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.

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.

Upper crustal structure of central Java, Indonesia, from transdimensional seismic ambient noise tomography

NASA Astrophysics Data System (ADS)

Zulfakriza, Z.; Saygin, E.; Cummins, P. R.; Widiyantoro, S.; Nugraha, A. D.; Lühr, B.-G.; Bodin, T.

2014-04-01

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. To overcome these difficulties, we apply the technique of ambient noise tomography (ANT) to data collected during the Merapi Amphibious Experiment (MERAMEX), which covered central Java with a temporary deployment of over 120 seismometers during 2004 May-October. More than 5000 Rayleigh wave Green's functions were extracted by cross-correlating the noise simultaneously recorded at available station pairs. We applied a fully non-linear 2-D Bayesian probabilistic inversion technique to the retrieved traveltimes. 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 ANT. 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.

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.

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

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

PubMed

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

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

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.

Structural architecture of oceanic plateau subduction offshore Eastern Java and the potential implications for geohazards

NASA Astrophysics Data System (ADS)

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

2011-01-01

The region offshore Eastern Java represents one of the few places where the early stage of oceanic plateau subduction is occurring. We study the little investigated Roo Rise oceanic plateau on the Indian plate, subducting beneath Eurasia. The presence of the abnormal bathymetric features entering the trench has a strong effect on the evolution of the subduction system, and causes additional challenges on the assessment of geohazard risks. We present integrated results of a refraction/wide-angle reflection tomography, gravity modelling, and multichannel reflection seismic imaging using data acquired in 2006 south of Java near 113°E. The composite structural model reveals the previously unresolved deep geometry of the oceanic plateau and the subduction zone. The oceanic plateau crust is on average 15 km thick and covers an area of about 100 000 km2. Within our profile the Roo Rise crustal thickness ranges between 18 and 12 km. The upper oceanic crust shows high degree of fracturing, suggesting heavy faulting. The forearc crust has an average thickness of 14 km, with a sharp increase to 33 km towards Java, as revealed by gravity modelling. The complex geometry of the backstop suggests two possible models for the structural formation within this segment of the margin: either accumulation of the Roo Rise crustal fragments above the backstop or alternatively uplift of the backstop caused by basal accumulation of crustal fragments. The subducting plateau is affecting the stress field within the accretionary complex and the backstop edge, which favours the initiation of large, potentially tsunamogenic earthquakes such as the 1994 Mw= 7.8 tsunamogenic event.

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.

A Java API for working with PubChem datasets.

PubMed

Southern, Mark R; Griffin, Patrick R

2011-03-01

PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

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.

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/

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework

Sequence stratigraphy, structural style, and age of deformation of the Malaita accretionary prism (Solomon arc-Ontong Java Plateau convergent zone)

NASA Astrophysics Data System (ADS)

Phinney, Eric J.; Mann, Paul; Coffin, Millard F.; Shipley, Thomas H.

2004-10-01

Possibilities for the fate of oceanic plateaus at subduction zones range from complete subduction of the plateau beneath the arc to complete plateau-arc accretion and resulting collisional orogenesis. Deep penetration, multi-channel seismic reflection (MCS) data from the northern flank of the Solomon Islands reveal the sequence stratigraphy, structural style, and age of deformation of an accretionary prism formed during late Neogene (5-0 Ma) convergence between the ˜33-km-thick crust of the Ontong Java oceanic plateau and the ˜15-km-thick Solomon island arc. Correlation of MCS data with the satellite-derived, free-air gravity field defines the tectonic boundaries and internal structure of the 800-km-long, 140-km-wide accretionary prism. We name this prism the "Malaita accretionary prism" or "MAP" after Malaita, the largest and best-studied island exposure of the accretionary prism in the Solomon Islands. MCS data, gravity data, and stratigraphic correlations to islands and ODP sites on the Ontong Java Plateau (OJP) reveal that the offshore MAP is composed of folded and thrust faulted sedimentary rocks and upper crystalline crust offscraped from the Solomon the subducting Ontong Java Plateau (Pacific plate) and transferred to the Solomon arc. With the exception of an upper, sequence of Quaternary? island-derived terrigenous sediments, the deformed stratigraphy of the MAP is identical to that of the incoming Ontong Java Plateau in the North Solomon trench. We divide the MAP into four distinct, folded and thrust fault-bounded structural domains interpreted to have formed by diachronous, southeast-to-northwest, and highly oblique entry of the Ontong Java Plateau into a former trench now marked by the Kia-Kaipito-Korigole (KKK) left-lateral strike-slip fault zone along the suture between the Solomon arc and the MAP. The structural style within each of the four structural domains consists of a parallel series of three to four fault propagation folds formed by the

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.

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.

A Java API for working with PubChem datasets

PubMed Central

Southern, Mark R.; Griffin, Patrick R.

2011-01-01

Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability: http://code.google.com/p/pubchemdb Contact: southern@scripps.edu PMID:21216779

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

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

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

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.

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.

Local Knowledge About The Structure, Function And Conversion Of Landscape In The Karangwangi Village, Cianjur, West Java, Indonesia

NASA Astrophysics Data System (ADS)

Ulfa Dwi Amelia, Fatiya; Iskandar, Johan

2017-10-01

Karangwangi people is one of indigenous people in West Java who has local knowledge about their nature thoroughly. They have local tradition about landscape ecosystem arrangement that based on sakral (sacred) norm. With this rule, local people will always try to preserve the sustainability of their natural environment. However, modernization, increasing population, decreasing forest, and increasing market economic penetration, causing this rule and structure of landscape in Karangwangi village has changed. Land conversion in Karangwangi was occur because of settlement and land investment by people outside the village. These behavior changes in tradition and landscape (structure, function and conversion) in Karangwangi may impact on their daily activities, and so do the changes in daily activities can change their behavior in tradition and landscape. This research was undertaken in the Village of Karangwangi, Sub-district of Cidaun, District of Cianjur, Province of West Java, Indonesia. This paper aims to identify how indigenous people in Karangwangi understand kinds of landscape and another conversion that was happen as a result of management. The method used in this paper is qualitative with ethno ecological approach. The resulted of the study show that local people in Karangwangi Village understand how chronological of landscape structure, function and conversion.

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.

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.

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.

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.

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%.

StrBioLib: a Java library for development of custom computational structural biology applications.

PubMed

Chandonia, John-Marc

2007-08-01

StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/

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/

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.

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.

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.

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…

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.

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.

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.

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

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.

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

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.

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…

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

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)

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.

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

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.

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.

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.

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.

Community Structure Of Coral Reefs In Saebus Island, Sumenep District, East Java

NASA Astrophysics Data System (ADS)

Rizmaadi, Mada; Riter, Johannes; Fatimah, Siti; Rifaldi, Riyan; Yoga, Arditho; Ramadhan, Fikri; Ambariyanto, Ambariyanto

2018-02-01

Increasing degradation coral reefs ecosystem has created many concerns. Reduction of this damage can only be done with good and proper management of coral reef ecosystem based on existing condition. The condition of coral reef ecosystem can be determined by assessing its community structure. This study investigates community structure of coral reef ecosystems around Saebus Island, Sumenep District, East Java, by using satellite imagery analysis and field observations. Satellite imagery analysis by Lyzenga methods was used to determine the observation stations and substrate distribution. Field observations were done by using Line Intercept Transect method at 4 stations, at the depth of 3 and 10 meters. The results showed that the percentage of coral reef coverage at the depth of 3 and 10 meters were 64.36% and 59.29%, respectively, and included in fine coverage category. This study found in total 25 genera from 13 families of corals at all stations. The most common species found were Acropora, Porites, and Pocillopora, while the least common species were Favites and Montastrea. Average value of Diversity, Uniformity and Dominancy indices were 2.94, 0.8 and 0.18 which include as medium, high, and low category, respectively. These results suggest that coral reef ecosystems around Saebus Island is in a good condition.

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.

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.

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.

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.

Chemozart: a web-based 3D molecular structure editor and visualizer platform.

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user-friendly interface is composed. More than 30 packages are used to compose this application which adds enough flexibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (application programming interface). JavaScript libraries which allow creation of web pages containing interactive three-dimensional molecular structures has also been made available. The application has been released under Apache 2 License and is available from the project website https://chemozart.com.

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.

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.

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…

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).

Earthquake effect on volcano and the geological structure in central java using tomography travel time method and relocation hypocenter by grid search method

NASA Astrophysics Data System (ADS)

Suharsono; Nurdian, S. W.; Palupi, I. R.

2016-11-01

Relocating hypocenter is a way to improve the velocity model of the subsurface. One of the method is Grid Search. To perform the distribution of the velocity in subsurface by tomography method, it is used the result of relocating hypocenter to be a reference for subsurface analysis in volcanic and major structural patterns, such as in Central Java. The main data of this study is the earthquake data recorded from 1952 to 2012 with the P wave number is 9162, the number of events is 2426 were recorded by 30 stations located in the vicinity of Central Java. Grid search method has some advantages they are: it can relocate the hypocenter more accurate because this method is dividing space lattice model into blocks, and each grid block can only be occupied by one point hypocenter. Tomography technique is done by travel time data that has had relocated with inversion pseudo bending method. Grid search relocated method show that the hypocenter's depth is shallower than before and the direction is to the south, the hypocenter distribution is modeled into the subduction zone between the continent of Eurasia with the Indo-Australian with an average angle of 14 °. The tomography results show the low velocity value is contained under volcanoes with value of -8% to -10%, then the pattern of the main fault structure in Central Java can be description by the results of tomography at high velocity that is from 8% to 10% with the direction is northwest and northeast-southwest.

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.

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.

Finding Chemical Structures Corresponding to a Set of Coordinates in Chemical Descriptor Space.

PubMed

Miyao, Tomoyuki; Funatsu, Kimito

2017-08-01

When chemical structures are searched based on descriptor values, or descriptors are interpreted based on values, it is important that corresponding chemical structures actually exist. In order to consider the existence of chemical structures located in a specific region in the chemical space, we propose to search them inside training data domains (TDDs), which are dense areas of a training dataset in the chemical space. We investigated TDDs' features using diverse and local datasets, assuming that GDB11 is the chemical universe. These two analyses showed that considering TDDs gives higher chance of finding chemical structures than a random search-based method, and that novel chemical structures actually exist inside TDDs. In addition to those findings, we tested the hypothesis that chemical structures were distributed on the limited areas of chemical space. This hypothesis was confirmed by the fact that distances among chemical structures in several descriptor spaces were much shorter than those among randomly generated coordinates in the training data range. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

EPA Pesticide Factsheets

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

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.

FlaME: Flash Molecular Editor - a 2D structure input tool for the web.

PubMed

Dallakian, Pavel; Haider, Norbert

2011-02-01

So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions.

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.

Velocity-depth ambiguity and the seismic structure of large igneous provinces: a case study from the Ontong Java Plateau

NASA Astrophysics Data System (ADS)

Korenaga, Jun

2011-05-01

The seismic structure of large igneous provinces provides unique constraints on the nature of their parental mantle, allowing us to investigate past mantle dynamics from present crustal structure. To exploit this crust-mantle connection, however, it is prerequisite to quantify the uncertainty of a crustal velocity model, as it could suffer from considerable velocity-depth ambiguity. In this contribution, a practical strategy is suggested to estimate the model uncertainty by explicitly exploring the degree of velocity-depth ambiguity in the model space. In addition, wide-angle seismic data collected over the Ontong Java Plateau are revisited to provide a worked example of the new approach. My analysis indicates that the crustal structure of this gigantic plateau is difficult to reconcile with the melting of a pyrolitic mantle, pointing to the possibility of large-scale compositional heterogeneity in the convecting mantle.

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

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.

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

Extracting and connecting chemical structures from text sources using chemicalize.org.

PubMed

Southan, Christopher; Stracz, Andras

2013-04-23

Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and

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).

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

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

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.

FlaME: Flash Molecular Editor - a 2D structure input tool for the web

PubMed Central

2011-01-01

Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions. PMID:21284863

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.

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

-Solomon Islands convergent zone; and (6) compare the structural and deformational pattern observed in the Solomon Islands to ancient oceanic plateaus preserved in Precambrian and Phanerozoic orogenic belts. Our main conclusion of this study is that 80% of the crustal thickness of the Ontong Java Plateau is subducted beneath the Solomon island arc; only the uppermost basaltic and sedimentary part of the crust (˜7 km) is preserved on the overriding plate by subduction-accretion processes. This observation is consistent with the observed imbricate structural style of plateaus and seamount chains preserved in both Precambrian and Phanerozoic orogenic belts.

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.

ACToR Chemical Structure processing using Open Source ...

EPA Pesticide Factsheets

ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

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.

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.

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.…

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.

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.

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.

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

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).

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.

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.

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.

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

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

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

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).

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…

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)

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.

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.

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.

jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

PubMed Central

2011-01-01

Background The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints, only a few open source implementations are available. The aim of this work is to introduce a library for exactly defined molecular decompositions, with a strong focus on the application of these features in machine learning and data mining. It provides several options such as search depth, distance cut-offs, atom- and pharmacophore typing. Furthermore, it provides the functionality to combine, to compare, or to export the fingerprints into several formats. Results We provide a Java 1.6 library for the decomposition of chemical graphs based on the open source Chemistry Development Kit toolkit. We reimplemented popular fingerprinting algorithms such as depth-first search fingerprints, extended connectivity fingerprints, autocorrelation fingerprints (e.g. CATS2D), radial fingerprints (e.g. Molprint2D), geometrical Molprint, atom pairs, and pharmacophore fingerprints. We also implemented custom fingerprints such as the all-shortest path fingerprint that only includes the subset of shortest paths from the full set of paths of the depth-first search fingerprint. As an application of jCompoundMapper, we provide a command-line executable binary. We measured the conversion speed and number of features for each encoding and described the composition of the features in detail. The quality of the encodings was tested using the default parametrizations in combination with a support vector machine on the Sutherland QSAR data sets. Additionally, we benchmarked the fingerprint encodings on the large-scale Ames toxicity benchmark using a large-scale linear support vector machine. The results were promising and could often compete with literature results. On the large Ames benchmark, for example, we obtained an AUC ROC performance of 0.87 with a reimplementation of

Neural network based chemical structure indexing.

PubMed

Rughooputh, S D; Rughooputh, H C

2001-01-01

Searches on chemical databases are presently dominated by the text-based content of a paper which can be indexed into a keyword searchable form. Such traditional searches can prove to be very time-consuming and discouraging to the less frequent scientist. We report a simple chemical indexing based on the molecular structure alone. The method used is based on a one-to-one correspondence between the chemical structure presented as an image to a neural network and the corresponding binary output. The method is direct and less cumbersome (compared with traditional methods) and proves to be robust, elegant, and very versatile.

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

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

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.

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.

Chemical structure of interfaces

NASA Technical Reports Server (NTRS)

Grunthaner, F. J.

1985-01-01

The interfacial structure of silicon/dielectric and silicon/metal systems is particularly amenable to analysis using a combination of surface spectroscopies together with a variety of chemical structures of Si/SiO2, Si/SiO2Si3N4, Si/Si2N2O, Si/SiO2/Al, and Si/Native Oxide interfaces using high resolution (0.350 eV FWHM) X ray photoelectron spectroscopy. The general structure of these dielectric interfaces entails a monolayer chemical transition layer at the Si/dielectric boundary. Amorphous Si substrates show a wide variety of hydrogenated Si and Si(OH) sub x states that are not observed in thermal oxidation of single crystal material. Extended SiO2 layers greater than 8 A in thickness are shown to be stoichiometric SiO2, but to exhibit a wide variety of local network structures. In the nitrogen containing systems, an approach to stoichiometric oxynitride compounds with interesting impurity and electron trapping properties are seen. In native oxides, substantial topographical nonuniformity in oxide thickness and composition are found. Analysis of metal/oxide interfacial layers is accomplished by analytical removal of the Si substrate by UHV XeF2 dry etching methods.

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.

Shallow Depth Study Using Gravity & Magnetics Data in Central Java - Yogyakarta

NASA Astrophysics Data System (ADS)

Fawzy Ismullah M, Muhammad; Altin Massinai, Muhammad; Maria

2018-03-01

Gravity and magnetics measurements carried out in Karangsambung - Bayat - Wonosari track, Central Java - Yogyakarta region as much as 34 points for subsurface identification. Modeling and interpretation using both data at 3 sections. Section A lies on Karangsambung area and reach to 1900 m. Section A showed formation of 0.000001 - 0.0014 nT and 2.00 - 2.80 g/cm3 like alluvium, basalt and tuff. Section B lies on Wates - Yogyakarta area and reach to 1700 m. Section B showed formation of (-0.01) - 0.02 nT and 2.40 - 3.00 g/cm3 like andesite intrusive and Merapi volcano sediments. Section C lies on Bayat - Wonosari area and reach to 2000 m. Section C showed formation of 0.00016 - 0.0005 nT and 2.30 - 3.14 g/cm3 like limestone, tuff and diorite intrusive. Based on modeling results from 2D structure inversion method can identify the formation of sediments from volcano activity on Karangsambung - Bayat - Wonosari track, Central Java - Yogyakarta region. The method of this study shows potential application for identify the formation of volcano activity from 2D structure.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

PubMed Central

Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

2015-01-01

Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

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.

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,…

Pure JavaScript Storyline Layout Algorithm

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

This is a JavaScript library for a storyline layout algorithm. Storylines are adept at communicating complex change by encoding time on the x-axis and using the proximity of lines in the y direction to represent interaction between entities. The library in this disclosure takes as input a list of objects containing an id, time, and state. The output is a data structure that can be used to conveniently render a storyline visualization. Most importantly, the library computes the y-coordinate of the entities over time that decreases layout artifacts including crossings, wiggles, and whitespace. This is accomplished through multi-objective, multi-stage optimizationmore » problem, where the output of one stage produces input and constraints for the next stage.« less

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…

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.

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

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.

ChemCalc: a building block for tomorrow's chemical infrastructure.

PubMed

Patiny, Luc; Borel, Alain

2013-05-24

Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data manipulation functionality that students and researchers need for chemical calculations. These services return their results as JSON (JavaScript Object Notation) objects, which facilitates their use for Web applications. The ChemCalc project http://www.chemcalc.org demonstrates this approach: we present three Web services related with mass spectrometry, namely isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. We also developed a complete Web application based on these three Web services, taking advantage of modern HTML5 and JavaScript libraries (ChemDoodle and jQuery).

Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

PubMed Central

Hay, Mark E.

2012-01-01

Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized. PMID:21141035

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…

Structural and Chemical Biology of Terpenoid Cyclases

PubMed Central

2017-01-01

The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function. PMID:28841019

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.

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

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.

Automated extraction of chemical structure information from digital raster images

PubMed Central

Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

2009-01-01

Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

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

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.

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.

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.

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.

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.

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

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/.

Temporal Control over Transient Chemical Systems using Structurally Diverse Chemical Fuels.

PubMed

Chen, Jack L-Y; Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Prins, Leonard J

2017-08-25

The next generation of adaptive, intelligent chemical systems will rely on a continuous supply of energy to maintain the functional state. Such systems will require chemical methodology that provides precise control over the energy dissipation process, and thus, the lifetime of the transiently activated function. This manuscript reports on the use of structurally diverse chemical fuels to control the lifetime of two different systems under dissipative conditions: transient signal generation and the transient formation of self-assembled aggregates. The energy stored in the fuels is dissipated at different rates by an enzyme, which installs a dependence of the lifetime of the active system on the chemical structure of the fuel. In the case of transient signal generation, it is shown that different chemical fuels can be used to generate a vast range of signal profiles, allowing temporal control over two orders of magnitude. Regarding self-assembly under dissipative conditions, the ability to control the lifetime using different fuels turns out to be particularly important as stable aggregates are formed only at well-defined surfactant/fuel ratios, meaning that temporal control cannot be achieved by simply changing the fuel concentration. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Deducing chemical structure from crystallographically determined atomic coordinates

PubMed Central

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

Classification of Chemicals Based On Structured Toxicity ...

EPA Pesticide Factsheets

Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-based classifications of chemicals were performed as a model application of ToxRefDB. These endpoints will ultimately provide the anchoring toxicity information for the development of predictive models and biological signatures utilizing in vitro assay data. Utilizing query and structured data mining approaches, toxicity profiles were uniformly generated for greater than 300 chemicals. Based on observation rate, species concordance and regulatory relevance, individual and aggregated effects have been selected to classify the chemicals providing a set of predictable endpoints. ToxRefDB exhibits the utility of transforming unstructured toxicity data into structured data and, furthermore, into computable outputs, and serves as a model for applying such data to address modern toxicological problems.

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…

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.

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.

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.

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

Surface wave tomography of the Ontong Java Plateau: Seismic probing of the largest igneous province

NASA Astrophysics Data System (ADS)

Richardson, William Philip

1998-12-01

Large igneous provinces (LIP), such as the gigantic Cretaceous oceanic plateaus, the Ontong-Java, the Manihiki and the Kerguelen, are part of a globally distributed diverse suite of massive crustal features considered to be episodic representations of mantle dynamics (Coffin and Eldholm, 1994). The Ontong Java Plateau in the central western Pacific is by far the largest (and presumably thickest) of these provinces and is believed to have been emplaced rapidly in the Aptian, ˜122 Ma (Tarduno et al., 1991). From 1994 to 1996 four PASSCAL broadband seismic stations were deployed in an array north of the OJP. Analysis was conducted on vertical component broadband seismograms from events recorded on the Micronesian Seismic Experiment array between January 1994 and March 1996. The purpose of this experiment is to investigate the crustal and upper mantle structure of the Ontong Java Plateau (OJP) employing surface wave tomographic methods. Using the partitioned waveform inversion method (Nolet, 1990) and earthquakes with published Centroid Moment Tensor (Dziewonski et al., 1981) solutions, we produce waveform fits from source-to-receiver paths that primarily sample the OJP. From these waveform fits, linearized constraints on shear velocity suggest: (1) a massively thickened crust over the center of the OJP-greater than 35km over central areas of the plateau while thinning off-center; (2) a pronounced low-velocity zone down to ˜300km depth-a robust result in agreement with recent geochemical predictions (Neal et al., 1997); (3) the probability of lateral heterogeneity across the OJP. Finally, by combining many single waveform inversions (van der Lee and Nolet, 1997b) a 3-D shear velocity model can be computed for the Ontong Java Plateau and the nearby Caroline Basin. New constraints on the crustal thickness (and hence the volume extruded) are presented, thereby adding to the understanding of the overall tectonic setting and possible emplacement mechanism of the structure.

Chemical structure and dynamics: Annual report 1996

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

Colson, S.D.; McDowell, R.S.

1997-03-01

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can bemore » brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.« less

Chemical datuments as scientific enablers.

PubMed

Rzepa, Henry S

2013-01-23

This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution of scientific journals are discussed.

Chemical datuments as scientific enablers

PubMed Central

2013-01-01

This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution of scientific journals are discussed. PMID:23343381

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...

Tracing crustal contamination along the Java segment of the Sunda Arc, Indonesia

NASA Astrophysics Data System (ADS)

Jolis, E. M.; Troll, V.; Deegan, F.; Blythe, L.; Harris, C.; Freda, C.; Hilton, D.; Chadwick, J.; Van Helden, M.

2012-04-01

Arc magmas typically display chemical and petrographic characteristics indicative of crustal input. Crustal contamination can take place either in the mantle source region or as magma traverses the upper crust (e.g. [1]). While source contamination is generally considered the dominant process (e.g. [2]), late-stage crustal contamination has been recognised at volcanic arcs too (e.g. [3]). In light of this, we aim to test the extent of upper crustal versus source contamination along the Java segment of the Sunda arc, which, due its variable upper crustal structure, is an exemplary natural laboratory. We present a detailed geochemical study of 7 volcanoes along a traverse from Anak-Krakatau in the Sunda strait through Java and Bali, to characterise the impact of the overlying crust on arc magma composition. Using rock and mineral elemental geochemistry, radiogenic (Sr, Nd and Pb) and, stable (O) isotopes, we show a correlation between upper crustal composition and the degree of upper crustal contamination. We find an increase in 87Sr/86Sr and δ18O values, and a decrease in 143Nd/144Nd values from Krakatau towards Merapi, indicating substantial crustal input from the thick continental basement present. Volcanoes to the east of Merapi and the Progo-Muria fault transition zone, where the upper crust is thinner, in turn, show considerably less crustal input in their isotopic signatures, indicating a stronger influence of the mantle source. Our new data represent a systematic and high-resolution arc-wide sampling effort that allows us to distinguish the effects of the upper crust on the compositional spectrum of individual volcanic systems along the Sunda arc. [1] Davidson, J.P, Hora, J.M, Garrison, J.M & Dungan, M.A 2005. Crustal Forensics in Arc Magmas. J. Geotherm. Res. 140, 157-170; [2] Debaille, V., Doucelance, R., Weis, D., & Schiano, P. 2005. Geochim. Cosmochim. Acta, 70,723-741; [3] Gasparon, M., Hilton, D.R., & Varne, R. 1994. Earth Planet. Sci. Lett., 126, 15-22.

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.

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.

LICSS - a chemical spreadsheet in microsoft excel.

PubMed

Lawson, Kevin R; Lawson, Jonty

2012-02-02

Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out.We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. LICSS is an Excel-based chemical spreadsheet with a difference:• It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel• It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation• It is free and extensibleLICSS is open source software and we hope sufficient detail is provided here to enable developers to add their

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.

[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.

Vegetation Structure of Ebony Leaf Monkey (Trachypithecus auratus) Habitat in Kecubung Ulolanang Nature Preservation Central Java-Indonesia

NASA Astrophysics Data System (ADS)

Ervina, Rahmawati; Wasiq, Hidayat Jafron

2018-02-01

Kecubung Ulolanang Nature Preservation is ebony leaf monkey's habitats in Central Java Indonesia. Continuously degradation of their population is caused by illegal hunting and habitat degradation that made this species being vulnerable. Habitat conservation is one of important aspects to prevent them from extinction. The purpose of this research was to analyze the vegetation's structure and composition, which was potentially, becomes habitat and food source for the monkeys. Data collected using purposive sampling with line transect method of four different level of vegetation. Data analysis used Important Value Index and Diversity Index. There were 43 species of vegetation at seedling stage, 18 species at sapling stage, 8 species at poles stage and 27 species at trees stage. Species that had the highest important value index at seedling was Stenochlaena palustri , at the sapling was Gnetum gnemon, at pole was Swietenia mahagoni and at tree was Tectona grandis . Species of trees those were potentially to become habitat (food source) for ebony leaf monkey were T. grandis, Dipterocarpus gracilis, Quercus sundaica and Ficus superba. The highest diversity index was at seedling gwoth stage.

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…

Shear wave velocity model beneath CBJI station West Java, Indonesia from joint inversion of teleseismic receiver functions and surface wave dispersion

NASA Astrophysics Data System (ADS)

Simanungkalit, R. H.; Anggono, T.; Syuhada; Amran, A.; Supriyanto

2018-03-01

Earthquake signal observations around the world allow seismologists to obtain the information of internal structure of the Earth especially the Earth’s crust. In this study, we used joint inversion of receiver functions and surface wave group velocities to investigate crustal structure beneath CBJI station in West Java, Indonesia. Receiver function were calculated from earthquakes with magnitude more than 5 and at distance 30°-90°. Surface wave group velocities were calculated using frequency time analysis from earthquakes at distance of 30°- 40°. We inverted shear wave velocity model beneath the station by conducting joint inversion from receiver functions and surface wave dispersions. We suggest that the crustal thickness beneath CBJI station, West Java, Indonesia is about 35 km.

CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules.

PubMed

Aguirre-Valderrama, Alonso; Dobado, José A

2008-12-01

Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.

One dimensional P wave velocity structure of the crust beneath west Java and accurate hypocentre locations from local earthquake inversion

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

Supardiyono; Santosa, Bagus Jaya; Physics Department, Faculty of Mathematics and Natural Sciences, Sepuluh Nopember Institute of Technology, Surabaya

A one-dimensional (1-D) velocity model and station corrections for the West Java zone were computed by inverting P-wave arrival times recorded on a local seismic network of 14 stations. A total of 61 local events with a minimum of 6 P-phases, rms 0.56 s and a maximum gap of 299 Degree-Sign were selected. Comparison with previous earthquake locations shows an improvement for the relocated earthquakes. Tests were carried out to verify the robustness of inversion results in order to corroborate the conclusions drawn out from our reasearch. The obtained minimum 1-D velocity model can be used to improve routine earthquakemore » locations and represents a further step toward more detailed seismotectonic studies in this area of West Java.« less

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.

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.

Ecological wisdom of Hindu-Javanese community settlement in Cetho Hamlet, Lawu Mountains, Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Ikhsan, Fauzan Ali; Setioko, Bambang; Suprapti, Atiek

2017-12-01

Dwelling culture of Java community has a long history. In Javanese community point of view, Javanese culture is not a homogeneous entity. There is a diversity characteristic of a regional nature of Javanese culture, which is caused by differences in the natural environment on the island of Java. Dwelling Culture settled in the mountains is a variant form of Javanese culture that has its own uniqueness. This study aimed to describe the local values of the rural settlement structure of in Lawu mountains with Hindu-Javanese culture background. This study used a qualitative approach with case study strategy. The locus of research is in the Cetho hamlet on the slopes of Mount Lawu Karanganyar, Central Java. The results showed that local values in the neighborhoods of Cetho hamlet is based on the Memayu Hayuning Bawana philosophy. These concepts are abstracted into various aspects of settlements in Cetho hamlet such as aspects of dwelling house setting, water management, and ritual activities related to environmental management. Memayu Hayuning Bawana philosophy becomes a cultural space coloring the ecological action of the population of Cetho hamlet. The comprehensive motivation of ecological action ultimately leads to one final goal, namely the desire to maintain a harmonic atmosphere with the surroundings.

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.

Why relevant chemical information cannot be exchanged without disclosing structures

NASA Astrophysics Data System (ADS)

Filimonov, Dmitry; Poroikov, Vladimir

2005-09-01

Both society and industry are interested in increasing the safety of pharmaceuticals. Potentially dangerous compounds could be filtered out at early stages of R&D by computer prediction of biological activity and ADMET characteristics. Accuracy of such predictions strongly depends on the quality & quantity of information contained in a training set. Suggestion that some relevant chemical information can be added to such training sets without disclosing chemical structures was generated at the recent ACS Symposium. We presented arguments that such safety exchange of relevant chemical information is impossible. Any relevant information about chemical structures can be used for search of either a particular compound itself or its close analogues. Risk of identifying such structures is enough to prevent pharma industry from relevant chemical information exchange.

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...

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.

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.

Petroleum system of Northwest Java basin based on gravity data analysis

NASA Astrophysics Data System (ADS)

Widianto, E.

2018-01-01

Energy management in the upstream oil and gas sector becomes very important for the country’s energy security. The renewal of energy resources and reserves becomes necessary and is a must. In the oil and gas industry, gravity data is usually used only for regional surveys, but with the development of instrumentation technology and gravity software development, this method can be used for assessing oil and gas survey stages from exploration to production. This study was conducted to evaluate aspects of petroleum system and exploration play concept in the part of Northwest Java Basin, covering source rock deposition regions (source kitchen area, migration direction), development of reservoirs, structural and stratigraphic trap, based on gravity data. This study uses data from Bouguer gravity anomaly map by filtering process to produce a residual map depicting sedimentation basin configuration. The mapping generated 20 sedimentary basins in Java Island with the total hydrocarbon resources of 113 BBOE (Billion Barrel of Oil Equivalent). The petroleum system analysis was conducted in the Northwest Basin section. The final map produced illustrates the condition of petroleum system and play concept that can be used as exploration direction, expectedly reducing the risk of drilling failure.

Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

NASA Astrophysics Data System (ADS)

Campbell, Erin Roberts

The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

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.

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.

Linking Supply Chain Governance and Biosecurity in the Context of HPAI Control in Western Java: A Value Chain Perspective

PubMed Central

Indrawan, Dikky; Rich, Karl M.; van Horne, Peter; Daryanto, Arief; Hogeveen, Henk

2018-01-01

Despite extensive efforts to control the highly pathogenic avian influenza (HPAI), it remains endemic in Western Java, Indonesia. To understand the limited effectiveness of HPAI control measures, it is important to map the complex structure of the poultry sector. The governance of the poultry value chain in particular, could play a pivotal role, yet there is limited information on the different chain governance structures and their impacts on HPAI control. This article uses value chain analysis (VCA), focusing on an in-depth assessment of governance structures as well as transaction cost economics and quantitative estimates of the market power of different chain actors, to establish a theoretical framework to examine biosecurity and HPAI control in the Western Java poultry chain. During the research, semi-structured interviews were conducted with key value-chain stakeholders, and the economic performance of identified actors was estimated. Results indicated the co-existence of four different poultry value chains in West Java: the integrator chain, the semi-automated slaughterhouse chain, the controlled slaughter-point chain, and the private slaughter-point chain. The integrator chain was characterized by the highest levels of coordination and a tight, hierarchical governance. In contrast, the other three types of value chains were less coordinated. The market power of the different actors within the four value chains also differed. In more integrated chains, slaughterhouses held considerable market power, while in more informal value chains, market power was in the hands of traders. The economic effects of HPAI and biosecurity measures also varied for the identified actors in the different value chains. Implementation of biosecurity and HPAI control measures was strongly related to the governance structure of the chain, with interactions between different chains and governance structures accentuating the risk of HPAI. Our findings highlight that a proper

Linking Supply Chain Governance and Biosecurity in the Context of HPAI Control in Western Java: A Value Chain Perspective.

PubMed

Indrawan, Dikky; Rich, Karl M; van Horne, Peter; Daryanto, Arief; Hogeveen, Henk

2018-01-01

Despite extensive efforts to control the highly pathogenic avian influenza (HPAI), it remains endemic in Western Java, Indonesia. To understand the limited effectiveness of HPAI control measures, it is important to map the complex structure of the poultry sector. The governance of the poultry value chain in particular, could play a pivotal role, yet there is limited information on the different chain governance structures and their impacts on HPAI control. This article uses value chain analysis (VCA), focusing on an in-depth assessment of governance structures as well as transaction cost economics and quantitative estimates of the market power of different chain actors, to establish a theoretical framework to examine biosecurity and HPAI control in the Western Java poultry chain. During the research, semi-structured interviews were conducted with key value-chain stakeholders, and the economic performance of identified actors was estimated. Results indicated the co-existence of four different poultry value chains in West Java: the integrator chain, the semi-automated slaughterhouse chain, the controlled slaughter-point chain, and the private slaughter-point chain. The integrator chain was characterized by the highest levels of coordination and a tight, hierarchical governance. In contrast, the other three types of value chains were less coordinated. The market power of the different actors within the four value chains also differed. In more integrated chains, slaughterhouses held considerable market power, while in more informal value chains, market power was in the hands of traders. The economic effects of HPAI and biosecurity measures also varied for the identified actors in the different value chains. Implementation of biosecurity and HPAI control measures was strongly related to the governance structure of the chain, with interactions between different chains and governance structures accentuating the risk of HPAI. Our findings highlight that a proper

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…

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.

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.

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

P and S velocity structure of the crust and the upper mantle beneath central Java from local tomography inversion

NASA Astrophysics Data System (ADS)

Koulakov, I.; Bohm, M.; Asch, G.; Lühr, B.-G.; Manzanares, A.; Brotopuspito, K. S.; Fauzi, Pak; Purbawinata, M. A.; Puspito, N. T.; Ratdomopurbo, A.; Kopp, H.; Rabbel, W.; Shevkunova, E.

2007-08-01

Here we present the results of local source tomographic inversion beneath central Java. The data set was collected by a temporary seismic network. More than 100 stations were operated for almost half a year. About 13,000 P and S arrival times from 292 events were used to obtain three-dimensional (3-D) Vp, Vs, and Vp/Vs models of the crust and the mantle wedge beneath central Java. Source location and determination of the 3-D velocity models were performed simultaneously based on a new iterative tomographic algorithm, LOTOS-06. Final event locations clearly image the shape of the subduction zone beneath central Java. The dipping angle of the slab increases gradually from almost horizontal to about 70°. A double seismic zone is observed in the slab between 80 and 150 km depth. The most striking feature of the resulting P and S models is a pronounced low-velocity anomaly in the crust, just north of the volcanic arc (Merapi-Lawu anomaly (MLA)). An algorithm for estimation of the amplitude value, which is presented in the paper, shows that the difference between the fore arc and MLA velocities at a depth of 10 km reaches 30% and 36% in P and S models, respectively. The value of the Vp/Vs ratio inside the MLA is more than 1.9. This shows a probable high content of fluids and partial melts within the crust. In the upper mantle we observe an inclined low-velocity anomaly which links the cluster of seismicity at 100 km depth with MLA. This anomaly might reflect ascending paths of fluids released from the slab. The reliability of all these patterns was tested thoroughly.

Informing rubella vaccination strategies in East Java, Indonesia through transmission modelling.

PubMed

Wu, Yue; Wood, James; Khandaker, Gulam; Waddington, Claire; Snelling, Thomas

2016-11-04

An estimated 110,000 babies are born with congenital rubella syndrome (CRS) worldwide annually; a significant proportion of cases occur in Southeast Asia. Rubella vaccine programs have led to successful control of rubella and CRS, and even the elimination of disease in many countries. However, if vaccination is poorly implemented it might increase the number of women reaching childbearing age who remain susceptible to rubella and thereby paradoxically increase CRS. We used an age-structured transmission model to compare seven alternative vaccine strategies for their impact on reducing CRS disease burden in East Java, a setting which is yet to implement a rubella vaccine program. We also investigated the robustness of model predictions to variation in vaccine coverage and other key epidemiological factors. Without rubella vaccination, approximately 700 babies are estimated to be born with CRS in East Java every year at an incidence of 0.77 per 1000live births. This incidence could be reduced to 0.0045 per 1000 live births associated with 99.9% annual reduction in rubella infections after 20 years if the existing two doses of measles vaccine are substituted with two doses of measles plus rubella combination vaccine with the same coverage (87.8% of 9-month-old infants and 80% of 6-year-old children). By comparison a single dose of rubella vaccine will take longer to reduce the burden of rubella and CRS and will be less robust to lower vaccine coverage. While the findings of this study should be informative for settings similar to East Java, the conclusions are dependent on vaccine coverage which would need consideration before applying to all of Indonesia and elsewhere in Asia. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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

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.

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

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.

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.

Using a Java Dynamic Tree to manage the terminology in a suite of medical applications.

PubMed

Yang, K; Evens, M W; Trace, D A

2008-01-01

Now that the National Library of Medicine has made SNOMED-CT widely available, we are trying to manage the terminology of a whole suite of medical applications and map our terminology into that in SNOMED. This paper describes the design and implementation of the Java Dynamic Tree that provides structure to our medical terminology and explains how it functions as the core of our system. The tree was designed to reflect the stages in a patient interview, so it contains components for identifying the patient and the provider, a large set of chief complaints, review of systems, physical examination, several history modules, medications, laboratory tests, imaging, and special procedures. The tree is mirrored in a commercial DBMS, which also stores multi-encounter patient data, disorder patterns for our Bayesian diagnostic system, and the data and rules for other expert systems. The DBMS facilitates the import and export of large terminology files. Our Java Dynamic Tree allows the health care provider to view the entire terminology along with the structure that supports it, as well as the mechanism for the generation of progress notes and other documents, in terms of a single hierarchical structure. Changes in terminology can be propagated through the system under the control of the expert. The import/ export facility has been a major help by replacing our original terminology by the terminology in SNOMED-CT.

The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.

PubMed

Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

2015-01-01

There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set

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.

Annual Report 1998: Chemical Structure and Dynamics

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

SD Colson; RS McDowell

1999-05-10

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generatedmore » can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).« less

Chemical structure of the Chromophoric Dissolved Organic Matter (CDOM) fluorescent matter.

NASA Astrophysics Data System (ADS)

Blough, N. V.; Del Vecchio, R.; Cartisano, C. M.; Bianca, M.

2017-12-01

The structure(s), distribution and dynamics of CDOM have been investigated over the last several decades largely through optical spectroscopy (including both absorption and fluorescence) due to the fairly inexpensive instrumentation and the easy-to-gather data (over thousands published papers from 1990-2016). Yet, the chemical structure(s) of the light absorbing and emitting species or constituents within CDOM has only recently being proposed and tested through chemical manipulation of selected functional groups (such as carbonyl and carboxylic/phenolic containing molecules) naturally occurring within the organic matter pool. Similarly, fitting models (among which the PArallel FACtor analysis, PARAFAC) have been developed to better understand the nature of a subset of DOM, the CDOM fluorescent matter (FDOM). Fluorescence spectroscopy coupled with chemical tests and PARAFAC analyses could potentially provide valuable insights on CDOM sources and chemical nature of the FDOM pool. However, despite that applications (and publications) of PARAFAC model to FDOM have grown exponentially since its first application/publication (2003), a large fraction of such publications has misinterpreted the chemical meaning of the delivered PARAFAC `components' leading to more confusion than clarification on the nature, distribution and dynamics of the FDOM pool. In this context, we employed chemical manipulation of selected functional groups to gain further insights on the chemical structure of the FDOM and we tested to what extent the PARAFAC `components' represent true fluorophores through a controlled chemical approach with the ultimate goal to provide insights on the chemical nature of such `components' (as well as on the chemical nature of the FDOM) along with the advantages and limitations of the PARAFAC application.

Organic chemical composition of mud from the LUSI mud volcano, Sidoarjo, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Rosenbauer, R. J.; Campbell, P.; Lam, A.

2009-12-01

Sidoarjo, East Java, Indonesia is the site of LUSI, a terrestrial mud volcano that has been erupting since May 29, 2006. In response to a U.S. Department of State request, the U.S. Geological Survey has been assisting the Indonesian Government to describe the geological and geochemical aspects and potential health risk of the mud eruption. We report here on the organic chemical composition of the mud. Organic chemical analyses were carried out by gas chromatography/mass spectroscopy following organic extraction by microwave-assisted solvent extraction and compound fractionation by adsorption chromatography. There is a petroliferous component in the mud that is fresh, immature, and nonbiodegraded. There is a complete suite of n-alkanes with a bell-shaped pattern typical of fresh petroleum with a Cmax around C20. The alkane content ranges from 0.12 to 1.01 mg/kg dry mud. The presence of certain hopanes (i.e. 17 α,21β(H)-30-norhopane and 17α,21β(H)-hopane) is also indicative of the presence of oil. The proportions of other biomarker compounds (pristane/phytane = 2.4) and the dominance of the C27 sterane (5α(H),14α(H),17α(H)-chlolestane) suggest that oil formed under oxic conditions and has a likely coastal marine or terrigenous source. The presence of oleanane indicates a Cretaceous or younger age for the petrogenic material. These geochemical parameters are consistent with Indonesian oil derived from Tertiary marlstone source rocks that contained kerogen deposited under oxic conditions, probably the upper Miocene Klasafet Formation. Polycyclic aromatic hydrocarbons (PAHs) are present and range in content from 0.1 to 2.2 mg/kg dry mud. The low molecular weight (LMW) PAHs, in particular, naphthalene and methyl-naphthalene are dominant except for perylene which is ubiquitous in the environment. The presence of both parent and higher homologue PAHs indicate a petrogenic rather than combustion source. PAHs are known carcinogens but toxicity data in sediments are

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…

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

PubMed

Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

2014-07-03

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

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.

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.

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.

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

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.

FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

PubMed

Erhard, Florian; Friedel, Caroline C; Zimmer, Ralf

2008-08-29

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary. In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment. FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

PubMed

Karthikeyan, Muthukumarasamy; Vyas, Renu

2016-01-01

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

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.

LICSS - a chemical spreadsheet in microsoft excel

PubMed Central

2012-01-01

Background Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visualisable chemical structures and data searchable by chemical as well as textual queries. Many such chemical spreadsheet tools are available, some operating in the familiar Microsoft Excel environment. However, within this group, the performance of Excel is often compromised, particularly in terms of the number of compounds which can usefully be stored on a sheet. Summary LICSS is a lightweight chemical spreadsheet within Microsoft Excel for Windows. LICSS stores structures solely as Smiles strings. Chemical operations are carried out by calling Java code modules which use the CDK, JChemPaint and OPSIN libraries to provide cheminformatics functionality. Compounds in sheets or charts may be visualised (individually or en masse), and sheets may be searched by substructure or similarity. All the molecular descriptors available in CDK may be calculated for compounds (in batch or on-the-fly), and various cheminformatic operations such as fingerprint calculation, Sammon mapping, clustering and R group table creation may be carried out. We detail here the features of LICSS and how they are implemented. We also explain the design criteria, particularly in terms of potential corporate use, which led to this particular implementation. Conclusions LICSS is an Excel-based chemical spreadsheet with a difference: • It can usefully be used on sheets containing hundreds of thousands of compounds; it doesn't compromise the normal performance of Microsoft Excel • It is designed to be installed and run in environments in which users do not have admin privileges; installation involves merely file copying, and sharing of LICSS sheets invokes automatic installation • It is free and extensible LICSS is open source software and we hope sufficient detail is provided

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.

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.

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

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.

Chemical compositions, methods of making the chemical compositions, and structures made from the chemical compositions

DOEpatents

Yang, Lei; Cheng, Zhe; Liu, Ze; Liu, Meilin

2015-01-13

Embodiments of the present disclosure include chemical compositions, structures, anodes, cathodes, electrolytes for solid oxide fuel cells, solid oxide fuel cells, fuel cells, fuel cell membranes, separation membranes, catalytic membranes, sensors, coatings for electrolytes, electrodes, membranes, and catalysts, and the like, are disclosed.

PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

EPA Science Inventory

Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

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.

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.

Applications of the Cambridge Structural Database in chemical education.

PubMed

Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

2010-10-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

Soil gas anomalies along the Watukosek fault system, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Sciarra, A.; Ruggiero, L.; Bigi, S.; Mazzini, A.

2017-12-01

Two soil gas surveys were carried out in the Sidoarjo district (East Java, Indonesia) to investigate the gas leaking properties along fractured zones that coincide with a strike-slip system in NE Java, the Watukosek Fault System. This structure has been the focus of attention since the beginning of the spectacular Lusi mud eruption on the 29th May 2006. This fault system appear to be a sinistral strike-slip system that originates from the Arjuno-Welirang volcanic complex, intersects the active Lusi eruption site displaying a system of antithetic faults, and extends towards the NE of Java where mud volcanic structures reside. In the Lusi region we completed two geochemical surveys (222Rn and 220Rn activity, CO2 and CH4 flux and concentration) along four profiles crossing the Watukosek fault system. In May 2015 two profiles ( 1.2 km long) were performed inside the 7 km2 embankment area framing the erupted mud breccia zone and across regions characterized by intense fracturing and surface deformation. In April 2017 two additional profiles ( 4 km long) were carried out in the northern and southern part outside the Lusi embankment mud eruption area, intersecting the direction of main Watukosek fault system. All the profiles highlight that the fractured zones have the highest 222Rn activity, CO2 and CH4 flux and concentration values. The relationship existing among the measured parameters suggest that the Watukosek fault system acts as a preferential pathway for active rise of deep fluids. In addition the longer profiles outside the embankment show very high average values of CO2 (5 - 8 %,v/v) and 222Rn (17 - 11.5 kBq/m3), while soil gas collected along the profiles inside the Lusi mud eruption are CH4-dominant (up to 4.5%,v/v).This suggests that inside the embankment area (i.e. covered by tens of meters thick deposits of erupted mud breccia) the seepage is overall methane-dominated. This is likely the result of microbial reactions ongoing in the organic-rich sediments

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.

Magnetic properties of fishes from rivers near Semarang, Central Java

NASA Astrophysics Data System (ADS)

Khumaedi; Nurbaiti, U.; Setyaningsi, N. E.

2018-03-01

Magnetic properties, in the form of magnetic susceptibility (χ) and frequency-dependent susceptibility (χ fd) were measured on scores of samples made of fishes from river nearby Semarang, Central Java. Semarang is one of the major cities in Indonesia, where the river systems are very likely to be contaminated by anthropogenic activities. The objective of this study is to identify the presence of heavy metals in the fishes that will determine the suitability of these fishes for healthy food. The results show that magnetic susceptibility varies from -0.3 to 13.8 × 10-8 m3/kg, while the frequency-dependent susceptibility is less than 3% indicating the predominance of ferromagnetic minerals. Quantitative chemical analyses on four samples show consistently high concentration of Ca, while Fe, Hg, Cu, Pb, Cd, and Ni present a few in some of the samples. This finding shows that the fishes are suitable for the ongoing research on environmental magnetism.

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…

[Construction of chemical information database based on optical structure recognition technique].

PubMed

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research

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

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

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

Earthquake disaster mitigation of Lembang Fault West Java with electromagnetic method

NASA Astrophysics Data System (ADS)

Widodo

2015-04-01

The Lembang fault is located around eight kilometers from Bandung City, West Java, Indonesia. The existence of this fault runs through densely populated settlement and tourism area. It is an active fault structure with increasing seismic activity where the 28 August 2011 earthquake occurred. The seismic response at the site is strongly influenced by local geological conditions. The ambient noise measurements from the western part of this fault give strong implication for a complex 3-D tectonic setting. Hence, near surface Electromagnetic (EM) measurements are carried out to understand the location of the local active fault of the research area. Hence, near surface EM measurements are carried out to understand the location of the local active fault and the top of the basement structure of the research area. The Transientelectromagnetic (TEM) measurements are carried out along three profiles, which include 35 TEM soundings. The results indicate that TEM data give detailed conductivity distribution of fault structure in the study area.

Earthquake disaster mitigation of Lembang Fault West Java with electromagnetic method

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

Widodo, E-mail: widodo@gf.itb.ac.id

The Lembang fault is located around eight kilometers from Bandung City, West Java, Indonesia. The existence of this fault runs through densely populated settlement and tourism area. It is an active fault structure with increasing seismic activity where the 28 August 2011 earthquake occurred. The seismic response at the site is strongly influenced by local geological conditions. The ambient noise measurements from the western part of this fault give strong implication for a complex 3-D tectonic setting. Hence, near surface Electromagnetic (EM) measurements are carried out to understand the location of the local active fault of the research area. Hence,more » near surface EM measurements are carried out to understand the location of the local active fault and the top of the basement structure of the research area. The Transientelectromagnetic (TEM) measurements are carried out along three profiles, which include 35 TEM soundings. The results indicate that TEM data give detailed conductivity distribution of fault structure in the study area.« less

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.

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.

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…

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.

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.

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.

PubMed

Weinbrand, Lina; Avihoo, Assaf; Barash, Danny

2013-11-15

In RNA design problems, it is plausible to assume that the user would be interested in preserving a particular RNA secondary structure motif, or fragment, for biological reasons. The preservation could be in structure or sequence, or both. Thus, the inverse RNA folding problem could benefit from considering fragment constraints. We have developed a new interactive Java application called RNA fragment-based inverse that allows users to insert an RNA secondary structure in dot-bracket notation. It then performs sequence design that conforms to the shape of the input secondary structure, the specified thermodynamic stability, the specified mutational robustness and the user-selected fragment after shape decomposition. In this shape-based design approach, specific RNA structural motifs with known biological functions are strictly enforced, while others can possess more flexibility in their structure in favor of preserving physical attributes and additional constraints. RNAfbinv is freely available for download on the web at http://www.cs.bgu.ac.il/~RNAexinv/RNAfbinv. The site contains a help file with an explanation regarding the exact use.

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…

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)

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.

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.

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.

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology

PubMed Central

Galdeano, Carles; Ciulli, Alessio

2017-01-01

Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity. PMID:27193077

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.

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.

Characterization of iron-phosphate-silicate chemical garden structures.

PubMed

Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

2012-02-28

Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life. © 2011 American Chemical Society

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…

TrackEtching - A Java based code for etched track profile calculations in SSNTDs

NASA Astrophysics Data System (ADS)

Muraleedhara Varier, K.; Sankar, V.; Gangadathan, M. P.

2017-09-01

A java code incorporating a user friendly GUI has been developed to calculate the parameters of chemically etched track profiles of ion-irradiated solid state nuclear track detectors. Huygen's construction of wavefronts based on secondary wavelets has been used to numerically calculate the etched track profile as a function of the etching time. Provision for normal incidence and oblique incidence on the detector surface has been incorporated. Results in typical cases are presented and compared with experimental data. Different expressions for the variation of track etch rate as a function of the ion energy have been utilized. The best set of values of the parameters in the expressions can be obtained by comparing with available experimental data. Critical angle for track development can also be calculated using the present code.

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.

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.

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.

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

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…

DSSR-enhanced visualization of nucleic acid structures in Jmol.

PubMed

Hanson, Robert M; Lu, Xiang-Jun

2017-07-03

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

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.

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.

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.

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.

Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

EPA Science Inventory

Background: The U.S. EPA ToxCastTM program is screening thousands of environmental chemicals for bioactivity using hundreds of high-throughput in vitro assays to build predictive models of toxicity. We represented chemicals based on bioactivity and chemical structure descriptors ...

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.

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

Effect of an Educational Intervention Related to Health and Nutrition on Pregnant Women in the Villages of Central Java Province, Indonesia

ERIC Educational Resources Information Center

Wijaya-Erhardt, Maria; Muslimatun, Siti; Erhardt, Juergen G.

2014-01-01

Objective: To assess the effects of a health and nutrition educational intervention on maternal knowledge, attitudes and practices. Design: Pre- and post-test design using structured interviews of pregnant women. Setting: Thirty-nine villages in Central Java Province, Indonesia. Method: Pregnant women (N = 252) at 12-20 weeks of gestation were…

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.

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.

Applications of the Cambridge Structural Database in chemical education1

PubMed Central

Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

2010-01-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

Rayleigh-wave tomography of the Ontong-Java Plateau

NASA Astrophysics Data System (ADS)

Richardson, W. Philip; Okal, Emile A.; Van der Lee, Suzan

2000-02-01

The deep structure of the Ontong-Java Plateau (OJP) in the westcentral Pacific is investigated through a 2-year deployment of four PASSCAL seismic stations used in a passive tomographic experiment. Single-path inversions of 230 Rayleigh waveforms from 140 earthquakes mainly located in the Solomon Trench confirm the presence of an extremely thick crust, with an average depth to the Mohorovičić discontinuity of 33 km. The thickest crusts (38 km) are found in the southcentral part of the plateau, around 2°S, 157°E. Lesser values remaining much thicker than average oceanic crust (15-26 km) are found on either side of the main structure, suggesting that the OJP spills over into the Lyra Basin to the west. Such thick crustal structures are consistent with formation of the plateau at the Pacific-Phoenix ridge at 121 Ma, while its easternmost part may have formed later (90 Ma) on more mature lithosphere. Single-path inversions also reveal a strongly developed low-velocity zone at asthenospheric depths in the mantle. A three-dimensional tomographic inversion resolves a low-velocity root of the OJP extending as deep as 300 km, with shear velocity deficiencies of ˜5%, suggesting the presence of a keel, dragged along with the plateau as the latter moves as part of the drift of the Pacific plate over the mantle.

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.

MICROBIAL TRANSFORMATION RATE CONSTANTS OF STRUCTURALLY DIVERSE MAN-MADE CHEMICALS

EPA Science Inventory

To assist in estimating microbially mediated transformation rates of man-made chemicals from their chemical structures, all second order rate constants that have been measured under conditions that make the values comparable have been extracted from the literature and combined wi...

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

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.

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.

Seismic imaging of a mid-lithospheric discontinuity beneath Ontong Java Plateau

NASA Astrophysics Data System (ADS)

Tharimena, Saikiran; Rychert, Catherine A.; Harmon, Nicholas

2016-09-01

Ontong Java Plateau (OJP) is a huge, completely submerged volcanic edifice that is hypothesized to have formed during large plume melting events ∼90 and 120 My ago. It is currently resisting subduction into the North Solomon trench. The size and buoyancy of the plateau along with its history of plume melting and current interaction with a subduction zone are all similar to the characteristics and hypothesized mechanisms of continent formation. However, the plateau is remote, and enigmatic, and its proto-continent potential is debated. We use SS precursors to image seismic discontinuity structure beneath Ontong Java Plateau. We image a velocity increase with depth at 28 ± 4 km consistent with the Moho. In addition, we image velocity decreases at 80 ± 5 km and 282 ± 7 km depth. Discontinuities at 60-100 km depth are frequently observed both beneath the oceans and the continents. However, the discontinuity at 282 km is anomalous in comparison to surrounding oceanic regions; in the context of previous results it may suggest a thick viscous root beneath OJP. If such a root exists, then the discontinuity at 80 km bears some similarity to the mid-lithospheric discontinuities (MLDs) observed beneath continents. One possibility is that plume melting events, similar to that which formed OJP, may cause discontinuities in the MLD depth range. Plume-plate interaction could be a mechanism for MLD formation in some continents in the Archean prior to the onset of subduction.

Resolving the Chemically Discrete Structure of Synthetic Borophene Polymorphs.

PubMed

Campbell, Gavin P; Mannix, Andrew J; Emery, Jonathan D; Lee, Tien-Lin; Guisinger, Nathan P; Hersam, Mark C; Bedzyk, Michael J

2018-05-09

Atomically thin two-dimensional (2D) materials exhibit superlative properties dictated by their intralayer atomic structure, which is typically derived from a limited number of thermodynamically stable bulk layered crystals (e.g., graphene from graphite). The growth of entirely synthetic 2D crystals, those with no corresponding bulk allotrope, would circumvent this dependence upon bulk thermodynamics and substantially expand the phase space available for structure-property engineering of 2D materials. However, it remains unclear if synthetic 2D materials can exist as structurally and chemically distinct layers anchored by van der Waals (vdW) forces, as opposed to strongly bound adlayers. Here, we show that atomically thin sheets of boron (i.e., borophene) grown on the Ag(111) surface exhibit a vdW-like structure without a corresponding bulk allotrope. Using X-ray standing wave-excited X-ray photoelectron spectroscopy, the positions of boron in multiple chemical states are resolved with sub-angström spatial resolution, revealing that the borophene forms a single planar layer that is 2.4 Å above the unreconstructed Ag surface. Moreover, our results reveal that multiple borophene phases exhibit these characteristics, denoting a unique form of polymorphism consistent with recent predictions. This observation of synthetic borophene as chemically discrete from the growth substrate suggests that it is possible to engineer a much wider variety of 2D materials than those accessible through bulk layered crystal structures.

Use of chemical-mechanical polishing for fabricating photonic bandgap structures

DOEpatents

Fleming, James G.; Lin, Shawn-Yu; Hetherington, Dale L.; Smith, Bradley K.

1999-01-01

A method is disclosed for fabricating a two- or three-dimensional photonic bandgap structure (also termed a photonic crystal, photonic lattice, or photonic dielectric structure). The method uses microelectronic integrated circuit (IC) processes to fabricate the photonic bandgap structure directly upon a silicon substrate. One or more layers of arrayed elements used to form the structure are deposited and patterned, with chemical-mechanical polishing being used to planarize each layer for uniformity and a precise vertical tolerancing of the layer. The use of chemical-mechanical planarization allows the photonic bandgap structure to be formed over a large area with a layer uniformity of about two-percent. Air-gap photonic bandgap structures can also be formed by removing a spacer material separating the arrayed elements by selective etching. The method is useful for fabricating photonic bandgap structures including Fabry-Perot resonators and optical filters for use at wavelengths in the range of about 0.2-20 .mu.m.

GREENER CHEMICAL PROCESS DESIGN ALTERNATIVES ARE REVEALED USING THE WASTE REDUCTION DECISION SUPPORT SYSTEM (WAR DSS)

EPA Science Inventory

The Waste Reduction Decision Support System (WAR DSS) is a Java-based software product providing comprehensive modeling of potential adverse environmental impacts (PEI) predicted to result from newly designed or redesigned chemical manufacturing processes. The purpose of this so...

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

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

Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

PubMed

Yabuzaki, Junko

2017-01-01

To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system 'Search similar carotenoids' using our original chemical fingerprint 'Carotenoid DB Chemical Fingerprints'. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool 'Search similar profiled organisms'. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. : http://carotenoiddb.jp. © The Author(s) 2017. Published by Oxford University Press.

Carotenoids Database: structures, chemical fingerprints and distribution among organisms

PubMed Central

2017-01-01

Abstract To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system ‘Search similar carotenoids’ using our original chemical fingerprint ‘Carotenoid DB Chemical Fingerprints’. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool ‘Search similar profiled organisms’. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. Database URL: http://carotenoiddb.jp PMID:28365725

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.

Alteration of submarine basaltic glass from the Ontong Java Plateau: A STXM and TEM study

NASA Astrophysics Data System (ADS)

Benzerara, K.; Menguy, N.; Banerjee, N. R.; Tyliszczak, Tolek; Brown, G. E.; Guyot, F.

2007-08-01

Frequent observations of tubular to vermicular microchannels in altered basalt glass have led to increasing appreciation of a possible significant role of microbes in the low-temperature alteration of seafloor basalt. We have examined such microchannel alteration features at the nanoscale in basalt glass shards from the Ontong Java Plateau using a combination of focused ion beam milling, transmission electron microscopy and scanning transmission X-ray microscopy. Three types of materials were found in ultrathin cross-sections cut through the microchannels by FIB milling: fresh basalt glass, amorphous Si-rich rims surrounding the microchannels, and palagonite within the microchannels. X-ray absorption spectroscopy at the C K-edge and Fe L 2,3-edges showed the presence of organic carbon in association with carbonates within the microchannels and partial oxidation of iron in palagonite compared with basalt glass. Although these observations alone cannot discriminate between a biotic or abiotic origin for the microchannels, they provide new information on their mineralogical and chemical composition and thus better constrain the physical and chemical conditions prevailing during the alteration process.

The Influence of Chemical Structure on the Strength of Rubber.

DTIC Science & Technology

1986-04-01

sticky, as if covered with an oily or tarry film. The debris from carbon-black-filled natural rubber vulcanizates is even more highly degraded , so...RD-RI66 355 THE INFLUENCE OF CHEMICAL STRUCTURE ON THE STRENGTH OF 1 1) RS 5355 RUBBER (U) KRON UNJY OH INST OF POLYMER SCIENCE UNCLSSIFEIDA N GENT...85-K-0222 .- Project NR 092-555 UTechnical Report No. 4 THE INFLUENCE OF CHEMICAL STRUCTURE ON THE * 4: STRENGTH OF RUBBER by S 2LECTE by A P R 0 9 I

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.

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.

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

Accretionary nature of the crust of Central and East Java (Indonesia) revealed by local earthquake travel-time tomography

NASA Astrophysics Data System (ADS)

Haberland, Christian; Bohm, Mirjam; Asch, Günter

2014-12-01

Reassessment of travel time data from an exceptionally dense, amphibious, temporary seismic network on- and offshore Central and Eastern Java (MERAMEX) confirms the accretionary nature of the crust in this segment of the Sunda subduction zone (109.5-111.5E). Traveltime data of P- and S-waves of 244 local earthquakes were tomographically inverted, following a staggered inversion approach. The resolution of the inversion was inspected by utilizing synthetic recovery tests and analyzing the model resolution matrix. The resulting images show a highly asymmetrical crustal structure. The images can be interpreted to show a continental fragment of presumably Gondwana origin in the coastal area (east of 110E), which has been accreted to the Sundaland margin. An interlaced anomaly of high seismic velocities indicating mafic material can be interpreted to be the mantle part of the continental fragment, or part of obducted oceanic lithosphere. Lower than average crustal velocities of the Java crust are likely to reflect ophiolitic and metamorphic rocks of a subduction melange.

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.

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.

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

PubMed

Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

2016-07-01

Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY

EPA Science Inventory

Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity

Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

Use of 13Cα Chemical-Shifts in Protein Structure Determination

PubMed Central

Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

2008-01-01

A physics-based method, aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts, is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid all-α-helical protein, namely the B. Subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank. PMID:17516673

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.

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).

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…

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.

Visualization of protein sequence features using JavaScript and SVG with pViz.js.

PubMed

Mukhyala, Kiran; Masselot, Alexandre

2014-12-01

pViz.js is a visualization library for displaying protein sequence features in a Web browser. By simply providing a sequence and the locations of its features, this lightweight, yet versatile, JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the Web is a common need in Bioinformatics. Although many Web sites have developed viewers to display these features, their implementations are usually focused on data from a specific source or use case. Some of these viewers can be adapted to fit other use cases but are not designed to be reusable. pViz makes it easy to display features as boxes aligned to a protein sequence with zooming functionality but also includes predefined renderings for secondary structure and post-translational modifications. The library is designed to further customize this view. We demonstrate such applications of pViz using two examples: a proteomic data visualization tool with an embedded viewer for displaying features on protein structure, and a tool to visualize the results of the variant_effect_predictor tool from Ensembl. pViz.js is a JavaScript library, available on github at https://github.com/Genentech/pviz. This site includes examples and functional applications, installation instructions and usage documentation. A Readme file, which explains how to use pViz with examples, is available as Supplementary Material A. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Priority setting in HIV/AIDS control in West Java Indonesia: an evaluation based on the accountability for reasonableness framework.

PubMed

Tromp, Noor; Prawiranegara, Rozar; Subhan Riparev, Harris; Siregar, Adiatma; Sunjaya, Deni; Baltussen, Rob

2015-04-01

Indonesia has insufficient resources to adequately respond to the HIV/AIDS epidemic, and thus faces a great challenge in prioritizing interventions. In many countries, such priority setting processes are typically ad hoc and not transparent leading to unfair decisions. Here, we evaluated the priority setting process in HIV/AIDS control in West Java province against the four conditions of the accountability for reasonableness (A4R) framework: relevance, publicity, appeals and revision, and enforcement. We reviewed government documents and conducted semi-structured qualitative interviews based on the A4R framework with 22 participants of the 5-year HIV/AIDS strategy development for 2008-13 (West Java province) and 2007-11 (Bandung). We found that criteria for priority setting were used implicitly and that the strategies included a wide range of programmes. Many stakeholders were involved in the process but their contribution could be improved and particularly the public and people living with HIV/AIDS could be better engaged. The use of appeal and publicity mechanisms could be more transparent and formally stated. Public regulations are not yet installed to ensure fair priority setting. To increase fairness in HIV/AIDS priority setting, West Java should make improvements on all four conditions of the A4R framework. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine © The Author 2014; all rights reserved.

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…

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.

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.

The Fragmented Manihiki Plateau - Key Region for Understanding the Break-up of the "Super" Large Igneous Province Ontong Java Nui

NASA Astrophysics Data System (ADS)

Hochmuth, K.; Gohl, K.; Uenzelmann-Neben, G.; Werner, R.

2014-12-01

The Manihiki Plateau of the western Pacific is one of the world - wide greatest Large Igneous Province (LIP) on oceanic crust. It is assumed that the Manihiki Plateau was emplaced as the centerpiece of the "Super-LIP" Ontong Java Nui by multiple volcanic phases during the Cretaceous Magnetic Quiet Period. The subsequent break-up of Ontong Java Nui led to fragmentation of the Manihiki Plateau into three sub-plateaus, which all exhibit individual relicts of the "Super-LIP" break-up. We examine two deep crustal seismic refraction/wide-angle reflection profiles crossing the two largest sub-plateaus of the Manihiki Plateau, the Western Plateaus and the High Plateau. Modeling of P- and S-wave velocities reveals surprising differences in the crustal structure between the two sub-plateaus. Whereas the High Plateau shows a constant crustal thickness of 20 km, relicts of multiple volcanic phases and break-up features at its margins, the model of the Western Plateaus reveals a crustal thickness decreasing from 17 km to only 9 km. There is only little evidence of secondary phases of volcanic activity. The main upper crustal structure on the Western Plateaus consists of fault systems and sedimentary basins. We infer that the High Plateau experienced phases of strong secondary volcanism, and that tectonic deformation was limited to its edges. The Western Plateaus, on the contrary, were deformed by crustal stretching and underwent only little to no secondary volcanism. This indicates that the two main sub-plateaus of the Manihiki Plateau experienced a different geological history and have played their individual parts in the break-up history of Ontong Java Nui.

The water quality and Cultivant enrichment potency of pond based on saprobic index at north coastal waters of Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Hidayat, Jafron W.

2018-05-01

Central Java is one of many areas which has long coastline, especially in the Northern Coast of Java Island. Intertidal activities occurred at this area may affect the transport of material and energy from surroundings. Cultivation activity supplies many inputs, i.e. feeds, chemicals (vitamin and mineral), including pollutants from feces and unconsumed feeds that affects the environment. One of water management is done through bioremediation by using vegetative agents (soft rehabilitation), such as seaweed and mangrove stands. The implementation of soft rehabilitation is highly depend on the existing environmental conditions of the ponds and surrounding waters. Therefore, it is very important to identify the condition of those waters first. The purpose of this study is to identify the quality of waters in the north coast of Central Java. Besides, it is also to analyze the potency of enriching cultivated commodity (cultivant), as well as a soft remediation mechanism using seaweed. The study was conducted in the coastal areas of Central Java, mainly to the locations commonly practicing cultivation in the pond waters; namely Brebes, Pemalang, Semarang, Demak, Pati and Jepara. Data were taken by sampling at least at 3 different sites as repetition, included ponds, public irrigations and coastline waters. The water sample was taken as much as 30 lt and filtered using plankton net no 25. Biodiversity of Shannon-Wiener Index (H'), evenness index (e) and Saprobic Index were used to analyze the plankton data. Result showed that plankton diversity in Central Java coasts were varied generally between 10 – 28 species. The most widely found species were Oscillatoria sp, Rhizosolenia styliformes, Surirella sp and Lyngbia conferoides. The diversity index varied from 1.83 to 2.9 with the stability status were between small to medium. The saprobic index showed a value between 0.33 up to 2.27; which indicated very small up to lightly contaminated status. The biggest stability

Automated workflows for data curation and standardization of chemical structures for QSAR modeling

EPA Science Inventory

Large collections of chemical structures and associated experimental data are publicly available, and can be used to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experime...

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.

THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

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.

Cleaner production options for reducing industrial waste: the case of batik industry in Malang, East Java-Indonesia

NASA Astrophysics Data System (ADS)

Sirait, M.

2018-01-01

The aim of this research is to conduct cleaner production options for improving the environmental performance during the production of batik industry, the case of UKM batik, Malang, East Java. Batik industry is one of small and medium textile industry which has contribution to economic growth in Malang. However, during production the batik, it generates wastewater that has potential to decrease the environmental performance. Wastewater from Celaket batik industry has BOD, COD, TSS, and pH level is far larger than the threshold of water quality standard as a result of use chemical substance during the dyes processing. In order to prevent generating wastewater, this study utilized cleaner production options, such as substitution of input material.Substitution of input material for dyes process was implemented by replacement chemical dyes (e.g.indigosol, nafthol, rapid) with natural dyes (e.g. Indigofero Tintoria). Modifying of technology/equipment was conducted by developing wastewater treatment equipment to reduce waste of batik production. The implementation of this strategy was carried out by changing input material from chemical dyes with natural dyes. The CP uptake could reduce significantly the environmental impact in term of reduction of COD, BOD, and TSS.

Static analysis of class invariants in Java programs

NASA Astrophysics Data System (ADS)

Bonilla-Quintero, Lidia Dionisia

2011-12-01

This paper presents a technique for the automatic inference of class invariants from Java bytecode. Class invariants are very important for both compiler optimization and as an aid to programmers in their efforts to reduce the number of software defects. We present the original DC-invariant analysis from Adam Webber, talk about its shortcomings and suggest several different ways to improve it. To apply the DC-invariant analysis to identify DC-invariant assertions, all that one needs is a monotonic method analysis function and a suitable assertion domain. The DC-invariant algorithm is very general; however, the method analysis can be highly tuned to the problem in hand. For example, one could choose shape analysis as the method analysis function and use the DC-invariant analysis to simply extend it to an analysis that would yield class-wide invariants describing the shapes of linked data structures. We have a prototype implementation: a system we refer to as "the analyzer" that infers DC-invariant unary and binary relations and provides them to the user in a human readable format. The analyzer uses those relations to identify unnecessary array bounds checks in Java programs and perform null-reference analysis. It uses Adam Webber's relational constraint technique for the class-invariant binary relations. Early results with the analyzer were very imprecise in the presence of "dirty-called" methods. A dirty-called method is one that is called, either directly or transitively, from any constructor of the class, or from any method of the class at a point at which a disciplined field has been altered. This result was unexpected and forced an extensive search for improved techniques. An important contribution of this paper is the suggestion of several ways to improve the results by changing the way dirty-called methods are handled. The new techniques expand the set of class invariants that can be inferred over Webber's original results. The technique that produces better

Using XML and Java for Astronomical Instrument Control

NASA Astrophysics Data System (ADS)

Koons, L.; Ames, T.; Evans, R.; Warsaw, C.; Sall, K.

1999-12-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests. Instrument description is too tightly coupled with details of implementation. NASA/Goddard Space Flight Center and AppNet, Inc. are developing a very general and highly extensible framework that applies to virtually any kind of instrument that can be controlled by a computer (e.g., telescopes, microscopes and printers). A key aspect of the object-oriented architecture, implemented in Java, involves software that is driven by an instrument description. The Astronomical Instrument Markup Language (AIML) is a domain-specific implementation of the more generalized Instrument Markup Language (IML). The software architecture combines the platform-independent processing capabilities of Java with the vendor-independent data description syntax of Extensible Markup Language (XML), a human-readable and machine-understandable way to describe structured data. IML is used to describe command sets (including parameters, datatypes, and constraints) and their associated formats, telemetry, and communication mechanisms. The software uses this description to present graphical user interfaces to control and monitor the instrument. Recent efforts have extended to command procedures (scripting) and representation of data pipeline inputs, outputs, and connections. Near future efforts are likely to include an XML description of data visualizations, as well as the potential use of XSL (Extensible Stylesheet Language) to permit astronomers to customize the user interface on several levels: per user, instrument, subsystem, or observatory-wide. Our initial prototyping effort was targeted for HAWC (High-resolution Airborne Wideband Camera), a first-light instrument of SOFIA (the Stratospheric Observatory for Infrared Astronomy

Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.

PubMed

Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

2014-10-22

In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or

Chemical modulation of electronic structure at the excited state

NASA Astrophysics Data System (ADS)

Li, F.; Song, C.; Gu, Y. D.; Saleem, M. S.; Pan, F.

2017-12-01

Spin-polarized electronic structures are the cornerstone of spintronics, and have thus attracted a significant amount of interest; in particular, researchers are looking into how to modulate the electronic structure to enable multifunctional spintronics applications, especially in half-metallic systems. However, the control of the spin polarization has only been predicted in limited two-dimensional systems with spin-polarized Dirac structures and is difficult to achieve experimentally. Here, we report the modulation of the electronic structure in the light-induced excited state in a typical half-metal, L a1 /2S r1 /2Mn O3 -δ . According to the spin-transport measurements, there appears a light-induced increase in magnetoresistance due to the enhanced spin scattering, which is closely associated with the excited spin polarization. Strikingly, the light-induced variation can be enhanced via alcohol processing and reduced by oxygen annealing. X-ray photoelectron spectroscopy measurements show that in the chemical process, a redox reaction occurs with a change in the valence of Mn. Furthermore, first-principles calculations reveal that the change in the valence of Mn alters the electronic structure and consequently modulates the spin polarization in the excited state. Our findings thus report a chemically tunable electronic structure, demonstrating interesting physics and the potential for multifunctional applications and ultrafast spintronics.

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.

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)

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.

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.

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.

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.

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/.

Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data

PubMed Central

Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander

2012-01-01

Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

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

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.

Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

ERIC Educational Resources Information Center

Rzepa, Henry S.

2016-01-01

Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

An Event-Related Potentials Study of Mental Rotation in Identifying Chemical Structural Formulas

ERIC Educational Resources Information Center

Huang, Chin-Fei; Liu, Chia-Ju

2012-01-01

The purpose of this study was to investigate how mental rotation strategies affect the identification of chemical structural formulas. This study conducted event-related potentials (ERPs) experiments. In addition to the data collected in the ERPs, a Chemical Structure Conceptual Questionnaire and interviews were also admin-istered for data…

Sharing chemical structures with peer-reviewed publications. Are we there yet?

EPA Science Inventory

In the domain of chemistry one of the greatest benefits to publishing research is that data are shared. Unfortunately, the vast majority of chemical structure data remain locked up in document form, primarily as PDF files. Despite the explosive growth of online chemical databases...

Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

PubMed Central

Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

2016-01-01

Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

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.

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...

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.

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

PubMed Central

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

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.

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...

Chemical-mechanical stability of the hierarchical structure of shell nacre

NASA Astrophysics Data System (ADS)

Sun, Jinmei; Guo, Wanlin

2010-02-01

The hierarchical structure and mechanical property of shell nacre are experimentally investigated from the new aspects of chemical stability and chemistry-mechanics coupling. Through chemical deproteinization or demineralization methods together with characterization techniques at micro/nano scales, it is found that the nacre of abalone, haliotis discus hannai, contains a hierarchical structure stacked with irregular aragonite platelets and interplatelet organic matrix thin layers. Yet the aragonite platelet itself is a nanocomposite consisting of nanoparticles and intraplatelet organic matrix framework. The mean diameter of the nanoparticles and the distribution of framework are quite different for different platelets. Though the interplatelet and intraplatelet organic matrix can be both decomposed by sodium hydroxide solution, the chemical stability of individual aragonite platelets is much higher than that of the microstructure stacked with them. Further, macroscopic bending test or nanoindentation experiment is performed on the micro/nanostructure of nacre after sodium hydroxide treatment. It is found that the Young’s modulus of both the stacked microstructure and nanocomposite platelet reduced. The reduction of the microstructure is more remark than that of the platelet. Therefore the chemical-mechanical stability of the nanocomposite platelet itself is much higher than that of the stacked microstructure of nacre.

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.

Chemical structure of wood charcoal by infrared spectroscopy and multivariate analysis

Treesearch

Nicole Labbe; David Harper; Timothy Rials; Thomas Elder

2006-01-01

In this work, the effect of temperature on charcoal structure and chemical composition is investigated for four tree species. Wood charcoal carbonized at various temperatures is analyzed by mid infrared spectroscopy coupled with multivariate analysis and by thermogravimetric analysis to characterize the chemical composition during the carbonization process. The...

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).

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

The Intersection of Structural and Chemical Biology - An Essential Synergy.

PubMed

Zuercher, William J; Elkins, Jonathan M; Knapp, Stefan

2016-01-21

The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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.

Chemical synthesis and NMR characterization of structured polyunsaturated triacylglycerols.

PubMed

Fauconnot, Laëtitia; Robert, Fabien; Villard, Renaud; Dionisi, Fabiola

2006-02-01

The chemical synthesis of pure triacylglycerol (TAG) regioisomers, that contain long chain polyunsaturated fatty acids, such as arachidonic acid (AA) or docosahexaenoic acid (DHA), and saturated fatty acids, such as lauric acid (La) or palmitic acid (P), at defined positions, is described. A single step methodology using (benzotriazol-1-yloxy)-tripyrrolidinophosphonium hexafluorophosphate (PyBOP), an activator of carboxyl group commonly used in peptide synthesis and occasionally used in carboxylic acid esterification, has been developed for structured TAG synthesis. Identification of the fatty acyl chains for each TAG species was confirmed by atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) and fatty acid positional distribution was determined by (1)H and (13)C NMR spectra. The generic described procedures can be applied to a large variety of substrates and was used for the production of specific triacylglycerols of defined molecular structures, with high regioisomeric purity. Combination of MS and NMR was shown to be an efficient tool for structural analysis of TAG. In particular, some NMR signals were demonstrated to be regioisomer specific, allowing rapid positional analysis of LC-PUFA containing TAG.

A SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES

EPA Science Inventory

Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

StrBioLib: a Java library for development of custom computationalstructural biology applications

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

Chandonia, John-Marc

2007-05-14

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure predictionmore » program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov« less

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.

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.

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.

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.

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

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.

Challenges to the implementation of the integrated management of childhood illness (IMCI) at community health centres in West Java province, Indonesia.

PubMed

Titaley, C R; Jusril, H; Ariawan, I; Soeharno, N; Setiawan, T; Weber, M W

2014-01-01

The integrated management of childhood illness (IMCI) is a comprehensive approach to child health, which has been adopted in Indonesia since 1997. This study aims to provide an overview of IMCI implementation at community health centres (puskesmas) in West Java province, Indonesia. Data were derived from a cross-sectional study conducted in 10 districts of West Java province, from November to December 2012. Semi-structured interviews were used to obtain information from staff at 80 puskesmas, including the heads (80 informants), pharmacy staff (79 informants) and midwives/nurses trained in IMCI (148 informants), using semi-structured interviews. Quantitative data were analysed using frequency tabulations and qualitative data were analysed by identifying themes that emerged in informants' responses. Almost all (N = 79) puskesmas implemented the IMCI strategy; however, only 64% applied it to all visiting children. Several barriers to IMCI implementation were identified, including shortage of health workers trained in IMCI (only 43% of puskesmas had all health workers in the child care unit trained in IMCI and 40% of puskesmas conducted on-the-job training). Only 19% of puskesmas had all the essential drugs and equipment for IMCI. Nearly all health workers acknowledged the importance of IMCI in their routine services and very few did not perceive its benefits. Lack of supervision from district health office staff and low community awareness regarding the importance of IMCI were reported. Complaints received from patients'families were generally related to the long duration of treatment and no administration of medication after physical examination. Interventions aiming to create local regulations endorsing IMCI implementation; promoting monitoring and supervision; encouraging on-the-job training for health workers; and strengthening training programmes, counselling and other promotional activities are important for promoting IMCI implementation in West Java province

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.

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. 

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

PubMed

Markiewicz, Tomasz

2011-03-30

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape.

PubMed

Ferreon, Allan Chris M; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A

2012-10-30

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson's disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 21 [urea][TMAO] ratio has a net neutral effect on the protein's dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

PubMed Central

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson’s disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 2∶1 [urea]∶[TMAO] ratio has a net neutral effect on the protein’s dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments. PMID:22826265

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

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins.

PubMed

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

Chemical modification of citrus pectin: Structural, physical and rheologial implications.

PubMed

Fracasso, Aline Francielle; Perussello, Camila Augusto; Carpiné, Danielle; Petkowicz, Carmen Lúcia de Oliveira; Haminiuk, Charles Windson Isidoro

2018-04-01

The present study aimed to investigate the physical, structural and rheological modifications caused by the chemical modification process of citrus pectin. Therefore, three commercial citrus pectins with different degree of esterification were chemically modified by sequential alkali and acidic hydrolytic process to produce modified citrus pectins (MCP) with special properties. The molar mass (M w ), degree of esterification (DE), monosaccharide composition, 13 C NMR spectra, homogeneity, morphology (SEM) and rheological behavior of both native and modified citrus pectins (MCP) were investigated. The chemical modification reduced the acid uronic content (up to 28.3%) and molar mass (up to 29.98%), however, showed little influence on the degree of esterification of native pectins. Modified citrus pectins presented higher amounts of neutral monosaccharides, mainly galactose, arabinose and rhamnose, typical of the Ramnogalacturonana-I (RG-I) region. Rheological tests indicated that the native and modified citrus pectins presented pseudoplastic behavior, however, the MCP samples were less viscous, compared to the native ones. Modified samples presented better dissolution in water and less strong gels, with good stability during oscillatory shearing at 25°C. This study aims to better understand the implications that chemical modifications may impose on the structure of citrus pectins. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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.

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

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

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.

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).

PubMed

Beaver, John E; Bourne, Philip E; Ponomarenko, Julia V

2007-02-21

Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools. The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site http://www.immuneepitope.org through the quick link 'Browse Records by 3D Structure.' The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required.

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.

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers.

PubMed

Monge, Aurélien; Arrault, Alban; Marot, Christophe; Morin-Allory, Luc

2006-08-01

The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, 'drug-like' and 'lead-like' properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million 'drug-like' molecules among which, more than one million are 'lead-like'. This study has been carried out using 'ScreeningAssistant', a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with 'in-house' scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. 'ScreeningAssistant' is freely available under the GPL license.

BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs

PubMed Central

Micklem, Gos

2014-01-01

Summary: The DAGViewer BioJS component is a reusable JavaScript component made available as part of the BioJS project and intended to be used to display graphs of structured data, with a particular emphasis on Directed Acyclic Graphs (DAGs). It enables users to embed representations of graphs of data, such as ontologies or phylogenetic trees, in hyper-text documents (HTML). This component is generic, since it is capable (given the appropriate configuration) of displaying any kind of data that is organised as a graph. The features of this component which are useful for examining and filtering large and complex graphs are described. Availability: http://github.com/alexkalderimis/dag-viewer-biojs; http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.8303. PMID:24627804

Chemical structure-based predictive model for methanogenic anaerobic biodegradation potential.

PubMed

Meylan, William; Boethling, Robert; Aronson, Dallas; Howard, Philip; Tunkel, Jay

2007-09-01

Many screening-level models exist for predicting aerobic biodegradation potential from chemical structure, but anaerobic biodegradation generally has been ignored by modelers. We used a fragment contribution approach to develop a model for predicting biodegradation potential under methanogenic anaerobic conditions. The new model has 37 fragments (substructures) and classifies a substance as either fast or slow, relative to the potential to be biodegraded in the "serum bottle" anaerobic biodegradation screening test (Organization for Economic Cooperation and Development Guideline 311). The model correctly classified 90, 77, and 91% of the chemicals in the training set (n = 169) and two independent validation sets (n = 35 and 23), respectively. Accuracy of predictions of fast and slow degradation was equal for training-set chemicals, but fast-degradation predictions were less accurate than slow-degradation predictions for the validation sets. Analysis of the signs of the fragment coefficients for this and the other (aerobic) Biowin models suggests that in the context of simple group contribution models, the majority of positive and negative structural influences on ultimate degradation are the same for aerobic and methanogenic anaerobic biodegradation.

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.

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…

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

Using XML and Java for Astronomical Instrumentation Control

NASA Technical Reports Server (NTRS)

Ames, Troy; Koons, Lisa; Sall, Ken; Warsaw, Craig

2000-01-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). ]ML is used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, and communication mechanisms. Although the current effort is targeted for the High-resolution Airborne Wideband Camera, a first-light instrument of the Stratospheric Observatory for Infrared Astronomy, the framework is designed to be generic and extensible so that it can be applied to any instrument.

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.

Structure and chemical composition of layers adsorbed at interfaces with champagne.

PubMed

Aguié-Béghin, V; Adriaensen, Y; Péron, N; Valade, M; Rouxhet, P; Douillard, R

2009-11-11

The structure and the chemical composition of the layer adsorbed at interfaces involving champagne have been investigated using native champagne, as well as ultrafiltrate (UFch) and ultraconcentrate (UCch) obtained by ultrafiltration with a 10(4) nominal molar mass cutoff. The layer adsorbed at the air/liquid interface was examined by surface tension and ellipsometry kinetic measurements. Brewster angle microscopy demonstrated that the layer formed on polystyrene by adsorption or drop evaporation was heterogeneous, with a domain structure presenting similarities with the layer adsorbed at the air/liquid interface. The surface chemical composition of polystyrene with the adlayer was determined by X-ray photoelectron spectroscopy (XPS). The contribution of champagne constituents varied according to the liquid (native, UFch, and UCch) and to the procedure of adlayer formation (evaporation, adsorption, and adsorption + rinsing). However, their chemical composition was not significantly influenced either by ultrafiltration or by the procedure of deposition on polystyrene. Modeling this composition in terms of classes of model compounds gave approximately 35% (w/w) of proteins and 65% (w/w) of polysaccharides. In the adlayer, the carboxyl groups or esters represent about 18% of carbon due to nonpolypeptidic compounds, indicating the presence of either uronic acids in the complex structure of pectic polysaccharides or of polyphenolic esters. This structural and chemical information and its relationship with the experimental procedures indicate that proteins alone cannot be used as a realistic model for the macromolecules forming the adsorption layer of champagne. Polysaccharides, the other major macromolecular components of champagne wine, are assembled with proteins at the interfaces, in agreement with the heterogeneous character of the adsorbed layer at interfaces.

Electronic and chemical structure of metal-silicon interfaces

NASA Technical Reports Server (NTRS)

Grunthaner, P. J.; Grunthaner, F. J.

1984-01-01

This paper reviews our current understanding of the near-noble metal silicides and the interfaces formed with Si(100). Using X-ray photoemission spectroscopy, we compare the chemical composition and electronic structure of the room temperature metal-silicon and reacted silicide-silicon interfaces. The relationship between the interfacial chemistry and the Schottky barrier heights for this class of metals on silicon is explored.

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.

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.

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.

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.

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;…

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

PubMed Central

2011-01-01

Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. Methods In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the

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.

Usability of HL7 and SNOMED CT standards in Java Persistence API environment.

PubMed

Antal, Gábor; Végh, Ádám Zoltán; Bilicki, Vilmos

2014-01-01

Due to the need for an efficient way of communication between the different stakeholders of healthcare (e.g. doctors, pharmacists, hospitals, patients etc.), the possibility of integrating different healthcare systems occurs. However, during the integration process several problems of heterogeneity might come up, which can turn integration into a difficult task. These problems motivated the development of healthcare information standards. The main goal of the HL7 family of standards is the standardization of communication between clinical systems and the unification of clinical document formats on the structural level. The SNOMED CT standard aims the unification of the healthcare terminology, thus the development of a standard on lexical level. The goal of this article is to introduce the usability of these two standards in Java Persistence API (JPA) environment, and to examine how standard-based system components can be efficiently generated. First, we shortly introduce the structure of the standards, their advantages and disadvantages. Then, we present an architecture design method, which can help to eliminate the possible structural drawbacks of the standards, and makes code generating tools applicable for the automatic production of certain system components.

TRAX-CHEM: A pre-chemical and chemical stage extension of the particle track structure code TRAX in water targets

NASA Astrophysics Data System (ADS)

Boscolo, D.; Krämer, M.; Durante, M.; Fuss, M. C.; Scifoni, E.

2018-04-01

The production, diffusion, and interaction of particle beam induced water-derived radicals is studied with the a pre-chemical and chemical module of the Monte Carlo particle track structure code TRAX, based on a step by step approach. After a description of the model implemented, the chemical evolution of the most important products of water radiolysis is studied for electron, proton, helium, and carbon ion radiation at different energies. The validity of the model is verified by comparing the calculated time and LET dependent yield with experimental data from literature and other simulation approaches.

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.

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…

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

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...

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.

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.

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.

Relationships between chemical structure, mechanical properties and materials processing in nanopatterned organosilicate fins.

PubMed

Stan, Gheorghe; Gates, Richard S; Hu, Qichi; Kjoller, Kevin; Prater, Craig; Jit Singh, Kanwal; Mays, Ebony; King, Sean W

2017-01-01

The exploitation of nanoscale size effects to create new nanostructured materials necessitates the development of an understanding of relationships between molecular structure, physical properties and material processing at the nanoscale. Numerous metrologies capable of thermal, mechanical, and electrical characterization at the nanoscale have been demonstrated over the past two decades. However, the ability to perform nanoscale molecular/chemical structure characterization has only been recently demonstrated with the advent of atomic-force-microscopy-based infrared spectroscopy (AFM-IR) and related techniques. Therefore, we have combined measurements of chemical structures with AFM-IR and of mechanical properties with contact resonance AFM (CR-AFM) to investigate the fabrication of 20-500 nm wide fin structures in a nanoporous organosilicate material. We show that by combining these two techniques, one can clearly observe variations of chemical structure and mechanical properties that correlate with the fabrication process and the feature size of the organosilicate fins. Specifically, we have observed an inverse correlation between the concentration of terminal organic groups and the stiffness of nanopatterned organosilicate fins. The selective removal of the organic component during etching results in a stiffness increase and reinsertion via chemical silylation results in a stiffness decrease. Examination of this effect as a function of fin width indicates that the loss of terminal organic groups and stiffness increase occur primarily at the exposed surfaces of the fins over a length scale of 10-20 nm. While the observed structure-property relationships are specific to organosilicates, we believe the combined demonstration of AFM-IR with CR-AFM should pave the way for a similar nanoscale characterization of other materials where the understanding of such relationships is essential.

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.

Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals.

PubMed

Trisciuzzi, Daniela; Alberga, Domenico; Mansouri, Kamel; Judson, Richard; Novellino, Ettore; Mangiatordi, Giuseppe Felice; Nicolotti, Orazio

2017-11-27

We present a practical and easy-to-run in silico workflow exploiting a structure-based strategy making use of docking simulations to derive highly predictive classification models of the androgenic potential of chemicals. Models were trained on a high-quality chemical collection comprising 1689 curated compounds made available within the CoMPARA consortium from the US Environmental Protection Agency and were integrated with a two-step applicability domain whose implementation had the effect of improving both the confidence in prediction and statistics by reducing the number of false negatives. Among the nine androgen receptor X-ray solved structures, the crystal 2PNU (entry code from the Protein Data Bank) was associated with the best performing structure-based classification model. Three validation sets comprising each 2590 compounds extracted by the DUD-E collection were used to challenge model performance and the effectiveness of Applicability Domain implementation. Next, the 2PNU model was applied to screen and prioritize two collections of chemicals. The first is a small pool of 12 representative androgenic compounds that were accurately classified based on outstanding rationale at the molecular level. The second is a large external blind set of 55450 chemicals with potential for human exposure. We show how the use of molecular docking provides highly interpretable models and can represent a real-life option as an alternative nontesting method for predictive toxicology.

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.

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.

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…

[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)

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.

Materials ``alchemy'': Shape-preserving chemical transformation of micro-to-macroscopic 3-D structures

NASA Astrophysics Data System (ADS)

Sandhage, Kenneth H.

2010-06-01

The scalable fabrication of nano-structured materials with complex morphologies and tailorable chemistries remains a significant challenge. One strategy for such synthesis consists of the generation of a solid structure with a desired morphology (a “preform”), followed by reactive conversion of the preform into a new chemistry. Several gas/solid and liquid/solid reaction processes that are capable of such chemical conversion into new micro-to-nano-structured materials, while preserving the macroscopic-to-microscopic preform morphologies, are described in this overview. Such shape-preserving chemical transformation of one material into another could be considered a modern type of materials “alchemy.”

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

Insight into Amyloid Structure Using Chemical Probes

PubMed Central

Reinke, Ashley A.; Gestwicki, Jason E.

2011-01-01

Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-β (Aβ) peptide. Over the past decade, it has become clear that these Aβ amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of Aβ peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

20180318 - Automated workflows for data curation and standardization of chemical structures for QSAR modeling (ACS Spring)

EPA Science Inventory

Large collections of chemical structures and associated experimental data are publicly available, and can be used to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experime...

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…

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.

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.

Prediction of biodegradability from chemical structure: Modeling or ready biodegradation test data

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

Loonen, H.; Lindgren, F.; Hansen, B.

1999-08-01

Biodegradation data were collected and evaluated for 894 substances with widely varying chemical structures. All data were determined according to the Japanese Ministry of International Trade and Industry (MITI) I test protocol. The MITI I test is a screening test for ready biodegradability and has been described by Organization for Economic Cooperation and Development (OECD) test guideline 301 C and European Union (EU) test guideline C4F. The chemicals were characterized by a set of 127 predefined structural fragments. This data set was used to develop a model for the prediction of the biodegradability of chemicals under standardized OECD and EUmore » ready biodegradation test conditions. Partial least squares (PLS) discriminant analysis was used for the model development. The model was evaluated by means of internal cross-validation and repeated external validation. The importance of various structural fragments and fragment interactions was investigated. The most important fragments include the presence of a long alkyl chain; hydroxy, ester, and acid groups (enhancing biodegradation); and the presence of one or more aromatic rings and halogen substituents (regarding biodegradation). More than 85% of the model predictions were correct for using the complete data set. The not readily biodegradable predictions were slightly better than the readily biodegradable predictions (86 vs 84%). The average percentage of correct predictions from four external validation studies was 83%. Model optimization by including fragment interactions improve the model predicting capabilities to 89%. It can be concluded that the PLS model provides predictions of high reliability for a diverse range of chemical structures. The predictions conform to the concept of readily biodegradable (or not readily biodegradable) as defined by OECD and EU test guidelines.« less

Drought Vulnerability Mapping with Geomorphological Approach in Yogyakarta Special Region (DIY) and Central Java

NASA Astrophysics Data System (ADS)

Sudaryatno

2016-11-01

This study aims to determine the level of vulnerability of the geomorphologic drought that occurred in Central Java and Yogyakarta Special Region. This study examines geomorphologic drought. Parameters used were slope, drainage, Available Water Capacity (AWC), permeability, landform, and land use. Landsat 8 and SRTM data were used for the extraction of physical parameters, such as slope, drainage, landform, and land use. The method used in this study is scoring and weighting. Query results were used for data classification by overlaying drought geomorphologic parameters. The expected outcome of this research is to map the geomorphologic drought vulnerability on Central Java and Yogyakarta Special Region. Drought vulnerability was divided into wet, normal and dry classes. Distribution of the dry class is frequent. Some of the dry classes are distributed on the steep till extremely steep slope region and on the structural and karsts landform. This was related to AWC value where region with high AWC contributed to the poor drainage of the soil, such as at Kulonprogo, Purworejo, Kebumen, Blora, Wonogiri, Purbalingga, Pekalongan, Jepara and Kudus regency. Normal classes are distributed on the sloping till steep slope, have moderate till well-drained soil and low AWC, such as at Gunung Kidul, Pati, Temanggung regency, and Magelang city. Wet classes are distributed on the flat or almost flat and sloping region. Most of the wet classes are distributed on volcanic hills and coastal area. Those regions are well-drained and the land uses are mostly for settlement and farming, such as at Sleman, Yogyakarta city, Klaten, Bantul, and Wonosobo regency.

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.

Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function.

PubMed

Väre, Ville Y P; Eruysal, Emily R; Narendran, Amithi; Sarachan, Kathryn L; Agris, Paul F

2017-03-16

RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

Electrostatic potential calculation for biomolecules--creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures.

PubMed

Rocchia, W; Neshich, G

2007-10-05

STING and Java Protein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and Java Protein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. BlueStar STING is available at http://www.cbi.cnptia.embrapa.br.

Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

3D seismic structures in different subduction zones (Central Java, Toba Caldera, Central Chile, Costa-Rica and others): common and particular features

NASA Astrophysics Data System (ADS)

Koulakov, I.

2009-12-01

We present several seismic models for different subduction zones derived using the LOTOS tomographic code based on travel times from local earthquakes. The quality and reliability of all these models are supported by various tests (odd/even test, reconstructions with different starting models and free parameters, synthetic modeling with realistic setup, etc). For two datasets (Central Chile and Costa-Rica) we present the results of anisotropic inversion, which determines the orientations and values of fastest and slowest velocities in each point of the study volume. Comparing the velocity models for all considered subduction zones reveals some common features and differences. For example, in all cases we observe a clear low velocity anomaly which appears to link the cluster of intermediate seismicity in the Benioff zone with the volcanoes of the main arc. This pattern is interpreted as paths of ascending fluids and melts which are related to phase transitions in the slab. However, the depths of the seismicity clusters and dipping angle of the low-velocity anomaly are considerably different. For example, beneath Toba the cluster is at 100-130 km depth, and the anomaly is vertical. In Central Java the anomaly is strongly inclined to the direction of the slab, while beneath Central Chile it has the opposite orientation. The amplitudes of velocity anomalies are considerably different. The strongest heterogeneity (up to 30% of negative anomaly) is observed in the crust beneath Central Java, while much lower amplitudes (~15%) are found beneath the Toba Caldera, where a catastrophic super-eruption took place about 70000 years ago. The anisotropic inversion reveal similar features in Costa-Rica and Central Java: trench perpendicular fast velocity orientations in the subducting plate and trench parallel orientations in the mantle wedge. This is consistent with shear wave splitting results obtained for many other subduction zones. Such anisotropy in the corner flow may be

jSynthesizer: A Java based first-motion synthetic seismogram tool

NASA Astrophysics Data System (ADS)

Sullivan, Mark

2009-10-01

Both researchers and educators need software tools to create synthetic seismograms to model earthquake sources. We have developed a program that generates first-motion synthetic seismograms that is highly interactive and suited to the needs of both research and education audiences. Implemented in the Java programming language, our program is available for use on Windows, Mac OS X and Linux operating systems. Our program allows the user to input the fault parameters strike, dip and slip angle, numerically or graphically using a lower hemisphere equal-area stereographic projection of the focal sphere of the earthquake. This representation is familiar to geologists and seismologists as the standard way of displaying the orientation of a fault in space. The user is also able to enter the relative location of the seismograph and the depth and crustal velocity structure in the vicinity of the earthquake. The direct P wave along with reflections off of layer boundaries near the source are generated using a constant ray-parameter approximation. The instrument response functions used by the Worldwide Standardized Seismogram Network and the attenuation response of the Earth's mantle are generated in the frequency domain and applied to generate the synthetic seismogram. Planned enhancements to this program will allow the simultaneous generation of seismograms at many stations as well as more complicated crustal structures.

Denaturation of collagen structures and their transformation under the physical and chemical effects

NASA Astrophysics Data System (ADS)

Ivankin, A.; Boldirev, V.; Fadeev, G.; Baburina, M.; Kulikovskii, A.; Vostrikova, N.

2017-11-01

The process of denaturation of collagen structures under the influence of physical and chemical factors play an important role in the manufacture of food technology and the production of drugs for medicine and cosmetology. The paper discussed the problem of the combined effects of heat treatment, mechanical dispersion and ultrasonic action on the structural changes of the animal collagen in the presence of weak protonated organic acids. Algorithm combined effects of physical and chemical factors as a result of the formation of the technological properties of products containing collagen has been shown.

Nutritional value of spiny lobsters (Panulirus sp.) from Southern Coast of Java

NASA Astrophysics Data System (ADS)

Haryono, F. Eko Dwi; Hutabarat, Sahala; Hutabarat, Johannes; Ambariyanto

2015-12-01

Five species of spiny lobsters are known to live in southern coast of Java. These lobsters are very popular seafood which was believed to have high nutritional value. However, nutrition content of these species from the area has not been investigated. This research was conducted to study nutrition content in these crustaceans. Five spiny lobsters i.e. Panulirus homarus, P. versicolor, P. ornatus, P. penicullatus, and P. longipes, were collected randomly from different locations at the southern coast of Java. Morphometric measurements were conducted prior to proximate analysis of these lobsters. All species of spiny lobsters investigated have similar carapace length. However, P. homarus and P. versicolor have the highest muscle weight. Proximate analysis shows that P. homarus also has high protein (24.18%) and carbohydrate content (55.68%) and lowest lipid content (6.18%) compare with other species. These results suggest that this lobster has best nutritional value for consumption.

Linear complexions: Confined chemical and structural states at dislocations

NASA Astrophysics Data System (ADS)

Kuzmina, M.; Herbig, M.; Ponge, D.; Sandlöbes, S.; Raabe, D.

2015-09-01

For 5000 years, metals have been mankind’s most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Chemical and structural biology of protein lysine deacetylases

PubMed Central

YOSHIDA, Minoru; KUDO, Norio; KOSONO, Saori; ITO, Akihiro

2017-01-01

Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD+-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer. Notably, drug discovery efforts have achieved success in developing HDAC-targeting therapeutics for treatment of several cancers. However, recent advancements in proteomics technology have revealed much broader aspects of HDACs beyond gene expression control. Not only histones but also a large number of cellular proteins are subject to acetylation by histone acetyltransferases (HATs) and deacetylation by HDACs. Furthermore, some of their structures can flexibly accept and hydrolyze other acyl groups on protein lysine residues. This review mainly focuses on structural aspects of HDAC enzymatic activity regulated by interaction with substrates, co-factors, small molecule inhibitors, and activators. PMID:28496053

Using a Java Web-based Graphical User Interface to access the SOHO Data Arch ive

NASA Astrophysics Data System (ADS)

Scholl, I.; Girard, Y.; Bykowski, A.

This paper presents the architecture of a Java web-based graphical interface dedicated to the access of the SOHO Data archive. This application allows local and remote users to search in the SOHO data catalog and retrieve the SOHO data files from the archive. It has been developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France), which is one of the European Archives for the SOHO data. This development is part of a joint effort between ESA, NASA and IAS in order to implement long term archive systems for the SOHO data. The software architecture is built as a client-server application using Java language and SQL above a set of components such as an HTTP server, a JDBC gateway, a RDBMS server, a data server and a Web browser. Since HTML pages and CGI scripts are not powerful enough to allow user interaction during a multi-instrument catalog search, this type of requirement enforces the choice of Java as the main language. We also discuss performance issues, security problems and portability on different Web browsers and operating syste ms.

Point Analysis in Java applied to histological images of the perforant pathway: a user's account.

PubMed

Scorcioni, Ruggero; Wright, Susan N; Patrick Card, J; Ascoli, Giorgio A; Barrionuevo, Germán

2008-01-01

The freeware Java tool Point Analysis in Java (PAJ), created to perform 3D point analysis, was tested in an independent laboratory setting. The input data consisted of images of the hippocampal perforant pathway from serial immunocytochemical localizations of the rat brain in multiple views at different resolutions. The low magnification set (x2 objective) comprised the entire perforant pathway, while the high magnification set (x100 objective) allowed the identification of individual fibers. A preliminary stereological study revealed a striking linear relationship between the fiber count at high magnification and the optical density at low magnification. PAJ enabled fast analysis for down-sampled data sets and a friendly interface with automated plot drawings. Noted strengths included the multi-platform support as well as the free availability of the source code, conducive to a broad user base and maximum flexibility for ad hoc requirements. PAJ has great potential to extend its usability by (a) improving its graphical user interface, (b) increasing its input size limit, (c) improving response time for large data sets, and (d) potentially being integrated with other Java graphical tools such as ImageJ.

Processes in KaffeOS: Isolation, Resource Management, and Sharing in Java

DTIC Science & Technology

2000-04-01

separation of garbage collection costs is not possible. Balfanz and Gong [2] describe a multi- processing JVM developed to explore the secu- rity...line in Java. In Proc. of the 7th HotOS, Rio Rico, AZ, Mar. 1999. IEEE Computer Society. [2] D. Balfanz and L. Gong. Experience with secure multi

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Ancient music instrument in east java: study about continuity and change in the 10-15 century

NASA Astrophysics Data System (ADS)

Pamungkas, H.; Thomas, N. A.; Nasution

2018-01-01

This research is included in art history, especially music art in East Java. The oldest evidence of musical instruments in this area is evidenced through the Jalatunda site, Trawas. On one of the relief panels found apsara (nymphs) plays vina (stringed instrument). This site was from the 10th century. Since then the relief of musical instruments more and more carved. This is apparent in some temples in East Java after the 11th century. Not only in terms of the number of instruments, but the type of musical instruments is also displayed more diverse. The inflatable instrument (xylophone), the percussion instrument (membraphone), or idiophone show diversity over time. The development is an interesting phenomenon in the life of music art. Problems in this research, whether within the period of 5 centuries (10-15 AD century) there is a change in how to play instrument. This research uses ethnographic analogy method. In the archaeological discipline, this method is used to reconstruct past lives through activities that can be found in temple reliefs in East Java.

Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

PubMed

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

Novel Plasmids and Resistance Phenotypes in Yersinia pestis: Unique Plasmid Inventory of Strain Java 9 Mediates High Levels of Arsenic Resistance

PubMed Central

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L.

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium. PMID:22479347

Information Theory and Voting Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures.

PubMed

Saeed, Faisal; Salim, Naomie; Abdo, Ammar

2013-07-01

Many consensus clustering methods have been applied in different areas such as pattern recognition, machine learning, information theory and bioinformatics. However, few methods have been used for chemical compounds clustering. In this paper, an information theory and voting based algorithm (Adaptive Cumulative Voting-based Aggregation Algorithm A-CVAA) was examined for combining multiple clusterings of chemical structures. The effectiveness of clusterings was evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster, and the results were compared with Ward's method. The chemical dataset MDL Drug Data Report (MDDR) and the Maximum Unbiased Validation (MUV) dataset were used. Experiments suggest that the adaptive cumulative voting-based consensus method can improve the effectiveness of combining multiple clusterings of chemical structures. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam

DOE PAGES

Lin, Feng; Markus, Isaac M.; Doeff, Marca M.; ...

2014-07-16

Our investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. But, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi 0.4Mn 0.4Co 0.18Ti 0.02O 2 particles, repeated electron beam irradiation induced a phase transition from an Rmore » $$\\bar{3}$$m layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from R$$\\bar{3}$$m 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, in using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.« less

From Structural Complexity to Structure-Property Relationships in Intermetallics: Development of Density Functional Theory-Chemical Pressure Analysis

NASA Astrophysics Data System (ADS)

Engelkemier, Joshua

The unparalleled structural diversity of intermetallic compounds provides nearly unlimited potential for the discovery and optimization of materials with useful properties, such as thermoelectricity, superconductivity, magnetism, hydrogen storage, superelasticity, and catalysis. This same diversity, however, creates challenges for understanding and controlling the unpredictable structure of intermetallic phases. Moreover, the fundamental design principles that have proven so powerful in molecular chemistry do not have simple analogues for metallic, solid state materials. One of these basic principles is the concept of atomic size effects. Especially in densely packed crystal structures where the need to fill space is in competition with the atoms' preferences for ideal interatomic distances, substitution of one element in a compound for another with similar chemical properties yet different atomic size can have dramatic effects on the ordering of the atoms (which in turn affects the electronic structure, vibrational properties, and materials properties). But because the forces that hold metallic phases together are less easily understood from a local perspective than covalent or ionic interactions in other kinds of materials, it is usually unclear whether the atoms are organized to optimize stabilizing, bonding interactions or rather forced to be close together despite repulsive, steric interactions. This dissertation details the development of a theoretical method, called Density Functional Theory-Chemical Pressure (DFT-CP) analysis, to address this issue. It works by converting the distribution of total energy density from a DFT calculation into a map of chemical pressure through a numerical approximation of the first derivative of energy with respect to voxel volume. The CP distribution is then carefully divided into contact volumes between neighboring atoms, from which it is possible to determine whether atoms are too close together (positive CP) or too far

Success Factors for Adoption of Real-Time Java

DTIC Science & Technology

2010-04-01

use Java in an effective way in order to achieve objectives If d ’t l t ti f bj ti d d ’t lt i t l i 9© 2010 Atego. All rights reserved. you on p an o...order to effectively use object-oriented programming practices. Te ps d’execution des algos 400 450 500 550 600 650 700 n m s TacticalPicture...find all garbage, nor to defragment the available free pool Common operations may have surprising effects (e.g. entering a mutual exclusion region

Nematodes of amphibians from Java, Indonesia, with a description of
new species, Meteterakis wonosoboensis n. sp. (Nematoda : Heterakoidea).

PubMed

Purwaningsih, Endang; Dewi, Kartika; Hasegawa, Hideo

2015-06-24

During a survey on the parasites of amphibians of Indonesia, toads (30 Bufo melanostictus) and 246 frogs (213 Fejervarya cancrivora, 11 F. limnocharis, 22 Rana macrodon from West Java and 68 F. cancrivora from Central Java) were examined for parasitic nematodes. Three species of nematodes were found and described, i.e. Meteterakis wonosoboensis n. sp. from Fejervaria cancrivora; Meteterakis japonica from Bufo melanostictus, F. cancrivora and F. limnocharis; and Chabaudus sp. from F. cancrivora, F. limnocharis and Rana macrodon. Meteterakis wonosoboensis n. sp. is distinguished from other species of the genus by the length and shape of spicules, the number of caudal papillae, the presence of gubernaculum in male and the presence of vulval flap in female. Bufo melanostictus and Java are recorded as new host and locality for M. japonica, respectively.

Influence of Chemical Conditions on the Nanoporous Structure of Silicate Aerogels

PubMed Central

Sinkó, Katalin

2010-01-01

Silica or various silicate aerogels can be characterized by highly porous, open cell, low density structures. The synthesis parameters influence the three-dimensional porous structures by modifying the kinetics and mechanism of hydrolysis and condensation processes. Numerous investigations have shown that the structure of porous materials can be tailored by variations in synthesis conditions (e.g., the type of precursors, catalyst, and surfactants; the ratio of water/precursor; the concentrations; the medium pH; and the solvent). The objectives of this review are to summarize and elucidate the effects of chemical conditions on the nanoporous structure of sol-gel derived silicate aerogels.

Java implementation of Class Association Rule algorithms

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

Tamura, Makio

2007-08-30

Java implementation of three Class Association Rule mining algorithms, NETCAR, CARapriori, and clustering based rule mining. NETCAR algorithm is a novel algorithm developed by Makio Tamura. The algorithm is discussed in a paper: UCRL-JRNL-232466-DRAFT, and would be published in a peer review scientific journal. The software is used to extract combinations of genes relevant with a phenotype from a phylogenetic profile and a phenotype profile. The phylogenetic profiles is represented by a binary matrix and a phenotype profile is represented by a binary vector. The present application of this software will be in genome analysis, however, it could be appliedmore » more generally.« less

Joint inversion of active and passive seismic data in Central Java

NASA Astrophysics Data System (ADS)

Wagner, Diana; Koulakov, I.; Rabbel, W.; Luehr, B.-G.; Wittwer, A.; Kopp, H.; Bohm, M.; Asch, G.

2007-08-01

Seismic and volcanic activities in Central Java, Indonesia, the area of interest of this study, are directly or indirectly related to the subduction of the Indo-Australian plate. In the framework of the MERapi AMphibious EXperiments (MERAMEX), a network consisting of about 130 seismographic stations was installed onshore and offshore in Central Java and operated for more than 150 days. In addition, 3-D active seismic experiments were carried out offshore. In this paper, we present the results of processing combined active and passive seismic data, which contain traveltimes from 292 local earthquakes and additional airgun shots along three offshore profiles. The inversion was performed using the updated LOTOS-06 code that allows processing for active and passive source data. The joint inversion of the active and passive data set considerably improves the resolution of the upper crust, especially in the offshore area in comparison to only passive data. The inversion results are verified using a series of synthetic tests. The resulting images show an exceptionally strong low-velocity anomaly (-30 per cent) in the backarc crust northward of the active volcanoes. In the upper mantle beneath the volcanoes, we observe a low-velocity anomaly inclined towards the slab, which probably reflects the paths of fluids and partially melted materials in the mantle wedge. The crust in the forearc appears to be strongly heterogeneous. The onshore part consists of two high-velocity blocks separated by a narrow low-velocity anomaly, which can be interpreted as a weakened contact zone between two rigid crustal bodies. The recent Java Mw = 6.3 earthquake (2006/05/26-UTC) occurred at the lower edge of this zone. Its focal strike slip mechanism is consistent with the orientation of this contact.

Establishing an Integrated Catchment Management (ICM) program in East Java, Indonesia.

PubMed

Booth, C A; Warianti, A; Wrigley, T

2001-01-01

The Brantas is one of Indonesia's most important catchments. It is the "rice bowl" of Java and nationally important for its industrial activity. Surabaya, Indonesia's second largest city, is located at the mouth of the Brantas River which is pivotal to the city's water supply. The challenges associated with the institutional framework for natural resource management in East Java parallels that of many states and provinces around the globe. It is multi-layered and complex. Integrated Catchment Management (ICM) may be defined as "the co-ordinated and sustainable management of land, water, soil vegetation, fauna and other natural resources on a water catchment basis". Over a period of six months, an ICM Strategy was researched and facilitated for the Brantas River Catchment in East Java via a short term advisor attachment. The aim of the Strategy is to improve coordination, co-operation, communication and consistency of government and community efforts towards sustaining the catchment's environmental, economic and social values. The attachment was part of the Pollution Control Implementation (PCI) Project funded by AusAid and the Indonesian Government. The ICM Strategy developed was broad based and addressed the priority natural resource management issues facing the Brantas Catchment. It was co-ordinated by BAPEDALDA, the Provincial Environmental Protection Agency, and developed by all agencies involved in natural resource management in the catchment. Various Universities and Non Government Organisations (NGOs) were also involved in the ICM process which developed the Strategy. At the conclusion of the attachment, a draft ICM Strategy and a proposed institutional framework had been developed. A working group of key agencies was also established to further enhance local "ownership", finalise timescales and implementation responsibilities within the Strategy and bring the institutional arrangements into being through a Governor's Decree.

Using Java to generate globally unique identifiers for DICOM objects.

PubMed

Kamauu, Aaron W C; Duvall, Scott L; Avrin, David E

2009-03-01

Digital imaging and communication in medicine (DICOM) specifies that all DICOM objects have globally unique identifiers (UIDs). Creating these UIDs can be a difficult task due to the variety of techniques in use and the requirement to ensure global uniqueness. We present a simple technique of combining a root organization identifier, assigned descriptive identifiers, and JAVA generated unique identifiers to construct DICOM compliant UIDs.

Java vs. Python Coverage of Introductory Programming Concepts: A Textbook Analysis

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Rague, Brian; Wolthuis, Stuart

2017-01-01

In this research, we compare two languages, Java and Python, by performing a content analysis of words in textbooks that describe important programming concepts. Our goal is to determine which language has better textbook support for teaching introductory programming courses. We used the TextSTAT program to count how often our list of concept…

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

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.

2014/2015 Investigations of the Ontong Java and Kerguelen Plateaus

NASA Astrophysics Data System (ADS)

Coffin, M. F.; Whittaker, J. M.

2013-12-01

The two largest oceanic plateaus, Ontong Java in the western Pacific, and Kerguelen in the southern Indian Ocean, will be the focus of scheduled multidisciplinary/interdisciplinary shipboard expeditions in 2014 and 2015. In mid-2014, scientists aboard the Schmidt Ocean Institute's RV Falkor will investigate the origin and evolution of two large atolls, Ontong Java and Nukumanu, surmounting the ca 122 Ma Ontong Java Plateau, as well how Kroenke Canyon, which deeply incises the plateau, formed and evolved. First-ever multibeam bathymetry and sub-bottom profiling data from the atolls and canyon will reveal their submarine and shallow sub-seafloor morphology, and, if combined with geochemical and geochronological analyses of potential igneous basement samples, will yield important information on their origin and evolution. The primary goals of this atoll and canyon project are: to test potential genetic relationships between a) the atolls and the OJP, and b) the atolls and Kroenke Canyon; to understand and model how atolls and canyons form and evolve on oceanic plateaus, isolated from terrestrial influences and subject to sea level fluctuations; and to contribute to understanding tsunami risk on low-lying atolls. In late 2014 and early 2015, researchers aboard Australia's new Marine National Facility, RV Investigator, will investigate active submarine hotspot volcanism on the Kerguelen Plateau and its consequences. The project's overall aim is to test the hypothesis that hydrothermal activity driven by active submarine magmatism fertilizes surface waters with iron that enhances primary biological productivity. Surmounting the Cretaceous plateau, Heard and McDonald Islands are among the world's most active hotspot volcanoes, and new multibeam bathymetry and sub-bottom profiling data will enable identification of candidate active submarine volcanoes, which we will sample. In the overlying water column, we will collect samples to test for the presence or absence of

First record of Puerulus mesodontus Chan, Ma & Chu, 2013 (Crustacea, Decapoda, Achelata, Palinuridae) from south of Java, Indonesia.

PubMed

Wardiatno, Yusli; Hakim, Agus Alim; Mashar, Ali; Butet, Nurlisa Alias; Adrianto, Luky; Farajallah, Achmad

2016-01-01

Three specimens of Puerulus mesodontus Chan, Ma & Chu, 2013 (Crustacea, Decapoda, Achelata, Palinuridae) were collected from Palabuhanratu Bay, southern Java, Indonesia. There is no previous record on the presence of the species in Indonesia. This finding represents the first record of this species in Java, Indonesia, and confirms that the species is present in the Indian Ocean. The morphological characters of the species are described. This paper contains a new distribution record of a lobster species from Indonesian waters.

CHEMICAL RIGIDIZATION OF EXPANDABLE STRUCTURES.

DTIC Science & Technology

The objective of this program was to develop a chemical rigidization process that could be activated by an on-command mechanism and be capable of...and rigidized in the high vacuum facilities atWright-Patterson AFB, Ohio and were delivered to the Air Force. A fail-safe chemical rigidization system...have been varied from fifteen minutes to two hours. The chemical system, a vinyl-type monomer, has exhibited a sustained shelf-life, under ambient

Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism

PubMed Central

Wildenhain, Jan; Spitzer, Michaela; Dolma, Sonam; Jarvik, Nick; White, Rachel; Roy, Marcia; Griffiths, Emma; Bellows, David S.; Wright, Gerard D.; Tyers, Mike

2016-01-01

The network structure of biological systems suggests that effective therapeutic intervention may require combinations of agents that act synergistically. However, a dearth of systematic chemical combination datasets have limited the development of predictive algorithms for chemical synergism. Here, we report two large datasets of linked chemical-genetic and chemical-chemical interactions in the budding yeast Saccharomyces cerevisiae. We screened 5,518 unique compounds against 242 diverse yeast gene deletion strains to generate an extended chemical-genetic matrix (CGM) of 492,126 chemical-gene interaction measurements. This CGM dataset contained 1,434 genotype-specific inhibitors, termed cryptagens. We selected 128 structurally diverse cryptagens and tested all pairwise combinations to generate a benchmark dataset of 8,128 pairwise chemical-chemical interaction tests for synergy prediction, termed the cryptagen matrix (CM). An accompanying database resource called ChemGRID was developed to enable analysis, visualisation and downloads of all data. The CGM and CM datasets will facilitate the benchmarking of computational approaches for synergy prediction, as well as chemical structure-activity relationship models for anti-fungal drug discovery. PMID:27874849