Tissue and Metabolomic Biomarkers of Recurrent Renal Cell Carcinoma

DTIC Science & Technology

2014-07-01

matrix : COG=1 COG= 2 COG=3 COG=4 COG=5 COG=6 b7h1.cutoff 0 0 0 ...0.473335 0.116014 0.366077 Variable importance matrix : COG=1 COG= 2 COG=3 COG=4 COG=5 COG=6 b7h1.cutoff 0 0 ...Variable importance matrix : COG=1 COG= 2 COG=3 COG=4 COG=5 COG=6 COG=7 COG=8 COG=9 COG=10 b7h1.cutoff 0 0 0 0 0

Probabilistic commodity-flow-based focusing of monitoring activities to facilitate early detection of Phytophthora ramorum outbreaks

Treesearch

Steven C. McKelvey; William D. Smith; Frank Koch

2012-01-01

This project summary describes a probabilistic model developed with funding support from the Forest Health Monitoring Program of the Forest Service, U.S. Department of Agriculture (BaseEM Project SO-R-08-01). The model has been implemented in SODBuster, a standalone software package developed using the Java software development kit from Sun Microsystems.

BRISK--research-oriented storage kit for biology-related data.

PubMed

Tan, Alan; Tripp, Ben; Daley, Denise

2011-09-01

In genetic science, large-scale international research collaborations represent a growing trend. These collaborations have demanding and challenging database, storage, retrieval and communication needs. These studies typically involve demographic and clinical data, in addition to the results from numerous genomic studies (omics studies) such as gene expression, eQTL, genome-wide association and methylation studies, which present numerous challenges, thus the need for data integration platforms that can handle these complex data structures. Inefficient methods of data transfer and access control still plague research collaboration. As science becomes more and more collaborative in nature, the need for a system that adequately manages data sharing becomes paramount. Biology-Related Information Storage Kit (BRISK) is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists. The software, documentation, Java source code and demo are available at http://genapha.icapture.ubc.ca/brisk/index.jsp. BRISK was developed in Java, and tested on an Apache Tomcat 6 server with a MySQL database. denise.daley@hli.ubc.ca.

Improving Aircraft Refueling Procedures at Naval Air Station Oceana

DTIC Science & Technology

2012-06-01

Station (NAS) Oceana, VA, using aircraft waiting time for fuel as a measure of performance. We develop a computer-assisted discrete-event simulation to...Station (NAS) Oceana, VA, using aircraft waiting time for fuel as a measure of performance. We develop a computer-assisted discrete-event simulation...server queue, with general interarrival and service time distributions gpm Gallons per minute JDK Java development kit M/M/1 Single-server queue

LIBMAKER

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

2015-08-01

Version 00 COG LibMaker contains various utilities to convert common data formats into a format usable by the COG - Multi-particle Monte Carlo Code System package, (C00777MNYCP01). Utilities included: ACEtoCOG - ACE formatted neutron data: Currently ENDFB7R0.BNL, ENDFB7R1.BNL, JEFF3.1, JEFF3.1.1, JEFF3.1.2, MCNP.50c, MCNP.51c, MCNP.55c, MCNP.66c, and MCNP.70c. ACEUtoCOG - ACEU formatted photonuclear data: Currently PN.MCNP.30c and PN.MCNP.70u. ACTLtoCOG - Creates a COG library from ENDL formatted activation data COG library. EDDLtoCOG - Creates a COG library from ENDL formatted LLNL deuteron data. ENDLtoCOG - Creates a COG library from ENDL formatted LLNL neutron data. EPDLtoCOG - Creates a COG librarymore » from ENDL formatted LLNL photon data. LEX - Creates a COG dictionary file. SAB.ACEtoCOG - Creates a COG library from ACE formatted S(a,b) data. SABtoCOG - Creates a COG library from ENDF6 formatted S(a,b) data. URRtoCOG - Creates a COG library from ACE formatted probability table data. This package also includes library checking and bit swapping capability.« less

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.

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

Candey, Robert M.; Harris, Bernard T.; Chimiak, Reine A.

2005-01-01

The Space Physics Data Facility (SPDF) Web services provides a distributed programming interface to a portion of the SPDF software. (A general description of Web services is available at http://www.w3.org/ and in many current software-engineering texts and articles focused on distributed programming.) The SPDF Web services distributed programming interface enables additional collaboration and integration of the SPDF software system with other software systems, in furtherance of the SPDF mission to lead collaborative efforts in the collection and utilization of space physics data and mathematical models. This programming interface conforms to all applicable Web services specifications of the World Wide Web Consortium. The interface is specified by a Web Services Description Language (WSDL) file. The SPDF Web services software consists of the following components: 1) A server program for implementation of the Web services; and 2) A software developer s kit that consists of a WSDL file, a less formal description of the interface, a Java class library (which further eases development of Java-based client software), and Java source code for an example client program that illustrates the use of the interface.

Visual Analysis of North Atlantic Hurricane Trends Using Parallel Coordinates and Statistical Techniques

DTIC Science & Technology

2008-07-07

analyzing multivariate data sets. The system was developed using the Java Development Kit (JDK) version 1.5; and it yields interactive performance on a... script and captures output from the MATLAB’s “regress” and “stepwisefit” utilities that perform simple and stepwise regression, respectively. The MATLAB...Statistical Association, vol. 85, no. 411, pp. 664–675, 1990. [9] H. Hauser, F. Ledermann, and H. Doleisch, “ Angular brushing of extended parallel coordinates

Math Description Engine Software Development Kit

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Smith, Stephanie L.; Dexter, Dan E.; Hodgson, Terry R.

2010-01-01

The Math Description Engine Software Development Kit (MDE SDK) can be used by software developers to make computer-rendered graphs more accessible to blind and visually-impaired users. The MDE SDK generates alternative graph descriptions in two forms: textual descriptions and non-verbal sound renderings, or sonification. It also enables display of an animated trace of a graph sonification on a visual graph component, with color and line-thickness options for users having low vision or color-related impairments. A set of accessible graphical user interface widgets is provided for operation by end users and for control of accessible graph displays. Version 1.0 of the MDE SDK generates text descriptions for 2D graphs commonly seen in math and science curriculum (and practice). The mathematically rich text descriptions can also serve as a virtual math and science assistant for blind and sighted users, making graphs more accessible for everyone. The MDE SDK has a simple application programming interface (API) that makes it easy for programmers and Web-site developers to make graphs accessible with just a few lines of code. The source code is written in Java for cross-platform compatibility and to take advantage of Java s built-in support for building accessible software application interfaces. Compiled-library and NASA Open Source versions are available with API documentation and Programmer s Guide at http:/ / prim e.jsc.n asa. gov.

NearFar: A computer program for nearside farside decomposition of heavy-ion elastic scattering amplitude

NASA Astrophysics Data System (ADS)

Cha, Moon Hoe

2007-02-01

The NearFar program is a package for carrying out an interactive nearside-farside decomposition of heavy-ion elastic scattering amplitude. The program is implemented in Java to perform numerical operations on the nearside and farside angular distributions. It contains a graphical display interface for the numerical results. A test run has been applied to the elastic O16+Si28 scattering at E=1503 MeV. Program summaryTitle of program: NearFar Catalogue identifier: ADYP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYP_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Computers: designed for any machine capable of running Java, developed on PC-Pentium-4 Operating systems under which the program has been tested: Microsoft Windows XP (Home Edition) Program language used: Java Number of bits in a word: 64 Memory required to execute with typical data: case dependent No. of lines in distributed program, including test data, etc.: 3484 Number of bytes distributed program, including test data, etc.: 142 051 Distribution format: tar.gz Other software required: A Java runtime interpreter, or the Java Development Kit, version 5.0 Nature of physical problem: Interactive nearside-farside decomposition of heavy-ion elastic scattering amplitude. Method of solution: The user must supply a external data file or PPSM parameters which calculates theoretical values of the quantities to be decomposed. Typical running time: Problem dependent. In a test run, it is about 35 s on a 2.40 GHz Intel P4-processor machine.

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 object providing the persistent data server is implemented using the Java progranu-ning language. It uses the JRB to store/retrieve data in/from a relational database server. The persistent data management system provides transaction and user management facilities which allow multi-user, distributed access to the stored data in a secure manner.

Arabidopsis COG Complex Subunits COG3 and COG8 Modulate Golgi Morphology, Vesicle Trafficking Homeostasis and Are Essential for Pollen Tube Growth

PubMed Central

Li, Yingxin; Li, Pengxiang; Gao, Caiji; Ding, Yu; Lan, Zhiyi; Shi, Zhixuan; Rui, Qingchen; Feng, Yihong; Liu, Yulong; Zhao, Yanxue; Wu, Chengyun; Zhang, Qian; Li, Yan; Jiang, Liwen

2016-01-01

Spatially and temporally regulated membrane trafficking events incorporate membrane and cell wall materials into the pollen tube apex and are believed to underlie the rapid pollen tube growth. In plants, the molecular mechanisms and physiological functions of intra-Golgi transport and Golgi integrity maintenance remain largely unclear. The conserved oligomeric Golgi (COG) complex has been implicated in tethering of retrograde intra-Golgi vesicles in yeast and mammalian cells. Using genetic and cytologic approaches, we demonstrate that T-DNA insertions in Arabidopsis COG complex subunits, COG3 and COG8, cause an absolute, male-specific transmission defect that can be complemented by expression of COG3 and COG8 from the LAT52 pollen promoter, respectively. No obvious abnormalities in the microgametogenesis of the two mutants are observed, but in vitro and in vivo pollen tube growth are defective. COG3 or COG8 proteins fused to green fluorescent protein (GFP) label the Golgi apparatus. In pollen of both mutants, Golgi bodies exhibit altered morphology. Moreover, γ-COP and EMP12 proteins lose their tight association with the Golgi. These defects lead to the incorrect deposition of cell wall components and proteins during pollen tube growth. COG3 and COG8 interact directly with each other, and a structural model of the Arabidopsis COG complex is proposed. We believe that the COG complex helps to modulate Golgi morphology and vesicle trafficking homeostasis during pollen tube tip growth. PMID:27448097

Consortium on the Genetics of Schizophrenia (COGS) assessment of endophenotypes for schizophrenia: an introduction to this Special Issue of Schizophrenia Research.

PubMed

Swerdlow, Neal R; Gur, Raquel E; Braff, David L

2015-04-01

The COGS is a multi-site NIMH-sponsored investigation of the genetic basis of 12 primary and multiple secondary quantitative endophenotypes in schizophrenia. Since 2003, COGS has completed studies using a family-based ascertainment strategy (COGS-1), and a case-control ascertainment strategy (COGS-2) (cumulative "n">4000). COGS-1 family study confirmed robust deficits in, and heritability of, these endophenotypes in schizophrenia, and provided evidence for a coherent genetic architecture underlying the risk for neurocognitive and neurophysiological deficits in this disorder. COGS-2 case-control findings, many reported herein, establish a foundation for fine genomic mapping and other analyses of these endophenotypes and risk genes for SZ. Several reports in this Special Issue compare findings of endophenotype deficits generated by fundamentally different COGS-1 vs. COGS-2 ascertainment strategies. Despite the expectation that family-based and case-control designs would establish demographically and potentially biologically distinct patient cohorts, findings generally revealed comparable patterns of endophenotype deficits across studies. The COGS-2 case-control design facilitated the accrual of a larger "n", permitting detailed analyses of factors moderating endophenotype performance. Some COGS-2 endophenotypes not assessed in COGS-1 are also reported, as is a new factor analytic strategy for identifying shared vs. unique factors among the COGS endophenotypes which can be used to develop composite variables with distinct genetic signatures. The path to date of COGS-1 endophenotype and genetic findings, followed by replication and extension in COGS-2, establishes benchmarks for endophenotype deficits in SZ and their moderation by specific factors, and clear expectations for informative findings from upcoming COGS-2 genetic analyses. Published by Elsevier B.V.

Consortium on the Genetics of Schizophrenia (COGS) assessment of endophenotypes for schizophrenia: An introduction to this Special Issue of schizophrenia research

PubMed Central

Swerdlow, Neal R.; Gur, Raquel E.; Braff, David L.

2014-01-01

Background The COGS is a multi-site NIMH-sponsored investigation of the genetic basis of 12 primary and multiple secondary quantitative endophenotypes in schizophrenia. Methods Since 2003, COGS has completed studies using a family-based ascertainment strategy (COGS-1), and a case–control ascertainment strategy (COGS-2) (cumulative “n” > 4000). Results COGS-1 family study confirmed robust deficits in, and heritability of, these endophenotypes in schizophrenia, and provided evidence for a coherent genetic architecture underlying the risk for neurocognitive and neurophysiological deficits in this disorder. COGS-2 case–control findings, many reported herein, establish a foundation for fine genomic mapping and other analyses of these endophenotypes and risk genes for SZ. Several reports in this Special Issue compare findings of endophenotype deficits generated by fundamentally different COGS-1 vs. COGS-2 ascertainment strategies. Despite the expectation that family-based and case–control designs would establish demographically and potentially biologically distinct patient cohorts, findings generally revealed comparable patterns of endophenotype deficits across studies. The COGS-2 case–control design facilitated the accrual of a larger “n”, permitting detailed analyses of factors moderating endophenotype performance. Some COGS-2 endophenotypes not assessed in COGS-1 are also reported, as is a new factor analytic strategy for identifying shared vs. unique factors among the COGS endophenotypes which can be used to develop composite variables with distinct genetic signatures. Discussion The path to date of COGS-1 endophenotype and genetic findings, followed by replication and extension in COGS-2, establishes benchmarks for endophenotype deficits in SZ and their moderation by specific factors, and clear expectations for informative findings from upcoming COGS-2 genetic analyses. PMID:25454799

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

PubMed Central

Meereis, Florian; Kaufmann, Michael

2008-01-01

Background The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries. Results Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at . Conclusion NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document. PMID:19014535

The COG database: new developments in phylogenetic classification of proteins from complete genomes

PubMed Central

Tatusov, Roman L.; Natale, Darren A.; Garkavtsev, Igor V.; Tatusova, Tatiana A.; Shankavaram, Uma T.; Rao, Bachoti S.; Kiryutin, Boris; Galperin, Michael Y.; Fedorova, Natalie D.; Koonin, Eugene V.

2001-01-01

The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih.gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis. PMID:11125040

Influences of posterior-located center of gravity on lumbar extension strength, balance, and lumbar lordosis in chronic low back pain.

PubMed

Kim, Dae-Hun; Park, Jin-Kyu; Jeong, Myeong-Kyun

2014-01-01

In patients with chronic low back pain, the center of gravity (COG) is abnormally located posterior to the center in most cases. The purpose of this study was to examine the effects of posterior-located COG on the functions (lumbar extension strength, and static and dynamic balance) and structure (lumbar lordosis angle and lumbosacral angle) of the lumbar spine. In this study, the COG of chronic low back pain patients who complained of only low back pain were examined using dynamic body balance equipment. A total of 164 subjects participated in the study (74 males and 90 females), and they were divided into two groups of 82 patients each. One group (n=82) consisted of patients whose COG was located at the center (C-COG); the other group (n=82) consisted of patients whose COG was located posterior to the center (P-COG). The following measures assessed the lumber functions and structures of the two groups: lumbar extension strength, moving speed of static and dynamic COGs, movement distance of the static and dynamic COGs, lumbar lordosis angle, and lumbosacral angle. The measured values were analyzed using independent t-tests. The group of patients with P-COG showed more decreases in lumbar extension strength, lumbar lordosis angle, and lumbosacral angle compared to the group of patients with C-COG. Also this group showed increases in moving speed and movement distance of the static COG. However, there were no differences in moving speed and movement distance of the dynamic COG between the two groups. These findings suggest that chronic LBP patients with P-COG have some disadvantages to establish lumbar extension strength and static and dynamic balance, which require specific efforts to maintain a neutral position and to control posture.

Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function

PubMed Central

Ungar, Daniel; Oka, Toshihiko; Brittle, Elizabeth E.; Vasile, Eliza; Lupashin, Vladimir V.; Chatterton, Jon E.; Heuser, John E.; Krieger, Monty; Waters, M. Gerard

2002-01-01

Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Three complexes that have previously been partially characterized include (a) the Golgi transport complex (GTC), identified in an in vitro membrane transport assay, (b) the ldlCp complex, identified in analyses of CHO cell mutants with defects in Golgi-associated glycosylation reactions, and (c) the mammalian Sec34 complex, identified by homology to yeast Sec34p, implicated in vesicular transport. We show that these three complexes are identical and rename them the conserved oligomeric Golgi (COG) complex. The COG complex comprises four previously characterized proteins (Cog1/ldlBp, Cog2/ldlCp, Cog3/Sec34, and Cog5/GTC-90), three homologues of yeast Sec34/35 complex subunits (Cog4, -6, and -8), and a previously unidentified Golgi-associated protein (Cog7). EM of ldlB and ldlC mutants established that COG is required for normal Golgi morphology. “Deep etch” EM of purified COG revealed an ∼37-nm-long structure comprised of two similarly sized globular domains connected by smaller extensions. Consideration of biochemical and genetic data for mammalian COG and its yeast homologue suggests a model for the subunit distribution within this complex, which plays critical roles in Golgi structure and function. PMID:11980916

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

PubMed

Makarova, Kira S; Sorokin, Alexander V; Novichkov, Pavel S; Wolf, Yuri I; Koonin, Eugene V

2007-11-27

An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover approximately 88% of the genes in a genome compared to a approximately 76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; approximately 40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems. The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: ftp://ftp.ncbi.nih.gov/pub/koonin/arCOGs/.

Mutations in proteins of the Conserved Oligomeric Golgi Complex affect polarity, cell wall structure, and glycosylation in the filamentous fungus Aspergillus nidulans.

PubMed

Gremillion, S K; Harris, S D; Jackson-Hayes, L; Kaminskyj, S G W; Loprete, D M; Gauthier, A C; Mercer, S; Ravita, A J; Hill, T W

2014-12-01

We have described two Aspergillus nidulans gene mutations, designated podB1 (polarity defective) and swoP1 (swollen cell), which cause temperature-sensitive defects during polarization. Mutant strains also displayed unevenness and abnormal thickness of cell walls. Un-polarized or poorly-polarized mutant cells were capable of establishing normal polarity after a shift to a permissive temperature, and mutant hyphae shifted from permissive to restrictive temperature show wall and polarity abnormalities in subsequent growth. The mutated genes (podB=AN8226.3; swoP=AN7462.3) were identified as homologues of COG2 and COG4, respectively, each predicted to encode a subunit of the multi-protein COG (Conserved Oligomeric Golgi) Complex involved in retrograde vesicle trafficking in the Golgi apparatus. Down-regulation of COG2 or COG4 resulted in abnormal polarization and cell wall staining. The GFP-tagged COG2 and COG4 homologues displayed punctate, Golgi-like localization. Lectin-blotting indicated that protein glycosylation was altered in the mutant strains compared to the wild type. A multicopy expression experiment showed evidence for functional interactions between the homologues COG2 and COG4 as well as between COG2 and COG3. To date, this work is the first regarding a functional role of the COG proteins in the development of a filamentous fungus. Copyright © 2014 Elsevier Inc. All rights reserved.

California Verbal Learning Test-II performance in schizophrenia as a function of ascertainment strategy: comparing the first and second phases of the Consortium on the Genetics of Schizophrenia (COGS).

PubMed

Stone, William S; Mesholam-Gately, Raquelle I; Braff, David L; Calkins, Monica E; Freedman, Robert; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Light, Gregory A; Nuechterlein, Keith H; Olincy, Ann; Radant, Allen D; Siever, Larry J; Silverman, Jeremy M; Sprock, Joyce; Sugar, Catherine A; Swerdlow, Neal R; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Seidman, Larry J

2015-04-01

The first phase of the Consortium on the Genetics of Schizophrenia (COGS-1) showed performance deficits in learning and memory on the California Verbal Learning Test, Second Edition (CVLT-II) in individuals with schizophrenia (SZ), compared to healthy comparison subjects (HCS). A question is whether the COGS-1 study, which used a family study design (i.e. studying relatively intact families), yielded "milder" SZ phenotypes than those acquired subsequently in the COGS-2 case-control design that did not recruit unaffected family members. CVLT-II performance was compared for the COGS-1 and COGS-2 samples. Analyses focused on learning, recall and recognition variables, with age, gender and education as covariates. Analyses of COGS-2 data explored effects of additional covariates and moderating factors in CVLT-II performance. 324 SZ subjects and 510 HCS had complete CVLT-II and covariate data in COGS-1, while 1356 SZ and 1036 HCS had complete data in COGS-2. Except for recognition memory, analysis of covariance showed significantly worse performance in COGS-2 on all CVLT-II variables for SZ and HCS, and remained significant in the presence of the covariates. Performance in each of the 5 learning trials differed significantly. However, effect sizes comparing cases and controls were comparable across the two studies. COGS-2 analyses confirmed SZ performance deficits despite effects of multiple significant covariates and moderating factors. CVLT-II performance was worse in COGS-2 than in COGS-1 for both the SZ and the HCS in this large cohort, likely due to cohort effects. Demographically corrected data yield a consistent pattern of performance across the two studies in SZ. Copyright © 2014. Published by Elsevier B.V.

PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.

PubMed

Meereis, Florian; Kaufmann, Michael

2004-10-15

The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (COGs). There are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for COGs containing (almost) exclusively proteins from (hyper)thermophilic genomes. However, public software to perform individually definable group-specific searches is not available. The tool described here exactly fills this gap. The software is accessible at http://www.uni-wh.de/pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the (current) 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes. This software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing (i) the presence and abundance of such COGs and (ii) the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

California Verbal Learning Test-II performance in schizophrenia as a function of ascertainment strategy: Comparing the first and second phases of the Consortium on the Genetics of Schizophrenia (COGS)

PubMed Central

Stone, William S.; Mesholam-Gately, Raquelle I.; Braff, David L.; Calkins, Monica E.; Freedman, Robert; Green, Michael F.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura C.; Light, Gregory A.; Nuechterlein, Keith H.; Olincy, Ann; Radant, Allen D.; Siever, Larry J.; Silverman, Jeremy M.; Sprock, Joyce; Sugar, Catherine A.; Swerdlow, Neal R.; Tsuang, Debby W.; Tsuang, Ming T.; Turetsky, Bruce I.; Seidman, Larry J.

2018-01-01

The first phase of the Consortium on the Genetics of Schizophrenia (COGS-1) showed performance deficits in learning and memory on the California Verbal Learning Test, Second Edition (CVLT-II) in individuals with schizophrenia (SZ), compared to healthy comparison subjects (HCS). A question is whether the COGS-1 study, which used a family study design (i.e. studying relatively intact families), yielded “milder” SZ phenotypes than those acquired subsequently in the COGS-2 case–control design that did not recruit unaffected family members. CVLT-II performance was compared for the COGS-1 and COGS-2 samples. Analyses focused on learning, recall and recognition variables, with age, gender and education as covariates. Analyses of COGS-2 data explored effects of additional covariates and moderating factors in CVLT-II performance. 324 SZ subjects and 510 HCS had complete CVLT-II and covariate data in COGS-1, while 1356 SZ and 1036 HCS had complete data in COGS-2. Except for recognition memory, analysis of covariance showed significantly worse performance in COGS-2 on all CVLT-II variables for SZ and HCS, and remained significant in the presence of the covariates. Performance in each of the 5 learning trials differed significantly. However, effect sizes comparing cases and controls were comparable across the two studies. COGS-2 analyses confirmed SZ performance deficits despite effects of multiple significant covariates and moderating factors. CVLT-II performance was worse in COGS-2 than in COGS-1 for both the SZ and the HCS in this large cohort, likely due to cohort effects. Demographically corrected data yield a consistent pattern of performance across the two studies in SZ. PMID:25497440

Neurocognitive performance in family-based and case-control studies of schizophrenia.

PubMed

Gur, Ruben C; Braff, David L; Calkins, Monica E; Dobie, Dorcas J; Freedman, Robert; Green, Michael F; Greenwood, Tiffany A; Lazzeroni, Laura C; Light, Gregory A; Nuechterlein, Keith H; Olincy, Ann; Radant, Allen D; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Sprock, Joyce; Stone, William S; Sugar, Catherine A; Swerdlow, Neal R; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Gur, Raquel E

2015-04-01

Neurocognitive deficits in schizophrenia (SZ) are established and the Consortium on the Genetics of Schizophrenia (COGS) investigated such measures as endophenotypes in family-based (COGS-1) and case-control (COGS-2) studies. By requiring family participation, family-based sampling may result in samples that vary demographically and perform better on neurocognitive measures. The Penn computerized neurocognitive battery (CNB) evaluates accuracy and speed of performance for several domains and was administered across sites in COGS-1 and COGS-2. Most tests were included in both studies. COGS-1 included 328 patients with SZ and 497 healthy comparison subjects (HCS) and COGS-2 included 1195 patients and 1009 HCS. Demographically, COGS-1 participants were younger, more educated, with more educated parents and higher estimated IQ compared to COGS-2 participants. After controlling for demographics, the two samples produced very similar performance profiles compared to their respective controls. As expected, performance was better and with smaller effect sizes compared to controls in COGS-1 relative to COGS-2. Better performance was most pronounced for spatial processing while emotion identification had large effect sizes for both accuracy and speed in both samples. Performance was positively correlated with functioning and negatively with negative and positive symptoms in both samples, but correlations were attenuated in COGS-2, especially with positive symptoms. Patients ascertained through family-based design have more favorable demographics and better performance on some neurocognitive domains. Thus, studies that use case-control ascertainment may tap into populations with more severe forms of illness that are exposed to less favorable factors compared to those ascertained with family-based designs.

Neurocognitive performance in family-based and case-control studies of schizophrenia

PubMed Central

Gur, Ruben C.; Braff, David L.; Calkins, Monica E.; Dobie, Dorcas J.; Freedman, Robert; Green, Michael F.; Greenwood, Tiffany A.; Lazzeroni, Laura C.; Light, Gregory A.; Nuechterlein, Keith H.; Olincy, Ann; Radant, Allen D.; Seidman, Larry J.; Siever, Larry J.; Silverman, Jeremy M.; Sprock, Joyce; Stone, William S.; Sugar, Catherine A.; Swerdlow, Neal R.; Tsuang, Debby W.; Tsuang, Ming T.; Turetsky, Bruce I.; Gur, Raquel E.

2014-01-01

Background Neurocognitive deficits in schizophrenia (SZ) are established and the Consortium on the Genetics of Schizophrenia (COGS) investigated such measures as endophenotypes in family-based (COGS-1) and case-control (COGS-2) studies. By requiring family participation, family-based sampling may result in samples that vary demographically and perform better on neurocognitive measures. Methods The Penn computerized neurocognitive battery (CNB) evaluates accuracy and speed of performance for several domains and was administered across sites in COGS-1 and COGS-2. Most tests were included in both studies. COGS-1 included 328 patients with SZ and 497 healthy comparison subjects (HCS) and COGS-2 included 1195 patients and 1009 HCS. Results Demographically, COGS-1 participants were younger, more educated, with more educated parents and higher estimated IQ compared to COGS-2 participants. After controlling for demographics, the two samples produced very similar performance profiles compared to their respective controls. As expected, performance was better and with smaller effect sizes compared to controls in COGS-1 relative to COGS-2. Better performance was most pronounced for spatial processing while emotion identification had large effect sizes for both accuracy and speed in both samples. Performance was positively correlated with functioning and negatively with negative and positive symptoms in both samples, but correlations were attenuated in COGS-2, especially with positive symptoms. Conclusions Patients ascertained through family-based design have more favorable demographics and better performance on some neurocognitive domains. Thus, studies that use case-control ascertainment may tap into populations with more severe forms of illness that are exposed to less favorable factors compared to those ascertained with family-based designs. PMID:25432636

Expanded microbial genome coverage and improved protein family annotation in the COG database

PubMed Central

Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

2015-01-01

Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the COGs is expected to become an important tool for microbial genomics. PMID:25428365

A quasi-randomized feasibility pilot study of specific treatments to improve emotion recognition and mental-state reasoning impairments in schizophrenia.

PubMed

Marsh, Pamela Jane; Polito, Vince; Singh, Subba; Coltheart, Max; Langdon, Robyn; Harris, Anthony W

2016-10-24

Impaired ability to make inferences about what another person might think or feel (i.e., social cognition impairment) is recognised as a core feature of schizophrenia and a key determinant of the poor social functioning that characterizes this illness. The development of treatments to target social cognitive impairments as a causal factor of impaired functioning in schizophrenia is of high priority. In this study, we investigated the acceptability, feasibility, and limited efficacy of 2 programs targeted at specific domains of social cognition in schizophrenia: "SoCog" Mental-State Reasoning Training (SoCog-MSRT) and "SoCog" Emotion Recognition Training (SoCog-ERT). Thirty-one participants with schizophrenia or schizoaffective disorder were allocated to either SoCog-MSRT (n = 19) or SoCog-ERT (n = 12). Treatment comprised 12 twice-weekly sessions for 6 weeks. Participants underwent assessments of social cognition, neurocognition and symptoms at baseline, post-training and 3-months after completing training. Attendance at training sessions was high with an average of 89.29 % attendance in the SoCog-MSRT groups and 85.42 % in the SoCog-ERT groups. Participants also reported the 2 programs as enjoyable and beneficial. Both SoCog-MSRT and SoCog-ERT groups showed increased scores on a false belief reasoning task and the Reading the Mind in the Eyes test. The SoCog-MSRT group also showed reduced personalising attributional biases in a small number of participants, while the SoCog-ERT group showed improved emotion recognition. The results are promising and support the feasibility and acceptability of the 2 SoCog programs as well as limited efficacy to improve social cognitive abilities in schizophrenia. There is also some evidence that skills for the recognition of basic facial expressions need specific training. Australian New Zealand Clinical Trials Registry ACTRN12613000978763 . Retrospectively registered 3/09/2013.

Measurements of characteristic parameters of extremely small cogged wheels with low module by means of low-coherence interferometry

NASA Astrophysics Data System (ADS)

Pakula, Anna; Tomczewski, Slawomir; Skalski, Andrzej; Biało, Dionizy; Salbut, Leszek

2010-05-01

This paper presents novel application of Low Coherence Interferometry (LCI) in measurements of characteristic parameters as circular pitch, foot diameter, heads diameter, in extremely small cogged wheels (cogged wheel diameter lower than θ=3 mm and module m = 0.15) produced from metal and ceramics. The most interesting issue concerning small diameter cogged wheels occurs during their production. The characteristic parameters of the wheel depend strongly on the manufacturing process and while inspecting small diameter wheels the shrinkage during the cast varies with the slight change of fabrication process. In the paper the LCI interferometric Twyman - Green setup with pigtailed high power light emitting diode, for cogged wheels measurement, is described. Due to its relatively big field of view the whole wheel can be examined in one measurement, without the necessity of numerical stitching. For purposes of small cogged wheel's characteristic parameters measurement the special binarization algorithm was developed and successfully applied. At the end the results of measurement of heads and foot diameters of two cogged wheels obtained by proposed LCI setup are presented and compared with the results obtained by the commercial optical profiler. The results of examination of injection moulds used for fabrication of measured cogged wheels are also presented. Additionally, the value of cogged wheels shrinkage is calculated as a conclusion for obtained results. Proposed method is suitable for complex measurements of small diameter cogged wheels with low module especially when there are no measurements standards for such objects.

Expanded microbial genome coverage and improved protein family annotation in the COG database.

PubMed

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2015-01-01

Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the COGs is expected to become an important tool for microbial genomics. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.

The DiaCog: A Prototype Tool for Visualizing Online Dialog Games' Interactions

ERIC Educational Resources Information Center

Yengin, Ilker; Lazarevic, Bojan

2014-01-01

This paper proposes and explains the design of a prototype learning tool named the DiaCog. The DiaCog visualizes dialog interactions within an online dialog game by using dynamically created cognitive maps. As a purposefully designed tool for enhancing learning effectiveness the DiaCog might be applicable to dialogs at discussion boards within a…

76 FR 13446 - Juniata Valley Railroad Company-Operation Exemption-SEDA-COG Joint Rail Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-11

... Railroad Company-Operation Exemption-SEDA-COG Joint Rail Authority Juniata Valley Railroad Company (JVRR... milepost 2.0 in Lewistown, Mifflin County, Pa. The line is owned or leased by SEDA-COG Joint Rail Authority (SEDA-COG). JVRR states that the line it proposes to operate is an extension of its existing line of...

76 FR 13445 - North Shore Railroad Company-Operation Exemption-SEDA-COG Joint Rail Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-11

... Railroad Company-Operation Exemption-SEDA-COG Joint Rail Authority North Shore Railroad Company (NSRR), a... milepost 2.0 in Berwick, Columbia County, Pa. The line is leased by SEDA-COG Joint Rail Authority (SEDA- COG). NSRR states that the line it proposes to operate is an extension of its existing line of...

76 FR 13445 - Lycoming Valley Railroad Company-Operation Exemption-SEDA-COG Joint Rail Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-11

... Railroad Company-Operation Exemption--SEDA--COG Joint Rail Authority Lycoming Valley Railroad Company (LVRR... milepost 0.4 in Muncy, Lycoming County, Pa. The line is owned or leased by SEDA-COG Joint Rail Authority (SEDA-COG). LVRR states that the line it proposes to operate is an extension of its existing line of...

Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

2015-01-01

With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection of archaeal Clusters of Orthologous Genes (arCOGs) to cover, on average, 91% of the protein-coding genes in 168 archaeal genomes. The new arCOGs were constructed using refined algorithms for orthology identification combined with extensive manual curation, including incorporation of the results of several completed and ongoing research projects in archaeal genomics. A new level of classification is introduced, superclusters that unit two or more arCOGs and more completely reflect gene family evolution than individual, disconnected arCOGs. Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality. In addition to their utility for genome annotation, arCOGs also are a platform for phylogenomic analysis. We explore this aspect of arCOGs by performing a phylogenomic study of the Thermococci that are traditionally viewed as the basal branch of the Euryarchaeota. The results of phylogenomic analysis that involved both comparison of multiple phylogenetic trees and a search for putative derived shared characters by using phyletic patterns extracted from the arCOGs reveal a likely evolutionary relationship between the Thermococci, Methanococci, and Methanobacteria. The arCOGs are expected to be instrumental for a comprehensive phylogenomic study of the archaea. PMID:25764277

New scoring methodology improves the sensitivity of the Alzheimer's Disease Assessment Scale-Cognitive subscale (ADAS-Cog) in clinical trials.

PubMed

Verma, Nishant; Beretvas, S Natasha; Pascual, Belen; Masdeu, Joseph C; Markey, Mia K

2015-11-12

As currently used, the Alzheimer's Disease Assessment Scale-Cognitive subscale (ADAS-Cog) has low sensitivity for measuring Alzheimer's disease progression in clinical trials. A major reason behind the low sensitivity is its sub-optimal scoring methodology, which can be improved to obtain better sensitivity. Using item response theory, we developed a new scoring methodology (ADAS-CogIRT) for the ADAS-Cog, which addresses several major limitations of the current scoring methodology. The sensitivity of the ADAS-CogIRT methodology was evaluated using clinical trial simulations as well as a negative clinical trial, which had shown an evidence of a treatment effect. The ADAS-Cog was found to measure impairment in three cognitive domains of memory, language, and praxis. The ADAS-CogIRT methodology required significantly fewer patients and shorter trial durations as compared to the current scoring methodology when both were evaluated in simulated clinical trials. When validated on data from a real clinical trial, the ADAS-CogIRT methodology had higher sensitivity than the current scoring methodology in detecting the treatment effect. The proposed scoring methodology significantly improves the sensitivity of the ADAS-Cog in measuring progression of cognitive impairment in clinical trials focused in the mild-to-moderate Alzheimer's disease stage. This provides a boost to the efficiency of clinical trials requiring fewer patients and shorter durations for investigating disease-modifying treatments.

76 FR 13446 - Nittany Bald and Eagle Railroad Company-Operation Exemption-SEDA-COG Joint Rail Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-11

... Eagle Railroad Company-Operation Exemption-SEDA- COG Joint Rail Authority Nittany Bald and Eagle... 0.0 and milepost 1.8 in Castanea, Clinton County, Pa. The line is owned or leased by SEDA-COG Joint Rail Authority (SEDA-COG). N&BE states that the line it proposes to operate is an extension of its...

Reduction of Cogging Torque in Dual Rotor Permanent Magnet Generator for Direct Coupled Wind Energy Systems

PubMed Central

Paulsamy, Sivachandran

2014-01-01

In wind energy systems employing permanent magnet generator, there is an imperative need to reduce the cogging torque for smooth and reliable cut in operation. In a permanent magnet generator, cogging torque is produced due to interaction of the rotor magnets with slots and teeth of the stator. This paper is a result of an ongoing research work that deals with various methods to reduce cogging torque in dual rotor radial flux permanent magnet generator (DRFPMG) for direct coupled stand alone wind energy systems (SAWES). Three methods were applied to reduce the cogging torque in DRFPMG. The methods were changing slot opening width, changing magnet pole arc width and shifting of slot openings. A combination of these three methods was applied to reduce the cogging torque to a level suitable for direct coupled SAWES. Both determination and reduction of cogging torque were carried out by finite element analysis (FEA) using MagNet Software. The cogging torque of DRFPMG has been reduced without major change in induced emf. A prototype of 1 kW, 120 rpm DRFPMG was fabricated and tested to validate the simulation results. The test results have good agreement with the simulation predictions. PMID:25202746

Reduction of cogging torque in dual rotor permanent magnet generator for direct coupled wind energy systems.

PubMed

Paulsamy, Sivachandran

2014-01-01

In wind energy systems employing permanent magnet generator, there is an imperative need to reduce the cogging torque for smooth and reliable cut in operation. In a permanent magnet generator, cogging torque is produced due to interaction of the rotor magnets with slots and teeth of the stator. This paper is a result of an ongoing research work that deals with various methods to reduce cogging torque in dual rotor radial flux permanent magnet generator (DRFPMG) for direct coupled stand alone wind energy systems (SAWES). Three methods were applied to reduce the cogging torque in DRFPMG. The methods were changing slot opening width, changing magnet pole arc width and shifting of slot openings. A combination of these three methods was applied to reduce the cogging torque to a level suitable for direct coupled SAWES. Both determination and reduction of cogging torque were carried out by finite element analysis (FEA) using MagNet Software. The cogging torque of DRFPMG has been reduced without major change in induced emf. A prototype of 1 kW, 120 rpm DRFPMG was fabricated and tested to validate the simulation results. The test results have good agreement with the simulation predictions.

Neurocognitive assessment in patients with a minor traumatic brain injury and an abnormal initial CT scan: Can cognitive evaluation assist in identifying patients who require surveillance CT brain imaging?

PubMed

Clements, Thomas W; Dunham, Michael; Kirkpatrick, Andrew; Rajakumar, Ruphus; Gratton, Carolyn; Lall, Rohan; McBeth, Paul; Ball, Chad G

2018-05-01

Evidence for repeat computed tomography (CT) in minor traumatic brain injury (mTBI) patients with intracranial pathology is scarce. The aim of this study was to investigate the utility of clinical cognitive assessment (COG) in defining the need for repeat imaging. COG performance was compared with findings on subsequent CT, and need for neurosurgery in mTBI patients (GCS 13-15 and positive CT findings). Of 152 patients, 65.8% received a COG (53.0% passed). Patients with passed COG underwent fewer repeat CT (43.4% vs. 78.7%; p = .001) and had shorter LOS (8.7 vs. 19.5; p < .05). Only 1 patient required neurosurgery after a passed COG. The negative predictive value of a normal COG was 90.6% (95%CI = 81.8%-95.4%). mTBI patients with an abnormal index CT who pass COG are less likely to undergo repeat CT head, and rarely require neurosurgery. The COG warrants further investigation to determine its role in omitting repeat head CT. Copyright © 2018 Elsevier Inc. All rights reserved.

The COG database: a tool for genome-scale analysis of protein functions and evolution

PubMed Central

Tatusov, Roman L.; Galperin, Michael Y.; Natale, Darren A.; Koonin, Eugene V.

2000-01-01

Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www.ncbi.nlm.nih.gov/COG ). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56–83% of the gene products from each of the complete bacterial and archaeal genomes and ~35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes. PMID:10592175

Adaptation effects in static postural control by providing simultaneous visual feedback of center of pressure and center of gravity.

PubMed

Takeda, Kenta; Mani, Hiroki; Hasegawa, Naoya; Sato, Yuki; Tanaka, Shintaro; Maejima, Hiroshi; Asaka, Tadayoshi

2017-07-19

The benefit of visual feedback of the center of pressure (COP) on quiet standing is still debatable. This study aimed to investigate the adaptation effects of visual feedback training using both the COP and center of gravity (COG) during quiet standing. Thirty-four healthy young adults were divided into three groups randomly (COP + COG, COP, and control groups). A force plate was used to calculate the coordinates of the COP in the anteroposterior (COP AP ) and mediolateral (COP ML ) directions. A motion analysis system was used to calculate the coordinates of the center of mass (COM) in both directions (COM AP and COM ML ). The coordinates of the COG in the AP direction (COG AP ) were obtained from the force plate signals. Augmented visual feedback was presented on a screen in the form of fluctuation circles in the vertical direction that moved upward as the COP AP and/or COG AP moved forward and vice versa. The COP + COG group received the real-time COP AP and COG AP feedback simultaneously, whereas the COP group received the real-time COP AP feedback only. The control group received no visual feedback. In the training session, the COP + COG group was required to maintain an even distance between the COP AP and COG AP and reduce the COG AP fluctuation, whereas the COP group was required to reduce the COP AP fluctuation while standing on a foam pad. In test sessions, participants were instructed to keep their standing posture as quiet as possible on the foam pad before (pre-session) and after (post-session) the training sessions. In the post-session, the velocity and root mean square of COM AP in the COP + COG group were lower than those in the control group. In addition, the absolute value of the sum of the COP - COM distances in the COP + COG group was lower than that in the COP group. Furthermore, positive correlations were found between the COM AP velocity and COP - COM parameters. The results suggest that the novel visual feedback training that incorporates the COP AP -COG AP interaction reduces postural sway better than the training using the COP AP alone during quiet standing. That is, even COP AP fluctuation around the COG AP would be effective in reducing the COM AP velocity.

Adolescents and Young Adults with Acute Lymphoblastic Leukemia and Acute Myeloid Leukemia: Impact of Care at Specialized Cancer Centers on Survival Outcome

PubMed Central

Wolfson, Julie; Sun, Can-Lan; Wyatt, Laura; Stock, Wendy; Bhatia, Smita

2017-01-01

Background Adolescents and young adults (AYA: 15-39y) with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) experience inferior survival when compared to children. Impact of care at NCI-designated Comprehensive Cancer Centers (CCC; or Children's Oncology Group sites [COG]) on survival disparities remains unstudied. Methods Using the Los Angeles Cancer registry, we identified 1,870 ALL or AML patients between 1 and 39y at diagnosis. Cox regression analyses assessed risk of mortality; younger age+CCC/COG served as the referent group. Logistic regression was used to determine odds of care at CCC/COG, adjusting for variables above. Results ALL outcome: AYAs at non-CCC/COG experienced inferior survival (15-21y: HR=1.9, p=0.005; 22-29y: HR=2.6, p<0.001; 30-39y: HR=3.0, p<0.001). Outcome at CCC/COG was comparable between children and young AYAs (15-21y: HR=1.3, p=0.3; 22-29y: HR=1.2, p=0.2) but was inferior for 30-39yo (HR=3.4, p<0.001). AML outcome: AYAs at non-CCC/COG experienced inferior outcome (15-21y: HR=1.8, p=0.02; 22-39y: HR=1.4, p=0.06). Outcome at CCC/COG was comparable between children and 15-21yo (HR=1.3, p=0.4) but was inferior for 22-39yo (HR=1.7, p=0.05). Access: 15-21yo were less likely to use CCC/COG than children (p<0.001). In 22-39yo, public/uninsured (ALL: p=0.004; AML<0.001), African-American/Hispanics (ALL: p=0.03), and 30-39yo (ALL: p=0.03) were less likely to use CCC/COG. Conclusions Poor survival in AYAs with ALL and AML is mitigated by care at CCC/COG. Barriers to CCC/COG care include public/uninsured, and African-American/Hispanic race/ethnicity. Impact Care at CCC/COG explains, in part, inferior outcomes in AYAs with ALL and AML. Key sociodemographic factors serve as barriers to care at specialized centers. PMID:28209594

Development of the beam extraction synchronization system at the Fermilab Booster

NASA Astrophysics Data System (ADS)

Seiya, K.; Chaurize, S.; Drennan, C. C.; Pellico, W.; Sullivan, T.; Triplett, A. K.; Waller, A. M.

2015-11-01

The new beam extraction synchronization control system called "Magnetic Cogging" was developed at the Fermilab Booster and it replaces a system called "RF Cogging" as part of the Proton Improvement Plan (PIP).[1] The flux throughput goal for the PIP is 2.2×1017 protons per hour, which is double the present flux. The flux increase will be accomplished by doubling the number of beam cycles which, in turn, will double the beam loss in the Booster accelerator if nothing else is done. The Booster accelerates beam from 400 MeV to 8 GeV and extracts it to the Main Injector (MI) or Recycler Ring (RR). Cogging controls the beam extraction gap position which is created early in the Booster cycle and synchronizes the gap to the rising edge of the Booster extraction kicker and the MI/RR injection kicker. The RF Cogging system controls the gap position by changing only the radial position of the beam thus limiting the beam aperture and creating beam loss due to beam scraping. The Magnetic Cogging system controls the gap position with the magnetic field of the dipole correctors while the radial position feedback keeps the beam on a central orbit. Also with Magnetic Cogging the gap creation can occur earlier in the Booster cycle when the removed particles are at a lower energy. Thus Magnetic Cogging reduces the deposited energy of the lost particles (beam energy loss) and results in less beam loss activation. Energy loss was reduced by 40% by moving the gap creation energy from 700 MeV to 400 MeV when the Booster Cogging system was switched from RF Cogging to Magnetic Cogging in March 2015.

Efficacy of a medical food on cognition in Alzheimer's disease: results from secondary analyses of a randomized, controlled trial.

PubMed

Kamphuis, P J G H; Verhey, F R J; Olde Rikkert, M G M; Twisk, J W R; Swinkels, S H N; Scheltens, P

2011-08-01

To investigate the extent that baseline cognitive impairment and intake adherence affected the 13-item Alzheimer's Disease Assessment Scale - cognitive subscale (ADAS-cog) intervention response of a medical food in Alzheimer's Disease (AD) patients. DESIGN/SETTING/PARTICIPANTS /INTERVENTION/MEASUREMENTS: This analysis was performed on data from a proof-of-concept study, consisting of a 12-week, double-blind, randomized, controlled, multicenter trial, followed by a similarly designed 12-week extension study. Patients with mild AD (Mini-Mental State Examination [MMSE] score of 20-26) were randomized to receive active or control product as a 125 ml daily drink. One of the co-primary outcome measures was the 13-item ADAS-cog. In this analysis, the study population was divided into two subgroups: patients with 'low' baseline ADAS-cog scores (<25.0) and patients with 'high' baseline ADAS-cog scores (≥25.0). Repeated Measures Models (RMM) were used to determine the relationship between ADAS-cog score and intervention. A significant treatment effect (F[1,319]=4.0, p=0.046) was shown in patients with 'high' baseline ADAS-cog, but not in patients with 'low' baseline ADAS-cog (F[1,250]=1.25, p=0.265). Overall, intake adherence was significantly correlated with ADAS-cog improvement in the active product group (correlation coefficient=-0.260; p=0.019), but not the control group. These data indicate that baseline ADAS-cog significantly influenced the effect of Souvenaid intervention on ADAS-cog outcome. A higher intake of active study product was also associated with greater cognitive benefit. These findings highlight the potential benefits of Souvenaid in AD patients and warrant confirmation in larger, controlled studies.

Model of the multipolar engine with decreased cogging torque by asymmetrical distribution of the magnets

NASA Astrophysics Data System (ADS)

Goryca, Zbigniew; Paduszyński, Kamil; Pakosz, Artur

2018-03-01

This paper presents the results of field calculations of cogging torque for a 12-pole torque motor with an 18-slot stator. A constant angular velocity magnet and the same size gap between n-1 magnets were assumed. In these conditions, the effect of change of the n-th gap between magnets on the cogging torque was tested. Due to considerable length of the machine the calculations were performed using a 2D model. The n-th gap for which the cogging torque assumed the lowest value was evaluated. The cogging torque of the machine with symmetrical magnetic circuit (the same size of gap between magnets) was compared to the one of the asymmetrical machine. With proper choice of asymmetry, the cogging torque for the machine decreased by four times.

Using the Cognitive Abilities Test (CogAT) 7 Nonverbal Battery to Identify the Gifted/Talented: An Investigation of Demographic Effects and Norming Plans

ERIC Educational Resources Information Center

Carman, Carol A.; Walther, Christine A. P.; Bartsch, Robert A.

2018-01-01

The nonverbal battery of the Cognitive Abilities Test (CogAT) is one of the two most common nonverbal measures used in gifted identification, yet the relationships between demographic variables and CogAT7 performance has not yet been fully examined. Additionally, the effect of using the CogAT7 nonverbal battery on the identification of diverse…

Development and construct validation of the Client-Centredness of Goal Setting (C-COGS) scale.

PubMed

Doig, Emmah; Prescott, Sarah; Fleming, Jennifer; Cornwell, Petrea; Kuipers, Pim

2015-07-01

Client-centred philosophy is integral to occupational therapy practice and client-centred goal planning is considered fundamental to rehabilitation. Evaluation of whether goal-planning practices are client-centred requires an understanding of the client's perspective about goal-planning processes and practices. The Client-Centredness of Goal Setting (C-COGS) was developed for use by practitioners who seek to be more client-centred and who require a scale to guide and evaluate individually orientated practice, especially with adults with cognitive impairment related to acquired brain injury. To describe development of the C-COGS scale and examine its construct validity. The C-COGS was administered to 42 participants with acquired brain injury after multidisciplinary goal planning. C-COGS scores were correlated with the Canadian Occupational Performance Measure (COPM) importance scores, and measures of therapeutic alliance, motivation, and global functioning to establish construct validity. The C-COGS scale has three subscales evaluating goal alignment, goal planning participation, and client-centredness of goals. The C-COGS subscale items demonstrated moderately significant correlations with scales measuring similar constructs. Findings provide preliminary evidence to support the construct validity of the C-COGS scale, which is intended to be used to evaluate and reflect on client-centred goal planning in clinical practice, and to highlight factors contributing to best practice rehabilitation.

A Mild Form of COG5 Defect Showing Early-Childhood-Onset Friedreich's-Ataxia-Like Phenotypes with Isolated Cerebellar Atrophy.

PubMed

Kim, Young Ok; Yun, Misun; Jeong, Jae Ho; Choi, Seong Min; Kim, Seul Kee; Yoon, Woong; Park, Chungoo; Hong, Yeongjin; Woo, Young Jong

2017-11-01

Progressive cerebellar ataxias are rare diseases during childhood, especially under 6 years of age. In a single family, three affected siblings exhibited Friedreich's-ataxia-like phenotypes before 2 years of age. They had progressive cerebellar atrophy, intellectual disability, and scoliosis. Although their phenotypes were similar to those observed in patients with autosomal recessive cerebellar ataxias, other phenotypes (e.g., seizure, movement disorders, ophthalmologic disturbance, cardiomyopathy, and cutaneous disorders) were not noted in this family. Whole-exome sequencing of the family members revealed one potential heterozygous mutation (c.1209delG, NM_181733.2; p.Met403IlefsX3, NP_859422.2) of the gene encoding conserved oligomeric Golgi complex subunit 5 (COG5). The heterozygous deletion at the fifth base in exon 12 of COG5 caused a frameshift and premature stop. Western blotting of COG5 proteins in the skin tissues from an affected proband showed a significantly decreased level of full length COG5 and smaller, aberrant COG5 proteins. We reported a milder form of COG5 defect showing Friedreich's-ataxia-like phenotypes without hypotonia, microcephaly, and short stature that were observed in most patients with COG5 defect. © 2017 The Korean Academy of Medical Sciences.

Predicting Operator Execution Times Using CogTool

NASA Technical Reports Server (NTRS)

Santiago-Espada, Yamira; Latorella, Kara A.

2013-01-01

Researchers and developers of NextGen systems can use predictive human performance modeling tools as an initial approach to obtain skilled user performance times analytically, before system testing with users. This paper describes the CogTool models for a two pilot crew executing two different types of a datalink clearance acceptance tasks, and on two different simulation platforms. The CogTool time estimates for accepting and executing Required Time of Arrival and Interval Management clearances were compared to empirical data observed in video tapes and registered in simulation files. Results indicate no statistically significant difference between empirical data and the CogTool predictions. A population comparison test found no significant differences between the CogTool estimates and the empirical execution times for any of the four test conditions. We discuss modeling caveats and considerations for applying CogTool to crew performance modeling in advanced cockpit environments.

Relationship of CogScreen-AE to flight simulator performance and pilot age.

PubMed

Taylor, J L; O'Hara, R; Mumenthaler, M S; Yesavage, J A

2000-04-01

We report on the relationship between CogScreen-Aeromedical Edition (AE) factor scores and flight simulator performance in aircraft pilots aged 50-69. Some 100 licensed, civilian aviators (average age 58+/-5.3 yr) performed aviation tasks in a Frasca model 141 flight simulator and the CogScreen-AE battery. The aviation performance indices were: a) staying on course; b) dialing in communication frequencies; c) avoiding conflicting traffic; d) monitoring cockpit instruments; e) executing the approach; and f) a summary score, which was the mean of these scores. The CogScreen predictors were based on a factor structure reported by Kay (11), which comprised 28 CogScreen scores. Through principal components analysis of Kay's nine factors, we reduced the number of predictors to five composite CogScreen scores: Speed/Working Memory (WM), Visual Associative Memory, Motor Coordination, Tracking, and Attribute Identification. Speed/WM scores had the highest correlation with the flight summary score, Spearman r(rho) = 0.57. A stepwise-forward multiple regression analysis indicated that four CogScreen variables could explain 45% of the variance in flight summary scores. Significant predictors, in order of entry, were: Speed/WM, Visual Associative Memory, Motor Coordination, and Tracking (p<0.05). Pilot age was found to significantly improve prediction beyond that which could be predicted by the four cognitive variables. In addition, there was some evidence for specific ability relationships between certain flight component scores and CogScreen scores, such as approach performance and tracking errors. These data support the validity of CogScreen-AE as a cognitive battery that taps skills relevant to piloting.

‘Sciencenet’—towards a global search and share engine for all scientific knowledge

PubMed Central

Lütjohann, Dominic S.; Shah, Asmi H.; Christen, Michael P.; Richter, Florian; Knese, Karsten; Liebel, Urban

2011-01-01

Summary: Modern biological experiments create vast amounts of data which are geographically distributed. These datasets consist of petabytes of raw data and billions of documents. Yet to the best of our knowledge, a search engine technology that searches and cross-links all different data types in life sciences does not exist. We have developed a prototype distributed scientific search engine technology, ‘Sciencenet’, which facilitates rapid searching over this large data space. By ‘bringing the search engine to the data’, we do not require server farms. This platform also allows users to contribute to the search index and publish their large-scale data to support e-Science. Furthermore, a community-driven method guarantees that only scientific content is crawled and presented. Our peer-to-peer approach is sufficiently scalable for the science web without performance or capacity tradeoff. Availability and Implementation: The free to use search portal web page and the downloadable client are accessible at: http://sciencenet.kit.edu. The web portal for index administration is implemented in ASP.NET, the ‘AskMe’ experiment publisher is written in Python 2.7, and the backend ‘YaCy’ search engine is based on Java 1.6. Contact: urban.liebel@kit.edu Supplementary Material: Detailed instructions and descriptions can be found on the project homepage: http://sciencenet.kit.edu. PMID:21493657

Adolescents and Young Adults with Acute Lymphoblastic Leukemia and Acute Myeloid Leukemia: Impact of Care at Specialized Cancer Centers on Survival Outcome.

PubMed

Wolfson, Julie; Sun, Can-Lan; Wyatt, Laura; Stock, Wendy; Bhatia, Smita

2017-03-01

Background: Adolescents and young adults (AYA; 15-39 years) with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) experience inferior survival when compared with children. Impact of care at NCI-designated Comprehensive Cancer Centers (CCC) or Children's Oncology Group sites (COG) on survival disparities remains unstudied. Methods: Using the Los Angeles cancer registry, we identified 1,870 ALL or AML patients between 1 and 39 years at diagnosis. Cox regression analyses assessed risk of mortality; younger age + CCC/COG served as the referent group. Logistic regression was used to determine odds of care at CCC/COG, adjusting for variables above. Results: ALL outcome: AYAs at non-CCC/COG experienced inferior survival (15-21 years: HR = 1.9, P = 0.005; 22-29 years: HR = 2.6, P < 0.001; 30-39 years: HR = 3.0, P < 0.001). Outcome at CCC/COG was comparable between children and young AYAs (15-21 years: HR = 1.3, P = 0.3; 22-29 years: HR = 1.2, P = 0.2) but was inferior for 30- to 39-year-olds (HR = 3.4, P < 0.001). AML outcome: AYAs at non-CCC/COG experienced inferior outcome (15-21 years: HR = 1.8, P = 0.02; 22-39 years: HR = 1.4, P = 0.06). Outcome at CCC/COG was comparable between children and 15- to 21-year-olds (HR = 1.3, P = 0.4) but was inferior for 22- to 39-year-olds (HR = 1.7, P = 0.05). Access: 15- to 21-year-olds were less likely to use CCC/COG than children ( P < 0.001). In 22- to 39-year-olds, public/uninsured (ALL: P = 0.004; AML<0.001), African American/Hispanics (ALL: P = 0.03), and 30- to 39-year-olds (ALL: P = 0.03) were less likely to use CCC/COG. Conclusions: Poor survival in AYAs with ALL and AML is mitigated by care at CCC/COG. Barriers to CCC/COG care include public/uninsured, and African American/Hispanic race/ethnicity. Impact: Care at CCC/COG explains, in part, inferior outcomes in AYAs with ALL and AML. Key sociodemographic factors serve as barriers to care at specialized centers. Cancer Epidemiol Biomarkers Prev; 26(3); 312-20. ©2017 AACR . ©2017 American Association for Cancer Research.

Toward improved guideline quality: using the COGS statement with GEM.

PubMed

Shiffman, Richard N; Michel, Georges

2004-01-01

The Conference on Guideline Standardization (COGS) was convened to create a standardized documentation checklist for clinical practice guidelines in an effort to promote guideline quality and facilitate implementation. The statement was created by a multidisciplinary panel using a rigorous consensus development methodology. The Guideline Elements Model (GEM) provides a standardized approach to representing guideline documents using XML. In this work, we demonstrate the sufficiency of GEM for describing COGS components. Using the mapping between COGS and GEM elements we built an XSLT application to examine a guideline's adherence (or non-adherence) to the COGS checklist. Once a guideline has been marked up according to the GEM hierarchy, its knowledge content can be reused in multiple ways.

Comparing of cogging torque reduction methods in permanent magnet machines with fractional slot windings

NASA Astrophysics Data System (ADS)

Pristup, A. G.; Toporkov, D. M.

2017-10-01

The results of the investigation of the cogging torque in permanent magnet synchronous machines, which is caused by the stator slotting and the rotor eccentricity, are presented in the paper. A new design of the machine has been developed in the course of the investigation, and the value of the cogging torque in this construction is less considerably compared to other constructions. In contrast to the available methods of the cogging torque reduction, the solution suggested not only decreases the level of the cogging torque but also has negligibly small influence on characteristics of the machine with the rotor eccentricity which is typical of the mass production and long-term usage.

Successful COG8 and PDF overlap is mediated by alterations in splicing and polyadenylation signals.

PubMed

Pereira-Castro, Isabel; Quental, Rita; da Costa, Luís T; Amorim, António; Azevedo, Luisa

2012-02-01

Although gene-free areas compose the great majority of eukaryotic genomes, a significant fraction of genes overlaps, i.e., unique nucleotide sequences are part of more than one transcription unit. In this work, the evolutionary history and origin of a same-strand gene overlap is dissected through the analysis of COG8 (component of oligomeric Golgi complex 8) and PDF (peptide deformylase). Comparative genomic surveys reveal that the relative locations of these two genes have been changing over the last 445 million years from distinct chromosomal locations in fish to overlapping in rodents and primates, indicating that the overlap between these genes precedes their divergence. The overlap between the two genes was initiated by the gain of a novel splice donor site between the COG8 stop codon and PDF initiation codon. Splicing is accomplished by the use of the PDF acceptor, leading COG8 to share the 3'end with PDF. In primates, loss of the ancestral polyadenylation signal for COG8 makes the overlap between COG8 and PDF mandatory, while in mouse and rat concurrent overlapping and non-overlapping Cog8 transcripts exist. Altogether, we demonstrate that the origin, evolution and preservation of the COG8/PDF same-strand overlap follow similar mechanistic steps as those documented for antisense overlaps where gain and/or loss of splice sites and polyadenylation signals seems to drive the process.

Cognitive Symptom Management and Rehabilitation Therapy (CogSMART) for veterans with traumatic brain injury: pilot randomized controlled trial.

PubMed

Twamley, Elizabeth W; Jak, Amy J; Delis, Dean C; Bondi, Mark W; Lohr, James B

2014-01-01

Traumatic brain injury (TBI) can result in cognitive impairments and persistent postconcussive symptoms that limit functional recovery, including return to work. We evaluated a 12 wk compensatory cognitive training intervention (Cognitive Symptom Management and Rehabilitation Therapy [CogSMART]) in the context of supported employment for Veterans with mild to moderate TBI. Participants were randomly assigned to receive 12 wk of supported employment plus CogSMART or enhanced supported employment that controlled for therapist attention (control). CogSMART sessions were delivered by the employment specialist and included psychoeducation regarding TBI; strategies to improve sleep, fatigue, headaches, and tension; and compensatory cognitive strategies in the domains of prospective memory, attention, learning and memory, and executive functioning. Compared with controls, those assigned to supported employment plus CogSMART demonstrated significant reductions in postconcussive symptoms (Cohen d = 0.97) and improvements in prospective memory functioning (Cohen d = 0.72). Effect sizes favoring CogSMART for posttraumatic stress disorder symptom severity, depressive symptom severity, and attainment of competitive work within 14 wk were in the small to medium range (Cohen d = 0.35-0.49). Those who received CogSMART rated the intervention highly. Results suggest that adding CogSMART to supported employment may improve postconcussive symptoms and prospective memory. These effects, as well as smaller effects on psychiatric symptoms and ability to return to work, warrant replication in a larger trial.

Validity and reliability of the G-Cog device for kinematic measurements.

PubMed

Chiementin, X; Crequy, S; Bertucci, W

2013-11-01

The aim of this study was to test the validity and the reliability of the G-Cog which is a new BMX powermeter allowing for the measurements of the acceleration on X-Y-Z axis (250 Hz) at the BMX rear wheel. These measurements allow computing lateral, angular, linear acceleration, angular, linear velocity and the distance. Mechanical measurements at submaximal intensities in standardized laboratory conditions and during maximal exercises in the field conditions were performed to analyse the reliability of the G-Cog accelerometers. The performances were evaluated in comparison with an industrial accelerometer and with 2 powermeters, the SRM and PowerTap. Our results in laboratory conditions show that the G-Cog measurements have low value of variation coefficient (CV=2.35%). These results suggest that the G-cog accelerometers measurements are reproducible. The ratio limits of agreement of the rear hub angular velocity differences between the SRM and the G-Cog were 1.010 × ÷ 1.024 (95%CI=0.986-1.034) and between PowerTap and G-Cog were 0.993 × ÷ 1.019 (95%CI=0.974-1.012). In conclusion, our results suggest that the G-Cog angular velocity measurements are valid and reliable compared with SRM and PowerTap and could be used to analyse the kinematics during BMX actual conditions. © Georg Thieme Verlag KG Stuttgart · New York.

Arterial pressure-based cardiac output monitoring: a multicenter validation of the third-generation software in septic patients.

PubMed

De Backer, Daniel; Marx, Gernot; Tan, Andrew; Junker, Christopher; Van Nuffelen, Marc; Hüter, Lars; Ching, Willy; Michard, Frédéric; Vincent, Jean-Louis

2011-02-01

Second-generation FloTrac software has been shown to reliably measure cardiac output (CO) in cardiac surgical patients. However, concerns have been raised regarding its accuracy in vasoplegic states. The aim of the present multicenter study was to investigate the accuracy of the third-generation software in patients with sepsis, particularly when total systemic vascular resistance (TSVR) is low. Fifty-eight septic patients were included in this prospective observational study in four university-affiliated ICUs. Reference CO was measured by bolus pulmonary thermodilution (iCO) using 3-5 cold saline boluses. Simultaneously, CO was computed from the arterial pressure curve recorded on a computer using the second-generation (CO(G2)) and third-generation (CO(G3)) FloTrac software. CO was also measured by semi-continuous pulmonary thermodilution (CCO). A total of 401 simultaneous measurements of iCO, CO(G2), CO(G3), and CCO were recorded. The mean (95%CI) biases between CO(G2) and iCO, CO(G3) and iCO, and CCO and iCO were -10 (-15 to -5)% [-0.8 (-1.1 to -0.4) L/min], 0 (-4 to 4)% [0 (-0.3 to 0.3) L/min], and 9 (6-13)% [0.7 (0.5-1.0) L/min], respectively. The percentage errors were 29 (20-37)% for CO(G2), 30 (24-37)% for CO(G3), and 28 (22-34)% for CCO. The difference between iCO and CO(G2) was significantly correlated with TSVR (r(2) = 0.37, p < 0.0001). A very weak (r(2) = 0.05) relationship was also observed for the difference between iCO and CO(G3). In patients with sepsis, the third-generation FloTrac software is more accurate, as precise, and less influenced by TSVR than the second-generation software.

Validation of the Chinese version of the CogState computerised cognitive assessment battery in Taiwanese patients with heart failure.

PubMed

Chou, Cheng-Chen; Pressler, Susan J; Giordani, Bruno; Fetzer, Susan Jane

2015-11-01

To evaluate the validity of the Chinese version of the CogState battery, a computerised cognitive testing among patients with heart failure in Taiwan. Cognitive deficits are common in patients with heart failure and a validated Chinese measurement is required for assessing cognitive change for this population. The CogState computerised battery is a measurement of cognitive function and has been validated in many languages, but not Chinese. A cross-sectional study. A convenience sample consisted of 76 women with heart failure and 64 healthy women in northern Taiwan. Women completed the Chinese version of the CogState battery and the Montreal Cognitive Assessment. Construct validity of the Chinese version of the battery was evaluated by exploratory factor analysis and known-group comparisons. Convergent validity of the CogState tasks was examined by Pearson correlation coefficients. Principal components factor analysis with promax rotation showed two factors reflecting the speed and memory dimensions of the tests. Scores for CogState battery tasks showed significant differences between the heart failure and healthy control group. Examination of convergent validity of the CogState found a significant association with the Montreal Cognitive Assessment. The Chinese CogState Battery has satisfactory construct and convergent validity to measure cognitive deficits in patients with heart failure in Taiwan. The Chinese CogState battery is a valid instrument for detecting cognitive deficits that may be subtle in the early stages, and identifying changes that provide insights into patients' abilities to implement treatment accurately and consistently. Better interventions tailored to the needs of the cognitive impaired population can be developed. © 2015 John Wiley & Sons Ltd.

A comparison of the COG and MCNP codes in computational neutron capture therapy modeling, Part I: boron neutron capture therapy models.

PubMed

Culbertson, C N; Wangerin, K; Ghandourah, E; Jevremovic, T

2005-08-01

The goal of this study was to evaluate the COG Monte Carlo radiation transport code, developed and tested by Lawrence Livermore National Laboratory, for neutron capture therapy related modeling. A boron neutron capture therapy model was analyzed comparing COG calculational results to results from the widely used MCNP4B (Monte Carlo N-Particle) transport code. The approach for computing neutron fluence rate and each dose component relevant in boron neutron capture therapy is described, and calculated values are shown in detail. The differences between the COG and MCNP predictions are qualified and quantified. The differences are generally small and suggest that the COG code can be applied for BNCT research related problems.

Cogging Torque Reduction Techniques for Spoke-type IPMSM

NASA Astrophysics Data System (ADS)

Bahrim, F. S.; Sulaiman, E.; Kumar, R.; Jusoh, L. I.

2017-08-01

A spoke-type interior permanent magnet synchronous motor (IPMSM) is extending its tentacles in industrial arena due to good flux-weakening capability and high power density. In many of the application, high strength of permanent magnet causes the undesirable effects of high cogging torque that can aggravate performance of the motor. High cogging torque is significantly produced by IPMSM due to the similar length and the effectiveness of the magnetic air-gap. The address of this study is to analyze and compare the cogging torque effect and performance of four common techniques for cogging torque reduction such as skewing, notching, pole pairing and rotor pole pairing. With the aid of 3-D finite element analysis (FEA) by JMAG software, a 6S-4P Spoke-type IPMSM with various rotor-PM configurations has been designed. As a result, the cogging torque effect reduced up to 69.5% for skewing technique, followed by 31.96%, 29.6%, and 17.53% by pole pairing, axial pole pairing and notching techniques respectively.

Robust differences in antisaccade performance exist between COGS schizophrenia cases and controls regardless of recruitment strategies.

PubMed

Radant, Allen D; Millard, Steven P; Braff, David L; Calkins, Monica E; Dobie, Dorcas J; Freedman, Robert; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Light, Gregory A; Meichle, Sean P; Nuechterlein, Keith H; Olincy, Ann; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Swerdlow, Neal R; Sugar, Catherine A; Tsuang, Ming T; Turetsky, Bruce I; Tsuang, Debby W

2015-04-01

The impaired ability to make correct antisaccades (i.e., antisaccade performance) is well documented among schizophrenia subjects, and researchers have successfully demonstrated that antisaccade performance is a valid schizophrenia endophenotype that is useful for genetic studies. However, it is unclear how the ascertainment biases that unavoidably result from recruitment differences in schizophrenia subjects identified in family versus case-control studies may influence patient-control differences in antisaccade performance. To assess the impact of ascertainment bias, researchers from the Consortium on the Genetics of Schizophrenia (COGS) compared antisaccade performance and antisaccade metrics (latency and gain) in schizophrenia and control subjects from COGS-1, a family-based schizophrenia study, to schizophrenia and control subjects from COGS-2, a corresponding case-control study. COGS-2 schizophrenia subjects were substantially older; had lower education status, worse psychosocial function, and more severe symptoms; and were three times more likely to be a member of a multiplex family than COGS-1 schizophrenia subjects. Despite these variations, which were likely the result of ascertainment differences (as described in the introduction to this special issue), the effect sizes of the control-schizophrenia differences in antisaccade performance were similar in both studies (Cohen's d effect size of 1.06 and 1.01 in COGS-1 and COGS-2, respectively). This suggests that, in addition to the robust, state-independent schizophrenia-related deficits described in endophenotype studies, group differences in antisaccade performance do not vary based on subject ascertainment and recruitment factors. Published by Elsevier B.V.

Robust differences in antisaccade performance exist between COGS schizophrenia cases and controls regardless of recruitment strategies

PubMed Central

Radant, Allen D.; Millard, Steven P.; Braff, David; Calkins, Monica E.; Dobie, Dorcas J.; Freedman, Robert; Green, Michael F.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura; Light, Gregory A.; Meichle, Sean; Nuechterlein, Keith H.; Olincy, Ann; Seidman, Larry J.; Siever, Larry; Silverman, Jeremy; Stone, William S.; Swerdlow, Neal R.; Sugar, Catherine; Tsuang, Ming T.; Turetsky, Bruce I.; Tsuang, Debby W.

2015-01-01

The impaired ability to make correct antisaccades (i.e., antisaccade performance) is well documented among schizophrenia subjects, and researchers have successfully demonstrated that antisaccade performance is a valid schizophrenia endophenotype that is useful for genetic studies. However, it is unclear how the ascertainment biases that unavoidably result from recruitment differences in schizophrenia subjects identified in family versus case-control studies may influence patient-control differences in antisaccade performance. To assess the impact of ascertainment bias, researchers from the Consortium on the Genetics of Schizophrenia (COGS) compared antisaccade performance and antisaccade metrics (latency and gain) in schizophrenia and control subjects from COGS-1, a family-based schizophrenia study, to schizophrenia and control subjects from COGS-2, a corresponding case-control study. COGS-2 schizophrenia subjects were substantially older; had lower education status, worse psychosocial function, and more severe symptoms; and were three times more likely to be a member of a multiplex family than COGS-1 schizophrenia subjects. Despite these variations, which were likely the result of ascertainment differences (as described in the introduction to this special issue), the effect sizes of the control-schizophrenia differences in antisaccade performance were similar in both studies (Cohen’s d effect size of 1.06 and 1.01 in COGS-1 and COGS-2, respectively). This suggests that, in addition to the robust, state-independent schizophrenia-related deficits described in endophenotype studies, group differences in antisaccade performance do not vary based on subject ascertainment and recruitment factors. PMID:25553977

Functional magnetic resonance imaging and transcranial magnetic stimulation: effects of motor imagery, movement and coil orientation.

PubMed

Niyazov, D M; Butler, A J; Kadah, Y M; Epstein, C M; Hu, X P

2005-07-01

To compare fMRI activations during movement and motor imagery to corresponding motor evoked potential (MEP) maps obtained with the TMS coil in three different orientations. fMRI activations during executed (EM) and imagined (IM) movements of the index finger were compared to MEP maps of the first dorsal interosseus (FDI) muscle obtained with the TMS coil in anterior, posterior and lateral handle positions. To ensure spatial registration of fMRI and MEP maps, a special grid was used in both experiments. No statistically significant difference was found between the TMS centers of gravity (TMS CoG) obtained with the three coil orientations. There was a significant difference between fMRI centers of gravity during IMs (IM CoG) and EMs (EM CoG), with IM CoGs localized on average 10.3mm anterior to those of EMs in the precentral gyrus. Most importantly, the IM CoGs closely matched cortical projections of the TMS CoGs while the EM CoGs were on average 9.5mm posterior to the projected TMS CoGs. TMS motor maps are more congruent with fMRI activations during motor imagery than those during EMs. These findings are not significantly affected by changing orientation of the TMS coil. Our results suggest that the discrepancy between fMRI and TMS motor maps may be largely due to involvement of the somatosensory component in the EM task.

Microbial community analysis using MEGAN.

PubMed

Huson, Daniel H; Weber, Nico

2013-01-01

Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de. © 2013 Elsevier Inc. All rights reserved.

Turning of COGS moves forward findings for hormonally mediated cancers.

PubMed

Sakoda, Lori C; Jorgenson, Eric; Witte, John S

2013-04-01

The large-scale Collaborative Oncological Gene-environment Study (COGS) presents new findings that further characterize the genetic bases of breast, ovarian and prostate cancers. We summarize and provide insights into this collection of papers from COGS and discuss the implications of the results and future directions for such efforts.

COGcollator: a web server for analysis of distant relationships between homologous protein families.

PubMed

Dibrova, Daria V; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Mulkidjanian, Armen Y

2017-11-29

The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs. We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server. Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1. This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf.

Creating Knock-outs of Conserved Oligomeric Golgi complex subunits using CRISPR-mediated gene editing paired with a selection strategy based on glycosylation defects associated with impaired COG complex function

PubMed Central

Blackburn, Jessica Bailey; Lupashin, Vladimir V.

2017-01-01

Summary The Conserved Oligomeric Golgi (COG) complex is a key evolutionally conserved multisubunit protein machinery that regulates tethering and fusion of intra-Golgi transport vesicles. The Golgi apparatus specifically promotes sorting and complex glycosylation of glycoconjugates. Without proper glycosylation and processing, proteins and lipids will be mislocalized and/or have impaired function. The Golgi glycosylation machinery is kept in homeostasis by a careful balance of anterograde and retrograde trafficking to ensure proper localization of the glycosylation enzymes and their substrates. This balance, like other steps of membrane trafficking, is maintained by vesicle trafficking machinery that includes COPI vesicular coat proteins, SNAREs, Rabs, and both coiled-coil and multi-subunit vesicular tethers. COG complex interacts with other membrane trafficking components and is essential for proper localization of Golgi glycosylation machinery. Here we describe using CRISPR-mediated gene editing coupled with a phenotype-based selection strategy directly linked to the COG complex’s role in glycosylation homeostasis to obtain COG complex subunit knock-outs (KOs). This has resulted in clonal KOs for each COG subunit in HEK293T cells and gives the ability to further probe the role of the COG complex in Golgi homeostasis. PMID:27632008

Examining the reliability of ADAS-Cog change scores.

PubMed

Grochowalski, Joseph H; Liu, Ying; Siedlecki, Karen L

2016-09-01

The purpose of this study was to estimate and examine ways to improve the reliability of change scores on the Alzheimer's Disease Assessment Scale, Cognitive Subtest (ADAS-Cog). The sample, provided by the Alzheimer's Disease Neuroimaging Initiative, included individuals with Alzheimer's disease (AD) (n = 153) and individuals with mild cognitive impairment (MCI) (n = 352). All participants were administered the ADAS-Cog at baseline and 1 year, and change scores were calculated as the difference in scores over the 1-year period. Three types of change score reliabilities were estimated using multivariate generalizability. Two methods to increase change score reliability were evaluated: reweighting the subtests of the scale and adding more subtests. Reliability of ADAS-Cog change scores over 1 year was low for both the AD sample (ranging from .53 to .64) and the MCI sample (.39 to .61). Reweighting the change scores from the AD sample improved reliability (.68 to .76), but lengthening provided no useful improvement for either sample. The MCI change scores had low reliability, even with reweighting and adding additional subtests. The ADAS-Cog scores had low reliability for measuring change. Researchers using the ADAS-Cog should estimate and report reliability for their use of the change scores. The ADAS-Cog change scores are not recommended for assessment of meaningful clinical change.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

PubMed

Wolf, Yuri I; Makarova, Kira S; Yutin, Natalya; Koonin, Eugene V

2012-12-14

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer. The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).

Science Opportunity Analyzer (SOA): Science Planning Made Simple

NASA Technical Reports Server (NTRS)

Streiffert, Barbara A.; Polanskey, Carol A.

2004-01-01

.For the first time at JPL, the Cassini mission to Saturn is using distributed science operations for developing their experiments. Remote scientists needed the ability to: a) Identify observation opportunities; b) Create accurate, detailed designs for their observations; c) Verify that their designs meet their objectives; d) Check their observations against project flight rules and constraints; e) Communicate their observations to other scientists. Many existing tools provide one or more of these functions, but Science Opportunity Analyzer (SOA) has been built to unify these tasks into a single application. Accurate: Utilizes JPL Navigation and Ancillary Information Facility (NAIF) SPICE* software tool kit - Provides high fidelity modeling. - Facilitates rapid adaptation to other flight projects. Portable: Available in Unix, Windows and Linux. Adaptable: Designed to be a multi-mission tool so it can be readily adapted to other flight projects. Implemented in Java, Java 3D and other innovative technologies. Conclusion: SOA is easy to use. It only requires 6 simple steps. SOA's ability to show the same accurate information in multiple ways (multiple visualization formats, data plots, listings and file output) is essential to meet the needs of a diverse, distributed science operations environment.

Material and Compression Properties of Cedrela odorata Gum Co-Processed with Plantain Starch and Microcrystalline Cellulose.

PubMed

Adetunji, Oladapo Adewale; Odeniyi, Michael Ayodele

2016-01-01

Many excipients used in tableting exhibit some undesirable properties such as poor flow, cohesion and lubricating characteristics, thus necessitating some modification to achieve the desired product. The objective of this study was to enhance the material, flow and compressional properties of Cedrela odorata gum (COG) (Family: Meliaceae) by co-processing with plantain starch (PS) and microcrystalline cellulose (MCC). The COG was co-processed with PS (or MCC) by physical co-grinding at ratio 1 : 1, 1 : 2 and 1 : 4, and characterized using morphological analysis, swelling index viscosity measurements, particle size analysis and FTIR spectra. The material, flow and compressional properties of the co-processed excipients were also evaluated. Results were analyzed using mean and standard deviation of data. There was a decrease in the degree of agglomeration of COG and a reduction in the size of the powdered gum. The co-processed excipients were more spherical than the native excipients. The COG had the highest viscosity, while MCC and COG : PS (1 : 2) showed the highest and lowest degrees of swelling at 27.0 ± 0.05°C respectively. Water absorption capacity of the component excipients improved with co-processing COG : MCC increasing from 171.8 ± 1.54 (1 : 1) to 214.8 ± 1.07 (1 : 2), while COG : PS increased from 95.2 ± 0.08 (1 : 1) to 206.2 ± 0.13. There was a decrease in the percentage solubility of the co-processed excipients with the highest and lowest solubility observed in COG (54.1 ± 0.07%) and PS (3.7 ± 0.16%), respectively. The FTIR spectra indicate no significant interaction between the excipients. The poor flow of the component excipients did not improve with co-processing; however, there was a significant increase in compressibility. Generally, COG co-processed with MCC showed better compression properties when compared with COG co-processed with PS. Co-processing of COD with MC or PS enhanced the characters of the component excipients, thus making the co-processed excipients suitable for direct compression of tablets without altering the chemical nature of the component excipients.

The development and validation of a carer questionnaire to assess cognitive function in neuropsychiatric patients.

PubMed

Randhawa, Sharan; Walterfang, Mark; Miller, Kathryn; Scholes, Amelia; Mocellin, Ramon; Velakoulis, Dennis

2007-07-01

The carer history is an integral part of the assessment of patients with cognitive impairment. We aimed to develop a comprehensive yet concise carer questionnaire, the CogRisk, which captures actuarial risk variables for cognitive impairment in addition to key symptoms suggestive of cognitive decline in a number of cognitive domains, and to then assess its validity and reliability in a neuropsychiatric population. Carers of patients assessed for cognitive impairment completed the CogRisk, and patients were clinically assessed using the Mini-Mental State Examination (MMSE) and Neuropsychiatry Unit COGnitive assessment tool (NUCOG). Reliability was assessed using test-retest and interrater measures and measures of internal consistency. Construct and concurrent validity was assessed using correlation between total and subscale scores on the CogRisk, total scores on the NUCOG and MMSE, and subscale scores on the NUCOG. Predictive validity was determined using measures of sensitivity and specificity and using receiver operating characteristic (ROC) methods. The CogRisk was completed by all carers in less than 10 min. The total CogRisk score correlated significantly with total MMSE and NUCOG scores (r=-0.511 and -0.563, respectively) and remained highly significant when age and education were controlled for. Internal consistency of CogRisk items was high (alpha=0.943). Intrarater reliability of the CogRisk was high with an intraclass correlation coefficient of .978 (P<.001), and interrater reliability between carers was also high at 0.868 (P<.05). Sensitivity and specificity for the detection of dementia were .70 and .73, respectively, with area under the ROC curve not significantly different from that of the MMSE or NUCOG. The CogRisk is a brief carer-rated tool of a patient's cognitive functioning developed for use within a neuropsychiatric setting. It exhibited good concurrent validity, internal consistency, and interrater and intrarater reliability. The CogRisk also demonstrated good sensitivity and specificity for dementia. The CogRisk provides carer information, which complements the clinical assessment and can be used to focus on direct carer interview.

The association of cognitive fatigue with menopause, depressive symptoms, and quality of life in ambulatory breast cancer patients.

PubMed

Miura, Kiyoko; Ando, Shoko; Imai, Tsuneo

2016-05-01

The causes of cancer-related fatigue, which can influence patients' activities, are multidimensional; however, little is known about the cognitive dimension. We examined the association of cognitive fatigue with menopause, depressive symptoms, and quality of life in ambulatory breast cancer patients after primary treatment. This descriptive, cross-sectional study recruited 20-64-year-old breast cancer patients in an outpatient setting. The patients (N = 93; mean age = 53 years) were divided into low (L-CogF) and high-cognitive fatigue (H-CogF) groups according to their scores on the cognitive fatigue subscale of the Cancer Fatigue Scale. We compared the groups on their sociodemographic and medical characteristics and scores on the Functional Assessment of Cancer Therapy-Breast (FACT-B) [a measure of quality of life (QOL)], Simplified Menopausal Index (SMI), and Self-Rating Questionnaire for Depression (SRQ-D). The L-CogF (n = 55) and H-CogF (n = 38) patients did not differ in age, years since diagnosis, marital status, educational background, or treatment history. Total and subscale FACT-B scores, except for physical well-being, were significantly lower in H-CogF participants than in L-CogF participants. SMI and SRQ-D scores were significantly higher in H-CogF participants. Employed H-CogF participants were concerned about keeping their jobs (p < 0.05). Breast cancer patients with high-cognitive fatigue suffer from severe menopause and depressive symptoms, and deteriorating QOL. Cognitive fatigue should be considered when interpreting patients' cognitive complaints.

The Earth System CoG Collaboration Environment

NASA Astrophysics Data System (ADS)

DeLuca, C.; Murphy, S.; Cinquini, L.; Treshansky, A.; Wallis, J. C.; Rood, R. B.; Overeem, I.

2013-12-01

The Earth System CoG supports collaborative Earth science research and product development in virtual organizations that span multiple projects and communities. It provides access to data, metadata, and visualization services along with tools that support open project governance, and it can be used to host individual projects or to profile projects hosted elsewhere. All projects on CoG are described using a project ontology - an organized common vocabulary - that exposes information needed for collaboration and decision-making. Projects can be linked into a network, and the underlying ontology enables consolidated views of information across the network. This access to information promotes the creation of active and knowledgeable project governance, at both individual and aggregate project levels. CoG is being used to support software development projects, model intercomparison projects, training classes, and scientific programs. Its services and ontology are customizable by project. This presentation will provide an overview of CoG, review examples of current use, and discuss how CoG can be used as knowledge and coordination hub for networks of projects in the Earth Sciences.

Should the SCOPA-COG be modified? A Rasch analysis perspective.

PubMed

Forjaz, M J; Frades-Payo, B; Rodriguez-Blazquez, C; Ayala, A; Martinez-Martin, P

2010-02-01

The SCales for Outcomes in PArkinson's disease-Cognition (SCOPA-COG) is a specific measure of cognitive function for Parkinson's disease (PD) patients. Previous studies, under the frame of the classic test theory, indicate satisfactory psychometric properties. The Rasch model, an item response theory approach, provides new information about the scale, as well as results in a linear scale. This study aims at analysing the SCOPA-COG according to the Rasch model and, on the basis of results, suggesting modification to the SCOPA-COG. Fit to the Rasch model was analysed using a sample of 384 PD patients. A good fit was obtained after rescoring for disordered thresholds. The person separation index, a reliability measure, was 0.83. Differential item functioning was observed by age for three items and by gender for one item. The SCOPA-COG is a unidimensional measure of global cognitive function in PD patients, with good scale targeting and no empirical evidence for use of the subscale scores. Its adequate reliability and internal construct validity were supported. The SCOPA-COG, with the proposed scoring scheme, generates true linear interval scores.

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

TMED6-COG8 is a novel molecular marker of TFE3 translocation renal cell carcinoma

PubMed Central

Xu, Yongcan; Rao, Qiu; Xia, Qiuyuan; Shi, Shanshan; Shi, Qunli; Ma, Henghui; Lu, Zhenfeng; Chen, Hui; Zhou, Xiaojun

2015-01-01

TFE3 translocation renal cell carcinoma is a highly aggressive malignancy which often occurs primarily in children and young adults. The pathognomonic molecular lesion in this subtype is a translocation event involving the TFE3 transcription factor at chromosome Xp11.2. Hence, the pathological diagnosis of an Xp11.2 translocation RCC is based upon morphology, TFE3 immunohistochemistry, or genetic analyses. However, due to the false-positive immunoreactivity for TFE3 IHC and expensive for TFE3 break-apart FISH assay, additional molecular markers are necessary to help provide early diagnose and individualization treatment. Owing to recent advances in microarray and RNA-Seq, Pflueger et al. have discovered that TMED6-COG8 is dramatically increased in TFE3 translocation RCCs, compared with clear cell RCCs and papillary RCCs, implying that TMED6-COG8 might be a new molecular tumor marker of TFE3 translocation RCCs. To extend this observation, we firstly validated the TMED6-COG8 expression level by qRT-PCR in RCCs including Xp11.2 translocation RCCs (n = 5), clear cell RCCs (n = 7) and papillary RCCs (n = 5). Then, we also examined the expression level of TMED6-COG8 chimera in Xp11.2 translocation alveolar soft part sarcoma. We found that TMED6-COG8 chimera expression level was higher in Xp11.2 translocation RCCs than in ASPS (P < 0.05). What’s more, the expression levels of TMED6-COG8 chimera in esophagus cancers (n = 32), gastric cancers (n = 11), colorectal cancers (n = 12), hepatocellular carcinomas (n = 10) and non-small-cell lung cancers (n = 12) were assessed. Unexpectedly, TMED6-COG8 chimera was decreased in these five human types. Therefore, our observations from this study indicated that TMED6-COG8 chimera might act as a novel diagnostic marker in Xp11.2 translocation RCCs. PMID:26045774

Neuropsychometric tests in cross sectional and longitudinal studies - a regression analysis of ADAS - cog, SKT and MMSE.

PubMed

Ihl, R; Grass-Kapanke, B; Jänner, M; Weyer, G

1999-11-01

In clinical and drug studies, different neuropsychometric tests are used. So far, no empirical data have been published to compare studies using different tests. The purpose of this study was to calculate a regression formula allowing a comparison of cross-sectional and longitudinal data from three neuropsychometric tests that are frequently used in drug studies (Alzheimer's Disease Assessment Scale, ADAS-cog; Syndrom Kurz Test, SKT; Mini Mental State Examination, MMSE). 177 patients with dementia according to ICD10 criteria were studied for the cross sectional and 61 for the longitudinal analysis. Correlations and linear regressions were calculated between tests. Significance was proven with ANOVA and t-tests using the SPSS statistical package. Significant Spearman correlations and slopes in the regression occurred in the cross sectional analysis (ADAS-cog-SKT r(s) = 0.77, slope = 0.45, SKT-ADAS-cog slope = 1.3, r2 = 0.59; ADAS-cog-MMSE r2 = 0.76, slope = -0.42, MMSE-ADAS-cog slope = -1.5, r2 = 0.64; MMSE-SKT r(s) = -0.79, slope = -0.87, SKT-MMSE slope = -0.71, r2 = 0.62; p<0.001 after Bonferroni correction; N = 177) and in the longitudinal analysis (SKT-ADAS-cog, r(s) = 0.48, slope = 0.69, ADAS-cog-SKT slope = 0.69, p<0.001, r2 = 0.32, MMSE-SKT, r(s) = 0.44, slope = -0.41, SKT-MMSE, slope = -0.55, p<0.001, r2 = 0.21). The results allow calculation of ADAS-scores when SKT scores are given, and vice versa. In longitudinal studies or in the course of the disease, scores assessed with the ADAS-cog and the SKT may now be statistically compared. In all comparisons, bottom and ceiling effects of the tests have to be taken into account.

Psychometric evaluation of ADAS-Cog and NTB for measuring drug response.

PubMed

Karin, A; Hannesdottir, K; Jaeger, J; Annas, P; Segerdahl, M; Karlsson, P; Sjögren, N; von Rosen, T; Miller, F

2014-02-01

To conduct a psychometric analysis to determine the adequacy of instruments that measure cognition in Alzheimer's disease trials. Both the Alzheimer's Disease Assessment Scale - Cognition (ADAS-Cog) and the Neuropsychological Test Battery (NTB) are validated outcome measures for clinical trials in Alzheimer's disease and are approved also for regulatory purposes. However, it is not clear how comparable they are in measuring cognitive function. In fact, many recent trials in Alzheimer's disease patients have failed and it has been questioned if ADAS-Cog still is a sensitive measure. The present paper examines the psychometric properties of ADAS-Cog and NTB, based on a post hoc analysis of data from a clinical trial (NCT01024660), which was conducted by AstraZeneca, in mild-to-moderate Alzheimer's disease (AD) patients, with a Mini Mental State Examination (MMSE) Total score 16-24. Acceptability, reliability, different types of validity and ability to detect change were assessed using relevant statistical methods. Total scores of both tests, as well as separate domains of both tests, including the Wechsler Memory Scale (WMS), Rey Auditory Verbal Learning Test (RAVLT) and Delis-Kaplan Executive Function System (D-KEFS) Verbal Fluency Condition, were analyzed. Overall, NTB performed well, with acceptable reliability and ability to detect change, while ADAS-Cog had insufficient psychometric properties, including ceiling effects in 8 out of a total of 11 ADAS-Cog items in mild AD patients, as well as low test-retest reliability in some of the items. Based on a direct comparison on the same patient sample, we see advantages of the NTB compared with the ADAS-Cog for the evaluation of cognitive function in the population of mild-to-moderate AD patients. The results suggest that not all of ADAS-Cog items are relevant for both mild and moderate AD population. This validation study demonstrates satisfactory psychometric properties of the NTB, while ADAS-Cog was found to be psychometrically inadequate. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Cogging Torque Estimation of Permanent Magnet Motors Resulting from Magnetic Anisotropy of Non-oriented Electrical Steel Sheets

NASA Astrophysics Data System (ADS)

Daikoku, Akihiro; Yamaguchi, Shinichi; Toide, Yukari; Fujiwara, Koji; Takahashi, Norio

This paper examines the cogging torque of permanent magnet motors resulting from the magnetic anisotropy of non-oriented steel sheets used for magnetic core. The cogging torque due to the magnetic anisotropy is calculated by FEM using two modeling methods; one is the newly developed method which takes account of the two-dimensional magnetic properties in arbitrary directions, and the other is the conventional method which uses only two magnetization curves both in rolling and transverse directions. In the proposed method, the measured magnetic properties are treated in two different ways; in the first way the data are used directly, and in the second way the data are interpolated using Bèzier surface. As a result, all of three models show the cogging torque component resulting from the magnetic anisotropy, that has less pulsation numbers per rotation than that of isotropic model. The difference of the cogging torque amplitude between the three models is small in the region of low magnetic flux density, however, it gradually becomes large along with the increase in magnetic flux density. The measured results of cogging torque is proximate to the results calculated by two-dimensional magnetic property method using the magnetic property data directly. The error is approximately 4% at the point where the cogging torque component resulting from the magnetic anisotropy is maximum.

The characteristics of patients with uncertain/mild cognitive impairment on the Alzheimer disease assessment scale-cognitive subscale.

PubMed

Pyo, Geunyeong; Elble, Rodger J; Ala, Thomas; Markwell, Stephen J

2006-01-01

The performances of the uncertain/mild cognitive impairment (MCI) patients on the Alzheimer Disease Assessment Scale-Cognitive (ADAS-Cog) subscale were compared with those of normal controls, Alzheimer disease patients with CDR 0.5, and Alzheimer disease patients with CDR 1.0. The Uncertain/MCI group was significantly different from normal controls and Alzheimer disease CDR 0.5 or 1.0 groups on the ADAS-Cog except on a few non-memory subtests. Age was significantly correlated with total error score in the normal group, but there was no significant correlation between age and ADAS-Cog scores in the patient groups. Education was not significantly correlated with the ADAS-Cog scores in any group. Regardless of age and educational level, there were clear differences between the normal group and the Uncertain/MCI group, especially on the total error scores. We found that the total error score of the ADAS-Cog was the most reliable variable in detecting patients with mild cognitive impairment. The present study demonstrated that the ADAS-Cog is a promising tool for detecting and studying patients with mild cognitive impairment. The results also indicated that demographic variables such as age and education do not play a significant role in the diagnosis of mild cognitive impaired patients based on the ADAS-Cog scores.

Comparison of centre of gravity and centre of pressure patterns in the golf swing.

PubMed

Smith, Aimée C; Roberts, Jonathan R; Kong, Pui Wah; Forrester, Stephanie E

2017-03-01

Analysing the centre of pressure (COP) and centre of gravity (COG) could reveal stabilising strategies used by golfers throughout the golf swing. This study identified and compared golfers' COP and COG patterns throughout the golf swing in medial-lateral (ML) and anterior-posterior (AP) directions using principal component analysis (PCA) and examined their relationship to clubhead velocity. Three-dimensional marker trajectories were collected using Vicon motion analysis and force plate data from two Kistler force plates for 22 low-handicap golfers during drives. Golfers' COG and COP were expressed as a percentage distance between their feet. PCA was performed on COG and COP in ML and AP directions. Relationships between principal component (PC) scores were examined using Pearson correlation and regression analysis used to examine the relationship with clubhead velocity. ML COP movements varied in magnitude (PC1), rate of change and timing (PC2 and PC3). The COP and COG PC1 scores were strongly correlated in both directions (ML: r = 0.90, P < .05; AP: r = 0.81, P < .05). Clubhead velocity, explained by three PCs (74%), related to timing and rate of change in COP ML near downswing (PC2 and PC3) and timing of COG ML late backswing (PC2). The relationship between COP ML and COG ML PC1 scores identified extremes of COP and COG patterns in golfers and could indicate a golfer's dynamic balance. Golfers with earlier movement of COP to the front foot (PC2) and rate of change (PC3) patterns in ML COP, prior to the downswing, may be more likely to generate higher clubhead velocity.

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities.

PubMed

Oberding, Lisa; Gieg, Lisa M

2016-01-05

Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.

A comparison of the COG and MCNP codes in computational neutron capture therapy modeling, Part II: gadolinium neutron capture therapy models and therapeutic effects.

PubMed

Wangerin, K; Culbertson, C N; Jevremovic, T

2005-08-01

The goal of this study was to evaluate the COG Monte Carlo radiation transport code, developed and tested by Lawrence Livermore National Laboratory, for gadolinium neutron capture therapy (GdNCT) related modeling. The validity of COG NCT model has been established for this model, and here the calculation was extended to analyze the effect of various gadolinium concentrations on dose distribution and cell-kill effect of the GdNCT modality and to determine the optimum therapeutic conditions for treating brain cancers. The computational results were compared with the widely used MCNP code. The differences between the COG and MCNP predictions were generally small and suggest that the COG code can be applied to similar research problems in NCT. Results for this study also showed that a concentration of 100 ppm gadolinium in the tumor was most beneficial when using an epithermal neutron beam.

Calculation of cogging force in a novel slotted linear tubular brushless permanent magnet motor

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

Zhu, Z.Q.; Hor, P.J.; Howe, D.

1997-09-01

There is an increasing requirement for controlled linear motion over short and long strokes, in the factory automation and packaging industries, for example. Linear brushless PM motors could offer significant advantages over conventional actuation technologies, such as motor driven cams and linkages and pneumatic rams--in terms of efficiency, operating bandwidth, speed and thrust control, stroke and positional accuracy, and indeed over other linear motor technologies, such as induction motors. Here, a finite element/analytical based technique for the prediction of cogging force in a novel topology of slotted linear brushless permanent magnet motor has been developed and validated. The various forcemore » components, which influence cogging are pre-calculated by the finite element analysis of some basic magnetic structures, facilitate the analytical synthesis of the resultant cogging force. The technique can be used to aid design for the minimization of cogging.« less

Development of Cogging at the Fermilab Booster

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

Seiya, K.; Chaurize, S.; Drennan, C.

2015-01-30

The development of magnetic cogging is part of the Fermilab Booster upgrade within the Proton Improvement Plan (PIP). The Booster is going to send 2.25E17 protons/hour which is almost double the present flux, 1.4E17 protons/hour to the Main Injector (MI) and Recycler (RR). The extraction kicker gap has to synchronize to the MI and RR injection bucket in order to avoid a beam loss at the rising edge of the extraction and injection kickers. Magnetic cogging is able to control the revolution frequency and the position of the gap using the magnetic field from dipole correctors while radial position feedbackmore » keeps the beam at the central orbit. The new cogging is expected to reduce beam loss due to the orbit changes and reduce beam energy loss when the gap is created. The progress of the magnetic cogging system development is going to be discussed in this paper.« less

Evaluation of the Earth System CoG Infrastructure in Supporting a Model Intercomparison Project

NASA Astrophysics Data System (ADS)

Wallis, J. C.; Rood, R. B.; Murphy, S.; Cinquini, L.; DeLuca, C.

2013-12-01

Earth System CoG is a web-based collaboration environment that combines data services with metadata and project management services. The environment is particularly suited to support software development and model intercomparison projects. CoG was recently used to support the National Climate Predictions and Projections Platform (NCPP) Quantitative Evaluation of Downscaling (QED-2013) workshop. QED-2013 was a workshop with a community approach for the objective, quantitative evaluation of techniques to downscale climate model predictions and projections. This paper will present a brief introduction to CoG, QED-2013, and findings from an ethnographic evaluation of how CoG supported QED-2013. The QED-2013 workshop focused on real-world application problems drawn from several sectors, and contributed to the informed use of downscaled data. This workshop is a part of a larger effort by NCPP and partner organizations to develop a standardized evaluation framework for local and regional climate information. The main goals of QED-2013 were to a) coordinate efforts for quantitative evaluation, b) develop software infrastructure, c) develop a repository of information, d) develop translational and guidance information, e) identify and engage key user communities, and f) promote collaboration and interoperability. CoG was a key player in QED-2013 support. NCPP was an early adopter of the CoG platform, providing valuable recommendations for overall development plus specific workshop-related requirements. New CoG features developed for QED-2013 included: the ability to publish images and associated metadata contained within XML files to its associated data node combine both artifacts into an integrated display. The ability to modify data search facets into scientifically relevant groups and display dynamic lists of workshop participants and their interests was also added to the interface. During the workshop, the QED-2013 project page on CoG provided meeting logistics, meeting materials, shared spaces and resources, and data services. The evaluation of CoG tools was focused on the usability of products rather than metrics, such as number of independent hits to a web site. We wanted to know how well CoG tools supported the workshop participants and their tasks. For instance, what workshop tasks could be performed within the CoG environment? Were these tasks performed there or with alternative tools? And do participants plan to use the tools after the workshop for other projects? Ultimately, we wanted to know if CoG contributed to NCPP's need for a flexible and extensible evaluation platform, and did it support the integration of dispersed resources, quantitative evaluation of climate projections, and the generation and management of interpretive information. Evaluation of the workshop and activity occurred during, at the end of, and after the workshop. During the workshop, an ethnographer observed and participated in the workshop, and collected short, semi-structured interviews with a subset of the participants. At the end of the workshop, an exit survey was administered to all the participants. After the workshop, a variety of methods were used to capture the impact of the workshop.

ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

PubMed

Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

2012-09-08

The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

PubMed Central

2012-01-01

Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836

The mini-cog: a cognitive 'vital signs' measure for dementia screening in multi-lingual elderly.

PubMed

Borson, S; Scanlan, J; Brush, M; Vitaliano, P; Dokmak, A

2000-11-01

The Mini-Cog, a composite of three-item recall and clock drawing, was developed as a brief test for discriminating demented from non-demented persons in a community sample of culturally, linguistically, and educationally heterogeneous older adults. All 129 who met criteria for probable dementia based on informant interviews and 120 with no history of cognitive decline were included; 124 were non-English speakers. Sensitivity, specificity, and diagnostic value of the Mini-Cog were compared with those of the Mini-Mental State Exam (MMSE) and Cognitive Abilities Screening Instrument (CASI). The Mini-Cog had the highest sensitivity (99%) and correctly classified the greatest percentage (96%) of subjects. Moreover, its diagnostic value was not influenced by education or language, while that of the CASI was adversely influenced by low education, and both education and language compromised the diagnostic value of the MMSE. Administration time for the Mini-Cog was 3 minutes vs 7 minutes for the MMSE. The Mini-Cog required minimal language interpretation and training to administer, and no test forms of scoring modifications were needed to compensate for the extensive linguistic and educational heterogeneity of the sample. Validation in clinical and population-based samples is warranted, as its brevity and ease of administration suggest that the Mini-Cog might be readily incorporated into general practice and senior care settings as a routine 'cognitive vital signs' measure. Copyright 2000 John Wiley & Sons, Ltd.

Concurrent CO2 Control and O2 Generation for Advanced Life Support

NASA Technical Reports Server (NTRS)

Paul, Heather L.; Duncan, Keith L.; Hagelin-Weaver, Helena E.; Bishop, Sean R.; Wachsman, Eric D.

2007-01-01

The electrochemical reduction of carbon dioxide (CO2) using ceramic oxygen generators (COGs) is well known and widely studied, however, conventional devices using yttria-stabilized zirconia (YSZ) electrolytes operate at temperatures greater than 700 C. Operating at such high temperatures increases system mass compared to lower temperature systems because of increased energy overhead to get the COG up to operating temperature and the need for heavier insulation and/or heat exchangers to reduce the COG oxygen (O2) output temperature for comfortable inhalation. Recently, the University of Florida developed novel ceramic oxygen generators employing a bilayer electrolyte of gadolinia-doped ceria and erbia-stabilized bismuth for NASA's future exploration of Mars. To reduce landed mass and operation expenditures during the mission, in-situ resource utilization was proposed using these COGs to obtain both lifesupporting oxygen and oxidant/propellant fuel, by converting CO2 from the Mars atmosphere. The results showed that oxygen could be reliably produced from CO2 at temperatures as low as 400 C. These results indicate that this technology could be adapted to CO2 removal from a spacesuit and other applications in which CO2 removal was an issue. The strategy proposed for CO2 removal for advanced life support systems employs a catalytic layer combined with a COG so that it is reduced all the way to solid carbon and oxygen. Hence, a three-phased approach was used for the development of a viable low weight COG for CO2 removal. First, to reduce the COG operating temperature a high oxide ion conductivity electrolyte was developed. Second, to promote full CO2 reduction while avoiding the problem of carbon deposition on the COG cathode, novel cathodes and a removable catalytic carbon deposition layer were designed. Third, to improve efficiency, a pre-stage for CO2 absorption was used to concentrate CO2 from the exhalate before sending it to the COG. These subsystems were then integrated into a single CO2 removal system. This paper describes our progress to date on these tasks.

Comparison of cognitive functioning as measured by the Ruff Figural Fluency Test and the CogState computerized battery within the LifeLines Cohort Study.

PubMed

Kuiper, Jisca S; Oude Voshaar, Richard C; Verhoeven, Floor E A; Zuidema, Sytse U; Smidt, Nynke

2017-05-12

The Ruff Figural Fluency Test (RFFT; a pencil and paper test) and the CogState (a computerized cognitive test battery) are well-validated and suitable tests to evaluate cognitive functioning in large observational studies at the population level. The LifeLines Cohort Study includes the RFFT as baseline measurement and incorporated the CogState as replacement for the RFFT at follow-up. It is unknown how these two tests relate to each other. Therefore, the aim of this study is to examine the correlation between the RFFT and the CogState and the impact of demographic characteristics on this association. A subcohort of the LifeLines Cohort Study, a large population based cohort study, participated in this study. Correlations between the RFFT and six subtasks of the CogState were examined. Subgroup analyses were performed to investigate the influence of age, education, and gender on the results. With sensitivity analyses we investigated the influence of computer experience and (physical) impairments. A total of 509 participants (mean age (SD): 53 years (14.6); range 18-87 years) participated in this study. All correlations between the RFFT and the CogState were statistically significant (except for the correlation between the RFFT error ratio and the CogState One Back Task), ranging from -0.39 to 0.28. Stratifying the analyses for age, education, and gender did not substantially affect our conclusions. Sensitivity analyses showed no substantial influence of level of computer experience or (physical) impairments. Correlations found in the present study were only weak to moderate, indicating that cognitive functioning measured by the RFFT does not measure the same components of cognitive functioning as six subtasks of the CogState. Computerized testing such as the CogState may be very well suited for large cohort studies to assess cognitive functioning in the general population and to identify cognitive changes as early as possible, as it is a less time- and labor intensive tool.

Alzheimer's Disease Assessment Scale-Cognitive subscale variants in mild cognitive impairment and mild Alzheimer's disease: change over time and the effect of enrichment strategies.

PubMed

Podhorna, Jana; Krahnke, Tillmann; Shear, Michael; Harrison, John E

2016-02-12

Development of new treatments for Alzheimer's disease (AD) has broadened into early interventions in individuals with modest cognitive impairment and a slow decline. The 11-item version of the Alzheimer's Disease Assessment Scale-Cognitive subscale (ADAS-Cog) was originally developed to measure cognition in patients with mild to moderate AD. Attempts to improve its properties for early AD by removing items prone to ceiling and/or by adding cognitive measures known to be impaired early have yielded a number of ADAS-Cog variants. Using Alzheimer's Disease Neuroimaging Initiative data, we compared the performance of the 3-, 5-, 11- and 13-item ADAS-Cog variants in subjects with early AD. Given the interest in enrichment strategies, we also examined this aspect with a focus on cerebrospinal fluid (CSF) markers. Subjects with mild cognitive impairment (MCI) and mild AD with available ADAS-Cog 13 and CSF data were analysed. The decline over time was defined by change from baseline. Direct cross-comparison of the ADAS-Cog variants was performed using the signal-to-noise ratio (SNR), with higher values reflecting increased sensitivity to detect change over time. The decline over time on any of the ADAS-Cog variants was minimal in subjects with MCI. Approximately half of subjects with MCI fulfilled enrichment criteria for positive AD pathology. The impact of enrichment was detectable but subtle in MCI. The annual decline in mild AD was more pronounced but still modest. More than 90 % of subjects with mild AD had positive AD pathology. SNRs were low in MCI but greater in mild AD. The numerically largest SNRs were seen for the ADAS-Cog 5 in MCI and for both the 5- and 13-item ADAS-Cog variants in mild AD, although associated confidence intervals were large. The possible value of ADAS-Cog expansion or reduction is less than compelling, particularly in MCI. In mild AD, adding items known to be impaired at early stages seems to provide more benefit than removing items on which subjects score close to ceiling.

Experimental validation of a distribution theory based analysis of the effect of manufacturing tolerances on permanent magnet synchronous machines

NASA Astrophysics Data System (ADS)

Boscaino, V.; Cipriani, G.; Di Dio, V.; Corpora, M.; Curto, D.; Franzitta, V.; Trapanese, M.

2017-05-01

An experimental study on the effect of permanent magnet tolerances on the performances of a Tubular Linear Ferrite Motor is presented in this paper. The performances that have been investigated are: cogging force, end effect cogging force and generated thrust. It is demonstrated that: 1) the statistical variability of the magnets introduces harmonics in the spectrum of the cogging force; 2) the value of the end effect cogging force is directly linked to the values of then remanence field of the external magnets placed on the slider; 3) the generated thrust and its statistical distribution depend on the remanence field of the magnets placed on the translator.

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities

PubMed Central

Oberding, Lisa; Gieg, Lisa M.

2016-01-01

Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data. PMID:27681901

Microbial genome analysis: the COG approach.

PubMed

Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Cogging force investigation of a free piston permanent magnet linear generator

NASA Astrophysics Data System (ADS)

Abdalla, I. I.; Zainal, A. E. Z.; Ramlan, N. A.; Firmansyah; Aziz, A. R. A.; Heikal, M. R.

2017-10-01

Better performance and higher efficiency of the vehicles can be achieved by using free piston engine, in which the piston is connected directly to the linear generator and waiving of any mechanical means. The free piston engine has the ability to overcome or reduce many of the challenges, such as the carbon dioxide (CO2) emission and fossil fuel consumption. The cogging force produces undesired vibration and acoustic noise in the generator. However, the cogging force must be minimized as much as possible, in order to have a high performance. This paper studies the effects of ferromagnetic materials on the cogging force of the permanent magnet linear generator (PMLG) to be used in a free piston engine using nonlinear finite-element analysis (FEA) under ANSYS Maxwell. The comparisons have been established for the cogging force of the PMLG under various translator velocities and three different ferromagnetic materials for the stator core, namely, Silicon Steel laminations, Mild Steel and Somaloy. It has been shown that the PMLG with a stator core made of Somaloy has a lower cogging force among them. Furthermore, the induced voltage of the PMLG at different accelerations has been studied. It is found that the PMLG with Mild Steel and Somaloy, respectively give larger induced voltage. Moreover, as the translator speed increase the induced voltage increased.

Metal Binding Properties of Escherichia coli YjiA, a Member of the Metal Homeostasis-Associated COG0523 Family of GTPases

PubMed Central

2013-01-01

GTPases are critical molecular switches involved in a wide range of biological functions. Recent phylogenetic and genomic analyses of the large, mostly uncharacterized COG0523 subfamily of GTPases revealed a link between some COG0523 proteins and metal homeostasis pathways. In this report, we detail the bioinorganic characterization of YjiA, a representative member of COG0523 subgroup 9 and the only COG0523 protein to date with high-resolution structural information. We find that YjiA is capable of binding several types of transition metals with dissociation constants in the low micromolar range and that metal binding affects both the oligomeric structure and GTPase activity of the enzyme. Using a combination of X-ray crystallography and site-directed mutagenesis, we identify, among others, a metal-binding site adjacent to the nucleotide-binding site in the GTPase domain that involves a conserved cysteine and several glutamate residues. Mutations of the coordinating residues decrease the impact of metal, suggesting that metal binding to this site is responsible for modulating the GTPase activity of the protein. These findings point toward a regulatory function for these COG0523 GTPases that is responsive to their metal-bound state. PMID:24449932

Comparison of the Classifier Oriented Gait Score and the Gait Profile Score based on imitated gait impairments.

PubMed

Christian, Josef; Kröll, Josef; Schwameder, Hermann

2017-06-01

Common summary measures of gait quality such as the Gait Profile Score (GPS) are based on the principle of measuring a distance from the mean pattern of a healthy reference group in a gait pattern vector space. The recently introduced Classifier Oriented Gait Score (COGS) is a pathology specific score that measures this distance in a unique direction, which is indicated by a linear classifier. This approach has potentially improved the discriminatory power to detect subtle changes in gait patterns but does not incorporate a profile of interpretable sub-scores like the GPS. The main aims of this study were to extend the COGS by decomposing it into interpretable sub-scores as realized in the GPS and to compare the discriminative power of the GPS and COGS. Two types of gait impairments were imitated to enable a high level of control of the gait patterns. Imitated impairments were realized by restricting knee extension and inducing leg length discrepancy. The results showed increased discriminatory power of the COGS for differentiating diverse levels of impairment. Comparison of the GPS and COGS sub-scores and their ability to indicate changes in specific variables supports the validity of both scores. The COGS is an overall measure of gait quality with increased power to detect subtle changes in gait patterns and might be well suited for tracing the effect of a therapeutic treatment over time. The newly introduced sub-scores improved the interpretability of the COGS, which is helpful for practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Open circuit V-I characteristics of a coreless ironless electric generator for low density wind power generation

NASA Astrophysics Data System (ADS)

Razali, Akhtar; Rahman, Fadhlur; Azlan, Syaiful; Razali Hanipah, Mohd; Azri Hizami, Mohd

2018-04-01

Cogging is an attraction of magnetism between permanent magnets and soft ironcore lamination in a conventional electric ironcore generator. The presence of cog in the generator is seen somehow restricted the application of the generator in an application where low rotational torque is required. Cog torque requires an additional input power to overcome, hence became one of the power loss sources. With the increasing of power output, the cogging is also proportionally increased. This leads to the increasing of the supplied power of the driver motor to overcome the cog. Therefore, this research is embarked to study fundamentally about the possibility of removing ironcore lamination in an electric generator. This research deals with removal of ironcore lamination in electric generator to eliminate cog torque. A confinement technique is proposed to confine and focus magnetic flux by introducing opposing permanent magnets arrangement. The concept is then fabricated and experimentally validated to qualify its no-load characteristics. The rotational torque and power output are measured and efficiency is then analyzed. Results indicated that the generator produced RMS voltage of 416VAC at rotational speed of 1762 RPM. Torque required to rotate the generator was at 2Nm for various rotational speed. The generator has shown 30% lesser rotational torque compared to the conventional ironcore type generator due to the absent of cogging torque in the system. Lesser rotational torque required to rotate has made this type of generator has a potential to be used for low wind density wind turbine application.

Geographic Access to Cancer Care and Mortality Among Adolescents.

PubMed

Tai, Eric; Hallisey, Elaine; Peipins, Lucy A; Flanagan, Barry; Lunsford, Natasha Buchanan; Wilt, Grete; Graham, Shannon

2018-02-01

Adolescents with cancer have had less improvement in survival than other populations in the United States. This may be due, in part, to adolescents not receiving treatment at Children's Oncology Group (COG) institutions, which have been shown to increase survival for some cancers. The objective of this ecologic study was to examine geographic distance to COG institutions and adolescent cancer mortality. We calculated cancer mortality among adolescents and sociodemographic and healthcare access factors in four geographic zones at selected distances surrounding COG facilities: Zone A (area within 10 miles of any COG institution), Zones B and C (concentric rings with distances from a COG institution of >10-25 miles and >25-50 miles, respectively), and Zone D (area outside of 50 miles). The adolescent cancer death rate was highest in Zone A at 3.21 deaths/100,000, followed by Zone B at 3.05 deaths/100,000, Zone C at 2.94 deaths/100,000, and Zone D at 2.88 deaths/100,000. The United States-wide death rate for whites without Hispanic ethnicity, blacks without Hispanic ethnicity, and persons with Hispanic ethnicity was 2.96 deaths/100,000, 3.10 deaths/100,000, and 3.26 deaths/100,000, respectively. Zone A had high levels of poverty (15%), no health insurance coverage (16%), and no vehicle access (16%). Geographic access to COG institutions, as measured by distance alone, played no evident role in death rate differences across zones. Among adolescents, socioeconomic factors, such as poverty and health insurance coverage, may have a greater impact on cancer mortality than geographic distance to COG institution.

The Impact of Cognitive Impairment in Dementia on Self-Care Domains in Diabetes Mellitus: A Systematic Search and Narrative Review.

PubMed

Santos, Tamsin; Lovell, Janaka; Shiell, Kerrie; Johnson, Marilyn; Ibrahim, Joseph E

2018-04-29

Self-management is integral to effective chronic disease management. Cognitive impairments (CogImp) associated with dementia have not previously been reviewed in diabetes mellitus (DM) self-care. (i) Whether CogImp associated with dementia impact self-care. (ii) Whether specific CogImp affects key DM self-care processes. A systematic literature search with a narrative review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. This review examined studies published from January, 2000 to February, 2016 describing the relationship between cognition and DM self-care domains in community dwelling older adults with dementia/CogImp. Eight studies met inclusion criteria. Decrements in all self-care domains were associated with CogImp. Problem solving was related to reduced disease knowledge (OR 0.87, 95% CI=0.49-1.55), resulting in poorer glycemic control. Decision-making impairments manifested as difficulties in adjusting insulin doses, leading to more hospital admissions. People without CogImp were better able to find/utilize resources by adhering to recommended management (OR 1.03, 95% CI=1.02-1.05). A lack of interaction with health care providers was demonstrated through reduced receipt of important routine investigation including eye examinations (ARR=0.85, 95% CI=0.85-0.86), HbA1c testing (ARR=0.96, 95% CI=0.96-0.97) and LDL-C testing (ARR=0.91, 95% CI=0.901-0.914). People without CogImp had better clinic attendance (OR 2.17, 95% CI=1.30-3.70). Action taking deficits were apparent through less self-testing of blood sugar levels (20.2% vs 24.4%, p=0.1) resulting in poorer glycemic control, self-care and more frequent micro/macrovascular complications. Persons with diabetes and CogImp, particularly in domains of learning, memory and executive function, were significantly impaired in all self-care tasks. This article is protected by copyright. All rights reserved.

Apolipoprotein E Mimetic Promotes Functional and Histological Recovery in Lysolecithin-Induced Spinal Cord Demyelination in Mice.

PubMed

Gu, Zhen; Li, Fengqiao; Zhang, Yi Ping; Shields, Lisa B E; Hu, Xiaoling; Zheng, Yiyan; Yu, Panpan; Zhang, Yongjie; Cai, Jun; Vitek, Michael P; Shields, Christopher B

2013-04-01

Considering demyelination is the pathological hallmark of multiple sclerosis (MS), reducing demyelination and/or promoting remyelination is a practical therapeutic strategy to improve functional recovery for MS. An apolipoprotein E (apoE)-mimetic peptide COG112 has previously demonstrated therapeutic efficacy on functional and histological recovery in a mouse experimental autoimmune encephalomyelitis (EAE) model of human MS. In the current study, we further investigated whether COG112 promotes remyelination and improves functional recovery in lysolecithin induced focal demyelination in the white matter of spinal cord in mice. A focal demyelination model was created by stereotaxically injecting lysolecithin into the bilateral ventrolateral funiculus (VLF) of T8 and T9 mouse spinal cords. Immediately after lysolecithin injection mice were treated with COG112, prefix peptide control or vehicle control for 21 days. The locomotor function of the mice was measured by the beam walking test and Basso Mouse Scale (BMS) assessment. The nerve transmission of the VLF of mice was assessed in vivo by transcranial magnetic motor evoked potentials (tcMMEPs). The histological changes were also examined by by eriochrome cyanine staining, immunohistochemistry staining and electron microscopy (EM) method. The area of demyelination in the spinal cord was significantly reduced in the COG112 group. EM examination showed that treatment with COG112 increased the thickness of myelin sheaths and the numbers of surviving axons in the lesion epicenter. Locomotor function was improved in COG112 treated animals when measured by the beam walking test and BMS assessment compared to controls. TcMMEPs also demonstrated the COG112-mediated enhancement of amplitude of evoked responses. The apoE-mimetic COG112 demonstrates a favorable combination of activities in suppressing inflammatory response, mitigating demyelination and in promoting remyelination and associated functional recovery in animal model of CNS demyelination. These data support that apoE-mimetic strategy may represent a promising therapy for MS and other demyelination disorders.

Developing an organizing framework to guide nursing research in the Children’s Oncology Group (COG)

PubMed Central

Kelly, Katherine Patterson; Hooke, Mary C.; Ruccione, Kathleen; Landier, Wendy; Haase, Joan

2014-01-01

Objectives To describe the development and application of an organizing research framework to guide COG Nursing research. Data Sources Research articles, reports and meeting minutes Conclusion An organizing research framework helps to outline research focus and articulate the scientific knowledge being produced by nurses in the pediatric cooperative group. Implication for Nursing Practice The use of an organizing framework for COG nursing research can facilitate clinical nurses’ understanding of how children and families sustain or regain optimal health when faced with a pediatric cancer diagnosis through interventions designed to promote individual and family resilience. The Children’s Oncology Group (COG) is the sole National Cancer Institute (NCI)-supported cooperative pediatric oncology clinical trials group and the largest organization in the world devoted exclusively to pediatric cancer research. It was founded in 2000 following the merger of the four legacy NCI-supported pediatric clinical trials groups (Children’s Cancer Group [CCG], Pediatric Oncology Group [POG], National Wilms Tumor Study Group, and Intergroup Rhabdomyosarcoma Study Group). The COG currently has over 200 member institutions across North America, Australia, New Zealand and Europe and a multidisciplinary membership of over 8,000 pediatric, radiation, and surgical oncologists, nurses, clinical research associates, pharmacists, behavioral scientists, pathologists, laboratory scientists, patient/parent advocates and other pediatric cancer specialists. The COG Nursing Discipline was formed from the merger of the legacy CCG and POG Nursing Committees, and current membership exceeds 2000 registered nurses. The discipline has a well-developed infrastructure that promotes nursing involvement throughout all levels of the organization, including representation on disease, protocol, scientific, executive and other administrative committees (e.g., nominating committee, data safety monitoring boards). COG nurses facilitate delivery of protocol-based treatments for children enrolled on COG protocols, and Nursing Discipline initiatives support nursing research, professional and patient/family education, evidence-based practice, and a patient-reported outcomes resource center. The research agenda of the Nursing Discipline is enacted through a well-established nursing scholar program. PMID:24559776

Indonesian kalkulator of oocytes (IKO): A smart application to determine our biological age

NASA Astrophysics Data System (ADS)

Wiweko, Budi; Narasati, Shabrina; Agung, Prince Gusti; Zesario, Aulia; Wibawa, Yohanes Satrya; Maidarti, Mila; Harzif, Achmad Kemal; Pratama, Gita; Sumapraja, Kanadi; Muharam, Raden; Hestiantoro, Andon

2018-02-01

Background: The use of smartphones and its associated application provides new opportunities for physicians. In current situations, there are still few applications are designed in the field of infertility and Assisted Reproductive Technologies (ART). A study conducted on 1616 subjects proved that AMH (Anti-Mullerian Hormone) could be used to predict a woman's biological age earlier than Follicle-Stimulating Hormone (FSH) and Antral Follicle Count (AFC). In this study, we describe the AMH nomogram that has been developed into a mobile application as "Indonesian Kalculator of Oocytes" (IKO). The software required to create IKO application was the Android 4.0.3 Ice Cream Sandwich and Java Application Development. The hardware specification that needed to develop the IKO apps were a 4.0-inch screen, 512 MB RAM (random-access memory), and CPU (central processing unit) with dual core 1.2 Ghz. The application is built using the Android SDK (Software Development Kit) and Java Application Development. In this application, we can predict the woman's biological age, some mature oocytes, and AMH level. This app is expected to help patients to plan effectively for pregnancy and help the doctor to choose the best intervention for patients who face infertility problems using Assisted Reproductive Technology (ART). IKO application can be downloaded for free on Google PlayStore and Apple Store.

The Relationship between Students' Performance on the Cognitive Abilities Test (CogAT) and the Fourth and Fifth Grade Reading and Math Achievement Tests in Ohio

ERIC Educational Resources Information Center

Warnimont, Chad S.

2010-01-01

The purpose of this quantitative study was to examine the relationship between students' performance on the Cognitive Abilities Test (CogAT) and the fourth and fifth grade Reading and Math Achievement Tests in Ohio. The sample utilized students from a suburban school district in Northwest Ohio. Third grade CogAT scores (2006-2007 school year), 4th…

Center of Gravity in the Asymmetric Environment: Applicable or Not

DTIC Science & Technology

2006-06-01

public release; distribution unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) The military concept of a Center of Gravity ( COG ) in...changed a great deal since the introduction of COG . And in today’s asymmetric environment, in which non-state actors use unconventional tactics, it is...becoming extremely difficult to apply the COG concept. The primary reason for this difficulty is that non-state actors do not operate as a unitary

Validation of COG10 and ENDFB6R7 on the Auk Workstation for General Application to Plutonium Systems

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

Percher, Catherine G

2011-08-08

The COG 10 code package1 on the Auk workstation is now validated with the ENBFB6R7 neutron cross section library for general application to plutonium (Pu) systems by comparison of the calculated keffective to the expected keffective of several relevant experimental benchmarks. This validation is supplemental to the installation and verification of COG 10 on the Auk workstation2.

Psychometric properties of Malay neuropsychiatry unit cognitive assessment tool among Alzheimer's disease patients in comparison to Malay Montreal Cognitive Assessment.

PubMed

Thong, Kai Shin; Chee, Kok Yoon; Ng, Chong Guan; Walterfang, Mark; Velakoulis, Dennis

2016-09-01

This study aims to establish psychometric properties of the Malay Neuropsychiatry Unit Cognitive Assessment Tool (Malay NuCOG) in Alzheimer's disease. NuCOG was translated to Malay language and compared with Montreal Cognitive Assessment Tool on 80 individuals. The Malay NuCOG showed good internal consistency and reliability (Cronbach's alpha = 0.895). It demonstrated 100% sensitivity and 87.5% specificity at the cutoff score of 78.50/100. The Malay NuCOG is a valid and reliable cognitive instrument that is sensitive and specific for the detection of dementia and has clinical advantages in its ability to examine individual cognitive domains. © 2015 Wiley Publishing Asia Pty Ltd.

Decreased serum levels of mature brain-derived neurotrophic factor (BDNF), but not its precursor proBDNF, in patients with major depressive disorder.

PubMed

Yoshida, Taisuke; Ishikawa, Masatomo; Niitsu, Tomihisa; Nakazato, Michiko; Watanabe, Hiroyuki; Shiraishi, Tetsuya; Shiina, Akihiro; Hashimoto, Tasuku; Kanahara, Nobuhisa; Hasegawa, Tadashi; Enohara, Masayo; Kimura, Atsushi; Iyo, Masaomi; Hashimoto, Kenji

2012-01-01

Meta-analyses have identified serum levels of brain-derived neurotrophic factor (BDNF) as a potential biomarker for major depressive disorder (MDD). However, at the time, commercially available human ELISA kits are unable to distinguish between proBDNF (precursor of BDNF) and mature BDNF because of limited BDNF antibody specificity. In this study, we examined whether serum levels of proBDNF, mature BDNF, and matrix metalloproteinase-9 (MMP-9), which converts proBDNF to mature BDNF, are altered in patients with MDD. Sixty-nine patients with MDD and 78 age- and gender-matched healthy subjects were enrolled. Patients were evaluated using 17 items on the Structured Interview Guide for the Hamilton Depression Rating Scale. Cognitive impairment was evaluated using the CogState battery. Serum levels of proBDNF, mature BDNF, and MMP-9 were measured using ELISA kits. Serum levels of mature BDNF in patients with MDD were significantly lower than those of normal controls. In contrast, there was no difference in the serum levels of proBDNF and MMP-9 between patients and normal controls. While neither proBDNF nor mature BDNF serum levels was associated with clinical variables, there were significant correlations between MMP-9 serum levels and the severity of depression, quality of life scores, and social function scores in patients. These findings suggest that mature BDNF may serve as a biomarker for MDD, and that MMP-9 may play a role in the pathophysiology of MDD. Further studies using larger sample sizes will be needed to investigate these results.

Which long-term care residents should be asked to complete a customer satisfaction survey?

PubMed

Van De Water, Margaret S; Kutner, Michael; Parmelee, Patricia A; Johnson, Theodore

2003-01-01

(1) To compare staff members' opinions of long-term care (LTC) residents' ability to complete a customer satisfaction survey (CSS) with a measure of cognition (MDS-COGS) derived from Minimum Data Set data; and (2) to examine the association between CSS answer reliability and MDS-COGS score. Retrospective comparison of the staff's assessment and MDS-COGS score for each respondent, as well as a prospective comparison of MDS-COGS scores with reliability measures from repeated survey administration. A 100-bed Veterans Affairs (VA) nursing home. We administered a CSS designed by our VA network following an assigned protocol. We later calculated each respondent's MDS-COGS score (grouped into 4 categories) and compared it with the staff's opinion of whether that resident was "capable of responding" (yes/no) to a CSS. We subsequently modified the CSS for low reading level and low vision, and randomly selected 40 LTC residents for repeated survey administration (T1 and T2 1 week later). Test-retest reliability was estimated by examining the extent to which T1 and T2 answers agreed (agreed exactly; meaningfully agreed as defined by VA network personnel who designed the survey; or meaningfully agreed as decided by paper authors). Staff judged that 25 of 76 LTC residents were not and 51 of 76 were capable of responding to the CSS. In 82% of cases, MDS-COGS score category and staff opinion agreed ("no cognitive impairment"/"mild-moderate cognitive impairment" with "able to complete"; and "moderate-severe cognitive impairment"/"severe cognitive impairment" with "unable to complete"). Cohen's kappa was 0.57 with a P value of <0.001. Of the 40 LTC residents randomly selected for repeated survey administration, 32 successfully completed surveys at T1 and T2. Higher MDS-COGS scores, suggesting greater cognitive impairment, were significantly associated with lower answer reliability. The answers given by LTC residents changed meaningfully (by network criteria) from T1 to T2 by 12%, 27%, and 28% across categories of no-to-mild cognitive impairment, mild-to-moderate impairment, and moderate-to-severe impairment, respectively. The rate of decline in reliability, however, was small for each unit of increase in MDS-COGS. Although the staff's opinions about residents' ability to complete a CSS were significantly associated with an objective MDS-COGS assessment, staff nonetheless failed on several occasions to let cognitively intact residents complete their own surveys. Although higher MDS-COGS scores were significantly related to lower reliability, there were no natural cut-points in the data to suggest a participate/do not participate line and the trend line between MDS-COGS level, and percent of questions answered reliably was not very strong. These results suggest that LTC residents with mild to moderate dementia might be capable of reliably answering certain types of customer satisfaction surveys.

Clinical global impression of cognition in schizophrenia (CGI-CogS): reliability and validity of a co-primary measure of cognition.

PubMed

Ventura, Joseph; Cienfuegos, Angel; Boxer, Oren; Bilder, Robert

2008-11-01

Cognitive deficits are core features of schizophrenia that have been associated reliably with functional outcomes and now are a focus of treatment research. New rating scales are needed to complement current psychometric testing procedures, both to enable wider clinical use, and to serve as endpoints in clinical trials. Subjects were 35 schizophrenia patient-and-caregiver pairs recruited from the UCLA and West Los Angeles VA Outpatient Psychiatry Departments. Participants were assessed with the Clinical Global Impression of Cognition in Schizophrenia (CGI-CogS), an interview-based rating scale of cognitive functioning, on 3 occasions (baseline, 1 month, and 3 months). A computerized neurocognitive battery (Cogtest), an assessment of functioning, and symptom measures were administered at two occasions (baseline and one month). The CGI-CogS ratings generally showed a high level of internal consistency (Cronbach's alpha=.69 to .96), adequate levels of inter-rater reliability (ICC's=.71 to .80), and high test-retest stability (ICC's=.92 to .95). Correlations of caregiver and rater global (but not "patient only rating") CGI-CogS ratings with neurocognitive performance were in the moderate range (r's=-.27 to -.48), while most of the correlations with functional outcome were moderate to high (r's=-.41 to -.72). In fact, the CGI-CogS ratings were significantly more correlated with Social Functioning than were objective neurocognitive test scores (p=.02) and showed a trend in the same direction for predicting Instrumental Functioning (p=.06). We found moderate correlations between CGI-CogS global ratings and PANSS positive (r's=.36 to .49) and SANS negative symptoms (r=.41 to .61), but not with BPRS depression (r's=.11 to .13). An interview-based measure of cognition demonstrated high internal consistency, good inter-rater reliability, and high test-retest reliability. Caregiver ratings appear to add important clinical information over patient-only ratings. The CGI-CogS showed moderate validity with respect to neurocognitive performance and functional outcome, and correlations of CGI-CogS with functional outcomes were stronger than correlations of objective neurocognitive performance with functional outcomes. The CGI-CogS appears to offer a reliable and valid method for clinical rating of cognitive deficits and their impact on everyday functioning in schizophrenia.

Residential care/assisted living staff may detect undiagnosed dementia using the minimum data set cognition scale.

PubMed

Zimmerman, Sheryl; Sloane, Philip D; Williams, Christianna S; Dobbs, Debra; Ellajosyula, Ratnavalli; Braaten, Alyssa; Rupnow, Marcia F T; Kaufer, Daniel I

2007-09-01

To estimate the sensitivity, specificity, and reliability of the Minimum Data Set Cognition Scale (MDS-COGS) in screening for undetected dementia when completed by direct care staff in residential care/assisted living (RC/AL) facilities and secondarily to determine the prevalence of dementia in the sample. A cross-sectional study in which staff were trained to complete the MDS-COGS. Research interviewers and a neuropsychologist obtained information on each participant. Two neurologists reviewed the data and examined the participant, rendering a probable diagnosis of dementia/non-dementia diagnosis. MDS-COGS results were compared with the neurologists' determination. Fourteen RC/AL facilities in North Carolina. Data were collected from 50 staff on 166 residents without a diagnosis of dementia. In addition to the MDS-COGS, measures included a comprehensive neuropsychological battery. Depression and other neuropsychiatric symptoms were also assessed. Neurologists determined that 38% of participants had probable dementia. An MDS-COGS cutpoint of 2 was highly specific (0.97) but not very sensitive (0.49) for dementia. Test-retest and interrater agreement for a negative screen were high (88% and 93%, respectively). The MDS-COGS is a simple, brief screen that RC/AL staff can complete. It will identify with high specificity a subset of residents with undetected dementia, allowing rapid identification of those likely to need dementia care. Caution needs to be exercised in light of its low sensitivity, because some with milder dementia will not be detected. Further work is needed to determine whether staff can and will use the MDS-COGS as a trigger for more-thorough assessment and to guide care and improve outcomes.

Deficient prepulse inhibition in schizophrenia detected by the multi-site COGS.

PubMed

Swerdlow, Neal R; Light, Gregory A; Sprock, Joyce; Calkins, Monica E; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Nuechterlein, Keith H; Radant, Allen D; Ray, Amrita; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Sugar, Catherine A; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L

2014-02-01

Startle inhibition by weak prepulses (PPI) is studied to understand the biology of information processing in schizophrenia patients and healthy comparison subjects (HCS). The Consortium on the Genetics of Schizophrenia (COGS) identified associations between PPI and single nucleotide polymorphisms in schizophrenia probands and unaffected relatives, and linkage analyses extended evidence for the genetics of PPI deficits in schizophrenia in the COGS-1 family study. These findings are being extended in a 5-site "COGS-2" study of 1800 patients and 1200 unrelated HCS to facilitate genetic analyses. We describe a planned interim analysis of COGS-2 PPI data. Eyeblink startle was measured in carefully screened HCS and schizophrenia patients (n=1402). Planned analyses of PPI (60 ms intervals) assessed effects of diagnosis, sex and test site, PPI-modifying effects of medications and smoking, and relationships between PPI and neurocognitive measures. 884 subjects met strict inclusion criteria. ANOVA of PPI revealed significant effects of diagnosis (p=0.0005) and sex (p<0.002), and a significant diagnosis×test site interaction. HCS>schizophrenia PPI differences were greatest among patients not taking 2nd generation antipsychotics, and were independent of smoking status. Modest but significant relationships were detected between PPI and performance in specific neurocognitive measures. The COGS-2 multi-site study detects schizophrenia-related PPI deficits reported in single-site studies, including patterns related to diagnosis, prepulse interval, sex, medication and other neurocognitive measures. Site differences were detected and explored. The target COGS-2 schizophrenia "endophenotype" of reduced PPI should prove valuable for identifying and confirming schizophrenia risk genes in future analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

Deficient prepulse inhibition in schizophrenia detected by the multi-site COGS

PubMed Central

Swerdlow, Neal R.; Light, Gregory A.; Sprock, Joyce; Calkins, Monica E.; Green, Michael F.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura C.; Nuechterlein, Keith H.; Radant, Allen D.; Ray, Amrita; Seidman, Larry J.; Siever, Larry J.; Silverman, Jeremy M.; Stone, William S.; Sugar, Catherine A.; Tsuang, Debby W.; Tsuang, Ming T.; Turetsky, Bruce I.; Braff, David L.

2014-01-01

Background Startle inhibition by weak prepulses (PPI) is studied to understand the biology of information processing in schizophrenia patients and healthy comparison subjects (HCS). The Consortium on the Genetics of Schizophrenia (COGS) identified associations between PPI and single nucleotide polymorphisms in schizophrenia probands and unaffected relatives, and linkage analyses extended evidence for the genetics of PPI deficits in schizophrenia in the COGS-1 family study. These findings are being extended in a 5-site “COGS-2” study of 1800 patients and 1200 unrelated HCS to facilitate genetic analyses. We describe a planned interim analysis of COGS-2 PPI data. Methods Eyeblink startle was measured in carefully screened HCS and schizophrenia patients (n=1402). Planned analyses of PPI (60 ms intervals) assessed effects of diagnosis, sex and test site, PPI-modifying effects of medications and smoking, and relationships between PPI and neurocognitive measures. Results 884 subjects met strict inclusion criteria. ANOVA of PPI revealed significant effects of diagnosis (p=0.0005) and sex (p<0.002), and a significant diagnosis × test site interaction. HCS > schizophrenia PPI differences were greatest among patients not taking 2nd generation antipsychotics, and were independent of smoking status. Modest but significant relationships were detected between PPI and performance in specific neurocognitive measures. Discussion The COGS-2 multi-site study detects schizophrenia-related PPI deficits reported in single-site studies, including patterns related to diagnosis, prepulse interval, sex, medication and other neurocognitive measures. Site differences were detected and explored. The target COGS-2 schizophrenia “endophenotype” of reduced PPI should prove valuable for identifying and confirming schizophrenia risk genes in future analyses. PMID:24405980

[Psychometric attributes of Scales for Outcomes in Parkinson's Disease-Cognition (SCOPA-Cog), Castilian language].

PubMed

Martínez-Martín, P; Frades-Payo, B; Rodríguez-Blázquez, C; Forjaz, M J; de Pedro-Cuesta, J

To test the psychometric attributes of the Scales for Outcomes in Parkinson's Disease-Cognition (SCOPA-Cog), in Castilian language. It is a multicenter, cross-sectional study carried out on 387 Parkinson's disease (PD) patients. They were 70% in Hoehn and Yahr stages 2 or 3; their mean age was 65,8 years and they underwent the disease for 8,1 years. Rater-based -SCOPA-Motor, modified Parkinson's Psychosis Rating Scale, Clinical Impression of Severity Index for PD (CISI-PD), Cumulative Illness Rating Scale-Geriatrics- and self-administered -SCOPA-Autonomic, SCOPA-Sleep, SCOPA-Psychosocial, Hospital Anxiety and Depression Scale, EuroQoL- assessments were applied. For SCOPA-Cog, the following psychometric attributes were analysed: acceptability, internal consistency, dimensionality, construct validity, and precision. A cut-off point for dementia and SCOPA-Cog score's predictors were explored. SCOPA-Cog was free from floor and ceiling effect. The internal consistency was satisfactory (alpha = 0,83) and the item-total correlation resulted equal or upper than 0,45. Two factors were identified (52% of variance), one of them formed by 3 out of the 4 memory-related items. The correlation with other measures was weak (rS < 0,35), except for the CISI-PD's item 'cognitive state' (rS = 0,51). SCOPA-Cog scored significantly different for Hoehn and Yahr stages and for patients grouped by age, age at onset of PD, and education. The standard error of measurement was 3,02. A cut-off point 19/20 reached 76% sensitivity and specificity for dementia. Age and age at onset of PD resulted the strongest predictors. SCOPA-Cog is a consistent, valid, and precise measure for assessment of the cognitive disorder in PD.

Validation of COG10 and ENDFB6R7 on the Auk Workstation for General Application to Highly Enriched Uranium Systems

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

Percher, Catherine G.

2011-08-08

The COG 10 code package1 on the Auk workstation is now validated with the ENBFB6R7 neutron cross section library for general application to highly enriched uranium (HEU) systems by comparison of the calculated keffective to the expected keffective of several relevant experimental benchmarks. This validation is supplemental to the installation and verification of COG 10 on the Auk workstation2.

A novel syndrome of hypohidrosis and intellectual disability is linked to COG6 deficiency.

PubMed

Shaheen, Ranad; Ansari, Shinu; Alshammari, Muneera J; Alkhalidi, Hisham; Alrukban, Hadeel; Eyaid, Wafaa; Alkuraya, Fowzan S

2013-07-01

Numerous syndromic forms of intellectual disability have been described including those with abnormal sweating pattern. To describe the clinical and molecular analysis of a large multiplex consanguineous Saudi family with an unusual constellation of severe intellectual disability, hypohidrosis, abnormal teeth, and acquired microcephaly. Clinical evaluation, autozygosity mapping, exome sequencing, and expression analysis. Autozygosity mapping revealed a single critical locus corresponding to chr13:39 338 062-40 857 430. Exome sequencing uncovered a deep intronic (NM_020751.2:c.1167-24A>G) variant in COG6 that largely replaces the consensus acceptor site, resulting in pronounced reduction of the normal transcript and consequent deficiency of COG6 protein. Patient cells also exhibited pronounced deficiency of STX6, consistent with the established stabilising effect of COG6 on STX6. Four additional patients representing two families of the same tribal origin as the original family were found to have the same mutation, confirming a founder effect. Remarkably, none of the patients displayed any detectable abnormality in the glycosylation pattern of transferrin, which contradicts a previously published report of a patient whose abnormal glycosylation pattern was presumed to be caused by a missense variant in COG6. Our data implicate COG6 in the pathogenesis of a novel hypohidrotic disorder in humans that is distinct from congenital disorders of glycosylation.

Discrepancies between cognition and decision making in older adults

PubMed Central

Boyle, Patricia A.; James, Bryan D.; Yu, Lei; Barnes, Lisa L.; Bennett, David A.

2015-01-01

Background and aims There is increasing clinical and legal interest in discrepancies between decision-making ability and cognition in old age, a stage of life when decisions have major ramifications. We investigated the frequency and correlates of such discrepancies in non-demented older adults participating in a large community-based cohort study of aging, the Rush Memory and Aging Project. Methods Participants [n = 689, mean age 81.8 (SD 7.6), mean education 15.2 (SD 3.1), 76.8 % female and 93.3 % white] completed a measure of financial and healthcare decision making (DM) and a battery of 19 neuropsychological tests from which a composite measure of global cognition (COG) was derived. Results Results indicated that 23.9 % of the sample showed a significant discrepancy between DM and COG abilities. Of these, 12.9 % showed DM < COG, while 11.0 % showed DM > COG. Logistic regression models showed older age, being non-white, greater temporal discounting, and greater risk aversion were associated with higher odds of being in the DM < COG group. Being male was associated with higher odds of being in the DM > COG group. Education, income, depressive symptoms, and impulsivity were not associated with a discrepancy. Only demographic associations (age, sex, and race) remained significant in a fully adjusted model with terms included for all factors. Conclusion These results support the consideration of decision making and cognition as potentially separate constructs. PMID:25995167

Discrepancies between cognition and decision making in older adults.

PubMed

Han, S Duke; Boyle, Patricia A; James, Bryan D; Yu, Lei; Barnes, Lisa L; Bennett, David A

2016-02-01

There is increasing clinical and legal interest in discrepancies between decision-making ability and cognition in old age, a stage of life when decisions have major ramifications. We investigated the frequency and correlates of such discrepancies in non-demented older adults participating in a large community-based cohort study of aging, the Rush Memory and Aging Project. Participants [n = 689, mean age 81.8 (SD 7.6), mean education 15.2 (SD 3.1), 76.8 % female and 93.3 % white] completed a measure of financial and healthcare decision making (DM) and a battery of 19 neuropsychological tests from which a composite measure of global cognition (COG) was derived. Results indicated that 23.9 % of the sample showed a significant discrepancy between DM and COG abilities. Of these, 12.9 % showed DM < COG, while 11.0 % showed DM > COG. Logistic regression models showed older age, being non-white, greater temporal discounting, and greater risk aversion were associated with higher odds of being in the DM < COG group. Being male was associated with higher odds of being in the DM > COG group. Education, income, depressive symptoms, and impulsivity were not associated with a discrepancy. Only demographic associations (age, sex, and race) remained significant in a fully adjusted model with terms included for all factors. These results support the consideration of decision making and cognition as potentially separate constructs.

Design and control of the phase current of a brushless dc motor to eliminate cogging torque

NASA Astrophysics Data System (ADS)

Jang, G. H.; Lee, C. J.

2006-04-01

This paper presents a design and control method of the phase current to reduce the torque ripple of a brushless dc (BLDC) motor by eliminating cogging torque. The cogging torque is the main source of torque ripple and consequently of speed error, and it is also the excitation source to generate the vibration and noise of a motor. This research proposes a modified current wave form, which is composed of main and auxiliary currents. The former is the conventional current to generate the commutating torque. The latter generates the torque with the same magnitude and opposite sign of the corresponding cogging torque at the given position in order to eliminate the cogging torque. Time-stepping finite element method simulation considering pulse-width-modulation switching method has been performed to verify the effectiveness of the proposed method, and it shows that this proposed method reduces torque ripple by 36%. A digital-signal-processor-based controller is also developed to implement the proposed method, and it shows that this proposed method reduces the speed ripple significantly.

A directed-overflow and damage-control N -glycosidase in riboflavin biosynthesis

DOE PAGES

Frelin, Océane; Huang, Lili; Hasnain, Ghulam; ...

2015-02-15

Plants and bacteria synthesize the essential human micronutrient riboflavin (vitamin B2) via the same multistep pathway. The early intermediates of this pathway are notoriously reactive, and may be overproduced in vivo because riboflavin biosynthesis enzymes lack feedback controls. Here we demonstrate disposal of riboflavin intermediates by COG3236 (DUF1768), a protein of previously unknown function that is fused to two different riboflavin pathway enzymes in plants and bacteria (RIBR and RibA, respectively). We present cheminformatic, biochemical, genetic, and genomic evidence to show that: (i) plant and bacterial COG3236 proteins cleave the N-glycosidic bond of the first two intermediates of riboflavin biosynthesis,more » yielding relatively innocuous products; (ii) certain COG3236 proteins are in a multienzyme riboflavin biosynthesis complex that gives them privileged access to riboflavin intermediates; and (iii) COG3236 action in Arabidopsis thaliana and Escherichia coli helps maintain flavin levels. We find COG3236 proteins thus illustrate two emerging principles in chemical biology: directed overflow metabolism, in which excess flux is diverted out of a pathway, and the pre-emption of damage from reactive metabolites.« less

New Cogging Torque Reduction Methods for Permanent Magnet Machine

NASA Astrophysics Data System (ADS)

Bahrim, F. S.; Sulaiman, E.; Kumar, R.; Jusoh, L. I.

2017-08-01

Permanent magnet type motors (PMs) especially permanent magnet synchronous motor (PMSM) are expanding its limbs in industrial application system and widely used in various applications. The key features of this machine include high power and torque density, extending speed range, high efficiency, better dynamic performance and good flux-weakening capability. Nevertheless, high in cogging torque, which may cause noise and vibration, is one of the threat of the machine performance. Therefore, with the aid of 3-D finite element analysis (FEA) and simulation using JMAG Designer, this paper proposed new method for cogging torque reduction. Based on the simulation, methods of combining the skewing with radial pole pairing method and skewing with axial pole pairing method reduces the cogging torque effect up to 71.86% and 65.69% simultaneously.

In-flight estimation of center of gravity position using all-accelerometers.

PubMed

Al-Rawashdeh, Yazan Mohammad; Elshafei, Moustafa; Al-Malki, Mohammad Fahad

2014-09-19

Changing the position of the Center of Gravity (CoG) for an aerial vehicle is a challenging part in navigation, and control of such vehicles. In this paper, an all-accelerometers-based inertial measurement unit is presented, with a proposed method for on-line estimation of the position of the CoG. The accelerometers' readings are used to find and correct the vehicle's angular velocity and acceleration using an Extended Kalman Filter. Next, the accelerometers' readings along with the estimated angular velocity and acceleration are used in an identification scheme to estimate the position of the CoG and the vehicle's linear acceleration. The estimated position of the CoG and motion measurements can then be used to update the control rules to achieve better trim conditions for the air vehicle.

Clouds Optically Gridded by Stereo COGS product

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

Oktem, Rusen; Romps, David

COGS product is a 4D grid of cloudiness covering a 6 km × 6 km × 6 km cube centered at the central facility of SGP site at a spatial resolution of 50 meters and a temporal resolution of 20 seconds. The dimensions are X, Y, Z, and time, where X,Y, Z, correspond to east-west, north-south, and altitude of the grid point, respectively. COGS takes on values 0, 1, and -1 denoting "cloud", "no cloud", and "not available". 

Oxygen Generation from Carbon Dioxide for Advanced Life Support

NASA Technical Reports Server (NTRS)

Bishop, s. R.; Duncan, K. L.; Hagelin-Weaver, H. E.; Neal, L.; Paul, H. L.; Wachsman, E. D.

2007-01-01

The partial electrochemical reduction of CO2 using ceramic oxygen generators (COGs) is well known and has been studied. Conventional COGs use yttria-stabilized zirconia (YSZ) electrolytes and operate at temperatures greater than 700 C (1, 2). Operating at a lower temperature has the advantage of reducing the mass of the ancillary components such as insulation. Moreover, complete reduction of metabolically produced CO2 (into carbon and oxygen) has the potential of reducing oxygen storage weight if the oxygen can be recovered. Recently, the University of Florida developed ceramic oxygen generators employing a bilayer electrolyte of gadolinia-doped ceria and erbia-stabilized bismuth oxide (ESB) for NASA s future exploration of Mars (3). The results showed that oxygen could be reliably produced from CO2 at temperatures as low as 400 C. These results indicate that this technology could be adapted to CO2 removal from a spacesuit and other applications in which CO2 removal is an issue. This strategy for CO2 removal in advanced life support systems employs a catalytic layer combined with a COG so that the CO2 is reduced completely to solid carbon and oxygen. First, to reduce the COG operating temperature, a thin, bilayer electrolyte was employed. Second, to promote full CO2 reduction while avoiding the problem of carbon deposition on the COG cathode, a catalytic carbon deposition layer was designed and the cathode utilized materials shown to be coke resistant. Third, a composite anode was used consisting of bismuth ruthenate (BRO) and ESB that has been shown to have high performance (4). The inset of figure 1 shows the conceptual design of the tubular COG and the rest of the figure shows schematically the test apparatus. Figure 2 shows the microstructure of a COG tube prior to testing. During testing, current is applied across the cell and initially CuO is reduced to copper metal by electrochemical pumping. Then the oxygen source becomes the CO/CO2. This presentation details the results of testing the COG.

Cogging Torque Minimization in Transverse Flux Machines

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

Husain, Tausif; Hasan, Iftekhar; Sozer, Yilmaz

2017-02-16

This paper presents the design considerations in cogging torque minimization in two types of transverse flux machines. The machines have a double stator-single rotor configuration with flux concentrating ferrite magnets. One of the machines has pole windings across each leg of an E-Core stator. Another machine has quasi-U-shaped stator cores and a ring winding. The flux in the stator back iron is transverse in both machines. Different methods of cogging torque minimization are investigated. Key methods of cogging torque minimization are identified and used as design variables for optimization using a design of experiments (DOE) based on the Taguchi method.more » A three-level DOE is performed to reach an optimum solution with minimum simulations. Finite element analysis is used to study the different effects. Two prototypes are being fabricated for experimental verification.« less

In-Flight Estimation of Center of Gravity Position Using All-Accelerometers

PubMed Central

Al-Rawashdeh, Yazan Mohammad; Elshafei, Moustafa; Al-Malki, Mohammad Fahad

2014-01-01

Changing the position of the Center of Gravity (CoG) for an aerial vehicle is a challenging part in navigation, and control of such vehicles. In this paper, an all-accelerometers-based inertial measurement unit is presented, with a proposed method for on-line estimation of the position of the CoG. The accelerometers' readings are used to find and correct the vehicle's angular velocity and acceleration using an Extended Kalman Filter. Next, the accelerometers' readings along with the estimated angular velocity and acceleration are used in an identification scheme to estimate the position of the CoG and the vehicle's linear acceleration. The estimated position of the CoG and motion measurements can then be used to update the control rules to achieve better trim conditions for the air vehicle. PMID:25244585

Toward the identification of molecular cogs.

PubMed

Dziubiński, Maciej; Lesyng, Bogdan

2016-04-05

Computer simulations of molecular systems allow determination of microscopic interactions between individual atoms or groups of atoms, as well as studies of intramolecular motions. Nevertheless, description of structural transformations at the mezoscopic level and identification of causal relations associated with these transformations is very difficult. Structural and functional properties are related to free energy changes. Therefore, to better understand structural and functional properties of molecular systems, it is required to deepen our knowledge of free energy contributions arising from molecular subsystems in the course of structural transformations. The method presented in this work quantifies the energetic contribution of each pair of atoms to the total free energy change along a given collective variable. Next, with the help of a genetic clustering algorithm, the method proposes a division of the system into two groups of atoms referred to as molecular cogs. Atoms which cooperate to push the system forward along a collective variable are referred to as forward cogs, and those which work in the opposite direction as reverse cogs. The procedure was tested on several small molecules for which the genetic clustering algorithm successfully found optimal partitionings into molecular cogs. The primary result of the method is a plot depicting the energetic contributions of the identified molecular cogs to the total Potential of Mean Force (PMF) change. Case-studies presented in this work should help better understand the implications of our approach, and were intended to pave the way to a future, publicly available implementation. © 2015 Wiley Periodicals, Inc.

Center-of-gravity effects in the perception of high front vowels

NASA Astrophysics Data System (ADS)

Jacewicz, Ewa; Feth, Lawrence L.

2002-05-01

When two formant peaks are close in frequency, changing their amplitude ratio can shift the perceived vowel quality. This center-of-gravity effect (COG) was studied particularly in back vowels whose F1 and F2 are close in frequency. Chistovich and Lublinskaja (1979) show that the effect occurs when the frequency separation between the formants does not exceed 3.5 bark. The COG and critical distance effects were manifested when a two-formant reference signal was matched by a single-formant target of variable frequency. This study investigates whether the COG effect extends to closely spaced higher formants as in English /i/ and /I/. In /i/, the frequency separation between F2, F3, and F4 does not exceed 3.5 bark, suggesting the existence of one COG which may affect all three closely spaced formants (F2=2030, F3=2970, F4=3400 Hz). In /I/, each of the F2-F3 and F3-F4 separations is less than 3.5 bark but the F2-F4 separation exceeds the critical distance, indicating two COGs (F2=1780, F3=2578, F4=3400 Hz). We examine the COG effects using matching of four-formant reference signals, in which we change the amplitude ratios, by two-formant targets with variable frequency of F2. The double-staircase adaptive procedure is used. [Work supported by an INRS award from NIH to R. Fox.

Outcomes of Patients With Relapsed Hepatoblastoma Enrolled on Children's Oncology Group (COG) Phase I and II Studies.

PubMed

Trobaugh-Lotrario, Angela D; Meyers, Rebecka L; Feusner, James H

2016-04-01

Data are limited regarding outcomes of patients treated for relapsed hepatoblastoma. We reviewed enrollment patterns and outcomes of patients with hepatoblastoma on Children's Oncology Group (COG) phase I/II studies. The medical literature was searched for reports of COG phase I/II studies using PUBMED as well as an inventory from the COG publications office searching manuscripts published from 2000 to 2014. Seventy-one patients with relapsed hepatoblastoma were enrolled on 23 separate COG phase I/II studies. Four studies collected α-fetoprotein (AFP) data, but none utilized AFP decline in assessing response. Most studies enrolled few patients with relapsed hepatoblastoma: 7 studies enrolled 1 patient, and another 7 studies enrolled 2 patients each. Only 9 studies enrolled 3 or more patients with relapsed hepatoblastoma. Four responses were reported. Dedicated strata and/or focus on 1 or 2 studies with compelling biological or clinical rationale for hepatoblastoma may improve accrual (and statistical significance of response data) of patients with relapsed hepatoblastoma. Prospective study of AFP decline versus RECIST response could help determine the optimal method of assessing response to identify potentially beneficial treatments in hepatoblastoma.

Indoor integrated navigation and synchronous data acquisition method for Android smartphone

NASA Astrophysics Data System (ADS)

Hu, Chunsheng; Wei, Wenjian; Qin, Shiqiao; Wang, Xingshu; Habib, Ayman; Wang, Ruisheng

2015-08-01

Smartphones are widely used at present. Most smartphones have cameras and kinds of sensors, such as gyroscope, accelerometer and magnet meter. Indoor navigation based on smartphone is very important and valuable. According to the features of the smartphone and indoor navigation, a new indoor integrated navigation method is proposed, which uses MEMS (Micro-Electro-Mechanical Systems) IMU (Inertial Measurement Unit), camera and magnet meter of smartphone. The proposed navigation method mainly involves data acquisition, camera calibration, image measurement, IMU calibration, initial alignment, strapdown integral, zero velocity update and integrated navigation. Synchronous data acquisition of the sensors (gyroscope, accelerometer and magnet meter) and the camera is the base of the indoor navigation on the smartphone. A camera data acquisition method is introduced, which uses the camera class of Android to record images and time of smartphone camera. Two kinds of sensor data acquisition methods are introduced and compared. The first method records sensor data and time with the SensorManager of Android. The second method realizes open, close, data receiving and saving functions in C language, and calls the sensor functions in Java language with JNI interface. A data acquisition software is developed with JDK (Java Development Kit), Android ADT (Android Development Tools) and NDK (Native Development Kit). The software can record camera data, sensor data and time at the same time. Data acquisition experiments have been done with the developed software and Sumsang Note 2 smartphone. The experimental results show that the first method of sensor data acquisition is convenient but lost the sensor data sometimes, the second method is much better in real-time performance and much less in data losing. A checkerboard image is recorded, and the corner points of the checkerboard are detected with the Harris method. The sensor data of gyroscope, accelerometer and magnet meter have been recorded about 30 minutes. The bias stability and noise feature of the sensors have been analyzed. Besides the indoor integrated navigation, the integrated navigation and synchronous data acquisition method can be applied to outdoor navigation.

Center of Gravity Analysis and Operational Design: Ensuring a Logical Linkage among National Strategic Objectives; Diplomatic, Informational, Military, and Economic Instruments of Power; and the Military Campaign

DTIC Science & Technology

2009-03-01

According to Dr. Joseph Strange, former professor at the US Marine Corps War College, COGs are “ physical or moral entities that are the primary components...of physical or moral strength, power and resistance. They don’t just contribute to strength; they ARE the strength. They offer resistance. They...affecting what Strange calls the physical strategic COGs (the ability COGs). Pape defines “denial strategies” as “thwarting the [adversary’s] military

Cost of goods sold and total cost of delivery for oral and parenteral vaccine packaging formats.

PubMed

Sedita, Jeff; Perrella, Stefanie; Morio, Matt; Berbari, Michael; Hsu, Jui-Shan; Saxon, Eugene; Jarrahian, Courtney; Rein-Weston, Annie; Zehrung, Darin

2018-03-14

Despite limitations of glass packaging for vaccines, the industry has been slow to implement alternative formats. Polymer containers may address many of these limitations, such as breakage and delamination. However, the ability of polymer containers to achieve cost of goods sold (COGS) and total cost of delivery (TCOD) competitive with that of glass containers is unclear, especially for cost-sensitive low- and lower-middle-income countries. COGS and TCOD models for oral and parenteral vaccine packaging formats were developed based on information from subject matter experts, published literature, and Kenya's comprehensive multiyear plan for immunization. Rotavirus and inactivated poliovirus vaccines (IPV) were used as representative examples of oral and parenteral vaccines, respectively. Packaging technologies evaluated included glass vials, blow-fill-seal (BFS) containers, preformed polymer containers, and compact prefilled auto-disable (CPAD) devices in both BFS and preformed formats. For oral vaccine packaging, BFS multi-monodose (MMD) ampoules were the least expensive format, with a COGS of $0.12 per dose. In comparison, oral single-dose glass vials had a COGS of $0.40. BFS MMD ampoules had the lowest TCOD of oral vaccine containers at $1.19 per dose delivered, and ten-dose glass vials had a TCOD of $1.61 per dose delivered. For parenteral vaccines, the lowest COGS was achieved with ten-dose glass vials at $0.22 per dose. In contrast, preformed CPAD devices had the highest COGS at $0.60 per dose. Ten-dose glass vials achieved the lowest TCOD of the parenteral vaccine formats at $1.56 per dose delivered. Of the polymer containers for parenteral vaccines, BFS MMD ampoules achieved the lowest TCOD at $1.89 per dose delivered, whereas preformed CPAD devices remained the most expensive format, at $2.25 per dose delivered. Given their potential to address the limitations of glass and reduce COGS and TCOD, polymer containers deserve further consideration as alternative approaches for vaccine packaging. Copyright © 2018 PATH. Published by Elsevier Ltd.. All rights reserved.

Genetics Home Reference: COG5-congenital disorder of glycosylation

MedlinePlus

... in my area? Other Names for This Condition carbohydrate deficient glycoprotein syndrome type IIi CDG IIi CDG2I ... the Golgi by the conserved oligomeric Golgi (COG) complex and the golgin TATA element modulatory factor (TMF). ...

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

PubMed

Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H

2006-01-01

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

A roadmap for cost-of-goods planning to guide economic production of cell therapy products.

PubMed

Lipsitz, Yonatan Y; Milligan, William D; Fitzpatrick, Ian; Stalmeijer, Evelien; Farid, Suzanne S; Tan, Kah Yong; Smith, David; Perry, Robert; Carmen, Jessica; Chen, Allen; Mooney, Charles; Fink, John

2017-12-01

Cell therapy products are frequently developed and produced without incorporating cost considerations into process development, contributing to prohibitively costly products. Herein we contextualize individual process development decisions within a broad framework for cost-efficient therapeutic manufacturing. This roadmap guides the analysis of cost of goods (COG) arising from tissue procurement, material acquisition, facility operation, production, and storage. We present the specific COG considerations related to each of these elements as identified through a 2013 International Society for Cellular Therapy COG survey, highlighting the differences between autologous and allogeneic products. Planning and accounting for COG at each step in the production process could reduce costs, allowing for more affordable market pricing to improve the long-term viability of the cell therapy product and facilitate broader patient access to novel and transformative cell therapies. Copyright © 2017 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Integrating Skills and Wills Instruction in Self-Regulated Science Text Reading for Secondary Students

NASA Astrophysics Data System (ADS)

Michalsky, Tova

2013-07-01

This study investigated the effectiveness of cognitive-metacognitive versus motivational components of the IMPROVE self-regulatory model, used while reading scientific texts, for 10th graders' scientific literacy and self-regulated learning (SRL). Three treatment groups (N = 198) received one type of self-addressable questions while reading scientific texts: cognitive-metacognitive (CogMet), motivational (Mot), or combined (CogMetMot). Control group received no self-addressed questions (noSRL). One measure assessed scientific literacy, and two measures assessed SRL: (a) as an aptitude-pre/post questionnaires assessing self-perceived SRL, and (b) as an event-audiotaping participants' thinking-aloud SRL behaviors in real-time learning experiences and data coding illustrating SRL changes. Findings indicated that treatment groups significantly outperformed the non-treatment group. No differences emerged between CogMet and Mot, whereas fully combined SRL support (CogMetMot) was most effective. Theoretical and practical implications of this preliminary study are discussed.

Performance and optimum characteristics by finite element analysis of a coreless ironless electric generator for low wind density power generation

NASA Astrophysics Data System (ADS)

Razali, Akhtar; Rahman, Fadhlur; Leong, Yap Wee; Razali Hanipah, Mohd; Azri Hizami, Mohd

2018-04-01

Cogging is an attraction of magnetism between permanent magnets and soft ironcore lamination in a conventional electric ironcore generator. The presence of cog in the generator is seen somehow restricted the application of the generator in an application where low rotational torque is required. Cog torque requires an additional input power to overcome, hence became one of the power loss sources. With the increasing of power output, the cogging is also proportionally increased. This leads to the increasing of the supplied power of the driver motor to overcome the cog. Therefore, this research is embarked to study fundamentally about the possibility of removing ironcore lamination in an electric generator. This research deals with removal of ironcore lamination in electric generator to eliminate cog torque. A confinement technique is proposed to confine and focus magnetic flux by introducing opposing permanent magnets arrangement. There were several parameters analysed using the JMAG Designer. Transient response analysis was used in the JMAG Designer. The parameters analysed were the number of coil turns per phase, gap distance between the magnet pairs as well as the magnet grade used. These few parameters were analysed under the open circuit condition. Results showed with the increasing of gap distance, output voltage produced decreased. The increment of number of turns in the coils and higher magnet grades used, these increased the output voltage of the generator. With the help of these results, a reference point is established to get optimum design parameter for fabrication of working prototype.

Cogging Torque Reduction in a Permanent Magnet Wind Turbine Generator: Preprint

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

Muljadi, E.; Green, J.

2002-01-01

In this paper, we investigate three design options to minimize cogging torque: uniformity of air gap, pole width, and skewing. Although the design improvement is intended for small wind turbines, it is also applicable to larger wind turbines.

Cogging effect minimization in PMSM position servo system using dual high-order periodic adaptive learning compensation.

PubMed

Luo, Ying; Chen, Yangquan; Pi, Youguo

2010-10-01

Cogging effect which can be treated as a type of position-dependent periodic disturbance, is a serious disadvantage of the permanent magnetic synchronous motor (PMSM). In this paper, based on a simulation system model of PMSM position servo control, the cogging force, viscous friction, and applied load in the real PMSM control system are considered and presented. A dual high-order periodic adaptive learning compensation (DHO-PALC) method is proposed to minimize the cogging effect on the PMSM position and velocity servo system. In this DHO-PALC scheme, more than one previous periods stored information of both the composite tracking error and the estimate of the cogging force is used for the control law updating. Asymptotical stability proof with the proposed DHO-PALC scheme is presented. Simulation is implemented on the PMSM servo system model to illustrate the proposed method. When the constant speed reference is applied, the DHO-PALC can achieve a faster learning convergence speed than the first-order periodic adaptive learning compensation (FO-PALC). Moreover, when the designed reference signal changes periodically, the proposed DHO-PALC can obtain not only faster convergence speed, but also much smaller final error bound than the FO-PALC. Copyright © 2010 ISA. Published by Elsevier Ltd. All rights reserved.

The golgin protein Coy1 functions in intra-Golgi retrograde transport and interacts with the COG complex and Golgi SNAREs

PubMed Central

Anderson, Nadine S.; Mukherjee, Indrani; Bentivoglio, Christine M.; Barlowe, Charles

2017-01-01

Extended coiled-coil proteins of the golgin family play prominent roles in maintaining the structure and function of the Golgi complex. Here we further investigate the golgin protein Coy1 and document its function in retrograde transport between early Golgi compartments. Cells that lack Coy1 displayed a reduced half-life of the Och1 mannosyltransferase, an established cargo of intra-Golgi retrograde transport. Combining the coy1Δ mutation with deletions in other putative retrograde golgins (sgm1Δ and rud3Δ) caused strong glycosylation and growth defects and reduced membrane association of the conserved oligomeric Golgi (COG) complex. In contrast, overexpression of COY1 inhibited the growth of mutant strains deficient in fusion activity at the Golgi (sed5-1 and sly1-ts). To map Coy1 protein interactions, coimmunoprecipitation experiments revealed an association with the COG complex and with intra-Golgi SNARE proteins. These physical interactions are direct, as Coy1 was efficiently captured in vitro by Lobe A of the COG complex and the purified SNARE proteins Gos1, Sed5, and Sft1. Thus our genetic, in vivo, and biochemical data indicate a role for Coy1 in regulating COG complex-dependent fusion of retrograde-directed COPI vesicles. PMID:28794270

Cognitive-Functional (Cog-Fun) Dyadic Intervention for Children with ADHD and Their Parents: Impact on Parenting Self-Efficacy.

PubMed

Hahn-Markowitz, Jeri; Berger, Itai; Manor, Iris; Maeir, Adina

2018-03-01

The family context of children with ADHD plays a role in intervention outcomes, especially when parents are involved in treatment. Parental participation in evidence-based treatment for ADHD may play a role in improving their own parenting self-efficacy (PSE) as well as child outcomes. This study examined the impact of Cognitive-Functional (Cog-Fun) intervention in occupational therapy (OT) for school-aged children with ADHD, on PSE. In this randomized controlled trial with crossover design, 107 children were allocated to intervention and waitlist control groups. Intervention participants (n = 50) received Cog-Fun after baseline assessment and waitlist controls (n = 49) received treatment 3 months later. Intervention participants received 3-month follow-up assessment. Treatment included 10 parent-child Cog-Fun weekly sessions. PSE was assessed with the Tool to measure Parenting Self-Efficacy (TOPSE). All children who began treatment completed it. Mixed ANOVA revealed significant Time x Group interaction effects on TOPSE scales of Play and Enjoyment, Control, Self-Acceptance, Knowledge and Learning and Total score, which showed significant improvement with moderate treatment effects for the intervention group. Results were replicated in the control group after crossover. The findings of this study suggest that Cog-Fun OT intervention may be effective for improving aspects of PSE among parents of children with ADHD.

Screening cognitive impairment among institutionalized older Chinese men in Taiwan: a new minimum data set-based dementia screening tool is needed.

PubMed

Lin, Chu-Sheng; Lin, Ming-Hsien; Peng, Li-Ning; Chen, Liang-Kung; Hwang, Shinn-Jang; Lan, Chung-Fu

2011-01-01

Dementia screening is of great importance in various health settings for older people, long-term care facilities are no exception. The need for an effective dementia screening tool being culture sensitive is important. Minimum data set (MDS) is a population instrument for health care management in the world, which also covers dementia screening. The main purpose of this study was to evaluate the effectiveness of the MDS-based dementia screening tools among older Chinese men in the Veteran Home in Taiwan. Overall, 576 participants (mean age: 80.9±5.3 years, all males, 92.7% physically independent), 18.6% had cognitive impairment according to the mini-mental state examination (MMSE) (mean score: 26.7±3.9). However, the prevalence of cognitive impairment was 5.5% by MDS cognitive performance scale (CPS) and 18.9% by MDS cognition scale (MDS-COGS). The screening results of CPS and MDS-COGS were highly interrelated (γ=0.93, p<0.001), and MMSE scores were also significantly associated with CPS and MDS-COGS status (γ=-0.50, p<0.001 and γ=-0.52, p<0.001, respectively). Although the prevalence of cognitive impairment by MMSE and MDS-COGS are similar, the results are significantly inconsistent (p<0.001). In conclusion, both MDS-COGS and CPS were significantly correlated with MMSE scores, but significant inconsistence was noted between screening results of MMSE, CPS and MDS-COGS. Further study is needed to develop MDS-based dementia screening tools for older Chinese men in Taiwan. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Male Reproductive Health After Childhood, Adolescent, and Young Adult Cancers: A Report From the Children's Oncology Group

PubMed Central

Kenney, Lisa B.; Cohen, Laurie E.; Shnorhavorian, Margarett; Metzger, Monika L.; Lockart, Barbara; Hijiya, Nobuko; Duffey-Lind, Eileen; Constine, Louis; Green, Daniel; Meacham, Lillian

2012-01-01

The majority of children, adolescents, and young adults diagnosed with cancer will become long-term survivors. Although cancer therapy is associated with many adverse effects, one of the primary concerns of young male cancer survivors is reproductive health. Future fertility is often the focus of concern; however, it must be recognized that all aspects of male health, including pubertal development, testosterone production, and sexual function, can be impaired by cancer therapy. Although pretreatment strategies to preserve reproductive health have been beneficial to some male patients, many survivors remain at risk for long-term reproductive complications. Understanding risk factors and monitoring the reproductive health of young male survivors are important aspects of follow-up care. The Children's Oncology Group Long-Term Follow-Up Guidelines for Survivors of Childhood, Adolescent, and Young Adult Cancer (COG-LTFU Guidelines) were created by the COG to provide recommendations for follow-up care of survivors at risk for long-term complications. The male health task force of the COG-LTFU Guidelines, composed of pediatric oncologists, endocrinologists, nurse practitioners, a urologist, and a radiation oncologist, is responsible for updating the COG-LTFU Guidelines every 2 years based on literature review and expert consensus. This review summarizes current task force recommendations for the assessment and management of male reproductive complications after treatment for childhood, adolescent, and young adult cancers. Issues related to male health that are being investigated, but currently not included in the COG-LTFU Guidelines, are also discussed. Ongoing investigation will inform future COG-LTFU Guideline recommendations for follow-up care to improve health and quality of life for male survivors. PMID:22649147

French version of the Functional Assessment of Cancer Therapy-Cognitive Function (FACT-Cog) version 3.

PubMed

Joly, F; Lange, M; Rigal, O; Correia, H; Giffard, B; Beaumont, J L; Clisant, S; Wagner, L

2012-12-01

Impairment of cognitive function, a common complaint in patients receiving chemotherapy, is usually measured through neuropsychological tests. Patient self-evaluation of cognitive difficulties is an important complement to those tests. The Functional Assessment of Cancer Therapy-Cognitive Function (FACT-Cog) is a self-report questionnaire with potential to be used in standard clinical practice as a tool for evaluating patient's cognitive function before, during, and after chemotherapy. The purpose of our study was to conduct linguistic validation of the French version of the FACT-Cog. Both qualitative and quantitative methods were used in this study. After undergoing a rigorous translation methodology, the French FACT-Cog version was pretested in France with 35 cancer patients undergoing chemotherapy treatment. Interviews were conducted with all patients to ascertain their understanding of each item. The validation of the final version was conducted among 63 cancer patients, and sociodemographic information was collected as well as brief measure of cognitive function and depression score. Patient comments obtained through the cognitive debriefing interviews indicated that patients understand the French FACT-Cog items as they are intended and that the measure is culturally appropriate. Internal consistency reliability of the subscales, evaluated using Cronbach's coefficient alpha, was high for all four subscales: Perceived Cognitive Impairments = 0.93, Impact On QOL = 0.85, Comments From Others = 0.70, and Perceived Cognitive Abilities = 0.89. All item-total correlations for each subscale were greater than 0.20, and most were greater than 0.50. Results from this study effectively demonstrate that the French FACT-Cog is a reliable instrument for the self-reporting of cognitive abilities in patients undergoing chemotherapy.

Reliability of the Client-Centeredness of Goal Setting (C-COGS) Scale in Acquired Brain Injury Rehabilitation.

PubMed

Doig, Emmah; Prescott, Sarah; Fleming, Jennifer; Cornwell, Petrea; Kuipers, Pim

2016-01-01

To examine the internal reliability and test-retest reliability of the Client-Centeredness of Goal Setting (C-COGS) scale. The C-COGS scale was administered to 42 participants with acquired brain injury after completion of multidisciplinary goal planning. Internal reliability of scale items was examined using item-partial total correlations and Cronbach's α coefficient. The scale was readministered within a 1-mo period to a subsample of 12 participants to examine test-retest reliability by calculating exact and close percentage agreement for each item. After examination of item-partial total correlations, test items were revised. The revised items demonstrated stronger internal consistency than the original items. Preliminary evaluation of test-retest reliability was fair, with an average exact percent agreement across all test items of 67%. Findings support the preliminary reliability of the C-COGS scale as a tool to evaluate and promote client-centered goal planning in brain injury rehabilitation. Copyright © 2016 by the American Occupational Therapy Association, Inc.

Apolipoprotein E-mimetics inhibit neurodegeneration and restore cognitive functions in a transgenic Drosophila model of Alzheimer's disease.

PubMed

Sarantseva, Svetlana; Timoshenko, Svetlana; Bolshakova, Olga; Karaseva, Eugenia; Rodin, Dmitry; Schwarzman, Alexander L; Vitek, Michael P

2009-12-07

Mutations of the amyloid precursor protein gene (APP) are found in familial forms of Alzheimer's disease (AD) and some lead to the elevated production of amyloid-beta-protein (Abeta). While Abeta has been implicated in the causation of AD, the exact role played by Abeta and its APP precursor are still unclear. In our study, Drosophila melanogaster transgenics were established as a model to analyze AD-like pathology caused by APP overexpression. We demonstrated that age related changes in the levels and pattern of synaptic proteins accompanied progressive neurodegeneration and impairment of cognitive functions in APP transgenic flies, but that these changes may be independent from the generation of Abeta. Using novel peptide mimetics of Apolipoprotein-E, COG112 or COG133 proved to be neuroprotective and significantly improved the learning and memory of APP transgenic flies. The development of neurodegeneration and cognitive deficits was corrected by injections of COG112 or COG133, novel mimetics of apolipoprotein-E (apoE) with neuroprotective activities.

An experimental study of the effect of mooring systems on the dynamics of a SPAR buoy-type floating offshore wind turbine

NASA Astrophysics Data System (ADS)

Hong, Sinpyo; Lee, Inwon; Park, Seong Hyeon; Lee, Cheolmin; Chun, Ho-Hwan; Lim, Hee Chang

2015-09-01

An experimental study of the effect of mooring systems on the dynamics of a SPAR buoy-type floating offshore wind turbine is presented. The effects of the Center of Gravity (COG), mooring line spring constant, and fair-lead location on the turbine's motion in response to regular waves are investigated. Experimental results show that for a typical mooring system of a SPAR buoy-type Floating Offshore Wind Turbine (FOWT), the effect of mooring systems on the dynamics of the turbine can be considered negligible. However, the pitch decreases notably as the COG increases. The COG and spring constant of the mooring line have a negligible effect on the fairlead displacement. Numerical simulation and sensitivity analysis show that the wind turbine motion and its sensitivity to changes in the mooring system and COG are very large near resonant frequencies. The test results can be used to validate numerical simulation tools for FOWTs.

The KICA Carer: informant information to enhance the Kimberley Indigenous Cognitive Assessment.

PubMed

Smith, K; Flicker, L; Atkinson, D; Dwyer, A; Lautenschlager, N T; Thomas, J; Almeida, O P; LoGiudice, D

2016-01-01

A quality dementia-screening tool is required for older remote Aboriginal Australians who have high rates of dementia and limited access to appropriate medical equipment and clinicians. The Kimberley Indigenous Cognitive Assessment (KICA Cog) is a valid cognitive test for dementia in Aboriginal and Torres Strait Islander peoples. The KICA cognitive informant questionnaire (KICA Carer) had yet to be analyzed to determine validity alone or in combination with the KICA Cog. The KICA Carer was completed by nominated informants of 349 remote-living Aboriginal Australians in the Kimberley region, Western Australia. Validity was assessed by comparing KICA Carer with Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) and International Classification of Diseases (ICD-10) consensus diagnoses based on a blinded specialist review. KICA Carer and KICA Cog were then compared to determine joint validity. A KICA Carer score of ≥3/16 gave optimum sensitivity (76.2%) and specificity (81.4%), area under curve (AUC) 0.89 (95% CI = 0.85, 0.94) with positive predictive value (PPV) of 35.8%, and negative predictive value (NPV) of 96.2%. A KICA Cog score of ≤33/39 gave a sensitivity of 92.9% and specificity of 89.9%, AUC 0.96 (95% CI = 0.94, 0.98), with PPV of 55.6% and NPV of 98.9%. Cut-off scores of KICA Cog ≤ 33/39 and KICA Carer ≥ 2/16 in series indicate possible dementia, with sensitivity of 90.5% and specificity of 93.5%. In this setting, PPV was 66.5% and NPV was 98.6%. The KICA Carer is an important tool to accurately screen dementia in remote Aboriginal Australians when the KICA Cog is unable to be used for a patient. It is readily accepted by caregivers. • For the best practice in the cognitive assessment of an Aboriginal Australian aged over 45 years, KICA Cog should be utilized. • In cases where Aboriginal patients are not assessed directly, KICA Carer should be conducted with an informant. A cut-off score of ≥3/16 should be used (these tools can be downloaded from www.wacha.org.au/kica.html).

Evaluation of Oxygen Concentrators and Chemical Oxygen Generators at Altitude and Temperature Extremes.

PubMed

Blakeman, Thomas C; Rodriquez, Dario; Britton, Tyler J; Johannigman, Jay A; Petro, Michael C; Branson, Richard D

2016-05-01

Oxygen cylinders are heavy and present a number of hazards, and liquid oxygen is too heavy and cumbersome to be used in far forward environments. Portable oxygen concentrators (POCs) and chemical oxygen generators (COGs) have been proposed as a solution. We evaluated 3 commercially available POCs and 3 COGs in a laboratory setting. Altitude testing was done at sea level and 8,000, 16,000, and 22,000 ft. Temperature extreme testing was performed after storing devices at 60°C and -35°C for 24 hours. Mean FIO2 decreased after storage at -35°C with Eclipse and iGo POCs and also at the higher volumes after storage at 60°C with the Eclipse. The iGo ceased to operate at 16,000 ft, but the Eclipse and Saros were unaffected by altitude. Oxygen flow, duration of operation, and total oxygen volume varied between COGs and within the same device type. Output decreased after storage at -35°C, but increased at each altitude as compared to sea level. This study showed significant differences in the performance of POCs and COGs after storage at temperature extremes and with the COGs at altitude. Clinicians must understand the performance characteristics of devices in all potential environments. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

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

Jin, H.G.; Sun, S.; Han, W.

This paper proposes a novel multifunctional energy system (MES), which cogenerates coke, hydrogen, and power, through the use of coal and coke oven gas (COG). In this system, a new type of coke oven, firing coal instead of COG as heating resource for coking, is adopted. The COG rich in H{sub 2} is sent to a pressure swing adsorption (PSA) unit to separate about 80% of hydrogen first, and then the PSA purge gas is fed to a combined cycle as fuel. The new system combines the chemical processes and power generation system, along with the integration of chemical conversionmore » and thermal energy utilization. In this manner, both the chemical energy of fuel and thermal energy can be used more effectively. With the same inputs of fuel and the same output of coking heat, the new system can produce about 65% more hydrogen than that of individual systems. As a result, the thermal efficiency of the new system is about 70%, and the exergy efficiency is about 66%. Compared with individual systems, the primary energy saving ratio can reach as high as 12.5%. Based on the graphical exergy analyses, we disclose that the integration of synthetic utilization of COG and coal plays a significant role in decreasing the exergy destruction of the MES system. The promising results obtained may lead to a clean coal technology that will utilize COG and coal more efficiently and economically.« less

The Impact of Cognitive Training on Cerebral White Matter in Community-Dwelling Elderly: One-Year Prospective Longitudinal Diffusion Tensor Imaging Study.

PubMed

Cao, Xinyi; Yao, Ye; Li, Ting; Cheng, Yan; Feng, Wei; Shen, Yuan; Li, Qingwei; Jiang, Lijuan; Wu, Wenyuan; Wang, Jijun; Sheng, Jianhua; Feng, Jianfeng; Li, Chunbo

2016-09-15

It has been shown that cognitive training (CogTr) is effective and recuperative for older adults, and can be used to fight against cognitive decline. In this study, we investigated whether behavioural gains from CogTr would extend to white matter (WM) microstructure, and whether training-induced changes in WM integrity would be associated with improvements in cognitive function, using diffusion tensor imaging (DTI). 48 healthy community elderly were either assigned to multi-domain or single-domain CogTr groups to receive 24 sessions over 12 weeks, or to a control group. DTI was performed at both baseline and 12-month follow-up. Positive effects of multi-domain CogTr on long-term changes in DTI indices were found in posterior parietal WM. Participants in the multi-domain group showed a trend of long-term decrease in axial diffusivity (AD) without significant change in fractional anisotropy (FA), mean diffusivity (MD) or radial diffusivity (RD), while those in the control group displayed a significant FA decrease, and an increase in MD and RD. In addition, significant relationships between an improvement in processing speed and changes in RD, MD and AD were found in the multi-domain group. These findings support the hypothesis that plasticity of WM can be modified by CogTr, even in late adulthood.

An Open Source Web Map Server Implementation For California and the Digital Earth: Lessons Learned

NASA Technical Reports Server (NTRS)

Sullivan, D. V.; Sheffner, E. J.; Skiles, J. W.; Brass, J. A.; Condon, Estelle (Technical Monitor)

2000-01-01

This paper describes an Open Source implementation of the Open GIS Consortium's Web Map interface. It is based on the very popular Apache WWW Server, the Sun Microsystems Java ServIet Development Kit, and a C language shared library interface to a spatial datastore. This server was initially written as a proof of concept, to support a National Aeronautics and Space Administration (NASA) Digital Earth test bed demonstration. It will also find use in the California Land Science Information Partnership (CaLSIP), a joint program between NASA and the state of California. At least one WebMap enabled server will be installed in every one of the state's 58 counties. This server will form a basis for a simple, easily maintained installation for those entities that do not yet require one of the larger, more expensive, commercial offerings.

A method for reduction of cogging torque in brushless DC motor considering the distribution of magnetization by 3DEMCN

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

Hur, J.; Hyun, D.S.; Hong, J.P.

1998-09-01

The method of reducing cogging torque and improving average torque has been studied by changing the dead zone angle of trapezoidal magnetization distribution of ring type rotor magnet in brushless DC motor (BLDCM). Because BLDCM has 3-D shape of overhang, 3-D analysis should be used for exact computation of its magnetic field. 3-D equivalent magnetic circuit network method (3-D EMCN) which can analyze an accurate 3-D magnetic field has been introduced. The analysis results of cogging torque using 3-D EMCN are compared with ones of 3-D finite element method (3-D FEM) and experimental data.

Investigation on the Room-temperature preparation of Cobalt hybrid/Graphene Nanocomposite and application in wastewater purification: Highly Efficient Removal of Congo Red

NASA Astrophysics Data System (ADS)

Wang, L. X.; Zhao, Y. F.; Meng, Q. M.

2018-01-01

Here, we are going to report a simple, low-cost and environmental friendly process to prepare the cobalt hybrid/graphene (Co/G) nanocomposite at room temperature. NaBH4 was used as the reducing agent. Such an approach can be extended to grow some other metal/G nanocomposites, for example, Ni/G, Co/G nanocomposite possesses narrow size-distribution and good dispersion. Because of the special appearance with large surface area, and the special synthesis process of the productions, adsorption experiments for Congo Red were carried out in synthetic wastewater. The CR removal ability of Co/G nanocomposite can reach 263.2 mg/g.

Computer-Based Cognitive Tools in Teacher Training: The COG-TECH Projects

ERIC Educational Resources Information Center

Orhun, Emrah

2003-01-01

The COG-TECH (Cognitive Technologies for Problem Solving and Learning) Network conducted three international projects between 1994 and 2001 under the auspices of the European Commission. The main purpose of these projects was to train teacher educators in the Mediterranean countries to use computers as effective pedagogical tools. The summer…

An open clinical trial assessing a novel training program for social cognitive impairment in schizophrenia.

PubMed

Marsh, Pamela; Langdon, Robyn; McGuire, Jonathan; Harris, Anthony; Polito, Vince; Coltheart, Max

2013-04-01

Social cognition is profoundly impaired in patients with schizophrenia. This study describes 'Mental-State Reasoning Training for Social Cognitive Impairment' (SoCog-MSRT), a 5-week program developed to improve social cognition in patients with schizophrenia. We aimed to investigate the feasibility of implementing SoCog-MSRT in a rehabilitation setting and to evaluate whether our training methods produced improvements. METHOD The feasibility and benefits of SoCog-MSRT were evaluated in an open clinical trial with 14 participants with schizophrenia or schizoaffective disorder. Training comprised 10 twice-weekly sessions, for 5 weeks, with a pre- and post-training assessment. There were significant improvements on: (a) a classic false-belief test of Theory of Mind (ToM); (b) inferring complex mental states from the eyes; and (c) a self-reported measure of social understanding. Some of these improvements were associated with baseline levels of working memory and premorbid Intelligence Quotient (IQ). CONCLUSIONS SoCog-MSRT can improve ToM abilities and social understanding, but individuals with poorer working memory and lower premorbid IQ may be less able to benefit from this type of training.

Apolipoprotein E Mimetic Peptide Increases Cerebral Glucose Uptake by Reducing Blood-Brain Barrier Disruption after Controlled Cortical Impact in Mice: An 18F-Fluorodeoxyglucose PET/CT Study.

PubMed

Qin, Xinghu; You, Hong; Cao, Fang; Wu, Yue; Peng, Jianhua; Pang, Jinwei; Xu, Hong; Chen, Yue; Chen, Ligang; Vitek, Michael P; Li, Fengqiao; Sun, Xiaochuan; Jiang, Yong

2017-02-15

Traumatic brain injury (TBI) disrupts the blood-brain barrier (BBB) and reduces cerebral glucose uptake. Vascular endothelial growth factor (VEGF) is believed to play a key role in TBI, and COG1410 has demonstrated neuroprotective activity in several models of TBI. However, the effects of COG1410 on VEGF and glucose metabolism following TBI are unknown. The current study aimed to investigate the expression of VEGF and glucose metabolism effects in C57BL/6J male mice subjected to experimental TBI. The results showed that controlled cortical impact (CCI)-induced vestibulomotor deficits were accompanied by increases in brain edema and the expression of VEGF, with a decrease in cerebral glucose uptake. COG1410 treatment significantly improved vestibulomotor deficits and glucose uptake and produced decreases in VEGF in the pericontusion and ipsilateral hemisphere of injury, as well as in brain edema and neuronal degeneration compared with the control group. These data support that COG1410 may have potential as an effective drug therapy for TBI.

Efficacy of Cognitive-Functional (Cog-Fun) Occupational Therapy Intervention Among Children With ADHD: An RCT.

PubMed

Hahn-Markowitz, Jeri; Berger, Itai; Manor, Iris; Maeir, Adina

2016-09-16

To examine the efficacy of a Cognitive-Functional (Cog-Fun) intervention for children with ADHD. Random allocation of 107 children to study or control groups preceded 10 parent-child weekly Cog-Fun sessions emphasizing executive strategy training in games and daily activities. Controls received treatment after crossover. Study participants were followed up 3 months post-treatment. Outcomes included parent/teacher ratings of executive functions, ADHD symptoms, and parent ratings of quality of life. Eight children withdrew prior to treatment. All children in both groups who began treatment completed it. Mixed effects ANOVA revealed significant Time × Group interaction effects on all parent-reported outcomes. Treatment effects were moderate to large, replicated after crossover in the control group and not moderated by medication. Parent-reported treatment gains in the study group were maintained at follow-up. No significant Time × Group interaction effects were found on teacher outcomes. Cog-Fun occupational therapy (OT) intervention shows positive context-specific effects on parent, but not teacher, ratings. © The Author(s) 2016.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

PubMed

Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A C; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

PubMed Central

Ferreira, Ari J. S.; Siam, Rania; Setubal, João C.; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S.; Dawe, Adam S.; Ghazy, Mohamed A.; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M.; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A. C.; Jankovic, Boris R.; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

Abundance and functional diversity of riboswitches in microbial communities

PubMed Central

Kazanov, Marat D; Vitreschak, Alexey G; Gelfand, Mikhail S

2007-01-01

Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes. Results Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198). Conclusion This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes. PMID:17908319

The CogBIAS longitudinal study protocol: cognitive and genetic factors influencing psychological functioning in adolescence.

PubMed

Booth, Charlotte; Songco, Annabel; Parsons, Sam; Heathcote, Lauren; Vincent, John; Keers, Robert; Fox, Elaine

2017-12-29

Optimal psychological development is dependent upon a complex interplay between individual and situational factors. Investigating the development of these factors in adolescence will help to improve understanding of emotional vulnerability and resilience. The CogBIAS longitudinal study (CogBIAS-L-S) aims to combine cognitive and genetic approaches to investigate risk and protective factors associated with the development of mood and impulsivity-related outcomes in an adolescent sample. CogBIAS-L-S is a three-wave longitudinal study of typically developing adolescents conducted over 4 years, with data collection at age 12, 14 and 16. At each wave participants will undergo multiple assessments including a range of selective cognitive processing tasks (e.g. attention bias, interpretation bias, memory bias) and psychological self-report measures (e.g. anxiety, depression, resilience). Saliva samples will also be collected at the baseline assessment for genetic analyses. Multilevel statistical analyses will be performed to investigate the developmental trajectory of cognitive biases on psychological functioning, as well as the influence of genetic moderation on these relationships. CogBIAS-L-S represents the first longitudinal study to assess multiple cognitive biases across adolescent development and the largest study of its kind to collect genetic data. It therefore provides a unique opportunity to understand how genes and the environment influence the development and maintenance of cognitive biases and provide insight into risk and protective factors that may be key targets for intervention.

The COG database: an updated version includes eukaryotes

PubMed Central

Tatusov, Roman L; Fedorova, Natalie D; Jackson, John D; Jacobs, Aviva R; Kiryutin, Boris; Koonin, Eugene V; Krylov, Dmitri M; Mazumder, Raja; Mekhedov, Sergei L; Nikolskaya, Anastasia N; Rao, B Sridhar; Smirnov, Sergei; Sverdlov, Alexander V; Vasudevan, Sona; Wolf, Yuri I; Yin, Jodie J; Natale, Darren A

2003-01-01

Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (~1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. Conclusion The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies. PMID:12969510

Puzzling with online games (BAM-COG): reliability, validity, and feasibility of an online self-monitor for cognitive performance in aging adults.

PubMed

Aalbers, Teun; Baars, Maria A E; Olde Rikkert, Marcel G M; Kessels, Roy P C

2013-12-03

Online interventions are aiming increasingly at cognitive outcome measures but so far no easy and fast self-monitors for cognition have been validated or proven reliable and feasible. This study examines a new instrument called the Brain Aging Monitor-Cognitive Assessment Battery (BAM-COG) for its alternate forms reliability, face and content validity, and convergent and divergent validity. Also, reference values are provided. The BAM-COG consists of four easily accessible, short, yet challenging puzzle games that have been developed to measure working memory ("Conveyer Belt"), visuospatial short-term memory ("Sunshine"), episodic recognition memory ("Viewpoint"), and planning ("Papyrinth"). A total of 641 participants were recruited for this study. Of these, 397 adults, 40 years and older (mean 54.9, SD 9.6), were eligible for analysis. Study participants played all games three times with 14 days in between sets. Face and content validity were based on expert opinion. Alternate forms reliability (AFR) was measured by comparing scores on different versions of the BAM-COG and expressed with an intraclass correlation (ICC: two-way mixed; consistency at 95%). Convergent validity (CV) was provided by comparing BAM-COG scores to gold-standard paper-and-pencil and computer-assisted cognitive assessment. Divergent validity (DV) was measured by comparing BAM-COG scores to the National Adult Reading Test IQ (NART-IQ) estimate. Both CV and DV are expressed as Spearman rho correlation coefficients. Three out of four games showed adequate results on AFR, CV, and DV measures. The games Conveyer Belt, Sunshine, and Papyrinth have AFR ICCs of .420, .426, and .645 respectively. Also, these games had good to very good CV correlations: rho=.577 (P=.001), rho=.669 (P<.001), and rho=.400 (P=.04), respectively. Last, as expected, DV correlations were low: rho=-.029 (P=.44), rho=-.029 (P=.45), and rho=-.134 (P=.28) respectively. The game Viewpoint provided less desirable results with an AFR ICC of .167, CV rho=.202 (P=.15), and DV rho=-.162 (P=.21). This study provides evidence for the use of the BAM-COG test battery as a feasible, reliable, and valid tool to monitor cognitive performance in healthy adults in an online setting. Three out of four games have good psychometric characteristics to measure working memory, visuospatial short-term memory, and planning capacity.

Clinical and histological characteristics of canine ocular gliovascular syndrome.

PubMed

Treadwell, Amy; Naranjo, Carolina; Blocker, Tiffany; Zarfoss, Mitzi; Dubielzig, Richard R

2015-09-01

To characterize the clinical, diagnostic, and histopathologic findings in dogs with canine ocular gliovascular syndrome (COGS). The archives at the Comparative Ocular Pathology Laboratory of Wisconsin (COPLOW) were used to identify eyes with COGS. Histopathological inclusion criteria included: a neovascular membrane extending from the optic nerve head or retina, clusters of spindle cells lacking vascularization within the vitreous, and histological signs of glaucoma. Special and immunohistochemical (IHC) staining techniques were performed. Clinical data, treatments, and outcomes were obtained from case records and information provided by submitting veterinarians. Thirty-seven eyes of 36 dogs were identified with COGS. The average age at diagnosis was 8.8 years (±2.2). The relative risk for a Labrador retriever affected by COGS was significantly greater (9.3 times) (P < 0.0001) when compared to all other dog breeds within the COPLOW database. Most dogs presented with hyphema and secondary glaucoma; average intraocular pressure was 39 mmHg (±19). Average time to enucleation or evisceration was 27 days. Vitreal cells stained positive with IHC for glial fibrillary acidic protein in 14 of 17 globes, and vascular endothelial growth factor was expressed in the vitreal cells in five of five globes. We have defined a syndrome associated with vitreal glial cell aggregates and neovascular proliferation from the optic nerve or retina, which leads to neovascular glaucoma. The inflammation and secondary glaucoma resulting from this syndrome appear poorly responsive to conventional medical therapies. The exact etiology of COGS remains undetermined, but a systemic etiology is unlikely. © 2014 American College of Veterinary Ophthalmologists.

Influence of Social Support on Older Adults with Cognitive Impairment, Depressive Symptoms, or Both Coexisting

ERIC Educational Resources Information Center

Millan-Calenti, Jose C.; Sanchez, Alba; Lorenzo-Lopez, Laura; Cao, Ricardo; Maseda, Ana

2013-01-01

The influence of social support dimensions (the extent of contact with others, the satisfaction with contacts, and the availability of help if sick or disabled) in elderly people with cognitive impairment (COG), depressive symptoms (DEP), or the co-occurrence of these symptoms (COG-DEP) was assessed in a cross-sectional analysis of a…

Potential of the Cogex Software Platform to Replace Logbooks in Capstone Design Projects

ERIC Educational Resources Information Center

Foley, David; Charron, François; Plante, Jean-Sébastien

2018-01-01

Recent technologies are offering the power to share and grow knowledge and ideas in unprecedented ways. The CogEx software platform was developed to take advantage of the digital world with innovative ideas to support designers work in both industrial and academic contexts. This paper presents a qualitative study on the usage of CogEx during…

The Cogs Are Coming: The Cognitive Augmentation Revolution

ERIC Educational Resources Information Center

Fulbright, Ron

2016-01-01

We are at the beginning of a new era in human history--the cognitive augmentation era. Until now, humans have had to do all of the thinking. The future will make it possible for humans to partner with cognitive systems doing some of the thinking themselves and in many ways thinking that is superior to humans. Together, humans and "cogs"…

Incremental Criterion Validity of the WJ-III COG Clinical Clusters: Marginal Predictive Effects beyond the General Factor

ERIC Educational Resources Information Center

McGill, Ryan J.

2015-01-01

The current study examined the incremental validity of the clinical clusters from the Woodcock-Johnson III Tests of Cognitive Abilities (WJ-III COG) for predicting scores on the Woodcock-Johnson III Tests of Achievement (WJ-III ACH). All participants were children and adolescents (N = 4,722) drawn from the nationally representative WJ-III…

Gaining New Military Capability: An Experiment in Concept Development.

DTIC Science & Technology

1998-01-01

Angeles Police Department ( LAPD ) were invited, at- tended, and made important contributions.1 ORGANIZING COG DISCUSSIONS We sought to structure COG...Terry Covington, RAND; Charles Duke, Los Angeles Police Department ; Gene Gritton, RAND; Thomas Karr, Lawrence Livermore Laboratory; LTC Will Irwin, USA...Munition Joint Requirements Oversight Council Joint Stand-off Weapon Joint Strategic Tracking and Radar System Laser radar Los Angeles Police

Comparative genomic analysis by microbial COGs self-attraction rate.

PubMed

Santoni, Daniele; Romano-Spica, Vincenzo

2009-06-21

Whole genome analysis provides new perspectives to determine phylogenetic relationships among microorganisms. The availability of whole nucleotide sequences allows different levels of comparison among genomes by several approaches. In this work, self-attraction rates were considered for each cluster of orthologous groups of proteins (COGs) class in order to analyse gene aggregation levels in physical maps. Phylogenetic relationships among microorganisms were obtained by comparing self-attraction coefficients. Eighteen-dimensional vectors were computed for a set of 168 completely sequenced microbial genomes (19 archea, 149 bacteria). The components of the vector represent the aggregation rate of the genes belonging to each of 18 COGs classes. Genes involved in nonessential functions or related to environmental conditions showed the highest aggregation rates. On the contrary genes involved in basic cellular tasks showed a more uniform distribution along the genome, except for translation genes. Self-attraction clustering approach allowed classification of Proteobacteria, Bacilli and other species belonging to Firmicutes. Rearrangement and Lateral Gene Transfer events may influence divergences from classical taxonomy. Each set of COG classes' aggregation values represents an intrinsic property of the microbial genome. This novel approach provides a new point of view for whole genome analysis and bacterial characterization.

The interactome of the copper transporter ATP7A belongs to a network of neurodevelopmental and neurodegeneration factors

PubMed Central

Comstra, Heather S; McArthy, Jacob; Rudin-Rush, Samantha; Hartwig, Cortnie; Gokhale, Avanti; Zlatic, Stephanie A; Blackburn, Jessica B; Werner, Erica; Petris, Michael; D’Souza, Priya; Panuwet, Parinya; Barr, Dana Boyd; Lupashin, Vladimir; Vrailas-Mortimer, Alysia; Faundez, Victor

2017-01-01

Genetic and environmental factors, such as metals, interact to determine neurological traits. We reasoned that interactomes of molecules handling metals in neurons should include novel metal homeostasis pathways. We focused on copper and its transporter ATP7A because ATP7A null mutations cause neurodegeneration. We performed ATP7A immunoaffinity chromatography and identified 541 proteins co-isolating with ATP7A. The ATP7A interactome concentrated gene products implicated in neurodegeneration and neurodevelopmental disorders, including subunits of the Golgi-localized conserved oligomeric Golgi (COG) complex. COG null cells possess altered content and subcellular localization of ATP7A and CTR1 (SLC31A1), the transporter required for copper uptake, as well as decreased total cellular copper, and impaired copper-dependent metabolic responses. Changes in the expression of ATP7A and COG subunits in Drosophila neurons altered synapse development in larvae and copper-induced mortality of adult flies. We conclude that the ATP7A interactome encompasses a novel COG-dependent mechanism to specify neuronal development and survival. DOI: http://dx.doi.org/10.7554/eLife.24722.001 PMID:28355134

Maximum power point tracking analysis of a coreless ironless electric generator for renewable energy application

NASA Astrophysics Data System (ADS)

Razali, Akhtar; Rahman, Fadhlur; Leong, Yap Wee; Razali Hanipah, Mohd; Azri Hizami, Mohd

2018-04-01

The magnetism attraction between permanent magnets and soft ironcore lamination in a conventional electric ironcore generator is often known as cogging. Cogging requires an additional input power to overcome, hence became one of the power loss sources. With the increasing of power output, the cogging is also proportionally increased. This leads to the increasing of the supplied power of the driver motor to overcome the cog. Therefore, this research is embarked to study fundamentally about the possibility of removing ironcore lamination in an electric generator to see its performance characteristic. In the maximum power point tracking test, the fabricated ironless coreless electricity generator was tested by applying the load on the ironless coreless electricity generator optimization to maximize the power generated, voltage and the current produced by the ironless coreless electricity generator when the rotational speed of the rotor increased throughout the test. The rotational torque and power output are measured, and efficiency is then analyzed. Results indicated that the generator produced RMS voltage of 200VAC at rotational speed of 318 RPM. Torque required to rotate the generator was at 10.8Nm. The generator had working efficiency of 77.73% and the power generated was at 280W.

Comparing clinical profiles in Alzheimer's disease and Parkinson's disease dementia.

PubMed

Farlow, Martin R; Schmitt, Frederick; Aarsland, Dag; Grossberg, George T; Somogyi, Monique; Meng, Xiangyi

2013-01-01

Greater understanding of differences in baseline impairment and disease progression in patients with Alzheimer's disease (AD) and Parkinson's disease dementia (PDD) may improve the interpretation of drug effects and the design of future studies. This was a retrospective analysis of three randomized, double-blind rivastigmine databases (one in PDD, two in AD). Impairment on the Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog), Alzheimer's Disease Cooperative Study-Activities of Daily Living (ADCS-ADL) scale, 10-item Neuropsychiatric Inventory (NPI-10) and the ADCS-Clinical Global Impression of Change (CGIC) was compared [standardized difference (Cohen's d), similar if <0.1]. Patients with AD or PDD had similar levels of impairment on the ADAS-cog and NPI-10. Scores on the ADCS-ADL scale (standardized difference = 0.47) and the ADAS-cog memory domain (total, 0.33; items, 0.10-0.58) were higher in AD; PDD patients were more impaired in the language (0.23) and praxis (0.34) domains. AD patients receiving placebo showed greater deterioration on the ADAS-cog (0.14) and improvement on the NPI-10 (0.11) compared with patients with PDD. Differing patterns of impairment occur in AD and PDD.

Nurse-Led Programs to Facilitate Enrollment to Children's Oncology Group Cancer Control Trials.

PubMed

Haugen, Maureen; Kelly, Katherine Patterson; Leonard, Marcia; Mills, Denise; Sung, Lillian; Mowbray, Catriona; Landier, Wendy

2016-09-01

The progress made over the past 50 years in disease-directed clinical trials has significantly increased cure rates for children and adolescents with cancer. The Children's Oncology Group (COG) is now conducting more studies that emphasize improving quality of life for young people with cancer. These types of clinical trials are classified as cancer control (CCL) studies by the National Cancer Institute and require different resources and approaches to facilitate adequate accrual and implementation at COG institutions. Several COG institutions that had previously experienced problems with low accruals to CCL trials have successfully implemented local nursing leadership for these types of studies. Successful models of nurses as institutional leaders and "champions" of CCL trials are described. © 2015 by Association of Pediatric Hematology/Oncology Nurses.

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

Husain, Tausif; Hasan, Iftekhar; Sozer, Yilmaz

This paper presents the design considerations in cogging torque minimization in two types of transverse flux machines. The machines have a double stator-single rotor configuration with flux concentrating ferrite magnets. One of the machines has pole windings across each leg of an E-Core stator. Another machine has quasi-U-shaped stator cores and a ring winding. The flux in the stator back iron is transverse in both machines. Different methods of cogging torque minimization are investigated. Key methods of cogging torque minimization are identified and used as design variables for optimization using a design of experiments (DOE) based on the Taguchi method.more » A three-level DOE is performed to reach an optimum solution with minimum simulations. Finite element analysis is used to study the different effects. Two prototypes are being fabricated for experimental verification.« less

Puzzling With Online Games (BAM-COG): Reliability, Validity, and Feasibility of an Online Self-Monitor for Cognitive Performance in Aging Adults

PubMed Central

Baars, Maria A E; Olde Rikkert, Marcel G M; Kessels, Roy P C

2013-01-01

Background Online interventions are aiming increasingly at cognitive outcome measures but so far no easy and fast self-monitors for cognition have been validated or proven reliable and feasible. Objective This study examines a new instrument called the Brain Aging Monitor–Cognitive Assessment Battery (BAM-COG) for its alternate forms reliability, face and content validity, and convergent and divergent validity. Also, reference values are provided. Methods The BAM-COG consists of four easily accessible, short, yet challenging puzzle games that have been developed to measure working memory (“Conveyer Belt”), visuospatial short-term memory (“Sunshine”), episodic recognition memory (“Viewpoint”), and planning (“Papyrinth”). A total of 641 participants were recruited for this study. Of these, 397 adults, 40 years and older (mean 54.9, SD 9.6), were eligible for analysis. Study participants played all games three times with 14 days in between sets. Face and content validity were based on expert opinion. Alternate forms reliability (AFR) was measured by comparing scores on different versions of the BAM-COG and expressed with an intraclass correlation (ICC: two-way mixed; consistency at 95%). Convergent validity (CV) was provided by comparing BAM-COG scores to gold-standard paper-and-pencil and computer-assisted cognitive assessment. Divergent validity (DV) was measured by comparing BAM-COG scores to the National Adult Reading Test IQ (NART-IQ) estimate. Both CV and DV are expressed as Spearman rho correlation coefficients. Results Three out of four games showed adequate results on AFR, CV, and DV measures. The games Conveyer Belt, Sunshine, and Papyrinth have AFR ICCs of .420, .426, and .645 respectively. Also, these games had good to very good CV correlations: rho=.577 (P=.001), rho=.669 (P<.001), and rho=.400 (P=.04), respectively. Last, as expected, DV correlations were low: rho=−.029 (P=.44), rho=−.029 (P=.45), and rho=−.134 (P=.28) respectively. The game Viewpoint provided less desirable results with an AFR ICC of .167, CV rho=.202 (P=.15), and DV rho=−.162 (P=.21). Conclusions This study provides evidence for the use of the BAM-COG test battery as a feasible, reliable, and valid tool to monitor cognitive performance in healthy adults in an online setting. Three out of four games have good psychometric characteristics to measure working memory, visuospatial short-term memory, and planning capacity. PMID:24300212

Incremental Validity of the WJ III COG: Limited Predictive Effects beyond the GIA-E

ERIC Educational Resources Information Center

McGill, Ryan J.; Busse, R. T.

2015-01-01

This study is an examination of the incremental validity of Cattell-Horn-Carroll (CHC) broad clusters from the Woodcock-Johnson III Tests of Cognitive Abilities (WJ III COG) for predicting scores on the Woodcock-Johnson III Tests of Achievement (WJ III ACH). The participants were children and adolescents, ages 6-18 (n = 4,722), drawn from the WJ…

A Comparison of Visual and Auditory Processing Tests on the Woodcock-Johnson Tests of Cognitive Ability, Revised and the Learning Efficiency Test-II.

ERIC Educational Resources Information Center

Bolen, L. M.; Kimball, D. J.; Hall, C. W.; Webster, R. E.

1997-01-01

Compares the visual and auditory processing factors of the Woodcock Johnson Tests of Cognitive Ability, Revised (WJR COG) and the visual and auditory memory factors of the Learning Efficiency Test, II (LET-II) among 120 college students. Results indicate two significant performance differences between the WJR COG and LET-II. (RJM)

Feel the Force of Cogs, Pulleys and Water Power

ERIC Educational Resources Information Center

Pugh, Julie

2016-01-01

Quarry Bank Mill in Cheshire was built in 1784 and was one of the first water-powered cotton mills of the Industrial Revolution. While the machines are now powered by electricity, the water wheel still turns and the machines run. Linking the two are cogs, shafts and belts, so it is possible to see how the power of the river was captured and then…

Adapted hydropower-driven water supply system: assessment of an underground application in an Indonesian karst area

NASA Astrophysics Data System (ADS)

Oberle, P.; Ikhwan, M.; Stoffel, D.; Nestmann, F.

2016-09-01

Populated karst landscapes can be found all over the world, although their natural boundary conditions mostly lead to distinct challenges regarding a sustainable water supply. Especially in developing and emerging countries, this situation aggravates since appropriate technologies and water management concepts are rarely available. Against this background, the interdisciplinary, German-Indonesian joint project " Integrated Water Resources Management (IWRM) Indonesia", funded by the German Federal Ministry of Education and Research (BMBF), focused on the development and exemplary implementation of adapted techniques to remedy the partly severe water scarcity in the region Gunung Sewu. This karst area, widely known as " Java's poorhouse", is located on the southern coast of Java Island and distinctly suffers from the mentioned constraints. Under the aegis of the Karlsruhe Institute of Technology (KIT), the conceptual and technical achievements of the "IWRM Indonesia" joint research project are characterized by a high potential for multiplication not only for karst areas but also for non-karst regions. One of the project's major accomplishments is the erection of an innovative hydropower-driven water supply facility located in a karst cave 100 m below ground and continuously supplying tens of thousands of people with fresh water. Referring to the plant's innovative character and the demanding conditions on-site, the implementation was a highly iterative process leading to today's autonomous operation by an Indonesian public authority. Based on the experiences gained during design, construction, operation and monitoring phase, this paper introduces an implementation approach for adapted technologies as well as a comprising technical and economical assessment of the plant's operation.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

PubMed

Powell, Bradford C; Hutchison, Clyde A

2006-01-19

Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene prediction. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

PubMed Central

Powell, Bradford C; Hutchison, Clyde A

2006-01-01

Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes. PMID:16423288

Feedforward ankle strategy of balance during quiet stance in adults

PubMed Central

Gatev, Plamen; Thomas, Sherry; Kepple, Thomas; Hallett, Mark

1999-01-01

We studied quiet stance investigating strategies for maintaining balance. Normal subjects stood with natural stance and with feet together, with eyes open or closed. Kinematic, kinetic and EMG data were evaluated and cross-correlated.Cross-correlation analysis revealed a high, positive, zero-phased correlation between anteroposterior motions of the centre of gravity (COG) and centre of pressure (COP), head and COG, and between linear motions of the shoulder and knee in both sagittal and frontal planes. There was a moderate, negative, zero-phased correlation between the anteroposterior motion of COP and ankle angular motion.Narrow stance width increased ankle angular motion, hip angular motion, mediolateral sway of the COG, and the correlation between linear motions of the shoulder and knee in the frontal plane. Correlations between COG and COP and linear motions of the shoulder and knee in the sagittal plane were decreased. The correlation between the hip angular sway in the sagittal and frontal planes was dependent on interaction between support and vision.Low, significant positive correlations with time lags of the maximum of cross-correlation of 250-300 ms were found between the EMG activity of the lateral gastrocnemius muscle and anteroposterior motions of the COG and COP during normal stance. Narrow stance width decreased both correlations whereas absence of vision increased the correlation with COP.Ankle mechanisms dominate during normal stance especially in the sagittal plane. Narrow stance width decreased the role of the ankle and increased the role of hip mechanisms in the sagittal plane, while in the frontal plane both increased.The modulation pattern of the lateral gastrocnemius muscle suggests a central program of control of the ankle joint stiffness working to predict the loading pattern. PMID:9882761

Spatial distribution of intermingling pools of projection neurons with distinct targets: A 3D analysis of the commissural ganglia in Cancer borealis.

PubMed

Follmann, Rosangela; Goldsmith, Christopher John; Stein, Wolfgang

2017-06-01

Projection neurons play a key role in carrying long-distance information between spatially distant areas of the nervous system and in controlling motor circuits. Little is known about how projection neurons with distinct anatomical targets are organized, and few studies have addressed their spatial organization at the level of individual cells. In the paired commissural ganglia (CoGs) of the stomatogastric nervous system of the crab Cancer borealis, projection neurons convey sensory, motor, and modulatory information to several distinct anatomical regions. While the functions of descending projection neurons (dPNs) which control downstream motor circuits in the stomatogastric ganglion are well characterized, their anatomical distribution as well as that of neurons projecting to the labrum, brain, and thoracic ganglion have received less attention. Using cell membrane staining, we investigated the spatial distribution of CoG projection neurons in relation to all CoG neurons. Retrograde tracing revealed that somata associated with different axonal projection pathways were not completely spatially segregated, but had distinct preferences within the ganglion. Identified dPNs had diameters larger than 70% of CoG somata and were restricted to the most medial and anterior 25% of the ganglion. They were contained within a cluster of motor neurons projecting through the same nerve to innervate the labrum, indicating that soma position was independent of function and target area. Rather, our findings suggest that CoG neurons projecting to a variety of locations follow a generalized rule: for all nerve pathway origins, the soma cluster centroids in closest proximity are those whose axons project down that pathway. © 2017 Wiley Periodicals, Inc.

Hybrid excited claw pole generator with skewed and non-skewed permanent magnets

NASA Astrophysics Data System (ADS)

Wardach, Marcin

2017-12-01

This article contains simulation results of the Hybrid Excited Claw Pole Generator with skewed and non-skewed permanent magnets on rotor. The experimental machine has claw poles on two rotor sections, between which an excitation control coil is located. The novelty of this machine is existence of non-skewed permanent magnets on claws of one part of the rotor and skewed permanent magnets on the second one. The paper presents the construction of the machine and analysis of the influence of the PM skewing on the cogging torque and back-emf. Simulation studies enabled the determination of the cogging torque and the back-emf rms for both: the strengthening and the weakening of magnetic field. The influence of the magnets skewing on the cogging torque and the back-emf rms have also been analyzed.

Mapping genomic features to functional traits through microbial whole genome sequences.

PubMed

Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

2014-01-01

Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.

The College Opportunity Grant Program of the California State Scholarship and Loan Commission; A Report on and Evaluation of the 1969 and 1970 COG Selection Procedures.

ERIC Educational Resources Information Center

Klingelhofer, Edwin L.

The College Opportunity Grant (COG) program was established by the California legislature in 1968 and was intended to provide monetary grants to financially needy students, primarily from ethnic minorities, to assist them while attending college. This paper contains: (1) a side-by-side description of the characteristics of the 1969 and 1970…

Public health implications from COGS and potential for risk stratification and screening.

PubMed

Burton, Hilary; Chowdhury, Susmita; Dent, Tom; Hall, Alison; Pashayan, Nora; Pharoah, Paul

2013-04-01

The PHG Foundation led a multidisciplinary program, which used results from COGS research identifying genetic variants associated with breast, ovarian and prostate cancers to model risk-stratified prevention for breast and prostate cancers. Implementing such strategies would require attention to the use and storage of genetic information, the development of risk assessment tools, new protocols for consent and programs of professional education and public engagement.

Support for the Annual Meeting (30th) of the Cognitive Science Society

DTIC Science & Technology

2008-10-01

Schunn Sponsors Co-Chairs: Jennifer Wiley and Christopher Sanchez Member Abstracts Chair: Hedderik Van Rijn Awards Chair: Niels Taatgen...The winner of the 2008 Marr Prize for Best Student Paper is: Michael Frank, Evelina Fedorenko, Edward Gibson (seepage 19 of the program) Language...Stellan Ohlsson, Ute Schmid, Alex Petrov, Hedderik van Rijn, Niels Taatgen. CogSci 2008 Final Program CogSci 2008 Sponsors, Exhibitors, & Advertisers

Development of a rapid screening instrument for mild cognitive impairment and undiagnosed dementia.

PubMed

Steenland, N Kyle; Auman, Courtney M; Patel, Purvi M; Bartell, Scott M; Goldstein, Felicia C; Levey, Allan I; Lah, James J

2008-11-01

Mild cognitive impairment (MCI) often presages development of Alzheimer's disease (AD). We recently completed a cross-sectional study to test the hypothesis that a combination of a brief cognitive screening instrument (Mini-Cog) with a functional scale (Functional Activities Questionnaire; FAQ) would accurately identify individuals with MCI and undiagnosed dementia. The Mini-Cog consists of a clock drawing task and 3-item recall, and takes less than 5 minutes to administer. The FAQ is a 30-item questionnaire completed by an informant. In addition to the Mini-Cog and FAQ, a traditional cognitive test battery was administered, and two neurologists and a neuropsychologist determined a consensus diagnosis of Normal, MCI, or Dementia. A classification tree algorithm was used to pick optimal cutpoints, and, using these cutpoints, the combined Mini-Cog and FAQ (MC-FAQ) predicted the consensus diagnosis with an accuracy of 83% and a weighted kappa of 0.81. When the population was divided into Normal and Abnormal, the sensitivity, specificity and positive predictive value were 89%, 90%, and 95%, respectively. The MC-FAQ discriminates individuals with MCI from cognitively normal individuals and those with dementia, and its ease of administration makes it an attractive screening instrument to aid detection of cognitive impairment in the elderly.

Efficacy of a Multimodal Cognitive Rehabilitation Including Psychomotor and Endurance Training in Parkinson's Disease

PubMed Central

Reuter, I.; Mehnert, S.; Sammer, G.; Oechsner, M.; Engelhardt, M.

2012-01-01

Mild cognitive impairment, especially executive dysfunction might occur early in the course of Parkinson's disease. Cognitive training is thought to improve cognitive performance. However, transfer of improvements achieved in paper and pencil tests into daily life has been difficult. The aim of the current study was to investigate whether a multimodal cognitive rehabilitation programme including physical exercises might be more successful than cognitive training programmes without motor training. 240 PD-patients were included in the study and randomly allocated to three treatment arms, group A cognitive training, group B cognitive training and transfer training and group C cognitive training, transfer training and psychomotor and endurance training. The primary outcome measure was the ADAS-Cog. The secondary outcome measure was the SCOPA-Cog. Training was conducted for 4 weeks on a rehabilitation unit, followed by 6 months training at home. Caregivers received an education programme. The combination of cognitive training using paper and pencil and the computer, transfer training and physical training seems to have the greatest effect on cognitive function. Thus, patients of group C showed the greatest improvement on the ADAS-Cog and SCOPA-COG and were more likely to continue with the training programme after the study. PMID:23008772

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.

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.

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.

The Umbra Simulation and Integration Framework Applied to Emergency Response Training

NASA Technical Reports Server (NTRS)

Hamilton, Paul Lawrence; Britain, Robert

2010-01-01

The Mine Emergency Response Interactive Training Simulation (MERITS) is intended to prepare personnel to manage an emergency in an underground coal mine. The creation of an effective training environment required realistic emergent behavior in response to simulation events and trainee interventions, exploratory modification of miner behavior rules, realistic physics, and incorporation of legacy code. It also required the ability to add rich media to the simulation without conflicting with normal desktop security settings. Our Umbra Simulation and Integration Framework facilitated agent-based modeling of miners and rescuers and made it possible to work with subject matter experts to quickly adjust behavior through script editing, rather than through lengthy programming and recompilation. Integration of Umbra code with the WebKit browser engine allowed the use of JavaScript-enabled local web pages for media support. This project greatly extended the capabilities of Umbra in support of training simulations and has implications for simulations that combine human behavior, physics, and rich media.

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.

A Phenomenological Study of the Preparation and Career Paths of Academic Deans in Church of God Institutions of Theological Education in Latin America and the Caribbean

ERIC Educational Resources Information Center

Contreras Flores, Jenniffer

2016-01-01

This study explored the preparation and career paths of academic deans in Church of God (COG) theological institutions located in Latin American and Caribbean. This study used a qualitative research approach and the in-depth interview method for data collection. A group of 14 academic deans that serve in COG theological schools and that…

Sociable Machines: Expressive Social Exchange between Humans and Robots

DTIC Science & Technology

2000-05-01

many occasions about theories on emotion. I’ve cornered Robert Irie’s again and again about auditory processing. I’ve bugged Matto Marjanovic throughout...development at the MIT Artificial Intel- ligence Lab (Brooks, Breazeal, Marjanovic , Scassellati & Williamson 1999). Cog is a general purpose humanoid...RA-2, 253-262. Brooks, R. A., Breazeal, C., Marjanovic , M., Scassellati, B. & Williamson, M. M. (1999), The Cog Project: Building a Humanoid Robot, in

Candidate old-growth on national forest system administered lands in California since the initiation of national forest management

Treesearch

William F. Laudenslayer

1985-01-01

The following is a report on the status of Candidate Old-growth (hereafter identified as COG) on National Forest System administered lands in California in the past, a t present, and in the immediate fhture. These r e s u l t s are based on information that may be speculative and contain inconsistencies, and therefore must be treated with caution. COG on these lands...

A model predictive current control of flux-switching permanent magnet machines for torque ripple minimization

NASA Astrophysics Data System (ADS)

Huang, Wentao; Hua, Wei; Yu, Feng

2017-05-01

Due to high airgap flux density generated by magnets and the special double salient structure, the cogging torque of the flux-switching permanent magnet (FSPM) machine is considerable, which limits the further applications. Based on the model predictive current control (MPCC) and the compensation control theory, a compensating-current MPCC (CC-MPCC) scheme is proposed and implemented to counteract the dominated components in cogging torque of an existing three-phase 12/10 FSPM prototyped machine, and thus to alleviate the influence of the cogging torque and improve the smoothness of electromagnetic torque as well as speed, where a comprehensive cost function is designed to evaluate the switching states. The simulated results indicate that the proposed CC-MPCC scheme can suppress the torque ripple significantly and offer satisfactory dynamic performances by comparisons with the conventional MPCC strategy. Finally, experimental results validate both the theoretical and simulated predictions.

Improvement of unbalanced illumination induced telecentricity within the exposure slit

NASA Astrophysics Data System (ADS)

Jang, Jonghoon; Lee, ByeongSoo; Kang, Young Seog; Chang, Chansam; Kong, Jeong-Heung; Kim, Young Ha; Bouman, Wim; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; de Boeij, Wim P.; van Bussel, Bart; Neefs, Patrick; Rijke, Arij

2016-03-01

Adjustment and control of the illumination pupil asymmetry is relevant for wafer alignment and overlay of lithography tools. Pupil asymmetries can cause a tilt in aerial image (Aerial Image Tilt, or AIT). This AIT, combined with a focus offset, leads to a horizontal image shift. Pupil asymmetries can be related to a shift of the entire illumination pupil (geometrical telecentricity) caused by illuminator misalign. Another type of pupil asymmetry is energetic imbalance (quantified by pupil Center of Gravity, COG). The scanner can show pupil variation across the exposure slit. In general the COG at the edge of the slit is often worse than in the center part of the slit. Recently, ASML has released the NXT:1980Di that is equipped with an enhanced illuminator to improve pupil COG variation across the slit. In this paper we explore the performance of this scanner system and show that the AIT variation across the slit is also reduced significantly.

Constraints on Generality (COG): A Proposed Addition to All Empirical Papers.

PubMed

Simons, Daniel J; Shoda, Yuichi; Lindsay, D Stephen

2017-11-01

Psychological scientists draw inferences about populations based on samples-of people, situations, and stimuli-from those populations. Yet, few papers identify their target populations, and even fewer justify how or why the tested samples are representative of broader populations. A cumulative science depends on accurately characterizing the generality of findings, but current publishing standards do not require authors to constrain their inferences, leaving readers to assume the broadest possible generalizations. We propose that the discussion section of all primary research articles specify Constraints on Generality (i.e., a "COG" statement) that identify and justify target populations for the reported findings. Explicitly defining the target populations will help other researchers to sample from the same populations when conducting a direct replication, and it could encourage follow-up studies that test the boundary conditions of the original finding. Universal adoption of COG statements would change publishing incentives to favor a more cumulative science.

Impact of the Cognitive-Functional (Cog-Fun) Intervention on Executive Functions and Participation Among Children With Attention Deficit Hyperactivity Disorder: A Randomized Controlled Trial.

PubMed

Hahn-Markowitz, Jeri; Berger, Itai; Manor, Iris; Maeir, Adina

We examined the effect of the Cognitive-Functional (Cog-Fun) occupational therapy intervention on executive functions and participation among children with attention deficit hyperactivity disorder (ADHD). We used a randomized, controlled study with a crossover design. One hundred and seven children age 7-10 yr diagnosed with ADHD were allocated to treatment or wait-list control group. The control group received treatment after a 3-mo wait. Outcome measures included the Behavior Rating Inventory of Executive Function (BRIEF) and the Canadian Occupational Performance Measure (COPM). Significant improvements were found on both the BRIEF and COPM after intervention with large treatment effects. Before crossover, significant Time × Group interactions were found on the BRIEF. This study supports the effectiveness of the Cog-Fun intervention in improving executive functions and participation among children with ADHD. Copyright © 2017 by the American Occupational Therapy Association, Inc.

Oxygen Generation from Carbon Dioxide for Advanced Life Support

NASA Technical Reports Server (NTRS)

Bishop, Sean; Duncan, Keith; Hagelin-Weaver, Helena; Neal, Luke; Sanchez, Jose; Paul, Heather L.; Wachsman, Eric

2007-01-01

The partial electrochemical reduction of carbon dioxide (CO2) using ceramic oxygen generators (COGs) is well known and widely studied. However, complete reduction of metabolically produced CO2 (into carbon and oxygen) has the potential of reducing oxygen storage weight for life support if the oxygen can be recovered. Recently, the University of Florida devel- oped novel ceramic oxygen generators employing a bilayer elec- trolyte of gadolinia-doped ceria and erbia-stabilized bismuth ox- ide (ESB) for NASA's future exploration of Mars. The results showed that oxygen could be reliably produced from CO2 at temperatures as low as 400 C. The strategy discussed here for advanced life support systems employs a catalytic layer com- bined with a COG cell so that CO2 is reduced all the way to solid carbon and oxygen without carbon buildup on the COG cell and subsequent deactivation.

JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Influence of neurophysiological hippotherapy on the transference of the centre of gravity among children with cerebral palsy.

PubMed

Maćków, Anna; Małachowska-Sobieska, Monika; Demczuk-Włodarczyk, Ewa; Sidorowska, Marta; Szklarska, Alicja; Lipowicz, Anna

2014-01-01

The aim of the study was to present the influence of neurophysiological hippotherapy on the transference of the centre of gravity (COG) among children with cerebral palsy (CP). The study involved 19 children aged 4-13 years suffering from CP who demonstrated an asymmetric (A/P) model of compensation. Body balance was studied with the Cosmogamma Balance Platform. An examination on this platform was performed before and after a session of neurophysiological hippotherapy. In order to compare the correlations and differences between the examinations, the results were analysed using Student's T-test for dependent samples at p ≤ 0.05 as the level of statistical significance and descriptive statistics were calculated. The mean value of the body's centre of gravity in the frontal plane (COG X) was 18.33 (mm) during the first examination, changing by 21.84 (mm) after neurophysiological hippotherapy towards deloading of the antigravity lower limb (p ≤ 0.0001). The other stabilographic parameters increased; however, only the change in average speed of antero - posterior COG oscillation was statistically significant (p = 0.0354). 1. One session of neurophysiological hippotherapy induced statistically significant changes in the position of the centre of gravity in the body in the frontal plane and the average speed of COG oscillation in the sagittal plane among CP children demonstrating an asymmetric model of compensation (A/P).

Adaptive, dose-finding phase 2 trial evaluating the safety and efficacy of ABT-089 in mild to moderate Alzheimer disease.

PubMed

Lenz, Robert A; Pritchett, Yili L; Berry, Scott M; Llano, Daniel A; Han, Shu; Berry, Donald A; Sadowsky, Carl H; Abi-Saab, Walid M; Saltarelli, Mario D

2015-01-01

ABT-089, an α4β2 neuronal nicotinic receptor partial agonist, was evaluated for efficacy and safety in mild to moderate Alzheimer disease patients receiving stable doses of acetylcholinesterase inhibitors. This phase 2 double-blind, placebo-controlled, proof-of-concept, and dose-finding study adaptively randomized patients to receive ABT-089 (5, 10, 15, 20, 30, or 35 mg once daily) or placebo for 12 weeks. The primary efficacy endpoint was the Alzheimer's Disease Assessment Scale, cognition subscale (ADAS-Cog) total score. A Bayesian response-adaptive randomization algorithm dynamically assigned allocation probabilities based on interim ADAS-Cog total scores. A normal dynamic linear model for dose-response relationships and a longitudinal model for predicting final ADAS-cog score were employed in the algorithm. Stopping criteria for futility or success were defined. The futility stopping criterion was met, terminating the study with 337 patients randomized. No dose-response relationship was observed and no dose demonstrated statistically significant improvement over placebo on ADAS-Cog or any secondary endpoint. ABT-089 was well tolerated at all dose levels. When administered as adjunctive therapy to acetylcholinesterase inhibitors, ABT-089 was not efficacious in mild to moderate Alzheimer disease. The adaptive study design enabled the examination of a broad dose range, enabled rapid determination of futility, and reduced patient exposure to nonefficacious doses of the investigational compound.

Airlift Operation Modeling Using Discrete Event Simulation (DES)

DTIC Science & Technology

2009-12-01

Java ......................................................................................................20 2. Simkit...JRE Java Runtime Environment JVM Java Virtual Machine lbs Pounds LAM Load Allocation Mode LRM Landing Spot Reassignment Mode LEGO Listener Event...SOFTWARE DEVELOPMENT ENVIRONMENT The following are the software tools and development environment used for constructing the models. 1. Java Java

Non-amidated and amidated members of the C-type allatostatin (AST-C) family are differentially distributed in the stomatogastric nervous system of the American lobster, Homarus americanus.

PubMed

Christie, Andrew E; Miller, Alexandra; Fernandez, Rebecca; Dickinson, Evyn S; Jordan, Audrey; Kohn, Jessica; Youn, Mina C; Dickinson, Patsy S

2018-01-13

The crustacean stomatogastric nervous system (STNS) is a well-known model for investigating neuropeptidergic control of rhythmic behavior. Among the peptides known to modulate the STNS are the C-type allatostatins (AST-Cs). In the lobster, Homarus americanus, three AST-Cs are known. Two of these, pQIRYHQCYFNPISCF (AST-C I) and GNGDGRLYWRCYFNAVSCF (AST-C III), have non-amidated C-termini, while the third, SYWKQCAFNAVSCFamide (AST-C II), is C-terminally amidated. Here, antibodies were generated against one of the non-amidated peptides (AST-C I) and against the amidated isoform (AST-C II). Specificity tests show that the AST-C I antibody cross-reacts with both AST-C I and AST-C III, but not AST-C II; the AST-C II antibody does not cross-react with either non-amidated peptide. Wholemount immunohistochemistry shows that both subclasses (non-amidated and amidated) of AST-C are distributed throughout the lobster STNS. Specifically, the antibody that cross-reacts with the two non-amidated peptides labels neuropil in the CoGs and the stomatogastric ganglion (STG), axons in the superior esophageal (son) and stomatogastric (stn) nerves, and ~ 14 somata in each commissural ganglion (CoG). The AST-C II-specific antibody labels neuropil in the CoGs, STG and at the junction of the sons and stn, axons in the sons and stn, ~ 42 somata in each CoG, and two somata in the STG. Double immunolabeling shows that, except for one soma in each CoG, the non-amidated and amidated peptides are present in distinct sets of neuronal profiles. The differential distributions of the two AST-C subclasses suggest that the two peptide groups are likely to serve different modulatory roles in the lobster STNS.

Localization of cortical primary motor area of the hand using navigated transcranial magnetic stimulation, BOLD and arterial spin labeling fMRI.

PubMed

Kallioniemi, Elisa; Pitkänen, Minna; Könönen, Mervi; Vanninen, Ritva; Julkunen, Petro

2016-11-01

Although the relationship between neuronavigated transcranial magnetic stimulation (nTMS) and functional magnetic resonance imaging (fMRI) has been widely studied in motor mapping, it is unknown how the motor response type or the choice of motor task affect this relationship. Centers of gravity (CoGs) and response maxima were measured with blood-oxygen-level dependent (BOLD) and arterial spin labeling (ASL) fMRI during motor tasks against nTMS CoGs and response maxima, which were mapped with motor evoked potentials (MEPs) and silent periods (SPs). No differences in motor representations (CoGs and response maxima) were observed in lateral-medial direction (p=0.265). fMRI methods localized the motor representation more posterior than nTMS (p<0.001). This was not affected by the BOLD fMRI motor task (p>0.999) nor nTMS response type (p>0.999). ASL fMRI maxima did not differ from the nTMS nor BOLD fMRI CoGs (p≥0.070), but the ASL CoG was deeper in comparison to other methods (p≤0.042). The BOLD fMRI motor task did not influence the depth of the motor representation (p≥0.745). The median Euclidean distances between the nTMS and fMRI motor representations varied between 7.7mm and 14.5mm and did not differ between the methods (F≤1.23, p≥0.318). The relationship between fMRI and nTMS mapped excitatory (MEP) and inhibitory (SP) responses, and whether the choice of motor task affects this relationship, have not been studied before. The congruence between fMRI and nTMS is good. The choice of nTMS motor response type nor BOLD fMRI motor task had no effect on this relationship. Copyright © 2016 Elsevier B.V. All rights reserved.

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes.

PubMed

Lin, Chieh-Hua; Lian, Chun-Yi; Hsiung, Chao Agnes; Chen, Feng-Chi

2011-10-05

Changes in transcriptional orientation ("CTOs") occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation. Furthermore, CTOs may cause deleterious disruptions of operon structure and/or gene regulations. The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous (dS) and nonsynonymous (dN) substitution rate between the genes that have experienced changes in transcriptional orientation (changed-orientation genes, "COGs") and those that do not (same-orientation genes, "SOGs"). The dN/dS ratio was also derived to evaluate the selection pressure on the analyzed genes. Confounding factors in the estimation of evolutionary rates, such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. We demonstrate that COGs have significantly higher dN and dS than SOGs when a series of confounding factors are controlled. However, the dN/dS ratios are similar between the two gene groups, suggesting that the increase in dS can sufficiently explain the increase in dN in COGs. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven. Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the replication-transcription confrontation, which is suggested to be the major cause of inversion-associated evolutionary rate increases. The real cause of such evolutionary rate increases remains unclear but is worth further explorations.

Prostate cancer detection in patients with prior negative biopsy undergoing cognitive-, robotic- or in-bore MRI target biopsy.

PubMed

Kaufmann, Sascha; Russo, Giorgio I; Bamberg, Fabian; Löwe, Lorenz; Morgia, Giuseppe; Nikolaou, Konstantin; Stenzl, Arnulf; Kruck, Stephan; Bedke, Jens

2018-05-01

To evaluate the detection rate among three different targeted biopsy approaches of robot-assisted MRI/TRUS fusion (RA-TB), mpMRI in-bore (MRGB), cognitive fusion guidance biopsy (COG-TB) for the detection of prostate cancer (PC) and clinically significant PC (csPC). Between 2014 and 2016, 156 patients with a lesion on mpMRI, performed in accordance with ESUR guidelines, due to cancer suspicion or on-going cancer suspicion after prior negative prostate biopsy, underwent targeted biopsy with RA-TB, MRGB or COG-TB. All lesions were rated according to PI-RADS v2. We compared detection rates between techniques. Models were constructed to predict the detection of overall PC and csPC and using a 1000 boot-strap sample. In the all cohort, 73, 45 and 38 patients underwent RA-TB, MRGB or COG-TB, respectively. Overall PC was found in 39 (52.42%), 23 (51.11%) and 11 (28.95%) (p = 0.04) patients of RA-TB, MRGB and COG-TB arm, respectively. As concerning the detection of csPC, it was found in 26 (35.62%),18 (40.0%) and 9 (23.68%) patients of RA-TB, MRGB and COG-TB arm (p = 0.27). Model 1 showed that RA-TB [OR: 10.08 (95% CI 1.95-51.97); p < 0.01] and MRGB [OR: 12.88 (95% CI 2.36-70.25); p < 0.01] were associated with overall PC detection in TB, while only MRGB was associated with csPC at TB (model 2) [OR: 5.72; (95% CI 1.40-23.35); p < 0.01]. The c-index for model 1 and model 2 was 0.86 and 0.85, respectively. We did not report significant complications between groups. In-bore biopsy and MRI/TRUS fusion-guided biopsy showed greater accuracy in detecting PC compared to cognitive fusion as modeled in a newly established normogram.

Efficacy and Cost-effectiveness of the Children’s Oncology Group Long-Term Follow-Up Screening Guidelines for Childhood Cancer Survivors at Risk of Treatment-related Heart Failure

PubMed Central

Wong, F. Lennie; Bhatia, Smita; Landier, Wendy; Francisco, Liton; Leisenring, Wendy; Hudson, Melissa M.; Armstrong, Gregory T.; Mertens, Ann; Stovall, Marilyn; Robison, Leslie L.; Lyman, Gary H.; Lipshultz, Steven E.; Armenian, Saro H.

2014-01-01

Background Childhood cancer survivors treated with anthracyclines are at high risk for asymptomatic left ventricular dysfunction (ALVD), subsequent heart failure (HF), and death. The consensus-based Children’s Oncology Group (COG) Long-Term Follow-Up Guidelines recommend lifetime echocardiographic screening for ALVD. Objective To evaluate the efficacy and cost-effectiveness of the COG Guidelines and to identify more cost-effective screening strategies. Design Simulation of life-histories using Markov health states. Data Sources Childhood Cancer Survivor Study; published literature. Target Population Childhood cancer survivors. Time Horizon Lifetime. Perspective Societal. Intervention Echocardiographic screening, followed by angiotensin-converting enzyme (ACE) inhibitor and beta-blocker therapies after ALVD diagnosis. Measurements Quality-adjusted life years (QALYs), costs, incremental cost-effectiveness ratios (ICERs) in dollars per QALY, and the cumulative incidence of HF. Results of Base-Case Analysis The COG Guidelines versus no screening have an ICER of $61,500, extend life expectancy by 6 months and QALYs by 1.6 months, and reduce the cumulative incidence of HF by 18% at 30 years after cancer diagnosis. However, less-frequent screenings are more cost-effective than the Guidelines, and maintain 80% of the health benefits. Results of Sensitivity Analysis The ICER was most sensitive to the magnitude of ALVD treatment efficacy; higher treatment efficacy resulted in lower ICER. Limitation Lifetime non-HF mortality and the cumulative incidence of HF more than 20 years after diagnosis were extrapolated; the efficacy of ACE inhibitor and beta-blocker therapy in childhood cancer survivors with ALVD is undetermined (or unknown). Conclusion The COG Guidelines could reduce the risk of HF in survivors at less than $100,000/QALY. Less-frequent screening achieves most of the benefits and would be more cost-effective than the COG Guidelines. Primary Funding Source Lance Armstrong Foundation, National Cancer Institute. PMID:24842414

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

Friedman-Hill, Ernest

Java Expert Shell System - Jess - is a rule engine and scripting environment written entirely in Sun's Java language, Jess was orginially inspired by the CLIPS expert system shell, but has grown int a complete, distinct JAVA-influenced environment of its own. Using Jess, you can build Java applets and applications that have the capacity to "reason" using knowledge you supply in the form of declarative rules. Jess is surprisingly fast, and for some problems is faster than CLIPS, in that many Jess scripts are valid CLIPS scripts and vice-versa. Like CLIPS, Jess uses the Rete algorithm to process rules,more » a very efficient mechanism for solving the difficult many-to-many matching problem. Jess adds many features to CLIPS, including backwards chaining and the ability to manipulate and directly reason about Java objects. Jess is also a powerful Java scripting environment, from which you can create Java objects and call Java methods without compiling any Java Code.« less

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).

Embodiment and Manipulation Learning Process for a Humanoid Hand.

DTIC Science & Technology

1995-05-01

Figures 1-1 Human somatotopic mappings 16 1-2 Human anatomy terminology 18 2-1 A picture of Cog 24 2-2 A picture of Cog’s hand 27 3-1 A... human anatomy terminologies shown in Figure 1-2 [24]. The mechanical hand constructed for this thesis have three fingers, each having two segments...and two joints, and a thumb with one segment and a joint, so the terms 18 CHAPTER 1. INTRODUCTION Saddle-joint of the thumb Figure 1-2: Human

A Square Peg in a Round Hole: A Case Study of Center Gravity Application in Counter Insurgency Warfare

DTIC Science & Technology

2011-06-01

paradigm historically based on conventional warfare and state-based actors. Underlying questions related to the research question are: Is there a CoG...analysis is still useful by proposing 5 new interpretations of this aged concept. This thesis will examine whether CoG is still useful in...cuts through the confusion and contradictions related to CoG by translating it functionally for the war-fighter. He does this through a

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

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

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…

The molecular basis of memory. Part 2: chemistry of the tripartite mechanism.

PubMed

Marx, Gerard; Gilon, Chaim

2013-06-19

We propose a tripartite mechanism to describe the processing of cognitive information (cog-info), comprising the (1) neuron, (2) surrounding neural extracellular matrix (nECM), and (3) numerous "trace" metals distributed therein. The neuron is encased in a polyanionic nECM lattice doped with metals (>10), wherein it processes (computes) and stores cog-info. Each [nECM:metal] complex is the molecular correlate of a cognitive unit of information (cuinfo), similar to a computer "bit". These are induced/sensed by the neuron via surface iontophoretic and electroelastic (piezoelectric) sensors. The generic cuinfo are used by neurons to biochemically encode and store cog-info in a rapid, energy efficient, but computationally expansive manner. Here, we describe chemical reactions involved in various processes that underline the tripartite mechanism. In addition, we present novel iconographic representations of various types of cuinfo resulting from"tagging" and cross-linking reactions, essential for the indexing cuinfo for organized retrieval and storage of memory.

Effectiveness of Cognitive-Functional (Cog-Fun) occupational therapy intervention for young children with attention deficit hyperactivity disorder: a controlled study.

PubMed

Maeir, Adina; Fisher, Orit; Bar-Ilan, Ruthie Traub; Boas, Naomi; Berger, Itai; Landau, Yael E

2014-01-01

The purpose of this study was to examine the effectiveness of the Cognitive-Functional (Cog-Fun) intervention for young children with attention deficit hyperactivity disorder (ADHD). Nineteen children ages 5-7 yr diagnosed with ADHD were allocated to treatment and wait-list control groups. After the 12-wk intervention, the control group was crossed over to treatment. Follow-up was conducted 3 mo after treatment. Outcome measures included the Behavior Rating Inventory of Executive Function and the Canadian Occupational Performance Measure. Before crossover, significant differences were found between groups in change scores on the outcome measures. After crossover, no significant differences were found in treatment effects, and significant moderate to large treatment effects were found for both COPM and BRIEF scores. Treatment gains were maintained at follow-up. The study supports the effectiveness of the Cog-Fun intervention in improving occupational performance and executive functions in daily life for young children with ADHD. Copyright © 2014 by the American Occupational Therapy Association, Inc.

Novel gas sensor with dual response under CO(g) exposure: Optical and electrical stimuli

NASA Astrophysics Data System (ADS)

Rocha, L. S. R.; Cilense, M.; Ponce, M. A.; Aldao, C. M.; Oliveira, L. L.; Longo, E.; Simoes, A. Z.

2018-05-01

In this work, a lanthanum (La) doped ceria (CeO2) film, which depicted a dual gas sensing response (electric and optical) for CO(g) detection, was obtained by the microwave-assisted hydrothermal (HAM) synthesis and deposited by the screen-printing technique, in order to prevent deaths by intoxication with this life-threatening gas. An electric response under CO(g) exposure was obtained, along with an extremely fast optical response for a temperature of 380 °C, associated with Ce+4 reduction and vacancy generation. A direct optical gap was found to be around 2.31 eV from UV-Vis results, which corresponds to a transition from valence band to 4f states. Due to the anomalous electron configuration of cerium atoms with 4f electrons in its reduced state, they are likely to present an electric conduction based on the small polaron theory with a hopping mechanism responsible for its dual sensing response with a complete reversible behaviour.

Java, Indonesia

NASA Image and Video Library

1996-01-20

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

COGNAT: a web server for comparative analysis of genomic neighborhoods.

PubMed

Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

2017-11-22

In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

Transcriptional regulation of the human mitochondrial peptide deformylase (PDF).

PubMed

Pereira-Castro, Isabel; Costa, Luís Teixeira da; Amorim, António; Azevedo, Luisa

2012-05-18

The last years of research have been particularly dynamic in establishing the importance of peptide deformylase (PDF), a protein of the N-terminal methionine excision (NME) pathway that removes formyl-methionine from mitochondrial-encoded proteins. The genomic sequence of the human PDF gene is shared with the COG8 gene, which encodes a component of the oligomeric golgi complex, a very unusual case in Eukaryotic genomes. Since PDF is crucial in maintaining mitochondrial function and given the atypical short distance between the end of COG8 coding sequence and the PDF initiation codon, we investigated whether the regulation of the human PDF is affected by the COG8 overlapping partner. Our data reveals that PDF has several transcription start sites, the most important of which only 18 bp from the initiation codon. Furthermore, luciferase-activation assays using differently-sized fragments defined a 97 bp minimal promoter region for human PDF, which is capable of very strong transcriptional activity. This fragment contains a potential Sp1 binding site highly conserved in mammalian species. We show that this binding site, whose mutation significantly reduces transcription activation, is a target for the Sp1 transcription factor, and possibly of other members of the Sp family. Importantly, the entire minimal promoter region is located after the end of COG8's coding region, strongly suggesting that the human PDF preserves an independent regulation from its overlapping partner. Copyright © 2012 Elsevier Inc. All rights reserved.

Genetic Variation in the Vesicular Monoamine Transporter: Preliminary associations with Cognitive Outcomes after Severe Traumatic Brain Injury

PubMed Central

Markos, Steven; Failla, Michelle D.; Ritter, Anne C; Dixon, C. Edward; Conley, Yvette P.; Ricker, Joseph H; Arenth, Patricia M.; Juengst, Shannon B.; Wagner, Amy K.

2015-01-01

Introduction Traumatic brain injury (TBI) frequently results in impaired cognition, a function that can be modulated by monoaminergic signaling. Genetic variation among monoaminergic genes may affect post-TBI cognitive performance. The vesicular monoamine transporter 2 (VMAT2) gene may be a novel source of genetic variation important for cognitive outcomes post-TBI given VMAT2’s role in monoaminergic neurotransmission. Objective Evaluate associations between VMAT2 variability and cognitive outcomes post-TBI. Methods We evaluated 136 white adults with severe TBI for variation in VMAT2 using a tagging single nucleotide polymorphism (tSNP) approach (rs363223, rs363226, rs363251, and rs363341). We show genetic variation interacts with assessed cognitive impairment [cognitive composite T-scores (Comp-Cog)] to influence functional cognition [Functional Independence Measure Cognitive subscale (FIM-Cog)] 6 and 12 months post-injury. Results Multivariate analyses at 6-months post-injury showed rs363226 genotype was associated with Comp-Cog (p=0.040) and interacted with Comp-Cog to influence functional cognition (p<0.001). G-homozygotes had the largest cognitive impairment, and their cognitive impairment had the greatest adverse effect on functional cognition. Discussion We provide the first evidence that genetic variation within VMAT2 is associated with cognitive outcomes following TBI. Further work is needed to validate this finding and elucidate mechanisms by which genetic variation affects monoaminergic signaling, mediating differences in cognitive outcomes. PMID:26828714

Evaluation of influence of stretching therapy and ergonomic factors on postural control in patients with chronic non-specific low back pain.

PubMed

Gawda, Piotr; Dmoszyńska-Graniczka, Magdalena; Pawlak, Halina; Cybulski, Marek; Kiełbus, Michał; Majcher, Piotr; Buczaj, Agnieszka; Buczaj, Marcin

2015-01-01

The vertical orientation of the body in the upright standing position is maintained by keeping the body's centre of gravity (COG) upright, above the base of support, by a dynamic interplay of visual, vestibular, and somatosensory control systems. The objectives of this study were: to compare the postural control strategy between people with and without low back pain (LBP), to estimate the influence of the stretching therapy on the postural control strategy, and to discover the relationship between the restriction of spine mobility and occurrence of some ergonomic factors. The study consisted of 32 patients with LBP and 25 healthy controls. Postural characteristics of the subjects were measured with the use of a computerized force platform. The software programme filters and measures COG sway velocity in different conditions. Additional measurements and tests were conducted in patients after stretching therapy. Based on survey research, all individuals were selected and evaluated from the aspect of ergonomics. The results of the COG sway velocity vary under the testing conditions. From the aspect of ergonomic attitude and influence of the rehabilitation, results varied in the groups. Ergonomic factors are often accompanied by the appearance of LBP. The restrictions within the musculoskeletal system cause disorders in muscle synergies, which is expressed by an increase in the angular velocity of the COG. In patients with chronic back pain syndrome, selected stretching therapy techniques improves the range of motion of the spine and reduces pain.

Influence of fear of falling on anticipatory postural control of medio-lateral stability during rapid leg flexion.

PubMed

Yiou, E; Deroche, T; Do, M C; Woodman, T

2011-04-01

During leg flexion from erect posture, postural stability is organized in advance during "anticipatory postural adjustments" (APA). During these APA, inertial forces are generated that propel the centre of gravity (CoG) laterally towards stance leg side. This study examined how fear of falling (FoF) may influence this anticipatory postural control of medio-lateral (ML) stability. Ten young healthy participants performed a series of leg flexions at maximal velocity from low and high surface heights (6 and 66 cm above ground, respectively). In this latter condition with increased FoF, stance foot was placed at the lateral edge of the support surface to induce maximal postural threat. Results showed that the amplitude of ML inertial forces generated during APA decreased with FoF; this decrease was compensated by an increase in APA duration so that the CoG position at time of swing foot-off was located further towards stance leg side. With these changes in ML APA, the CoG was propelled in the same final (unipodal) position above stance foot as in condition with low FoF. These results contrast with those obtained in the literature during quiet standing which showed that FoF did not have any influence on the ML component of postural control. It is proposed that ML APA are modified with increased FoF, in such a way that the risk of a sideway fall induced by the large CoG motion is attenuated.

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.…

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.

Data Processing for a High Resolution Preclinical PET Detector Based on Philips DPC Digital SiPMs

NASA Astrophysics Data System (ADS)

Schug, David; Wehner, Jakob; Goldschmidt, Benjamin; Lerche, Christoph; Dueppenbecker, Peter Michael; Hallen, Patrick; Weissler, Bjoern; Gebhardt, Pierre; Kiessling, Fabian; Schulz, Volkmar

2015-06-01

In positron emission tomography (PET) systems, light sharing techniques are commonly used to readout scintillator arrays consisting of scintillation elements, which are smaller than the optical sensors. The scintillating element is then identified evaluating the signal heights in the readout channels using statistical algorithms, the center of gravity (COG) algorithm being the simplest and mostly used one. We propose a COG algorithm with a fixed number of input channels in order to guarantee a stable calculation of the position. The algorithm is implemented and tested with the raw detector data obtained with the Hyperion-II D preclinical PET insert which uses Philips Digital Photon Counting's (PDPC) digitial SiPMs. The gamma detectors use LYSO scintillator arrays with 30 ×30 crystals of 1 ×1 ×12 mm3 in size coupled to 4 ×4 PDPC DPC 3200-22 sensors (DPC) via a 2-mm-thick light guide. These self-triggering sensors are made up of 2 ×2 pixels resulting in a total of 64 readout channels. We restrict the COG calculation to a main pixel, which captures most of the scintillation light from a crystal, and its (direct and diagonal) neighboring pixels and reject single events in which this data is not fully available. This results in stable COG positions for a crystal element and enables high spatial image resolution. Due to the sensor layout, for some crystals it is very likely that a single diagonal neighbor pixel is missing as a result of the low light level on the corresponding DPC. This leads to a loss of sensitivity, if these events are rejected. An enhancement of the COG algorithm is proposed which handles the potentially missing pixel separately both for the crystal identification and the energy calculation. Using this advancement, we show that the sensitivity of the Hyperion-II D insert using the described scintillator configuration can be improved by 20-100% for practical useful readout thresholds of a single DPC pixel ranging from 17-52 photons. Furthermore, we show that the energy resolution of the scanner is superior for all readout thresholds if singles with a single missing pixel are accepted and correctly handled compared to the COG method only accepting singles with all neighbors present by 0-1.6% (relative difference). The presented methods can not only be applied to gamma detectors employing DPC sensors, but can be generalized to other similarly structured and self-triggering detectors, using light sharing techniques, as well.

Maximum likelihood positioning algorithm for high-resolution PET scanners

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

Gross-Weege, Nicolas, E-mail: nicolas.gross-weege@pmi.rwth-aachen.de, E-mail: schulz@pmi.rwth-aachen.de; Schug, David; Hallen, Patrick

2016-06-15

Purpose: In high-resolution positron emission tomography (PET), lightsharing elements are incorporated into typical detector stacks to read out scintillator arrays in which one scintillator element (crystal) is smaller than the size of the readout channel. In order to identify the hit crystal by means of the measured light distribution, a positioning algorithm is required. One commonly applied positioning algorithm uses the center of gravity (COG) of the measured light distribution. The COG algorithm is limited in spatial resolution by noise and intercrystal Compton scatter. The purpose of this work is to develop a positioning algorithm which overcomes this limitation. Methods:more » The authors present a maximum likelihood (ML) algorithm which compares a set of expected light distributions given by probability density functions (PDFs) with the measured light distribution. Instead of modeling the PDFs by using an analytical model, the PDFs of the proposed ML algorithm are generated assuming a single-gamma-interaction model from measured data. The algorithm was evaluated with a hot-rod phantom measurement acquired with the preclinical HYPERION II {sup D} PET scanner. In order to assess the performance with respect to sensitivity, energy resolution, and image quality, the ML algorithm was compared to a COG algorithm which calculates the COG from a restricted set of channels. The authors studied the energy resolution of the ML and the COG algorithm regarding incomplete light distributions (missing channel information caused by detector dead time). Furthermore, the authors investigated the effects of using a filter based on the likelihood values on sensitivity, energy resolution, and image quality. Results: A sensitivity gain of up to 19% was demonstrated in comparison to the COG algorithm for the selected operation parameters. Energy resolution and image quality were on a similar level for both algorithms. Additionally, the authors demonstrated that the performance of the ML algorithm is less prone to missing channel information. A likelihood filter visually improved the image quality, i.e., the peak-to-valley increased up to a factor of 3 for 2-mm-diameter phantom rods by rejecting 87% of the coincidences. A relative improvement of the energy resolution of up to 12.8% was also measured rejecting 91% of the coincidences. Conclusions: The developed ML algorithm increases the sensitivity by correctly handling missing channel information without influencing energy resolution or image quality. Furthermore, the authors showed that energy resolution and image quality can be improved substantially by rejecting events that do not comply well with the single-gamma-interaction model, such as Compton-scattered events.« less

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.

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

Bonachea, D.; Dickens, P.; Thakur, R.

There is a growing interest in using Java as the language for developing high-performance computing applications. To be successful in the high-performance computing domain, however, Java must not only be able to provide high computational performance, but also high-performance I/O. In this paper, we first examine several approaches that attempt to provide high-performance I/O in Java - many of which are not obvious at first glance - and evaluate their performance on two parallel machines, the IBM SP and the SGI Origin2000. We then propose extensions to the Java I/O library that address the deficiencies in the Java I/O APImore » and improve performance dramatically. The extensions add bulk (array) I/O operations to Java, thereby removing much of the overhead currently associated with array I/O in Java. We have implemented the extensions in two ways: in a standard JVM using the Java Native Interface (JNI) and in a high-performance parallel dialect of Java called Titanium. We describe the two implementations and present performance results that demonstrate the benefits of the proposed extensions.« less

Near Net-Shape, Ultra High Melting, Erosion Resistant Carbide/Metal Composites with Tailored Fibrillar Microstructures via the Displacive Compensation of Porosity Process

DTIC Science & Technology

2006-11-26

vapor species, formed over tungsten trioxide powder, is 1.25xl0Ŗ atm at 1400°C and 1 atm total pressure (assuming an oxygen partial pressure greater...with CO(g). ■19- These hollow tungsten fibers were then carburized via reaction with CO(g) to generate the polycrystalline WC-based fibers shown in...of tungsten carbide via reaction with a hafnium-copper melt," Ada Mater., 57(13), 3924-3931 (2009).) The kinetic mechanism of incongruent reduction

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

Telescope Automation and Remote Observing System (TAROS)

NASA Astrophysics Data System (ADS)

Wilson, G.; Czezowski, A.; Hovey, G. R.; Jarnyk, M. A.; Nielsen, J.; Roberts, B.; Sebo, K.; Smith, D.; Vaccarella, A.; Young, P.

2005-12-01

TAROS is a system that will allow for the Australian National University telescopes at a remote location to be operated automatically or interactively with authenticated control via the internet. TAROS is operated by a Java front-end GUI and employs the use of several Java technologies - such as Java Message Service (JMS) for communication between the telescope and the remote observer, Java Native Interface to integrate existing data acquisition software written in C++ (CICADA) with new Java programs and the JSky collection of Java GUI components for parts of the remote observer client. In this poster the design and implementation of TAROS is described.

Project LITE - Light Inquiry Through Experiments

NASA Astrophysics Data System (ADS)

Brecher, K.

2004-12-01

Hands-on, inquiry-based, constructivist activity offers students a powerful way to explore, uncover and ultimately gain a feel for the nature of science. In order to make practicable a more genuine approach to learning astronomy, we have undertaken the development of hands-on (and eyes-on) materials that can be used in introductory undergraduate astronomy courses. These materials focus on light and optics. Over the past several years as part of Project LITE (Light Inquiry Through Experiments), we have developed a kit of optical materials that is integrated with a set of Java applets. The combined kit and software allows students to do actual experiments concerning geometrical optics, fluorescence, phosphorescence, polarization and other topics by making use of the photons that are emitted by their computer screens. We have also developed a suite of over 100 Flash applets that allow students to directly explore many aspects of visual perception. A major effort of the project concerns spectroscopy, since it is arguably the most important tool used by astronomers to disentangle the nature of the universe. It is also one of the most challenging subjects to teach in undergraduate astronomy courses. The spectroscopy component of Project LITE includes take-home laboratory materials and experiments that are integrated with web-based software. We have also developed a novel quantitative handheld binocular spectrometer (patent pending). Our major spectroscopic software is called the Spectrum Explorer (SPEX). It allows students to create, manipulate and explore all types of spectra including blackbody, power law, emission and absorption. We are now extending the SPEX capabilities to help students gain easy access to the astronomical spectra included in the NVO databases. All of the Project LITE software can be found http://lite.bu.edu. Project LITE is supported by Grant #DUE-0125992 from the NSF Division of Undergraduate Education.

Education Office Application Design and Development

NASA Technical Reports Server (NTRS)

Johnson, Jamie E.

2013-01-01

The content of this project focuses on designing and implementing a new prototype website for the Kennedy Intern Tracking System (KITS). The goal of the new website is to allow the user to search for interns based on several different categories and fields. In hence, making it easier to find a count of interns matching a set of criteria. The KSC office of education is the primary users of KITS, their job is to recruit interns year-round. As a secondary goal, each user will be able to generate a report of their searches onto a portable document format (PDF) me. The results of each search will be set to a limited amount per page. This site will be used for Kennedy Space Center internal purposes only. After the implementations are done, a visual walk through using screen shots will be used to guide the users through all of the different scenarios that are likely to occur when the users are navigating through the site. In addition, a demo of the site will be presented to the KSC Office of Education. JavaScript and JQuery are the languages that will focus on the functionality of the implementation. Hyper Text Markup Language will be used to form the foundation for the body structure of the website. Ruby will be the programming language used to elevate the prototype to a dynamic website and enable the programmer to finish with in an efficient time frame. Cascading Style Sheet will be the language used for the design and styling purposes. Rails is the framework that the new website will be built upon. By default, the database will be managed by Sequel Lite (SQLite). All users will need to be granted special privileges in order to use the site.

Pre-Clinical and Clinical Evaluation of High Resolution, Mobile Gamma Camera and Positron Imaging Devices

DTIC Science & Technology

2007-11-01

accuracy. FPGA ADC data acquisition is controlled by distributed Java -based software. Java -based server application sits on each of the acquisition...JNI ( Java Native Interface) is used to allow Java indirect control of the USB driver. Fig. 5. Photograph of mobile electronics rack...supplies with the monitor and keyboard. The server application on each of these machines is controlled by a remote client Java -based application

Seeing the LITE

NASA Astrophysics Data System (ADS)

Brecher, K.

2000-12-01

We are developing a number of eyes-on experiments, lecture demonstrations and Web based JAVA applets about light, optics, color and visual perception as part of `Project LITE - Light Inquiry Through Experiments'. These are intended for incorporation into introductory level university science courses in astronomy, physics and other disciplines. In this presentation, several of the new LITE demonstrations applicable to large astronomy and physics classes will be shown. One demonstration involves novel materials to display Rayleigh scattering (blue skies, red sunsets and interstellar reddening - NOT redshift!) - including polarization effects. Others employ incandescent bulbs, LED's and laser pointers to illustrate fluorescence, diffraction and other physical and quantum optics phenomena. Still other demonstrations utilize transparent plastic moire overlays as well as computer animated moire patterns to show a variety of astronomical and physical phenomena. We will also display some of our applets posted at the Project LITE Web site (http://www.bu.edu/smec/lite) as well as the associated kit of optical materials we have developed for use by individual students in their own homes or dormitory rooms. This work was supported in part by NSF grant # DUE-9950551.

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.

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation.

PubMed

Reck, Michael; Tomasch, Jürgen; Deng, Zhiluo; Jarek, Michael; Husemann, Peter; Wagner-Döbler, Irene

2015-07-04

The complex microbiome of the gut has an enormous impact on human health. Analysis of the transcriptional activity of microorganisms through mRNA sequencing (metatranscriptomics) opens a completely new window into their activity in vivo, but it is highly challenging due to numerous technical and bioinformatical obstacles. Here we present an optimized pipeline for extraction of high quality mRNA from stool samples. Comparison of three commercially available RNA extraction kits with the method of Zoetendal revealed that the Powermicrobiome Kit (MoBio) performed best with respect to RNA yield and purity. Next, the influence of the stabilization reagent during sample storage for up to 15 days was studied. RIN analysis and qRT-PCR of spiked-in and indigenous genes revealed that RNA Later preserved mRNA integrity most efficiently, while samples conserved in RNA Protect showed substantial mRNA decay. Using the optimized pipeline developed here, recovery rates for spiked-in E.coli cells expressing fluorescing proteins were 8.7-9.7% for SuperfolderGFP and 14.7-17.8% for mCherry. The mRNA of stabilized stool samples as well as of snap-frozen controls was sequenced with Illumina Hiseq, yielding on average 74 million reads per sample. PCoA analysis, taxonomic classification using Kraken and functional classification using bwa showed that the transcriptomes of samples conserved in RNA Later were unchanged for up to 6 days even at room temperature, while RNA Protect was inefficient for storage durations exceeding 24 h. However, our data indicate that RNA Later introduces a bias which is then maintained throughout storage, while RNA Protect conserved samples are initially more similar to the snap frozen controls. RNA Later conserved samples had a reduced abundance of e.g. Prevotellaceae transcripts and were depleted for e.g. COG category "Carbohydrate transport and metabolism". Since the overall similarity between all stool transcriptional profiles studied here was >0.92, these differences are unlikely to affect global comparisons, but should be taken into account when rare but critically important members of the stool microbiome are being studied.

Efficacy of higher-dose 13.3 mg/24 h (15 cm2) rivastigmine patch on the Alzheimer's Disease Assessment Scale-cognitive subscale: domain and individual item analysis.

PubMed

Alva, Gustavo; Isaacson, Richard; Sadowsky, Carl; Grossberg, George; Meng, Xiangyi; Somogyi, Monique

2014-09-01

Rivastigmine displays dose-dependent efficacy on cognition in patients with Alzheimer's disease (AD), as measured by the Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog). Subanalysis of the OPTIMA (OPtimising Transdermal Exelon In Mild-to-moderate Alzheimer's disease) study aimed to define ADAS-cog domains by factor analysis of individual items. Efficacy of 13.3 mg/24 h versus 9.5 mg/24 h rivastigmine patch on individual items and newly derived domains was assessed. OPTIMA was a 48-week, double-blind (DB) study in patients with mild-to-moderate AD. Patients meeting pre-defined decline criteria during open-label treatment with 9.5 mg/24 h patch were randomized in the DB phase to 13.3 mg/24 h (n = 280) or 9.5 mg/24 h (n = 287) patch. ADAS-cog change from baseline was a co-primary outcome measure. Factor analysis categorized ADAS-cog items into newly derived domains. Change from DB-baseline was calculated for domains and individual items. Numerically, less decline was displayed with 13.3 mg/24 h versus 9.5 mg/24 h patch in the total ADAS-cog score at all time points (significant at Week 24, p = 0.027). Factor analysis identified two domains: memory and language. Significantly, less decline was observed on the memory domain with 13.3 mg/24 h versus 9.5 mg/24 h patch at Weeks 12, 24, and 48 (p < 0.05; observed cases). Three items (following commands, orientation, and word recognition) displayed numerically less decline with 13.3 mg/24 h versus 9.5 mg/24 h patch at all time points. No significant between-group differences were observed on the language domain. Results suggest that the greater cognitive efficacy of 13.3 mg/24 h versus 9.5 mg/24 h rivastigmine patch is driven primarily by effects on memory, particularly in the areas of following commands, orientation, and word recognition. Copyright © 2014 John Wiley & Sons, Ltd.

CogChamps - a model of implementing evidence-based care in hospitals: study protocol.

PubMed

Travers, Catherine; Graham, Frederick; Henderson, Amanda; Beattie, Elizabeth

2017-03-14

Delirium and dementia (cognitive impairment; CI), are common in older hospital patients, and both are associated with serious adverse outcomes. Despite delirium often being preventable, it is frequently not recognized in hospital settings, which may be because hospital nurses have not received adequate education or training in recognizing or caring for those with CI. However, the most effective way of increasing nurses' awareness about delirium and dementia, and initiating regular patient screening and monitoring to guide best practices for these patients in hospital settings is not known. Hence this current project, conducted in 2015-2017, aims to redress this situation by implementing a multi-component non-pharmacological evidence-based intervention for patients with CI, through educating and mentoring hospital nurses to change their practice. The development of the practice change component is informed by recent findings from implementation science that focuses on facilitation as the active ingredient in knowledge uptake and utilization. This component focuses on educating and empowering experienced nurses to become Cognition Champions (CogChamps) across six wards in a large Australian tertiary referral hospital. The CogChamps will, in turn, educate other nursing team members to more effectively care for patients with CI. The hospital leadership team are supportive of the project and are directly involved in selecting the CogChamps. CogChamps will be provided with comprehensive education in evidence-based delirium assessment, prevention and management, and practice change management skills. They will receive continuing support from research and education staff about raising awareness, upskilling other staff in delirium assessment and in the adoption of best practices for preventing and managing delirium. Both qualitative and quantitative data are being collected at multiple time-points to evaluate process, impact and outcome, and to provide clarity regarding the most effective aspects of the intervention. This paper describes the study protocol for the implementation of multi-component evidence-based non-pharmacological practices designed to improve the care of older hospital patients with CI. Findings will inform subsequent initiatives directed towards enhancing the capacity of the nursing workforce to implement best practices for providing high quality care for this growing patient population throughout their acute care hospital stay.

Xenopatients 2.0: reprogramming the epigenetic landscapes of patient-derived cancer genomes.

PubMed

Menendez, Javier A; Alarcón, Tomás; Corominas-Faja, Bruna; Cuyàs, Elisabet; López-Bonet, Eugeni; Martin, Angel G; Vellon, Luciano

2014-01-01

In the science-fiction thriller film Minority Report, a specialized police department called "PreCrime" apprehends criminals identified in advance based on foreknowledge provided by 3 genetically altered humans called "PreCogs". We propose that Yamanaka stem cell technology can be similarly used to (epi)genetically reprogram tumor cells obtained directly from cancer patients and create self-evolving personalized translational platforms to foresee the evolutionary trajectory of individual tumors. This strategy yields a large stem cell population and captures the cancer genome of an affected individual, i.e., the PreCog-induced pluripotent stem (iPS) cancer cells, which are immediately available for experimental manipulation, including pharmacological screening for personalized "stemotoxic" cancer drugs. The PreCog-iPS cancer cells will re-differentiate upon orthotopic injection into the corresponding target tissues of immunodeficient mice (i.e., the PreCrime-iPS mouse avatars), and this in vivo model will run through specific cancer stages to directly explore their biological properties for drug screening, diagnosis, and personalized treatment in individual patients. The PreCog/PreCrime-iPS approach can perform sets of comparisons to directly observe changes in the cancer-iPS cell line vs. a normal iPS cell line derived from the same human genetic background. Genome editing of PreCog-iPS cells could create translational platforms to directly investigate the link between genomic expression changes and cellular malignization that is largely free from genetic and epigenetic noise and provide proof-of-principle evidence for cutting-edge "chromosome therapies" aimed against cancer aneuploidy. We might infer the epigenetic marks that correct the tumorigenic nature of the reprogrammed cancer cell population and normalize the malignant phenotype in vivo. Genetically engineered models of conditionally reprogrammable mice to transiently express the Yamanaka stemness factors following the activation of phenotypic copies of specific cancer diseases might crucially evaluate a "reprogramming cure" for cancer. A new era of xenopatients 2.0 generated via nuclear reprogramming of the epigenetic landscapes of patient-derived cancer genomes might revolutionize the current personalized translational platforms in cancer research.

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…

Development and assessment of a composite score for memory in the Alzheimer's Disease Neuroimaging Initiative (ADNI).

PubMed

Crane, Paul K; Carle, Adam; Gibbons, Laura E; Insel, Philip; Mackin, R Scott; Gross, Alden; Jones, Richard N; Mukherjee, Shubhabrata; Curtis, S McKay; Harvey, Danielle; Weiner, Michael; Mungas, Dan

2012-12-01

We sought to develop and evaluate a composite memory score from the neuropsychological battery used in the Alzheimer's Disease (AD) Neuroimaging Initiative (ADNI). We used modern psychometric approaches to analyze longitudinal Rey Auditory Verbal Learning Test (RAVLT, 2 versions), AD Assessment Schedule - Cognition (ADAS-Cog, 3 versions), Mini-Mental State Examination (MMSE), and Logical Memory data to develop ADNI-Mem, a composite memory score. We compared RAVLT and ADAS-Cog versions, and compared ADNI-Mem to RAVLT recall sum scores, four ADAS-Cog-derived scores, the MMSE, and the Clinical Dementia Rating Sum of Boxes. We evaluated rates of decline in normal cognition, mild cognitive impairment (MCI), and AD, ability to predict conversion from MCI to AD, strength of association with selected imaging parameters, and ability to differentiate rates of decline between participants with and without AD cerebrospinal fluid (CSF) signatures. The second version of the RAVLT was harder than the first. The ADAS-Cog versions were of similar difficulty. ADNI-Mem was slightly better at detecting change than total RAVLT recall scores. It was as good as or better than all of the other scores at predicting conversion from MCI to AD. It was associated with all our selected imaging parameters for people with MCI and AD. Participants with MCI with an AD CSF signature had somewhat more rapid decline than did those without. This paper illustrates appropriate methods for addressing the different versions of word lists, and demonstrates the additional power to be gleaned with a psychometrically sound composite memory score.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

PubMed Central

2012-01-01

Background Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Results Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Conclusions Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world. PMID:22691113

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.

PubMed

Roy Chowdhury, Anindya; Dutta, Chitra

2012-06-12

Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

Conduction velocity of the uterine contraction in serial magnetomyogram (MMG) data: event based simulation and validation.

PubMed

Furdea, Adrian; Preissl, Hubert; Lowery, Curtis L; Eswaran, Hari; Govindan, Rathinaswamy B

2011-01-01

We propose a novel approach to calculate the conduction velocity (CV) of the uterine contraction bursts in magnetomyogram (MMG) signals measured using a multichannel SQUID array. For this purpose, we partition the sensor coordinates into four different quadrants and identify the contractile bursts using a previously proposed Hilbert-wavelet transform approach. If contractile burst is identified in more than one quadrant, we calculate the center of gravity (CoG) in each quadrant for each time point as the sum of the product of the sensor coordinates with the Hilbert amplitude of the MMG signals normalized by the sum of the Hilbert amplitude of the signals over all sensors. Following this we compute the delay between the CoGs of all (six) possible quadrant pairs combinations. As a first step, we validate this approach by simulating a stochastic model based on independent second-order autoregressive processes (AR2) and we divide them into 30 second disjoint windows and insert burst activity at specific time instances in preselected sensors. Also we introduce a lag of 5 ± 1 seconds between different quadrants. Using our approach we calculate the CoG of the signals in a quadrant. To this end, we compute the delay between CoGs obtained from different quadrants and show that our approach is able to reliably capture the delay incorporated in the model. We apply the proposed approach to 19 serial MMG data obtained from two subjects and show an increase in the CV as the subjects approached labor.

Effectiveness of computerized cognitive rehabilitation training on symptomatological, neuropsychological and work function in patients with schizophrenia.

PubMed

Lee, Woo Kyeong

2013-06-01

There has been plenty of interest in cognitive rehabilitation for schizophrenia here in Korea since the year 2000. But the efficacy studies of cognitive remediation intervention are still deficient. The primary purpose of this study was to develop a computer-assisted cognitive remediation program and conduct a clinical trial in a group of schizophrenic patients. Sixty patients with schizophrenia were randomly assigned to a computerized cognitive rehabilitation (Cog-trainer) group plus usual rehabilitation (UR) or to a usual rehabilitation (UR) group only. Clinical, neuropsychological and functional outcome variables were assessed at baseline and after intervention. The Cog-trainer group received 20 sessions of computerized cognitive remediation training over 3 months. This training program consists of 10 units, with each unit being divided into three stages: (i) practice; (ii) application; and (iii) advanced. Compared to the UR group, the Cog-trainer exhibited a significant improvement in attention, concentration and working memory. The Cog-trainer group also showed improvement in the work quality subscale of the work behavior inventory. However, there were no significant benefits of computerized cognitive remediation where symptoms were concerned. These results indicate that computerized cognitive rehabilitation training can contribute to an improvement in the cognitive function of people with schizophrenia. The changes in cognitive outcomes can also contribute to improvement in job functioning. Further study of generalization to other functional outcome measures will be necessary. Long-term follow-up studies are needed to confirm the maintenance of such improvements. Copyright © 2013 Wiley Publishing Asia Pty Ltd.

Endocrine-Disrupting Activities and Organic Contaminants Associated with Oil and Gas Operations in Wyoming Groundwater.

PubMed

Kassotis, Christopher D; Vu, Danh C; Vo, Phuc H; Lin, Chung-Ho; Cornelius-Green, Jennifer N; Patton, Sharyle; Nagel, Susan C

2018-04-05

Unconventional oil and natural gas (UOG) operations couple horizontal drilling with hydraulic fracturing to access previously inaccessible fossil fuel deposits. Hydraulic fracturing, a common form of stimulation, involves the high-pressure injection of water, chemicals, and sand to fracture the target layer and release trapped natural gas and/or oil. Spills and/or discharges of wastewater have been shown to impact surface, ground, and drinking water. The goals of this study were to characterize the endocrine activities and measure select organic contaminants in groundwater from conventional oil and gas (COG) and UOG production regions of Wyoming. Groundwater samples were collected from each region, solid-phase extracted, and assessed for endocrine activities (estrogen, androgen, progesterone, glucocorticoid, and thyroid receptor agonism and antagonism), using reporter gene assays in human endometrial cells. Water samples from UOG and conventional oil areas exhibited greater ER antagonist activities than water samples from conventional gas areas. Samples from UOG areas tended to exhibit progesterone receptor antagonism more often, suggesting there may be a UOG-related impact on these endocrine activities. We also report UOG-specific contaminants in Pavillion groundwater extracts, and these same chemicals at high concentrations in a local UOG wastewater sample. A unique suite of contaminants was observed in groundwater from a permitted drinking water well at a COG well pad and not at any UOG sites; high levels of endocrine activities (most notably, maximal estrogenic activity) were noted there, suggesting putative impacts on endocrine bioactivities by COG. As such, we report two levels of evidence for groundwater contamination by both UOG and COG operations in Wyoming.

Age and rate of cognitive decline in Alzheimer disease: implications for clinical trials.

PubMed

Bernick, Charles; Cummings, Jeffrey; Raman, Rema; Sun, Xiaoying; Aisen, Paul

2012-07-01

Factors that affect the rate of progression of Alzheimer disease (AD) need to be considered in the clinical trial designs of potential disease-modifying therapies. To determine the influence of age on AD course in a clinical trial setting. Pooled cohort study from 3 AD clinical trials of 18-month duration conducted by the Alzheimer Disease Cooperative Study group. Alzheimer disease research centers from across the United States. Four hundred seventy-one subjects with mild to moderate AD assigned to the placebo arm of 3 clinical trials. The relationships between baseline age and rate of change in the Alzheimer Disease Assessment Scale–cognitive subscale (ADAS-cog) 11, Mini-Mental State Examination, Clinical Dementia Rating scale Sum of Boxes score, Alzheimer Disease Cooperative Study–activities of daily living scale, and Neuropsychiatric Inventory were analyzed using a mixed-effect regression model. Sample size calculation for possible future AD clinical trials lasting 18 months using the results of the change in ADAS-cog 11 by tertiles of age groups. Older age at baseline was associated with a slower rate of decline in the ADAS-cog 11 and the Mini-Mental State Examination scores. Almost twice as many subjects aged 80 years and older compared with those aged younger than 70 years would be required to demonstrate a 30% treatment effect on the ADAS-cog 11 in an 18-month AD trial. Subject age is an important factor to consider when defining the study population in and analyzing data from AD trials of potential disease-modifying therapies.

Further delineation of COG8-CDG: A case with novel compound heterozygous mutations diagnosed by targeted exome sequencing.

PubMed

Yang, Aram; Cho, Sung Yoon; Jang, Ja-Hyun; Kim, Jinsup; Kim, Sook Za; Lee, Beom Hee; Yoo, Han-Wook; Jin, Dong-Kyu

2017-08-01

Congenital disorders of glycosylation (CDG) are a rapidly expanding group of inherited metabolic disorders with highly variable clinical presentations caused by deficient glycosylation of proteins and/or lipids. CDG-IIh is a very rare subgroup of CDG caused by mutations in the conserved oligomeric Golgi (COG) complex gene, COG8, and so far, only two cases have been reported in the medical literature. Here, we describe an 8-year-old Korean boy with psychomotor retardation, hypotonia, failure to thrive, elevated serum liver enzymes, microcephaly, and talipes equinovarus. A liver biopsy of the patient showed only interface hepatitis with mild lobular activity, and brain magnetic resonance imaging revealed cerebellar atrophy. Compared with the previous two reported cases, our patient showed relatively mild psychomotor retardation without a seizure history. The transferrin isoelectric focusing profiles in the patient showed a CDG type II pattern with increased disialo- and trisialo-transferrin. Targeted exome sequencing was performed to screen all CDG type II-related genes, and two novel frameshift mutations were found: c.171dupG (p.Leu58Alafs*29) and c.1656dupC (p.Ala553Argfs*15) in COG8. The parents were heterozygous carriers of each variant. CDG should be included in the initial differential diagnosis for children with a suspected unknown syndrome or unclassified inherited metabolic disorder or children with diverse clinical presentations, such as psychomotor retardation, hypotonia, skeletal deformity, microcephaly, cerebellar atrophy, and unexplained transient elevated liver enzyme. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

The analysis of ensembles of moderately saturated interstellar lines

NASA Technical Reports Server (NTRS)

Jenkins, E. B.

1986-01-01

It is shown that the combined equivalent widths for a large population of Gaussian-like interstellar line components, each with different central optical depths tau(0) and velocity dispersions b, exhibit a curve of growth (COG) which closely mimics that of a single, pure Gaussian distribution in velocity. Two parametric distributions functions for the line populations are considered: a bivariate Gaussian for tau(0) and b and a power law distribution for tau(0) combined with a Gaussian dispersion for b. First, COGs for populations having an extremely large number of nonoverlapping components are derived, and the implications are shown by focusing on the doublet-ratio analysis for a pair of lines whose f-values differ by a factor of two. The consequences of having, instead of an almost infinite number of lines, a relatively small collection of components added together for each member of a doublet are examined. The theory of how the equivalent widths grow for populations of overlapping Gaussian profiles is developed. Examples of the composite COG analysis applied to existing collections of high-resolution interstellar line data are presented.

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

Jun Shen; Zhi-zhong Wang; Huai-wang Yang

About 15 billion Nm{sup 3} coke oven gas (COG) is emitted into the air in Shanxi Province in China as air pollutants. It is also a waste of precious chemical resources. In this study, COG was purified respectively by four methods including refrigeration, fiberglass, silica gel, and molecular sieve. Purified COG was separated by a prism membrane into two gas products. One consists mainly of H{sub 2} ({gt}90 vol %) and the other is rich in CH{sub 4} ({gt}60 vol %) with their exact compositions to vary with the membrane separation pressure and outlet gas flow ratio. The gas richmore » in CH{sub 4} was partially oxidized with oxygen in a high-temperature fixed-bed quartz reactor charged with coke particles of 10 mm size. At 1200-1300{sup o}C, a CH{sub 4} conversion of {gt}99% could be obtained. The H{sub 2}/CO ratio in the synthesis product gas can be adjusted in the range 0.3-1.4, very favorable for further C1 synthesis. 10 refs., 17 figs., 1t ab.« less

Component Composition for Embedded Systems Using Semantic Aspect-Oriented Programming

DTIC Science & Technology

2004-10-01

real - time systems for the defense community. Our research focused on Real-Time Java implementation and analysis techniques. Real-Time Java is important for the defense community because it holds out the promise of enabling developers to apply COTS Java technology to specialized military embedded systems. It also promises to allow the defense community to utilize a large Java-literate workforce for building defense systems. Our research has delivered several techniques that may make Real-Time Java a better platform for developing embedded

Scalable and Precise Abstraction of Programs for Trustworthy Software

DTIC Science & Technology

2017-01-01

calculus for core Java. • 14 months: A systematic abstraction of core Java. • 18 months: A security auditor for core Java. • 24 months: A contract... auditor for full Java. • 42 months: A web-deployed service for security auditing. Approved for Public Release; Distribution Unlimited 4 4.0 RESULTS

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…

SimPackJ/S: a web-oriented toolkit for discrete event simulation

NASA Astrophysics Data System (ADS)

Park, Minho; Fishwick, Paul A.

2002-07-01

SimPackJ/S is the JavaScript and Java version of SimPack, which means SimPackJ/S is a collection of JavaScript and Java libraries and executable programs for computer simulations. The main purpose of creating SimPackJ/S is that we allow existing SimPack users to expand simulation areas and provide future users with a freeware simulation toolkit to simulate and model a system in web environments. One of the goals for this paper is to introduce SimPackJ/S. The other goal is to propose translation rules for converting C to JavaScript and Java. Most parts demonstrate the translation rules with examples. In addition, we discuss a 3D dynamic system model and overview an approach to 3D dynamic systems using SimPackJ/S. We explain an interface between SimPackJ/S and the 3D language--Virtual Reality Modeling Language (VRML). This paper documents how to translate C to JavaScript and Java and how to utilize SimPackJ/S within a 3D web environment.

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.

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.

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.

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.

Exploring cogging free magnetic gears

NASA Astrophysics Data System (ADS)

Borgers, Stefan; Völkel, Simeon; Schöpf, Wolfgang; Rehberg, Ingo

2018-06-01

The coupling of two rotating spherical magnets is investigated experimentally, with particular emphasis on those motions in which the driven magnet follows the driving one with a uniform angular speed, which is a feature of the so called cogging free couplings. The experiment makes use of standard equipment and digital image processing. The theory for these couplings is based on fundamental dipole-dipole interactions with analytically accessible solutions. Technical applications of this kind of coupling are foreseeable particularly for small machines, an advantage which also comes in handy for classroom demonstrations of this feature of the fundamental concept of dipole-dipole coupling.

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

Bower, G.

We summarize the current status and future developments of the North American Group's Java-based system for studying physics and detector design issues at a linear collider. The system is built around Java Analysis Studio (JAS) an experiment-independent Java-based utility for data analysis. Although the system is an integrated package running in JAS, many parts of it are also standalone Java utilities.

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.

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.

CogState computerized memory tests in patients with brain metastases: secondary endpoint results of NRG Oncology RTOG 0933.

PubMed

Caine, Chip; Deshmukh, Snehal; Gondi, Vinai; Mehta, Minesh; Tomé, Wolfgang; Corn, Benjamin W; Kanner, Andrew; Rowley, Howard; Kundapur, Vijayananda; DeNittis, Albert; Greenspoon, Jeffrey Noah; Konski, Andre A; Bauman, Glenn S; Raben, Adam; Shi, Wenyin; Wendland, Merideth; Kachnic, Lisa

2016-01-01

Whole brain radiotherapy (WBRT) is associated with memory dysfunction. As part of NRG Oncology RTOG 0933, a phase II study of WBRT for brain metastases that conformally avoided the hippocampal stem cell compartment (HA-WBRT), memory was assessed pre- and post-HA-WBRT using both traditional and computerized memory tests. We examined whether the computerized tests yielded similar findings and might serve as possible alternatives for assessment of memory in multi-institution clinical trials. Adult patients with brain metastases received HA-WBRT to 30 Gy in ten fractions and completed Hopkins Verbal Learning Test-Revised (HVLT-R), CogState International Shopping List Test (ISLT) and One Card Learning Test (OCLT), at baseline, 2 and 4 months. Tests' completion rates were 52-53 % at 2 months and 34-42 % at 4 months. All baseline correlations between HVLT-R and CogState tests were significant (p ≤ 0.003). At baseline, both CogState tests and one component of HVLT-R differentiated those who were alive at 6 months and those who had died (p ≤ 0.01). At 4 months, mean relative decline was 7.0 % for HVLT-R Delayed Recall and 18.0 % for ISLT Delayed Recall. OCLT showed an 8.0 % increase. A reliable change index found no significant changes from baseline to 2 and 4 months for ISLT Delayed Recall (z = -0.40, p = 0.34; z = -0.68, p = 0.25) or OCLT (z = 0.15, p = 0.56; z = 0.41, p = 0.66). Study findings support the possibility that hippocampal avoidance may be associated with preservation of memory test performance, and that these computerized tests also may be useful and valid memory assessments in multi-institution adult brain tumor trials.

The importance of endophenotypes in schizophrenia research.

PubMed

Braff, David L

2015-04-01

Endophenotypes provide a powerful neurobiological platform from which we can understand the genomic and neural substrates of schizophrenia and other common complex neuropsychiatric disorders. The Consortium on the Genetics of Schizophrenia (COGS) has conducted multisite studies on carefully selected key neurocognitive and neurophysiological endophenotypes in 300 families (COGS-1) and then in a follow up multisite case-control study of 2471 subjects (COGS-2). Endophenotypes are neurobiologically informed quantitative measures that show deficits in probands and their first degree relatives. They are more amenable to statistical analysis than are "fuzzy" qualitative clinical traits or confoundingly heterogeneous diagnostic categories. Endophenotypes are also viewed as uniquely informative in traditional diagnosis-based as well as emerging NIMH Research Domain (RDoC) contexts, offering a bridge between the two approaches to psychopathology classification and research. Endo- or intermediate phenotypes are heritable, and in the COGS-1 cohort their level of heritability is in the same range as is the heritability of schizophrenia itself, using the same statistical methods and subjects to assess both. Because we can demonstrate endophenotypes link to both gene networks and neural circuits on the one hand and also to real-life function, endophenotypes provide a critically important bridge for "connecting the dots" between genes, cells, circuits, information processing, neurocognition and functional impairment and personalized treatment selection in schizophrenia patients. By connecting schizophrenia risk genes with neurobiologically informed endophenotypes, and via the use of association, linkage, sequencing, stem cell and other strategies, we can provide our field with new neurobiologically informed information in our efforts to understand and treat schizophrenia. Evolving views, data and new analytic strategies about schizophrenia risk, pathology and treatment are described in this Viewpoint and in the accompanying Special Issue reports. Published by Elsevier B.V.

Extent and Location of the Excitatory and Inhibitory Cortical Hand Representation Maps: A Navigated Transcranial Magnetic Stimulation Study.

PubMed

Pitkänen, Minna; Kallioniemi, Elisa; Julkunen, Petro

2015-09-01

Voluntary muscle action and control are modulated by the primary motor cortex, which is characterized by a well-defined somatotopy. Muscle action and control depend on a sensitive balance between excitatory and inhibitory mechanisms in the cortex and in the corticospinal tract. The cortical locations evoking excitatory and inhibitory responses in brain stimulation can be mapped, for example, as a pre-surgical procedure. The purpose of this study was to find the differences between excitatory and inhibitory motor representations mapped using navigated transcranial magnetic stimulation (nTMS). The representations of small hand muscles were mapped to determine the areas and the center of gravities (CoGs) in both hemispheres of healthy right-handed volunteers. The excitatory representations were obtained via resting motor evoked potential (MEP) mapping, with and without a stimulation grid. The inhibitory representations were mapped using the grid and measuring corticospinal silent periods (SPs) during voluntary muscle contraction. The excitatory representations were larger on the dominant hemisphere compared with the non-dominant (p < 0.05). The excitatory CoGs were more medial (p < 0.001) and anterior (p < 0.001) than the inhibitory CoGs. The use of the grid did not influence the areas or the CoGs. The results support the common hypothesis that the MEP and SP representations are located at adjacent sites. Furthermore, the dominant hemisphere seems to be better organized for controlling excitatory motor functions with respect to TMS. In addition, the inhibitory representations could provide further information about motor reorganization and aid in surgery planning when the functional cortical representations are located in abnormal cortical regions.

Informant-related effects of neurofeedback and cognitive training in children with ADHD including a waiting control phase: a randomized-controlled trial.

PubMed

Minder, Franziska; Zuberer, Agnieszka; Brandeis, Daniel; Drechsler, Renate

2018-02-02

There is controversy regarding the clinical efficacy of neurofeedback (NF) and computerized cognitive training (CogT) as treatments for ADHD. Meta-analyses claim that probably blinded teachers observe smaller effects than parents, because they are less biased. We investigated informant-specific effects by manipulating the involvement of informants, by controlling for waiting time effects, and by adding a blinded outcome measure. Seventy-seven children with ADHD were randomly allocated to slow cortical potential NF or to individualized CogT (of attention, working memory or inhibition). The training was conducted in schools (NF: n = 19, CogT: n = 19) or in outpatient clinics (NF: n = 19, CogT: n = 20). Three assessments were scheduled: baseline, followed by a waiting period, pre-training, and post-training. Multivariate Analyses of Variance were conducted to assess parent- and teacher-rated changes in ADHD symptoms and executive functions (EF), and changes according to standardized classroom observations. Both treatments resulted in significant improvements according to informants, with larger effects for parents (ADHD symptoms: parent η p 2  = .32; teacher η p 2  = .10), and according to observations (η p 2  = .19). The setting had no effect on outcome. Considerable waiting time effects were revealed for ADHD symptom ratings by both informants, for EF ratings only by teachers. Changed classroom behavior was uncorrelated with teacher-rated changes. Overall, the results do not support the notion that teachers are more objective while being as sensitive to change as parents. The three sources seem to contribute differential and mostly unrelated pieces of information to the evaluation of treatments.

Substrate-Triggered Exosite Binding: Synergistic Dendrimer/Folic Acid Action for Achieving Specific, Tight-Binding to Folate Binding Protein.

PubMed

Chen, Junjie; van Dongen, Mallory A; Merzel, Rachel L; Dougherty, Casey A; Orr, Bradford G; Kanduluru, Ananda Kumar; Low, Philip S; Marsh, E Neil G; Banaszak Holl, Mark M

2016-03-14

Polymer-ligand conjugates are designed to bind proteins for applications as drugs, imaging agents, and transport scaffolds. In this work, we demonstrate a folic acid (FA)-triggered exosite binding of a generation five poly(amidoamine) (G5 PAMAM) dendrimer scaffold to bovine folate binding protein (bFBP). The protein exosite is a secondary binding site on the protein surface, separate from the FA binding pocket, to which the dendrimer binds. Exosite binding is required to achieve the greatly enhanced binding constants and protein structural change observed in this study. The G5Ac-COG-FA1.0 conjugate bound tightly to bFBP, was not displaced by a 28-fold excess of FA, and quenched roughly 80% of the initial fluorescence. Two-step binding kinetics were measured using the intrinsic fluorescence of the FBP tryptophan residues to give a KD in the low nanomolar range for formation of the initial G5Ac-COG-FA1.0/FBP* complex, and a slow conversion to the tight complex formed between the dendrimer and the FBP exosite. The extent of quenching was sensitive to the choice of FA-dendrimer linker chemistry. Direct amide conjugation of FA to G5-PAMAM resulted in roughly 50% fluorescence quenching of the FBP. The G5Ac-COG-FA, which has a longer linker containing a 1,2,3-triazole ring, exhibited an ∼80% fluorescence quenching. The binding of the G5Ac-COG-FA1.0 conjugate was compared to poly(ethylene glycol) (PEG) conjugates of FA (PEGn-FA). PEG2k-FA had a binding strength similar to that of FA, whereas other PEG conjugates with higher molecular weight showed weaker binding. However, no PEG conjugates gave an increased degree of total fluorescence quenching.

Utility, reliability, sensitivity and validity of an online test system designed to monitor changes in cognitive function in clinical trials.

PubMed

Wesnes, Keith A; Brooker, Helen; Ballard, Clive; McCambridge, Laura; Stenton, Robert; Corbett, Anne

2017-12-01

The advent of long-term remotely conducted clinical trials requires assessments which can be administered online. This paper considers the utility, reliability, sensitivity and validity of an internet-based system for measuring changes in cognitive function which is being used in one such trial. The Platform for Research Online to investigate Genetics and Cognition in Ageing is a 10-year longitudinal and entirely remote study launched in November 2015. The CogTrack TM System is being used to monitor changes in important aspects of cognitive function using tests of attention, information processing and episodic memory. On study entry, the participants performed CogTrack TM up to three times over seven days, and these data are evaluated in this paper. During the first six months of the study, 14 531 individuals aged 50 to 94 years enrolled and performed the CogTrack TM System, 8627 of whom completed three test sessions. On the first administration, 99.4% of the study tasks were successfully completed. Repeated testing showed training/familiarisation effects on four of the ten measures which had largely stabilised by the third test session. The factor structure of the various measures was found to be robust. Evaluation of the influence of age identified clinically relevant declines over the age range of the population on one or more measures from all tasks. The results of these analyses identify CogTrack TM to be a practical and valid method to reliably, sensitively, remotely and repeatedly collect cognitive data from large samples of individuals aged 50 and over. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Differential effects of water-based exercise on the cognitive function in independent elderly adults.

PubMed

Sato, Daisuke; Seko, Chihiro; Hashitomi, Tatsuya; Sengoku, Yasuo; Nomura, Takeo

2015-04-01

Physical exercise has been reported to be the most effective method to improve cognitive function and brain health, but there is as yet no research on the effect of water-based exercise. The aim of the present study was to compare the effects of water-based exercise with and without cognitive stimuli on cognitive and physical functions. The design is a single-blind randomized controlled study. Twenty-one participants were randomly assigned to a normal water-based exercise (Nor-WE) group or a cognitive water-based exercise (Cog-WE) group. The exercise sessions were divided into two exercise series: a 10-min series of land-based warm-up, consisting of flexibility exercises, and a 50-min series of exercises in water. The Nor-WE consisted of 10 min of walking, 30 min of strength and stepping exercise, including stride over, and 10 min of stretching and relaxation in water. The Cog-WE consisted of 10 min of walking, 30 min of water-cognitive exercises, and 10 min of stretching and relaxation in water. Cognitive function, physical function, and ADL were measured before the exercise intervention (pre-intervention) and 10 weeks after the intervention (post-intervention). Participation in the Cog-WE performed significantly better on the pegboard test and the choice stepping reaction test and showed a significantly improved attention, memory, and learning, and in the general cognitive function (measured as the total score in the 5-Cog test). Participation in the Nor-WE dramatically improved walking ability and lower limb muscle strength. Our results reveal that the benefits elderly adults may obtain from water-based exercise depend on the characteristics of each specific exercise program. These findings highlight the importance of prescription for personalized water-based exercises to elderly adults to improve cognitive function.

An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.

PubMed

Cuadrat, Rafael R C; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M; Mattoso, Marta; Dávila, Alberto M R

2014-08-01

A key focus in 21(st) century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools.

Modeling of postural stability borders during heel-toe rocking.

PubMed

Murnaghan, Chantelle D; Elston, Beth; Mackey, Dawn C; Robinovitch, Stephen N

2009-08-01

To maintain balance during movements such as bending and reaching, the CNS must generate muscle forces to counteract destabilizing torques produced by gravitational (position-dependent) and inertial (acceleration-dependent) forces. This may create a trade-off between the attainable frequency and amplitude of movements. We used experiments and mathematical modeling to examine this relationship during the task of heel-toe rocking. During the experiments, participants (n=15) rocked about the ankles in the sagittal plane with maximum attainable amplitude at a frequency of 0.33 Hz or 0.66 Hz. As the frequency doubled, the maximum anterior position of the whole-body centre-of-gravity (COG) with respect to the ankle decreased by 11% of foot length (from 11.9 cm (S.D. 1.6) to 9.2 cm (S.D. 1.2); p<0.001), the minimum anterior position of the COG increased by 8% of foot length (from 1.6 cm to 3.5 cm in front on the ankle; p<0.0005), and the ankle stiffness increased from 787 Nm/rad (S.D. 156) to 1625 Nm/rad (S.D. 339). However, there was no difference between conditions in the maximum anterior position of the COP (p=0.51), the minimum anterior position of the COP (p=0.23), or the peak ankle torque (p=0.39). An inverted pendulum model driven by a rotational spring predicted the measured ankle stiffness to within 0.9% (S.D. 6.8), and the maximum anterior COG position to within 1.2% (S.D. 4.0). These results indicate that COG amplitude decreases with increasing rocking frequency, due to (a) invariability in peak ankle torque and (b) the need to allocate torque between gravitational and inertial components, the latter of which scales with the square of frequency.

An Orthology-Based Analysis of Pathogenic Protozoa Impacting Global Health: An Improved Comparative Genomics Approach with Prokaryotes and Model Eukaryote Orthologs

PubMed Central

Cuadrat, Rafael R. C.; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M.; Mattoso, Marta

2014-01-01

Abstract A key focus in 21st century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools. PMID:24960463

Extended "Timed Up and Go" assessment as a clinical indicator of cognitive state in Parkinson's disease.

PubMed

Evans, Tess; Jefferson, Alexa; Byrnes, Michelle; Walters, Sue; Ghosh, Soumya; Mastaglia, Frank L; Power, Brian; Anderton, Ryan S

2017-04-15

To evaluate a modified extended Timed Up and Go (extended-TUG) assessment against a panel of validated clinical assessments, as an indicator of Parkinson's disease (PD) severity and cognitive impairment. Eighty-seven participants with idiopathic PD were sequentially recruited from a Movement Disorders Clinic. An extended-TUG assessment was employed which required participants to stand from a seated position, walk in a straight line for 7m, turn 180° and then return to the start, in a seated position. The extended-TUG assessment duration was correlated to a panel of clinical assessments, including the Unified Parkinson's Disease Rating Scale (MDS-UPDRS), Quality of Life (PDQ-39), Scales for Outcomes in Parkinson's Disease (SCOPA-Cog), revised Addenbrooke's Cognitive Index (ACE-R) and Barratt's Impulsivity Scale 11 (BIS-11). Extended-TUG time was significantly correlated to MDS-UPDRS III score and to SCOPA-Cog, ACE-R (p<0.001) and PDQ-39 scores (p<0.01). Generalized linear models determined the extended-TUG to be a sole variable in predicting ACE-R or SCOPA-Cog scores. Patients in the fastest extended-TUG tertile were predicted to perform 8.3 and 13.4 points better in the SCOPA-Cog and ACE-R assessments, respectively, than the slowest group. Patients who exceeded the dementia cut-off scores with these instruments exhibited significantly longer extended-TUG times. Extended-TUG performance appears to be a useful indicator of cognition as well as motor function and quality of life in PD, and warrants further evaluation as a first line assessment tool to monitor disease severity and response to treatment. Poor extended-TUG performance may identify patients without overt cognitive impairment form whom cognitive assessment is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

Poor Performance on a Preoperative Cognitive Screening Test Predicts Postoperative Complications in Older Orthopedic Surgical Patients.

PubMed

Culley, Deborah J; Flaherty, Devon; Fahey, Margaret C; Rudolph, James L; Javedan, Houman; Huang, Chuan-Chin; Wright, John; Bader, Angela M; Hyman, Bradley T; Blacker, Deborah; Crosby, Gregory

2017-11-01

The American College of Surgeons and the American Geriatrics Society have suggested that preoperative cognitive screening should be performed in older surgical patients. We hypothesized that unrecognized cognitive impairment in patients without a history of dementia is a risk factor for development of postoperative complications. We enrolled 211 patients 65 yr of age or older without a diagnosis of dementia who were scheduled for an elective hip or knee replacement. Patients were cognitively screened preoperatively using the Mini-Cog and demographic, medical, functional, and emotional/social data were gathered using standard instruments or review of the medical record. Outcomes included discharge to place other than home (primary outcome), delirium, in-hospital medical complications, hospital length-of-stay, 30-day emergency room visits, and mortality. Data were analyzed using univariate and multivariate analyses. Fifty of 211 (24%) patients screened positive for probable cognitive impairment (Mini-Cog less than or equal to 2). On age-adjusted multivariate analysis, patients with a Mini-Cog score less than or equal to 2 were more likely to be discharged to a place other than home (67% vs. 34%; odds ratio = 3.88, 95% CI = 1.58 to 9.55), develop postoperative delirium (21% vs. 7%; odds ratio = 4.52, 95% CI = 1.30 to 15.68), and have a longer hospital length of stay (hazard ratio = 0.63, 95% CI = 0.42 to 0.95) compared to those with a Mini-Cog score greater than 2. Many older elective orthopedic surgical patients have probable cognitive impairment preoperatively. Such impairment is associated with development of delirium postoperatively, a longer hospital stay, and lower likelihood of going home upon hospital discharge.

The Effects of Simulated Wildland Firefighting Tasks on Core Temperature and Cognitive Function under Very Hot Conditions.

PubMed

Williams-Bell, F Michael; Aisbett, Brad; Murphy, Bernadette A; Larsen, Brianna

2017-01-01

Background: The severity of wildland fires is increasing due to continually hotter and drier summers. Firefighters are required to make life altering decisions on the fireground, which requires analytical thinking, problem solving, and situational awareness. This study aimed to determine the effects of very hot (45°C; HOT) conditions on cognitive function following periods of simulated wildfire suppression work when compared to a temperate environment (18°C; CON). Methods: Ten male volunteer firefighters intermittently performed a simulated fireground task for 3 h in both the CON and HOT environments, with cognitive function tests (paired associates learning and spatial span) assessed at baseline (cog 1) and during the final 20-min of each hour (cog 2, 3, and 4). Reaction time was also assessed at cog 1 and cog 4. Pre- and post- body mass were recorded, and core and skin temperature were measured continuously throughout the protocol. Results: There were no differences between the CON and HOT trials for any of the cognitive assessments, regardless of complexity. While core temperature reached 38.7°C in the HOT (compared to only 37.5°C in the CON; p < 0.01), core temperature declined during the cognitive assessments in both conditions (at a rate of -0.15 ± 0.20°C·hr -1 and -0.63 ± 0.12°C·hr -1 in the HOT and CON trial respectively). Firefighters also maintained their pre-exercise body mass in both conditions, indicating euhydration. Conclusions: It is likely that this maintenance of euhydration and the relative drop in core temperature experienced between physical work bouts was responsible for the preservation of firefighters' cognitive function in the present study.

Predictors of Sustained Response to Rivastigmine in Patients With Alzheimer's Disease: A Retrospective Analysis

PubMed Central

Grossberg, George T.; Somogyi, Monique; Meng, Xiangyi

2011-01-01

Objective: The cholinesterase inhibitor rivastigmine is approved for the treatment of mild to moderate Alzheimer's disease. However, it is not possible to predict which individuals will benefit from treatment. This retrospective analysis of an international, 24-week, randomized, double-blind trial aimed to identify the percentage of persons with Alzheimer's disease who have a sustained response with rivastigmine patch, rivastigmine capsules, or placebo; to determine the magnitude of the sustained treatment response; and to investigate baseline patient characteristics predictive of the observed sustained response. Method: Patients who improved on the Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog) and Alzheimer's Disease Cooperative Study-Activities of Daily Living scale (ADCS-ADL) at week 16 and maintained at least the week 16 improvement at week 24 were identified as sustained responders. Treatment differences and baseline predictive factors were assessed in patients demonstrating a 1-, 2-, 3-, 4-, or 5-point sustained improvement. The first patient was screened in November 2003 and the last patient completed the study in January 2006. Results: More persons with Alzheimer's disease had sustained improvements on the ADAS-cog and ADCS-ADL with rivastigmine versus placebo. Sustained improvements of 4 or 5 points on the ADAS-cog or ADCS-ADL were demonstrated in the 9.5-mg/24-h rivastigmine patch (24% and 36% of patients, respectively) and 12-mg/d capsule groups (28% on both outcome measures). Factors predictive of a sustained response to treatment included baseline Mini-Mental State Examination, ADAS-cog, and ADCS-ADL scores and treatment, country of treatment, and time since first symptom was diagnosed by a physician. Conclusions: Understanding factors predictive of sustained cholinesterase inhibitor treatment response should help to optimize Alzheimer's disease management and encourage compliance by allowing more realistic expectations of treatment effects. PMID:21977379

Predictors of sustained response to rivastigmine in patients with Alzheimer's disease: a retrospective analysis.

PubMed

Sadowsky, Carl H; Grossberg, George T; Somogyi, Monique; Meng, Xiangyi

2011-01-01

The cholinesterase inhibitor rivastigmine is approved for the treatment of mild to moderate Alzheimer's disease. However, it is not possible to predict which individuals will benefit from treatment. This retrospective analysis of an international, 24-week, randomized, double-blind trial aimed to identify the percentage of persons with Alzheimer's disease who have a sustained response with rivastigmine patch, rivastigmine capsules, or placebo; to determine the magnitude of the sustained treatment response; and to investigate baseline patient characteristics predictive of the observed sustained response. Patients who improved on the Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog) and Alzheimer's Disease Cooperative Study-Activities of Daily Living scale (ADCS-ADL) at week 16 and maintained at least the week 16 improvement at week 24 were identified as sustained responders. Treatment differences and baseline predictive factors were assessed in patients demonstrating a 1-, 2-, 3-, 4-, or 5-point sustained improvement. The first patient was screened in November 2003 and the last patient completed the study in January 2006. More persons with Alzheimer's disease had sustained improvements on the ADAS-cog and ADCS-ADL with rivastigmine versus placebo. Sustained improvements of 4 or 5 points on the ADAS-cog or ADCS-ADL were demonstrated in the 9.5-mg/24-h rivastigmine patch (24% and 36% of patients, respectively) and 12-mg/d capsule groups (28% on both outcome measures). Factors predictive of a sustained response to treatment included baseline Mini-Mental State Examination, ADAS-cog, and ADCS-ADL scores and treatment, country of treatment, and time since first symptom was diagnosed by a physician. Understanding factors predictive of sustained cholinesterase inhibitor treatment response should help to optimize Alzheimer's disease management and encourage compliance by allowing more realistic expectations of treatment effects.

The Effects of Simulated Wildland Firefighting Tasks on Core Temperature and Cognitive Function under Very Hot Conditions

PubMed Central

Williams-Bell, F. Michael; Aisbett, Brad; Murphy, Bernadette A.; Larsen, Brianna

2017-01-01

Background: The severity of wildland fires is increasing due to continually hotter and drier summers. Firefighters are required to make life altering decisions on the fireground, which requires analytical thinking, problem solving, and situational awareness. This study aimed to determine the effects of very hot (45°C; HOT) conditions on cognitive function following periods of simulated wildfire suppression work when compared to a temperate environment (18°C; CON). Methods: Ten male volunteer firefighters intermittently performed a simulated fireground task for 3 h in both the CON and HOT environments, with cognitive function tests (paired associates learning and spatial span) assessed at baseline (cog 1) and during the final 20-min of each hour (cog 2, 3, and 4). Reaction time was also assessed at cog 1 and cog 4. Pre- and post- body mass were recorded, and core and skin temperature were measured continuously throughout the protocol. Results: There were no differences between the CON and HOT trials for any of the cognitive assessments, regardless of complexity. While core temperature reached 38.7°C in the HOT (compared to only 37.5°C in the CON; p < 0.01), core temperature declined during the cognitive assessments in both conditions (at a rate of −0.15 ± 0.20°C·hr−1 and −0.63 ± 0.12°C·hr−1 in the HOT and CON trial respectively). Firefighters also maintained their pre-exercise body mass in both conditions, indicating euhydration. Conclusions: It is likely that this maintenance of euhydration and the relative drop in core temperature experienced between physical work bouts was responsible for the preservation of firefighters' cognitive function in the present study. PMID:29114230

Anesthesia Basics

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

Asthma Diary

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

World Reference Center for Arboviruses.

DTIC Science & Technology

1984-01-01

viral antigen in Avian sera. .. . ... ....... . ... .. . ... . .......... 97 Effect of hibernation of EEE virus circulation and antibody Development...viruses were isolated from a variety of mosquito species collected on several different islands in the Indonesian archipelago (Sumatra, Kalimantan, Java ...vishnui Java 15 Jun 81 7180 Cx. tritaeniorhynchus Java 13 Jul 81 7887 Cx. tritaeniorhynchus Java 26-27 Jul 81 8442 Cx. tritaeniorhynchus Bali 10 Dec 80

An Interface Transformation Strategy for AF-IPPS

DTIC Science & Technology

2012-12-01

Representational State Transfer (REST) and Java Enterprise Edition ( Java EE) to implement a reusable “translation service.” For SOAP and REST protocols, XML and...of best-of-breed open source software. The product baseline is summarized in the following table: Product Function Description Java Language...Compiler & Runtime JBoss Application Server Applications, Messaging, Translation Java EE Application Server Ruby on Rails Applications Ruby Web

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).

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

Web-based three-dimensional geo-referenced visualization

NASA Astrophysics Data System (ADS)

Lin, Hui; Gong, Jianhua; Wang, Freeman

1999-12-01

This paper addresses several approaches to implementing web-based, three-dimensional (3-D), geo-referenced visualization. The discussion focuses on the relationship between multi-dimensional data sets and applications, as well as the thick/thin client and heavy/light server structure. Two models of data sets are addressed in this paper. One is the use of traditional 3-D data format such as 3-D Studio Max, Open Inventor 2.0, Vis5D and OBJ. The other is modelled by a web-based language such as VRML. Also, traditional languages such as C and C++, as well as web-based programming tools such as Java, Java3D and ActiveX, can be used for developing applications. The strengths and weaknesses of each approach are elaborated. Four practical solutions for using VRML and Java, Java and Java3D, VRML and ActiveX and Java wrapper classes (Java and C/C++), to develop applications are presented for web-based, real-time interactive and explorative visualization.

Cardiac Catheterization (For Teens)

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

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 accommodated by the Java megathrust, and a much smaller parallel motion accommodated along the Baribis (∼ 5 ± 0.2 mm /yr) and Kendeng (∼ 2.3 ± 0.7 mm /yr) Thrusts. Our study highlights a correlation between the geodetically inferred active faults and historical seismic catalogs, emphasizing the importance of considering crustal fault activity within Java in future seismic assessments.

Opening up Architectures of Software-Intensive Systems: A Functional Decomposition to Support System Comprehension

DTIC Science & Technology

2007-10-01

Architecture ................................................................................ 14 Figure 2. Eclipse Java Model...16 Figure 3. Eclipse Java Model at the Source Code Level...24 Figure 9. Java Source Code

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Molecular cogs of the insect circadian clock.

PubMed

Shirasu, Naoto; Shimohigashi, Yasuyuki; Tominaga, Yoshiya; Shimohigashi, Miki

2003-08-01

During the last five years, enormous progress has been made in understanding the molecular basis of circadian systems, mainly by molecular genetic studies using the mouse and fly. Extensive evidence has revealed that the core clock machinery involves "clock genes" and "clock proteins" functioning as molecular cogs. These participate in transcriptional/translational feedback loops and many homologous clock-components in the fruit fly Drosophila are also expressed in mammalian clock tissues with circadian rhythms. Thus, the mechanisms of the central clock seem to be conserved across animal kingdom. However, some recent studies imply that the present widely accepted molecular models of circadian clocks may not always be supported by the experimental evidence.

Female Reproductive Health After Childhood, Adolescent, and Young Adult Cancers: Guidelines for the Assessment and Management of Female Reproductive Complications

PubMed Central

Metzger, Monika L.; Meacham, Lillian R.; Patterson, Briana; Casillas, Jacqueline S.; Constine, Louis S.; Hijiya, Nobuko; Kenney, Lisa B.; Leonard, Marcia; Lockart, Barbara A.; Likes, Wendy; Green, Daniel M.

2013-01-01

Purpose As more young female patients with cancer survive their primary disease, concerns about reproductive health related to primary therapy gain relevance. Cancer therapy can often affect reproductive organs, leading to impaired pubertal development, hormonal regulation, fertility, and sexual function, affecting quality of life. Methods The Children's Oncology Group Long-Term Follow-Up Guidelines for Survivors of Childhood, Adolescent, and Young Adult Cancer (COG-LTFU Guidelines) are evidence-based recommendations for screening and management of late effects of therapeutic exposures. The guidelines are updated every 2 years by a multidisciplinary panel based on current literature review and expert consensus. Results This review summarizes the current task force recommendations for the assessment and management of female reproductive complications after treatment for childhood, adolescent, and young adult cancers. Experimental pretreatment as well as post-treatment fertility preservation strategies, including barriers and ethical considerations, which are not included in the COG-LTFU Guidelines, are also discussed. Conclusion Ongoing research will continue to inform COG-LTFU Guideline recommendations for follow-up care of female survivors of childhood cancer to improve their health and quality of life. PMID:23382474

Sensitivity of the curve-to-growth technique utilized in rocket experiments to determine the line shape of solar He I resonance lines

NASA Technical Reports Server (NTRS)

Wu, C. Y. R.; Ogawa, H. S.

1986-01-01

The sensitivity of the curve-of-growth (COG) technique utilized in rocket measurements to determine the line profiles of the solar He I resonance emissions is theoretically examined with attention to the possibility of determining the line core shape using this technique. The line at 584.334 A is chosen as an illustration. Various possible source functions of the solar line have been assumed in the computation of the integrated transmitted intensity. A recent observational data set obtained by the present researchers is used as the constraint of the computation. It is confirmed that the COG technique can indeed provide a good measurement of the solar line width. However, to obtain detailed knowledge of the solar profile at line center and in the core region, (1) it is necessary to be able to carry out relative solar flux measurements with a 1-percent or better precision, and (2) it must be possible to measure the He gas pressure in the absorption cell to lower than 0.1 mtorr. While these numbers apply specifically to the present geometry, the results are readily scaled to other COG measurements using other experimental parameters.

Genetics in arterial calcification: pieces of a puzzle and cogs in a wheel.

PubMed

Rutsch, Frank; Nitschke, Yvonne; Terkeltaub, Robert

2011-08-19

Artery calcification reflects an admixture of factors such as ectopic osteochondral differentiation with primary host pathological conditions. We review how genetic factors, as identified by human genome-wide association studies, and incomplete correlations with various mouse studies, including knockout and strain analyses, fit into "pieces of the puzzle" in intimal calcification in human atherosclerosis, and artery tunica media calcification in aging, diabetes mellitus, and chronic kidney disease. We also describe in sharp contrast how ENPP1, CD73, and ABCC6 serve as "cogs in a wheel" of arterial calcification. Specifically, each is a minor component in the function of a much larger network of factors that exert balanced effects to promote and suppress arterial calcification. For the network to normally suppress spontaneous arterial calcification, the "cogs" ENPP1, CD73, and ABCC6 must be present and in working order. Monogenic ENPP1, CD73, and ABCC6 deficiencies each drive a molecular pathophysiology of closely related but phenotypically different diseases (generalized arterial calcification of infancy (GACI), pseudoxanthoma elasticum (PXE) and arterial calcification caused by CD73 deficiency (ACDC)), in which premature onset arterial calcification is a prominent but not the sole feature.

The Consortium on the Genetics of Schizophrenia: Neurocognitive Endophenotypes

PubMed Central

Gur, Raquel E.; Calkins, Monica E.; Gur, Ruben C.; Horan, William P.; Nuechterlein, Keith H.; Seidman, Larry J.; Stone, William S.

2007-01-01

The Consortium on the Genetics of Schizophrenia (COGS) is a 7-site collaboration that examines the genetic architecture of quantitative endophenotypes in families with schizophrenia. Here we review the background and rationale for selecting neurocognitive tasks as endophenotypic measures in genetic studies. Criteria are outlined for the potential of measures as endophenotypic vulnerability markers. These include association with illness, state independence (ie, adequate test-retest stability, adequate between-site reliability, impairments in patients not due to medications, impairments observed regardless of illness state), heritability, findings of higher rates in relatives of probands than in the general population, and cosegregation within families. The COGS required that, in addition, the measures be “neurocognitive” and thus linked to neurobiology and that they be feasible in multisite studies. The COGS neurocognitive assessment includes measures of attention, verbal memory, working memory, and a computerized neurocognitive battery that also includes facial processing tasks. Here we describe data demonstrating that these neurobehavioral measures meet criteria for endophenotypic candidacy. We conclude that quantitative neurocognitive endophenotypes need further evidence for efficacy in identifying genetic effects but have the potential of providing unprecedented insight into gene-environment interaction related to dimensions of brain and behavior in health and disease. PMID:17101692

Effects of Lacunar Infarctions on Cognitive Impairment in Patients with Cerebral Autosomal-Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy

PubMed Central

Choi, Jay Chol; Kang, Sa-Yoon; Kang, Ji-Hoon; Na, Hae Ri; Park, Ji-Kang

2011-01-01

Background and Purpose Cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited microangiopathy caused by mutations in the Notch3 gene. Although previous studies have shown an association between lacunar infarction and cognitive impairment, the relationship between MRI parameters and cognition remains unclear. In this study we investigated the influence of MRI parameters on cognitive impairment in CADASIL. Methods We applied a prospective protocol to 40 patients. MRI analysis included the normalized volume of white-matter hyperintensities (nWMHs), number of lacunes, and number of cerebral microbleeds. Cognition was assessed with the aid of psychometric tests [Mini-Mental State Examination (MMSE), Alzheimer's Disease Assessment Scale-cognition (ADAS-cog), Trail-Making Test, and Stroop interference (Stroop IF)]. Results A multivariate regression analysis revealed that the total number of lacunes influenced the performance in the MMSE, ADAS-cog, and Stroop IF, while nWMHs had a strong univariate association with ADAS-cog and Stroop IF scores. However, this association disappeared in the multivariate analysis. Conclusions These findings demonstrate that the number of lacunes is the main predictive factor of cognitive impairment in CADASIL. PMID:22259617

Novel Control Scheme of Power Assisted Wheelchair for Preventing Overturn (Part II)-Variable Assistance Ratio Control Based on Estimation of Center-of-Gravity Angle and Phase Plane-

NASA Astrophysics Data System (ADS)

Hata, Naoki; Seki, Hirokazu; Koyasu, Yuichi; Hori, Yoichi

Aged people and disabled people who have difficulty in walking are increasing. As one of mobility support, significance of a power assisted wheelchair which assists driving force using electric motors and spreads their living areas has been enhanced. However, the increased driving force often causes a dangerous overturn of wheelchair. This paper proposes a novel control method to prevent power assisted wheelchair from overturning. The man-wheelchair system can be regarded as an inverse pendulum model when the front wheels are rising. The center-of-gravity (COG) angle of the model is the most important information directly-linked to overturn. Behavior of the system can be analyzed using phase plane as shown in this paper. The COG angle cannot be directly measured using a sensor, therefore, COG observer based on its velocity is proposed. On the basis of the analysis on phase plane, a novel control method with variable assistance ratio to prevent a dangerous overturn is proposed. The effectiveness of the proposed method is verified by the practical experiments on the flat ground and uphill slope.

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

PubMed

Natale, D A; Shankavaram, U T; Galperin, M Y; Wolf, Y I; Aravind, L; Koonin, E V

2000-01-01

Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and predicted protein functions provide for a significant improvement in genome annotation. A differential genome display approach helps in a systematic investigation of common and distinct features of gene repertoires and in some cases reveals unexpected connections that may be indicative of functional similarities between phylogenetically distant organisms and of lateral gene exchange.

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

PubMed Central

Natale, Darren A; Shankavaram, Uma T; Galperin, Michael Y; Wolf, Yuri I; Aravind, L; Koonin, Eugene V

2000-01-01

Background: Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. Results: A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. Conclusions: Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and predicted protein functions provide for a significant improvement in genome annotation. A differential genome display approach helps in a systematic investigation of common and distinct features of gene repertoires and in some cases reveals unexpected connections that may be indicative of functional similarities between phylogenetically distant organisms and of lateral gene exchange. PMID:11178258

Limits of Stability and Adaptation to Wearing Rocker Bottom Shoes.

PubMed

Vieira, Edgar Ramos; Guerrero, Gerardo; Holt, Daniel; Arreaza, Monica; Veroes, Valentina; Brunt, Denis

2014-06-01

Stability and balance are fundamental during static and dynamic activities. The effects of wearing rocker bottom sole (RBS) shoes on the limits of stability (LOS) and adaptation to wearing RBS shoes need to be investigated. The objectives of this study were to evaluate the LOS when wearing RBS shoes, and to evaluate if people improve their stability while wearing RBS shoes over time. Eleven female subjects with no lower extremity impairments participated in the study. The LOS were tested at baseline and weeks 3 and 6 using a Neurocom SMART EquiTest equipment. Center of pressure (CoP) was determined using force plates, and the center of gravity (CoG) position was estimated from the CoP measures and subjects' anthropometry. Subjects performed a series of tasks that involved leaning in different directions so as to move the vertical projection of their CoG. End-point excursions of the CoG floor projection were calculated as a percentage of the distance between the starting position and the target. Considering the body as an inverted pendulum, we recorded the average angular velocity of the inverted pendulum during the movements and quantified directional control as a percentage of movement toward versus away from the target. Shoe types were compared using paired t tests, and sessions were compared using repeated measures ANOVA. The angular velocities of the inverted pendulum (ie, CoG velocity) were not significantly different between shoe conditions in the front and back directions at baseline (4 ± 3 with RBS vs 5 ± 2 deg/sec with regular shoes, and 4 ± 1 vs 6 ± 4 deg/sec). Front directional control of the CoG was significantly worse with RBS shoes at weeks 3 and 6 ( P < .015). Front end-point excursions were also lower with RBS shoes both at baseline and week 6 ( P < .014). There were no significant changes over time. The findings indicate that the LOS were negatively affected by wearing RBS shoes and that people do not improve their stability while wearing these shoes even after a 6-week period of use. This study shows that wearing RBS shoes increase instability and the instability remains even after wearing these shoes for six weeks.

Senses and Your 8- to 12-Month-Old

MedlinePlus

... FrameworkServlet.doGet(FrameworkServlet.java:549) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache. ...

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

Multi-National Information Sharing -- Cross Domain Collaborative Information Environment (CDCIE) Solution. Revision 4

DTIC Science & Technology

2005-04-12

Hardware, Database, and Operating System independence using Java • Enterprise-class Architecture using Java2 Enterprise Edition 1.4 • Standards based...portal applications. Compliance with the Java Specification Request for Portlet APIs (JSR-168) (Portlet API) and Web Services for Remote Portals...authentication and authorization • Portal Standards using Java Specification Request for Portlet APIs (JSR-168) (Portlet API) and Web Services for Remote

Simulation for Dynamic Situation Awareness and Prediction III

DTIC Science & Technology

2010-03-01

source Java ™ library for capturing and sending network packets; 4) Groovy – an open source, Java -based scripting language (version 1.6 or newer). Open...DMOTH Analyzer application. Groovy is an open source dynamic scripting language for the Java Virtual Machine. It is consistent with Java syntax...between temperature, pressure, wind and relative humidity, and 3) a precipitation editing algorithm. The Editor can be used to prepare scripted changes

JNDMS Task Authorization 2 Report

DTIC Science & Technology

2013-10-01

uses Barnyard to store alarms from all DREnet Snort sensors in a MySQL database. Barnyard is an open source tool designed to work with Snort to take...Technology ITI Information Technology Infrastructure J2EE Java 2 Enterprise Edition JAR Java Archive. This is an archive file format defined by Java ...standards. JDBC Java Database Connectivity JDW JNDMS Data Warehouse JNDMS Joint Network and Defence Management System JNDMS Joint Network Defence and

Hardware Assisted Stealthy Diversity (CHECKMATE)

DTIC Science & Technology

2013-09-01

applicable across multiple architectures. Figure 29 shows an example an attack against an interpreted environment with a Java executable. CHECKMATE can...Architectures ARM PPCx86 Java VM Java VMJava VM Java Executable Attack APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED 33 a user executes “/usr/bin/wget...Server 1 - Administration Server 2 – Database ( mySQL ) Server 3 – Web server (Mongoose) Server 4 – File server (SSH) Server 5 – Email server

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.

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.

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

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Increasing the uptake of long-acting and permanent methods of family planning: A qualitative study with village midwives in East Java and Nusa Tenggara Barat Provinces, Indonesia.

PubMed

Titaley, Christiana R; Wijayanti, Ratna U; Damayanti, Rita; Setiawan, Agus Dwi; Dadun; Dachlia, Dini; Siagian, Ferdinand; Suparno, Heru; Saputri, Dwi Astuti Yunita; Harlan, Sarah; Wahyuningrum, Yunita; Storey, Douglas

2017-10-01

this analysis aims to explore midwives' insights into the provision of long-acting and permanent methods of contraception (LAPMs) in the selected areas of East Java and Nusa Tenggara Barat (NTB) Provinces, Indonesia. a qualitative study using in-depth interviews was conducted with 12 village midwives from 12 villages, to explore their perceptions and experiences in delivering family planning services. the study was carried out in May-June 2013, as part of the baseline assessment in the Improving Contraceptive Method Mix (ICMM) study. We interviewed 12 village midwives working in 12 villages in six study districts: Tuban, Kediri, and Lumajang Districts in East Java Province; and Lombok Barat, Lombok Timur, and Sumbawa Districts in NTB Province. an interview guideline was used in all interviews. It covered several topics, such as community perceptions of LAPMs, availability of contraception and related equipment, availability of human resources, and midwives' efforts to improve LAPM coverage. All interviews were recorded and transcribed. Content and thematic analyses were carried out by grouping and coding the information based on the identified themes and topics. according to village midwives interviewed in this study, community-level acceptance of LAPMs has increased over time; however, some still prefer using short-acting methods for a long period. The reasons include lack of awareness about the benefits and side effects of LAPMs, fear of surgical procedures, rumored consequences (for example, that LAPMs would limit women's ability to perform hard physical labor), and religious beliefs. There were several challenges reported by village midwives in delivering LAPM services, such as confusion about midwives' eligibility to provide LAPM services, lack of Contraceptive Technology Update (CTU) and counseling trainings, and shortage of supporting equipment (such as exam tables and IUD and implant insertion kits). There were several strategies implemented by village midwives to improve LAPM use, including strengthening the counseling services, accompanying clients to higher health facilities to obtain LAPM services, and providing services for groups of clients. All village midwives emphasized the importance of strengthening collaboration among stakeholders to increase the uptake of LAPM services. as midwives are the main family planning providers in Indonesia, efforts to address their challenges is essential. Enabling a supportive policy environment, strengthening promotional activities, increasing the number of training programs designed for village midwives-in addition to enhancing inter-sectoral collaboration-are some recommendations to improve LAPM uptake in study areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spatial Modeling Tools for Cell Biology

DTIC Science & Technology

2006-10-01

multiphysics modeling expertise. A graphical user interface (GUI) for CoBi, JCoBi, was written in Java and interactive 3D graphics. CoBi has been...tools (C++ and Java ) to simulate complex cell and organ biology problems. CoBi has been designed to interact with the other Bio-SPICE software...fall of 2002. VisIt supports C++, Python and Java interfaces. The C++ and Java interfaces make it possible to provide alternate user interfaces for

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

DTIC Science & Technology

2008-03-01

Machine [29]. OC4J applications support Java Servlets , Web services, and the following J2EE specific standards: Extensible Markup Language (XML...IMAP Internet Message Access Protocol IP Internet Protocol IT Information Technology xviii J2EE Java Enterprise Environment JSR 168 Java ...LDAP), World Wide Web Distributed Authoring and Versioning (WebDav), Java Specification Request 168 (JSR 168), and Web Services for Remote

CPU Performance Counter-Based Problem Diagnosis for Software Systems

DTIC Science & Technology

2009-09-01

application servers and implementation techniques), this thesis only used the Enterprise Java Bean (EJB) SessionBean version of RUBiS. The PHP and Servlet ...collection statistics at the Java Virtual Machine (JVM) level can be reused for any Java application. Other examples of gray-box instrumentation include path...used gray-box approaches. For example, PinPoint [11, 14] and [29] use request tracing to diagnose Java exceptions, endless calls, and null calls in

Interactive Vulnerability Analysis Enhancement Results

DTIC Science & Technology

2012-12-01

from JavaEE web based applications to other non-web based Java programs. Technology developed in this effort should be generally applicable to other...Generating a rule is a 2 click process that requires no input from the user. • Task 3: Added support for non- Java EE applications Aspect’s...investigated a variety of Java -based technologies and how IAST can support them. We were successful in adding support for Scala, a popular new language, and

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.

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.

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.

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

Dr. George L. Mesina; Steven P. Miller

The XMGR5 graphing package [1] for drawing RELAP5 [2] plots is being re-written in Java [3]. Java is a robust programming language that is available at no cost for most computer platforms from Sun Microsystems, Inc. XMGR5 is an extension of an XY plotting tool called ACE/gr extended to plot data from several US Nuclear Regulatory Commission (NRC) applications. It is also the most popular graphing package worldwide for making RELAP5 plots. In Section 1, a short review of XMGR5 is given, followed by a brief overview of Java. In Section 2, shortcomings of both tkXMGR [4] and XMGR5 aremore » discussed and the value of converting to Java is given. Details of the conversion to Java are given in Section 3. The progress to date, some conclusions and future work are given in Section 4. Some screen shots of the Java version are shown.« less

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.

49 CFR 173.161 - Chemical kits and first aid kits.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Chemical kits and first aid kits. 173.161 Section... Class 7 § 173.161 Chemical kits and first aid kits. (a) Chemical kits and First aid kits must conform to... 10 kg. (b) Chemical kits and First aid kits are excepted from the specification packaging...

49 CFR 173.161 - Chemical kits and first aid kits.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 2 2012-10-01 2012-10-01 false Chemical kits and first aid kits. 173.161 Section... Class 7 § 173.161 Chemical kits and first aid kits. (a) Applicability. Chemical kits and first aid kits... assigned to the chemical kit and first aid kit as a whole must be the most stringent packing group assigned...

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

DTIC Science & Technology

2015-06-01

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

Practical Application of Model Checking in Software Verification

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Skakkebaek, Jens Ulrik

1999-01-01

This paper presents our experiences in applying the JAVA PATHFINDER (J(sub PF)), a recently developed JAVA to SPIN translator, in the finding of synchronization bugs in a Chinese Chess game server application written in JAVA. We give an overview of J(sub PF) and the subset of JAVA that it supports and describe the abstraction and verification of the game server. Finally, we analyze the results of the effort. We argue that abstraction by under-approximation is necessary for abstracting sufficiently smaller models for verification purposes; that user guidance is crucial for effective abstraction; and that current model checkers do not conveniently support the computational models of software in general and JAVA in particular.

Software Assurance Measurement -- State of the Practice

DTIC Science & Technology

2013-11-01

quality and productivity. 30+ languages, C/C++, Java , .NET, Oracle, PeopleSoft, SAP, Siebel, Spring, Struts, Hibernate , and all major databases. ChecKing...NET 39 ActionScript 39 Ada 40 C/C++ 40 Java 41 JavaScript 42 Objective-C 42 Opa 42 Packages 42 Perl 42 PHP 42 Python 42 Formal Methods...Suite—A tool for Ada, C, C++, C#, and Java code that comprises various analyses such as architecture checking, interface analyses, and clone detection

PSPVDC: An Adaptation of the PSP that Incorporates Verified Design by Contract

DTIC Science & Technology

2013-05-01

characteristics mentioned above, including the following: • Java Modeling Language (JML) implements DbC in Java . VDbC can then be carried out using tools like...Extended Static Checking (ESC/ Java ) [Cok 2005] or TACO [Galeotti 2010]. • Perfect Developer [Crocker 2003] is a specification and modeling language...These are written in the language employed in the environment (e.g., as Java Boolean expressions, if JML is used) which we call the carrier lan

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 ability to associate services with actions. Several Java technologies have been incorporated into JAS, including Swing, Internal Frames, Java Beans, XML, JavaScript, JavaHelp, and Jini. Additional information is contained in the original extended abstract.

'Sciencenet'--towards a global search and share engine for all scientific knowledge.

PubMed

Lütjohann, Dominic S; Shah, Asmi H; Christen, Michael P; Richter, Florian; Knese, Karsten; Liebel, Urban

2011-06-15

Modern biological experiments create vast amounts of data which are geographically distributed. These datasets consist of petabytes of raw data and billions of documents. Yet to the best of our knowledge, a search engine technology that searches and cross-links all different data types in life sciences does not exist. We have developed a prototype distributed scientific search engine technology, 'Sciencenet', which facilitates rapid searching over this large data space. By 'bringing the search engine to the data', we do not require server farms. This platform also allows users to contribute to the search index and publish their large-scale data to support e-Science. Furthermore, a community-driven method guarantees that only scientific content is crawled and presented. Our peer-to-peer approach is sufficiently scalable for the science web without performance or capacity tradeoff. The free to use search portal web page and the downloadable client are accessible at: http://sciencenet.kit.edu. The web portal for index administration is implemented in ASP.NET, the 'AskMe' experiment publisher is written in Python 2.7, and the backend 'YaCy' search engine is based on Java 1.6.

Iris: Constructing and Analyzing Spectral Energy Distributions with the Virtual Observatory

NASA Astrophysics Data System (ADS)

Laurino, O.; Budynkiewicz, J.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2014-05-01

We present Iris 2.0, the latest release of the Virtual Astronomical Observatory application for building and analyzing Spectral Energy Distributions (SEDs). With Iris, users may read in and display SEDs inspect and edit any selection of SED data, fit models to SEDs in arbitrary spectral ranges, and calculate confidence limits on best-fit parameters. SED data may be loaded into the application from VOTable and FITS files compliant with the International Virtual Observatoy Alliance interoperable data models, or retrieved directly from NED or the Italian Space Agency Science Data Center; data in non-standard formats may also be converted within the application. Users may seamlessy exchange data between Iris and other Virtual Observatoy tools using the Simple Application Messaging Protocol. Iris 2.0 also provides a tool for redshifting, interpolating, and measuring integratd fluxes, and allows simple aperture corrections for individual points and SED segments. Custom Python functions, template models and template libraries may be imported into Iris for fitting SEDs. Iris may be extended through Java plugins; users can install third-party packages, or develop their own plugin using Iris' Software Development Kit. Iris 2.0 is available for Linux and Mac OS X systems.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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.

MoCog1: A computer simulation of recognition-primed human decision making, considering emotions

NASA Technical Reports Server (NTRS)

Gevarter, William B.

1992-01-01

The successful results of the first stage of a research effort to develop a versatile computer model of motivated human cognitive behavior are reported. Most human decision making appears to be an experience-based, relatively straightforward, largely automatic response to situations, utilizing cues and opportunities perceived from the current environment. The development, considering emotions, of the architecture and computer program associated with such 'recognition-primed' decision-making is described. The resultant computer program (MoCog1) was successfully utilized as a vehicle to simulate earlier findings that relate how an individual's implicit theories orient the individual toward particular goals, with resultant cognitions, affects, and behavior in response to their environment.

MoCog1: A computer simulation of recognition-primed human decision making

NASA Technical Reports Server (NTRS)

Gevarter, William B.

1991-01-01

The results of the first stage of a research effort to develop a 'sophisticated' computer model of human cognitive behavior are described. Most human decision making is an experience-based, relatively straight-forward, largely automatic response to internal goals and drives, utilizing cues and opportunities perceived from the current environment. The development of the architecture and computer program (MoCog1) associated with such 'recognition-primed' decision making is discussed. The resultant computer program was successfully utilized as a vehicle to simulate earlier findings that relate how an individual's implicit theories orient the individual toward particular goals, with resultant cognitions, affects, and behavior in response to their environment.

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.

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)

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.

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.

Structural Technology Evaluation and Analysis Program (STEAP). Delivery Order 0035: Dynamics and Control and Computational Design of Flapping Wing Micro Air Vehicles

DTIC Science & Technology

2012-10-01

library as a principal Requestor. The M3CT requestor is written in Java , leveraging the cross platform deployment capabilities needed for a broadly...each application to the Java programming language, the independently generated sources are wrapped with JNA or Groovy. The Java wrapping process...unlimited. Figure 13. Leveraging Languages Once the underlying product is available to the Java source as a library, the application leverages

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.

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.

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

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.

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/.

Novel Advancements in Internet-Based Real Time Data Technologies

NASA Technical Reports Server (NTRS)

Myers, Gerry; Welch, Clara L. (Technical Monitor)

2002-01-01

AZ Technology has been working with MSFC Ground Systems Department to find ways to make it easier for remote experimenters (RPI's) to monitor their International Space Station (ISS) payloads in real-time from anywhere using standard/familiar devices. AZ Technology was awarded an SBIR Phase I grant to research the technologies behind and advancements of distributing live ISS data across the Internet. That research resulted in a product called "EZStream" which is in use on several ISS-related projects. Although the initial implementation is geared toward ISS, the architecture and lessons learned are applicable to other space-related programs. This paper presents the high-level architecture and components that make up EZStream. A combination of commercial-off-the-shelf (COTS) and custom components were used and their interaction will be discussed. The server is powered by Apache's Jakarta-Tomcat web server/servlet engine. User accounts are maintained in a My SQL database. Both Tomcat and MySQL are Open Source products. When used for ISS, EZStream pulls the live data directly from NASA's Telescience Resource Kit (TReK) API. TReK parses the ISS data stream into individual measurement parameters and performs on-the- fly engineering unit conversion and range checking before passing the data to EZStream for distribution. TReK is provided by NASA at no charge to ISS experimenters. By using a combination of well established Open Source, NASA-supplied. and AZ Technology-developed components, operations using EZStream are robust and economical. Security over the Internet is a major concern on most space programs. This paper describes how EZStream provides for secure connection to and transmission of space- related data over the public Internet. Display pages that show sensitive data can be placed under access control by EZStream. Users are required to login before being allowed to pull up those web pages. To enhance security, the EZStream client/server data transmissions can be encrypted to preclude interception. EZStream was developed to make use of a host of standard platforms and protocols. Each are discussed in detail in this paper. The I3ZStream server is written as Java Servlets. This allows different platforms (i.e. Windows, Unix, Linux . Mac) to host the server portion. The EZStream client component is written in two different flavors: JavaBean and ActiveX. The JavaBean component is used to develop Java Applet displays. The ActiveX component is used for developing ActiveX-based displays. Remote user devices will be covered including web browsers on PC#s and scaled-down displays for PDA's and smart cell phones. As mentioned. the interaction between EZStream (web/data server) and TReK (data source) will be covered as related to ISS. EZStream is being enhanced to receive and parse binary data stream directly. This makes EZStream beneficial to both the ISS International Partners and non-NASA applications (i.e. factory floor monitoring). The options for developing client-side display web pages will be addressed along with the development of tools to allow creation of display web pages by non-programmers.

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

Leveraging annotation-based modeling with Jump.

PubMed

Bergmayr, Alexander; Grossniklaus, Michael; Wimmer, Manuel; Kappel, Gerti

2018-01-01

The capability of UML profiles to serve as annotation mechanism has been recognized in both research and industry. Today's modeling tools offer profiles specific to platforms, such as Java, as they facilitate model-based engineering approaches. However, considering the large number of possible annotations in Java, manually developing the corresponding profiles would only be achievable by huge development and maintenance efforts. Thus, leveraging annotation-based modeling requires an automated approach capable of generating platform-specific profiles from Java libraries. To address this challenge, we present the fully automated transformation chain realized by Jump, thereby continuing existing mapping efforts between Java and UML by emphasizing on annotations and profiles. The evaluation of Jump shows that it scales for large Java libraries and generates profiles of equal or even improved quality compared to profiles currently used in practice. Furthermore, we demonstrate the practical value of Jump by contributing profiles that facilitate reverse engineering and forward engineering processes for the Java platform by applying it to a modernization scenario.

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.

A novel cryptochrome-dependent oscillator in Neurospora crassa.

PubMed

Nsa, Imade Y; Karunarathna, Nirmala; Liu, Xiaoguang; Huang, Howard; Boetteger, Brittni; Bell-Pedersen, Deborah

2015-01-01

Several lines of evidence suggest that the circadian clock is constructed of multiple molecular feedback oscillators that function to generate robust rhythms in organisms. However, while core oscillator mechanisms driving specific behaviors are well described in several model systems, the nature of other potential circadian oscillators is not understood. Using genetic approaches in the fungus Neurospora crassa, we uncovered an oscillator mechanism that drives rhythmic spore development in the absence of the well-characterized FRQ/WCC oscillator (FWO) and in constant light, conditions under which the FWO is not functional. While this novel oscillator does not require the FWO for activity, it does require the blue-light photoreceptor CRYPTOCHROME (CRY); thus, we call it the CRY-dependent oscillator (CDO). The CDO was uncovered in a strain carrying a mutation in cog-1 (cry-dependent oscillator gate-1), has a period of ∼1 day in constant light, and is temperature-compensated. In addition, cog-1 cells lacking the circadian blue-light photoreceptor WC-1 respond to blue light, suggesting that alternate light inputs function in cog-1 mutant cells. We show that the blue-light photoreceptors VIVID and CRY compensate for each other and for WC-1 in CRY-dependent oscillator light responses, but that WC-1 is necessary for circadian light entrainment. Copyright © 2015 by the Genetics Society of America.

A Novel Cryptochrome-Dependent Oscillator in Neurospora crassa

PubMed Central

Nsa, Imade Y.; Karunarathna, Nirmala; Liu, Xiaoguang; Huang, Howard; Boetteger, Brittni; Bell-Pedersen, Deborah

2015-01-01

Several lines of evidence suggest that the circadian clock is constructed of multiple molecular feedback oscillators that function to generate robust rhythms in organisms. However, while core oscillator mechanisms driving specific behaviors are well described in several model systems, the nature of other potential circadian oscillators is not understood. Using genetic approaches in the fungus Neurospora crassa, we uncovered an oscillator mechanism that drives rhythmic spore development in the absence of the well-characterized FRQ/WCC oscillator (FWO) and in constant light, conditions under which the FWO is not functional. While this novel oscillator does not require the FWO for activity, it does require the blue-light photoreceptor CRYPTOCHROME (CRY); thus, we call it the CRY-dependent oscillator (CDO). The CDO was uncovered in a strain carrying a mutation in cog-1 (cry-dependent oscillator gate-1), has a period of ∼1 day in constant light, and is temperature-compensated. In addition, cog-1 cells lacking the circadian blue-light photoreceptor WC-1 respond to blue light, suggesting that alternate light inputs function in cog-1 mutant cells. We show that the blue-light photoreceptors VIVID and CRY compensate for each other and for WC-1 in CRY-dependent oscillator light responses, but that WC-1 is necessary for circadian light entrainment. PMID:25361899

Cephalometric norms for orthognathic surgery for North India (Eastern Uttar Pradesh).

PubMed

Gulati, Rajeev; Jain, Shikha

2011-01-01

The present study was aimed at development of the cephalometric norms for orthognathic surgery for the population of eastern Uttar Pradesh in North India. This study was conducted at a dental college. The study sample consisted of 50 males and 50 females. Each lateral cephalogram was taken in occlusion and subsequently traced. All reference points, landmarks, and measurements were made according to cephalometrics for orthognathic surgery (COGS) system. The statistical analysis involved calculation of mean and standard deviation for each of the 23 parameters assessed for each subject. The data was subsequently compared with COGS study by using Normal (Z) test. The norms were derived for the purvanchal population of North India and these were found to be quite distinct compared to those obtained from COGS study with respect to specific parameters. Male subjects indicated greater prominence of chin relative to the face, decreased posterior divergence, infraeruption of upper and lower molar as well as lower incisors, decreased total effective length of the maxilla, tendency towards Class III occlusion, and procumbent lower incisors. Female subjects, however, indicated increased anterior cranial base length, greater prominence of chin relative to the face, prognathic maxilla and mandible, increased middle third facial height, infraerupted lower incisors, increased mandibular body length, and procumbent lower incisors.

Executive function impairment in community elderly subjects with questionable dementia.

PubMed

Lam, Linda C W; Lui, Victor W C; Chiu, Helen F K; Chan, Sandra S M; Tam, Cindy W C

2005-01-01

The neurocognitive profile of community-dwelling Chinese subjects with 'questionable' dementia was studied. One hundred and fifty-four ambulatory Chinese subjects were recruited from local social centers for the elderly. Each subject was examined using the Clinical Dementia Rating (CDR), the Cantonese version of the Mini-Mental State Examination (CMMSE), the Chinese version of the Alzheimer's Disease Assessment Scale-Cognitive Subscale (ADAS-Cog), the Category Verbal Fluency Test (CVFT), digit and visual span tests, and the Cambridge Neurological Inventory. The neurocognitive profile of nondemented subjects (CDR 0) was compared with that of subjects with 'questionable' dementia (CDR 0.5). Subjects with 'questionable' dementia were older, and had lower educational levels and global cognitive assessment scores than the controls (CMMSE and ADAS-Cog; t tests, p < 0.001). In addition, they also had significantly lower scores in delayed recall, reverse span, verbal fluency tests and worse performance in complex motor tasks related to executive function (Mann-Whitney tests, p < 0.001). Logistic regression analysis revealed that ADAS-Cog, CVFT, and reverse visual span were significant predictors for the CDR of 'questionable' dementia. Aside from memory impairment, executive function deficits were also present in subjects with 'questionable' dementia. To identify groups cognitively at risk for dementia, concomitant assessments of memory and executive function are suggested.

Effects of general principles of person transfer techniques on low back joint extension moment.

PubMed

Katsuhira, Junji; Yamasaki, Syun; Yamamoto, Sumiko; Maruyama, Hitoshi

2010-01-01

The purpose of this study was to examine the effects of general principles of person transfer techniques specifically on the low back joint extension moment. These effects were examined by the following measurable quantitative parameters: 1) trunk bending angle, 2) knee flexion angle, 3) distance between the centers of gravity (COGs) of the caregiver and patient, representing the distance between the caregiver and patient, and 4) the vertical component of the ground reaction force representing the amount of the weight-bearing load on the caregiver's low back during transfers with and without assistive devices. Twenty students each took the role of caregiver, and one healthy adult simulated a patient. The participants performed three different transfer tasks: without any assistive device, with the patient wearing a low back belt, and with the caregiver using a transfer board. We found that the distance between the COGs and the vertical component of the ground reaction force, but not the trunk bending and knee flexion angles, were the variables that affected the low back joint extension moment. Our results suggest that the general principle of decreasing the distance between COGs is most effective for decreasing the low back joint extension moment during transfers under all conditions.

Gaze and viewing angle influence visual stabilization of upright posture

PubMed Central

Ustinova, KI; Perkins, J

2011-01-01

Focusing gaze on a target helps stabilize upright posture. We investigated how this visual stabilization can be affected by observing a target presented under different gaze and viewing angles. In a series of 10-second trials, participants (N = 20, 29.3 ± 9 years of age) stood on a force plate and fixed their gaze on a figure presented on a screen at a distance of 1 m. The figure changed position (gaze angle: eye level (0°), 25° up or down), vertical body orientation (viewing angle: at eye level but rotated 25° as if leaning toward or away from the participant), or both (gaze and viewing angle: 25° up or down with the rotation equivalent of a natural visual perspective). Amplitude of participants’ sagittal displacement, surface area, and angular position of the center of gravity (COG) were compared. Results showed decreased COG velocity and amplitude for up and down gaze angles. Changes in viewing angles resulted in altered body alignment and increased amplitude of COG displacement. No significant changes in postural stability were observed when both gaze and viewing angles were altered. Results suggest that both the gaze angle and viewing perspective may be essential variables of the visuomotor system modulating postural responses. PMID:22398978

Castor oil for induction of labour: a retrospective study.

PubMed

Neri, Isabella; Dante, Giulia; Pignatti, Lucrezia; Salvioli, Chiara; Facchinetti, Fabio

2018-08-01

The aim of this study is to investigate the safety and efficacy of castor oil to induce labour. A retrospective observational case control study was conducted over five years. Castor oil was proposed to women referred to the Birth Centre (Castor Oil group (COG)). They were compared to women who chose to be followed by the traditional doctor-led unit (control group (CG)). Castor oil was administered in a 60 ml single dose in 200 ml of warm water. Inclusion criteria were gestational age between 40 and 41 weeks plus premature rupture of membranes between 12 and 18 hours or amniotic fluid index ≤4 or Bishop Score of ≤4 or absence of spontaneous labour over 41 + 4 weeks. Pharmacological induction of labour was required for 18 women in the COG (45%) and 36 in the CG (90%) (p < .001). The mode of delivery differed significantly between groups: women assuming castor oil showed a higher incidence of vaginal delivery, whereas the incidence of caesarean section was lower in the COG, but no statistical significance was reached. The use of castor oil is related to a higher probability of labour initiation within 24 hours. Castor oil can be considered a safe non-pharmacological method for labour induction.

The effect of shoe type on static and dynamic balance during treadmill walking in young healthy women.

PubMed

Kim, Mi-Kyoung; Kong, Byung-Sun; Yoo, Kyung-Tae

2017-09-01

[Purpose] The purpose of this study was to analyze the effect of various shoes on the static and dynamic balance of young women in their 20s. [Subjects and Methods] The subjects of the study were 15 healthy young women and repeated measured design. The subjects walked on the treadmill at a speed of 4 km/h for 30 minutes wearing three types of shoes: sneaker, rain boots, and combat boots. Balance was measured by a Romberg test and a limits of stability test. One-way ANOVA was used for statistical analysis. [Results] As the results of the Romberg test, the main effect of time was shown in the EO-COG area, EO-COG length, and EO-COG velocity. As the results of the limits of stability test, the main effects of time in LT, RT, FW, and total. There were significant differences in the LT in the sneaker group, the rain boots group, and the LT and RT in the combat boots group between the pre- and post-test. [Conclusion] The characteristics of shoes such as the materials, hardness, and thickness of the soles, the coefficient of friction of the outsoles, and the collar height affected the static and dynamic balance.

The effect of shoe type on static and dynamic balance during treadmill walking in young healthy women

PubMed Central

Kim, Mi-Kyoung; Kong, Byung-Sun; Yoo, Kyung-Tae

2017-01-01

[Purpose] The purpose of this study was to analyze the effect of various shoes on the static and dynamic balance of young women in their 20s. [Subjects and Methods] The subjects of the study were 15 healthy young women and repeated measured design. The subjects walked on the treadmill at a speed of 4 km/h for 30 minutes wearing three types of shoes: sneaker, rain boots, and combat boots. Balance was measured by a Romberg test and a limits of stability test. One-way ANOVA was used for statistical analysis. [Results] As the results of the Romberg test, the main effect of time was shown in the EO-COG area, EO-COG length, and EO-COG velocity. As the results of the limits of stability test, the main effects of time in LT, RT, FW, and total. There were significant differences in the LT in the sneaker group, the rain boots group, and the LT and RT in the combat boots group between the pre- and post-test. [Conclusion] The characteristics of shoes such as the materials, hardness, and thickness of the soles, the coefficient of friction of the outsoles, and the collar height affected the static and dynamic balance. PMID:28932007

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.

Motor cortex evaluation by nTMS after surgery of central region tumors: a feasibility study.

PubMed

Forster, Marie-Thérèse; Senft, Christian; Hattingen, Elke; Lorei, Mario; Seifert, Volker; Szelényi, Andrea

2012-08-01

Largely discussed during the past decade, motor cortex reorganization in brain tumor surgery has been investigated only by few studies. We therefore aimed to investigate cortical motor representation after resection of perirolandic WHO grade II and III gliomas using navigated transcranial magnetic stimulation (nTMS). Five patients were examined before neurosurgery and after a follow-up period of 17.7 ± 6.8 months. As a control, five healthy age-matched subjects were equally studied by nTMS in two sessions spaced 12.6 (range 2-35) days apart. Resting motor thresholds (RMT), hotspots and centers of gravity (CoG) were identified for the first dorsal interosseous (FDI), abductor pollicis brevis (APB), extensor digitorum (EXT), tibialis anterior (TA) and abductor hallucis (AH) muscles. Euclidian distances, coefficients of variance and intraclass correlation coefficients (ICC) were calculated. Healthy subjects showed moderate to excellent reliability measurement of RMT (ICC = 0.69-0.94). Average displacement of CoGs across sessions was 0.68 ± 0.34 cm in the dominant and 0.76 ± 0.38 cm in the non-dominant hemisphere; hotspots moved 0.87 ± 0.51 cm and 0.83 ± 0.45 cm, respectively. In one patient these parameters differed significantly from the control group (p < 0.05 for both CoGs and hotspots). Overall, all patients' CoGs moved 1.12 ± 0.93 cm, and hotspots were 1.06 ± 0.7 cm apart. In both patients and healthy subjects, movement of assessed parameters was more important along the X- than the Y-axis. nTMS allows evaluating cortical reorganization after brain tumor surgery. It may contribute to the understanding of neurofunctional dynamics, thus influencing therapeutic strategy.

Cognitive complaints and predictors of perceived cognitive dysfunction in adults with major depressive disorder: Findings from the Cognitive Dysfunction in Asians with Depression (CogDAD) study.

PubMed

Srisurapanont, Manit; Mok, Yee Ming; Yang, Yen Kuang; Chan, Herng-Nieng; Della, Constantine D; Zainal, Nor Zuraida; Jambunathan, Stephen; Amir, Nurmiati; Kalita, Pranab

2018-05-01

Several studies have described the presence of perceived cognitive dysfunction amongst Asian patients with major depressive disorder (MDD). To date, no study has been conducted investigating the predictors of perceived cognitive dysfunction amongst Asian MDD patients. This was a post-hoc analysis of the Cognitive Dysfunction in Asian patients with Depression (CogDAD) study. Descriptive statistics were used to describe the most common cognitive complaints by patients. Univariate and multivariate analyses were performed to determine variables associated with perceived cognitive dysfunction (Perceived Deficit Questionnaire-Depression, PDQ-D). The CogDAD study population is comprised of MDD patients with mild-to-moderate depression (Patient Health Questionnaire 9-item [PHQ-9]: 11.3 ± 6.9) who reported perceived cognitive dysfunction (PDQ-D = 22.6 ± 16.2). The most common cognitive complaints were: mind drifting (42.3%), trouble making decision (39.6%) and trouble concentrating (38.0%). Predictors of perceived cognitive dysfunction were: being Southeast Asians (vs. Taiwanese) (p < 0.001), current episode longer than 8 weeks (vs. 1-8 weeks) (p < 0.05), the presence of disability (vs. no disability) (p < 0.05), younger age (p < 0.01), and higher PHQ-9 total scores (p < 0.001). The causal relationship between predictive variables and PDQ-D could not be tested due to the cross-sectional nature of the study. Furthermore, a neuropsychological test was not included in the CogDAD study and use of concomitant medications, including anti-depressants, could have impacted patient's perceived cognitive ability. The present study results suggest a potential role for subjective cognitive assessment in patients with MDD who are young, with long durations of depression or severe depression. Copyright © 2018 Elsevier B.V. All rights reserved.

Executive cognitive tests for the evaluation of patients with Parkinson’s disease

PubMed Central

Sobreira, Emmanuelle Silva Tavares; Pena, Marina Ceres Silva; Silva Filho, José Humberto; Souza, Carolina Pinto; Oliveira, Guiomar Nascimento; Tumas, Vitor; do Vale, Francisco de Assis Carvalho

2008-01-01

Parkinson’s disease (PD) is characterized by changes in movement, which are later followed by cognitive, behavioral and psychological changes. The objective of the present study was to correlate different tests used to examine executive functions in PD patients followed at a specialized outpatient clinic. Methods Thirty-five patients with idiopathic PD aged 63.0 years on average and with mean schooling of 5.5±4.2 years, were examined using the following tests: Mattis Dementia Rating Scale (MDRS), Scales for Outcomes of Parkinson’s Disease-Cognition (SCOPA-COG), Wisconsin Card Sorting Test (WCST), Frontal Assessment Battery (FAB), Digit Span – Inverse Order (IO) (a subtest of the WAIS III) and Verbal Fluency Test (category animals). Results Significant correlations were detected between FAB and MDRS Conceptualization (0.814), MDRS Initiation/Perseveration (I/P) and SCOPA-COG Executive Function (0.643), FAB and MDRS I/P (0.601), FAB and Verbal Fluency (0.602), MDRS I/P and MDRS Conceptualization (0.558), Verbal Fluency and MDRS I/P (0.529), MDRS Attention and SCOPA-COG Executive Function (0.495), MDRS Conceptualization and SCOPA-COG Executive Function (0.520), FAB and Digit Span (OI) (0.503), Verbal Fluency and MDRS Conceptualization (0.501), and WCST perseverative errors and FAB (–0.379), WCST perseverative errors and MDRS Conceptualization (0.445), WCST perseverative errors and MDRS I/P (–0.407) and WCST categories completed and MDRS Conceptualization (0.382). Discussion The results demonstrated strong correlations between most of the tests applied, but no associations were detected between the WCST and the other tests, a fact that may be explained by the heterogeneity of scores obtained in the tests by the patients evaluated. A difficulty of the present study was the lack of a control groups for the establishment of adequate standards for this population. PMID:29213572

To what degree does cognitive impairment in Alzheimer's disease predict dependence of patients on caregivers?

PubMed Central

Caro, Jaime; Ward, Alexandra; Ishak, Khajak; Migliaccio-Walle, Kristen; Getsios, Denis; Papadopoulos, George; Torfs, Koen

2002-01-01

Background Patients with Alzheimer's disease experience a progressive loss of cognitive function, and the ability to independently perform activities of daily life. Sometimes a dependent stage is reached quite early in the disease, when caregivers decide that the patients can no longer be left alone safely. This is an important aspect of Alzheimer's for patients, their families, and also health care providers. Understanding the relationship between a patient's current cognitive status and their need for care may assist clinicians when recommending an appropriate management plan. In this study, we investigated the relationship of cognitive function to dependence on caregivers before the patients reach a severe stage of the disease. Methods Data were obtained on 1,289 patients with mild-to-moderate Alzheimer's disease studied in two randomised clinical trials of galantamine (Reminyl®). Cognition was assessed using the cognitive part of the Alzheimer's Disease Assessment Scale (ADAS-cog) and Mini-Mental State Examination (MMSE). Patients were considered dependent if they required >12 hours of supervision each day or had high care needs. The Disability Assessment for Dementia (DAD) scale was also used as a measure of dependence. Disability was predicted directly using MMSE and ADAS-cog and compared to predictions from converted scores. Results The odds ratio of dependence was significantly higher amongst the patients with worse cognitive impairment, adjusting for age, gender and antipsychotic medication use. For example, a 4-point difference in ADAS-cog score was associated with an increase of 17% (95% CI 11–23) in the adjusted odds for >12 hours of supervision, and of 35% (95% CI 28–43) for dependence. Disability predicted directly using actual ADAS-cog and scores converted from MMSE values had close agreement using the models developed. Conclusion In patients with mild-to-moderate Alzheimer's disease, even relatively small degrees of poorer cognitive function increased the risk of losing the ability to live independently. PMID:12184819

Are automatic postural responses in patients with Parkinson's disease abnormal due to their stooped posture?

PubMed

Bloem, B R; Beckley, D J; van Dijk, J G

1999-02-01

Abnormal automatic postural responses are thought to contribute to balance impairment in Parkinson's disease. However, because postural responses are modifiable by stance, we have speculated that some postural abnormalities in patients with Parkinson's disease are secondary to their stooped stance. We have studied this assumption by assessing automatic postural responses in 30 healthy subjects who were instructed either to stand upright or to assume a typical parkinsonian posture. During both conditions, subjects received 20 serial 4 degrees 'toe-up' rotational perturbations from a supporting forceplate. We recorded short-latency (SL) and medium-latency (ML) responses from stretched gastrocnemius muscles and long-latency (LL) responses from shortened tibialis anterior muscles. We also assessed changes in the center of foot pressure (CFP) and the center of gravity (COG). The results were qualitatively compared to a previously described group of patients with Parkinson's disease who, under these circumstances, typically have large ML responses, small LL responses and insufficient voluntary postural corrections, accompanied by a slow rate of backward CFP displacement and an increased posterior COG displacement. The stooped posture resulted in unloading of medial gastrocnemius muscles and loading of tibialis anterior muscles. Onset latencies of stretch responses in gastrocnemius muscles were delayed in stooped subjects, but the onset of LL responses was markedly reduced. Amplitudes of both ML and LL responses were reduced in stooped subjects. Prestimulus COG and, to a lesser extent, CFP were shifted forwards in stooped subjects. Posterior COG displacement and the rate of backward CFP displacement were diminished in stooped subjects. Voluntary postural corrections were unchanged while standing stooped. These results indicate that some postural abnormalities of patients with Parkinson's disease (most notably the reduced LL responses) can be reproduced in healthy subjects mimicking a stooped parkinsonian posture. Other postural abnormalities (most notably the increased ML responses and insufficient voluntary responses) did not appear in stooped controls and may contribute to balance impairment in Parkinson's disease.

Impact of Androgen Deprivation Therapy on Self-Reported Cognitive Function in Men with Prostate Cancer.

PubMed

Marzouk, Shireen; Naglie, Gary; Tomlinson, George; Duff Canning, Sarah; Breunis, Henriette; Timilshina, Narhari; Alibhai, Shabbir M H

2018-03-01

Although androgen deprivation therapy is widely used to treat prostate cancer, its effects on cognitive function are unclear. To our knowledge no prior report has examined the impact of androgen deprivation therapy on self-reported cognitive function. Three groups of men 50 years old or older who were matched on age and education were enrolled in the study, including 81 with prostate cancer starting on continuous androgen deprivation therapy, 84 controls with prostate cancer not receiving androgen deprivation therapy and 85 healthy controls. Two scales from the FACT-Cog (Functional Assessment of Cancer Therapy-Cognitive subscale) version 3 were used to assess self-reported cognitive function. Changes in cognitive scores with time were analyzed by 2 approaches, including 1) multivariable regression and 2) calculation of the proportion of subjects per group with a decrease of 1 SD or more. Multivariable regression was applied to assess predictors of a decline in self-reported cognitive function. We also examined relationships between the FACT-Cog and a neuropsychological battery of 15 tests. Mean participant age was 69 years (range 50 to 87). The mean educational level was 15 years (range 8 to 24). FACT-Cog scores were similar at baseline across the cohorts. Neither analytical approach revealed that androgen deprivation therapy was associated with changes in self-reported cognitive function on either FACT-Cog scale. Mood and fatigue correlated with changes in self-reported cognitive function. The relationship between self-reported and objective cognitive measures was weak (maximum Spearman correlation coefficient 0.14) and only 2 of 30 correlations were statistically significant. A total of 12 months of androgen deprivation therapy were not associated with self-reported cognitive function changes in older men with nonmetastatic prostate cancer. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Comparison of pathway and center of gravity of the calcaneus on non-involved and involved sides according to eccentric and concentric strengthening in patients with achilles tendinopathy.

PubMed

Yu, Jaeho; Lee, Gyuchang

2012-01-01

This study compares the changes in pathway and center of gravity (COG) on the calcaneus of non-involved and involved sides according to eccentric and concentric strengthening in patients with unilateral Achilles tendinopathy. The goal was to define the biomechanical changes according to eccentric strengthening for the development of clinical guidelines. Eighteen patients with Achilles tendinopathy were recruited at the K Rehabilitation Hospital in Seoul. The subjects were instructed to perform 5 sessions of concentric strengthening. The calcaneal pathway was measured using a three-dimensional (3D) motion analyzer, and COG was measured by a force plate. Subsequently, eccentric strengthening was implemented, and identical variables were measured. Concentric and eccentric strengthening was carried out on both the involved and non-involved sides. There was no significant difference in the calcaneal pathway in patients with Achilles tendinopathy during concentric and eccentric strengthening. However, during eccentric strengthening, the calcaneal pathway significantly increased on the involved side compared to the non-involved side for all variables excluding the z-axis. COG significantly decreased on the involved side when compared to the non-involved side in patients with Achilles tendinopathy during eccentric and concentric strengthening. During concentric strengthening, all variables of the COG significantly increased on the involved side compared to the non-involved side. Compared with eccentric strengthening, concentric strengthening decreased the stability of ankle joints and increased the movement distance of the calcaneus in patients with Achilles tendinopathy. Furthermore, eccentric strengthening was verified to be an effective exercise method for prevention of Achilles tendinopathy through the reduction of forward and backward path length of foot pressure. The regular application of eccentric strengthening was found to be effective in the secondary prevention of Achilles tendinopathy in a clinical setting.

Cognitive versus Software-Assisted Registration: Development of a New Nomogram Predicting Prostate Cancer at MRI-Targeted Biopsies.

PubMed

Kaufmann, Sascha; Russo, Giorgio I; Thaiss, Wolfgang; Notohamiprodjo, Mike; Bamberg, Fabian; Bedke, Jens; Morgia, Giuseppe; Nikolaou, Konstantin; Stenzl, Arnulf; Kruck, Stephan

2018-04-03

Multiparametric magnetic resonance imaging (mpMRI) is gaining acceptance to guide targeted biopsy (TB) in prostate cancer (PC) diagnosis. We aimed to compare the detection rate of software-assisted fusion TB (SA-TB) versus cognitive fusion TB (COG-TB) for PC and to evaluate potential clinical features in detecting PC and clinically significant PC (csPC) at TB. This was a retrospective cohort study of patients with rising and/or persistently elevated prostate-specific antigen (PSA) undergoing mpMRI followed by either transperineal SA-TB or transrectal COG-TB. The analysis showed a matched-paired analysis between SA-TB versus COG-TB without differences in clinical or radiological characteristics. Differences among detection of PC/csPC among groups were analyzed. A multivariable logistic regression model predicting PC at TB was fitted. The model was evaluated using the receiver operating characteristic-derived area under the curve, goodness of fit test, and decision-curve analyses. One hundred ninety-one and 87 patients underwent SA-TB or COG-TB, respectively. The multivariate logistic analysis showed that SA-TB was associated with overall PC (odds ratio [OR], 5.70; P < .01) and PC at TB (OR, 3.00; P < .01) but not with overall csPC (P = .40) and csPC at TB (P = .40). A nomogram predicting PC at TB was constructed using the Prostate Imaging Reporting and Data System version 2.0, age, PSA density and biopsy technique, showing improved clinical risk prediction against a threshold probability of 10% with a c-index of 0.83. In patients with suspected PC, software-assisted biopsy detects most cancers and outperforms the cognitive approach in targeting magnetic resonance imaging-visible lesions. Furthermore, we introduced a prebiopsy nomogram for the probability of PC in TB. Copyright © 2018 Elsevier Inc. All rights reserved.

Cogs in the endless machine: lakes, climate change and nutrient cycles: a review.

PubMed

Moss, Brian

2012-09-15

Lakes have, rather grandly, been described as sentinels, integrators and regulators of climate change (Williamson et al., Limnol. Oceanogr. 2009; 54: 2273-82). Lakes are also part of the continuum of the water cycle, cogs in a machine that processes water and elements dissolved and suspended in myriad forms. Assessing the changes in the functioning of the cogs and the machine with respect to these substances as climate changes is clearly important, but difficult. Many other human-induced influences, not least eutrophication, that impact on catchment areas and consequently on lakes, have generally complicated the recording of recent change in sediment records and modern sets of data. The least confounded evidence comes from remote lakes in mountain and polar regions and suggests effects of warming that include mobilisation of ions and increased amounts of phosphorus. A cottage industry has arisen in deduction and prediction of the future effects of climate change on lakes, but the results are very general and precision is marred not only by confounding influences but by the complexity of the lake system and the infinite variety of possible future scenarios. A common conclusion, however, is that warming will increase the intensity of symptoms of eutrophication. Direct experimentation, though expensive and still unusual and confined to shallow lake and wetland systems is perhaps the most reliable approach. Results suggest increased symptoms of eutrophication, and changes in ecosystem structure, but in some respects are different from those deduced from comparisons along latitudinal gradients or by inference from knowledge of lake behaviour. Experiments have shown marked increases in community respiration compared with gross photosynthesis in mesocosm systems and it may be that the most significant churnings of these cogs in the earth-air-water machine will be in their influence on the carbon cycle, with possibly large positive feedback effects on warming. Copyright © 2011 Elsevier B.V. All rights reserved.

Alterations in blood pressure, antioxidant status and caspase 8 expression in cobalt chloride-induced cardio-renal dysfunction are reversed by Ocimum gratissimum and gallic acid in Wistar rats.

PubMed

Akinrinde, A S; Oyagbemi, A A; Omobowale, T O; Asenuga, E R; Ajibade, T O

2016-07-01

The protective abilities of the chloroform extract of Ocimum gratissimum (COG) and gallic acid against cobalt chloride (CoCl2) - induced cardiac and renal toxicity were evaluated. Rats were exposed to CoCl2 (350ppm) for 7 days, either alone, or in combination with COG (100 and 200mg/kg) or gallic acid (120mg/kg). CoCl2 given alone, caused significant increases (p<0.05) in oxidative stress parameters (hydrogen peroxide, H2O2 and malondialdehyde, MDA) and increased expression of the apoptotic initiator caspase 8 in the heart and kidneys. There was significant reduction (p<0.05) in reduced glutathione (GSH) in cardiac and renal tissues; reduction in superoxide dismutase (SOD) activity in the kidneys and adaptive increases in Glutathione S-transferase (GST) and catalase (CAT). CoCl2 also produced significant reduction (p<0.05) in systolic (SBP), diastolic (DBP) and mean arterial (MAP) blood pressures. Oral COG and gallic acid treatment significantly reduced (p<0.05) the levels of H2O2 and MDA; with reduced expression of caspase 8 and restoration of GSH levels, GPx, SOD and CAT activities, howbeit, to varying degrees in the heart and kidneys. COG (200mg/kg) was most effective in restoring the blood pressures in the rats to near control levels. CoCl2-induced histopathological lesions including myocardial infarction and inflammation and renal tubular necrosis and inflammation were effectively ameliorated by the treatments administered. This study provides evidence for the protective roles of O. gratissimum and gallic acid by modulation of CoCl2-induced alterations in blood pressure, antioxidant status and pro-apoptotic caspase 8 in Wistar rats. Copyright © 2016 Elsevier GmbH. All rights reserved.

Clinical trial of an inhibitor of RAGE-Aβ interactions in Alzheimer disease.

PubMed

Galasko, Douglas; Bell, Joanne; Mancuso, Jessica Y; Kupiec, James W; Sabbagh, Marwan N; van Dyck, Christopher; Thomas, Ronald G; Aisen, Paul S

2014-04-29

To examine safety, tolerability, and efficacy of PF-04494700, an inhibitor of the receptor for advanced glycation end products (RAGE), in mild to moderate Alzheimer disease (AD). Double-blind, placebo-controlled trial at 40 academic centers (United States). Subjects with AD and Mini-Mental State Examination score 14-26 were randomized to PF-04494700 60 mg/day × 6 days, then 20 mg daily (high dose); 15 mg/day × 6 days, then 5 mg daily (low dose); or placebo, for 18 months. Clinical and laboratory measures were used to evaluate safety and tolerability. The primary efficacy measure was the Alzheimer's Disease Assessment Scale-cognitive (ADAS-cog). Secondary measures assessed clinical stage, function, behavior, MRI, and CSF biomarkers. A total of 399 subjects were randomized. In a prespecified interim analysis, when 50% of subjects had completed the 6-month visit, the high dose was associated with confusion, falls, and greater ADAS-cog decline and was discontinued. A second prespecified analysis compared low-dose and placebo groups for futility and safety approximately 12 months after all subjects were randomized. This analysis met criteria for futility, and treatment was discontinued. There were no safety concerns in the low-dose group. Analyses including post-futility data showed decreased decline on the ADAS-cog in the low-dose group at month 18. Other clinical and biomarker measures showed no differences between low-dose treatment and placebo. PF-04494700 at 20 mg/d was associated with increased adverse events and cognitive decline. At 5 mg/d, PF-04494700 had a good safety profile. A potential benefit for this low dose on the ADAS-cog is not conclusive, because of high dropout and discontinuation rates subsequent to the interim analyses. This study provides Class I evidence that in patients with AD high-dose PF-04494700 increased cognitive decline at 6 months and Class IV evidence that low-dose PF-04494700 slowed cognitive decline at 18 months.

A Comparative Evaluation of Normal Tissue Doses for Patients Receiving Radiation Therapy for Hodgkin Lymphoma on the Childhood Cancer Survivor Study and Recent Children's Oncology Group Trials

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

Zhou, Rachel; Ng, Angela; Constine, Louis S.

Purpose: Survivors of pediatric Hodgkin lymphoma (HL) are recognized to have an increased risk of delayed adverse health outcomes related to radiation therapy (RT). However, the necessary latency required to observe these late effects means that the estimated risks apply to outdated treatments. We sought to compare the normal tissue dose received by children treated for HL and enrolled in the Childhood Cancer Survivor Study (CCSS) (diagnosed 1970-1986) with that of patients treated in recent Children's Oncology Group (COG) trials (enrolled 2002-2012). Methods and Materials: RT planning data were obtained for 50 HL survivors randomly sampled from the CCSS cohortmore » and applied to computed tomography planning data sets to reconstruct the normal tissue dosimetry. For comparison, the normal tissue dosimetry data were obtained for all 191 patients with full computed tomography–based volumetric RT planning on COG protocols AHOD0031 and AHOD0831. Results: For early-stage patients, the mean female breast dose in the COG patients was on average 83.5% lower than that for CCSS patients, with an absolute reduction of 15.5 Gy. For advanced-stage patients, the mean breast dose was decreased on average by 70% (11.6 Gy average absolute dose reduction). The mean heart dose decreased on average by 22.9 Gy (68.6%) and 17.6 Gy (56.8%) for early- and advanced-stage patients, respectively. All dose comparisons for breast, heart, lung, and thyroid were significantly lower for patients in the COG trials than for the CCSS participants. Reductions in the prescribed dose were a major contributor to these dose reductions. Conclusions: These are the first data quantifying the significant reduction in the normal tissue dose using actual, rather than hypothetical, treatment plans for children with HL. These findings provide useful information when counseling families regarding the risks of contemporary RT.« less

Cognitive Assessment of Patients With Alzheimer's Disease by Telemedicine: Pilot Study

PubMed Central

Carotenuto, Anna; Rea, Raffaele; Ricci, Giovanna; Fasanaro, Angiola Maria; Amenta, Francesco

2018-01-01

Background Approximately 46.8 million people are living with dementia worldwide and their number will grow in the next years. Any potential treatment should be administered as early as possible because it is important to provide an early cognitive assessment and to regularly monitor the mental function of patients. Information and communication technologies can be helpful to reach and follow patients without displacing them, but there may be doubts about the reliability of cognitive tests performed by telemedicine. Objective The purpose of this study was to evaluate the reliability of the Mini Mental State Examination (MMSE) and the Alzheimer’s Disease Assessment Scale cognitive subscale (ADAS-cog) tests administered in hospital by videoconference to patients with mild to moderate Alzheimer's disease. Methods The tests were administered to 28 Alzheimer's disease outpatients (8 male, mean age 73.88, SD 7.45 years; 20 female mean age 76.00, SD 5.40 years) recruited and followed in the Alzheimer’s Unit of the A Cardarelli National Hospital (Naples, Italy) at baseline and after 6, 12, 18, and 24 months of observation. Patients were evaluated first face-to-face by a psychologist and then, after 2 weeks, by another psychologist via videoconference in hospital. Results This study showed no differences in the MMSE and ADAS-cog scores when the tests were administered face-to-face or by videoconference, except in patients with more pronounced cognitive deficits (MMSE<17), in which the assessment via videoconference overestimated the cognitive impairment (face to face, MMSE mean 13.9, SD 4.9 and ADAS-cog mean 9.0, SD 3.8; videoconference, MMSE mean 42.8, SD 12.5 and ADAS-cog mean 56.9, SD 5.5). Conclusions We found that videoconferencing is a reliable approach to document cognitive stability or decline, and to measure treatment effects in patients with mild to moderate dementia. A more extended study is needed to confirm these results. PMID:29752254

Transfer of adapted water supply technologies through a demonstration and teaching facility

NASA Astrophysics Data System (ADS)

Nestmann, F.; Oberle, P.; Ikhwan, M.; Stoffel, D.; Blaß, H. J.; Töws, D.; Schmidt, S.

2016-09-01

Water scarcity can be defined as a lack of sufficient water resources or as the limited or even missing access to a safe water supply. Latter can be classified as `economic water scarcity' which among others can commonly be met in tropical and subtropical karst regions of emerging and developing countries. Karst aquifers, mostly consisting of limestone and carbonate rock, show high infiltration rates which leads to a lack of above ground storage possibilities. Thus, the water will drain rapidly into the underground and evolve vast river networks. Considering the lack of appropriate infrastructure and limited human capacities in the affected areas, these underground water resources cannot be exploited adequately. Against this, background innovative and adapted technologies are required to utilize hard-to-access water resources in a sustainable way. In this context, the German-Indonesian joint R&D project "Integrated Water Resources Management (IWRM) Indonesia" dealt with the development of highly adaptable water technologies and management strategies. Under the aegis of the Karlsruhe Institute of Technology (KIT) and funded by the German Ministry of Education and Research (BMBF), these innovative technical concepts were exemplarily implemented to remedy this deficiency in the model region Gunung Sewu, a karst area situated on the southern coast of Java Island, Indonesia. The experiences gained through the interdisciplinary joint R&D activities clearly showed that even in the case of availability of appropriate technologies, a comprising transfer of knowhow and the buildup of capabilities (Capacity Development) is inevitable to sustainably implement and disseminate new methods. In this context, an adapted water supply facility was developed by KIT which hereafter shall serve for demonstration, teaching, and research purposes. The plant's functionality, its teaching and research concept, as well as the design process, which was accomplished in collaboration with the University Gadjah Mada (UGM), Yogyakarta, Indonesia, is the content of this present paper.

Automatic Web-based Calibration of Network-Capable Shipboard Sensors

DTIC Science & Technology

2007-09-01

Server, Java , Applet, and Servlet . 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT Unclassified 18. SECURITY CLASSIFICATION OF THIS PAGE...49 b. Sensor Applet...........................................................................49 3. Java Servlet ...Table 1. Required System Environment Variables for Java Servlet Development. ......25 Table 2. Payload Data Format of the POST Requests from

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…

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...

Development, Deployment, and Cost Effectiveness of a Self-Administered Stereo Non Mydriatic Automated Retinal Camera (SNARC) Containing Automated Retinal Lesion (ARL) Detection Using Adaptive Optics

DTIC Science & Technology

2010-10-01

Requirements Application Server  BEA Weblogic Express 9.2 or higher  Java v5Apache Struts v2  Hibernate v2  C3PO  SQL*Net client / JDBC Database Server...designed for the desktop o An HTML and JavaScript browser-based front end designed for mobile Smartphones - A Java -based framework utilizing Apache...Technology Requirements The recommended technologies are as follows: Technology Use Requirements Java Application Provides the backend application

Malware Memory Analysis for Non-Specialists: Investigating Publicly Available Memory Image for the Stuxnet Worm

DTIC Science & Technology

2013-11-01

may be considered moderately suspicious. [20, 21, 22 and 23] PID 1580 (jqs.exe) is using port 5152, a port associated to with Java Quick Starter [26...spoolsv.exe 0x01000000 True False True \\WINDOWS\\system32\\spoolsv.exe 1580 jqs.exe 0x00400000 True False True \\Program Files\\ Java \\jre6\\bin\\jqs.exe 1664...Files\\ Java \\ Java Update\\jusched.exe 1816 VMUpgradeHelp er 0x00400000 True False True \\Program Files\\VMware\\VMware Tools\\VMUpgradeHelper.exe 1872

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.

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.

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.

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.

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.

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.

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.

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.

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/

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.

Radotinib induces high cytotoxicity in c-KIT positive acute myeloid leukemia cells.

PubMed

Heo, Sook-Kyoung; Noh, Eui-Kyu; Kim, Jeong Yi; Jo, Jae-Cheol; Choi, Yunsuk; Koh, SuJin; Baek, Jin Ho; Min, Young Joo; Kim, Hawk

2017-06-05

Previously, we reported that radotinib, a BCR-ABL1 tyrosine kinase inhibitor, induced cytotoxicity in acute myeloid leukemia (AML) cells. However, the effects of radotinib in the subpopulation of c-KIT-positive AML cells were unclear. We observed that low-concentration radotinib had more potent cytotoxicity in c-KIT-positive cells than c-KIT-negative cells from AML patients. To address this issue, cell lines with high c-KIT expression, HEL92.1.7, and moderate c-KIT expression, H209, were selected. HEL92.1.7 cells were grouped into intermediate and high c-KIT expression populations. The cytotoxicity of radotinib against the HEL92.1.7 cell population with intermediate c-KIT expression was not different from that of the population with high c-KIT expression. When H209 cells were grouped into c-KIT expression-negative and c-KIT expression-positive populations, radotinib induced cytotoxicity in the c-KIT-positive population, but not the c-KIT-negative population. Thus, radotinib induces cytotoxicity in c-KIT-positive cells, regardless of the c-KIT expression intensity. Therefore, radotinib induces significant cytotoxicity in c-KIT-positive AML cells, suggesting that radotinib is a potential target agent for the treatment of c-KIT-positive malignancies including AML. Copyright © 2017 Elsevier B.V. All rights reserved.

Techni-kits and Techni-kit Building Systems

NASA Technical Reports Server (NTRS)

Callender, E. D.; Hartsough, C.; Morris, R. V.; Yamamoto, Y.

1985-01-01

Techni-kits consists of theories, methods, standards and computer based tools that assist in design of information-intensive systems. Techni-kit "building system" is techni-kit that builds techni-kits.

Children’s Oncology Group’s 2013 Blueprint for Research: Soft Tissue Sarcomas

PubMed Central

Hawkins, Douglas S.; Spunt, Sheri L.; Skapek, Stephen X.

2013-01-01

In the US, approximately 850-900 children are diagnosed each year with soft tissue sarcomas (STS). Key findings from recent clinical trials include safe reduction in therapy for low risk rhabdomyosarcoma (RMS), validation of FOXO1 fusion as a prognostic factor, a modest improvement in outcome for high-risk RMS, and a biologically-designed non-cytotoxic therapy for pediatric desmoid tumor. Planned Phase 2 trials include targeted agents for VEGF/PDGF, mTOR, and IGF-1R for children with RMS and VEGF for children with non-RMS STS (NRSTS). For RMS, COG Phase 3 trials potentially will explore VEGF/mTOR inhibition or chemotherapy interval compression. For NRSTS, a COG Phase 3 trial will explore VEGF inhibition. PMID:23255356

A decrease in ubiquitination and resulting prolonged life-span of KIT underlies the KIT overexpression-mediated imatinib resistance of KIT mutation-driven canine mast cell tumor cells.

PubMed

Kobayashi, Masato; Kuroki, Shiori; Kurita, Sena; Miyamoto, Ryo; Tani, Hiroyuki; Tamura, Kyoichi; Bonkobara, Makoto

2017-10-01

Overexpression of KIT is one of the mechanisms that contributes to imatinib resistance in KIT mutation-driven tumors. Here, the mechanism underlying this overexpression of KIT was investigated using an imatinib-sensitive canine mast cell tumor (MCT) line CoMS, which has an activating mutation in KIT exon 11. A KIT-overexpressing imatinib-resistant subline, rCoMS1, was generated from CoMS cells by their continuous exposure to increasing concentrations of imatinib. Neither a secondary mutation nor upregulated transcription of KIT was detected in rCoMS1 cells. A decrease in KIT ubiquitination, a prolonged KIT life-span, and KIT overexpression were found in rCoMS1 cells. These events were suppressed by withdrawal of imatinib and were re-induced by re‑treatment with imatinib. These findings suggest that imatinib elicited overexpression of KIT via suppression of its ubiquitination. These results also indicated that imatinib-induced overexpression of KIT in rCoMS1 cells was not a permanently acquired feature but was a reversible response of the cells. Moreover, the pan deubiquitinating enzyme inhibitor PR619 prevented imatinib induction of KIT overexpression, suggesting that the imatinib-induced decrease in KIT ubiquitination could be mediated by upregulation and/or activation of deubiquitinating enzyme(s). It may be possible that a similar mechanism of KIT overexpression underlies the acquisition of imatinib resistance in some human tumors that are driven by KIT mutation.

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,…

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…

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…

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.

Monitoring Java Programs with Java PathExplorer

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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

Wickstrom, Gregory Lloyd; Gale, Jason Carl; Ma, Kwok Kee

The Sandia Secure Processor (SSP) is a new native Java processor that has been specifically designed for embedded applications. The SSP's design is a system composed of a core Java processor that directly executes Java bytecodes, on-chip intelligent IO modules, and a suite of software tools for simulation and compiling executable binary files. The SSP is unique in that it provides a way to control real-time IO modules for embedded applications. The system software for the SSP is a 'class loader' that takes Java .class files (created with your favorite Java compiler), links them together, and compiles a binary. Themore » complete SSP system provides very powerful functionality with very light hardware requirements with the potential to be used in a wide variety of small-system embedded applications. This paper gives a detail description of the Sandia Secure Processor and its unique features.« less

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.

Oncogenic signaling by Kit tyrosine kinase occurs selectively on the Golgi apparatus in gastrointestinal stromal tumors

PubMed Central

Obata, Y; Horikawa, K; Takahashi, T; Akieda, Y; Tsujimoto, M; Fletcher, J A; Esumi, H; Nishida, T; Abe, R

2017-01-01

Gastrointestinal stromal tumors (GISTs) are caused by gain-of-function mutations in the Kit receptor tyrosine kinase. Most primary GIST patients respond to the Kit inhibitor imatinib, but this drug often becomes ineffective because of secondary mutations in the Kit kinase domain. The characteristic intracellular accumulation of imatinib-sensitive and -resistant Kit protein is well documented, but its relationship to oncogenic signaling remains unknown. Here, we show that in cancer tissue from primary GIST patients as well as in cell lines, mutant Kit accumulates on the Golgi apparatus, whereas normal Kit localizes to the plasma membrane (PM). In imatinib-resistant GIST with a secondary Kit mutation, Kit localizes predominantly on the Golgi apparatus. Both imatinib-sensitive and imatinib-resistant Kit (Kit(mut)) become fully auto-phosphorylated only on the Golgi and only if in a complex-glycosylated form. Kit(mut) accumulates on the Golgi during the early secretory pathway, but not after endocytosis. The aberrant kinase activity of Kit(mut) prevents its export from the Golgi to the PM. Furthermore, Kit(mut) on the Golgi signals and activates the phosphatidylinositol 3-kinase–Akt (PI3K–Akt) pathway, signal transducer and activator of transcription 5 (STAT5), and the Mek–Erk pathway. Blocking the biosynthetic transport of Kit(mut) to the Golgi from the endoplasmic reticulum inhibits oncogenic signaling. PM localization of Kit(mut) is not required for its signaling. Activation of Src-family tyrosine kinases on the Golgi is essential for oncogenic Kit signaling. These results suggest that the Golgi apparatus serves as a platform for oncogenic Kit signaling. Our study demonstrates that Kit(mut)’s pathogenicity is related to its mis-localization, and may offer a new strategy for treating imatinib-resistant GISTs. PMID:28192400

Protein kinase C-δ-mediated recycling of active KIT in colon cancer.

PubMed

Park, Misun; Kim, Won Kyu; Song, Meiying; Park, Minhee; Kim, Hyunki; Nam, Hye Jin; Baek, Sung Hee; Kim, Hoguen

2013-09-15

Abnormal signaling through receptor tyrosine kinase (RTK) moieties is important in tumorigenesis and drug targeting of colorectal cancers. Wild-type KIT (WT-KIT), a RTK that is activated upon binding with stem cell factor (SCF), is highly expressed in some colon cancers; however, little is known about the functional role of SCF-dependent KIT activation in colon cancer pathogenesis. We aimed to elucidate the conditions and roles of WT-KIT activation in colon cancer tumorigenesis. Colorectal cancers with KIT expression were characterized by immunoblotting and immunohistochemistry. The biologic alterations after KIT-SCF binding were analyzed with or without protein kinase C (PKC) activation. We found that WT-KIT was expressed in a subset of colon cancer cell lines and was activated by SCF, leading to activation of downstream AKT and extracellular signal-regulated kinase (ERK) signaling pathways. We also showed that KIT expression gradually decreased, after prolonged SCF stimulation, due to lysosomal degradation. Degradation of WT-KIT after SCF binding was significantly rescued when PKC was activated. We also showed the involvement of activated PKC-δ in the recycling of WT-KIT. We further showed that a subset of colorectal cancers exhibit expressions of both WT-KIT and activated PKC-δ and that expression of KIT is correlated with poor patient survival (P = 0.004). Continuous downstream signal activation after KIT-SCF binding is accomplished through PKC-δ-mediated recycling of KIT. This sustained KIT activation may contribute to tumor progression in a subset of colon cancers with KIT expression and might provide the rationale for a therapeutic approach targeting KIT. ©2013 AACR.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Cardiac c-Kit Biology Revealed by Inducible Transgenesis.

PubMed

Gude, Natalie A; Firouzi, Fareheh; Broughton, Kathleen M; Ilves, Kelli; Nguyen, Kristine P; Payne, Christina R; Sacchi, Veronica; Monsanto, Megan M; Casillas, Alexandria R; Khalafalla, Farid G; Wang, Bingyan J; Ebeid, David E; Alvarez, Roberto; Dembitsky, Walter P; Bailey, Barbara A; van Berlo, Jop; Sussman, Mark A

2018-06-22

Biological significance of c-Kit as a cardiac stem cell marker and role(s) of c-Kit+ cells in myocardial development or response to pathological injury remain unresolved because of varied and discrepant findings. Alternative experimental models are required to contextualize and reconcile discordant published observations of cardiac c-Kit myocardial biology and provide meaningful insights regarding clinical relevance of c-Kit signaling for translational cell therapy. The main objectives of this study are as follows: demonstrating c-Kit myocardial biology through combined studies of both human and murine cardiac cells; advancing understanding of c-Kit myocardial biology through creation and characterization of a novel, inducible transgenic c-Kit reporter mouse model that overcomes limitations inherent to knock-in reporter models; and providing perspective to reconcile disparate viewpoints on c-Kit biology in the myocardium. In vitro studies confirm a critical role for c-Kit signaling in both cardiomyocytes and cardiac stem cells. Activation of c-Kit receptor promotes cell survival and proliferation in stem cells and cardiomyocytes of either human or murine origin. For creation of the mouse model, the cloned mouse c-Kit promoter drives Histone2B-EGFP (enhanced green fluorescent protein; H2BEGFP) expression in a doxycycline-inducible transgenic reporter line. The combination of c-Kit transgenesis coupled to H2BEGFP readout provides sensitive, specific, inducible, and persistent tracking of c-Kit promoter activation. Tagging efficiency for EGFP+/c-Kit+ cells is similar between our transgenic versus a c-Kit knock-in mouse line, but frequency of c-Kit+ cells in cardiac tissue from the knock-in model is 55% lower than that from our transgenic line. The c-Kit transgenic reporter model reveals intimate association of c-Kit expression with adult myocardial biology. Both cardiac stem cells and a subpopulation of cardiomyocytes express c-Kit in uninjured adult heart, upregulating c-Kit expression in response to pathological stress. c-Kit myocardial biology is more complex and varied than previously appreciated or documented, demonstrating validity in multiple points of coexisting yet heretofore seemingly irreconcilable published findings. © 2018 American Heart Association, Inc.

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…

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…

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.

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…

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…

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…

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.

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…

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…

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...

Advantage of using a home-made ELISA kit for detection of Helicobacter pylori infection over commercially imported kits.

PubMed

Mohammadi, M; Talebkhan, Y; Khalili, G; Mahboudi, F; Massarrat, S; Zamaninia, L; Oghalaei, A

2008-01-01

To evaluate a home-made ELISA kit for detection of Helicobacter pylori (Hp) infection and comparison of its immunologic criteria with those of foreign commercial kits. A home-made IgG ELISA kit was developed using soluble antigenic fractions of Hp proteins. Confirmed sera were tested and serological criteria were evaluated through assessment of 199 serum samples. The accuracy, sensitivity and specificity values of home-made kit were 92, 92 and 90.4%, respectively. These immunologic criteria for Trinity kit were 95.2, 95.2 and 95% in comparison with IBL kit (91.3, 92.2 and 88.5%), BIOHIT kit (72.4, 41.6 and 94.1%) and HelicoBlot2.1 (94.2, 93.4 and 100%). Kappa agreement assessment demonstrated that two of the imported ELISA kits had fair to moderate agreement with the home-made kit while the other one had a poor agreement value. Apart from comparable values between the home-made kit and the most efficient imported kit (Trinity) there was significant cost benefit. Therefore, we recommend the home-made kit as a suitable substitution for detection of Hp infection in the Iranian population.

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

Evaluation of the kinase domain of c-KIT in canine cutaneous mast cell tumors

PubMed Central

Webster, Joshua D; Kiupel, Matti; Yuzbasiyan-Gurkan, Vilma

2006-01-01

Background Mutations in the c-KIT proto-oncogene have been implicated in the progression of several neoplastic diseases, including gastrointestinal stromal tumors and mastocytosis in humans, and cutaneous mast cell tumors (MCTs) in canines. Mutations in human mastocytosis patients primarily occur in c-KIT exon 17, which encodes a portion of its kinase domain. In contrast, deletions and internal tandem duplication (ITD) mutations are found in the juxtamembrane domain of c-KIT in approximately 15% of canine MCTs. In addition, ITD c-KIT mutations are significantly associated with aberrant KIT protein localization in canine MCTs. However, some canine MCTs have aberrant KIT localization but lack ITD c-KIT mutations, suggesting that other mutations or other factors may be responsible for aberrant KIT localization in these tumors. Methods In order to characterize the prevalence of mutations in the phospho-transferase portion of c-KIT's kinase domain in canine MCTs exons 16–20 of 33 canine MCTs from 33 dogs were amplified and sequenced. Additionally, in order to determine if mutations in c-KIT exon 17 are responsible for aberrant KIT localization in MCTs that lack juxtamembrane domain c-KIT mutations, c-KIT exon 17 was amplified and sequenced from 18 canine MCTs that showed an aberrant KIT localization pattern but did not have ITD c-KIT mutations. Results No mutations or polymorphisms were identified in exons 16–20 of any of the MCTs examined. Conclusion In conclusion, mutations in the phospho-transferase portion of c-KIT's kinase domain do not play an important role in the progression of canine cutaneous MCTs, or in the aberrant localization of KIT in canine MCTs. PMID:16579858

Adult cardiac stem cells are multipotent and robustly myogenic: c-kit expression is necessary but not sufficient for their identification.

PubMed

Vicinanza, Carla; Aquila, Iolanda; Scalise, Mariangela; Cristiano, Francesca; Marino, Fabiola; Cianflone, Eleonora; Mancuso, Teresa; Marotta, Pina; Sacco, Walter; Lewis, Fiona C; Couch, Liam; Shone, Victoria; Gritti, Giulia; Torella, Annalaura; Smith, Andrew J; Terracciano, Cesare Mn; Britti, Domenico; Veltri, Pierangelo; Indolfi, Ciro; Nadal-Ginard, Bernardo; Ellison-Hughes, Georgina M; Torella, Daniele

2017-12-01

Multipotent adult resident cardiac stem cells (CSCs) were first identified by the expression of c-kit, the stem cell factor receptor. However, in the adult myocardium c-kit alone cannot distinguish CSCs from other c-kit-expressing (c-kit pos ) cells. The adult heart indeed contains a heterogeneous mixture of c-kit pos cells, mainly composed of mast and endothelial/progenitor cells. This heterogeneity of cardiac c-kit pos cells has generated confusion and controversy about the existence and role of CSCs in the adult heart. Here, to unravel CSC identity within the heterogeneous c-kit-expressing cardiac cell population, c-kit pos cardiac cells were separated through CD45-positive or -negative sorting followed by c-kit pos sorting. The blood/endothelial lineage-committed (Lineage pos ) CD45 pos c-kit pos cardiac cells were compared to CD45 neg (Lineage neg /Lin neg ) c-kit pos cardiac cells for stemness and myogenic properties in vitro and in vivo. The majority (~90%) of the resident c-kit pos cardiac cells are blood/endothelial lineage-committed CD45 pos CD31 pos c-kit pos cells. In contrast, the Lin neg CD45 neg c-kit pos cardiac cell cohort, which represents ⩽10% of the total c-kit pos cells, contain all the cardiac cells with the properties of adult multipotent CSCs. These characteristics are absent from the c-kit neg and the blood/endothelial lineage-committed c-kit pos cardiac cells. Single Lin neg c-kit pos cell-derived clones, which represent only 1-2% of total c-kit pos myocardial cells, when stimulated with TGF-β/Wnt molecules, acquire full transcriptome and protein expression, sarcomere organisation, spontaneous contraction and electrophysiological properties of differentiated cardiomyocytes (CMs). Genetically tagged cloned progeny of one Lin neg c-kit pos cell when injected into the infarcted myocardium, results in significant regeneration of new CMs, arterioles and capillaries, derived from the injected cells. The CSC's myogenic regenerative capacity is dependent on commitment to the CM lineage through activation of the SMAD2 pathway. Such regeneration was not apparent when blood/endothelial lineage-committed c-kit pos cardiac cells were injected. Thus, among the cardiac c-kit pos cell cohort only a very small fraction has the phenotype and the differentiation/regenerative potential characteristics of true multipotent CSCs.

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.

Summary of Synoptic Meteorological Observations. Indonesian Coastal Marine Areas. Volume 2. Area 8 - West Borneo, Area 9 - Karimata Strait, Area 10 - Southwest Java Sea, Area 11 - South Central Java, Area 12 - Southeast Java, Area 13 - Southeast Java Sea, Area 14 - Northeast Java Sea

DTIC Science & Technology

1975-04-01

5 ’ :00 0 1’.20 2. 219 39 : .:0 :00 .0 A.. AP99 120 , ~ ~ ~ ~ ~ -y- ,M -.7yT ,, T , . , .,77M III II P~ kID : (¢E(’Ll) 9•3-977AREA 0009 KARIMATA STRAIT...TYPE OTHER WEATHER PHENOMENA kNO 01D RAIN PAIN VAIL RAIG SNOW OTHER HAI. PORN AT PCPN PAST ?HOR FOG FOG WO SMOKE SPRAY NO SHoR PON FRZN 06 TIME HOUR LTNG...NAONO DIR RAIN RAIN ORIL RCZG SNOW OTHER HAIL PCORN A? FCN PAST THOR OTOH HAZE SPRy NOUST SI ? R G PUG W SMOK SPRAY No PHft PCN PRN OPTM OR LTNG Wa PORN

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.

The Category Cued Recall test in very mild Alzheimer's disease: discriminative validity and correlation with semantic memory functions.

PubMed

Vogel, A; Mortensen, E L; Gade, A; Waldemar, G

2007-01-01

Episodic memory tests that measure cued recall may be particularly effective in the diagnosis of early Alzheimer's disease (AD) because they examine both episodic and semantic memory functions. The Category Cued Recall (CCR) test provides superordinate semantic cues at encoding and retrieval, and high discriminative validity has been claimed for this test. The aim of this study was to investigate the discriminative validity for this test when compared with the 10-word memory list from Alzheimer's Disease Assessment Scale (ADAS-cog) that measures free recall. The clinical diagnosis of AD was taken as the standard. It was also investigated whether the two episodic memory tests correlated with measures of semantic memory. The tests were administered to 35 patients with very mild AD (Mini Mental State Examination score >22) and 28 control subjects. Both tests had high sensitivity (>88%) with high specificity (>89%). One out of the five semantic memory tests was significantly correlated to performances on CCR, whereas delayed recall on the ADAS-cog memory test was significantly correlated to two semantic tests. In conclusion, the discriminative validity of the CCR test and the ADAS-cog memory test was equivalent in very mild AD. This may be because CCR did not tap more semantic processes, which are impaired in the earliest phases of AD, than a test of free recall.

Computerized Posturographic Measurement in Elderly Women with Unilateral Knee Osteoarthritis

PubMed Central

Lim, Kil-Byung

2012-01-01

Objective To identify the subtle change of postural control in elderly patients with unilateral knee osteoarthritis (OA) with computerized dynamic posturography. Method Twenty-two healthy women and twenty-six women with unilateral knee OA, aged 60 and over, were enrolled. The computerized posturographic measures included a weight bearing pattern during squatting and sit-to-stand, sway velocity of center of gravity (COG) during one leg standing, on-axis velocity and directional control of COG during rhythmic weight shift, rising index during sit-to-stand, end sway during tandem walk, and movement time during step up/over. Results It was shown that patients bore significantly less weight on the affected side during the 30° and 60° squat and sit-to-stand. Sway velocity of COG during one leg standing was greater whereas the on-axis velocity and directional control during the front/back rhythmic weight shift were significantly lower in the patient group. The rising index during sit-to-stand was significantly lower and movement time during step up/over with the affected side was significantly longer in patients. Conclusion This study demonstrated in detail a decline of postural balance by utilizing computerized posturography in elderly women with unilateral knee OA. They had less weight-bearing, more sway, and less ability of intentional postural control on the affected side. PMID:23185725

The Effects of Shoulder Slings on Balance in Patients With Hemiplegic Stroke.

PubMed

Sohn, Min Kyun; Jee, Sung Ju; Hwang, Pyoungsik; Jeon, Yumi; Lee, Hyunkeun

2015-12-01

To investigate the effects of a shoulder sling on balance in patients with hemiplegia. Twenty-seven hemiplegic stroke patients (right 13, left 14) were enrolled in this study. The subjects' movement in their centers of gravity (COGs) during their static and dynamic balance tests was measured with their eyes open in each sling condition-without a sling, with Bobath's axillary support (Bobath sling), and with a simple arm sling. The percent times in quadrant, overall, anterior/posterior, and medial/lateral stability indexes were measured using a posturography platform (Biodex Balance System SD). Functional balance was evaluated using the Berg Balance Scale and the Trunk Impairment Scale. All balance tests were performed with each sling in random order. The COGs of right hemiplegic stroke patients and all hemiplegic stroke patients shifted to, respectively, the right and posterior quadrants during the static balance test without a sling (p<0.05). This weight asymmetry pattern did not improve with either the Bobath or the simple arm sling. There was no significant improvement in any stability index during either the static or the dynamic balance tests in any sling condition. The right and posterior deviations of the hemiplegic stroke patients' COGs were maintained during the application of the shoulder slings, and there were no significant effects of the shoulder slings on the patients' balance in the standing still position.

Susceptibility of the MMPI-2-RF neurological complaints and cognitive complaints scales to over-reporting in simulated head injury.

PubMed

Bolinger, Elizabeth; Reese, Caitlin; Suhr, Julie; Larrabee, Glenn J

2014-02-01

We examined the effect of simulated head injury on scores on the Neurological Complaints (NUC) and Cognitive Complaints (COG) scales of the Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF). Young adults with a history of mild head injury were randomly assigned to simulate head injury or give their best effort on a battery of neuropsychological tests, including the MMPI-2-RF. Simulators who also showed poor effort on performance validity tests (PVTs) were compared with controls who showed valid performance on PVTs. Results showed that both scales, but especially NUC, are elevated in individuals simulating head injury, with medium to large effect sizes. Although both scales were highly correlated with all MMPI-2-RF over-reporting validity scales, the relationship of Response Bias Scale to both NUC and COG was much stronger in the simulators than controls. Even accounting for over-reporting on the MMPI-2-RF, NUC was related to general somatic complaints regardless of group membership, whereas COG was related to both psychological distress and somatic complaints in the control group only. Neither scale was related to actual neuropsychological performance, regardless of group membership. Overall, results provide further evidence that self-reported cognitive symptoms can be due to many causes, not necessarily cognitive impairment, and can be exaggerated in a non-credible manner.

Flexure mechanism-based parallelism measurements for chip-on-glass bonding

NASA Astrophysics Data System (ADS)

Jung, Seung Won; Yun, Won Soo; Jin, Songwan; Kim, Bo Sun; Jeong, Young Hun

2011-08-01

Recently, liquid crystal displays (LCDs) have played vital roles in a variety of electronic devices such as televisions, cellular phones, and desktop/laptop monitors because of their enhanced volume, performance, and functionality. However, there is still a need for thinner LCD panels due to the trend of miniaturization in electronic applications. Thus, chip-on-glass (COG) bonding has become one of the most important aspects in the LCD panel manufacturing process. In this study, a novel sensor was developed to measure the parallelism between the tooltip planes of the bonding head and the backup of the COG main bonder, which has previously been estimated by prescale pressure films in industry. The sensor developed in this study is based on a flexure mechanism, and it can measure the total pressing force and the inclination angles in two directions that satisfy the quantitative definition of parallelism. To improve the measurement accuracy, the sensor was calibrated based on the estimation of the total pressing force and the inclination angles using the least-squares method. To verify the accuracy of the sensor, the estimation results for parallelism were compared with those from prescale pressure film measurements. In addition, the influence of parallelism on the bonding quality was experimentally demonstrated. The sensor was successfully applied to the measurement of parallelism in the COG-bonding process with an accuracy of more than three times that of the conventional method using prescale pressure films.

Effect of rivastigmine or memantine add-on therapy is affected by butyrylcholinesterase genotype in patients with probable Alzheimer's disease.

PubMed

Han, Hyun Jeong; Kwon, Jay C; Kim, Jung Eun; Kim, Shin Gyeom; Park, Jong-Moo; Park, Kyung Won; Park, Key Chung; Park, Kee Hyung; Moon, So Young; Seo, Sang Won; Choi, Seong Hye; Cho, Soo-Jin

2015-01-01

The K variant of butyrylcholinesterase (BCHE-K) exhibits a reduced acetylcholine-hydrolyzing capacity; so the clinical response to rivastigmine may differ in Alzheimer's disease (AD) patients with the BCHE-K gene. To investigate the clinical response to rivastigmine transdermal patch monotherapy or memantine plus rivastigmine transdermal patch therapy in AD patients based on the BCHE-K gene. A total of 146 probable AD patients consented to genetic testing for butyrylcholinesterase and underwent the final efficacy evaluations. Responders were defined as patients with an equal or better score on the Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog) at 16 weeks compared to their baseline score. BCHE-K carriers showed a lower responder rate on the ADAS-cog than non-carriers (38.2 vs. 61.7%, p = 0.02), and this trend was evident in AD patients with apolipoprotein E ε 4 (35 vs. 60.7%, p = 0.001). The presence of the BCHE-K allele predicted a worse response on the ADAS-cog (odds ratio 0.35, 95% confidence interval 0.14-0.87), after adjusting for demographic and baseline cognitive and functional variables. The BCHE-K genotype may be related to a poor cognitive response to rivastigmine patch or memantine add-on therapy, especially in the presence of apolipoprotein E ε 4.

A Biomarker Combining Imaging and Neuropsychological Assessment for Tracking Early Alzheimer's Disease in Clinical Trials.

PubMed

Verma, Nishant; Beretvas, S Natasha; Pascual, Belen; Masdeu, Joseph C; Markey, Mia K

2018-03-14

Combining optimized cognitive (Alzheimer's Disease Assessment Scale- Cognitive subscale, ADAS-Cog) and atrophy markers of Alzheimer's disease for tracking progression in clinical trials may provide greater sensitivity than currently used methods, which have yielded negative results in multiple recent trials. Furthermore, it is critical to clarify the relationship among the subcomponents yielded by cognitive and imaging testing, to address the symptomatic and anatomical variability of Alzheimer's disease. Using latent variable analysis, we thoroughly investigated the relationship between cognitive impairment, as assessed on the ADAS-Cog, and cerebral atrophy. A biomarker was developed for Alzheimer's clinical trials that combines cognitive and atrophy markers. Atrophy within specific brain regions was found to be closely related with impairment in cognitive domains of memory, language, and praxis. The proposed biomarker showed significantly better sensitivity in tracking progression of cognitive impairment than the ADAS-Cog in simulated trials and a real world problem. The biomarker also improved the selection of MCI patients (78.8±4.9% specificity at 80% sensitivity) that will evolve to Alzheimer's disease for clinical trials. The proposed biomarker provides a boost to the efficacy of clinical trials focused in the mild cognitive impairment (MCI) stage by significantly improving the sensitivity to detect treatment effects and improving the selection of MCI patients that will evolve to Alzheimer's disease. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The KEEPS-Cognitive and Affective Study: baseline associations between vascular risk factors and cognition.

PubMed

Wharton, Whitney; Gleason, Carey E; Dowling, N Maritza; Carlsson, Cynthia M; Brinton, Eliot A; Santoro, M Nanette; Neal-Perry, Genevieve; Taylor, Hugh; Naftolin, Frederick; Lobo, Rogerio A; Merriam, George; Manson, Joann E; Cedars, Marcelle I; Miller, Virginia M; Black, Dennis M; Budoff, Matthew; Hodis, Howard N; Harman, S Mitchell; Asthana, Sanjay

2014-01-01

Midlife vascular risk factors influence later cognitive decline and Alzheimer's disease (AD). The decrease in serum estradiol levels during menopause has been associated with cognitive impairment and increased vascular risk, such as high blood pressure (BP), which independently contributes to cognitive dysfunction and AD. We describe the extent to which vascular risk factors relate to cognition in healthy, middle-aged, recently postmenopausal women enrolled in the Kronos Early Estrogen Prevention Cognitive and Affective Study (KEEPS-Cog) at baseline. KEEPS-Cog is a double-blind, randomized, placebo-controlled, parallel group, clinical trial, investigating the efficacy of low-dose, transdermal 17β-estradiol and oral conjugated equine estrogen on cognition. All results are cross-sectional and represent baseline data only. Analyses confirm that the KEEPS-Cog cohort (n = 571) was middle aged (mean 52.7 years, range 42-59 years), healthy, and free of cognitive dysfunction. Higher systolic BP was weakly related to poorer performance in auditory working memory and attention (p = 0.004; adjusted for multiple comparisons p = 0.10). This relationship was not associated with endogenous hormone levels, and systolic BP was not related to any other cognitive domain. BP levels may be more sensitive than other vascular risk factors in detecting subtle differences in cognitive task performance in healthy, recently menopausal women. Lower BP early in menopause may affect cognitive domains known to be associated with AD.

The Effects of Shoulder Slings on Balance in Patients With Hemiplegic Stroke

PubMed Central

Sohn, Min Kyun; Jee, Sung Ju; Hwang, Pyoungsik; Jeon, Yumi

2015-01-01

Objective To investigate the effects of a shoulder sling on balance in patients with hemiplegia. Methods Twenty-seven hemiplegic stroke patients (right 13, left 14) were enrolled in this study. The subjects' movement in their centers of gravity (COGs) during their static and dynamic balance tests was measured with their eyes open in each sling condition-without a sling, with Bobath's axillary support (Bobath sling), and with a simple arm sling. The percent times in quadrant, overall, anterior/posterior, and medial/lateral stability indexes were measured using a posturography platform (Biodex Balance System SD). Functional balance was evaluated using the Berg Balance Scale and the Trunk Impairment Scale. All balance tests were performed with each sling in random order. Results The COGs of right hemiplegic stroke patients and all hemiplegic stroke patients shifted to, respectively, the right and posterior quadrants during the static balance test without a sling (p<0.05). This weight asymmetry pattern did not improve with either the Bobath or the simple arm sling. There was no significant improvement in any stability index during either the static or the dynamic balance tests in any sling condition. Conclusion The right and posterior deviations of the hemiplegic stroke patients' COGs were maintained during the application of the shoulder slings, and there were no significant effects of the shoulder slings on the patients' balance in the standing still position. PMID:26798614

Recommendations for the return of research results to study participants and guardians: a report from the Children's Oncology Group.

PubMed

Fernandez, Conrad V; Ruccione, Kathleen; Wells, Robert J; Long, Jay B; Pelletier, Wendy; Hooke, Mary C; Pentz, Rebecca D; Noll, Robert B; Baker, Justin N; O'Leary, Maura; Reaman, Gregory; Adamson, Peter C; Joffe, Steven

2012-12-20

The Children's Oncology Group (COG) strongly supports the widely recognized principle that research participants should be offered a summary of study results. The mechanism by which to do so in a cooperative research group setting has not been previously described. On the basis of a review of the available empirical and theoretic literature and on iterative, multidisciplinary discussion, a COG Return of Results Task Force (RRTF) offered detailed recommendations for the return of results to research study participants. The RRTF established guidelines for the notification of research participants and/or their parents/guardians about the availability of research results, a mechanism for and timing of sharing results via registration on the COG public Web site, the scope of the research to be shared, the target audience, and a process for creating and vetting lay summaries of study results. The RRTF recognized the challenges in adequately conveying complex scientific results to audiences with varying levels of health literacy and recommended that particularly sensitive or complex results be returned using direct personal contact. The RRTF also recommended evaluation of the cost, effectiveness, and impact of sharing results. These recommendations provide a framework for the offering and returning of results to participants. They can be used by individual investigators, multi-investigator research collaboratives, and large cooperative groups.

Recommendations for the Return of Research Results to Study Participants and Guardians: A Report From the Children's Oncology Group

PubMed Central

Fernandez, Conrad V.; Ruccione, Kathleen; Wells, Robert J.; Long, Jay B.; Pelletier, Wendy; Hooke, Mary C.; Pentz, Rebecca D.; Noll, Robert B.; Baker, Justin N.; O'Leary, Maura; Reaman, Gregory; Adamson, Peter C.; Joffe, Steven

2012-01-01

Purpose The Children's Oncology Group (COG) strongly supports the widely recognized principle that research participants should be offered a summary of study results. The mechanism by which to do so in a cooperative research group setting has not been previously described. Methods On the basis of a review of the available empirical and theoretic literature and on iterative, multidisciplinary discussion, a COG Return of Results Task Force (RRTF) offered detailed recommendations for the return of results to research study participants. Results The RRTF established guidelines for the notification of research participants and/or their parents/guardians about the availability of research results, a mechanism for and timing of sharing results via registration on the COG public Web site, the scope of the research to be shared, the target audience, and a process for creating and vetting lay summaries of study results. The RRTF recognized the challenges in adequately conveying complex scientific results to audiences with varying levels of health literacy and recommended that particularly sensitive or complex results be returned using direct personal contact. The RRTF also recommended evaluation of the cost, effectiveness, and impact of sharing results. Conclusion These recommendations provide a framework for the offering and returning of results to participants. They can be used by individual investigators, multi-investigator research collaboratives, and large cooperative groups. PMID:23109703

Pathologic Stimulus Determines Lineage Commitment of Cardiac C-kit+ Cells.

PubMed

Chen, Zhongming; Zhu, Wuqiang; Bender, Ingrid; Gong, Wuming; Kwak, Il-Youp; Yellamilli, Amritha; Hodges, Thomas J; Nemoto, Natsumi; Zhang, Jianyi; Garry, Daniel J; van Berlo, Jop H

2017-12-12

Although cardiac c-kit + cells are being tested in clinical trials, the circumstances that determine lineage differentiation of c-kit + cells in vivo are unknown. Recent findings suggest that endogenous cardiac c-kit + cells rarely contribute cardiomyocytes to the adult heart. We assessed whether various pathological stimuli differentially affect the eventual cell fates of c-kit + cells. We used single-cell sequencing and genetic lineage tracing of c-kit + cells to determine whether various pathological stimuli would result in different fates of c-kit + cells. Single-cell sequencing of cardiac CD45 - c-kit + cells showed innate heterogeneity, indicative of the existence of vascular and mesenchymal c-kit + cells in normal hearts. Cardiac pressure overload resulted in a modest increase in c-kit-derived cardiomyocytes, with significant increases in the numbers of endothelial cells and fibroblasts. Doxorubicin-induced acute cardiotoxicity did not increase c-kit-derived endothelial cell fates but instead induced cardiomyocyte differentiation. Mechanistically, doxorubicin-induced DNA damage in c-kit + cells resulted in expression of p53. Inhibition of p53 blocked cardiomyocyte differentiation in response to doxorubicin, whereas stabilization of p53 was sufficient to increase c-kit-derived cardiomyocyte differentiation. These results demonstrate that different pathological stimuli induce different cell fates of c-kit + cells in vivo. Although the overall rate of cardiomyocyte formation from c-kit + cells is still below clinically relevant levels, we show that p53 is central to the ability of c-kit + cells to adopt cardiomyocyte fates, which could lead to the development of strategies to preferentially generate cardiomyocytes from c-kit + cells. © 2017 American Heart Association, Inc.

DEVELOPMENT AND DEMONSTRATION OF NOVEL LOW-NOx BURNERS IN THE STEEL INDUSTRY

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

Cygan, David

Gas Technology Institute (GTI), together with Hamworthy Peabody Combustion Incorporated (formerly Peabody Engineering Corporation), the University of Utah, and Far West Electrochemical have developed and demonstrated an innovative combustion system suitable for natural gas and coke-oven gas firing within the steel industry. The combustion system is a simple, low-cost, energy-efficient burner that can reduce NOx by more than 75%. The U.S. steel industry needs to address NOx control at its steelmaking facilities. A significant part of NOx emissions comes from gas-fired boilers. In steel plants, byproduct gases – blast furnace gas (BFG) and coke-oven gas (COG) – are widely usedmore » together with natural gas to fire furnaces and boilers. In steel plants, natural gas can be fired together with BFG and COG, but, typically, the addition of natural gas raises NOx emissions, which can already be high because of residual fuel-bound nitrogen in COG. The Project Team has applied its expertise in low-NOx burners to lower NOx levels for these applications by combining advanced burner geometry and combustion staging with control strategies tailored to mixtures of natural gas and byproduct fuel gases. These methods reduce all varieties of NOx – thermal NOx produced by high flame temperatures, prompt NOx produced by complex chain reactions involving radical hydrocarbon species and NOx from fuel-bound nitrogen compounds such as ammonia found in COG. The Project Team has expanded GTI’s highly successful low-NOx forced internal recirculation (FIR) burner, previously developed for natural gas-fired boilers, into facilities that utilize BFG and COG. For natural gas firing, these burners have been shown to reduce NOx emissions from typical uncontrolled levels of 80-100 vppm to single-digit levels (9 vppm). This is done without the energy efficiency penalties incurred by alternative NOx control methods, such as external flue gas recirculation (FGR), water injection, and selective non-catalytic reduction. The FIR burner was previously demonstrated on firetube and watertube boilers, and these units are still operating at several industrial and commercial boiler sites in sizes ranging from 2.5 to 60 million Btu/h. This report covers the development of an innovative combustion system suitable for natural gas or coke-oven gas firing within the steel industry. The prototype FIR burner was evaluated on a 20 million Btu/h watertube boiler. Acceptable burner performance was obtained when firing natural gas and simulated coke-oven gas doped with ammonia. The laboratory data reveals a direct relationship between NOx formation and the ammonia concentration in the fuel. In addition, NOx formation increases as the primary stoichiometric ratio (PSR) increases. Representative ammonia concentrations, as documented in the steel industry, ranged from 200 to 500 vppm. When the laboratory burner/boiler was operated with 500 vppm ammonia in the fuel, NOx emissions ranged from 50 to 75 vppm. This, conservatively, is 75% less than state-of-the-art burner performance. When the burner is operated with 200 vppm ammonia in the fuel, the corresponding NOx emissions would range from 30 to 45 vppm, 84% less than present burner technology. During field evaluation on a 174 million Btu/h industrial prototype burner both natural gas and actual COG from on-site generation were tested. Despite the elevated hydrogen cyanide and ammonia content in the COG throughout the test program, the FIR burner showed an improvement over baseline emissions. At full load; 167 million Btu/h, NOx emissions were relatively low at 169 vppm. This represents a 30% reduction compared to baseline emissions not accounting for the higher hydrogen cyanide content in the COG. CO emissions remained below 20 vppm and were stable across the firing range. This represents a 68% reduction compared to baseline CO emissions. When firing natural gas, emissions were stable as firing rate increased over the range. At low fire; 45 million Btu/h, NOx emissions where 33 vppm and increased at full load; 144 million Btu/h, to 49 vppm. CO emissions fluctuated with the oxygen content and remained below 135 vppm during all tests. The boiler’s maximum output was not achieved due to a limitation dictated by the host site natural gas supply. The FIR burner benefits the public by simultaneously addressing the problems of air pollution and energy conservation through a low-NOx combustion technology that does not increase energy consumption. Continuing activities include the negotiation of a license with Hamworthy Peabody Combustion, Incorporated (Hamworthy Peabody) to commercialize the FIR burner for steel industry applications. Hamworthy Peabody is one of the largest U.S. manufacturers of combustion equipment for boilers in the Steel Industry, and has stated their intention to commercialize the FIR burner.« less

Receptor tyrosine kinase (c-Kit) inhibitors: a potential therapeutic target in cancer cells

PubMed Central

Abbaspour Babaei, Maryam; Kamalidehghan, Behnam; Saleem, Mohammad; Huri, Hasniza Zaman; Ahmadipour, Fatemeh

2016-01-01

c-Kit, a receptor tyrosine kinase, is involved in intracellular signaling, and the mutated form of c-Kit plays a crucial role in occurrence of some cancers. The function of c-Kit has led to the concept that inhibiting c-Kit kinase activity can be a target for cancer therapy. The promising results of inhibition of c-Kit for treatment of cancers have been observed in some cancers such as gastrointestinal stromal tumor, acute myeloid leukemia, melanoma, and other tumors, and these results have encouraged attempts toward improvement of using c-Kit as a capable target for cancer therapy. This paper presents the findings of previous studies regarding c-Kit as a receptor tyrosine kinase and an oncogene, as well as its gene targets and signaling pathways in normal and cancer cells. The c-Kit gene location, protein structure, and the role of c-Kit in normal cell have been discussed. Comprehending the molecular mechanism underlying c-Kit-mediated tumorogenesis is consequently essential and may lead to the identification of future novel drug targets. The potential mechanisms by which c-Kit induces cellular transformation have been described. This study aims to elucidate the function of c-Kit for future cancer therapy. In addition, it has c-Kit inhibitor drug properties and their functions have been listed in tables and demonstrated in schematic pictures. This review also has collected previous studies that targeted c-Kit as a novel strategy for cancer therapy. This paper further emphasizes the advantages of this approach, as well as the limitations that must be addressed in the future. Finally, although c-Kit is an attractive target for cancer therapy, based on the outcomes of treatment of patients with c-Kit inhibitors, it is unlikely that Kit inhibitors alone can lead to cure. It seems that c-Kit mutations alone are not sufficient for tumorogenesis, but do play a crucial role in cancer occurrence. PMID:27536065

Proper Plugin Protocols

DTIC Science & Technology

2011-12-28

specify collaboration constraints that occur in Java and XML frameworks and that the collaboration constraints from these frameworks matter in practice. (a...programming language boundaries, and Chapter 6 and Appendix A demonstrate that Fusion can specify constraints across both Java and XML in practice. (c...designed JUnit, Josh Bloch designed Java Collec- tions, and Krzysztof Cwalina designed the .NET Framework APIs. While all of these frameworks are very

Notice and Credits Page - NOAA's National Weather Service

Science.gov Websites

- Visolve is a software application (free for personal use) that transforms colors of the computer display Mac OS X 10.2 or later. (Purchase) - A 30-day free trial of eyePilot is available from eyePilot web site - http://www.colorhelper.com/ Java Java Virtual Machine - free download from java.com Adobe Reader

Tomcat, Oracle & XML Web Archive

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

Cothren, D. C.

2008-01-01

The TOX (Tomcat Oracle & XML) web archive is a foundation for development of HTTP-based applications using Tomcat (or some other servlet container) and an Oracle RDBMS. Use of TOX requires coding primarily in PL/SQL, JavaScript, and XSLT, but also in HTML, CSS and potentially Java. Coded in Java and PL/SQL itself, TOX provides the foundation for more complex applications to be built.

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…

Digitizing Consumption Across the Operational Spectrum

DTIC Science & Technology

2014-09-01

Figure 14.  Java -implemented Dictionary and Query: Result ............................................22  Figure 15.  Global Database Architecture...format. Figure 14 is an illustration of the query submitted in Java and the result which would be shown using the data shown in Figure 13. Figure...13. NoSQL (key, value) Dictionary Example 22 Figure 14. Java -implemented Dictionary and Query: Result While a

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.

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

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.

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.

Identification of rice supply chain risk to DKI Jakarta through Cipinang primary rice market

NASA Astrophysics Data System (ADS)

Sugiarto, D.; Ariwibowo, A.; Mardianto, I.; Surjasa, D.

2018-01-01

This paper identifies several sources of risks in DKI Jakarta rice supply chain that through Cipinang Primary Rice Market (CPRM). Secondary data from several sources were collected and analysed using pareto chart and time series analysis. Based on the pareto analysis, it was known that there was a change in the order of suppliers whereas in 2011, 80% of the supply came only from Cirebon, Karawang and Bandung (West Java Province). While in 2015 the main source of supply changed to Cirebon, Central Java and Karawang. Linear trend equation using decomposition model for Cirebon and Karawang showed trend of decreasing monthly supply while Central Java had a positive trend. Harvest area of wetland paddy in Cirebon and Karawang showed a negative trend in the last 6 years. The data also showed that West Java Province was the province with the largest rice crop area affected by plant organism attack and drought disaster in 2015. DKI Jakarta had several potential supply chain risks from rice supply, drought risk and pests risk where the province of West Java, which previously could become a major supplier began to require supply assistance from other provinces, especially Central Java.

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.

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.

Pediatric MATCH Infographic

Cancer.gov

Infographic explaining NCI-COG Pediatric MATCH, a cancer treatment clinical trial for children and adolescents, from 1 to 21 years of age, that is testing the use of precision medicine for pediatric cancers.

Research of centroiding algorithms for extended and elongated spot of sodium laser guide star

NASA Astrophysics Data System (ADS)

Shao, Yayun; Zhang, Yudong; Wei, Kai

2016-10-01

Laser guide stars (LGSs) increase the sky coverage of astronomical adaptive optics systems. But spot array obtained by Shack-Hartmann wave front sensors (WFSs) turns extended and elongated, due to the thickness and size limitation of sodium LGS, which affects the accuracy of the wave front reconstruction algorithm. In this paper, we compared three different centroiding algorithms , the Center-of-Gravity (CoG), weighted CoG (WCoG) and Intensity Weighted Centroid (IWC), as well as those accuracies for various extended and elongated spots. In addition, we compared the reconstructed image data from those three algorithms with theoretical results, and proved that WCoG and IWC are the best wave front reconstruction algorithms for extended and elongated spot among all the algorithms.

Designing physics video hooks for science students

NASA Astrophysics Data System (ADS)

McHugh, M.; McCauley, V.

2016-01-01

This paper offers an insight into the design structure of physics video hooks that were developed by the Science Education Resource design team in the school of education (SOE) in National University of Ireland, Galway (NUI Galway). A hook, is an instructional technique used to stimulate student attention (Hunter 1994, Lemov 2010), interest (Jewett 2013) and engagement (McCrory 2011, Riendeau 2013). The physics video hooks followed a design framework that is illustrated below by breaking down the centre of gravity (COG) hook. Various design principles and elements embedded within the COG hook are presented with examples and the time they occur within the video. The intention of this article is that the design can be replicated and modified to aid teachers and designers in the development of a multitude of classroom based multimedia resources.

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

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.

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.

SHP-1 Binds and Negatively Modulates the c-Kit Receptor by Interaction with Tyrosine 569 in the c-Kit Juxtamembrane Domain

PubMed Central

Kozlowski, Maya; Larose, Louise; Lee, Fai; Le, Duc Mingh; Rottapel, Robert; Siminovitch, Katherine A.

1998-01-01

The SH2 domain-containing SHP-1 tyrosine phosphatase has been shown to negatively regulate a broad spectrum of growth factor- and cytokine-driven mitogenic signaling pathways. Included among these is the cascade of intracellular events evoked by stem cell factor binding to c-Kit, a tyrosine kinase receptor which associates with and is dephosphorylated by SHP-1. Using a series of glutathione S-transferase (GST) fusion proteins containing either tyrosine-phosphorylated segments of the c-Kit cytosolic region or the SH2 domains of SHP-1, we have shown that SHP-1 interacts with c-Kit by binding selectively to the phosphorylated c-Kit juxtamembrane region and that the association of c-Kit with the larger of the two SHP-1 isoforms may be mediated through either the N-terminal or C-terminal SHP-1 SH2 domain. The results of binding assays with mutagenized GST-Kit juxtamembrane fusion proteins and competitive inhibition assays with phosphopeptides encompassing each c-Kit juxtamembrane region identified the tyrosine residue at position 569 as the major site for binding of SHP-1 to c-Kit and suggested that tyrosine 567 contributes to, but is not required for, this interaction. By analysis of Ba/F3 cells retrovirally transduced to express c-Kit receptors, phenylalanine substitution of c-Kit tyrosine residue 569 was shown to be associated with disruption of c-Kit–SHP-1 binding and induction of hyperproliferative responses to stem cell factor. Although phenylalanine substitution of c-Kit tyrosine residue 567 in the Ba/F3–c-Kit cells did not alter SHP-1 binding to c-Kit, the capacity of a second c-Kit-binding tyrosine phosphatase, SHP-2, to associate with c-Kit was markedly reduced, and the cells again showed hyperproliferative responses to stem cell factor. These data therefore identify SHP-1 binding to tyrosine 569 on c-Kit as an interaction pivotal to SHP-1 inhibitory effects on c-Kit signaling, but they indicate as well that cytosolic protein tyrosine phosphatases other than SHP-1 may also negatively regulate the coupling of c-Kit engagement to proliferation. PMID:9528781

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 terrestrial input into the Java Sea was limited to approx. 15 km off the river mouth. Both cores off Kalimantan and the core off Java close to the Bengawan Solo had similar Corg contents (~0.8%) and molar C/N-ratios (11-19). δ13Corg of -24‰ and low carbonate contents (~7%) indicate an even higher contribution of terrigenous organic matter off the Kalimantan rivers than off the Bengawan Solo, where δ13Corg of -22‰ and CaCO3 contents of ~17% rather point to marine phytoplankton as major organic matter source. Our preliminary results indicate a higher input of terrigenous organic matter from Kalimantan than from Java and show little evidence for anthropogenic impact on organic matter inputs into the Java Sea during the late Holocene.

Comparison of three DNA extraction kits to establish maximum yield and quality of coral-associated microbial DNA

USGS Publications Warehouse

Baker, Erin J.; Kellogg, Christina A.

2014-01-01

Coral microbiology is an expanding field, yet there is no standard DNA extraction protocol. Although many researchers depend on commercial extraction kits, no specific kit has been optimized for use with coral samples. Both soil and plant DNA extraction kits from MO BIO Laboratories, Inc., have been used by many research groups for this purpose. MO BIO recently replaced their PowerPlant® kit with an improved PowerPlantPro kit, but it was unclear how these changes would affect the kit’s use with coral samples. In order to determine which kit produced the best results, we conducted a comparison between the original PowerPlant kit, the new PowerPlantPro kit, and an alternative kit, PowerSoil, using samples from several different coral genera. The PowerPlantPro kit had the highest DNA yields, but the lack of 16S rRNA gene amplification in many samples suggests that much of the yield may be coral DNA rather than microbial DNA. The most consistent positive amplifications came from the PowerSoil kit.

Doing Mathematics with Bicycle Gear Ratios.

ERIC Educational Resources Information Center

Stump, Sheryl L.

2000-01-01

Describes an activity in which students examine bicycle chain-rings, cogs, and gear ratios as a means of exploring algebraic relationships, data collection, scatter plots, and lines of best fit. (KHR)

Identification of mutations in the coding sequence of the proto-oncogene c-kit in a human mast cell leukemia cell line causing ligand-independent activation of c-kit product.

PubMed Central

Furitsu, T; Tsujimura, T; Tono, T; Ikeda, H; Kitayama, H; Koshimizu, U; Sugahara, H; Butterfield, J H; Ashman, L K; Kanayama, Y

1993-01-01

The c-kit proto-oncogene encodes a receptor tyrosine kinase. Binding of c-kit ligand, stem cell factor (SCF) to c-kit receptor (c-kitR) is known to activate c-kitR tyrosine kinase, thereby leading to autophosphorylation of c-kitR on tyrosine and to association of c-kitR with substrates such as phosphatidylinositol 3-kinase (PI3K). In a human mast cell leukemia cell line HMC-1, c-kitR was found to be constitutively phosphorylated on tyrosine, activated, and associated with PI3K without the addition of SCF. The expression of SCF mRNA transcript in HMC-1 cells was not detectable by means of PCR after reverse transcription (RT-PCR) analysis, suggesting that the constitutive activation of c-kitR was ligand independent. Sequencing of whole coding region of c-kit cDNA revealed that c-kit genes of HMC-1 cells were composed of a normal, wild-type allele and a mutant allele with two point mutations resulting in intracellular amino acid substitutions of Gly-560 for Val and Val-816 for Asp. Amino acid sequences in the regions of the two mutations are completely conserved in all of mouse, rat, and human c-kit. In order to determine the causal role of these mutations in the constitutive activation, murine c-kit mutants encoding Gly-559 and/or Val-814, corresponding to human Gly-560 and/or Val-816, were constructed by site-directed mutagenesis and expressed in a human embryonic kidney cell line, 293T cells. In the transfected cells, both c-kitR (Gly-559, Val-814) and c-kitR (Val-814) were abundantly phosphorylated on tyrosine and activated in immune complex kinase reaction in the absence of SCF, whereas tyrosine phosphorylation and activation of c-kitR (Gly-559) or wild-type c-kitR was modest or little, respectively. These results suggest that conversion of Asp-816 to Val in human c-kitR may be an activating mutation and responsible for the constitutive activation of c-kitR in HMC-1 cells. Images PMID:7691885

Distributed Planning in a Mixed-Initiative Environment

DTIC Science & Technology

2008-06-01

Knowledge Sources Control Remote Blackboard Remote Knowledge Sources Remot e Data Remot e Data Java Distributed Blackboard Figure 3 - Distributed...an interface agent or planning agent and the second type is a critic agent. Agents in the DEEP architecture extend and use the Java Agent...chosen because it is fully implemented in Java , and supports these requirements. 2.3.3 Interface Agents Interface agents are the interfaces through

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

[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.

Generic Bluetooth Data Module

DTIC Science & Technology

2002-09-01

to Ref (1). 34 RS232.java Serial Coomunication port class To Bluetooth module HCI.java Host Control Interface class L2CAP.java Logical Link Control...standard protocol for transporting IP datagrams over point-to-point link . It is designed to run over RFCOMM to accomplish point-to-point connections...Control and Adaption Host Controller Interface Link Manager Baseband / Link Controller Radio Figure 2. Bluetooth layers (From Ref. [3].) C

Distinct cellular properties of oncogenic KIT receptor tyrosine kinase mutants enable alternative courses of cancer cell inhibition

PubMed Central

Shi, Xiarong; Sousa, Leiliane P.; Mandel-Bausch, Elizabeth M.; Tome, Francisco; Reshetnyak, Andrey V.; Hadari, Yaron; Schlessinger, Joseph; Lax, Irit

2016-01-01

Large genomic sequencing analysis as part of precision medicine efforts revealed numerous activating mutations in receptor tyrosine kinases, including KIT. Unfortunately, a single approach is not effective for inhibiting cancer cells or treating cancers driven by all known oncogenic KIT mutants. Here, we show that each of the six major KIT oncogenic mutants exhibits different enzymatic, cellular, and dynamic properties and responds distinctly to different KIT inhibitors. One class of KIT mutants responded well to anti-KIT antibody treatment alone or in combination with a low dose of tyrosine kinase inhibitors (TKIs). A second class of KIT mutants, including a mutant resistant to imatinib treatment, responded well to a combination of TKI with anti-KIT antibodies or to anti-KIT toxin conjugates, respectively. We conclude that the preferred choice of precision medicine treatments for cancers driven by activated KIT and other RTKs may rely on clear understanding of the dynamic properties of oncogenic mutants. PMID:27482095

Megakaryocytes compensate for Kit insufficiency in murine arthritis.

PubMed

Cunin, Pierre; Penke, Loka R; Thon, Jonathan N; Monach, Paul A; Jones, Tatiana; Chang, Margaret H; Chen, Mary M; Melki, Imene; Lacroix, Steve; Iwakura, Yoichiro; Ware, Jerry; Gurish, Michael F; Italiano, Joseph E; Boilard, Eric; Nigrovic, Peter A

2017-05-01

The growth factor receptor Kit is involved in hematopoietic and nonhematopoietic development. Mice bearing Kit defects lack mast cells; however, strains bearing different Kit alleles exhibit diverse phenotypes. Herein, we investigated factors underlying differential sensitivity to IgG-mediated arthritis in 2 mast cell-deficient murine lines: KitWsh/Wsh, which develops robust arthritis, and KitW/Wv, which does not. Reciprocal bone marrow transplantation between KitW/Wv and KitWsh/Wsh mice revealed that arthritis resistance reflects a hematopoietic defect in addition to mast cell deficiency. In KitW/Wv mice, restoration of susceptibility to IgG-mediated arthritis was neutrophil independent but required IL-1 and the platelet/megakaryocyte markers NF-E2 and glycoprotein VI. In KitW/Wv mice, platelets were present in numbers similar to those in WT animals and functionally intact, and transfer of WT platelets did not restore arthritis susceptibility. These data implicated a platelet-independent role for the megakaryocyte, a Kit-dependent lineage that is selectively deficient in KitW/Wv mice. Megakaryocytes secreted IL-1 directly and as a component of circulating microparticles, which activated synovial fibroblasts in an IL-1-dependent manner. Transfer of WT but not IL-1-deficient megakaryocytes restored arthritis susceptibility to KitW/Wv mice. These findings identify functional redundancy among Kit-dependent hematopoietic lineages and establish an unanticipated capacity of megakaryocytes to mediate IL-1-driven systemic inflammatory disease.

Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night.

PubMed

Kiseleva, Olga; Poverennaya, Ekaterina; Shargunov, Alexander; Lisitsa, Andrey

2018-02-01

Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the "speed" of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui.googlecode.com ) into total result of proteoforms identification and optimized set of engines working simultaneously. We also compared the results of our search combination with Mascot results using protein kit UPS2, containing 48 human proteins. We selected combination of X!Tandem, MS-GF[Formula: see text] and OMMSA as the most time-efficient and productive combination of search. We added homemade java-script to automatize pipeline from file picking to report generation. These settings resulted in rise of the efficiency of our customized pipeline unobtainable by manual scouting: the analysis of 192 files searched against human proteome (42153 entries) downloaded from UniProt took 11[Formula: see text]h.

Development and Technical Validation of the Mobile Based Assistive Listening System: A Smartphone-Based Remote Microphone.

PubMed

Lopez, Esteban Alejandro; Costa, Orozimbo Alves; Ferrari, Deborah Viviane

2016-10-01

The purpose of this research note is to describe the development and technical validation of the Mobile Based Assistive Listening System (MoBALS), a free-of-charge smartphone-based remote microphone application. MoBALS Version 1.0 was developed for Android (Version 2.1 or higher) and was coded with Java using Eclipse Indigo with the Android Software Development Kit. A Wi-Fi router with background traffic and 2 affordable smartphones were used for debugging and technical validation comprising, among other things, multicasting capability, data packet loss, and battery consumption. MoBALS requires at least 2 smartphones connected to the same Wi-Fi router for signal transmission and reception. Subscriber identity module cards or Internet connections are not needed. MoBALS can be used alone or connected to a hearing aid or cochlear implant via direct audio input. Maximum data packet loss was 99.28%, and minimum battery life was 5 hr. Other relevant design specifications and their implementation are described. MoBALS performed as a remote microphone with enhanced accessibility features and avoids overhead expenses by using already-available and affordable technology. The further development and technical revalidation of MoBALS will be followed by clinical evaluation with persons with hearing impairment.

Constructing Adverse Outcome Pathways: a Demonstration of ...

EPA Pesticide Factsheets

Adverse outcome pathway (AOP) provides a conceptual framework to evaluate and integrate chemical toxicity and its effects across the levels of biological organization. As such, it is essential to develop a resource-efficient and effective approach to extend molecular initiating events (MIEs) of chemicals to their downstream phenotypes of a greater regulatory relevance. A number of ongoing public phenomics (high throughput phenotyping) efforts have been generating abundant phenotypic data annotated with ontology terms. These phenotypes can be analyzed semantically and linked to MIEs of interest, all in the context of a knowledge base integrated from a variety of ontologies for various species and knowledge domains. In such analyses, two phenotypic profiles (PPs; anchored by genes or diseases) each characterized by multiple ontology terms are compared for their semantic similarities within a common ontology graph, but across boundaries of species and knowledge domains. Taking advantage of publicly available ontologies and software tool kits, we have implemented an OS-Mapping (Ontology-based Semantics Mapping) approach as a Java application, and constructed a network of 19383 PPs as nodes with edges weighed by their pairwise semantic similarity scores. Individual PPs were assembled from public phenomics data. Out of possible 1.87×108 pairwise connections among these nodes, about 71% of them have similarity scores between 0.2 and the maximum possible of 1.0.

Signal transduction by normal isoforms and W mutant variants of the Kit receptor tyrosine kinase.

PubMed

Reith, A D; Ellis, C; Lyman, S D; Anderson, D M; Williams, D E; Bernstein, A; Pawson, T

1991-09-01

Germline mutations at the Dominant White Spotting (W) and Steel (Sl) loci have provided conclusive genetic evidence that c-kit mediated signal transduction pathways are essential for normal mouse development. We have analysed the interactions of normal and mutant W/c-kit gene products with cytoplasmic signalling proteins, using transient c-kit expression assays in COS cells. In addition to the previously identified c-kit gene product (Kit+), a second normal Kit isoform (KitA+) containing an in-frame insertion, Gly-Asn-Asn-Lys, within the extracellular domain, was detected in murine mast cell cultures and mid-gestation placenta. Both Kit+ and KitA+ isoforms showed increased autophosphorylation and enhanced association with phosphatidylinositol (PI) 3' kinase and PLC gamma 1, when stimulated with recombinant soluble Steel factor. No association or increase in phosphorylation of GAP and two GAP-associated proteins, p62 and p190, was observed. The two isoforms had distinct activities in the absence of exogenous soluble Steel factor; Kit+, but not KitA+, showed constitutive tyrosine phosphorylation that was accompanied by a low constitutive level of association with PI-3' kinase and PLC gamma 1. Introduction of the point substitutions associated with W37 (Glu582----Lys) or W41 (Val831----Met) mutant alleles into c-kit expression constructs abolished (W37) or reduced (W41) the Steel factor-induced association of the Kit receptor with signalling proteins in a manner proportional to the overall severity of the corresponding W mutant phenotype. These data suggest a diversity of normal Kit signalling pathways and indicate that W mutant phenotypes result from primary defects in the Kit receptor that affect its interaction with cytoplasmic signalling proteins.

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.

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.