat in web application, other approaches for displaying interactive mathematics in the web browser are needed. One such alternative could be our open-source project JSXGraph. It is a cross-browser library for displaying interactive geometry, function plotting, graphs, and data visualization in a web…

  10. PDDL4J: a planning domain description library for java

    NASA Astrophysics Data System (ADS)

    Pellier, D.; Fiorino, H.

    2018-01-01

    PDDL4J (Planning Domain Description Library for Java) is an open source toolkit for Java cross-platform developers meant (1) to provide state-of-the-art planners based on the Pddl language, and (2) to facilitate research works on new planners. In this article, we present an overview of the Automated Planning concepts and languages. We present some planning systems and their most significant applications. Then, we detail the Pddl4j toolkit with an emphasis on the available informative structures, heuristics and search algorithms.

  11. Spatial modeling for estimation of earthquakes economic loss in West Java

    NASA Astrophysics Data System (ADS)

    Retnowati, Dyah Ayu; Meilano, Irwan; Riqqi, Akhmad; Hanifa, Nuraini Rahma

    2017-07-01

    Indonesia has a high vulnerability towards earthquakes. The low adaptive capacity could make the earthquake become disaster that should be concerned. That is why risk management should be applied to reduce the impacts, such as estimating the economic loss caused by hazard. The study area of this research is West Java. The main reason of West Java being vulnerable toward earthquake is the existence of active faults. These active faults are Lembang Fault, Cimandiri Fault, Baribis Fault, and also Megathrust subduction zone. This research tries to estimates the value of earthquakes economic loss from some sources in West Java. The economic loss is calculated by using HAZUS method. The components that should be known are hazard (earthquakes), exposure (building), and the vulnerability. Spatial modeling is aimed to build the exposure data and make user get the information easier by showing the distribution map, not only in tabular data. As the result, West Java could have economic loss up to 1,925,122,301,868,140 IDR ± 364,683,058,851,703.00 IDR, which is estimated from six earthquake sources with maximum possibly magnitude. However, the estimation of economic loss value in this research is the worst case earthquakes occurrence which is probably over-estimated.

  12. Spatial durbin error model for human development index in Province of Central Java.

    NASA Astrophysics Data System (ADS)

    Septiawan, A. R.; Handajani, S. S.; Martini, T. S.

    2018-05-01

    The Human Development Index (HDI) is an indicator used to measure success in building the quality of human life, explaining how people access development outcomes when earning income, health and education. Every year HDI in Central Java has improved to a better direction. In 2016, HDI in Central Java was 69.98 %, an increase of 0.49 % over the previous year. The objective of this study was to apply the spatial Durbin error model using angle weights queen contiguity to measure HDI in Central Java Province. Spatial Durbin error model is used because the model overcomes the spatial effect of errors and the effects of spatial depedency on the independent variable. Factors there use is life expectancy, mean years of schooling, expected years of schooling, and purchasing power parity. Based on the result of research, we get spatial Durbin error model for HDI in Central Java with influencing factors are life expectancy, mean years of schooling, expected years of schooling, and purchasing power parity.

  13. Collaborative Scheduling Using JMS in a Mixed Java and .NET Environment

    NASA Technical Reports Server (NTRS)

    Wang, Yeou-Fang; Wax, Allan; Lam, Ray; Baldwin, John; Borden, Chet

    2006-01-01

    A collaborative framework/environment was proto-typed to prove the feasibility of scheduling space flight missions on NASA's Deep Space Network (DSN) in a distributed fashion. In this environment, effective collaboration relies on efficient communications among all flight mission and DSN scheduling users. There-fore, messaging becomes critical to timely event notification and data synchronization. In the prototype, a rapid messaging system using Java Message Service (JMS) in a mixed Java and .NET environment is established. This scheme allows both Java and .NET applications to communicate with each other for data synchronization and schedule negotiation. The JMS approach we used is based on a centralized messaging scheme. With proper use of a high speed messaging system, all users in this collaborative framework can communicate with each other to generate a schedule collaboratively to meet DSN and projects tracking needs.

  14. Seismicity of the Earth 1900-2012 Java and vicinity

    USGS Publications Warehouse

    Jones, Eric S.; Hayes, Gavin P.; Bernardino, Melissa; Dannemann, Fransiska K.; Furlong, Kevin P.; Benz, Harley M.; Villaseñor, Antonio

    2014-01-01

    The Sunda convergent margin extends for 5,600 km from the Bay of Bengal and the Andaman Sea, both located northwest of the map area, towards the island of Sumba in the southeast, and then continues eastward as the Banda arc system. This tectonically active margin is a result of the India and Australia plates converging with and subducting beneath the Sunda plate at a rate of approximately 50 to 70 mm/yr. The main physiographic feature associated with this convergent margin is the Sunda-Java Trench, which stretches for 3,000 km parallel to the Java and Sumatra land masses and terminates at 120° E. The convergence of the Indo-Australia and Sunda plates produces two active volcanic arcs: Sunda, which extends from 105 to 122° E and Banda, which extends from 122 to 128° E. The Sunda arc results solely from relatively simple oceanic plate subduction, while the Banda arc represents the transition from oceanic subduction to continental collision, where a complex, broad deforming zone is found. Based on modern activity, the Banda arc can be divided into three distinct zones: an inactive section, the Wetar Zone, bound by two active segments, the Flores Zone in the west and the Damar Zone in the east. The lack of volcanism in the Wetar Zone is attributed to the collision of Australia with the Sunda plate. The absence of gap in volcanic activity is underlain by a gap in intermediate depth seismicity, which is in contrast to nearly continuous, deep seismicity below all three sections of the arc. The Flores Zone is characterized by down-dip compression in the subducted slab at intermediate depths and late Quaternary uplift of the forearc. These unusual features, along with GPS data interpretations indicate that the Flores Zone marks the transition between subduction of oceanic crust in the west and the collision of continental crust in the east. The Java section of the Sunda arc is considered relatively aseismic historically when compared to the highly seismically active

  15. Potential Development Essential Oil Production of Central Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Alighiri, D.; Eden, W. T.; Supardi, K. I.; Masturi; Purwinarko, A.

    2017-04-01

    Indonesia is the source of raw essential oil in the world. Essential oils are used in various types of industries such as food and beverage, flavour, fragrance, perfumery, pharmaceuticals, and cosmetics. However, the development of Indonesian essential oil industry has not been encouraging for the production of essential oils, further it is unable to meet global demand. Besides that, the quality of volatile oil resulted cannot meet the international market standards. Based on the facts, the potential of Indonesian essential oils needs to be developed to provide added value, through increased production, improved quality and product diversification. One part of Indonesia having abundant of raw essential oil source is Central Java. Central Java has the quite large potential production of essential oils. Some essential oils produced from refining industry owned by the government, private and community sectors include cananga oils (Boyolali district), clove oils (Semarang district), patchouli oils (Brebes district, Pemalang district, and Klaten district). The main problem in the development of plants industries that producing essential oil in Central Java is low crops production, farming properties, quality of essential oils are diverse, providing poor-quality products and volatile oil price fluctuations. Marketing constraints of Central Java essential oils are quite complex supply chain. In general, marketing constraints of essential oils due to three factors, namely the low quality due to type of essential oil business that generally shaped small businesses with different capital and technology, domestic marketing is still a buyer-market (price determined by the buyer) because of weak bargaining position processors businessman, and prices fluctuate (domestic and foreign) due to uncontrolled domestic production and inter-country competition among manufacturers.

  16. An oceanic plateau subduction offshore Eastern Java

    NASA Astrophysics Data System (ADS)

    Shulgin, A.; Kopp, H.; Mueller, C.; Planert, L.; Lueschen, E.; Flueh, E. R.; Djajadihardja, Y.

    2010-12-01

    The area offshore Java represents one of a few places globally where the early stage of subduction of an oceanic plateau is observed. We study the little investigated Roo Rise oceanic plateau on the Indian plate, subducting beneath Eurasia.Our study area is located south of eastern Java and covers the edge of the Roo Rise plateau, the Java trench and the entire forearc section. For the first time the detailed deep structure of the Roo Rise is studied, subduction of which has a significant effect on the forearc dynamics and evolution and the increase of the geohazards risks. The tsunamogenic earthquakes of 1994 and 2006 are associated with the oceanic plateau edge been subducted. We present integrated results of a refraction/wide-angle reflection tomography, gravity modeling, and multichannel reflection seismic imaging using data acquired in 2006 along a corridor centered around 113°E and composed of a 340 km long N-S profile and a 130 km long E-W oriented profile. The composite structural models reveal the previously unresolved deep geometry of the collision zone and the structure of the oceanic plateau. The crustal thickness of the Roo Rise plateau is ranging from 18 to 12 km. The structure of the upper crust of the incoming oceanic plate shows the extreme degree of fracturing in its top section, and is associated with a plate bending. The forearc Moho has a depth range from 16 to 20 km. The gravity modeling requires a sharp crustal thickness increase below Java. Within our profiles we do not recover any direct evidence for the presence of the bathymetric features on the oceanic plate currently present below the accretionary prism, responsible for the tsunamogenic earthquake triggering. However vertical variations of the forearc basement edge are observed on the trench-parallel profile, which opens a discussion on the origin of such basement undulations, together with a localized patchy uplift character of the forearc high.The complex geometry of the backstop

  17. GC-MS analysis of clove (Syzygium aromaticum) bud essential oil from Java and Manado

    NASA Astrophysics Data System (ADS)

    Amelia, B.; Saepudin, E.; Cahyana, A. H.; Rahayu, D. U.; Sulistyoningrum, A. S.; Haib, J.

    2017-07-01

    The largest clove production contributors in Indonesia are mostly coming from Java and Manado. Different flavor among clove origins is caused by chemical constituents in clove oil. Unfortunately, scientific research and publications about flavor in clove from Indonesia's origin are still limited. The objective of this research is to determine significant differences of constituents in terms of flavor in clove oil originated from Java and Manado. The essential oils were isolated from cut clove bud samples by steam distillation method. The chemical constituents of clove bud oil were analyzed by using gas chromatography-mass spectrometry (GC-MS). Constituents were then identified by comparing the results of the chromatogram and reference retention time using Wiley mass spectra library (Wiley W9N11). Thirty-six and thirty-four chemical constituents were identified based on GC-MS from clove oil collected from Java and Manado, respectively. Major classes of compounds are sesquiterpenes, phenyl propanoid, oxygenated sesquiterpenes, and esters. Different compositions in major constituents were found between both origins. Clove Java contained eugenol (55.60 %), eugenyl acetate (20.54 %), caryophyllene (14.84 %), and α-humulene (2.75 %). While, in clove Manado, the composition were eugenol (74.64 %), caryophyllene (12.79 %), eugenyl acetate (8.70 %), and α-humulene (1.53 %). Moreover, minor constituents β-elemene (0.04 %), α-cadinene (0.05 %) and ledol (0.06 %) were existed only in clove Java, while clove Manado had some unique minor constituents which were not found in clove Java, i.e. β-gurjunene (0.04 %), γ-cadinene %), and humulene oxide (0.05 %). In conclusion, both clove oils from Java and Manado contained same major chemical constituents but different in their composition. In addition, some minor constituents existed only in specific origin.

  18. Identifying Intraplate Mechanism by B-Value Calculations in the South of Java Island

    NASA Astrophysics Data System (ADS)

    Bagus Suananda Y., Ida; Aufa, Irfan; Harlianti, Ulvienin

    2018-03-01

    Java is the most populous island in Indonesia with 50 million people live there. This island geologically formed at the Eurasia plate margin by the subduction of the Australian oceanic crust. At the south part of Java, beside the occurrence of 2-plate convergence earthquake (interplate), there are also the activities of the intraplate earthquake. Research for distinguish this 2 different earthquake type is necessary for estimating the behavior of the earthquake that may occur. The aim of this research is to map the b-value in the south of Java using earthquake data from 1963 until 2008. The research area are divided into clusters based on the epicenter mapping results with magnitude more than 4 and three different depth (0-30 km, 30-60 km, 60-100 km). This location clustering indicate group of earthquakes occurred by the same structure or mechanism. On some cluster in the south of Java, b-value obtained are between 0.8 and 1.25. This range of b-value indicates the region was intraplate earthquake zone, with 0.72-1.2 b-value range is the indication of intraplate earthquake zone. The final validation is to determine the mechanism of a segment done by correlating the epicenter and b-value plot with the available structural geology data. Based on this research, we discover that the earthquakes occur in Java not only the interplate earthquake, the intraplate earthquake also occurred here. By identifying the mechanism of a segment in the south of Java, earthquake characterization that may occur can be done for developing the accurate earthquake disaster mitigation system.

  19. SST cooling along coastal Java and Sumatra during positive Indian Ocean Dipole events

    NASA Astrophysics Data System (ADS)

    Delman, A. S.; McClean, J.; Sprintall, J.; Talley, L. D.; Bryan, F.; Johnson, B. K.; Carton, J.

    2016-02-01

    The evolution of positive Indian Ocean Dipole (pIOD) events is driven in part by anomalous SST cooling near the coasts of Java and Sumatra. However, the mechanisms and timeline of surface temperature changes near these two islands are distinct. Satellite data and mixed layer budgets in a forced ocean model simulation with 0.1° spatial resolution were used to characterize the dominant influences on SST in each region during pIOD events. Along the south coast of Java, where upwelling from southeasterly trade winds happens seasonally in June-September, strengthening/weakening of the trade winds has little effect on the interannual variability of SST. Instead, remotely-forced upwelling Kelvin waves are the primary mechanism for producing anomalous Java SST cooling in the early stages of a pIOD event. Other mechanisms that affect Java SST anomalies include inflows from the interior Indonesian Seas, mesoscale eddies, and air-sea heat fluxes; these influences can hasten the decay of cool Java SST anomalies and therefore may impact the strength and duration of pIOD events. Along the west coast of Sumatra, surface cooling is initially delayed by a deeper thermocline and a salinity-stratified barrier layer. Hence upwelling Kelvin waves do not substantially affect SST near Sumatra during the first 2-3 months of Java SST cooling; however, they do help drive surface cooling near Sumatra once the barrier layer has been sufficiently eroded by waters of decreasing temperature and increasing salinity. Upwelling Kelvin wave activity in the equatorial Indian Ocean starting in April is also shown to be a robust predictor of pIOD events later in the calendar year.

  20. A Standalone Vision Impairments Simulator for Java Swing Applications

    NASA Astrophysics Data System (ADS)

    Oikonomou, Theofanis; Votis, Konstantinos; Korn, Peter; Tzovaras, Dimitrios; Likothanasis, Spriridon

    A lot of work has been done lately in an attempt to assess accessibility. For the case of web rich-client applications several tools exist that simulate how a vision impaired or colour-blind person would perceive this content. In this work we propose a simulation tool for non-web JavaTM Swing applications. Developers and designers face a real challenge when creating software that has to cope with a lot of interaction situations, as well as specific directives for ensuring an accessible interaction. The proposed standalone tool will assist them to explore user-centered design and important accessibility issues for their JavaTM Swing implementations.

  1. Applications of Java and Vector Graphics to Astrophysical Visualization

    NASA Astrophysics Data System (ADS)

    Edirisinghe, D.; Budiardja, R.; Chae, K.; Edirisinghe, G.; Lingerfelt, E.; Guidry, M.

    2002-12-01

    We describe a series of projects utilizing the portability of Java programming coupled with the compact nature of vector graphics (SVG and SWF formats) for setup and control of calculations, local and collaborative visualization, and interactive 2D and 3D animation presentations in astrophysics. Through a set of examples, we demonstrate how such an approach can allow efficient and user-friendly control of calculations in compiled languages such as Fortran 90 or C++ through portable graphical interfaces written in Java, and how the output of such calculations can be packaged in vector-based animation having interactive controls and extremely high visual quality, but very low bandwidth requirements.

  2. Zika Virus, a Cause of Fever in Central Java, Indonesia

    DTIC Science & Technology

    1981-01-01

    ZIKA VIRUS , A CAUSE OF FEVER IN CENTRAL JAVA, INDONESIA J.G. Olson, T.G. Ksiazek, Suhandiman and Triwibowo REPORT NO. TR-879 NAMRU- DT1 &, AUG 0 9...75, No. 3, 1981 Zika virus , a cause of fever in Central Java, Indonesia J. G. OLSON’, T. G. KSIAZEK’, SUHANDIMAN 2 AND TRIwIBOWO 2 ’U.S. Naval...more days on admission. A physician member of the team recorded the Introduction patient’s age, sex and date of onset of symptoms and Zika virus ( ZIKA

  3. Implementing the Gaia Astrometric Global Iterative Solution (AGIS) in Java

    NASA Astrophysics Data System (ADS)

    O'Mullane, William; Lammers, Uwe; Lindegren, Lennart; Hernandez, Jose; Hobbs, David

    2011-10-01

    This paper provides a description of the Java software framework which has been constructed to run the Astrometric Global Iterative Solution for the Gaia mission. This is the mathematical framework to provide the rigid reference frame for Gaia observations from the Gaia data itself. This process makes Gaia a self calibrated, and input catalogue independent, mission. The framework is highly distributed typically running on a cluster of machines with a database back end. All code is written in the Java language. We describe the overall architecture and some of the details of the implementation.

  4. Controls on dissolved organic matter (DOM) degradation in a headwater stream: the influence of photochemical and hydrological conditions in determining light-limitation or substrate-limitation of photo-degradation

    NASA Astrophysics Data System (ADS)

    Cory, R. M.; Harrold, K. H.; Neilson, B. T.; Kling, G. W.

    2015-11-01

    We investigated how absorption of sunlight by chromophoric dissolved organic matter (CDOM) controls the degradation and export of DOM from Imnavait Creek, a beaded stream in the Alaskan Arctic. We measured concentrations of dissolved organic carbon (DOC), as well as concentrations and characteristics of CDOM and fluorescent dissolved organic matter (FDOM), during ice-free periods of 2011-2012 in the pools of Imnavait Creek and in soil waters draining to the creek. Spatial and temporal patterns in CDOM and FDOM in Imnavait Creek were analyzed in conjunction with measures of DOM degradation by sunlight and bacteria and assessments of hydrologic residence times and in situ UV exposure. CDOM was the dominant light attenuating constituent in the UV and visible portion of the solar spectrum, with high attenuation coefficients ranging from 86 ± 12 m-1 at 305 nm to 3 ± 1 m-1 in the photosynthetically active region (PAR). High rates of light absorption and thus light attenuation by CDOM contributed to thermal stratification in the majority of pools in Imnavait Creek under low-flow conditions. In turn, thermal stratification increased the residence time of water and DOM, and resulted in a separation of water masses distinguished by contrasting UV exposure (i.e., UV attenuation by CDOM with depth resulted in bottom waters receiving less UV than surface waters). When the pools in Imnavait Creek were stratified, DOM in the pool bottom water closely resembled soil water DOM in character, while the concentration and character of DOM in surface water was reproduced by experimental photo-degradation of bottom water. These results, in combination with water column rates of DOM degradation by sunlight and bacteria, suggest that photo-degradation is the dominant process controlling DOM fate and export in Imnavait Creek. A conceptual model is presented showing how CDOM amount and lability interact with incident UV light and water residence time to determine whether photo

  5. An Evaluation of Nitrate, fDOM, and Turbidity Sensors in New Hampshire Streams

    NASA Astrophysics Data System (ADS)

    Snyder, Lisle; Potter, Jody D.; McDowell, William H.

    2018-03-01

    A state-of-the-art network of water quality sensors was established in 2012 to gather year-round high temporal frequency hydrochemical data in streams and rivers throughout the state of New Hampshire. This spatially extensive network includes eight headwater stream and two main stem river monitoring sites, spanning a variety of stream orders and land uses. Here we evaluate the performance of nitrate, fluorescent dissolved organic matter (fDOM), and turbidity sensors included in the sensor network. Nitrate sensors were first evaluated in the laboratory for interference by different forms of dissolved organic carbon (DOC), and then for accuracy in the field across a range of hydrochemical conditions. Turbidity sensors were assessed for their effectiveness as a proxy for concentrations of total suspended solids (TSS) and total particulate C and N, and fDOM as a proxy for concentrations of dissolved organic matter. Overall sensor platform performance was also examined by estimating percentage of data loss due to sensor failures or related malfunctions. Although laboratory sensor trials show that DOC can affect optical nitrate measurements, our validations with grab samples showed that the optical nitrate sensors provide a reliable measurement of NO3 concentrations across a wide range of conditions. Results showed that fDOM is a good proxy for DOC concentration (r2 = 0.82) but is a less effective proxy for dissolved organic nitrogen (r2 = 0.41). Turbidity measurements from sensors correlated well with TSS (r2 = 0.78), PC (r2 = 0.53), and PN (r2 = 0.51).

  6. Building interactive virtual environments for simulated training in medicine using VRML and Java/JavaScript.

    PubMed

    Korocsec, D; Holobar, A; Divjak, M; Zazula, D

    2005-12-01

    Medicine is a difficult thing to learn. Experimenting with real patients should not be the only option; simulation deserves a special attention here. Virtual Reality Modelling Language (VRML) as a tool for building virtual objects and scenes has a good record of educational applications in medicine, especially for static and animated visualisations of body parts and organs. However, to create computer simulations resembling situations in real environments the required level of interactivity and dynamics is difficult to achieve. In the present paper we describe some approaches and techniques which we used to push the limits of the current VRML technology further toward dynamic 3D representation of virtual environments (VEs). Our demonstration is based on the implementation of a virtual baby model, whose vital signs can be controlled from an external Java application. The main contributions of this work are: (a) outline and evaluation of the three-level VRML/Java implementation of the dynamic virtual environment, (b) proposal for a modified VRML Timesensor node, which greatly improves the overall control of system performance, and (c) architecture of the prototype distributed virtual environment for training in neonatal resuscitation comprising the interactive virtual newborn, active bedside monitor for vital signs and full 3D representation of the surgery room.

  7. Subduction erosion off central Java: transition from accretion to erosion manifested by wide-angle seismic studies

    NASA Astrophysics Data System (ADS)

    Wittwer, A.; Flueh, E.; Rabbel, W.; Wagner, D.

    2006-12-01

    In this study, offshore wide-angle data acquired by ocean bottom instruments of a combined onshore- offshore investigation of the tectonic framework of central Java will be presented. The joint interdisciplinary project MERAMEX (Merapi Amphibious Experiment) was carried out in order to characterize the subduction of the Indo-Australian plate beneath Eurasia. The interpretation of three wide-angle data profiles, modelled with forward raytracing, indicates that the subduction of the Roo Rise with its thickened oceanic crust strongly influences the subduction zone. The dip angle of the downgoing oceanic plate is 10° and its crustal thickness increases to the east from 8 km to 9 km between both dip profiles off central Java. Large scale forearc uplift is manifested in isolated forearc highs, reaching water depths of only 1000 m compared to 2000 m water depth off western Java, and results from oceanic basement relief subduction. A broad band of seamounts trends E-W at approximately 10°S. Its incipient subduction off central Java causes frontal erosion of the margin here and leads to mass wasting due to oversteepening of the upper trench wall. A suite of wide-angle profiles off southern Sumatra to central Java indicates a clear change in the tectonic environment between longitude 108°E and 109°E. The well-developed accretionary wedge off southern Sumatra and western Java changes into a small frontal prism with steep slope angles of the upper plate off central Java.

  8. Land subsidence threats and its management in the North Coast of Java

    NASA Astrophysics Data System (ADS)

    Sarah, D.; Soebowo, E.

    2018-02-01

    Cities on the north coast of Java such as Jakarta, Semarang, Pekalongan, and Surabaya are vulnerable to environmental pressures such as sea level change and land subsidence. Land subsidence can be caused by natural and anthropogenic processes. Geologically, the north coastal plain of Java consists of unconsolidated Holocene alluvial deposit. The recent alluvial deposit is prone to compaction, and further aggravated by anthropogenic forces such as groundwater extraction and land development. Understanding the complex interaction of natural and manmade factors is essential to establish mitigation strategy. Although the impacts of land subsidence are widely felt, many do not realize that land subsidence is taking place. This paper presents a brief review of the land subsidence threats in the North coast of Java and proposes a recommendation for suitable management response.

  9. JPLEX: Java Simplex Implementation with Branch-and-Bound Search for Automated Test Assembly

    ERIC Educational Resources Information Center

    Park, Ryoungsun; Kim, Jiseon; Dodd, Barbara G.; Chung, Hyewon

    2011-01-01

    JPLEX, short for Java simPLEX, is an automated test assembly (ATA) program. It is a mixed integer linear programming (MILP) solver written in Java. It reads in a configuration file, solves the minimization problem, and produces an output file for postprocessing. It implements the simplex algorithm to create a fully relaxed solution and…

  10. Real-time Java simulations of multiple interference dielectric filters

    NASA Astrophysics Data System (ADS)

    Kireev, Alexandre N.; Martin, Olivier J. F.

    2008-12-01

    An interactive Java applet for real-time simulation and visualization of the transmittance properties of multiple interference dielectric filters is presented. The most commonly used interference filters as well as the state-of-the-art ones are embedded in this platform-independent applet which can serve research and education purposes. The Transmittance applet can be freely downloaded from the site http://cpc.cs.qub.ac.uk. Program summaryProgram title: Transmittance Catalogue identifier: AEBQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5778 No. of bytes in distributed program, including test data, etc.: 90 474 Distribution format: tar.gz Programming language: Java Computer: Developed on PC-Pentium platform Operating system: Any Java-enabled OS. Applet was tested on Windows ME, XP, Sun Solaris, Mac OS RAM: Variable Classification: 18 Nature of problem: Sophisticated wavelength selective multiple interference filters can include some tens or even hundreds of dielectric layers. The spectral response of such a stack is not obvious. On the other hand, there is a strong demand from application designers and students to get a quick insight into the properties of a given filter. Solution method: A Java applet was developed for the computation and the visualization of the transmittance of multilayer interference filters. It is simple to use and the embedded filter library can serve educational purposes. Also, its ability to handle complex structures will be appreciated as a useful research and development tool. Running time: Real-time simulations

  11. Bioavialability of Dom Photochemically Released from Resuspended Sediments

    NASA Astrophysics Data System (ADS)

    Avery, G. B., Jr.; Rainey, D. H.; Mead, R. N.; Skrabal, S. A.; Kieber, R. J.; Felix, J. D.; Helms, J. R.

    2016-02-01

    Little is known regarding the bioavailability of dissolved organic matter (DOM) released photochemically from resuspended estuarine sediments. Sediments were collected from two sites along the Cape Fear River estuary, NC, USA, size fractionated in 0.2 µm filtered Gulf Stream seawater and exposed to simulated sunlight for six hours. Light exposed samples resulted in increases of dissolved organic carbon (DOC) (34 ± 3 µM), chromophoric dissolved organic matter (CDOM) (a300nm, 2.7 m-1), and fluorescent dissolved organic matter (FDOM) (78.6 quinine sulfate equivalents (QSE)) compared to dark controls. Ultra high resolution mass spectrometric characterization indicated the photoreleased DOM was more oxidized and condensed based upon van Kreevlan analysis. Samples were then filtered and inoculated to a final ratio of 4% with coastal water sample filtered through a100 µm net to remove larger grazing organisms and particles while keeping most of bacterial community intact. All three parameters were monitored during a 30 day-long incubation in the dark to assess biological consumption and alteration. Previously light exposed samples had double (20 vs. 9 µM) the amount of DOC consumed compared to samples not previously exposed to light and twice the loss of CDOM (a300nm, 0.6 vs. 0.3 m-1) compared to samples not previously exposed to light. Previously light exposed samples resulted in a threefold loss of FDOM (9.5 QSE) compared to samples not previously exposed to light (2.8 QSE). Results of this study are important because they demonstrate dissolved organic matter released photochemically from resuspended sediments is more bioavailable than ambient material likely fueling secondary productivity and impacting ecosystem functioning in coastal regions.

  12. MSAViewer: interactive JavaScript visualization of multiple sequence alignments

    PubMed Central

    Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E.; Rost, Burkhard; Goldberg, Tatyana

    2016-01-01

    Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: msa@bio.sh PMID:27412096

  13. A High-Availability, Distributed Hardware Control System Using Java

    NASA Technical Reports Server (NTRS)

    Niessner, Albert F.

    2011-01-01

    Two independent coronagraph experiments that require 24/7 availability with different optical layouts and different motion control requirements are commanded and controlled with the same Java software system executing on many geographically scattered computer systems interconnected via TCP/IP. High availability of a distributed system requires that the computers have a robust communication messaging system making the mix of TCP/IP (a robust transport), and XML (a robust message) a natural choice. XML also adds the configuration flexibility. Java then adds object-oriented paradigms, exception handling, heavily tested libraries, and many third party tools for implementation robustness. The result is a software system that provides users 24/7 access to two diverse experiments with XML files defining the differences

  14. Waveform identification and retracking analyses of Jason-2 altimeter satellite data for improving sea surface height estimation in Southern Java Island Waters and Java Sea, Indonesia

    NASA Astrophysics Data System (ADS)

    Nababan, Bisman; Hakim, Muhammad R.; Panjaitan, James P.

    2018-05-01

    Indonesian waters containing many small islands and shallow waters leads to a less accurate of sea surface height (SSH) estimation from satellite altimetry. Little efforts are also given for the validation of SSH estimation from the satellite in Indonesian waters. The purpose of this research was to identify and retrack waveforms of Jason-2 altimeter satellite data in southern Java island waters and Java Sea using several retrackers and performed improvement percentage analyses for new SSH estimation. The study used data of the Sensor Geophysical Data Record type D (SGDR-D) of Jason-2 satellite altimeter of the year 2010 in the southern Java island waters and 2012-2014 in Java Sea. Waveform retracking analyses were conducted using several retrackers (Offset Center of Gravity, Ice, Threshold, and Improved Threshold) and examined using a world reference undulation geoid of EGM08 and Oceanic retracker. Result showed that shape and pattern of waveforms were varied in all passes, seasons, and locations specifically along the coastal regions. In general, non-Brownish and complex waveforms were identified along coastal region specifically within the distance of 0-10 km from the shoreline. In contrary, generally Brownish waveforms were found in offshore. However, Brownish waveform can also be found within coastal region and non-Brownish waveforms within offshore region. The results were also showed that the four retrackers produced a better SSH estimation in coastal region. However, there was no dominant retracker to improve the accuracy of the SSH estimate.

  15. Scientific Programming Using Java and C: A Remote Sensing Example

    NASA Technical Reports Server (NTRS)

    Prados, Donald; Johnson, Michael; Mohamed, Mohamed A.; Cao, Chang-Yong; Gasser, Jerry; Powell, Don; McGregor, Lloyd

    1999-01-01

    This paper presents results of a project to port code for processing remotely sensed data from the UNIX environment to Windows. Factors considered during this process include time schedule, cost, resource availability, reuse of existing code, rapid interface development, ease of integration, and platform independence. The approach selected for this project used both Java and C. By using Java for the graphical user interface and C for the domain model, the strengths of both languages were utilized and the resulting code can easily be ported to other platforms. The advantages of this approach are discussed in this paper.

  16. Concentration and spectroscopic characteristics of DOM in surface runoff and fracture flow in a cropland plot of a loamy soil.

    PubMed

    Xian, Qingsong; Li, Penghui; Liu, Chen; Cui, Junfang; Guan, Zhuo; Tang, Xiangyu

    2018-05-01

    Being crucial for predicting the impact of source inputs on a watershed in rainfall events, an understanding of the dynamics and characteristics of dissolved organic matter (DOM) export from the soil under particular land use types, particularly those associated with underground flows is still largely lacking. A field study was carried out using a 1500m 2 slope farmland plot in the hilly area of Sichuan Basin, Southwest China. The discharge of surface runoff and fracture flow was recorded and samples were collected in four representative rainfall events. For DOM characterization, concentration of dissolved organic carbon (DOC) and absorbance/excitation-emission matrix (EEM) fluorescence were analyzed. Soil water potential was also determined using tensiometers for understanding the runoff generation mechanisms. The DOC values for both surface and fracture flow showed significant responses to rainfall, with hydrological path being the primary factor in determining DOM dynamics. EEM-PARAFAC analyses indicated that the soil DOM mainly consisted of two terrestrial humic-like components with peaks located at Ex/Em 270(380)/480nm (C1) and 250(320)/410nm (C2), respectively. Concentrations of these components also responded strongly to rainfall, fluctuating in good agreement with the corresponding DOCs. Although there was no change in the presence of the components themselves, their relative distributions varied during precipitation, with the C1/C2 ratio increasing with the proportion of soil pre-event water. As the dynamic changes of soil DOM characteristics can be successfully captured using spectroscopic techniques, they may serve as a tracer for understanding hydrological paths based on their potential correlations with water source differences during rains. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Evaluating the ameliorative effect of natural dissolved organic matter (DOM) quality on copper toxicity to Daphnia magna: improving the BLM.

    PubMed

    Al-Reasi, Hassan A; Smith, D Scott; Wood, Chris M

    2012-03-01

    Various quality predictors of seven different natural dissolved organic matter (DOM) and humic substances were evaluated for their influence on protection of Daphnia magna neonates against copper (Cu) toxicity. Protection was examined at 3 and 6 mg l(-1) of dissolved organic carbon (DOC) of each DOM isolate added to moderately hard, dechlorinated water. Other water chemistry parameters (pH, concentrations of DOC, calcium, magnesium and sodium) were kept relatively constant. Predictors included absorbance ratios Abs(254/365) (index of molecular weight) and Abs-octanol(254)/Abs-water(254) (index of lipophilicity), specific absorption coefficient (SAC(340); index of aromaticity), and fluorescence index (FI; index of source). In addition, the fluorescent components (humic-like, fulvic-like, tryptophan-like, and tyrosine-like) of the isolates were quantified by parallel factor analysis (PARAFAC). Up to 4-fold source-dependent differences in protection were observed amongst the different DOMs. Significant correlations in toxicity amelioration were found with Abs(254/365), Abs-octanol(254)/Abs-water(254), SAC(340), and with the humic-like fluorescent component. The relationships with FI were not significant and there were no relationships with the tryptophan-like or tyrosine-like fluorescent components at 3 mg C l(-1), whereas a negative correlation was seen with the fulvic-like component. In general, the results indicate that larger, optically dark, more lipophilic, more aromatic DOMs of terrigenous origin, with higher humic-like content, are more protective against Cu toxicity. A method for incorporating SAC(340) as a DOM quality indicator into the Biotic Ligand Model is presented; this may increase the accuracy for predicting Cu toxicity in natural waters.

  18. Interactive Learning with Java Applets: Using Interactive, Web-Based Java Applets to Present Science in a Concrete, Meaningful Manner

    ERIC Educational Resources Information Center

    Corder, Greg

    2005-01-01

    Science teachers face challenges that affect the quality of instruction. Tight budgets, limited resources, school schedules, and other obstacles limit students' opportunities to experience science that is visual and interactive. Incorporating web-based Java applets into science instruction offers a practical solution to these challenges. The…

  19. Descriptive Statistics and Cluster Analysis for Extreme Rainfall in Java Island

    NASA Astrophysics Data System (ADS)

    E Komalasari, K.; Pawitan, H.; Faqih, A.

    2017-03-01

    This study aims to describe regional pattern of extreme rainfall based on maximum daily rainfall for period 1983 to 2012 in Java Island. Descriptive statistics analysis was performed to obtain centralization, variation and distribution of maximum precipitation data. Mean and median are utilized to measure central tendency data while Inter Quartile Range (IQR) and standard deviation are utilized to measure variation of data. In addition, skewness and kurtosis used to obtain shape the distribution of rainfall data. Cluster analysis using squared euclidean distance and ward method is applied to perform regional grouping. Result of this study show that mean (average) of maximum daily rainfall in Java Region during period 1983-2012 is around 80-181mm with median between 75-160mm and standard deviation between 17 to 82. Cluster analysis produces four clusters and show that western area of Java tent to have a higher annual maxima of daily rainfall than northern area, and have more variety of annual maximum value.

  20. WWWinda Orchestrator: a mechanism for coordinating distributed flocks of Java Applets

    NASA Astrophysics Data System (ADS)

    Gutfreund, Yechezkal-Shimon; Nicol, John R.

    1997-01-01

    The WWWinda Orchestrator is a simple but powerful tool for coordinating distributed Java applets. Loosely derived from the Linda programming language developed by David Gelernter and Nicholas Carriero of Yale, WWWinda implements a distributed shared object space called TupleSpace where applets can post, read, or permanently store arbitrary Java objects. In this manner, applets can easily share information without being aware of the underlying communication mechanisms. WWWinda is a very useful for orchestrating flocks of distributed Java applets. Coordination event scan be posted to WWWinda TupleSpace and used to orchestrate the actions of remote applets. Applets can easily share information via the TupleSpace. The technology combines several functions in one simple metaphor: distributed web objects, remote messaging between applets, distributed synchronization mechanisms, object- oriented database, and a distributed event signaling mechanisms. WWWinda can be used a s platform for implementing shared VRML environments, shared groupware environments, controlling remote devices such as cameras, distributed Karaoke, distributed gaming, and shared audio and video experiences.

  1. Activity Scratchpad Prototype: Simplifying the Rover Activity Planning Cycle

    NASA Technical Reports Server (NTRS)

    Abramyan, Lucy

    2005-01-01

    The Mars Exploration Rover mission depends on the Science Activity Planner as its primary interface to the Spirit and Opportunity Rovers. Scientists alternate between a series of mouse clicks and keyboard inputs to create a set of instructions for the rovers. To accelerate planning by minimizing mouse usage, a rover planning editor should receive the majority of inputted commands from the keyboard. Thorough investigation of the Eclipse platform's Java editor has provided the understanding of the base model for the Activity Scratchpad. Desirable Eclipse features can be mapped to specific rover planning commands, such as auto-completion for activity titles and content assist for target names. A custom editor imitating the Java editor's features was created with an XML parser for experimenting purposes. The prototype editor minimized effort for redundant tasks and significantly improved the visual representation of XML syntax by highlighting keywords, coloring rules, folding projections, and providing hover assist, templates and an outline view of the code.

  2. Implementation of integrated heterogeneous electronic electrocardiography data into Maharaj Nakorn Chiang Mai Hospital Information System.

    PubMed

    Khumrin, Piyapong; Chumpoo, Pitupoom

    2016-03-01

    Electrocardiography is one of the most important non-invasive diagnostic tools for diagnosing coronary heart disease. The electrocardiography information system in Maharaj Nakorn Chiang Mai Hospital required a massive manual labor effort. In this article, we propose an approach toward the integration of heterogeneous electrocardiography data and the implementation of an integrated electrocardiography information system into the existing Hospital Information System. The system integrates different electrocardiography formats into a consistent electrocardiography rendering by using Java software. The interface acts as middleware to seamlessly integrate different electrocardiography formats. Instead of using a common electrocardiography protocol, we applied a central format based on Java classes for mapping different electrocardiography formats which contains a specific parser for each electrocardiography format to acquire the same information. Our observations showed that the new system improved the effectiveness of data management, work flow, and data quality; increased the availability of information; and finally improved quality of care. © The Author(s) 2014.

  3. JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

    PubMed

    Rosen, Jebediah; Handy, Kyle; Gillan, André; Smith, Rob

    2017-11-06

    Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.

  4. Predictors of Errors of Novice Java Programmers

    ERIC Educational Resources Information Center

    Bringula, Rex P.; Manabat, Geecee Maybelline A.; Tolentino, Miguel Angelo A.; Torres, Edmon L.

    2012-01-01

    This descriptive study determined which of the sources of errors would predict the errors committed by novice Java programmers. Descriptive statistics revealed that the respondents perceived that they committed the identified eighteen errors infrequently. Thought error was perceived to be the main source of error during the laboratory programming…

  5. Interactive Economics Instruction with Java and CGI.

    ERIC Educational Resources Information Center

    Gerdes, Geoffrey R.

    2000-01-01

    States that this Web site is based on the conviction that Web-based materials must contain interactive modules to achieve value beyond that obtained by conventional media. Discusses three applets that can be reached at the homepage of the Web site by selecting the Java applets link. (CMK)

  6. Seasonal variation in the nature of DOM in a river and drinking water reservoir of a closed catchment.

    PubMed

    Awad, John; van Leeuwen, John; Chow, Christopher W K; Smernik, Ronald J; Anderson, Sharolyn J; Cox, Jim W

    2017-01-01

    Dissolved organic matter (DOM) in surface waters used for drinking purposes can vary markedly in character depending on its source within catchments and the timing and intensity of rainfall events. Here we report the findings of a study on the character and concentration of DOM in waters collected during different seasons from Myponga River and Reservoir, South Australia. The character of DOM was assessed in terms of its treatability by enhanced coagulation and potential for disinfection by-product i.e. trihalomethane (THM) formation. During the wet seasons (winter and spring), water samples from the river had higher DOC concentrations (X¯: 21 mg/L) and DOM of higher average molecular weight (AMW: 1526 Da) than waters collected during the dry seasons (summer and autumn: DOC: 13 mg/L; AMW: 1385 Da). Even though these features led to an increase in the percentage removal of organics by coagulation with alum (64% for wet compared with 53% for dry season samples) and a lower alum dose rate (10 versus 15 mg alum/mg DOC removal), there was a higher THM formation potential (THMFP) from wet season waters (treated waters: 217 μg/L vs 172 μg/L). For reservoir waters, samples collected during the wet seasons had an average DOC concentration (X¯: 15 mg/L), percentage removal of organics by alum (54%), alum dose rates (13 mg/mg DOC) and THMFP (treated waters: 207 μg/L) that were similar to samples collected during the dry seasons (mean DOC: 15 mg/L; removal of organics: 52%; alum dose rate: 13 mg/mg DOC; THMFP: 212 μg/L for treated waters). These results show that DOM present in river waters and treatability by alum are highly impacted by seasonal environmental variations. However these in reservoir waters exhibit less seasonal variability. Storage of large volumes of water in the reservoir enables mixing of influent waters and stabilization of water quality. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  7. Playing jigsaw with large igneous provinces - a plate-tectonic reconstruction of Ontong Java Nui

    NASA Astrophysics Data System (ADS)

    Hochmuth, Katharina; Gohl, Karsten; Uenzelmann-Neben, Gabriele; Werner, Reinhard

    2015-04-01

    Ontong Java Nui is a Cretaceous large igneous province (LIP), which was rifted apart into various smaller plateaus shortly after its emplacement around 125 Ma in the central Pacific. It incorporated the Ontong Java Plateau, the Hikurangi Plateau and the Manihiki Plateau as well as multiple smaller fragments, which have been subducted. Its size has been estimated to be approximately 0.8% of the Earth's surface. A volcanic edifice of this size has potentially had a great impact on the environment such as its CO2 release. The break-up of the "Super"-LIP is poorly constrained, because the break-up and subsequent seafloor spreading occurred within the Cretaceous Quiet Period. The Manihiki Plateau is presumably the centerpiece of this "Super"-LIP and shows by its margins and internal fragmentation that its tectonic and volcanic activity is related to the break-up of Ontong Java Nui. By incorporating two new seismic refraction/wide-angle reflection lines across two of the main sub-plateaus of the Manihiki Plateau, we can classify the break-up modes of the individual margins of the Manihiki Plateau. The Western Plateaus experienced crustal stretching due to the westward motion of the Ontong Java Plateau. The High Plateau shows sharp strike-slip movements at its eastern boundary towards an earlier part of Ontong Java Nui, which is has been subducted, and a rifted margin with a strong volcanic overprint at its southern edges towards the Hikurangi Plateau. These observations allow us a re-examination of the conjugate margins of the Hikurangi Plateau and the Ontong Java Plateau. The repositioning of the different plateaus leads to the conclusion that Ontong Java Nui was larger (~1.2% of the Earth's surface at emplacement) than previously anticipated. We use these finding to improve the plate tectonic reconstruction of the Cretaceous Pacific and to illuminate the role of the LIPs within the plate tectonic circuit in the western and central Pacific.

  8. Java-based cryptosystem for PACS and tele-imaging

    NASA Astrophysics Data System (ADS)

    Tjandra, Donny; Wong, Stephen T. C.; Yu, Yuan-Pin

    1998-07-01

    Traditional PACS systems are based on two-tier client server architectures, and require the use of costly, high-end client workstations for image viewing. Consequently, PACS systems using the two-tier architecture do not scale well as data increases in size and complexity. Furthermore, use of dedicated viewing workstations incurs costs in deployment and maintenance. To address these issues, the use of digital library technologies, such as the World Wide Web, Java, and CORBA, is being explored to distribute PACS data to serve a broader range of healthcare providers in an economic and efficient manner. Integration of PACS systems with digital library technologies allows access to medical information through open networks such as the Internet. However, use of open networks to transmit medical data introduces problems with maintaining privacy and integrity of patient information. Cryptography and digital timestamping is used to protect sensitive information from unauthorized access or tampering. A major concern when using cryptography and digital timestamping is the performance degradation associated with the mathematical calculations needed to encrypt/decrypt an image dataset, or to calculate the hash value of an image. The performance issue is compounded by the extra layer associated with the CORBA middleware, and the use of programming languages interpreted at the client side, such as Java. This paper study the extent to which Java-based cryptography and digital timestamping affects performance in a PACS system integrated with digital library technologies.

  9. Monitoring 2015 drought in West Java using Normalized Difference Water Index (NDWI)

    NASA Astrophysics Data System (ADS)

    Febrina Amalo, Luisa; Ma’rufah, Ummu; Ayu Permatasari, Prita

    2018-05-01

    Drought is a slow developing phenomenon that accumulates over period and affecting various sectors. It is one of natural hazards that occurs each year, particularly in Indonesia over Australian Monsoon period. During drought event, vegetation’s cover can be affected by water stress. Normalized Difference Water Index (NDWI) is a method for water resource assessment and known to be strongly related to the plant water content. NDWI is produced from MODIS bands Near-infrared (NIR) and Short Wave Infrared (SWIR). This research aims to monitor drought using NDWI in West Java during El Niño 2015 and its impact on rainfall variability. The result showed rainfall was decreased significantly starting from May-June, then increased in November. According to NDWI, it also showed that mostly West Java Region affected by drought during May-November. Very strong drought occurred on September-November. On December, areal extent of drought was decreasing significantly because rainfall had increased during November. Generally, areal extent of drought in West Java was dominated by strong and moderate drought. It implied that El Niño 2015, give great impact on increasing drought and decreasing rainfall in West Java. NDWI can be detected drought occurrence as it have good correlation with rainfall spatially.

  10. Transformations of the chemical compositions of high molecular weight DOM along a salinity transect: Using two dimensional correlation spectroscopy and principal component analysis approaches

    NASA Astrophysics Data System (ADS)

    Abdulla, Hussain A. N.; Minor, Elizabeth C.; Dias, Robert F.; Hatcher, Patrick G.

    2013-10-01

    In a study of chemical transformations of estuarine high-molecular-weight (HMW, >1000 Da) dissolved organic matter (DOM) collected over a period of two years along a transect through the Elizabeth River/Chesapeake Bay system to the coastal Atlantic Ocean off Virginia, USA, δ13C values, N/C ratios, and principal component analysis (PCA) of the solid-state 13C NMR (nuclear magnetic resonance) spectra of HMW-DOM show an abrupt change in both its sources and chemical structural composition occurring around salinity 20. HMW-DOM in the lower salinity region had lighter isotopic values, higher aromatic and lower carbohydrate contents relative to that in the higher salinity region. These changes around a salinity of 20 are possibly due to introduction of a significant amount of new carbon (autotrophic DOM) to the transect. PC-1 loadings plot shows that spatially differing DOM components are similar to previously reported 13C NMR spectra of heteropolysaccharides (HPS) and carboxyl-rich alicyclic molecules (CRAM). Applying two dimensional correlation spectroscopy techniques to 1H NMR spectra from the same samples reveals increases in the contribution of N-acetyl amino sugars, 6-deoxy sugars, and sulfated polysaccharides to HPS components along the salinity transect, which suggests a transition from plant derived carbohydrates to marine produced carbohydrates within the HMW-DOM pool. In contrast to what has been suggested previously, our combined results from 13C NMR, 1H NMR, and FTIR indicate that CRAM consists of at least two different classes of compounds (aliphatic polycarboxyl compounds and lignin-like compounds).

  11. Strategies for teaching object-oriented concepts with Java

    NASA Astrophysics Data System (ADS)

    Sicilia, Miguel-Ángel

    2006-03-01

    A considerable amount of experiences in teaching object-oriented concepts using the Java language have been reported to date, some of which describe language pitfalls and concrete learning difficulties. In this paper, a number of additional issues that have been experienced as difficult for students to master, along with approaches intended to overcome them, are addressed. Concretely, practical issues regarding associations, interfaces, genericity and exceptions are described. These issues suggest that more emphasis is required on presenting Java programs as derivations of conceptual models, in order to guarantee that a thorough design of the object structure actually precedes implementation issues. In addition, common student misunderstandings about the uses of interfaces and exceptions point to the necessity of introducing both specific design philosophies and also a clear distinction between design-for-reuse and more specific implementation issues.

  12. The simulation of 3D structure of groundwater system based on Java/Java3D

    NASA Astrophysics Data System (ADS)

    Yang, Xiaodong; Cui, Weihong; Wang, Peifa; Huang, Yongqi

    2007-06-01

    With the singular development of Internet technique and 3DGIS as well as VR and the imminence demand of 3D visualization from Groundwater information management field, how to display, roam, anatomize and analyze of 3D structure of Groundwater system on Internet have become a research hotspot in hydrogeology field. We simulated the 3D Groundwater resource structure of Taiyuan basin and implemented displaying, roaming, anatomizing and analyzing functions on Internet by Java 3D.

  13. MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

    PubMed

    Marchetti, Luca; Manca, Vincenzo

    2015-04-15

    MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Improving the interactivity and functionality of Web-based radiology teaching files with the Java programming language.

    PubMed

    Eng, J

    1997-01-01

    Java is a programming language that runs on a "virtual machine" built into World Wide Web (WWW)-browsing programs on multiple hardware platforms. Web pages were developed with Java to enable Web-browsing programs to overlay transparent graphics and text on displayed images so that the user could control the display of labels and annotations on the images, a key feature not available with standard Web pages. This feature was extended to include the presentation of normal radiologic anatomy. Java programming was also used to make Web browsers compatible with the Digital Imaging and Communications in Medicine (DICOM) file format. By enhancing the functionality of Web pages, Java technology should provide greater incentive for using a Web-based approach in the development of radiology teaching material.

  15. An Investigation of Factors Related to Self-Efficacy for Java Programming among Engineering Students

    ERIC Educational Resources Information Center

    Askar, Petek; Davenport, David

    2009-01-01

    The purpose of this study was to examine the factors related to self-efficacy for Java programming among first year engineering students. An instrument assessing Java programming self-efficacy was developed from the computer programming self-efficacy scale of Ramalingam & Wiedenbeck. The instrument was administered at the beginning of the…

  16. Volcanoes in Central Java, Indonesia

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The Indonesian island of Java (8.0S, 112.0) has over 35 active volcanoes, some of which are the most explosive in the world, and form an east/west line of peaks the length of the island. Five are in this image and at least one is thought to be currently active. The plume flowing north from Welirang (just east of the central cloud mass) is believed to be steam emissions. Also, the lack of vegetation at the peak indicates volcanic activity.

  17. MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

    PubMed

    Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

    2016-11-15

    The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

  18. Ambient Noise Tomography of central Java, with Transdimensional Bayesian Inversion

    NASA Astrophysics Data System (ADS)

    Zulhan, Zulfakriza; Saygin, Erdinc; Cummins, Phil; Widiyantoro, Sri; Nugraha, Andri Dian; Luehr, Birger-G.; Bodin, Thomas

    2014-05-01

    Delineating the crustal structure of central Java is crucial for understanding its complex tectonic setting. However, seismic imaging of the strong heterogeneity typical of such a tectonically active region can be challenging, particularly in the upper crust where velocity contrasts are strongest and steep body wave ray-paths provide poor resolution. We have applied ambient noise cross correlation of pair stations in central Java, Indonesia by using the MERapi Amphibious EXperiment (MERAMEX) dataset. The data were collected between May to October 2004. We used 120 of 134 temporary seismic stations for about 150 days of observation, which covered central Java. More than 5000 Rayleigh wave Green's function were extracted by cross-correlating the noise simultaneously recorded at available station pairs. We applied a fully nonlinear 2D Bayesian inversion technique to the retrieved travel times. Features in the derived tomographic images correlate well with previous studies, and some shallow structures that were not evident in previous studies are clearly imaged with Ambient Noise Tomography. The Kendeng Basin and several active volcanoes appear with very low group velocities, and anomalies with relatively high velocities can be interpreted in terms of crustal sutures and/or surface geological features.

  19. Java-based browsing, visualization and processing of heterogeneous medical data from remote repositories.

    PubMed

    Masseroli, M; Bonacina, S; Pinciroli, F

    2004-01-01

    The actual development of distributed information technologies and Java programming enables employing them also in the medical arena to support the retrieval, integration and evaluation of heterogeneous data and multimodal images in a web browser environment. With this aim, we used them to implement a client-server architecture based on software agents. The client side is a Java applet running in a web browser and providing a friendly medical user interface to browse and visualize different patient and medical test data, integrating them properly. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. Based on the Java Advanced Imaging API, processing and analysis tools were developed to support the evaluation of remotely retrieved bioimages through the quantification of their features in different regions of interest. The Java platform-independence allows the centralized management of the implemented prototype and its deployment to each site where an intranet or internet connection is available. Giving healthcare providers effective support for comprehensively browsing, visualizing and evaluating medical images and records located in different remote repositories, the developed prototype can represent an important aid in providing more efficient diagnoses and medical treatments.

  20. Rickettsia felis in Xenopsylla cheopis, Java, Indonesia

    PubMed Central

    Jiang, Ju; Soeatmadji, Djoko W.; Henry, Katherine M.; Ratiwayanto, Sutanti; Bangs, Michael J.

    2006-01-01

    Rickettsia typhi and R. felis, etiologic agents of murine typhus and fleaborne spotted fever, respectively, were detected in Oriental rat fleas (Xenopsylla cheopis) collected from rodents and shrews in Java, Indonesia. We describe the first evidence of R. felis in Indonesia and naturally occurring R. felis in Oriental rat fleas. PMID:16965716

  1. Verification of Java Programs using Symbolic Execution and Invariant Generation

    NASA Technical Reports Server (NTRS)

    Pasareanu, Corina; Visser, Willem

    2004-01-01

    Software verification is recognized as an important and difficult problem. We present a norel framework, based on symbolic execution, for the automated verification of software. The framework uses annotations in the form of method specifications an3 loop invariants. We present a novel iterative technique that uses invariant strengthening and approximation for discovering these loop invariants automatically. The technique handles different types of data (e.g. boolean and numeric constraints, dynamically allocated structures and arrays) and it allows for checking universally quantified formulas. Our framework is built on top of the Java PathFinder model checking toolset and it was used for the verification of several non-trivial Java programs.

  2. Java across Different Curricula, Courses and Countries Using a Common Pool of Teaching Material

    ERIC Educational Resources Information Center

    Ivanovic, Mirjana; Budimac, Zoran; Mishev, Anastas; Bothe, Klaus; Jurca, Ioan

    2013-01-01

    Under the auspices of a DAAD funded educational project, a subproject devoted to different aspects of teaching the Java programming language started several years ago. The initial intention of the subproject was to attract members of the subproject to prepare some teaching materials for teaching essentials of the Java programming language. During…

  3. The influence of DOM and microbial processes on arsenic release from karst during ASR operations in the Floridan Aquifer

    NASA Astrophysics Data System (ADS)

    Jin, J.; Zimmerman, A. R.

    2011-12-01

    The mobilization of subsurface As poses a serious threat to human health, particularly in a region such as Florida where population is heavily dependent on highly porous karstic aquifers for drinking water. Injection water used in aquifer storage and recovery (ASR) or aquifer recharge (AR) operations is commonly high in dissolved organic matter (DOM) and OM can also be present in the subsurface carbonate rock. Using batch incubation experiments, this study examined the role of core preservation methods, as well as the influence of labile and more refractory DOM on the mobilization of As from carbonate rock. Incubation experiments used sealed reaction vessels with preserved and homogenized core materials collected via coring the Suwannee Formation in southwest Florida and treatment additions consisting of 1) source water (SW) enriched in sterilized soil DOM, 2) SW enriched in soil DOM and microbes, and 3) SW enriched in sodium acetate. During an initial equilibration phase in native groundwater (NGW) with low dissolved oxygen (DO; Phase 1), we found the greatest As release of the whole incubation. In the beginning of Phase 2 (N2 headspace) in which NGW was replaced with treatment solutions, there was little As release except in the vessel with Na-acetate added, which also had the lowest ORP. At the start of Phase 3, when incubations were exposed to air, most vessels saw more ion (including As) release into solution. Vessel with Na-acetate had less As release in Phase 3 than in Phase 2. During all experimental phases, treatments of DOM or microbe additions had no apparent effect on the amount of As release. The core materials was found contain significant amount of indigenous DOM (about 8 g OC/kg core) which was released during the incubation so DOC concentrations displayed no clear pattern among different treatments. At least three abiotic As mobilization mechanisms may play a role in As released during different stages of the experiment. Desorption of As from iron

  4. BounceBack capsules for reduction of DOMS after eccentric exercise: a randomized, double-blind, placebo-controlled, crossover pilot study.

    PubMed

    Udani, Jay K; Singh, Betsy B; Singh, Vijay J; Sandoval, Elizabeth

    2009-06-05

    Delayed onset muscle soreness (DOMS) is muscle pain and discomfort experienced approximately one to three days after exercise. DOMS is thought to be a result of microscopic muscle fiber tears that occur more commonly after eccentric exercise rather than concentric exercise. This study sought to test the efficacy of a proprietary dietary supplement, BounceBack, to alleviate the severity of DOMS after standardized eccentric exercise. The study was a randomized, double-blind, placebo-controlled, crossover study. Ten healthy community-dwelling untrained subjects, ranging in age from 18-45 years, were enrolled. Mean differences within and between groups were assessed inferentially at each data collection time-point using t-tests for all outcome measures. In this controlled pilot study, intake of BounceBack capsules for 30 days resulted in a significant reduction in standardized measures of pain and tenderness post-eccentric exercise compared to the placebo group. There were trends towards reductions in plasma indicators of inflammation (high sensitivity C-reactive protein) and muscle damage (creatine phosphokinase and myoglobin). BounceBack capsules were able to significantly reduce standardized measures of pain and tenderness at several post-eccentric exercise time points in comparison to placebo. The differences in the serological markers of DOMS, while not statistically significant, appear to support the clinical findings. The product appears to have a good safety profile and further study with a larger sample size is warranted based on the current results.

  5. BounceBack™ capsules for reduction of DOMS after eccentric exercise: a randomized, double-blind, placebo-controlled, crossover pilot study

    PubMed Central

    Udani, Jay K; Singh, Betsy B; Singh, Vijay J; Sandoval, Elizabeth

    2009-01-01

    Background Delayed onset muscle soreness (DOMS) is muscle pain and discomfort experienced approximately one to three days after exercise. DOMS is thought to be a result of microscopic muscle fiber tears that occur more commonly after eccentric exercise rather than concentric exercise. This study sought to test the efficacy of a proprietary dietary supplement, BounceBack™, to alleviate the severity of DOMS after standardized eccentric exercise. Methods The study was a randomized, double-blind, placebo-controlled, crossover study. Ten healthy community-dwelling untrained subjects, ranging in age from 18–45 years, were enrolled. Mean differences within and between groups were assessed inferentially at each data collection time-point using t-tests for all outcome measures. Results In this controlled pilot study, intake of BounceBack™ capsules for 30 days resulted in a significant reduction in standardized measures of pain and tenderness post-eccentric exercise compared to the placebo group. There were trends towards reductions in plasma indicators of inflammation (high sensitivity C-reactive protein) and muscle damage (creatine phosphokinase and myoglobin). Conclusion BounceBack™ capsules were able to significantly reduce standardized measures of pain and tenderness at several post-eccentric exercise time points in comparison to placebo. The differences in the serological markers of DOMS, while not statistically significant, appear to support the clinical findings. The product appears to have a good safety profile and further study with a larger sample size is warranted based on the current results. PMID:19500355

  6. A Sociolinguistic Study of Differential Object Marking (DOM) in Two Varieties of Contemporary Spanish

    ERIC Educational Resources Information Center

    Balasch Rodriguez, Sonia

    2011-01-01

    This sociolinguistic-variationist investigation sheds light on two little-studied issues concerning Spanish DOM, or variable use of a before animate "direct objects" (DOs), in vernacular language: the complex interaction of co-occurring linguistic (type of verb; definiteness, specificity, grammatical number, topicality, type and…

  7. Characterising DOC, DON and DOP flux in two contrasting lowland UK catchments: impacts of contrasting source character and connectivity on reach scale DOM signature

    NASA Astrophysics Data System (ADS)

    Yates, C. A.; Johnes, P.; Spencer, R. G.

    2012-12-01

    Riverine DOM is a significant component of C, N and P transport from source to sea. Research to date has focused on characterising DOC in upland and boreal moorland and forested catchments. Here we present the results of an investigation of DOM character and DOC, DON and DOP flux relative to C, N and P flux in two contrasting lowland UK catchments: the Wylye and Millersford Brook. Both were sampled at daily frequency at 3 sites over a 2 year period, (2010-11 WY, 2011-12 WY) with fluorescence EEMs and UV-Vis determined weekly. The Wylye is a Chalk catchment, underlain by a major aquifer. It has predominantly calcareous brown earth soils, intensive arable agriculture, scattered farms and riparian villages with a major settlement in the lower reaches of the river. There are few natural organic sources in the catchment and flows are baseflow dominated with a BFI of 0.93. DOC (NPOC) concentrations averaged 2.59 mg C/l in water year 2011-12, while Total N concentrations averaged 10.0 mg N/l, with DON averaging 0.9 mg N/l, and Total P concentrations averaged 0.18 mg/l with DOP averaging 0.026 mg/l. Millersford Brook drains peaty soils over glacial sands and clays, with moorland and forestry as the dominant land uses. Flows are dominated by overland and subsurface quick flow through with a BFI of 0.34. There is some low intensity grazing, no fertiliser use and no dwellings in the headwaters of the catchment. As a result nutrient concentrations are lower, but C flux is higher, with mean annual concentrations in WY 2011-12 of 0.93 mg TN/l, 0.051 mg TP/l, 8.83 mg DOC/l, 0.55 mg DON/l and 0.029 mg DOP/l. DOM character in Millersford Brook is comparable for that observed in other catchments with peaty soils and low acid neutralising capacity. The character of DOM varies along the length of the river, with HMW compounds dominating the signal in the headwaters, and LMW fluorescence intensities added to the signal in the lower reaches of the river, where septic tank effluent

  8. Java-based PACS and reporting system for nuclear medicine

    NASA Astrophysics Data System (ADS)

    Slomka, Piotr J.; Elliott, Edward; Driedger, Albert A.

    2000-05-01

    In medical imaging practice, images and reports often need be reviewed and edited from many locations. We have designed and implemented a Java-based Remote Viewing and Reporting System (JaRRViS) for a nuclear medicine department, which is deployed as a web service, at the fraction of the cost dedicated PACS systems. The system can be extended to other imaging modalities. JaRRViS interfaces to the clinical patient databases of imaging workstations. Specialized nuclear medicine applets support interactive displays of data such as 3-D gated SPECT with all the necessary options such as cine, filtering, dynamic lookup tables, and reorientation. The reporting module is implemented as a separate applet using Java Foundation Classes (JFC) Swing Editor Kit and allows composition of multimedia reports after selection and annotation of appropriate images. The reports are stored on the server in the HTML format. JaRRViS uses Java Servlets for the preparation and storage of final reports. The http links to the reports or to the patient's raw images with applets can be obtained from JaRRViS by any Hospital Information System (HIS) via standard queries. Such links can be sent via e-mail or included as text fields in any HIS database, providing direct access to the patient reports and images via standard web browsers.

  9. JDiffraction: A GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields

    NASA Astrophysics Data System (ADS)

    Piedrahita-Quintero, Pablo; Trujillo, Carlos; Garcia-Sucerquia, Jorge

    2017-05-01

    JDiffraction, a GPGPU-accelerated JAVA library for numerical propagation of scalar wave fields, is presented. Angular spectrum, Fresnel transform, and Fresnel-Bluestein transform are the numerical algorithms implemented in the methods and functions of the library to compute the scalar propagation of the complex wavefield. The functionality of the library is tested with the modeling of easy to forecast numerical experiments and also with the numerical reconstruction of a digitally recorded hologram. The performance of JDiffraction is contrasted with a library written for C++, showing great competitiveness in the apparently less complex environment of JAVA language. JDiffraction also includes JAVA easy-to-use methods and functions that take advantage of the computation power of the graphic processing units to accelerate the processing times of 2048×2048 pixel images up to 74 frames per second.

  10. Designing and developing portable large-scale JavaScript web applications within the Experiment Dashboard framework

    NASA Astrophysics Data System (ADS)

    Andreeva, J.; Dzhunov, I.; Karavakis, E.; Kokoszkiewicz, L.; Nowotka, M.; Saiz, P.; Tuckett, D.

    2012-12-01

    Improvements in web browser performance and web standards compliance, as well as the availability of comprehensive JavaScript libraries, provides an opportunity to develop functionally rich yet intuitive web applications that allow users to access, render and analyse data in novel ways. However, the development of such large-scale JavaScript web applications presents new challenges, in particular with regard to code sustainability and team-based work. We present an approach that meets the challenges of large-scale JavaScript web application design and development, including client-side model-view-controller architecture, design patterns, and JavaScript libraries. Furthermore, we show how the approach leads naturally to the encapsulation of the data source as a web API, allowing applications to be easily ported to new data sources. The Experiment Dashboard framework is used for the development of applications for monitoring the distributed computing activities of virtual organisations on the Worldwide LHC Computing Grid. We demonstrate the benefits of the approach for large-scale JavaScript web applications in this context by examining the design of several Experiment Dashboard applications for data processing, data transfer and site status monitoring, and by showing how they have been ported for different virtual organisations and technologies.

  11. Empowerment model of biomass in west java

    NASA Astrophysics Data System (ADS)

    Mulyana, C.; Fitriani, N. I.; Saad, A.; Yuliah, Y.

    2017-06-01

    Scarcity of fossil energy accelerates the search of renewable energy sources as the substitution. In West Java, biomass has potential to be developed into bio-briquette because the resources are abundant. The objectives of this research are mapping the potency of biomass as bio-briquette in West Java, and making the model of the empowerment biomass potential involving five fundamental step which are raw material, pre-processing process, conversion mechanism, products, and end user. The main object of this model focused on 3 forms which are solid, liquid, and gas which was made by involving the community component as the owner biomass, district government, academics and researcher communities, related industries as users of biomass, and the central government as the policy holders and investors as a funder. In the model was described their respective roles and mutual relationship one with another so that the bio-briquette as a substitute of fossil fuels can be realized. Application of this model will provide the benefits in renewability energy sources, environmental, socio economical and energy security.

  12. Access Control of Web- and Java-Based Applications

    NASA Technical Reports Server (NTRS)

    Tso, Kam S.; Pajevski, Michael J.

    2013-01-01

    Cybersecurity has become a great concern as threats of service interruption, unauthorized access, stealing and altering of information, and spreading of viruses have become more prevalent and serious. Application layer access control of applications is a critical component in the overall security solution that also includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. An access control solution, based on an open-source access manager augmented with custom software components, was developed to provide protection to both Web-based and Javabased client and server applications. The DISA Security Service (DISA-SS) provides common access control capabilities for AMMOS software applications through a set of application programming interfaces (APIs) and network- accessible security services for authentication, single sign-on, authorization checking, and authorization policy management. The OpenAM access management technology designed for Web applications can be extended to meet the needs of Java thick clients and stand alone servers that are commonly used in the JPL AMMOS environment. The DISA-SS reusable components have greatly reduced the effort for each AMMOS subsystem to develop its own access control strategy. The novelty of this work is that it leverages an open-source access management product that was designed for Webbased applications to provide access control for Java thick clients and Java standalone servers. Thick clients and standalone servers are still commonly used in businesses and government, especially for applications that require rich graphical user interfaces and high-performance visualization that cannot be met by thin clients running on Web browsers

  13. [Using ultraviolet-visible ( UV-Vis) absorption spectrum to estimate the dissolved organic matter (DOM) concentration in water, soils and sediments of typical water-level fluctuation zones of the Three Gorges Reservoir areas].

    PubMed

    Li, Lu-lu; Jiang, Tao; Lu, Song; Yan, Jin-long; Gao, Jie; Wei, Shi-qiang; Wang, Ding-yong; Guo, Nian; Zhao, Zhena

    2014-09-01

    Dissolved organic matter (DOM) is a very important component in terrestrial ecosystem. Chromophoric dissolved organic matter (CDOM) is a significant constituent of DOM, which can be measured by ultraviolet-visible (UV-Vis) absorption spectrum. Thus the relationship between CDOM and DOM was investigated and established by several types of models including single-wavelength model, double-wavelength model, absorption spectrum slope (S value) model and three-wavelength model, based on the UV-Vis absorption coefficients of soil and sediment samples (sampled in July of 2012) and water samples (sampled in November of 2012) respectively. The results suggested that the three-wavelength model was the best for fitting, and the determination coefficients of water, soil and sediment data were 0. 788, 0. 933 and 0. 856, respectively. Meanwhile, the nominal best model was validated with the UV-Vis data of 32 soil samples and 36 water samples randomly collected in 2013, showing the RRMSE and MRE were 16. 5% and 16. 9% respectively for soil DOM samples, 10. 32% and 9. 06% respectively for water DOM samples, which further suggested the prediction accuracy was higher in water DOM samples as compared with that in soil DOM samples.

  14. Fractionation and characterization of dissolved organic matter (DOM) in refinery wastewater by revised phase retention and ion-exchange adsorption solid phase extraction followed by ESI FT-ICR MS.

    PubMed

    Fang, Zhi; He, Chen; Li, Yongyong; Chung, Keng H; Xu, Chunming; Shi, Quan

    2017-01-01

    Although the progress of high resolution mass spectrometry in the past decade has enabled the molecular characterization of dissolved organic matter (DOM) in water as a whole, fractionation of DOM is necessary for a comprehensive characterization due to its super-complex nature. Here we proposed a method for the fractionation of DOM in a wastewater based on solubility and acidic-basic properties. Solid phase extraction (SPE) cartridges with reversed phase retention and ion-exchange adsorption capacities, namely MAX and MCX, were used in succession to fractionate a petroleum refinery wastewater into four fractions: hydrophobic acid (HOA), hydrophobic neutral (HON), hydrophobic base (HOB), and hydrophilic substance (HIS) fractions. According to the total organic carbon (TOC) analysis, 72.6% (in term of TOC) of DOM was extracted in hydrophobic fractions, in which HON was the most abundant. Hydrophobic extracts were characterized by negative and positive ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), respectively. Compounds with multiple oxygen atoms were predominant in the HOA, which were responded strongly in the negative ESI MS. Nitrogen containing compounds were the major detected species by positive ion ESI in all hydrophobic fractions. The molecular composition of the DOM were discussed based on the FT-ICR MS results. The fractionation provided salt free samples which enables the direct analysis of the fractions by ESI and a deep insight into the molecular composition of DOM in the wastewater. The method is potential for routine evaluation of DOM in industry wastewaters, as well as environmental water samples. Copyright © 2016. Published by Elsevier B.V.

  15. An oceanic plateau subduction: A case study offshore Eastern Java.

    NASA Astrophysics Data System (ADS)

    Shulgin, Alexey; Kopp, Heidrun; Mueller, Christian; Planert, Lars; Lueschen, Ewald; Flueh, Ernst; Djajadihardja, Yusuf

    2010-05-01

    The area offshore Java represents one of a few places globally where the early stage of subduction of an oceanic plateau is observed. Our study area is located south of eastern Java and covers the edge of the Roo Rise plateau, the Java trench and the entire forearc section. For the first time the detailed deep structure of the Roo Rise is studied, subduction of which has a significant effect on the forearc dynamics and evolution and the increase of the geohazards risks. The tsunamogenic earthquakes of 1994 and 2006 are associated with the oceanic plateau edge been subducted. We present integrated results of a refraction/wide-angle reflection tomography, gravity modeling, and multichannel reflection seismic imaging using data acquired in 2006 along a corridor centered around 113°E and composed of a 340 km long N-S profile and a 130 km long E-W oriented profile. The composite structural models reveal the previously unresolved deep geometry of the collision zone and the structure of the oceanic plateau. The crustal thickness of the Roo Rise plateau is ranging from 18 to 12 km. The structure of the upper crust of the incoming oceanic plate shows the extreme degree of fracturing in its top section, and is associated with a plate bending. The forearc Moho has a depth range from 16 to 20 km. The gravity modeling requires a sharp crustal thickness increase below Java. Within our profiles we do not recover any direct evidence for the presence of the bathymetric features on the oceanic plate currently present below the accretionary prism, responsible for the tsunamogenic earthquake triggering. However vertical variations of the forearc basement edge are observed on the trench-parallel profile, which opens a discussion on the origin of such basement undulations, together with a localized patchy uplift character of the forearc high.

  16. The spirit of democracy in the implementation of public information policy at the provincial government of West Java

    NASA Astrophysics Data System (ADS)

    Sjoraida, D. F.; Asmawi, A.; Anwar, R. K.

    2018-03-01

    This article analyses the implementation of Law Number 14/2008 on Public Information Disclosure on the Provincial Government of West Java. This descriptive-qualitative study presents a discussion of the spirit of democracy in the implementation of the abovem-entioned policy in West Java Province. With the theory of policy implementation and democratization, data obtains that the element of democratic spirit in the implementation of public information policy in the government of West Java is quite thick. Therefore, there must be a massification of the implementation of the law in West Java, especially its socialization to districts/cities and society in general. It was found that the democratization of the West Java Provincial Government in implementing the Act has been well received in the community. However, the lack of publicity about this Law can reduce the strength of moral messages that exist in the law to the public.

  17. Relationships between anopheline mosquitoes and topography in West Timor and Java, Indonesia.

    PubMed

    Ndoen, Ermi; Wild, Clyde; Dale, Pat; Sipe, Neil; Dale, Mike

    2010-08-26

    Malaria is a serious health issue in Indonesia. Mosquito control is one aspect of an integrated malaria management programme. To focus resources on priority areas, information is needed about the vectors and their habitats. This research aimed to identify the relationship between anopheline mosquitoes and topography in West Timor and Java. Study areas were selected in three topographic types in West Timor and Java. These were: coastal plain, hilly (rice field) and highland. Adult mosquitoes were captured landing on humans identified to species level and counted. Eleven species were recorded, four of which were significant for malaria transmission: Anopheles aconitus, Anopheles barbirostris, Anopheles subpictus and Anopheles sundaicus. Each species occupied different topographies, but only five were significantly associated: Anopheles annularis, Anopheles vagus and Anopheles subpictus (Java only) with hilly rice fields; Anopheles barbirostris, Anopheles maculatus and Anopheles subpictus (West Timor only) with coastal areas. Information on significant malaria vectors associated with specific topography is useful for planning the mosquito control aspect of malaria management.

  18. NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.

    PubMed

    Lagnel, Jacques; Tsigenopoulos, Costas S; Iliopoulos, Ioannis

    2009-03-15

    NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST. Supplementary data are available at Bioinformatics online.

  19. A geostationary Earth orbit satellite model using Easy Java Simulation

    NASA Astrophysics Data System (ADS)

    Wee, Loo Kang; Hwee Goh, Giam

    2013-01-01

    We develop an Easy Java Simulation (EJS) model for students to visualize geostationary orbits near Earth, modelled using a Java 3D implementation of the EJS 3D library. The simplified physics model is described and simulated using a simple constant angular velocity equation. We discuss four computer model design ideas: (1) a simple and realistic 3D view and associated learning in the real world; (2) comparative visualization of permanent geostationary satellites; (3) examples of non-geostationary orbits of different rotation senses, periods and planes; and (4) an incorrect physics model for conceptual discourse. General feedback from the students has been relatively positive, and we hope teachers will find the computer model useful in their own classes.

  20. Controls on dissolved organic matter (DOM) degradation in a headwater stream: the influence of photochemical and hydrological conditions in determining light-limitation or substrate-limitation of photo-degradation

    NASA Astrophysics Data System (ADS)

    Cory, R. M.; Harrold, K. H.; Neilson, B. T.; Kling, G. W.

    2015-07-01

    We investigated how absorption of sunlight by chromophoric dissolved organic matter (CDOM) controls the degradation and export of DOM from Imnavait Creek, a beaded stream in the Alaskan Arctic. We measured concentrations of dissolved organic carbon (DOC), as well as concentrations and characteristics of CDOM and fluorescent dissolved organic matter (FDOM), during ice-free periods of 2011-2012 in the pools of Imnavait Creek and in soil waters draining to the creek. Spatial and temporal patterns in CDOM and FDOM in Imnavait Creek were analyzed in conjunction with measures of DOM degradation by sunlight and bacteria and assessments of hydrologic residence times and in situ UV exposure. CDOM was the dominant light attenuating constituent in the UV and visible portion of the solar spectrum, with high attenuation coefficients ranging from 86 ± 12 m-1 at 305 nm to 3 ± 1 m-1 in the photosynthetically active region (PAR). High rates of light absorption and thus light attenuation by CDOM contributed to thermal stratification in the majority of pools in Imnavait Creek under low-flow conditions. In turn, thermal stratification increased the residence time of water and DOM, and resulted in a separation of water masses distinguished by contrasting UV exposure (i.e., UV attenuation by CDOM with depth resulted in bottom waters receiving less UV than surface waters). When the pools in Imnavait Creek were stratified, DOM in the pool bottom water closely resembled soil water DOM in character, while the concentration and character of DOM in surface water was reproduced by experimental photo-degradation of bottom water. These results, in combination with water column rates of DOM degradation by sunlight and bacteria, suggest that photo-degradation is the dominant process controlling DOM fate and export in Imnavait Creek. A conceptual model is presented showing how CDOM amount and lability interact with incident UV light and water residence time to determine whether photo

  1. Java Source Code Analysis for API Migration to Embedded Systems

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

    Winter, Victor; McCoy, James A.; Guerrero, Jonathan

    Embedded systems form an integral part of our technological infrastructure and oftentimes play a complex and critical role within larger systems. From the perspective of reliability, security, and safety, strong arguments can be made favoring the use of Java over C in such systems. In part, this argument is based on the assumption that suitable subsets of Java’s APIs and extension libraries are available to embedded software developers. In practice, a number of Java-based embedded processors do not support the full features of the JVM. For such processors, source code migration is a mechanism by which key abstractions offered bymore » APIs and extension libraries can made available to embedded software developers. The analysis required for Java source code-level library migration is based on the ability to correctly resolve element references to their corresponding element declarations. A key challenge in this setting is how to perform analysis for incomplete source-code bases (e.g., subsets of libraries) from which types and packages have been omitted. This article formalizes an approach that can be used to extend code bases targeted for migration in such a manner that the threats associated the analysis of incomplete code bases are eliminated.« less

  2. Shuttle Data Center File-Processing Tool in Java

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Miller, Walter H.

    2006-01-01

    A Java-language computer program has been written to facilitate mining of data in files in the Shuttle Data Center (SDC) archives. This program can be executed on a variety of workstations or via Web-browser programs. This program is partly similar to prior C-language programs used for the same purpose, while differing from those programs in that it exploits the platform-neutrality of Java in implementing several features that are important for analysis of large sets of time-series data. The program supports regular expression queries of SDC archive files, reads the files, interleaves the time-stamped samples according to a chosen output, then transforms the results into that format. A user can choose among a variety of output file formats that are useful for diverse purposes, including plotting, Markov modeling, multivariate density estimation, and wavelet multiresolution analysis, as well as for playback of data in support of simulation and testing.

  3. JGromacs: a Java package for analyzing protein simulations.

    PubMed

    Münz, Márton; Biggin, Philip C

    2012-01-23

    In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

  4. JANIS: NEA JAva-based Nuclear Data Information System

    NASA Astrophysics Data System (ADS)

    Soppera, Nicolas; Bossant, Manuel; Cabellos, Oscar; Dupont, Emmeric; Díez, Carlos J.

    2017-09-01

    JANIS (JAva-based Nuclear Data Information System) software is developed by the OECD Nuclear Energy Agency (NEA) Data Bank to facilitate the visualization and manipulation of nuclear data, giving access to evaluated nuclear data libraries, such as ENDF, JEFF, JENDL, TENDL etc., and also to experimental nuclear data (EXFOR) and bibliographical references (CINDA). It is available as a standalone Java program, downloadable and distributed on DVD and also a web application available on the NEA website. One of the main new features in JANIS is the scripting capability via command line, which notably automatizes plots generation and permits automatically extracting data from the JANIS database. Recent NEA software developments rely on these JANIS features to access nuclear data, for example the Nuclear Data Sensitivity Tool (NDaST) makes use of covariance data in BOXER and COVERX formats, which are retrieved from the JANIS database. New features added in this version of the JANIS software are described along this paper with some examples.

  5. Cognitive characteristics of learning Java, an object-oriented programming language

    NASA Astrophysics Data System (ADS)

    White, Garry Lynn

    Industry and Academia are moving from procedural programming languages (e.g., COBOL) to object-oriented programming languages, such as Java for the Internet. Past studies in the cognitive aspects of programming have focused primarily on procedural programming languages. Some of the languages used have been Pascal, C, Basic, FORTAN, and COBOL. Object-oriented programming (OOP) represents a new paradigm for computing. Industry is finding that programmers are having difficulty shifting to this new programming paradigm. This instruction in OOP is currently starting in colleges and universities across the country. What are the cognitive aspects for this new OOP language Java? When is a student developmentally ready to handle the cognitive characteristics of the OOP language Java? Which cognitive teaching style is best for this OOP language Java? Questions such as the aforementioned are the focus of this research Such research is needed to improve understanding of the learning process and identify students' difficulties with OOP methods. This can enhance academic teaching and industry training (Scholtz, 1993; Sheetz, 1997; Rosson, 1990). Cognitive development as measured by the Propositional Logic Test, cognitive style as measured by the Hemispheric Mode Indicator, and physical hemispheric dominance as measured by a self-report survey were obtained from thirty-six university students studying Java programming. Findings reveal that physical hemispheric dominance is unrelated to cognitive and programming language variables. However, both procedural and object oriented programming require Piaget's formal operation cognitive level as indicated by the Propositional Logic Test. This is consistent with prior research A new finding is that object oriented programming also requires formal operation cognitive level. Another new finding is that object oriented programming appears to be unrelated to hemispheric cognitive style as indicated by the Hemispheric Mode Indicator (HMI

  6. Providing the Persistent Data Storage in a Software Engineering Environment Using Java/COBRA and a DBMS

    NASA Technical Reports Server (NTRS)

    Dhaliwal, Swarn S.

    1997-01-01

    An investigation was undertaken to build the software foundation for the WHERE (Web-based Hyper-text Environment for Requirements Engineering) project. The TCM (Toolkit for Conceptual Modeling) was chosen as the foundation software for the WHERE project which aims to provide an environment for facilitating collaboration among geographically distributed people involved in the Requirements Engineering process. The TCM is a collection of diagram and table editors and has been implemented in the C++ programming language. The C++ implementation of the TCM was translated into Java in order to allow the editors to be used for building various functionality of the WHERE project; the WHERE project intends to use the Web as its communication back- bone. One of the limitations of the translated software (TcmJava), which militated against its use in the WHERE project, was persistent data management mechanisms which it inherited from the original TCM; it was designed to be used in standalone applications. Before TcmJava editors could be used as a part of the multi-user, geographically distributed applications of the WHERE project, a persistent storage mechanism must be built which would allow data communication over the Internet, using the capabilities of the Web. An approach involving features of Java, CORBA (Common Object Request Broker), the Web, a middle-ware (Java Relational Binding (JRB)), and a database server was used to build the persistent data management infrastructure for the WHERE project. The developed infrastructure allows a TcmJava editor to be downloaded and run from a network host by using a JDK 1.1 (Java Developer's Kit) compatible Web-browser. The aforementioned editor establishes connection with a server by using the ORB (Object Request Broker) software and stores/retrieves data in/from the server. The server consists of a CORBA object or objects depending upon whether the data is to be made persistent on a single server or multiple servers. The CORBA

  7. High Molecular Weight (HMW) Dissolved Organic Matter (DOM) in Seawater: Chemical Structure, Sources and Cycling

    DTIC Science & Technology

    1999-06-01

    source for APS three species of phytoplankton, Thalassiossira weissflogii, Emiliania huxleyi and Phaeocystis, were cultured in seawater and their HMW...DOM exudates examined by a variety of analytical techniques. Both the T. weissflogii and E. huxleyi exudates contain compounds that resemble APS

  8. HEP data analysis using jHepWork and Java.

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

    Chekanov, S.; High Energy Physics

    2009-03-23

    A role of Java in high-energy physics (HEP) and recent progress in development of a platform-independent data-analysis framework, jHepWork, is discussed. The framework produces professional graphics and has many libraries for data manipulation.

  9. The response of water quality variation in Poyang Lake (Jiangxi, People's Republic of China) to hydrological changes using historical data and DOM fluorescence.

    PubMed

    Yao, Xin; Wang, Shengrui; Ni, Zhaokui; Jiao, Lixin

    2015-02-01

    Poyang Lake is a unique wetland system that has evolved in response to natural seasonal fluctuations in water levels. To better characterize the response of water quality to hydrological variation, historical data were analyzed in combination with dissolved organic matter (DOM) fluorescence samplings conducted in situ. Historical data showed that long-term changes in water quality are mainly controlled by the sewage inputs to Poyang Lake. Monthly changes in water quality recorded during 2008 and 2012 suggest that water level may be the most important factor for water quality during a hydrological year. DOM fluorescence samples were identified as three humic-like components (C1, C2, and C3) and a protein-like component (C4). These obvious compositional changes in DOM fluorescence were considered to be related to the hydrodynamic differences controlled by water regimen. Principal component analysis (PCA) showed higher C1 and C2 signals during a normal season than the wet season, whereas C3 was lower, and C4 was higher in the dry season than in the wet or normal seasons. From the open lake to the Yangtze River mouth, increased C3 component carried by backflows of the Yangtze River to the lake resulted in these unique variations of PCA factor 2 scores during September. These obvious compositional changes in DOM fluorescence were considered to be related to the hydrodynamic differences controlled by water regimen. DOM fluorescence could be a proxy for capturing rapid changes in water quality and thereby provide an early warning signal for the quality of water supply.

  10. Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

    NASA Astrophysics Data System (ADS)

    Halder, P.; Chakraborty, A.; Deb Roy, P.; Das, H. S.

    2014-09-01

    In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Catalogue identifier: AETB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571570 No. of bytes in distributed program

  11. High Resolution Hypocenter Relocation for Events in Central Java, Indonesia using Double-Difference Technique

    NASA Astrophysics Data System (ADS)

    Sahara, D. P.; Widiyantoro, S.; Nugraha, A. D.; Sule, R.; Luehr, B. G.

    2010-12-01

    Seismic and volcanic activities in Central Java are highly related to the subduction of the Indo-Australian plate. In the MERapi AMphibious Experiments (MERAMEX), a network consisting of 169 seismographic stations was installed onshore and offshore in central Java and recorded 282 events during the operation. In this study, we present the results of relative hypocenters relocation by using Double Difference (DD) method to image the subduction beneath the volcanic chain in central Java. The DD method is an iterative procedure using Least Square optimization to determine high-resolution hypocenter locations over large distances. This relocation method uses absolute travel-time measurements and/or cross-correlation of P- and S-wave differential travel-time measurements. The preliminary results of our study showed that the algorithm could collapse the diffused event locations obtained from previous study into a sharp image of seismicity structure and reduce the residual travel time errors significantly (7 - 60%). As a result, narrow regions of a double seismic zone which correlated with the subducting slab can be determined more accurately. The dip angle of the slab increases gradually from almost horizontal beneath offshore to very steep (65-80 degrees) beneath the northern part of central Java. The aseismic gap at depths of 140 km - 185 km is also depicted clearly. The next step of the ongoing research is to provide detailed quantitative constraints on the structures of the mantle wedge and crust beneath central Java and to show the ascending paths of fluids and partially molten materials below the volcanic arc by applying Double-Difference Tomography method (TomoDD).

  12. Modelling of land use change in Indramayu District, West Java Province

    NASA Astrophysics Data System (ADS)

    Handayani, L. D. W.; Tejaningrum, M. A.; Damrah, F.

    2017-01-01

    Indramayu District into a strategic area for a stopover and overseas from East Java area because Indramayu District passed the north coast main lane, which is the first as the economic lifeblood of the Java Island. Indramayu District is part of mainstream economic Java pathways so that physical development of the area and population density as well as community activities grew by leaps and bounds. Growth acceleration raised the level of land use change. Land use change and population activities in coastal area would reduce the carrying capacity and impact on environmental quality. This research aim to analyse landuse change of years 2000 and 2011 in Indramayu District. Using this land use change map, we can predict the condition of landuse change of year 2022 in Indramayu District. Cellular Automata Markov (Markov CA) Method is used to create a spatial model of land use changes. The results of this study are predictive of land use in 2022 and the suitability with Spatial Plan (RTRW). A settlement increase predicted to continue in the future the designation of the land according to the spatial plan should be maintained.

  13. Promoting innovative business in the fishery sector in West Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Nurhayati, A.; Aisah, I.; Supriatna, A. K.

    2018-04-01

    West Java represents an important fisheries production center in Indonesia, owing to the abundant capture and aquaculture resources. However, the intrinsic characteristics of fish products such as perishable, voluminous, and seasonal currently prevent fisheries from having brought significant economic contribution to the province. In line with it, this research was aimed to analyze and identify leverage factors that will lead to fishery-based innovative business in West Java. Data used in this research were primary and secondary ones, which were collected through surveys involving 30 respondents representing fish processors and the same number representing consumers. A Focus Group Discussion (FGD) was also carried out to verify the collected data. Analytical tools adopted in this research were fishery triangle product model. Based on the analyses, it was found factors influencing the success of a fishery innovative business in West Java, Indonesia were consecutively: the existence of derivative products, product processing innovativeness, product price competitiveness, market place, and promotion. Based on the fishery trianggle product model, it was found that fish onboard handling, post-harvest handling, and procesing was in the development stage and therefore these production nodes need a particularly high attention.

  14. Monitoring the UPS and Downs of Sumatra and Java with D-Insar Time-Series

    NASA Astrophysics Data System (ADS)

    Chaussard, E.; Amelung, F.

    2010-12-01

    We performed, for the first time, a global D-InSAR survey of the Indonesian islands of Sumatra and Java to define locations where deformation is occurring. The goals of this study are 1) to create an inventory of actively deforming volcanic centers and 2) monitor all types of ground motion. This work provides ground deformation data for previously unmonitored areas and can assist the Indonesian authorities to improve hazards assessment. The D-InSAR survey covers an area of about 500 000 km2 and 3000 km long on the islands of Sumatra, Java and Bali. We used ALOS data from 45 tracks and more than 1500 granules obtained from the Alaska Satellite Facility (ASF) through the US Government Research Consortium (USGRC). We completed more than 1000 interferograms spanning a period from the end of 2006 to the beginning of 2009. L-band SAR images enable deformation mapping at global scales even in highly vegetated areas where C-band signal experiences loss of coherence. To identify locations where ground deformations are occurring, we used multiple SAR acquisitions of the same area and performed time series analysis using the Small BAseline Subset (SBAS) method. Interferograms with a maximum spatial baseline of 3000 m were phase-unwrapped and subsequently inverted for the phase with respect to the first acquisition. Temporal coherence of each pixel is computed on the set of interferograms in order to select only pixels with high temporal coherence. The compiled InSAR velocity map reveals the background level of activity of the 84 volcanic centers constituting the Sumatra, Java and Bali volcanic arcs. We identified possible uplift at 6 volcanic centers: Agung (Bali), Lamongan (Java), Lawu (Java), Slamet (Java), Kerinci (Sumatra) and Sinabung (Sumatra). Moreover, we identified subsidence in 5 major cities and 1 coastal area. Subsidence rates range from 6 cm/yr in Medan, the largest city of Sumatra, to more than 15 cm/yr in Jakarta. These major subsidence areas are probably due

  15. Distriblets: Java-Based Distributed Computing on the Web.

    ERIC Educational Resources Information Center

    Finkel, David; Wills, Craig E.; Brennan, Brian; Brennan, Chris

    1999-01-01

    Describes a system for using the World Wide Web to distribute computational tasks to multiple hosts on the Web that is written in Java programming language. Describes the programs written to carry out the load distribution, the structure of a "distriblet" class, and experiences in using this system. (Author/LRW)

  16. JIP: Java image processing on the Internet

    NASA Astrophysics Data System (ADS)

    Wang, Dongyan; Lin, Bo; Zhang, Jun

    1998-12-01

    In this paper, we present JIP - Java Image Processing on the Internet, a new Internet based application for remote education and software presentation. JIP offers an integrate learning environment on the Internet where remote users not only can share static HTML documents and lectures notes, but also can run and reuse dynamic distributed software components, without having the source code or any extra work of software compilation, installation and configuration. By implementing a platform-independent distributed computational model, local computational resources are consumed instead of the resources on a central server. As an extended Java applet, JIP allows users to selected local image files on their computers or specify any image on the Internet using an URL as input. Multimedia lectures such as streaming video/audio and digital images are integrated into JIP and intelligently associated with specific image processing functions. Watching demonstrations an practicing the functions with user-selected input data dramatically encourages leaning interest, while promoting the understanding of image processing theory. The JIP framework can be easily applied to other subjects in education or software presentation, such as digital signal processing, business, mathematics, physics, or other areas such as employee training and charged software consumption.

  17. The analysis of export commodity competitiveness in Central Java Province at period 2011-2015

    NASA Astrophysics Data System (ADS)

    Elysi, M. G.; Darsono; Riptanti, E. W.

    2018-03-01

    This study aims to determine the competitiveness of furniture export in Central Java Province Indonesia in terms of comparative and competitive advantages and to formulate the strategies to enhance the competitiveness of furniture export in Central Java Province. Descriptive analytic method was used for this research. Data used in this research are primary and secondary data. Data were analyzed using RCA (Revealed Comparative Advantage), TSI (Trade Specialization Index) and SOAR (Strength, Opportunity, Aspiration, Result). The results showed that furniture commodity in Central Java Province had strong comparative competitiveness with the value of RCA>1 and had strong competitiveness with positive index values in the range of 0 to 1. Based on SOAR analysis, strategy measures can be formulated, namely maintaining the existing and expanding targeted markets, improving product designs (innovations) and improving raw materials efficiency.

  18. Geographically Weighted Regression Model with Kernel Bisquare and Tricube Weighted Function on Poverty Percentage Data in Central Java Province

    NASA Astrophysics Data System (ADS)

    Nugroho, N. F. T. A.; Slamet, I.

    2018-05-01

    Poverty is a socio-economic condition of a person or group of people who can not fulfil their basic need to maintain and develop a dignified life. This problem still cannot be solved completely in Central Java Province. Currently, the percentage of poverty in Central Java is 13.32% which is higher than the national poverty rate which is 11.13%. In this research, data of percentage of poor people in Central Java Province has been analyzed through geographically weighted regression (GWR). The aim of this research is therefore to model poverty percentage data in Central Java Province using GWR with weighted function of kernel bisquare, and tricube. As the results, we obtained GWR model with bisquare and tricube kernel weighted function on poverty percentage data in Central Java province. From the GWR model, there are three categories of region which are influenced by different of significance factors.

  19. Insights on the Optical Properties of Estuarine DOM - Hydrological and Biological Influences.

    PubMed

    Santos, Luísa; Pinto, António; Filipe, Olga; Cunha, Ângela; Santos, Eduarda B H; Almeida, Adelaide

    2016-01-01

    Dissolved organic matter (DOM) in estuaries derives from a diverse array of both allochthonous and autochthonous sources. In the estuarine system Ria de Aveiro (Portugal), the seasonality and the sources of the fraction of DOM that absorbs light (CDOM) were inferred using its optical and fluorescence properties. CDOM parameters known to be affected by aromaticity and molecular weight were correlated with physical, chemical and meteorological parameters. Two sites, representative of the marine and brackish water zones of the estuary, and with different hydrological characteristics, were regularly surveyed along two years, in order to determine the major influences on CDOM properties. Terrestrial-derived compounds are the predominant source of CDOM in the estuary during almost all the year and the two estuarine zones presented distinct amounts, as well as absorbance and fluorescence characteristics. Freshwater inputs have major influence on the dynamics of CDOM in the estuary, in particular at the brackish water zone, where accounted for approximately 60% of CDOM variability. With a lower magnitude, the biological productivity also impacted the optical properties of CDOM, explaining about 15% of its variability. Therefore, climate changes related to seasonal and inter-annual variations of the precipitation amounts might impact the dynamics of CDOM significantly, influencing its photochemistry and the microbiological activities in estuarine systems.

  20. Contemporary Mobilization of Legacy Pb Stores by DOM in a Boreal Peatland.

    PubMed

    Jeremiason, Jeff D; Baumann, Erin I; Sebestyen, Stephen D; Agather, Alison M; Seelen, Emily A; Carlson-Stehlin, Benjamin J; Funke, Meghan M; Cotner, James B

    2018-03-20

    We examined how different landscape areas in a catchment containing a northern ombrotrophic peatland and upland mineral soils responded to dramatic decreases in atmospheric deposition of lead (Pb). Pb concentrations in the outflow stream from the peatland measured from 2009-2015 indicated continued mobilization and export of Pb derived from historic inputs to the bog. In contrast, Pb concentrations in surface peat and runoff from upland mineral soils have declined in response to reductions in atmospheric deposition. Relative to the early 1980s, Pb concentrations in the streamflow decreased only ∼50%, while Pb in surface peat and upland subsurface runoff decreased by more than 90%. Water level fluctuations in the slow-accumulating peat have allowed dissolved organic matter (DOM) to continue mobilizing Pb deposited in the peatland decades earlier. Strong correlations between dissolved organic carbon (DOC) and Pb concentrations in outflow from the peatland and in bog porewaters demonstrate Pb mobility related to DOM production. Peat stores of Pb in 2016 were less than or equal to those reported in the early 1980s despite the dry mass inventory increasing by 60-80%. Much of the loss in Pb stored in peat can be accounted for by stream runoff from the peatland.

  1. Nested generalized linear mixed model with ordinal response: Simulation and application on poverty data in Java Island

    NASA Astrophysics Data System (ADS)

    Widyaningsih, Yekti; Saefuddin, Asep; Notodiputro, Khairil A.; Wigena, Aji H.

    2012-05-01

    The objective of this research is to build a nested generalized linear mixed model using an ordinal response variable with some covariates. There are three main jobs in this paper, i.e. parameters estimation procedure, simulation, and implementation of the model for the real data. At the part of parameters estimation procedure, concepts of threshold, nested random effect, and computational algorithm are described. The simulations data are built for 3 conditions to know the effect of different parameter values of random effect distributions. The last job is the implementation of the model for the data about poverty in 9 districts of Java Island. The districts are Kuningan, Karawang, and Majalengka chose randomly in West Java; Temanggung, Boyolali, and Cilacap from Central Java; and Blitar, Ngawi, and Jember from East Java. The covariates in this model are province, number of bad nutrition cases, number of farmer families, and number of health personnel. In this modeling, all covariates are grouped as ordinal scale. Unit observation in this research is sub-district (kecamatan) nested in district, and districts (kabupaten) are nested in province. For the result of simulation, ARB (Absolute Relative Bias) and RRMSE (Relative Root of mean square errors) scale is used. They show that prov parameters have the highest bias, but more stable RRMSE in all conditions. The simulation design needs to be improved by adding other condition, such as higher correlation between covariates. Furthermore, as the result of the model implementation for the data, only number of farmer family and number of medical personnel have significant contributions to the level of poverty in Central Java and East Java province, and only district 2 (Karawang) of province 1 (West Java) has different random effect from the others. The source of the data is PODES (Potensi Desa) 2008 from BPS (Badan Pusat Statistik).

  2. Effects of a Case-Based Reasoning System on Student Performance in a Java Programming Course

    ERIC Educational Resources Information Center

    Schmidt, Cecil

    2007-01-01

    The purpose of this study was to determine if a case-based reasoning tool would improve a student's understanding of the complex concepts in a Java programming course. Subjects for the study were randomly assigned from two sections of an introductory Java programming course. Posttests were used to measure the effects of the case-based reasoning…

  3. Extraction of essential oil from baby Java orange (Citrus sinensis) solid waste using water and steam distillation

    NASA Astrophysics Data System (ADS)

    Dewi, I. A.; Prastyo, A. M.; Wijana, S.

    2018-03-01

    Baby java orange (Citrus sinensis) is commonly consumed as juice. Processing of baby java orange leaves organic waste which consist of the mesocarp, exocarp, seed, and wall of the orange. Therefore, it is necessary to process baby java orange waste to be valuable products. The purpose of this study was to provide added value to unutilized baby java orange waste, and to find out the pretreatment of time-delay process that maximize the yield of essential oil produced. Essential oil processing can be done by water and steam distillation. The study used randomized block design with one factor namely distillation time-delay process by air drying consisted of 4 levels i.e. the distillation delay for 2, 4, 6, and 8 days. The best treatment was determined based on the yield. The best essential oil from baby java orange waste was obtained from the treatment of distillation delay-process of 8 days. This pretreatment generated yield value of 0.63% with moisture content of 24.21%. By estimating the price of essential oil showed that this effort not only reduced the bulky organic waste but also provided potential economical value.

  4. Strategies for Teaching Object-Oriented Concepts with Java

    ERIC Educational Resources Information Center

    Sicilia, Miguel-Angel

    2006-01-01

    A considerable amount of experiences in teaching object-oriented concepts using the Java language have been reported to date, some of which describe language pitfalls and concrete learning difficulties. In this paper, a number of additional issues that have been experienced as difficult for students to master, along with approaches intended to…

  5. Developing LED UV fluorescence sensors for online monitoring DOM and predicting DBPs formation potential during water treatment.

    PubMed

    Li, Wen-Tao; Jin, Jing; Li, Qiang; Wu, Chen-Fei; Lu, Hai; Zhou, Qing; Li, Ai-Min

    2016-04-15

    Online monitoring dissolved organic matter (DOM) is urgent for water treatment management. In this study, high performance size exclusion chromatography with multi-UV absorbance and multi-emission fluorescence scans were applied to spectrally characterize samples from 16 drinking water sources across Yangzi River and Huai River Watersheds. The UV absorbance indices at 254 nm and 280 nm referred to the same DOM components and concentration, and the 280 nm UV light could excite both protein-like and humic-like fluorescence. Hence a novel UV fluorescence sensor was developed out using only one UV280 light-emitting diode (LED) as light source. For all samples, enhanced coagulation was mainly effective for large molecular weight biopolymers; while anion exchange further substantially removed humic substances. During chlorination tests, UVA280 and UVA254 showed similar correlations with yields of disinfection byproducts (DBPs); the humic-like fluorescence obtained from LED sensors correlated well with both trihalomethanes and haloacetic acids yields, while the correlation between protein-like fluorescence and trihalomethanes was relatively poor. Anion exchange exhibited more reduction of DBPs yields as well as UV absorbance and fluorescence signals than enhanced coagulation. The results suggest that the LED UV fluorescence sensors are very promising for online monitoring DOM and predicting DBPs formation potential during water treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Java Image I/O for VICAR, PDS, and ISIS

    NASA Technical Reports Server (NTRS)

    Deen, Robert G.; Levoe, Steven R.

    2011-01-01

    This library, written in Java, supports input and output of images and metadata (labels) in the VICAR, PDS image, and ISIS-2 and ISIS-3 file formats. Three levels of access exist. The first level comprises the low-level, direct access to the file. This allows an application to read and write specific image tiles, lines, or pixels and to manipulate the label data directly. This layer is analogous to the C-language "VICAR Run-Time Library" (RTL), which is the image I/O library for the (C/C++/Fortran) VICAR image processing system from JPL MIPL (Multimission Image Processing Lab). This low-level library can also be used to read and write labeled, uncompressed images stored in formats similar to VICAR, such as ISIS-2 and -3, and a subset of PDS (image format). The second level of access involves two codecs based on Java Advanced Imaging (JAI) to provide access to VICAR and PDS images in a file-format-independent manner. JAI is supplied by Sun Microsystems as an extension to desktop Java, and has a number of codecs for formats such as GIF, TIFF, JPEG, etc. Although Sun has deprecated the codec mechanism (replaced by IIO), it is still used in many places. The VICAR and PDS codecs allow any program written using the JAI codec spec to use VICAR or PDS images automatically, with no specific knowledge of the VICAR or PDS formats. Support for metadata (labels) is included, but is format-dependent. The PDS codec, when processing PDS images with an embedded VIAR label ("dual-labeled images," such as used for MER), presents the VICAR label in a new way that is compatible with the VICAR codec. The third level of access involves VICAR, PDS, and ISIS Image I/O plugins. The Java core includes an "Image I/O" (IIO) package that is similar in concept to the JAI codec, but is newer and more capable. Applications written to the IIO specification can use any image format for which a plug-in exists, with no specific knowledge of the format itself.

  7. Acute, fatal Sarcocystis calchasi-associated hepatitis in Roller pigeons (Columbia livia f. dom.) at Philadelphia Zoo

    USDA-ARS?s Scientific Manuscript database

    Four Roller pigeons (Columba livia f. dom.) at the Philadelphia Zoo died suddenly. Necropsy examination revealed macroscopic hepatitis. Microscopically, the predominant lesions were in liver, characterized with necrosis and mixed cell inflammatory response. Sarcocystis calchasi-like schizonts and fr...

  8. Handle with care: the impact of using Java applets in Web-based studies on dropout and sample composition.

    PubMed

    Stieger, Stefan; Göritz, Anja S; Voracek, Martin

    2011-05-01

    In Web-based studies, Web browsers are used to display online questionnaires. If an online questionnaire relies on non-standard technologies (e.g., Java applets), it is often necessary to install a particular browser plug-in. This can lead to technically induced dropout because some participants lack the technological know-how or the willingness to install the plug-in. In two thematically identical online studies conducted across two time points in two different participant pools (N = 1,527 and 805), we analyzed whether using a Java applet produces dropout and distortion of demographics in the final sample. Dropout was significantly higher on the Java applet questionnaire page than on the preceding and subsequent questionnaire pages. Age-specific effects were found only in one sample (i.e., dropouts were older), whereas sex-specific effects were found in both samples (i.e., women dropped out more frequently than men on the Java applet page). These results additionally support the recommendation that using additional technologies (e.g., Java applets) can be dangerous in producing a sample that is biased toward both younger and male respondents.

  9. Fractionation of Java Citronella Oil and Citronellal Purification by Batch Vacuum Fractional Distillation

    NASA Astrophysics Data System (ADS)

    Eden, W. T.; Alighiri, D.; Cahyono, E.; Supardi, K. I.; Wijayati, N.

    2018-04-01

    The aim of this work was to assess the performance of a vacuum fractionating column for the fractionation of Java Citronella Oil (Cymbopogon winterianus) and citronellal purification during batch mode operation at vacuum -76 cmHg and reflux ratios 5:1. Based on GC-MS analysis of Java Citronella Oil is known that citronellal, citronellol, and geraniol has yielded 21,59%; 7,43%; and 34,27%, respectively. Fractional distillation under reduced pressure and continued redistilled are needed to isolate the component of Java Citronella Oil. Redistilled can improve the purity, then distillate collected while the temperature changed. In the first distillate yielded citronellal with a purity of 75.67%. The first distillate obtained residue rhodinol product will then be carried back to separation into citronellol and geraniol. The purity of citronellol reached 80,65% purity, whereas geraniol reached 76.63% purity. Citronellal Purification resulting citronellal to 95.10% purity and p-menthane-3,8-diol reached 75.95% purity.

  10. Geological structure analysis in Central Java using travel time tomography technique of S waves

    NASA Astrophysics Data System (ADS)

    Palupi, I. R.; Raharjo, W.; Nurdian, S. W.; Giamboro, W. S.; Santoso, A.

    2016-11-01

    Java is one of the islands in Indonesia that is prone to the earthquakes, in south of Java, there is the Australian Plate move to the Java island and press with perpendicular direction. This plate movement formed subduction zone and cause earthquakes. The earthquake is the release of energy due to the sudden movement of the plates. When an earthquake occurs, the energy is released and record by seismometers in the waveform. The first wave recorded is called the P waves (primary) and the next wave is called S waves (secondary). Both of these waves have different characteristics in terms of propagation and direction of movement. S wave is composed of waves of Rayleigh and Love waves, with each direction of movement of the vertical and horizontal, subsurface imaging by using S wave tomography technique can describe the type of the S wave through the medium. The variation of wave velocity under Central Java (esearch area) is ranging from -10% to 10% at the depth of 20, 30 and 40 km, the velocity decrease with the depth increase. Moho discontinuity is lies in the depth of 32 km under the crust, it is indicates there is strong heterogenity in Moho.

  11. Hierarchical time series bottom-up approach for forecast the export value in Central Java

    NASA Astrophysics Data System (ADS)

    Mahkya, D. A.; Ulama, B. S.; Suhartono

    2017-10-01

    The purpose of this study is Getting the best modeling and predicting the export value of Central Java using a Hierarchical Time Series. The export value is one variable injection in the economy of a country, meaning that if the export value of the country increases, the country’s economy will increase even more. Therefore, it is necessary appropriate modeling to predict the export value especially in Central Java. Export Value in Central Java are grouped into 21 commodities with each commodity has a different pattern. One approach that can be used time series is a hierarchical approach. Hierarchical Time Series is used Buttom-up. To Forecast the individual series at all levels using Autoregressive Integrated Moving Average (ARIMA), Radial Basis Function Neural Network (RBFNN), and Hybrid ARIMA-RBFNN. For the selection of the best models used Symmetric Mean Absolute Percentage Error (sMAPE). Results of the analysis showed that for the Export Value of Central Java, Bottom-up approach with Hybrid ARIMA-RBFNN modeling can be used for long-term predictions. As for the short and medium-term predictions, it can be used a bottom-up approach RBFNN modeling. Overall bottom-up approach with RBFNN modeling give the best result.

  12. Java RMI Software Technology for the Payload Planning System of the International Space Station

    NASA Technical Reports Server (NTRS)

    Bryant, Barrett R.

    1999-01-01

    The Payload Planning System is for experiment planning on the International Space Station. The planning process has a number of different aspects which need to be stored in a database which is then used to generate reports on the planning process in a variety of formats. This process is currently structured as a 3-tier client/server software architecture comprised of a Java applet at the front end, a Java server in the middle, and an Oracle database in the third tier. This system presently uses CGI, the Common Gateway Interface, to communicate between the user-interface and server tiers and Active Data Objects (ADO) to communicate between the server and database tiers. This project investigated other methods and tools for performing the communications between the three tiers of the current system so that both the system performance and software development time could be improved. We specifically found that for the hardware and software platforms that PPS is required to run on, the best solution is to use Java Remote Method Invocation (RMI) for communication between the client and server and SQLJ (Structured Query Language for Java) for server interaction with the database. Prototype implementations showed that RMI combined with SQLJ significantly improved performance and also greatly facilitated construction of the communication software.

  13. [Oceanography and King Dom Carlos I's collection of iconography].

    PubMed

    Jardim, Maria Estela; Peres, Isabel Marília; Ré, Pedro Barcia; Costa, Fernanda Madalena

    2014-01-01

    After the Challenger expedition (1872-1878), other nations started to show interest in oceanographic research and organizing their own expeditions. As of 1885, Prince Albert I of Monaco conducted oceanographic campaigns with the collaboration of some of the best marine biologists and physical oceanographers of the day, inventing new techniques and instruments for the oceanographic work. Prince Albert's scientific activity certainly helped kindle the interest of his friend, Dom Carlos I, king of Portugal, in the study of the oceans and marine life. Both shared the need to use photography to document their studies. This article analyzes the role of scientific photography in oceanography, especially in the expeditions organized by the Portuguese monarch.

  14. JGromacs: A Java Package for Analyzing Protein Simulations

    PubMed Central

    2011-01-01

    In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

  15. Using Runtime Analysis to Guide Model Checking of Java Programs

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Norvig, Peter (Technical Monitor)

    2001-01-01

    This paper describes how two runtime analysis algorithms, an existing data race detection algorithm and a new deadlock detection algorithm, have been implemented to analyze Java programs. Runtime analysis is based on the idea of executing the program once. and observing the generated run to extract various kinds of information. This information can then be used to predict whether other different runs may violate some properties of interest, in addition of course to demonstrate whether the generated run itself violates such properties. These runtime analyses can be performed stand-alone to generate a set of warnings. It is furthermore demonstrated how these warnings can be used to guide a model checker, thereby reducing the search space. The described techniques have been implemented in the b e grown Java model checker called PathFinder.

  16. Developing Multimedia Courseware for the Internet's Java versus Shockwave.

    ERIC Educational Resources Information Center

    Majchrzak, Tina L.

    1996-01-01

    Describes and compares two methods for developing multimedia courseware for use on the Internet: an authoring tool called Shockwave, and an object-oriented language called Java. Topics include vector graphics, browsers, interaction with network protocols, data security, multithreading, and computer languages versus development environments. (LRW)

  17. JANIS-2: An Improved Version of the NEA Java-based Nuclear Data Information System

    NASA Astrophysics Data System (ADS)

    Soppera, N.; Henriksson, H.; Nouri, A.; Nagel, P.; Dupont, E.

    2005-05-01

    JANIS (JAva-based Nuclear Information Software) is a display program designed to facilitate the visualisation and manipulation of nuclear data. Its objective is to allow the user of nuclear data to access numerical and graphical representations without prior knowledge of the storage format. It offers maximum flexibility for the comparison of different nuclear data sets. Features included in the latest release are described such as direct access to centralised databases through JAVA Servlet technology.

  18. JANIS-2: An Improved Version of the NEA Java-based Nuclear Data Information System

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

    Soppera, N.; Henriksson, H.; Nagel, P.

    2005-05-24

    JANIS (JAva-based Nuclear Information Software) is a display program designed to facilitate the visualisation and manipulation of nuclear data. Its objective is to allow the user of nuclear data to access numerical and graphical representations without prior knowledge of the storage format. It offers maximum flexibility for the comparison of different nuclear data sets. Features included in the latest release are described such as direct access to centralised databases through JAVA Servlet technology.

  19. Composition of dissolved organic matter (DOM) from periodically submerged soils in the Three Gorges Reservoir areas as determined by elemental and optical analysis, infrared spectroscopy, pyrolysis-GC-MS and thermally assisted hydrolysis and methylation.

    PubMed

    Jiang, Tao; Kaal, Joeri; Liang, Jian; Zhang, Yaoling; Wei, Shiqiang; Wang, Dingyong; Green, Nelson W

    2017-12-15

    Soil-derived dissolved organic matter (DOM) has a major influence in biogeochemical processes related to contaminant dynamics and greenhouse gas emissions, due to its reactivity and its bridging role between the soil and aquatic systems. Within the Three Gorges Reservoir (TGR, China) area, an extensive water-fluctuation zone periodically submerges the surrounding soils. Here we report a characterization study of soil-derived DOM across the TGR areas, using elemental and optical analysis, infrared spectroscopy (FTIR), pyrolysis-GC-MS (Py-GC-MS) and thermally assisted hydrolysis and methylation (THM-GC-MS). The results showed that the soil DOM from the TGR area is a mixture of "allochthonous" (i.e., plant-derived/terrigenous) and "autochthonous" (i.e., microbial) origins. The terrigenous DOM is composed primarily of phenolic and aliphatic structures from lignin and aliphatic biopolymers (i.e. cutin, suberin), respectively. Multivariate statistics differentiated between two fractions of the microbial DOM, i.e. chitin-derived, perhaps from fungi and arthropods in soil, and protein-derived, partially sourced from algal or aquatic organisms. Molecular proxies of source and degradation state were in good agreement with optical parameters such as SUVA 254 , the fluorescence index (FI) and the humification index (HIX). The combined use of elemental analysis, fluorescence spectroscopy, and Py-GC-MS provides rigorous and detailed DOM characterization, whereas THM-GC-MS is useful for more precise but qualitative identification of the different phenolic (cinnamyl, p-hydroxyphenyl, guaiacyl, syringyl and tannin-derived) and aliphatic materials. With the multi-methodological approach used in this study, FTIR was the least informative, in part, because of the interference of inorganic matter in the soil DOM samples. The soil DOM from the TGR's water fluctuation zone exhibited considerable compositional diversity, mainly related to the balance between DOM source (microbial- or

  20. Predicting reactivity of model DOM compounds towards chlorine with mediated electrochemical oxidation.

    PubMed

    de Vera, Glen Andrew; Gernjak, Wolfgang; Radjenovic, Jelena

    2017-05-01

    Chlorine demand of a water sample depends on the characteristics of dissolved organic matter (DOM). It is an important parameter for water utilities used to assess oxidant and/or disinfectant consumption of source waters during treatment and distribution. In this study, model compounds namely resorcinol, tannic acid, vanillin, cysteine, tyrosine, and tryptophan were used to represent the reactive moieties of complex DOM mixtures. The reactivity of these compounds was evaluated in terms of Cl 2 demand and electron donating capacity (EDC). The EDC was determined by mediated electrochemical oxidation (MEO) which involves the use of 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) as an electron shuttle. The Cl 2 demand of readily oxidizable compounds (resorcinol, tannic acid, vanillin, and cysteine) was found to correlate well with EDC (R 2  = 0.98). The EDC values (mol e - /mol C) of the model compounds are as follows: 1.18 (cysteine) > 0.77 (resorcinol) > 0.59 (vanillin) > 0.52 (tannic acid) > 0.36 (tryptophan) > 0.19 (tyrosine). To determine the effect of pre-oxidation on EDC, ozone was added (0.1 mol O 3 /mol C) into each model compound solution. Ozonation caused a general decrease in EDC (10-40%), chlorine demand (10-30%), and UV absorbance (10-40%), except for tyrosine which showed both increased UV 275 and EDC. Before and after ozonation, 24 h disinfection byproduct (DBP) formation potential tests (Cl 2 residual = 1.5 mg/L) were conducted to evaluate the use of EDC for DBP formation prediction. The results indicate that there was no significant correlation between the EDC of the model compounds and the formation potentials of adsorbable organic chlorine, trichloromethane, and trichloroacetic acid. This suggests that while EDC correlates with Cl 2 demand, chlorine consumption may not directly translate to DBP formation because oxidation reactions may dominate over substitution reactions. Overall, this study provides useful insights

  1. Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

    PubMed Central

    Muin, Michael; Fontelo, Paul

    2006-01-01

    Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

  2. Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.

    PubMed

    Muin, Michael; Fontelo, Paul

    2006-11-03

    The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications.

  3. A distributed computing system for magnetic resonance imaging: Java-based processing and binding of XML.

    PubMed

    de Beer, R; Graveron-Demilly, D; Nastase, S; van Ormondt, D

    2004-03-01

    Recently we have developed a Java-based heterogeneous distributed computing system for the field of magnetic resonance imaging (MRI). It is a software system for embedding the various image reconstruction algorithms that we have created for handling MRI data sets with sparse sampling distributions. Since these data sets may result from multi-dimensional MRI measurements our system has to control the storage and manipulation of large amounts of data. In this paper we describe how we have employed the extensible markup language (XML) to realize this data handling in a highly structured way. To that end we have used Java packages, recently released by Sun Microsystems, to process XML documents and to compile pieces of XML code into Java classes. We have effectuated a flexible storage and manipulation approach for all kinds of data within the MRI system, such as data describing and containing multi-dimensional MRI measurements, data configuring image reconstruction methods and data representing and visualizing the various services of the system. We have found that the object-oriented approach, possible with the Java programming environment, combined with the XML technology is a convenient way of describing and handling various data streams in heterogeneous distributed computing systems.

  4. Java Library for Input and Output of Image Data and Metadata

    NASA Technical Reports Server (NTRS)

    Deen, Robert; Levoe, Steven

    2003-01-01

    A Java-language library supports input and output (I/O) of image data and metadata (label data) in the format of the Video Image Communication and Retrieval (VICAR) image-processing software and in several similar formats, including a subset of the Planetary Data System (PDS) image file format. The library does the following: It provides low-level, direct access layer, enabling an application subprogram to read and write specific image files, lines, or pixels, and manipulate metadata directly. Two coding/decoding subprograms ("codecs" for short) based on the Java Advanced Imaging (JAI) software provide access to VICAR and PDS images in a file-format-independent manner. The VICAR and PDS codecs enable any program that conforms to the specification of the JAI codec to use VICAR or PDS images automatically, without specific knowledge of the VICAR or PDS format. The library also includes Image I/O plugin subprograms for VICAR and PDS formats. Application programs that conform to the Image I/O specification of Java version 1.4 can utilize any image format for which such a plug-in subprogram exists, without specific knowledge of the format itself. Like the aforementioned codecs, the VICAR and PDS Image I/O plug-in subprograms support reading and writing of metadata.

  5. Seismic hazard analysis with PSHA method in four cities in Java.

    NASA Astrophysics Data System (ADS)

    Elistyawati, Y.; Palupi, I. R.; Suharsono

    2016-11-01

    In this study the tectonic earthquakes was observed through the peak ground acceleration through the PSHA method by dividing the area of the earthquake source. This study applied the earthquake data from 1965 - 2015 that has been analyzed the completeness of the data, location research was the entire Java with stressed in four large cities prone to earthquakes. The results were found to be a hazard map with a return period of 500 years, 2500 years return period, and the hazard curve were four major cities (Jakarta, Bandung, Yogyakarta, and the city of Banyuwangi). Results Java PGA hazard map 500 years had a peak ground acceleration within 0 g ≥ 0.5 g, while the return period of 2500 years had a value of 0 to ≥ 0.8 g. While, the PGA hazard curves on the city's most influential source of the earthquake was from sources such as fault Cimandiri backgroud, for the city of Bandung earthquake sources that influence the seismic source fault dent background form. In other side, the city of Yogyakarta earthquake hazard curve of the most influential was the source of the earthquake background of the Opak fault, and the most influential hazard curve of Banyuwangi earthquake was the source of Java and Sumba megatruts earthquake.

  6. BAOBAB: a Java editor for large phylogenetic trees.

    PubMed

    Dutheil, J; Galtier, N

    2002-06-01

    BAOBAB is a Java user interface dedicated to viewing and editing large phylogenetic trees. Original features include: (i) a colour-mediated overview of magnified subtrees; (ii) copy/cut/paste of (sub)trees within or between windows; (iii) compressing/ uncompressing subtrees; and (iv) managing sequence files together with tree files. http://www.univ-montp2.fr/~genetix/.

  7. Global tectonic significance of the Solomon Islands and Ontong Java Plateau convergent zone

    NASA Astrophysics Data System (ADS)

    Mann, Paul; Taira, Asahiko

    2004-10-01

    Oceanic plateaus, areas of anomalously thick oceanic crust, cover about 3% of the Earth's seafloor and are thought to mark the surface location of mantle plume "heads". Hotspot tracks represent continuing magmatism associated with the remaining plume conduit or "tail". It is presently controversial whether voluminous and mafic oceanic plateau lithosphere is eventually accreted at subduction zones, and, therefore: (1) influences the eventual composition of continental crust and; (2) is responsible for significantly higher rates of continental growth than growth only by accretion of island arcs. The Ontong Java Plateau (OJP) of the southwestern Pacific Ocean is the largest and thickest oceanic plateau on Earth and the largest plateau currently converging on an island arc (Solomon Islands). For this reason, this convergent zone is a key area for understanding the fate of large and thick plateaus on reaching subduction zones. This volume consists of a series of four papers that summarize the results of joint US-Japan marine geophysical studies in 1995 and 1998 of the Solomon Islands-Ontong Java Plateau convergent zone. Marine geophysical data include single and multi-channel seismic reflection, ocean-bottom seismometer (OBS) refraction, gravity, magnetic, sidescan sonar, and earthquake studies. Objectives of this introductory paper include: (1) review of the significance of oceanic plateaus as potential contributors to continental crust; (2) review of the current theories on the fate of oceanic plateaus at subduction zones; (3) establish the present-day and Neogene tectonic setting of the Solomon Islands-Ontong Java Plateau convergent zone; (4) discuss the controversial sequence and timing of tectonic events surrounding Ontong Java Plateau-Solomon arc convergence; (5) present a series of tectonic reconstructions for the period 20 Ma (early Miocene) to the present-day in support of our proposed timing of major tectonic events affecting the Ontong Java Plateau

  8. Seventeen-year evaluation of breast cancer screening: the DOM project, The Netherlands. Diagnostisch Onderzoek (investigation) Mammacarcinoom.

    PubMed Central

    Miltenburg, G. A.; Peeters, P. H.; Fracheboud, J.; Collette, H. J.

    1998-01-01

    The DOM project is a non-randomized population-based breast cancer screening programme in Utrecht which started in 1974-75. The 17-year effect has been evaluated by a case-control study of breast cancer deaths during the period 1975-92 in women living in the city of Utrecht, born between 1911 and 1925, whose breast cancers were diagnosed after the initiation of the DOM project. Controls (three for each case) were defined as women having the same year of birth as the case, living in the city of Utrecht at the time the case died, and having had the opportunity of screening in the DOM project. Screening in the period 1975-92 indicated a breast cancer mortality reduction of 46% (odds ratio of 0.54, 95% confidence interval 0.37-0.79). The strongest protective effect was found at a screening interval of 2 years or less (mortality reduction of 62%, odds ratio of 0.38), and for the highest number of screens (mortality reduction of 68%, odds ratio of 0.32 for more than four screens). Exclusion of breast cancer deaths that occurred within 1 year of diagnosis, to allow for 'lead-time' bias, gave an odds ratio of 0.61. Early diagnosis of breast cancer by screening reduces breast cancer mortality in the long term. Bias due to the study design may slightly overestimate the protective effect. A screening programme with a 2-yearly, or smaller, interval between successive screens will improve the protection of screening. PMID:9764591

  9. Effects of dissolved organic matters (DOMs) on membrane fouling in anaerobic ceramic membrane bioreactors (AnCMBRs) treating domestic wastewater.

    PubMed

    Yue, Xiaodi; Koh, Yoong Keat Kelvin; Ng, How Yong

    2015-12-01

    Anaerobic membrane bioreactors (AnMBRs) have been regarded as a potential solution to achieve energy neutrality in the future wastewater treatment plants. Coupling ceramic membranes into AnMBRs offers great potential as ceramic membranes are resistant to corrosive chemicals such as cleaning reagents and harsh environmental conditions such as high temperature. In this study, ceramic membranes with pore sizes of 80, 200 and 300 nm were individually mounted in three anaerobic ceramic membrane bioreactors (AnCMBRs) treating real domestic wastewater to examine the treatment efficiencies and to elucidate the effects of dissolved organic matters (DOMs) on fouling behaviours. The average overall chemical oxygen demands (COD) removal efficiencies could reach around 86-88%. Although CH4 productions were around 0.3 L/g CODutilised, about 67% of CH4 generated was dissolved in the liquid phase and lost in the permeate. When filtering mixed liquor of similar properties, smaller pore-sized membranes fouled slower in long-term operations due to lower occurrence of pore blockages. However, total organic removal efficiencies could not explain the fouling behaviours. Liquid chromatography-organic carbon detection, fluorescence spectrophotometer and high performance liquid chromatography coupled with fluorescence and ultra-violet detectors were used to analyse the DOMs in detail. The major foulants were identified to be biopolymers that were produced in microbial activities. One of the main components of biopolymers--proteins--led to different fouling behaviours. It is postulated that the proteins could pass through porous cake layers to create pore blockages in membranes. Hence, concentrations of the DOMs in the soluble fraction of mixed liquor (SML) could not predict membrane fouling because different components in the DOMs might have different interactions with membranes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. JCell--a Java-based framework for inferring regulatory networks from time series data.

    PubMed

    Spieth, C; Supper, J; Streichert, F; Speer, N; Zell, A

    2006-08-15

    JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

  11. Space Radar Image of Central Java, Indonesia

    NASA Image and Video Library

    1999-04-15

    The summits of two large volcanoes in Central Java, Indonesia are shown in the center of this radar image. Lava flows of different ages and surface roughness appear in shades of green and yellow surrounding the summit of Mt. Merbabu (mid-center) and Mt. Merapi (lower center). Mt. Merapi erupted on November 28, 1994 about six weeks after this image was taken. The eruption killed more than 60 people and forced the evacuation of more than 6,000 others. Thousands of other residents were put on alert due to the possibility of volcanic debris mudflows, called lahars, that threatened nearby towns. Mt. Merapi is located approximately 40 kilometers (25 miles) north of Yogyakarta, the capital of Central Java. The older volcano at the top of the image is unnamed. Lake Rawapening is the dark blue feature in the upper right. The light blue area southeast of the lake is the city of Salatiga. Directly south of Salatiga and southeast of Mt. Merapi is the city of Boyolali. Scientists are studying Mt. Merapi as part of the international "Decade Volcanoes" project, because of its recent activity and potential threat to local populations. The radar data are being used to identify and distinguish a variety of volcanic features. http://photojournal.jpl.nasa.gov/catalog/PIA01782

  12. Tooth enamel surface micro-hardness with dual species Streptococcus biofilm after exposure to Java turmeric (Curcuma xanthorrhiza Roxb.) extract

    NASA Astrophysics Data System (ADS)

    Isjwara, F. R. G.; Hasanah, S. N.; Utami, Sri; Suniarti, D. F.

    2017-08-01

    Streptococcus biofilm on tooth surfaces can decrease mouth environment pH, thus causing enamel demineralization that can lead to dental caries. Java Turmeric extract has excellent antibacterial effects and can maintain S. mutans biofilm pH at neutral levels for 4 hours. To analyze the effect of Java Turmeric extract on tooth enamel micro-hardness, the Java Turmeric extract was added on enamel tooth samples with Streptococcus dual species biofilm (S. sanguinis and S. mutans). The micro-hardness of enamel was measured by Knoop Hardness Tester. Results showed that Curcuma xanthorrhiza Roxb. could not maintain tooth enamel surface micro-hardness. It is concluded that Java Turmeric extract ethanol could not inhibit the hardness of enamel with Streptococcus dual species biofilm.

  13. Three-dimensionally ordered macroporous (3DOM) gold-nanoparticle-doped titanium dioxide (GTD) photonic crystals modified electrodes for hydrogen peroxide biosensor.

    PubMed

    Li, Jianlin; Han, Tao; Wei, Nannan; Du, Jiangyan; Zhao, Xiangwei

    2009-12-15

    Gold nanoparticles have been introduced into the wall framework of titanium dioxide photonic crystals by the colloidal crystal template technique. The three-dimensionally ordered macroporous gold-nanoparticle-doped titanium dioxide (3DOM GTD) film was modified on the indium-tin oxide (ITO) electrode surface and used for the hydrogen peroxide biosensor. The direct electron transfer and electrocatalysis of horseradish peroxidase (HRP) immobilized on this film have been investigated. The 3DOM GTD film could provide a good microenvironment for retaining the biological bioactivity, large internal area, and superior conductivity. The HRP/3DOM GTD/ITO electrode exhibited two couples of redox peaks corresponding to the HRP intercalated in the mesopores and adsorbed on the external surface of the film with the formal potential of -0.19 and -0.52V in 0.1M PBS (pH 7.4), respectively. The HRP intercalated in the mesopores showed a surface-controlled process with a single proton transfer. The direct electron transfer between the adsorbed HRP and the electrode is achieved without the aid of an electron mediator. The H(2)O(2) biosensor displayed a rapid eletrocatalytic response (less than 3s), a wide linear range from 0.5 microM to 1.4mM with a detection limit of 0.2 microM, high sensitivity (179.9 microAmM(-1)), good stability and reproducibility. Compared with the free-Au doped titanium dioxide photonic crystals modified electrode, the GTD modified electrode could greatly enhance the response current signal, linear detection range and higher sensitivity. The 3DOM GTD provided a new matrix for protein immobilization and direct transfer study and opened a way for low conductivity electrode biosensor.

  14. Evaluating Changes in the Molecular Composition and Optical Properties of Pacific Ocean Dissolved Organic Matter (DOM) caused by Borodeuteride Reduction

    NASA Astrophysics Data System (ADS)

    Bianca, M.; Blough, N. V.; Del Vecchio, R.; Cartisano, C. M.; Schmitt-Kopplin, P.; Gonsior, M.

    2016-02-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR MS) is a powerful tool to obtain detailed molecular information for complex DOM and was combined in this study with optical measurements to determine the molecular fingerprint of Pacific Ocean DOM before and after borodeuteride reduction. Selective chemical reductions, using sodium borodeuteride, has been previously demonstrated to produce unique mass markers of ketone and aldehyde-containing species in ultrahigh resolution mass spectrometry. These functional groups have also been proposed to be responsible for chromophoric dissolved organic matter (CDOM) long wavelength optical properties through charge transfer interactions and their chemical reduction has shown to irreversibly alter the CDOM optical properties. ESI-FT-ICR MS coupled with borodeuteride reduction was thus applied to reference material, Suwannee River Fulvic Acid (SRFA), and CDOM extracts collected from Station ALOHA, in the North Pacific Ocean during December 2014. Results showed distinct differences between samples collected at different depths, indicating that the combination of FT-ICR-MS with borodeuteride reduction is a useful analytical tool to further understand marine DOM molecular composition. When this method is combined with optical measurements, specific insights into the CDOM composition can also be obtained.

  15. Facile synthesis of iron oxide nanoparticle and synergistic effect of iron nanoparticle in the presence of sunlight for the degradation of DOM from textile wastewater

    NASA Astrophysics Data System (ADS)

    Parvin, Fahmida; Nayna, Omme Kulsum; Tareq, Shafi M.; Rikta, Sharmin Yousuf; Kamal, Abdul KI

    2018-05-01

    This study explores the capacity of synthesized Fe2O3 nanoparticles (NPs) under sunlight for the degradation of dissolved organic matter (DOM) from synthetic (Procion blue dye) solution as well as from textile wastewater (TWW). Fe2O3 NPs were properly synthesized and confirmed by UV absorbance, FTIR spectra and SEM image analysis. Photocatalytic degradation of DOM from TWW and synthetic solution was performed by catalyst Fe2O3 NPs (5 mg/L) in the presence of solar irradiation (up to 40 h). The DOM degradation of the TWW and synthetic solution has been analyzed by fluorescence 3D excitation emission matrix (3D EEM). Synergistic effect was expected and it was found that the rate of decrease of fluorescence intensity increased with time. Within 20 h, for the synthetic solution, reduction of fluorescence intensity (80%) reaches an equilibrium. In contrast, the rate of decrease in the fluorescence intensity is highest (91%) in 40 h of irradiation for TWW. This reduction of fluorescence intensity indicates the degradation of DOM and can be expressed well by second-order model kinetics. Reduction of TOC, BOD5 and COD load again validated the degradation of DOM from TWW by catalyst Fe2O3 NPs-induced solar irradiation. We applied the treated wastewater on the plant to observe the reusability of the treated TWW, and the morphological data analysis of the plant demonstrates that the catalyst Fe2O3 NPs-induced solar-irradiated wastewater exhibits less adverse impact on plant morphology.

  16. Tatool: a Java-based open-source programming framework for psychological studies.

    PubMed

    von Bastian, Claudia C; Locher, André; Ruflin, Michael

    2013-03-01

    Tatool (Training and Testing Tool) was developed to assist researchers with programming training software, experiments, and questionnaires. Tatool is Java-based, and thus is a platform-independent and object-oriented framework. The architecture was designed to meet the requirements of experimental designs and provides a large number of predefined functions that are useful in psychological studies. Tatool comprises features crucial for training studies (e.g., configurable training schedules, adaptive training algorithms, and individual training statistics) and allows for running studies online via Java Web Start. The accompanying "Tatool Online" platform provides the possibility to manage studies and participants' data easily with a Web-based interface. Tatool is published open source under the GNU Lesser General Public License, and is available at www.tatool.ch.

  17. Stand-Damage Model with Java (Version 3.0)

    Treesearch

    George Racin; J.J. Colbert

    2004-01-01

    NOTE: Instructions for ordering the cd-rom with the software are included on the front cover of the linked publication. The Stand-Damage Model with Java is a distance-independent tree-growth simulator. The model follows the life of a forest stand represented by species and diameter-class widths. The user supplies the initial state of the stand along with management...

  18. Application of Semiparametric Spline Regression Model in Analyzing Factors that In uence Population Density in Central Java

    NASA Astrophysics Data System (ADS)

    Sumantari, Y. D.; Slamet, I.; Sugiyanto

    2017-06-01

    Semiparametric regression is a statistical analysis method that consists of parametric and nonparametric regression. There are various approach techniques in nonparametric regression. One of the approach techniques is spline. Central Java is one of the most densely populated province in Indonesia. Population density in this province can be modeled by semiparametric regression because it consists of parametric and nonparametric component. Therefore, the purpose of this paper is to determine the factors that in uence population density in Central Java using the semiparametric spline regression model. The result shows that the factors which in uence population density in Central Java is Family Planning (FP) active participants and district minimum wage.

  19. Influence of Coastal Upwelling on SST Trends along the South Coast of Java

    PubMed Central

    Varela, R.; Santos, F.; Gómez-Gesteira, M.; Álvarez, I.; Costoya, X.; Días, J. M.

    2016-01-01

    The south coast of Java has warmed at a much lower rate than adjacent ocean locations over the last three decades (1982–2015). This behavior can be observed during the upwelling season (July-October) and it is especially patent in August and September when upwelling attains the highest values. Although different warming rates (ocean-coast) had been previously observed in other areas around the world, this behavior was always linked to situations where upwelling increased or remained unchanged. South Java warming is observed at ocean locations and cooling near shore but under a scenario of decreasing upwelling (~30% in some cases). The origin of coastal cooling is due to changes in the vertical structure of the water column. A vein of subsurface water, which has cooled at a rate higher than 0.3°C per decade, is observed to enter from the northwestern part of the study area following the South Java Current. This water only manifests at surface near coast, where it is pumped up by coastal upwelling. PMID:27606676

  20. Upper crustal structure beneath East Java from ambient noise tomography: A preliminary result

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

    Martha, Agustya Adi; Graduate Research on Earthquakes and Active Tectonics, Institut Teknologi Bandung, Bandung; Widiyantoro, Sri

    East Java has a fairly complex geological structure. Physiographically East Java can be divided into three zones, i.e. the Southern Mountains zone in the southern part, the Kendeng zone in the middle part, and the Rembang zone in the northern part. Most of the seismic hazards in this region are due to processes in the upper crust. In this study, the Ambient Noise Tomography (ANT) method is used to image the upper crustal structure beneath East Java. We have used seismic waveform data recorded by 8Meteorological, Climatological and Geophysical Agency (BMKG) stationary seismographic stations and 16 portable seismographs installed formore » 2 to 8 weeks. The data were processed to obtain waveforms fromnoise cross-correlation between pairs of seismographic stations. Our preliminary results indicate that the Kendeng zone, an area of low gravity anomaly, is associated with a low velocity zone. On the other hand, the southern mountain range, which has a high gravity anomaly, is related to a high velocity anomaly as shown by our tomographic images.« less

  1. Freshwater DOM quantity and quality from a two-component model of UV absorbance

    USGS Publications Warehouse

    Carter, Heather T.; Tipping, Edward; Koprivnjak, Jean-Francois; Miller, Matthew P.; Cookson, Brenda; Hamilton-Taylor, John

    2012-01-01

    We present a model that considers UV-absorbing dissolved organic matter (DOM) to consist of two components (A and B), each with a distinct and constant spectrum. Component A absorbs UV light strongly, and is therefore presumed to possess aromatic chromophores and hydrophobic character, whereas B absorbs weakly and can be assumed hydrophilic. We parameterised the model with dissolved organic carbon concentrations [DOC] and corresponding UV spectra for c. 1700 filtered surface water samples from North America and the United Kingdom, by optimising extinction coefficients for A and B, together with a small constant concentration of non-absorbing DOM (0.80 mg DOC L-1). Good unbiased predictions of [DOC] from absorbance data at 270 and 350 nm were obtained (r2 = 0.98), the sum of squared residuals in [DOC] being reduced by 66% compared to a regression model fitted to absorbance at 270 nm alone. The parameterised model can use measured optical absorbance values at any pair of suitable wavelengths to calculate both [DOC] and the relative amounts of A and B in a water sample, i.e. measures of quantity and quality. Blind prediction of [DOC] was satisfactory for 9 of 11 independent data sets (181 of 213 individual samples).

  2. Insights on the Optical Properties of Estuarine DOM – Hydrological and Biological Influences

    PubMed Central

    Santos, Luísa; Pinto, António; Filipe, Olga; Cunha, Ângela; Santos, Eduarda B. H.

    2016-01-01

    Dissolved organic matter (DOM) in estuaries derives from a diverse array of both allochthonous and autochthonous sources. In the estuarine system Ria de Aveiro (Portugal), the seasonality and the sources of the fraction of DOM that absorbs light (CDOM) were inferred using its optical and fluorescence properties. CDOM parameters known to be affected by aromaticity and molecular weight were correlated with physical, chemical and meteorological parameters. Two sites, representative of the marine and brackish water zones of the estuary, and with different hydrological characteristics, were regularly surveyed along two years, in order to determine the major influences on CDOM properties. Terrestrial-derived compounds are the predominant source of CDOM in the estuary during almost all the year and the two estuarine zones presented distinct amounts, as well as absorbance and fluorescence characteristics. Freshwater inputs have major influence on the dynamics of CDOM in the estuary, in particular at the brackish water zone, where accounted for approximately 60% of CDOM variability. With a lower magnitude, the biological productivity also impacted the optical properties of CDOM, explaining about 15% of its variability. Therefore, climate changes related to seasonal and inter-annual variations of the precipitation amounts might impact the dynamics of CDOM significantly, influencing its photochemistry and the microbiological activities in estuarine systems. PMID:27195702

  3. The Utility of CDOM for Improving the Resolution of Riverine DOM Fluxes and Biogeochemical Function

    NASA Astrophysics Data System (ADS)

    Spencer, R. G.; Aiken, G.; Mann, P. J.; Holmes, R. M.; Niggemann, J.; Dittmar, T.; Hernes, P.; Stubbins, A.

    2014-12-01

    A major historical limitation to geochemical studies assessing fluvial fluxes of dissolved organic matter (DOM) has been the issue of both temporal and spatial scaling. Examples will be presented from watersheds around the world highlighting how chromophoric dissolved organic matter (CDOM) measurements can be utilized as proxies for more intensive and expensive analytical analyses (e.g. molecular-level organic biomarkers). Utilizing these refined CDOM loads for terrigenous biomarkers results in improved temporal resolution and a significant change in flux estimates. Examining CDOM and dissolved organic carbon (DOC) flux data from an assortment of terrestrial biomes we establish a robust relationship between CDOM and DOC loads. The application of this relationship allows future studies to derive DOC loads from CDOM utilizing emerging in-situ or remote sensing technologies and thus refine river-to-ocean DOC fluxes, as well as exploit historic imagery to examine how fluxes may have changed. Calculated CDOM yields from a range of rivers are correlated to watershed percent wetland and highlight the importance of certain regions with respect to CDOM flux to the coastal ocean. This approach indicates that future studies might predict CDOM and DOC yields for different watershed types that could then be readily converted to loads providing for the estimation of CDOM and DOC export from ungauged watersheds. Examination of CDOM yields also highlights important geographical regions for future study with respect to the role of terrigenous CDOM in ocean color budgets and CDOM's role in biogeochemical processes. Finally, examples will be presented linking CDOM parameters to DOM composition and biogeochemical properties with the aim of providing measurements to improve the spatial and especially temporal resolution of the role DOM plays in fluvial networks.

  4. Web Based Nasal Surgical Simulator Using VRML and Java.

    PubMed

    Yuan-Yuan, Zhao; Guo-Hong, Zhou; De-Rong, Ye

    2005-01-01

    This paper describes a nasal surgical simulator that we have designed and implemented to run on the WWW using VRML and Java. In this paper we concentrate on implementation details such as collision detection and the usage of our simulator. At last, we discuss the advantage and disadvantave of the simulator.

  5. Estimation of toxicity using a Java based software tool

    EPA Science Inventory

    A software tool has been developed that will allow a user to estimate the toxicity for a variety of endpoints (such as acute aquatic toxicity). The software tool is coded in Java and can be accessed using a web browser (or alternatively downloaded and ran as a stand alone applic...

  6. Analysis of time series for postal shipments in Regional VII East Java Indonesia

    NASA Astrophysics Data System (ADS)

    Kusrini, DE; Ulama, B. S. S.; Aridinanti, L.

    2018-03-01

    The change of number delivery goods through PT. Pos Regional VII East Java Indonesia indicates that the trend of increasing and decreasing the delivery of documents and non-documents in PT. Pos Regional VII East Java Indonesia is strongly influenced by conditions outside of PT. Pos Regional VII East Java Indonesia so that the prediction the number of document and non-documents requires a model that can accommodate it. Based on the time series plot monthly data fluctuations occur from 2013-2016 then the model is done using ARIMA or seasonal ARIMA and selected the best model based on the smallest AIC value. The results of data analysis about the number of shipments on each product sent through the Sub-Regional Postal Office VII East Java indicates that there are 5 post offices of 26 post offices entering the territory. The largest number of shipments is available on the PPB (Paket Pos Biasa is regular package shipment/non-document ) and SKH (Surat Kilat Khusus is Special Express Mail/document) products. The time series model generated is largely a Random walk model meaning that the number of shipment in the future is influenced by random effects that are difficult to predict. Some are AR and MA models, except for Express shipment products with Malang post office destination which has seasonal ARIMA model on lag 6 and 12. This means that the number of items in the following month is affected by the number of items in the previous 6 months.

  7. JavaScript DNA translator: DNA-aligned protein translations.

    PubMed

    Perry, William L

    2002-12-01

    There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

  8. A comparison study of 2006 Java earthquake and other Tsunami earthquakes

    NASA Astrophysics Data System (ADS)

    Ji, C.; Shao, G.

    2006-12-01

    We revise the slip processes of July 17 2006 Java earthquakes by combined inverting teleseismic body wave, long period surface waves, as well as the broadband records at Christmas island (XMIS), which is 220 km away from the hypocenter and so far the closest observation for a Tsunami earthquake. Comparing with the previous studies, our approach considers the amplitude variations of surface waves with source depths as well as the contribution of ScS phase, which usually has amplitudes compatible with that of direct S phase for such low angle thrust earthquakes. The fault dip angles are also refined using the Love waves observed along fault strike direction. Our results indicate that the 2006 event initiated at a depth around 12 km and unilaterally rupture southeast for 150 sec with a speed of 1.0 km/sec. The revised fault dip is only about 6 degrees, smaller than the Harvard CMT (10.5 degrees) but consistent with that of 1994 Java earthquake. The smaller fault dip results in a larger moment magnitude (Mw=7.9) for a PREM earth, though it is dependent on the velocity structure used. After verified with 3D SEM forward simulation, we compare the inverted result with the revised slip models of 1994 Java and 1992 Nicaragua earthquakes derived using the same wavelet based finite fault inversion methodology.

  9. Adsorptive removal of dissolved organic matter (DOM) in landfill leachate by iron oxide nanoparticles (FeONPs)

    NASA Astrophysics Data System (ADS)

    Ghani, Zaidi Ab; Yusoff, Mohd Suffian; Zaman, Nastaein Qamaruz; Andas, Jeyashelly; Aziz, Hamidi Abdul

    2017-10-01

    A study was conducted to investigate the efficiency of iron oxide nanoparticle (FeONPs) adsorption for removing of DOM in landfill leachate. FeONPs was directly prepared via sodium borohydride (KBH4) reduction method. Adsorption kinetics, isotherm and thermodynamic studies were developed to design the model for DOM removal. Pseudo first-order and pseudo second-order model have been studied to fit the experimental data. The regression results showed that the adsorption kinetics were more accurately represented by a pseudo second-order model. The Weber-Morris intraparticle diffusion model was used to analyze the adsorption kinetics data. The plot of qt versus t1/2 represents multi linearity, which showed that the adsorption processes occurred in more than one step. Adsorption isotherms were analyzed by Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich, isotherms model. Equilibrium data were well fitted to the Dubinin- Radushkevich isotherm model. Maximum monolayer adsorption based on Langmuir was calculated to be 21.74 mg/g. Thermodynamic parameters such as free energy changes (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) were evaluated between temperatures of 25 °C and 40 °C. The ΔG° was noticed progressively decrease from -9.620 -9.820 -10.021, and -10.222 kJ/mol as the temperature increase. The ΔH° and ΔS° values were found to be 2.350 kJ/mol and 40.165 J/mol.K respectively. The results showed that the overall adsorption process was endothermic and spontaneous. The results from this study suggested that FeNPs could be a viable adsorbent in managing higher DOM problems associated with landfill leachate.

  10. H5N1 surveillance in migratory birds in Java, Indonesia.

    PubMed

    Stoops, Arthur C; Barbara, Katie A; Indrawan, Mochamad; Ibrahim, Ima N; Petrus, Wicaksana B; Wijaya, Susan; Farzeli, Arik; Antonjaya, Ungke; Sin, Lim W; Hidayatullah, N; Kristanto, Ige; Tampubolon, A M; Purnama, S; Supriatna, Adam; Burgess, Timothy H; Williams, Maya; Putnam, Shannon D; Tobias, Steve; Blair, Patrick J

    2009-12-01

    We sought to elucidate the role of migratory birds in transmission of H5N1 in an enzoonotic area. Resident, captive, and migratory birds were sampled at five sites in Java, Indonesia. Mist nets were used to trap birds. Birds were identified to species. RNA was extracted from swabs and reverse transcriptase polymerase chain reaction (RT-PCR) conducted for the HA and M genes of H5N1. Antibodies were detected by enzyme-linked immunosorbent assay and hemagglutination inhibition test. Between October 2006 and September 2007, a total of 4,067 captive, resident, and migratory birds comprising 98 species in 23 genera were sampled. The most commonly collected birds were the common sandpiper (6% of total), striated heron (3%), and the domestic chicken (14%). The overall prevalence of H5N1 antibodies was 5.3%. A significantly higher percentage of captive birds (16.1%) showed antibody evidence of H5N1 exposure when compared to migratory or resident birds. The greatest number of seropositive birds in each category were Muschovy duck (captive), striated heron (resident), and the Pacific golden plover (migratory). Seven apparently well captive birds yielded molecular evidence of H5N1 infection. Following amplification, the HA, NA, and M genes were analyzed. Phylogenetic analysis of the HA gene showed that the isolates were 97% similar to EU124153.1 A/chicken/West Java/Garut May 2006, an isolate obtained in a similar region of West Java. While no known markers of neuraminidase inhibitor resistance were found within the NA gene, M segment analysis revealed the V27A mutation known to confer resistance to adamantanes. Our results demonstrate moderate serologic evidence of H5N1 infection in captive birds, sampled in five sites in Java, Indonesia, but only occasional infection in resident and migratory birds. These data imply that in an enzoonotic region of Indonesia the role of migratory birds in transmission of H5N1 is limited.

  11. QSPIN: A High Level Java API for Quantum Computing Experimentation

    NASA Technical Reports Server (NTRS)

    Barth, Tim

    2017-01-01

    QSPIN is a high level Java language API for experimentation in QC models used in the calculation of Ising spin glass ground states and related quadratic unconstrained binary optimization (QUBO) problems. The Java API is intended to facilitate research in advanced QC algorithms such as hybrid quantum-classical solvers, automatic selection of constraint and optimization parameters, and techniques for the correction and mitigation of model and solution errors. QSPIN includes high level solver objects tailored to the D-Wave quantum annealing architecture that implement hybrid quantum-classical algorithms [Booth et al.] for solving large problems on small quantum devices, elimination of variables via roof duality, and classical computing optimization methods such as GPU accelerated simulated annealing and tabu search for comparison. A test suite of documented NP-complete applications ranging from graph coloring, covering, and partitioning to integer programming and scheduling are provided to demonstrate current capabilities.

  12. Skeleton microstructure of Porites lutea in Kondang Merak, Malang, East Java

    NASA Astrophysics Data System (ADS)

    Luthfi, Oktiyas Muzaky; Sontodipoero, R. M. Agung M. Rizqon; Isdianto, Andik; Setyohadi, Daduk; Jauhari, Alfan; Januarsa, I. Nyoman

    2017-11-01

    Research on coral microstructure in Indonesia, especially in East Java is rarely done. Therefore, this study aims to examine the shape of Aragonite Crystal coral Porites lutea in Pantai Kondak Merak, East Java, especially in 1998 which is the time of El Nino and has a global impact on coral growth. The shape of the aragonite crystal on the reef can be seen using the Scanning Electron Microscopy-Energy Dispersion X-Ray (SEM - EDX). Based on the coral aragonite crystal form, the increasing temperature in 1998 was not proven to have a devastating effect on the growth of corals of Pantai Kondang Merak. In contrast, the temperature at this site should support corals in order to grow rapidly, but there are other environmental factors that ultimately inhibit the growth of the coral.

  13. Attenuation relation for strong motion in Eastern Java based on appropriate database and method

    NASA Astrophysics Data System (ADS)

    Mahendra, Rian; Rohadi, Supriyanto; Rudyanto, Ariska

    2017-07-01

    The selection and determination of attenuation relation has become important for seismic hazard assessment in active seismic region. This research initially constructs the appropriate strong motion database, including site condition and type of the earthquake. The data set consisted of large number earthquakes of 5 ≤ Mw ≤ 9 and distance less than 500 km that occurred around Java from 2009 until 2016. The location and depth of earthquake are being relocated using double difference method to improve the quality of database. Strong motion data from twelve BMKG's accelerographs which are located in east Java is used. The site condition is known by using dominant period and Vs30. The type of earthquake is classified into crustal earthquake, interface, and intraslab based on slab geometry analysis. A total of 10 Ground Motion Prediction Equations (GMPEs) are tested using Likelihood (Scherbaum et al., 2004) and Euclidean Distance Ranking method (Kale and Akkar, 2012) with the associated database. The evaluation of these methods lead to a set of GMPEs that can be applied for seismic hazard in East Java where the strong motion data is collected. The result of these methods found that there is still high deviation of GMPEs, so the writer modified some GMPEs using inversion method. Validation was performed by analysing the attenuation curve of the selected GMPE and observation data in period 2015 up to 2016. The results show that the selected GMPE is suitable for estimated PGA value in East Java.

  14. Dusk to dawn activity patterns of anopheline mosquitoes in West Timor and Java, Indonesia.

    PubMed

    Ndoen, Ermi; Wild, Clyde; Dale, Pat; Sipe, Neil; Dale, Mike

    2011-05-01

    Malaria is a serious health issue in Indonesia. We investigated the dusk to dawn anopheline mosquito activity patterns, host-seeking and resting locations in coastal plain, hilly and highland areas in West Timor and Java. Adult mosquitoes were captured landing on humans or resting in houses or animal barns. Data analyzed were: mosquito night-time activities; period of peak activity; night-time activity in specific periods of time and for mosquito resting locations. Eleven species were recorded; data were sparse for some species therefore detailed analyses were performed for four species only. In Java Anopheles vagus was common, with a bimodal pattern of high activity. In West Timor, its activity peaked around midnight. Other species with peak activity around the middle of the night were An. barbirostris and An. subpictus. Most species showed no biting and resting preference for indoors or outdoors, although An. barbirostris preferred indoors in West Timor, but outdoors in Java. An. aconitus and An. annularis preferred resting in human dwellings; An. subpictus and An. vagus preferred resting in animal barns. An. barbirostris preferred resting in human dwellings in West Timor and in animal barns in Java. The information is useful for planning the mosquito control aspect of malaria management. For example, where mosquito species have peak activity at night indoors, bednets and indoor residual spraying should reduce malaria risk, but where mosquitoes are most active outdoors, other options may be more effective.

  15. PAEs and BPA removal in landfill leachate with Fenton process and its relationship with leachate DOM composition.

    PubMed

    He, Pin-Jing; Zheng, Zhong; Zhang, Hua; Shao, Li-Ming; Tang, Qiong-Yao

    2009-08-15

    An increasing attention has been paid to the trace endocrine disrupting compounds (EDCs) in landfill leachate. In this paper, the removal of EDCs including phthalic acid esters (PAEs) and bisphenol A (BPA) from the fresh and mature landfill leachate by Fenton treatment was studied. More than 40% of PAEs and about 62% of BPA were removed from the raw mature leachate while only 20% of PAEs and 37% of BPA in the raw fresh leachate were reduced, respectively. After the fresh and mature leachates were spiked with PAEs to 1.5 mg L(-1) and BPA to 0.08 mg L(-1), the removal efficiencies of BPA and PAEs increased to more than 88%. The results indicated that the removing efficiencies of the EDCs in the leachate had a relationship with their concentrations, and that the trace levels of EDCs in leachate challenged the treatment capacity of the Fenton process. Most of the EDCs in the enriched leachate were removed by oxidation, which had no clear correlation with the hydrophobicity of the EDCs. The flocculation played an important role in the removal of di-(2-ethylhexyl) phthalate that could not be completely oxidized in the Fenton process, in that the EDCs with high n-octanol/water partition coefficient inclined to precipitate after the Fenton process. The dissolved organic matter (DOM) in the fresh leachate inhibited the EDCs removal more than the DOM in the mature leachate did. Both the composition of the leachate DOM and the characteristics of the EDCs determined the removing efficiencies of the EDCs in the Fenton process.

  16. The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance.

    PubMed

    Ferraro, Jeffrey P; Ye, Ye; Gesteland, Per H; Haug, Peter J; Tsui, Fuchiang Rich; Cooper, Gregory F; Van Bree, Rudy; Ginter, Thomas; Nowalk, Andrew J; Wagner, Michael

    2017-05-31

    This study evaluates the accuracy and portability of a natural language processing (NLP) tool for extracting clinical findings of influenza from clinical notes across two large healthcare systems. Effectiveness is evaluated on how well NLP supports downstream influenza case-detection for disease surveillance. We independently developed two NLP parsers, one at Intermountain Healthcare (IH) in Utah and the other at University of Pittsburgh Medical Center (UPMC) using local clinical notes from emergency department (ED) encounters of influenza. We measured NLP parser performance for the presence and absence of 70 clinical findings indicative of influenza. We then developed Bayesian network models from NLP processed reports and tested their ability to discriminate among cases of (1) influenza, (2) non-influenza influenza-like illness (NI-ILI), and (3) 'other' diagnosis. On Intermountain Healthcare reports, recall and precision of the IH NLP parser were 0.71 and 0.75, respectively, and UPMC NLP parser, 0.67 and 0.79. On University of Pittsburgh Medical Center reports, recall and precision of the UPMC NLP parser were 0.73 and 0.80, respectively, and IH NLP parser, 0.53 and 0.80. Bayesian case-detection performance measured by AUROC for influenza versus non-influenza on Intermountain Healthcare cases was 0.93 (using IH NLP parser) and 0.93 (using UPMC NLP parser). Case-detection on University of Pittsburgh Medical Center cases was 0.95 (using UPMC NLP parser) and 0.83 (using IH NLP parser). For influenza versus NI-ILI on Intermountain Healthcare cases performance was 0.70 (using IH NLP parser) and 0.76 (using UPMC NLP parser). On University of Pisstburgh Medical Center cases, 0.76 (using UPMC NLP parser) and 0.65 (using IH NLP parser). In all but one instance (influenza versus NI-ILI using IH cases), local parsers were more effective at supporting case-detection although performances of non-local parsers were reasonable.

  17. Hydrocarbon potential assessment of Ngimbang formation, Rihen field of Northeast Java Basin

    NASA Astrophysics Data System (ADS)

    Pandito, R. H.; Haris, A.; Zainal, R. M.; Riyanto, A.

    2017-07-01

    The assessment of Ngimbang formation at Rihen field of Northeast Java Basin has been conducted to identify the hydrocarbon potential by analyzing the response of passive seismic on the proven reservoir zone and proposing a tectonic evolution model. In the case of petroleum exploration in Northeast Java basin, the Ngimbang formation cannot be simply overemphasized. East Java Basin has been well known as one of the mature basins producing hydrocarbons in Indonesia. This basin was stratigraphically composed of several formations from the old to the young i.e., the basement, Ngimbang, Kujung, Tuban, Ngerayong, Wonocolo, Kawengan and Lidah formation. All of these formations have proven to become hydrocarbon producer. The Ngrayong formation, which is geologically dominated by channels, has become a production formation. The Kujung formation that has been known with the reef build up has produced more than 102 million barrel of oil. The Ngimbang formation so far has not been comprehensively assessed in term its role as a source rock and a reservoir. In 2013, one exploratory well has been drilled at Ngimbang formation and shown a gas discovery, which is indicated on Drill Stem Test (DST) reading for more than 22 MMSCFD of gas. This discovery opens new prospect in exploring the Ngimbang formation.

  18. A preliminary study of paleotsunami deposit along the south coast of East Java: Pacitan-Banyuwangi

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

    Anugrah, Suci D.; Istiyanati; Zaim, Yahdi

    Along the southern coast of East Java Indonesia, at a number of localities, it can be identified and attempted to assign the age of tsunami deposit. Laboratory analyses were conducted also to support this study such as Granulometry, Paleontology and radiometric dating analysis. The presence of tsunami 1994 deposit in the area of Pancer, Lampon, Prigi and Grajagan was found, as a result of 7.8 Magnitude Banyuwangi Earthquake. The radiometric dating analysis also identified some paleotsunami deposit of about 1921 and 1930 in the area of Prigi and Teleng. This paleotsunami is assumed to have a correlation with an earthquakemore » in the south of Java at the same time. An outcrop in the Prigi and Teleng strongly convinced the fact of an earthquake generated tsunami in the south of Java in the year of about 1921 and 1930.« less

  19. The competitiveness of medicinal plants in Central Java Indonesia

    NASA Astrophysics Data System (ADS)

    Riptanti, E. W.; Qonita, R. A.; Fajarningsih, R. U.

    2018-03-01

    Indonesia hold a potential opportunity to be a pharmaceutical production country. In the other side, Indonesia facing agriculture product and market competition internationally and domestically. Improving competitiveness of specific products are aimed to hit the export market and also to be able to compete with import products in domestic market. Considering Indonesian market opportunity, therefore we perform this study aiming to examine the competitiveness of medicinal plants in Central Java area. The basic method applied in this study was descriptive and data sources are primary and secondary data. Data were analyzed using Revealed Comparative Advantage (RCA) and Trade Specialization Index (TSI) approaches. According to the study, we reveal that medicinal plant commodities in Central Java province have average score 8.52, indicating a strong comparative advantage in global markets, while the commodities appear to have average score of 0.97 at 0 to 1 range, representing a strong competitiveness. Those results are attributed to natural and environmental condition, as well as high demand of global market. This competitiveness will encourage traditional/modern medicinal industries in global market.

  20. JAva GUi for Applied Research (JAGUAR) v 3.0

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

    JAGUAR is a Java software tool for automatically rendering a graphical user interface (GUI) from a structured input specification. It is designed as a plug-in to the Eclipse workbench to enable users to create, edit, and externally execute analysis application input decks and then view the results. JAGUAR serves as a GUI for Sandia's DAKOTA software toolkit for optimization and uncertainty quantification. It will include problem (input deck)set-up, option specification, analysis execution, and results visualization. Through the use of wizards, templates, and views, JAGUAR helps uses navigate the complexity of DAKOTA's complete input specification. JAGUAR is implemented in Java, leveragingmore » Eclipse extension points and Eclipse user interface. JAGUAR parses a DAKOTA NIDR input specification and presents the user with linked graphical and plain text representations of problem set-up and option specification for DAKOTA studies. After the data has been input by the user, JAGUAR generates one or more input files for DAKOTA, executes DAKOTA, and captures and interprets the results« less

  1. Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder

    NASA Technical Reports Server (NTRS)

    Staats, Matt

    2009-01-01

    We present work on a prototype tool based on the JavaPathfinder (JPF) model checker for automatically generating tests satisfying the MC/DC code coverage criterion. Using the Eclipse IDE, developers and testers can quickly instrument Java source code with JPF annotations covering all MC/DC coverage obligations, and JPF can then be used to automatically generate tests that satisfy these obligations. The prototype extension to JPF enables various tasks useful in automatic test generation to be performed, such as test suite reduction and execution of generated tests.

  2. A new small karst-dwelling species of Cyrtodactylus (Reptilia: Squamata: Gekkonidae) from Java, Indonesia.

    PubMed

    Riyanto, Awal; Bauer, Aaron M; Yudha, Donan Satria

    2014-04-07

    A new small karst-dwelling species of the genus Cyrtodactylus is described from East Java and Special Province of Yogyakarta, Indonesia. Cyrtodactylus semiadii sp. nov. is a small species (SVL to 47.1 mm in females, 42.1 mm in males) distinguished from all other congeners by unique characters combination: short, robust, cylindrical tail, indistinct ventrolateral folds, absence of precloacal groove, absence of enlarged femoral scales, absence of precloacal and femoral pores and lack of enlarged median subcaudal scales. It is the third member of the genus recorded from Java

  3. Add Java extensions to your wiki: Java applets can bring dynamic functionality to your wiki pages

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

    Scarberry, Randall E.

    Virtually everyone familiar with today’s world wide web has encountered the free online encyclopedia Wikipedia many times. What you may not know is that Wikipedia is driven by an excellent open-source product called MediaWiki which is available to anyone for free. This has led to a proliferation of wiki sites devoted to just about any topic one can imagine. Users of a wiki can add content -- all that is required of them is that they type in their additions into their web browsers using the simple markup language called wikitext. Even better, the developers of wikitext made it extensible.more » With a little server-side development of your own, you can add your own custom syntax. Users aware of your extensions can then utilize them on their wiki pages with a few simple keystrokes. These extensions can be custom decorations, formatting, web applications, and even instances of the venerable old Java applet. One example of a Java applet extension is the Jmol extension (REF), used to embed a 3-D molecular viewer. This article will walk you through the deployment of a fairly elaborate applet via a MediaWiki extension. By no means exhaustive -- an entire book would be required for that -- it will demonstrate how to give the applet resize handles using using a little Javascript and CSS coding and some popular Javascript libraries. It even describes how a user may customize the extension somewhat using a wiki template. Finally, it explains a rudimentary persistence mechanism which allows applets to save data directly to the wiki pages on which they reside.« less

  4. Identification of the terebrantian thrips (Insecta, Thysanoptera) associated with cultivated plants in Java, Indonesia

    PubMed Central

    Sartiami, Dewi; Mound, Laurence A.

    2013-01-01

    Abstract An illustrated identification key is provided to 49 species of Thysanoptera, Terebrantia that have been found in association with cultivated plants in Java. This is the first published identification system to this group of insects from Indonesia, and includes 15 species not previously recorded from Indonesia, and a further three species not previously recorded from Java. A table is provided indicating the plants from which thrips were taken. PMID:23794915

  5. Machado de Assis's "Dom Casmurro" and "Soneto De Natal": The Calculated Mediocrity of a Mute Prophet

    ERIC Educational Resources Information Center

    Lewis, Christopher T.

    2016-01-01

    Joaquim Maria Machado de Assis's poem "Soneto de Natal" and the chapter "Um soneto" from his novel "Dom Casmurro" exhibit striking points of intersection that describe the same process: the creation of a sonnet. In the novel, Bentinho abandons his attempt with only a first and last line. "Soneto de Natal"…

  6. Cost-effectiveness of scaling up voluntary counselling and testing in West-Java, Indonesia.

    PubMed

    Tromp, Noor; Siregar, Adiatma; Leuwol, Barnabas; Komarudin, Dindin; van der Ven, Andre; van Crevel, Reinout; Baltussen, Rob

    2013-01-01

    to evaluate the costs-effectiveness of scaling up community-based VCT in West-Java. the Asian epidemic model (AEM) and resource needs model (RNM) were used to calculate incremental costs per HIV infection averted and per disability-adjusted life years saved (DALYs). Locally monitored demographic, epidemiological behavior and cost data were used as model input. scaling up community-based VCT in West-Java will reduce the overall population prevalence by 36% in 2030 and costs US$248 per HIV infection averted and US$9.17 per DALY saved. Cost-effectiveness estimation were most sensitive to the impact of VCT on condom use and to the population size of clients of female sex workers (FSWs), but were overall robust. The total costs for scaling up community-based VCT range between US$1.3 and 3.8 million per year and require the number of VCT integrated clinics at public community health centers to increase from 73 in 2010 to 594 in 2030. scaling up community-based VCT seems both an effective and cost-effective intervention. However, in order to prioritize VCT in HIV/AIDS control in West-Java, issues of budget availability and organizational capacity should be addressed.

  7. The July 17, 2006 Java Tsunami: Tsunami Modeling and the Probable Causes of the Extreme Run-up

    NASA Astrophysics Data System (ADS)

    Kongko, W.; Schlurmann, T.

    2009-04-01

    On 17 July 2006, an Earthquake magnitude Mw 7.8 off the south coast of west Java, Indonesia generated tsunami that affected over 300 km of south Java coastline and killed more than 600 people. Observed tsunami heights and field measurement of run-up distributions were uniformly scattered approximately 5 to 7 m along a 200 km coastal stretch; remarkably, a locally focused tsunami run-up height exceeding 20 m at Nusakambangan Island has been observed. Within the framework of the German Indonesia Tsunami Early Warning System (GITEWS) Project, a high-resolution near-shore bathymetrical survey equipped by multi-beam echo-sounder has been recently conducted. Additional geodata have been collected using Intermap Technologies STAR-4 airborne interferometric SAR data acquisition system on a 5 m ground sample distance basis in order to establish a most-sophisticated Digital Terrain Model (DTM). This paper describes the outcome of tsunami modelling approaches using high resolution data of bathymetry and topography being part of a general case study in Cilacap, Indonesia, and medium resolution data for other area along coastline of south Java Island. By means of two different seismic deformation models to mimic the tsunami source generation, a numerical code based on the 2D nonlinear shallow water equations is used to simulate probable tsunami run-up scenarios. Several model tests are done and virtual points in offshore, near-shore, coastline, as well as tsunami run-up on the coast are collected. For the purpose of validation, the model results are compared with field observations and sea level data observed at several tide gauges stations. The performance of numerical simulations and correlations with observed field data are highlighted, and probable causes for the extreme wave heights and run-ups are outlined. References Ammon, C.J., Kanamori, K., Lay, T., and Velasco, A., 2006. The July 2006 Java Tsunami Earthquake, Geophysical Research Letters, 33(L24308). Fritz, H

  8. Towards Formalizing the Java Security Architecture of JDK 1.2

    DTIC Science & Technology

    1998-01-01

    and Richard E. Newman for their contributions to this paper. References 1. Balfanz , D. and Gong, L.: Experience with Secure Multi-Processing in Java...Privacy, IEEE Computer Society, Oakland, California, Pages 122-136, 1992. 18. Wallach, D. S., Balfanz , D., Dean, D., and Felton, E. W.: Extensible

  9. Cyclone: java-based querying and computing with Pathway/Genome databases.

    PubMed

    Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

    2007-05-15

    Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

  10. Programming with non-heap memory in the real time specification for Java

    NASA Technical Reports Server (NTRS)

    Bollella, G.; Canham, T.; Carson, V.; Champlin, V.; Dvorak, D.; Giovannoni, B.; Indictor, M.; Meyer, K.; Reinholtz, A.; Murray, K.

    2003-01-01

    The Real-Time Specification for Java (RTSJ) provides facilities for deterministic, real-time execution in a language that is otherwise subject to variable latencies in memory allocation and garbage collection.

  11. Hypocenter Determination Using a Non-Linear Method for Events in West Java, Indonesia: A Preliminary Result

    NASA Astrophysics Data System (ADS)

    Rosalia, Shindy; Widiyantoro, Sri; Nugraha, Andri Dian; Ash Shiddiqi, Hasbi; Supendi, Pepen; Wandono

    2017-04-01

    West Java, part of the Sunda Arc, has relatively high seismicity due to subduction activity and faulting. The first step of tomography study in order to infer the geometry of the structure beneath West Java is to conduct precise earthquake hypocenter determination. In this study, we used earthquake waveform data taken from the regional Meteorological, Climatological, Geophysical Agency (BMKG) network from South Sumatra to central Java. We have repicked P and S arrival times from about 800 events in the period from April 2009 to December 2015. We selected the events which have azimuthal gap < 210° and phase more than 8. The non-linear method employed in this study used the oct-tree sampling algorithm from NonLinLoc program to determine the earthquake hypocenters. The hypocenter location results give better clustering earthquakes which are correlated well with geological structure in the study region. We also compared our results with BMKG catalog data and found that the average hypocenter location difference is about 12 km in latitude direction, 9.5 km in longitude direction, and the average focal depth difference is about 19.5 km. For future studies, we will conduct tomographic imaging to invert 3-D seismic velocity structure beneath the western part of Java.

  12. The effect of green supply chain management implementation to marketing performance through company competitiveness (study on paper industry in West Java)

    NASA Astrophysics Data System (ADS)

    Hijuzaman, O.; Rahayu, A.; Kusnendi

    2018-05-01

    The purpose of this study was to determine and analyze the effect of direct and indirect implementation of Green Supply-Chain Management (GSCM) on the Performance Marketing and Competitiveness Mediation Paper Company in West Java province. Object This research is the paper company that existed in West Java Province, which amounts to 30 companies as well as a sample of research, while variables studied are Variable Green Supply- Chain Management, Company Competitiveness Variable and Variable of Paper Marketing Industry Performance in West Java Province. The method used SEM with Variance Based or Component Based with Software used is SmartPLS 3.0. On this research are identified that no effect of Competitiveness on Marketing Performance in Paper Companies in West Java Province.

  13. Simulation Tools for Power Electronics Courses Based on Java Technologies

    ERIC Educational Resources Information Center

    Canesin, Carlos A.; Goncalves, Flavio A. S.; Sampaio, Leonardo P.

    2010-01-01

    This paper presents interactive power electronics educational tools. These interactive tools make use of the benefits of Java language to provide a dynamic and interactive approach to simulating steady-state ideal rectifiers (uncontrolled and controlled; single-phase and three-phase). Additionally, this paper discusses the development and use of…

  14. Fluorescence excitation-emission matrix spectroscopy analysis of landfill leachate DOM in coagulation-flocculation process.

    PubMed

    Zhu, Guocheng; Wang, Chuang; Dong, Xingwei

    2017-06-01

    Landfill leachate contains a variety of organic matters, some of which can be excited and emit fluorescence signal. In order to degrade these organic matters, the pretreatment of the leachate is needed, which can improve the degradation performance of post-treatment process. Coagulation-flocculation is one of the important pretreatment processes to treat landfill leachate. Assessing the chemical compositions of landfill leachate is helpful in the understanding of their sources and fates as well as the mechanistic behaviors in the water environment. The present work aimed to use fluorescence excitation-emission matrix spectroscopy (EEMs) to characterize the chemical fractions of landfill leachate dissolved organic matter (DOM) in conjunction with parallel factor analysis (PARAFAC). Results showed that the DOM of landfill leachate tested in this study was identified resulting from microbial input, which included five typical characteristic peaks and four kinds of PARAFAC fractions. These fractions were mainly composed of hydrophobic macromolecule humic acid-like (HM-HA), hydrophilic intermediate molecular fulvic acid-like (HIM-FA), and hydrophilic small molecule protein-like substances (HSM-PS). HM-HA and HIM-FA were found to be easier to remove than HSM-PS. Further research on HSM-PS removal by coagulation-flocculation still needs to be improved.

  15. Event Reconstruction for Many-core Architectures using Java

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

    Graf, Norman A.; /SLAC

    Although Moore's Law remains technically valid, the performance enhancements in computing which traditionally resulted from increased CPU speeds ended years ago. Chip manufacturers have chosen to increase the number of core CPUs per chip instead of increasing clock speed. Unfortunately, these extra CPUs do not automatically result in improvements in simulation or reconstruction times. To take advantage of this extra computing power requires changing how software is written. Event reconstruction is globally serial, in the sense that raw data has to be unpacked first, channels have to be clustered to produce hits before those hits are identified as belonging tomore » a track or shower, tracks have to be found and fit before they are vertexed, etc. However, many of the individual procedures along the reconstruction chain are intrinsically independent and are perfect candidates for optimization using multi-core architecture. Threading is perhaps the simplest approach to parallelizing a program and Java includes a powerful threading facility built into the language. We have developed a fast and flexible reconstruction package (org.lcsim) written in Java that has been used for numerous physics and detector optimization studies. In this paper we present the results of our studies on optimizing the performance of this toolkit using multiple threads on many-core architectures.« less

  16. Exploring ethnomathematics in Central Java

    NASA Astrophysics Data System (ADS)

    Zaenuri; Dwidayati, N.

    2018-03-01

    This research was intended to: (1) explore the forms of ethnomathematics and (2) analyze the integration of ethnomathematic at elementary and intermediate educations. This research used surveys as the main method. The data were collected by means of questionnaires, observations and documentation as well as literature reviews. The data were then analyzed descriptively and qualitatively. The analyses showed the following results: (1) ethnomathematics within the cultures of communities in northern coastal areas of Java Island were in the forms of: (a) cultural buildings (Menara Kudus), (b) non-cultural buildings, traditional foods and (c) batik motifs, and (2) various forms of ethnomathematics in the communities studied relate to the concepts of mathematics that they could be integrated into mathematic learning-teaching activities both in elementary and intermediate levels.

  17. Biochars induced modification of dissolved organic matter (DOM) in soil and its impact on mobility and bioaccumulation of arsenic and cadmium.

    PubMed

    Li, Gang; Khan, Sardar; Ibrahim, Muhammad; Sun, Tian-Ran; Tang, Jian-Feng; Cotner, James B; Xu, Yao-Yang

    2018-04-15

    Biochar application has attracted great attention due to its diverse uses and benefits in the fields of environmental management and agriculture. Biochar modifies the composition of dissolved organic matter (DOM) in soil, which directly or indirectly controls the mobility of metal contaminants and their bioaccumulation. In this study, ten different hydrothermal biochars pyrolysed from mushroom waste (MSBC), soybean straw (SBBC), sewage sludge (SSBC), peanut shells (PNBC) and rice straw (RSBC) at two pyrolysis temperatures (200 °C and 350 °C) were used to investigate DOM changes in soil solution and their effects on metal availability and bioaccumulation. Biochar induced modification of soil DOM which was characterized by spectroscopic analysis of water soluble organic carbon, specific absorbance (SUVA 254 ), UV-vis absorption, spectral slope (S R ) and the absorption coefficient. Regarding rice plant growth, the biochar effects on biomass were greatly varied. Biochars (except for RSBC and MSBC) prepared at high temperature significantly (P ≤ 0.05) suppressed the availability of As and Cd in soil and their subsequent bioaccumulation in rice plants. The highest reduction (88%) in bioaccumulated As was observed in rice grown on soil amended with SBBC prepared at 350 °C (the highest temperature for hydrothermal technique). The addition of biochars (except RSBC and MSBC) prepared at high temperature markedly (p < 0.05) decreased AsIII (30-92%), while the effects on dimethylarsenic acid (DMA) and arsenate (AsV) concentrations were not significant except for SSBC350 (prepared at 350 °C) treatment. These results highlight the potential of biochar-DOM interactions as an important mechanism for suppressing the mobility and bioaccumulation of As and Cd in biochar-amended paddy agricultural systems. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Changes in DOM Character and Composition during Spring Snow Melt in the Jemez River Basin Critical Zone Observatory.

    NASA Astrophysics Data System (ADS)

    Thompson, M.; Olshansky, Y.; Chorover, J.

    2017-12-01

    Dynamics of dissolved organic matter (DOM) in stream waters are important indicators of internal processes in the critical zone, such as decomposition and mobilization of soil organic matter, hydrologic flow paths, potential for metal mobilization and nutrient redistribution. Previous studies indicate that DOM concentration was highest during peak snow melt in the La Jara catchment located in the Jemez River Basin Critical Zone Observatory (Perdrial et al., 2014). We postulate that the molecular composition and character of DOM changes with the advance of spring snow melt. Water samples were collected from two flumes located at the outlets of the La Jara Creek and from a zero order basin within this catchment through the spring snowmelt from March 1 to May 15 2017. DOM concentration increased with stream discharge. Quantification of molecular changes was conducted using Fourier transform infrared spectroscopy (FTIR), which showed the variation in carboxyl abundance (wavenumbers 1680, 1600 and 1410 cm-1) correlated with dissolved organic carbon concentration, indicating that this component is relatively a constant fraction of the organic carbon exported through the stream during spring snowmelt. In contrast, amide vibrations (3550, 1640 and 670 cm-1) were shown to decrease with the advance of spring snowmelt. This trend further corresponded to a decrease in the ratio of carboxylic acid (above) to aromatic (1622, 1490, 955 cm-1) moieties, suggesting either a flush of compounds accumulated prior to spring snow melt, or increased decomposition of plant derived material in the soil that was then transported to the stream. Aliphatic components (2965, 2925 and 2865 cm-1) decreased from the beginning to the middle of sampling period, then showed an increase toward the end of snowmelt. O-Alkyl peak (1150 and 1073 cm-1) varied without a clear trend during the spring snowmelt. These changes in O-Alkyl and aliphatic compounds may be related to microbial derived compounds and

  19. Implications of effluent organic matter and its hydrophilic fraction on zinc(II) complexation in rivers under strong urban pressure: aromaticity as an inaccurate indicator of DOM-metal binding.

    PubMed

    Louis, Yoann; Pernet-Coudrier, Benoît; Varrault, Gilles

    2014-08-15

    The zinc binding characteristics of dissolved organic matter (DOM) fractions from the Seine River Basin were studied after being separated and extracted according to their polarity: hydrophobic, transphilic, and hydrophilic. The applied experimental methodology was based on a determination of labile zinc species by means of differential pulse anodic stripping voltammetry (DPASV) at increasing concentrations of total zinc on a logarithmic scale and at fixed levels of: pH, ionic strength, and temperature. Fitting the DOM fractions with two discrete classes of ligands successfully allowed determining the conditional zinc binding constants (Ki) as well as total ligand density (LiT). The binding constants obtained for each DOM fraction were then compared and discussed with respect to the hydrophobic/hydrophilic nature and sample origin. Results highlighted a strong complexation of zinc to the effluent organic matter and especially the most hydrophilic fraction, which also displayed a very low specific UV absorbance. Although the biotic ligand model takes into account the quality of DOM through UV absorbance in the predictions of metal bioavailability and toxicity, this correction is not efficient for urban waters. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. DOM in stream water and soil solution in two small, bordering catchments in central Sweden

    NASA Astrophysics Data System (ADS)

    Norström, Sara H.; Bylund, Dan

    2013-04-01

    Seasonal variations in dissolved organic matter (DOM) and the influence of wood ash application on DOM were studied in two first order streams draining two small, bordering forested catchments. The catchments, 40 and 50 h respectively, were situated in Bispgården (63°07N, 16°70E), central Sweden with forest consisting of mainly 50 to 80 year-old Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). Seasonal variations in the stream water were measured during 2003-2007, and wood ash was applied in one of the catchments in the fall of 2004. In addition to stream water samples, sampling of soil solution in the riparian zone was made in one of the catchments during 2003-2006. The quantity of DOM differed between the streams, but the seasonal patterns for the two streams were correlated during 2003 and 2004. After wood ash treatment, dissolved organic carbon (DOC) increased significantly in the stream draining the treated catchment. 17 different low molecular mass organic acids (LMMOAs) were measured in the stream water during the whole study period. The most abundant LMMOAs were oxalic- and lactic acid, of which peak concentrations of oxalic acid coincided with those of DOC, while no such relation between the concentrations of DOC and lactic acid could be seen in either of the streams. Some of the most common acids in the soil solution, shikimic acid, citric acid and malic acid were rarely found in the stream water and only then in very low concentrations, thus appearing not to have made the transition from soil to stream water in the same manner as oxalic acid. The wood ash application did not affect the total LMMOA concentration and there was no difference during the investigated period. Of the 17 analysed LMMOAs, only malonic acid appeared affected by wood ash application, with a significant increase during both 2005 and 2006.

  1. Differential fluorescence EEMs can be used to assess treatability of DOM during drinking water production

    NASA Astrophysics Data System (ADS)

    Lavonen, Elin; Kothawala, Dolly; Tranvik, Lars; Köhler, Stephan

    2014-05-01

    Fluorescence spectroscopy has been widely used to characterize fluorescent dissolved organic matter (FDOM) in various waters including during drinking water production. Commonly used techniques for data treatment include peak picking, indexes calculated from 2D emission spectra and modelling of fluorescence components using parallel factor analysis (PARAFAC). However, peak picking and indexes only use limited information from the fluorescence EEMs and PARAFAC requires a larger dataset and experience to perform. Because DOM is a major issue in drinking water production, and personnel at water treatment plants usually have limited time for advanced analysis we have developed a simple way of assessing the treatability of DOM in different waters using differential fluorescence. With this approach the removed fraction of FDOM is calculated from samples taken before and after a particular treatment process and the percentage of removed material assessed. Samples have been collected from four large water treatment plants in Sweden and analyzed for 3Dfluorescence, absorbance and DOC. The selective removal of DOM during e.g. flocculation and slow sand filtration as well as differences in experienced treatability between the treatment plants was described with differential fluorescence. Chemical flocculation is selective towards FDOM with red-shifted emission across the entire EEM. Red-shift has earlier been connected to condensation (i.e. decrease in H/C) and positively correlated to molecular size indicating that larger, humified molecules are being preferentially removed. During the biological process of slow sand filtration compounds with blue-shifted emission are targeted demonstrating selective removal of more freshly produced, microbial material. Disinfection with UV/NH2Cl and NaOCl was found to only target material with protein-like fluorescence suggesting that FDOM of this nature could be responsible for unwanted consumption of disinfection agent. Targeted removal

  2. HYDROXYL RADICAL/OZONE RATIOS DURING OZONATION PROCESSES. II. THE EFFECT OF TEMPERATURE, PH, ALKALINITY, AND DOM PROPERTIES

    EPA Science Inventory

    The influence of temperature, pH, alkalinity, and type and concentration of the dissolved organic matter (DOM) on the rate of ozone (O3) decomposition, O3-exposure, .OH-exposure and the ratio Rct of the concentrations of .OH and O3 has been studied. For a standardized single ozon...

  3. A kickball game for ankle rehabilitation by JAVA, JNI, and VRML

    NASA Astrophysics Data System (ADS)

    Choi, Hyungjeen; Ryu, Jeha; Lee, Chansu

    2004-03-01

    This paper presents development of a virtual environment that can be applied to the ankle rehabilitation procedure. We developed a virtual football stadium to intrigue a patient, where two degree of freedom (DOF) plate-shaped object is oriented to kick a ball falling from the sky in accordance with the data from the ankle's dorisflexion/plantarflexion and inversion/eversion motion on the moving platform of the K-Platform. This Kickball Game is implemented by Virtual Reality Modeling Language (VRML). To control virtual objects, data from the K-Platform are transmitted through the communication module implemented in C++. Java, Java Native Interface (JNI) and VRML plug-in are combined together so as to interface the communication module with the virtual environment by VRML. This game may be applied to the Active Range of Motion (AROM) exercise procedure that is one of the ankle rehabilitation procedures.

  4. Changes in polyphenolics during maturation of Java plum (Syzygium cumini Lam.).

    PubMed

    Lestario, Lydia Ninan; Howard, Luke R; Brownmiller, Cindi; Stebbins, Nathan B; Liyanage, Rohana; Lay, Jackson O

    2017-10-01

    Java plum (Syzygium cumini Lam.) is a rich source of polyphenolics with many purported health benefits, but the effect of maturation on polyphenolic content is unknown. Freeze-dried samples of Java plum from seven different maturity stages were analyzed for anthocyanin, flavonol, flavanonol and hydrolysable tannin composition by HPLC. Anthocyanins were first detected at the green-pink stage of maturity and increased throughout maturation with the largest increase occurring from the dark purple to black stages of maturation. Levels of gallotannins, ellagitannins, flavonols, gallic acid and ellagic acid were highest at early stages of maturation and decreased as the fruit ripened. For production of antioxidant-rich nutraceutical ingredients, fruit should be harvested immature to obtain extracts rich in hydrolysable tannins and flavonols. The exceptional anthocyanin content of black fruit may prove useful as a source of a natural colorant. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Implementing a Java Based GUI for RICH Detector Analysis

    NASA Astrophysics Data System (ADS)

    Lendacky, Andrew; Voloshin, Andrew; Benmokhtar, Fatiha

    2016-09-01

    The CLAS12 detector at Thomas Jefferson National Accelerator Facility (TJNAF) is undergoing an upgrade. One of the improvements is the addition of a Ring Imaging Cherenkov (RICH) detector to improve particle identification in the 3-8 GeV/c momentum range. Approximately 400 multi anode photomultiplier tubes (MAPMTs) are going to be used to detect Cherenkov Radiation in the single photoelectron spectra (SPS). The SPS of each pixel of all MAPMTs have been fitted to a mathematical model of roughly 45 parameters for 4 HVs, 3 OD. Out of those parameters, 9 can be used to evaluate the PMTs performance and placement in the detector. To help analyze data when the RICH is operational, a GUI application was written in Java using Swing and detector packages from TJNAF. To store and retrieve the data, a MySQL database program was written in Java using the JDBC package. Using the database, the GUI pulls the values and produces histograms and graphs for a selected PMT at a specific HV and OD. The GUI will allow researchers to easily view a PMT's performance and efficiency to help with data analysis and ring reconstruction when the RICH is finished.

  6. Important property of polymer spheres for the preparation of three-dimensionally ordered macroporous (3DOM) metal oxides by the ethylene glycol method: the glass-transition temperature.

    PubMed

    Sadakane, Masahiro; Sasaki, Keisuke; Nakamura, Hiroki; Yamamoto, Takashi; Ninomiya, Wataru; Ueda, Wataru

    2012-12-21

    We demonstrate that the glass-transition temperature (T(g)) of a polymer sphere template is a crucial factor in the production of three-dimensionally ordered macroporous (3DOM) materials. Metal nitrate dissolved in ethylene glycol-methanol was infiltrated into the void of a face-centered, close-packed colloidal crystal of poly(methyl methacrylate) (PMMA)-based spheres. The metal nitrate reacts with EG to form a metal oxalate (or metal glycoxylate) solid (nitrate oxidation) in the void of the template when the metal nitrate-EG-PMMA composite is heated. Further heating converts metal oxalate to metal oxide and removes PMMA to form 3DOM materials. We investigated the effect of T(g) of PMMA templates and obtained clear evidence that the solidification temperature of the metal precursor solution (i.e., nitration oxidation temperature) should be lower than the T(g) of the polymer spheres to obtain a well-ordered 3DOM structure.

  7. On The Impact of Climate Change to Agricultural Productivity in East Java

    NASA Astrophysics Data System (ADS)

    Kuswanto, Heri; Salamah, Mutiah; Mumpuni Retnaningsih, Sri; Dwi Prastyo, Dedy

    2018-03-01

    Many researches showed that climate change has significant impact on agricultural sector, which threats the food security especially in developing countries. It has been observed also that the climate change increases the intensity of extreme events. This research investigated the impact climate to the agricultural productivity in East Java, as one of the main rice producers in Indonesia. Standard regression as well as panel regression models have been performed in order to find the best model which is able to describe the climate change impact. The analysis found that the fixed effect model of panel regression outperforms the others showing that climate change had negatively impacted the rice productivity in East Java. The effect in Malang and Pasuruan were almost the same, while the impact in Sumenep was the least one compared to other districts.

  8. Early Supplemental Feeding and Spontaneous Play in West Java, Indonesia.

    ERIC Educational Resources Information Center

    Walka, Helen; Pollitt, Ernesto; Triana, Nina; Jahari, Abas B.

    This study examined the effects of nutritional supplements on the duration and level of spontaneous play of 55 mildly to moderately malnourished toddlers living within the tea plantations of West Java, Indonesia. Infants were randomly assigned by their day care centers to one of three supplement groups: (1) energy and micronutrient supplements;…

  9. PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

    PubMed Central

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2006-01-01

    Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

  10. ImageJ: Image processing and analysis in Java

    NASA Astrophysics Data System (ADS)

    Rasband, W. S.

    2012-06-01

    ImageJ is a public domain Java image processing program inspired by NIH Image. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

  11. Project Golden Gate: towards real-time Java in space missions

    NASA Technical Reports Server (NTRS)

    Dvorak, Daniel; Bollella, Greg; Canham, Tim; Carson, Vanessa; Champlin, Virgil; Giovannoni, Brian; Indictor, Mark; Meyer, Kenny; Murray, Alex; Reinholtz, Kirk

    2004-01-01

    This paper describes the problem domain and our experimentation with the first commercial implementation of the Real Time Specification for Java. The two main issues explored in this report are: (1) the effect of RTSJ's non-heap memory on the programming model, and (2) performance benchmarking of RTSJ/Linux relative to C++/VxWorks.

  12. An Ethernet Java Applet for a Course for Non-Majors.

    ERIC Educational Resources Information Center

    Holliday, Mark A.

    1997-01-01

    Details the topics of a new course that introduces computing and communication technology to students not majoring in computer science. Discusses the process of developing a Java applet (a program that can be invoked through a World Wide Web browser) that illustrates the protocol used by ethernet local area networks to determine which computer can…

  13. Advances in the spatially distributed ages-w model: parallel computation, java connection framework (JCF) integration, and streamflow/nitrogen dynamics assessment

    USDA-ARS?s Scientific Manuscript database

    AgroEcoSystem-Watershed (AgES-W) is a modular, Java-based spatially distributed model which implements hydrologic and water quality (H/WQ) simulation components under the Java Connection Framework (JCF) and the Object Modeling System (OMS) environmental modeling framework. AgES-W is implicitly scala...

  14. Collection of process data after cardiac surgery: initial implementation with a Java-based intranet applet.

    PubMed

    Ratcliffe, M B; Khan, J H; Magee, K M; McElhinney, D B; Hubner, C

    2000-06-01

    Using a Java-based intranet program (applet), we collected postoperative process data after coronary artery bypass grafting. A Java-based applet was developed and deployed on a hospital intranet. Briefly, the nurse entered patient process data using a point and click interface. The applet generated a nursing note, and process data were saved in a Microsoft Access database. In 10 patients, this method was validated by comparison with a retrospective chart review. In 45 consecutive patients, weekly control charts were generated from the data. When aberrations from the pathway occurred, feedback was initiated to restore the goals of the critical pathway. The intranet process data collection method was verified by a manual chart review with 98% sensitivity. The control charts for time to extubation, intensive care unit stay, and hospital stay showed a deviation from critical pathway goals after the first 20 patients. Feedback modulation was associated with a return to critical pathway goals. Java-based applets are inexpensive and can collect accurate postoperative process data, identify critical pathway deviations, and allow timely feedback of process data.

  15. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

    PubMed

    Balaur, Irina; Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J; Auffray, Charles

    2017-04-01

    The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . ibalaur@eisbm.org. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  16. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

    PubMed Central

    Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J.; Auffray, Charles

    2017-01-01

    Abstract Summary: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. Availability and Implementation: The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/. The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework. Contact: ibalaur@eisbm.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27993779

  17. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

    PubMed

    Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

    2012-03-01

    We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Context-sensitive trace inlining for Java.

    PubMed

    Häubl, Christian; Wimmer, Christian; Mössenböck, Hanspeter

    2013-12-01

    Method inlining is one of the most important optimizations in method-based just-in-time (JIT) compilers. It widens the compilation scope and therefore allows optimizing multiple methods as a whole, which increases the performance. However, if method inlining is used too frequently, the compilation time increases and too much machine code is generated. This has negative effects on the performance. Trace-based JIT compilers only compile frequently executed paths, so-called traces, instead of whole methods. This may result in faster compilation, less generated machine code, and better optimized machine code. In the previous work, we implemented a trace recording infrastructure and a trace-based compiler for [Formula: see text], by modifying the Java HotSpot VM. Based on this work, we evaluate the effect of trace inlining on the performance and the amount of generated machine code. Trace inlining has several major advantages when compared to method inlining. First, trace inlining is more selective than method inlining, because only frequently executed paths are inlined. Second, the recorded traces may capture information about virtual calls, which simplify inlining. A third advantage is that trace information is context sensitive so that different method parts can be inlined depending on the specific call site. These advantages allow more aggressive inlining while the amount of generated machine code is still reasonable. We evaluate several inlining heuristics on the benchmark suites DaCapo 9.12 Bach, SPECjbb2005, and SPECjvm2008 and show that our trace-based compiler achieves an up to 51% higher peak performance than the method-based Java HotSpot client compiler. Furthermore, we show that the large compilation scope of our trace-based compiler has a positive effect on other compiler optimizations such as constant folding or null check elimination.

  19. GEODATA: Information System Based on Geospatial for Early Warning Tracking and Analysis Agricultural Plant Diseases in Central Java

    NASA Astrophysics Data System (ADS)

    Prasetyo, S. Y. J.; Agus, Y. H.; Dewi, C.; Simanjuntak, B. H.; Hartomo, K. D.

    2017-03-01

    The Government of Indonesia is currently faced with the problems of food, especially rice. It needs in large numbers that have to import from neighboring countries. Actually, the Indonesian government has the ability to produce rice to meet national needs but is still faced with the problem of pest attack rice annually increasing extent. One of the factors is that geographically Indonesia located on the migration path of world rice insect pests (called BPH or Brown Planthoppers) (Nilaparvata lugens Stal.) It leads endemic status annually. One proposed strategy to be applied is to use an early warning system based on a specific region of the main pest population. The proposed information system called GEODATA. GEODATA is Geospatial Outbreak of Disease Tracking and Analysis. The system works using a library ESSA (Exponential Smoothing - Spatial Autocorrelation) developed in previous studies in Satya Wacana Christian University. GEODATA built to meet the qualifications required surveillance device by BMKG (Indonesian Agency of Meteorology, Climatology and Geophysics’ Central Java Provinces), BPTPH (Indonesian Agency of Plant Protection and Horticulture) Central Java Provinces, BKP-KP District Boyolali, Central Java, (Indonesian Agency of Food Security and Agriculture Field Supervisor, District Boyolali, Central Java Provinces) and farmer groups. GIS GEODATA meets the needs of surveillance devices that include: (1) mapping of the disease, (2) analysis of the dynamics of the disease, and (3) prediction of attacks / disease outbreaks in a particular region. GIS GEODATA is currently under implementation in the laboratory field observations of plant pest in Central Java province, Indonesia.

  20. Recent structural studies on Dom34/aPelota and Hbs1/aEF1α: important factors for solving general problems of ribosomal stall in translation

    PubMed Central

    Kobayashi, Kan; Ishitani, Ryuichiro; Nureki, Osamu

    2013-01-01

    In the translation process, translating ribosomes usually move on an mRNA until they reach the stop codon. However, when ribosomes translate an aberrant mRNA, they stall. Then, ribosomes are rescued from the aberrant mRNA, and the aberrant mRNA is subsequently degraded. In eukaryotes, Pelota (Dom34 in yeast) and Hbs1 are responsible for solving general problems of ribosomal stall in translation. In archaea, aPelota and aEF1α, homologous to Pelota and Hbs1, respectively, are considered to be involved in that process. In recent years, great progress has been made in determining structures of Dom34/aPelota and Hbs1/aEF1α. In this review, we focus on the functional roles of Dom34/aPelota and Hbs1/aEF1α in ribosome rescue, based on recent structural studies of them. We will also present questions to be answered by future work. PMID:27493551

  1. Anatomy of the western Java plate interface from depth-migrated seismic images

    NASA Astrophysics Data System (ADS)

    Kopp, H.; Hindle, D.; Klaeschen, D.; Oncken, O.; Reichert, C.; Scholl, D.

    2009-11-01

    Newly pre-stack depth-migrated seismic images resolve the structural details of the western Java forearc and plate interface. The structural segmentation of the forearc into discrete mechanical domains correlates with distinct deformation styles. Approximately 2/3 of the trench sediment fill is detached and incorporated into frontal prism imbricates, while the floor sequence is underthrust beneath the décollement. Western Java, however, differs markedly from margins such as Nankai or Barbados, where a uniform, continuous décollement reflector has been imaged. In our study area, the plate interface reveals a spatially irregular, nonlinear pattern characterized by the morphological relief of subducted seamounts and thicker than average patches of underthrust sediment. The underthrust sediment is associated with a low velocity zone as determined from wide-angle data. Active underplating is not resolved, but likely contributes to the uplift of the large bivergent wedge that constitutes the forearc high. Our profile is located 100 km west of the 2006 Java tsunami earthquake. The heterogeneous décollement zone regulates the friction behavior of the shallow subduction environment where the earthquake occurred. The alternating pattern of enhanced frictional contact zones associated with oceanic basement relief and weak material patches of underthrust sediment influences seismic coupling and possibly contributed to the heterogeneous slip distribution. Our seismic images resolve a steeply dipping splay fault, which originates at the décollement and terminates at the sea floor and which potentially contributes to tsunami generation during co-seismic activity.

  2. Anatomy of the western Java plate interface from depth-migrated seismic images

    USGS Publications Warehouse

    Kopp, H.; Hindle, D.; Klaeschen, D.; Oncken, O.; Reichert, C.; Scholl, D.

    2009-01-01

    Newly pre-stack depth-migrated seismic images resolve the structural details of the western Java forearc and plate interface. The structural segmentation of the forearc into discrete mechanical domains correlates with distinct deformation styles. Approximately 2/3 of the trench sediment fill is detached and incorporated into frontal prism imbricates, while the floor sequence is underthrust beneath the d??collement. Western Java, however, differs markedly from margins such as Nankai or Barbados, where a uniform, continuous d??collement reflector has been imaged. In our study area, the plate interface reveals a spatially irregular, nonlinear pattern characterized by the morphological relief of subducted seamounts and thicker than average patches of underthrust sediment. The underthrust sediment is associated with a low velocity zone as determined from wide-angle data. Active underplating is not resolved, but likely contributes to the uplift of the large bivergent wedge that constitutes the forearc high. Our profile is located 100 km west of the 2006 Java tsunami earthquake. The heterogeneous d??collement zone regulates the friction behavior of the shallow subduction environment where the earthquake occurred. The alternating pattern of enhanced frictional contact zones associated with oceanic basement relief and weak material patches of underthrust sediment influences seismic coupling and possibly contributed to the heterogeneous slip distribution. Our seismic images resolve a steeply dipping splay fault, which originates at the d??collement and terminates at the sea floor and which potentially contributes to tsunami generation during co-seismic activity. ?? 2009 Elsevier B.V.

  3. JavaScript Access to DICOM Network and Objects in Web Browser.

    PubMed

    Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

    2017-10-01

    Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

  4. The Model of Landscape Development in Big Cities Of Central Java

    NASA Astrophysics Data System (ADS)

    Darmawan, E.; Murtini, T. W.

    2018-05-01

    The existence of urban parks as a part of urban green space is very important for the environment and the citizen of the city, and inseparable part from the urban landscape. In its development, the existence of an urban parks could create a safe, comfortable, productive, and visually aesthetical environment. The problem arising now is a view that the urban parks are often unsuitable with the surrounding. Therefore, the parks are not functional and does not have significant visual. So that, this research is aimed to reveal model of landscape development in big cities in Central Java. The method used is descriptive qualitative that can describe the detail of problem, in determining the plan to overcome the problem. The research location will focused on big cities in Central Java with potential landscape that can be improved. The results of the research will be composed in an international scientific journals and is expected to be a reference in the field of urban landscape arrangement.

  5. Teaching Introductory Programming to IS Students: Java Problems and Pitfalls

    ERIC Educational Resources Information Center

    Pendergast, Mark O.

    2006-01-01

    This paper examines the impact the use of the Java programming language has had on the way our students learn to program and the success they achieve. The importance of a properly constructed first course in programming cannot be overstated. A course well experienced will leave students with good programming habits, the ability to learn on their…

  6. [Background and characteristics of migration to urban areas in Java].

    PubMed

    Kawamoto, I

    1985-06-01

    A review of urbanization trends in Java, Indonesia, is presented, with the focus on the background and characteristics of migrants to urban areas. Comparisons are made between the characteristics of laborers in the informal sector (housemaids) and those of factory workers, and between migrants from rural areas and those from other urban areas. (summary in ENG)

  7. Migration Imaging of the Java Subduction Zones

    NASA Astrophysics Data System (ADS)

    Dokht, Ramin M. H.; Gu, Yu Jeffrey; Sacchi, Mauricio D.

    2018-02-01

    Imaging of tectonically complex regions can greatly benefit from dense network data and resolution enhancement techniques. Conventional methods in the analysis of SS precursors stack the waveforms to obtain an average discontinuity depth, but smearing due to large Fresnel zones can degrade the fine-scale topography on the discontinuity. To provide a partial solution, we introduce a depth migration algorithm based on the common scattering point method while considering nonspecular diffractions from mantle transition zone discontinuities. Our analysis indicates that, beneath the Sunda arc, the depth of the 410 km discontinuity (the 410) is elevated by 30 km and the 660 km discontinuity (the 660) is depressed by 20-40 km; the region of the strongest anticorrelation is correlated with the morphology of the subducting Indo-Australian slab. In eastern Java, a "flat" 410 coincides with a documented slab gap, showing length scales greater than 400 km laterally and 200 km vertically. This observation could be explained by the arrival of a buoyant oceanic plateau at the Java trench at approximately 8 Ma ago, which may have caused a temporary cessation of subduction and formed a tear in the subducting slab. Our results highlight contrasting depths of the 410 and 660 along the shallow-dipping slab below the Banda trench. The 660, however, becomes significantly uplifted beneath the Banda Sea, which is accompanied by enhanced reflection amplitudes. We interpret these observations as evidence for a subslab low-velocity zone, possibly related to the lower mantle upwelling beneath the subducting slab.

  8. Vertical Stratification of Peat Pore Water Dissolved Organic Matter Composition in a Peat Bog in Northern Minnesota: Pore Water DOM composition in a peat bog

    DOE PAGES

    Tfaily, Malak M.; Wilson, Rachel M.; Cooper, William T.; ...

    2018-01-29

    Here, we characterized dissolved organic matter (DOM) composition throughout the peat column at the Marcell S1 forested bog in northern Minnesota and tested the hypothesis that redox oscillations associated with cycles of wetting and drying at the surface of the fluctuating water table correlate with increased carbon, sulfur, and nitrogen turn over. We found significant vertical stratification of DOM molecular composition and excitation-emission matrix parallel factor analysis components within the peat column. In particular, the intermediate depth zone (~ 50 cm) was identified as a zone where maximum decomposition and turnover is taking place. Surface DOM was dominated by inputsmore » from surface vegetation. The intermediate depth zone was an area of high organic matter reactivity and increased microbial activity with diagenetic formation of many unique compounds, among them polycyclic aromatic compounds that contain both nitrogen and sulfur heteroatoms. These compounds have been previously observed in coal-derived compounds and were assumed to be responsible for coal's biological activity. Biological processes triggered by redox oscillations taking place at the intermediate depth zone of the peat profile at the S1 bog are assumed to be responsible for the formation of these heteroatomic PACs in this system. Alternatively, these compounds could stem from black carbon and nitrogen derived from fires that have occurred at the site in the past. Surface and deep DOM exhibited more similar characteristics, compared to the intermediate depth zone, with the deep layer exhibiting greater input of microbially degraded organic matter than the surface suggesting that the entire peat profile consists of similar parent material at different degrees of decomposition and that lateral and vertical advection of pore water from the surface to the deeper horizons is responsible for such similarities. Lastly, our findings suggest that molecular composition of DOM in peatland pore

  9. Vertical Stratification of Peat Pore Water Dissolved Organic Matter Composition in a Peat Bog in Northern Minnesota: Pore Water DOM composition in a peat bog

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

    Tfaily, Malak M.; Wilson, Rachel M.; Cooper, William T.

    We characterized dissolved organic matter (DOM) composition throughout the peat column at the Marcell S1 forested bog in northern Minnesota and tested the hypothesis that redox oscillations associated with cycles of wetting and drying at the surface of the fluctuating water table correlate with increased carbon, sulfur and nitrogen turn over. We found significant vertical stratification of DOM molecular composition and EEM-PARAFAC components within the peat column. In particular the intermediate depth zone (~ 50 cm) was identified as a zone where maximum decomposition and turnover is taking place. Surface DOM was dominated by inputs from surface vegetation. The intermediate-depthmore » zone was an area of high organic matter reactivity and increased microbial activity with diagenetic formation of many unique compounds, among them polycyclic aromatic compounds (PAC) that contain both nitrogen and sulfur heteroatoms. These compounds have been previously observed in coal-derived compounds and were assumed to be responsible for coal's biological activity. Biological processes triggered by redox oscillations taking place at the intermediate depth zone of the peat profile at the S1 bog are assumed to be responsible for the formation of these heteroatomic PACs in this system. Alternatively these compounds could stem from black carbon and nitrogen derived from fires that have occurred at the site in the past. Surface and deep DOM exhibited more similar characteristics, compared to the intermediate-depth zone, with the deep layer exhibiting greater input of microbially degraded organic matter than the surface suggesting that the entire peat profile consists of similar parent material at different degrees of decomposition and that lateral and vertical advection of pore water from the surface to the deeper horizons is responsible for such similarities. Our findings suggest that molecular composition of DOM in peatland pore water is dynamic and is a function of ecosystem

  10. Vertical Stratification of Peat Pore Water Dissolved Organic Matter Composition in a Peat Bog in Northern Minnesota: Pore Water DOM composition in a peat bog

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

    Tfaily, Malak M.; Wilson, Rachel M.; Cooper, William T.

    Here, we characterized dissolved organic matter (DOM) composition throughout the peat column at the Marcell S1 forested bog in northern Minnesota and tested the hypothesis that redox oscillations associated with cycles of wetting and drying at the surface of the fluctuating water table correlate with increased carbon, sulfur, and nitrogen turn over. We found significant vertical stratification of DOM molecular composition and excitation-emission matrix parallel factor analysis components within the peat column. In particular, the intermediate depth zone (~ 50 cm) was identified as a zone where maximum decomposition and turnover is taking place. Surface DOM was dominated by inputsmore » from surface vegetation. The intermediate depth zone was an area of high organic matter reactivity and increased microbial activity with diagenetic formation of many unique compounds, among them polycyclic aromatic compounds that contain both nitrogen and sulfur heteroatoms. These compounds have been previously observed in coal-derived compounds and were assumed to be responsible for coal's biological activity. Biological processes triggered by redox oscillations taking place at the intermediate depth zone of the peat profile at the S1 bog are assumed to be responsible for the formation of these heteroatomic PACs in this system. Alternatively, these compounds could stem from black carbon and nitrogen derived from fires that have occurred at the site in the past. Surface and deep DOM exhibited more similar characteristics, compared to the intermediate depth zone, with the deep layer exhibiting greater input of microbially degraded organic matter than the surface suggesting that the entire peat profile consists of similar parent material at different degrees of decomposition and that lateral and vertical advection of pore water from the surface to the deeper horizons is responsible for such similarities. Lastly, our findings suggest that molecular composition of DOM in peatland pore

  11. A troglomorphic spider from Java (Araneae, Ctenidae, Amauropelma)

    PubMed Central

    Miller, Jeremy; Rahmadi, Cahyo

    2012-01-01

    Abstract A new troglomorphic spider from caves in Central Java, Indonesia, is described and placed in the ctenid genus Amauropelma Raven, Stumkat & Gray, until now containing only species from Queensland, Australia. Only juveniles and mature females of the new species are known. We give our reasons for placing the new species in Amauropelma, discuss conflicting characters, and make predictions about the morphology of the as yet undiscovered male that will test our taxonomic hypothesis. The description includes DNA barcode sequence data. PMID:22303127

  12. Variations of DOM quality in inflows of a drinking water reservoir: linking of van Krevelen diagrams with EEMF spectra by rank correlation.

    PubMed

    Herzsprung, Peter; von Tümpling, Wolf; Hertkorn, Norbert; Harir, Mourad; Büttner, Olaf; Bravidor, Jenny; Friese, Kurt; Schmitt-Kopplin, Philippe

    2012-05-15

    Elevated concentrations of dissolved organic matter (DOM) such as humic substances in raw water pose significant challenges during the processing of the commercial drinking water supplies. This is a relevant issue in Saxony, Central East Germany, and many other regions worldwide, where drinking water is produced from raw waters with noticeable presence of chromophoric DOM (CDOM), which is assumed to originate from forested watersheds in spring regions of the catchment area. For improved comprehension of DOM molecular composition, the seasonal and spatial variations of humic-like fluorescence and elemental formulas in the catchment area of the Muldenberg reservoir were recorded by excitation emission matrix fluorescence (EEMF) and ultrahigh-resolution mass spectrometry (FT-ICR-MS). The Spearman rank correlation was applied to link the EEMF intensities with exact molecular formulas and their corresponding relative mass peak abundances. Thereby, humic-like fluorescence could be allocated to the pool of oxygen-rich and relatively unsaturated components with stoichiometries similar to those of tannic acids, which are suspected to have a comparatively high disinfection byproduct formation potential associated with the chlorination of raw water. Analogous relationships were established for UV absorption at 254 nm (UV(254)) and dissolved organic carbon (DOC) and compared to the EEMF correlation.

  13. A contribution to regional stratigraphic correlations of the Afro-Brazilian depression - The Dom João Stage (Brotas Group and equivalent units - Late Jurassic) in Northeastern Brazilian sedimentary basins

    NASA Astrophysics Data System (ADS)

    Kuchle, Juliano; Scherer, Claiton Marlon dos Santos; Born, Christian Correa; Alvarenga, Renata dos Santos; Adegas, Felipe

    2011-04-01

    The Dom João Stage comprises an interval with variable thickness between 100 and 1200 m, composed of fluvial, eolian and lacustrine deposits of Late Jurassic age, based mainly on the lacustrine ostracod fauna (although the top deposits may extend into the Early Cretaceous). These deposits comprise the so-called Afro-Brazilian Depression, initially characterized as containing the Brotas Group of the Recôncavo Basin (which includes the Aliança and the Sergi Formations) and subsequently extended into the Tucano, Jatobá, Camamu, Almada, Sergipe, Alagoas and Araripe Basins in northeastern Brazil, encompassing the study area of this paper. The large occurrence area of the Dom João Stage gives rise to discussions about the depositional connectivity between the basins, and the real extension of sedimentation. In the first studies of this stratigraphic interval, the Dom João Stage was strictly associated with the rift phase, as an initial stage (decades of 1960-70), but subsequent analyses considered the Dom João as an intracratonic basin or pre-rift phase - without any relation to the active mechanics of a tectonic syn-rift phase (decades of 1980-2000). The present work developed an evolutionary stratigraphic and tectonic model, based on the characterization of depositional sequences, internal flooding surfaces, depositional systems arrangement and paleoflow directions. Several outcrops on the onshore basins were used to build composite sections of each basin, comprising facies, architectural elements, depositional systems, stratigraphic and lithostratigraphic frameworks, and paleocurrents. In addition to that, over a hundred onshore and offshore exploration wells were used (only 21 of which are showed) to map the depositional sequences and generate correlation sections. These show the characteristics and relations of the Dom João Stage in each studied basin, and they were also extended to the Gabon Basin. The results indicate that there were two main phases during

  14. Assessment of Differential Uplift Along South Java, Indonesia from Terrace Elevations Mapped with Structure from Motion Photogrammetry

    NASA Astrophysics Data System (ADS)

    Andreini, J.; Bunds, M. P.; Harris, R. A.; Yulianto, E.; Horns, D. M.; Prasetyadi, C.; Putra, P. S.

    2016-12-01

    Assessment of Differential Uplift Along South Java, Indonesia from Terrace Elevations Mapped with Structure from Motion Photogrammetry Jeremy Andreini, Michael Bunds, Ronald Harris, Eko Yulianto, Carolus Prasetyadi, Daniel Horns, Purna Putra Is differential uplift occurring on the south coast of Java? Java is on the southern edge of the Sunda plate, above the subducting Indo-Australian plate. Its south coast is 300 km north of the Java Trench and south of the volcanic arc that runs the length of Java. We are investigating relations between marine terraces and convergence, normal faulting associated with tectonically induced basin subsidence, eustatic sea level change, and variations in sediment supply from volcanic activity. Exposed bedrock along the coast includes upper Miocene basinal limestone, and localized exposure of underlying Miocene reef deposits and Oligo-miocene volcanic basement. Differential uplift in the past is implied by north-south trending horst-like ridges of Miocene reef sediment and volcanic basement that have been exhumed from greater depth than adjacent upper Miocene strata. We utilized Quaternary terrace elevations at four locations (Pangamalang, Pangandaran, Karanghawu, and Pacitan). Elevations were measured using traverses with handheld GPS units, profiles made with RTK GPS, and digital surface models (DSMs).The DSMs have 5 cm pixels and were constructed using structure-from-motion (SfM) software to process photos collected with quadcopters equipped with a 24 Mpixel Sony A5100 camera; their vertical RMS error relative to checkpoints measured on bare ground is 6 cm. SfM processing was done in the field with a specially built portable workstation. Four sets of terraces (T) with the following elevations were identified: T1 0-.5 m, T2 2 m, T3 17 m, T4 22 m. We interpret T1 to be the modern wave-cut platform, T2 to represent Holocene uplift of a Holocene terrace or possibly modern deposition, T3 to result from Marine Isotope Stage 5e. T4 occurs

  15. Higher Education and the Labour Market in the Java Region, Indonesia.

    ERIC Educational Resources Information Center

    Notodihardjo, Hardjono; Sanyal, Bikas C.

    Based on a survey of college students, graduates, and employers throughout Java, this report examines (1) reasons for pursuing higher education, channels of career information, frequency of and reasons for students changing majors, and the performance of the higher education system; (2) occupational expectations and their determinants; (3) methods…

  16. A Multi-Disciplinary Approach to Tsunami Disaster Prevention in Java, Indonesia

    NASA Astrophysics Data System (ADS)

    Horns, D. M.; Hall, S.; Harris, R. A.

    2016-12-01

    The island of Java in Indonesia is the most densely populated island on earth, and is situated within one of the most tectonically active regions on the planet. Deadly tsunamis struck Java in 1994 and 2006. We conducted an assessment of tsunami hazards on the south coast of Java using a team of geologists, public health professionals, and disaster education specialists. The social science component included tsunami awareness surveys, education in communities and schools, evacuation drills, and evaluation. We found that the evacuation routes were generally appropriate for the local hazard, and that most people were aware of the routes and knew how to use them. However, functional tsunami warning systems were lacking in most areas and knowledge of natural warning signs was incomplete. We found that while knowledge of when to evacuate improved after our educational lesson, some incorrect beliefs persisted (e.g. misconceptions about types of earthquakes able to generate tsunamis and how far inland tsunamis can reach). There was a general over-reliance on government to alert when evacuation is needed as well as reluctance on the part of local leaders to take initiative to sound tsunami alerts. Many people on earth who are at risk of tsunamis live in areas where the government lacks resources to maintain a functional tsunami warning system. The best hope for protecting those people is direct education working within the local cultural belief system. Further collaboration is needed with government agencies to design consistent and repeated messages challenging misperceptions about when to evacuate and to encourage individuals to take personal responsibility based on natural warning signs.

  17. The effects of d-lysergic acid diethylamide (LSD), 2,5-dimethoxy-4-methylamphetamine (DOM) and d-amphetamine on operant responding in control and 6-hydroxydopamine-treated rats.

    PubMed

    Commissaris, R; Lyness, W H; Cordon, J J; Moore, K E; Rech, R H

    1980-11-01

    The purpose of the present study was to determine the role of central catecholaminergic neuronal systems in the effects of LSD, DOM and d-amphetamine on fixed ratio (FR) operant responding in rats. Food-deprived male rats were trained to press a bar for food reinforcement on a FR-40 schedule. Control responding on this schedule is characterized by a rapid, constant rate of responding (approximately 100 responses/min) throughout a 40 min test session. LSD and DOM, as with other hallucinogens, produced dose-dependent periods of nonresponding or "pausing," followed by reinstatement of responding at or near the control rate. Administration of the non-hallucinogen, d-amphetamine, did not produce "pausing," but caused the response rate to slow and become erratic. In animals pretreated intraventricularly with 6-hydroxydopamine (6-OHDA; 200 micrograms/10 microliter X 2), the response to LSD and DOM was unchanged, while the response to d-amphetamine was significantly diminished. The neurotoxin significantly decreased brain catecholamines to less than 25 percent of control in al regions examined, without altering 5-HT concentrations in these same regions. These data demonstrate that the effects of LSD and DOM on FR-40 responding are quite different from those of d-amphetamine, and that this difference may be due to the extent of catecholamine involvement in the effects of these agents.

  18. Velocity Model Analysis Based on Integrated Well and Seismic Data of East Java Basin

    NASA Astrophysics Data System (ADS)

    Mubin, Fathul; Widya, Aviandy; Eka Nurcahya, Budi; Nurul Mahmudah, Erma; Purwaman, Indro; Radityo, Aryo; Shirly, Agung; Nurwani, Citra

    2018-03-01

    Time to depth conversion is an important processof seismic interpretationtoidentify hydrocarbonprospectivity. Main objectives of this research are to minimize the risk of error in geometry and time to depth conversion. Since it’s using a large amount of data and had been doing in the large scale of research areas, this research can be classified as a regional scale research. The research was focused on three horizons time interpretation: Top Kujung I, Top Ngimbang and Basement which located in the offshore and onshore areas of east Java basin. These three horizons was selected because they were assumed to be equivalent to the rock formation, which is it has always been the main objective of oil and gas exploration in the East Java Basin. As additional value, there was no previous works on velocity modeling for regional scale using geological parameters in East Java basin. Lithology and interval thickness were identified as geological factors that effected the velocity distribution in East Java Basin. Therefore, a three layer geological model was generated, which was defined by the type of lithology; carbonate (layer 1: Top Kujung I), shale (layer 2: Top Ngimbang) and Basement. A statistical method using three horizons is able to predict the velocity distribution on sparse well data in a regional scale. The average velocity range for Top Kujung I is 400 m/s - 6000 m/s, Top Ngimbang is 500 m/s - 8200 m/s and Basement is 600 m/s - 8000 m/s. Some velocity anomalies found in Madura sub-basin area, caused by geological factor which identified as thick shale deposit and high density values on shale. Result of velocity and depth modeling analysis can be used to define the volume range deterministically and to make geological models to prospect generation in details by geological concept.

  19. Models for Train Passenger Forecasting of Java and Sumatra

    NASA Astrophysics Data System (ADS)

    Sartono

    2017-04-01

    People tend to take public transportation to avoid high traffic, especially in Java. In Jakarta, the number of railway passengers is over than the capacity of the train at peak time. This is an opportunity as well as a challenge. If it is managed well then the company can get high profit. Otherwise, it may lead to disaster. This article discusses models for the train passengers, hence, finding the reasonable models to make a prediction overtimes. The Box-Jenkins method is occupied to develop a basic model. Then, this model is compared to models obtained using exponential smoothing method and regression method. The result shows that Holt-Winters model is better to predict for one-month, three-month, and six-month ahead for the passenger in Java. In addition, SARIMA(1,1,0)(2,0,0) is more accurate for nine-month and twelve-month oversee. On the other hand, for Sumatra passenger forecasting, SARIMA(1,1,1)(0,0,2) gives a better approximation for one-month ahead, and ARIMA model is best for three-month ahead prediction. The rest, Trend Seasonal and Liner Model has the least of RMSE to forecast for six-month, nine-month, and twelve-month ahead.

  20. Experimental Study of Fouling Behavior of Main Substances (BSA, HA, SA) of Dissolved Organic Matter (DOM) in Dead-end Membrane Filtration

    NASA Astrophysics Data System (ADS)

    Sun, Yongjun; Zhu, Kexin; Khan, Bushra; Du, Xinpei; Hou, Lei; Zhao, Shuang; Li, Ping; Liu, Songbai; Song, Peng; Zhang, Hong; Jiang, Shuihong; Wang, Zhan; Zha, Shenghua

    2018-01-01

    In this study, the fouling behavior of PES ultrafiltration (UF) membrane with different DOM fractions including bovine serum albumin (BSA), sodium alginate (SA) and humic acid (HA) was systematically investigated. The result showed that the fouling mechanism of HA was cake formation while that of BSA and SA was caused by both pore blocking and cake formation due to the different particle size. Moreover, membrane fouling became more severe with the increase of feed concentration and TMP and it could be accurately described by the cake-complete model. The pore blocking resistance for SA was larger than that for BSA, whereas the cake resistance followed the sequence SA>BSA>HA. This observation offered insight into the differences in fouling behavior of the various DOM components and was further used as guidance for practical application.