Three-dimensional user interfaces for scientific visualization

NASA Technical Reports Server (NTRS)

Vandam, Andries

1995-01-01

The main goal of this project is to develop novel and productive user interface techniques for creating and managing visualizations of computational fluid dynamics (CFD) datasets. We have implemented an application framework in which we can visualize computational fluid dynamics user interfaces. This UI technology allows users to interactively place visualization probes in a dataset and modify some of their parameters. We have also implemented a time-critical scheduling system which strives to maintain a constant frame-rate regardless of the number of visualization techniques. In the past year, we have published parts of this research at two conferences, the research annotation system at Visualization 1994, and the 3D user interface at UIST 1994. The real-time scheduling system has been submitted to SIGGRAPH 1995 conference. Copies of these documents are included with this report.

Interactive graphical computer-aided design system

NASA Technical Reports Server (NTRS)

Edge, T. M.

1975-01-01

System is used for design, layout, and modification of large-scale-integrated (LSI) metal-oxide semiconductor (MOS) arrays. System is structured around small computer which provides real-time support for graphics storage display unit with keyboard, slave display unit, hard copy unit, and graphics tablet for designer/computer interface.

Cooperative Data Sharing: Simple Support for Clusters of SMP Nodes

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Balley, David H. (Technical Monitor)

1997-01-01

Libraries like PVM and MPI send typed messages to allow for heterogeneous cluster computing. Lower-level libraries, such as GAM, provide more efficient access to communication by removing the need to copy messages between the interface and user space in some cases. still lower-level interfaces, such as UNET, get right down to the hardware level to provide maximum performance. However, these are all still interfaces for passing messages from one process to another, and have limited utility in a shared-memory environment, due primarily to the fact that message passing is just another term for copying. This drawback is made more pertinent by today's hybrid architectures (e.g. clusters of SMPs), where it is difficult to know beforehand whether two communicating processes will share memory. As a result, even portable language tools (like HPF compilers) must either map all interprocess communication, into message passing with the accompanying performance degradation in shared memory environments, or they must check each communication at run-time and implement the shared-memory case separately for efficiency. Cooperative Data Sharing (CDS) is a single user-level API which abstracts all communication between processes into the sharing and access coordination of memory regions, in a model which might be described as "distributed shared messages" or "large-grain distributed shared memory". As a result, the user programs to a simple latency-tolerant abstract communication specification which can be mapped efficiently to either a shared-memory or message-passing based run-time system, depending upon the available architecture. Unlike some distributed shared memory interfaces, the user still has complete control over the assignment of data to processors, the forwarding of data to its next likely destination, and the queuing of data until it is needed, so even the relatively high latency present in clusters can be accomodated. CDS does not require special use of an MMU, which can add overhead to some DSM systems, and does not require an SPMD programming model. unlike some message-passing interfaces, CDS allows the user to implement efficient demand-driven applications where processes must "fight" over data, and does not perform copying if processes share memory and do not attempt concurrent writes. CDS also supports heterogeneous computing, dynamic process creation, handlers, and a very simple thread-arbitration mechanism. Additional support for array subsections is currently being considered. The CDS1 API, which forms the kernel of CDS, is built primarily upon only 2 communication primitives, one process initiation primitive, and some data translation (and marshalling) routines, memory allocation routines, and priority control routines. The entire current collection of 28 routines provides enough functionality to implement most (or all) of MPI 1 and 2, which has a much larger interface consisting of hundreds of routines. still, the API is small enough to consider integrating into standard os interfaces for handling inter-process communication in a network-independent way. This approach would also help to solve many of the problems plaguing other higher-level standards such as MPI and PVM which must, in some cases, "play OS" to adequately address progress and process control issues. The CDS2 API, a higher level of interface roughly equivalent in functionality to MPI and to be built entirely upon CDS1, is still being designed. It is intended to add support for the equivalent of communicators, reduction and other collective operations, process topologies, additional support for process creation, and some automatic memory management. CDS2 will not exactly match MPI, because the copy-free semantics of communication from CDS1 will be supported. CDS2 application programs will be free to carefully also use CDS1. CDS1 has been implemented on networks of workstations running unmodified Unix-based operating systems, using UDP/IP and vendor-supplied high- performance locks. Although its inter-node performance is currently unimpressive due to rudimentary implementation technique, it even now outperforms highly-optimized MPI implementation on intra-node communication due to its support for non-copy communication. The similarity of the CDS1 architecture to that of other projects such as UNET and TRAP suggests that the inter-node performance can be increased significantly to surpass MPI or PVM, and it may be possible to migrate some of its functionality to communication controllers.

Uniform Interfaces for Distributed Systems.

DTIC Science & Technology

1980-05-01

in data str ’.ctures on stable storage (such as disk). The Virtual Terminals associated with a particular user (i.e., rM display terminal) are all...vec MESSAGESIZE let error = nil [S ReceiveAny (msg) // The copy is made so that lower-level routines may // munge the message template without losing

The APA Style Converter: a Web-based interface for converting articles to APA style for publication.

PubMed

Li, Ping; Cunningham, Krystal

2005-05-01

The APA Style Converter is a Web-based tool with which authors may prepare their articles in APA style according to the APA Publication Manual (5th ed.). The Converter provides a user-friendly interface that allows authors to copy and paste text and upload figures through the Web, and it automatically converts all texts, references, and figures to a structured article in APA style. The output is saved in PDF or RTF format, ready for either electronic submission or hardcopy printing.

Assessment Report Sandia National Laboratories Fuel Cycle Technologies Quality Assurance Evaluation of FY15 SNL FCT M2 Milestone Deliverables

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

Appel, Gordon John

Sandia National Laboratories (SNL) Fuel Cycle Technologies (FCT) program activities are conducted in accordance with FCT Quality Assurance Program Document (FCT-QAPD) requirements. The FCT-QAPD interfaces with SNL approved Quality Assurance Program Description (SNL-QAPD) as explained in the Sandia National Laboratories QA Program Interface Document for FCT Activities (Interface Document). This plan describes SNL's FY16 assessment of SNL's FY15 FCT M2 milestone deliverable's compliance with program QA requirements, including SNL R&A requirements. The assessment is intended to confirm that SNL's FY15 milestone deliverables contain the appropriate authenticated review documentation and that there is a copy marked with SNL R&A numbers.

The Evolution of Computer Based Learning Software Design: Computer Assisted Teaching Unit Experience.

ERIC Educational Resources Information Center

Blandford, A. E.; Smith, P. R.

1986-01-01

Describes the style of design of computer simulations developed by Computer Assisted Teaching Unit at Queen Mary College with reference to user interface, input and initialization, input data vetting, effective display screen use, graphical results presentation, and need for hard copy. Procedures and problems relating to academic involvement are…

Software-defined network abstractions and configuration interfaces for building programmable quantum networks

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

Dasari, Venkat; Sadlier, Ronald J; Geerhart, Mr. Billy

Well-defined and stable quantum networks are essential to realize functional quantum applications. Quantum networks are complex and must use both quantum and classical channels to support quantum applications like QKD, teleportation, and superdense coding. In particular, the no-cloning theorem prevents the reliable copying of quantum signals such that the quantum and classical channels must be highly coordinated using robust and extensible methods. We develop new network abstractions and interfaces for building programmable quantum networks. Our approach leverages new OpenFlow data structures and table type patterns to build programmable quantum networks and to support quantum applications.

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

PubMed Central

2018-01-01

Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that ‘leftover’ proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles. PMID:29518071

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis.

PubMed

Holland, David O; Johnson, Margaret E

2018-03-01

Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that 'leftover' proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles.

BAOBAB: a Java editor for large phylogenetic trees.

PubMed

Dutheil, J; Galtier, N

2002-06-01

BAOBAB is a Java user interface dedicated to viewing and editing large phylogenetic trees. Original features include: (i) a colour-mediated overview of magnified subtrees; (ii) copy/cut/paste of (sub)trees within or between windows; (iii) compressing/ uncompressing subtrees; and (iv) managing sequence files together with tree files. http://www.univ-montp2.fr/~genetix/.

Figure 2 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

Cancer.gov

Grouping and sorting genomic data in IGV. The IGV user interface displaying 202 glioblastoma samples from TCGA. Samples are grouped by tumor subtype (second annotation column) and data type (first annotation column) and sorted by copy number of the EGFR locus (middle column). Adapted from Figure 1; Robinson et al. 2011

Software-defined network abstractions and configuration interfaces for building programmable quantum networks

NASA Astrophysics Data System (ADS)

Dasari, Venkat R.; Sadlier, Ronald J.; Geerhart, Billy E.; Snow, Nikolai A.; Williams, Brian P.; Humble, Travis S.

2017-05-01

Well-defined and stable quantum networks are essential to realize functional quantum communication applications. Quantum networks are complex and must use both quantum and classical channels to support quantum applications like QKD, teleportation, and superdense coding. In particular, the no-cloning theorem prevents the reliable copying of quantum signals such that the quantum and classical channels must be highly coordinated using robust and extensible methods. In this paper, we describe new network abstractions and interfaces for building programmable quantum networks. Our approach leverages new OpenFlow data structures and table type patterns to build programmable quantum networks and to support quantum applications.

A brain computer interface-based explorer.

PubMed

Bai, Lijuan; Yu, Tianyou; Li, Yuanqing

2015-04-15

In recent years, various applications of brain computer interfaces (BCIs) have been studied. In this paper, we present a hybrid BCI combining P300 and motor imagery to operate an explorer. Our system is mainly composed of a BCI mouse, a BCI speller and an explorer. Through this system, the user can access his computer and manipulate (open, close, copy, paste, and delete) files such as documents, pictures, music, movies and so on. The system has been tested with five subjects, and the experimental results show that the explorer can be successfully operated according to subjects' intentions. Copyright © 2014 Elsevier B.V. All rights reserved.

78 FR 11129 - Office of Engineering and Technology Seeks Comment on Updated OET-69 Software

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-15

... cell level, and also speeds calculations since the study grid only needs to be established one time... who choose to file by paper must file an original and one copy of each filing. If more than one docket... interface (implemented in Java), used to establish the parameters of the study and which draws data from...

7 CFR 1755.910 - RUS specification for outside plant housings and serving area interface systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... accordance with 5 U.S.C. 552(a) and 1 CFR part 51. A copy of the UL standard is available for inspection... approved by the Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 7 CFR part 51... or nonmetallic materials in different sizes and configurations to suit a variety of applications. The...

Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.

PubMed

Ma, Buyong; Pan, Yongping; Gunasekaran, K; Venkataraghavan, R Babu; Levine, Arnold J; Nussinov, Ruth

2005-03-15

p53, the tumor suppressor protein, functions as a dimer of dimers. However, how the tetramer binds to the DNA is still an open question. In the crystal structure, three copies of the p53 monomers (containing chains A, B, and C) were crystallized with the DNA-consensus element. Although the structure provides crucial data on the p53-DNA contacts, the active oligomeric state is unclear because the two dimeric (A-B and B-C) interfaces present in the crystal cannot both exist in the tetramer. Here, we address the question of which of these two dimeric interfaces may be more biologically relevant. We analyze the sequence and structural properties of the p53-p53 dimeric interfaces and carry out extensive molecular dynamics simulations of the crystal structures of the human and mouse p53 dimers. We find that the A-B interface residues are more conserved than those of the B-C. Molecular dynamics simulations show that the A-B interface can provide a stable DNA-binding motif in the dimeric state, unlike B-C. Our results indicate that the interface between chains A-B in the p53-DNA complex constitutes a better candidate for a stable biological interface, whereas the B-C interface is more likely to be due to crystal packing. Thus, they have significant implications toward our understanding of DNA binding by p53 as well as p53-mediated interactions with other proteins.

The Raid distributed database system

NASA Technical Reports Server (NTRS)

Bhargava, Bharat; Riedl, John

1989-01-01

Raid, a robust and adaptable distributed database system for transaction processing (TP), is described. Raid is a message-passing system, with server processes on each site to manage concurrent processing, consistent replicated copies during site failures, and atomic distributed commitment. A high-level layered communications package provides a clean location-independent interface between servers. The latest design of the package delivers messages via shared memory in a configuration with several servers linked into a single process. Raid provides the infrastructure to investigate various methods for supporting reliable distributed TP. Measurements on TP and server CPU time are presented, along with data from experiments on communications software, consistent replicated copy control during site failures, and concurrent distributed checkpointing. A software tool for evaluating the implementation of TP algorithms in an operating-system kernel is proposed.

Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

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

Bowers, Geoffrey

United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

New Initiatives for Electronic Scholarly Publishing: Academic Information Sources on the Internet

DTIC Science & Technology

2004-12-01

parallel with the changing economics of publishing. A strong movement, among researchers and academics ( user community), seeks to free scientific...interface between the user and a vast amount of published and unpublished information (Oppenheim 1997: 398), which was made available in hard copy, via...have implemented facilities that enable the user to exercise clear options for selectively retrieving material (OpCit), to discuss and rank the articles

Handling of the demilitarized zone using service providers in SAP

NASA Astrophysics Data System (ADS)

Iovan, A.; Robu, R.

2016-02-01

External collaboration needs to allow data access from the Internet. In a trusted Internet collaboration scenario where the external user works on the same data like the internal user direct access to the data in the Intranet is required. The paper presents a solution to get access to certain data in the Enterprise Resource Planning system, having the User Interface on a system in the Demilitarized Zone and the database on a system which is located in the trusted area. Using the Service Provider Interface framework, connections between separate systems can be created in different areas of the network. The paper demonstrates how to connect the two systems, one in the Demilitarized Zone and one in the trusted area, using SAP ERP 6.0 with Enhancement Package 7. In order to use the Service Provider Interface SAP Business Suite Foundation component must be installed in both systems. The advantage of using the Service Provider Interface framework is that the external user works on the same data like the internal user (and not on copies). This assures data consistency and less overhead for backup and security systems.

Improvements to the National Transport Code Collaboration Data Server

NASA Astrophysics Data System (ADS)

Alexander, David A.

2001-10-01

The data server of the National Transport Code Colaboration Project provides a universal network interface to interpolated or raw transport data accessible by a universal set of names. Data can be acquired from a local copy of the Iternational Multi-Tokamak (ITER) profile database as well as from TRANSP trees of MDS Plus data systems on the net. Data is provided to the user's network client via a CORBA interface, thus providing stateful data server instances, which have the advantage of remembering the desired interpolation, data set, etc. This paper will review the status and discuss the recent improvements made to the data server, such as the modularization of the data server and the addition of hdf5 and MDS Plus data file writing capability.

The UMLS Knowledge Sources: Tools for Building Better User Interfaces

PubMed Central

Lindberg, Donald A. B.; Humphreys, Betsy L.

1990-01-01

The current focus of the National Library of Medicine's Unified Medical Language System (UMLS) project is the development, testing, and evaluation of the first versions of three new knowledge sources: the Metathesaurus, the Semantic Network, and the Information Sources Map. These three knowledge sources can be used by interface programs to conduct an intelligent interaction with the user and to make the conceptual link between the user's question and relevant machine-readable information. NLM is providing experimental copies of the initial versions of the UMLS knowledge sources in exchange for feedback on ways they can and should be improved. The hope is that the results of such experimentation will provide both immediate improvements in biomedical information service and useful suggestions for enhancements to the UMLS.

Copy Hiding Application Interface

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

Jones, Holger; Poliakoff, David; Robinson, Peter

2016-10-06

CHAI is a light-weight framework which abstracts the automated movement of data (e.g. to/from Host/Device) via RAJA like performance portability programming model constructs. It can be viewed as a utility framework and an adjunct to FAJA (A Performance Portability Framework). Performance Portability is a technique that abstracts the complexities of modern Heterogeneous Architectures while allowing the original program to undergo incremental minimally invasive code changes in order to adapt to the newer architectures.

Determination of real-time polymerase chain reaction uncertainty of measurement using replicate analysis and a graphical user interface with Fieller’s theorem

PubMed Central

Stuart, James Ian; Delport, Johan; Lannigan, Robert; Zahariadis, George

2014-01-01

BACKGROUND: Disease monitoring of viruses using real-time polymerase chain reaction (PCR) requires knowledge of the precision of the test to determine what constitutes a significant change. Calculation of quantitative PCR confidence limits requires bivariate statistical methods. OBJECTIVE: To develop a simple-to-use graphical user interface to determine the uncertainty of measurement (UOM) of BK virus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV) real-time PCR assays. METHODS: Thirty positive clinical samples for each of the three viral assays were repeated once. A graphical user interface was developed using a spreadsheet (Excel, Microsoft Corporation, USA) to enable data entry and calculation of the UOM (according to Fieller’s theorem) and PCR efficiency. RESULTS: The confidence limits for the BK virus, CMV and EBV tests were ∼0.5 log, 0.5 log to 1.0 log, and 0.5 log to 1.0 log, respectively. The efficiencies of these assays, in the same order were 105%, 119% and 90%. The confidence limits remained stable over the linear range of all three tests. DISCUSSION: A >5 fold (0.7 log) and a >3-fold (0.5 log) change in viral load were significant for CMV and EBV when the results were ≤1000 copies/mL and >1000 copies/mL, respectively. A >3-fold (0.5 log) change in viral load was significant for BK virus over its entire linear range. PCR efficiency was ideal for BK virus and EBV but not CMV. Standardized international reference materials and shared reporting of UOM among laboratories are required for the development of treatment guidelines for BK virus, CMV and EBV in the context of changes in viral load. PMID:25285125

Determination of real-time polymerase chain reaction uncertainty of measurement using replicate analysis and a graphical user interface with Fieller's theorem.

PubMed

Stuart, James Ian; Delport, Johan; Lannigan, Robert; Zahariadis, George

2014-07-01

Disease monitoring of viruses using real-time polymerase chain reaction (PCR) requires knowledge of the precision of the test to determine what constitutes a significant change. Calculation of quantitative PCR confidence limits requires bivariate statistical methods. To develop a simple-to-use graphical user interface to determine the uncertainty of measurement (UOM) of BK virus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV) real-time PCR assays. Thirty positive clinical samples for each of the three viral assays were repeated once. A graphical user interface was developed using a spreadsheet (Excel, Microsoft Corporation, USA) to enable data entry and calculation of the UOM (according to Fieller's theorem) and PCR efficiency. The confidence limits for the BK virus, CMV and EBV tests were ∼0.5 log, 0.5 log to 1.0 log, and 0.5 log to 1.0 log, respectively. The efficiencies of these assays, in the same order were 105%, 119% and 90%. The confidence limits remained stable over the linear range of all three tests. A >5 fold (0.7 log) and a >3-fold (0.5 log) change in viral load were significant for CMV and EBV when the results were ≤1000 copies/mL and >1000 copies/mL, respectively. A >3-fold (0.5 log) change in viral load was significant for BK virus over its entire linear range. PCR efficiency was ideal for BK virus and EBV but not CMV. Standardized international reference materials and shared reporting of UOM among laboratories are required for the development of treatment guidelines for BK virus, CMV and EBV in the context of changes in viral load.

Distributed computing system with dual independent communications paths between computers and employing split tokens

NASA Technical Reports Server (NTRS)

Rasmussen, Robert D. (Inventor); Manning, Robert M. (Inventor); Lewis, Blair F. (Inventor); Bolotin, Gary S. (Inventor); Ward, Richard S. (Inventor)

1990-01-01

This is a distributed computing system providing flexible fault tolerance; ease of software design and concurrency specification; and dynamic balance of the loads. The system comprises a plurality of computers each having a first input/output interface and a second input/output interface for interfacing to communications networks each second input/output interface including a bypass for bypassing the associated computer. A global communications network interconnects the first input/output interfaces for providing each computer the ability to broadcast messages simultaneously to the remainder of the computers. A meshwork communications network interconnects the second input/output interfaces providing each computer with the ability to establish a communications link with another of the computers bypassing the remainder of computers. Each computer is controlled by a resident copy of a common operating system. Communications between respective ones of computers is by means of split tokens each having a moving first portion which is sent from computer to computer and a resident second portion which is disposed in the memory of at least one of computer and wherein the location of the second portion is part of the first portion. The split tokens represent both functions to be executed by the computers and data to be employed in the execution of the functions. The first input/output interfaces each include logic for detecting a collision between messages and for terminating the broadcasting of a message whereby collisions between messages are detected and avoided.

Development of the FITS tools package for multiple software environments

NASA Technical Reports Server (NTRS)

Pence, W. D.; Blackburn, J. K.

1992-01-01

The HEASARC is developing a package of general purpose software for analyzing data files in FITS format. This paper describes the design philosophy which makes the software both machine-independent (it runs on VAXs, Suns, and DEC-stations) and software environment-independent. Currently the software can be compiled and linked to produce IRAF tasks, or alternatively, the same source code can be used to generate stand-alone tasks using one of two implementations of a user-parameter interface library. The machine independence of the software is achieved by writing the source code in ANSI standard Fortran or C, using the machine-independent FITSIO subroutine interface for all data file I/O, and using a standard user-parameter subroutine interface for all user I/O. The latter interface is based on the Fortran IRAF Parameter File interface developed at STScI. The IRAF tasks are built by linking to the IRAF implementation of this parameter interface library. Two other implementations of this parameter interface library, which have no IRAF dependencies, are now available which can be used to generate stand-alone executable tasks. These stand-alone tasks can simply be executed from the machine operating system prompt either by supplying all the task parameters on the command line or by entering the task name after which the user will be prompted for any required parameters. A first release of this FTOOLS package is now publicly available. The currently available tasks are described, along with instructions on how to obtain a copy of the software.

Latest generation interconnect technologies in APEnet+ networking infrastructure

NASA Astrophysics Data System (ADS)

Ammendola, Roberto; Biagioni, Andrea; Cretaro, Paolo; Frezza, Ottorino; Lo Cicero, Francesca; Lonardo, Alessandro; Martinelli, Michele; Stanislao Paolucci, Pier; Pastorelli, Elena; Rossetti, Davide; Simula, Francesco; Vicini, Piero

2017-10-01

In this paper we present the status of the 3rd generation design of the APEnet board (V5) built upon the 28nm Altera Stratix V FPGA; it features a PCIe Gen3 x8 interface and enhanced embedded transceivers with a maximum capability of 12.5Gbps each. The network architecture is designed in accordance to the Remote DMA paradigm. The APEnet+ V5 prototype is built upon the Stratix V DevKit with the addition of a proprietary, third party IP core implementing multi-DMA engines. Support for zero-copy communication is assured by the possibility of DMA-accessing either host and GPU memory, offloading the CPU from the chore of data copying. The current implementation plateaus to a bandwidth for memory read of 4.8GB/s. Here we describe the hardware optimization to the memory write process which relies on the use of two independent DMA engines and an improved TLB.

Integrated Graphene-Based Optoelectronic Devices Used for Ultrafast Optical-THz Photodetectors, Modulators and Emitters

DTIC Science & Technology

2015-04-03

08 and AFRL/ CA policy clarification memorandum dated 16 Jan 09. This report is available to the general public, including foreign nationals. Copies... doped graphene micro-ribbon array and a quantum-well electron gas sitting at an interface between a half-space of air and another half-space of a... doped semiconductor substrate which supports a surface-plasmon mode in our system. The coupling between a spatially-modulated total electromagnetic

EEG correlates of P300-based brain-computer interface (BCI) performance in people with amyotrophic lateral sclerosis

NASA Astrophysics Data System (ADS)

Mak, Joseph N.; McFarland, Dennis J.; Vaughan, Theresa M.; McCane, Lynn M.; Tsui, Phillippa Z.; Zeitlin, Debra J.; Sellers, Eric W.; Wolpaw, Jonathan R.

2012-04-01

The purpose of this study was to identify electroencephalography (EEG) features that correlate with P300-based brain-computer interface (P300 BCI) performance in people with amyotrophic lateral sclerosis (ALS). Twenty people with ALS used a P300 BCI spelling application in copy-spelling mode. Three types of EEG features were found to be good predictors of P300 BCI performance: (1) the root-mean-square amplitude and (2) the negative peak amplitude of the event-related potential to target stimuli (target ERP) at Fz, Cz, P3, Pz, and P4; and (3) EEG theta frequency (4.5-8 Hz) power at Fz, Cz, P3, Pz, P4, PO7, PO8 and Oz. A statistical prediction model that used a subset of these features accounted for >60% of the variance in copy-spelling performance (p < 0.001, mean R2 = 0.6175). The correlations reflected between-subject, rather than within-subject, effects. The results enhance understanding of performance differences among P300 BCI users. The predictors found in this study might help in: (1) identifying suitable candidates for long-term P300 BCI operation; (2) assessing performance online. Further work on within-subject effects needs to be done to establish whether P300 BCI user performance could be improved by optimizing one or more of these EEG features.

Phast4Windows: A 3D graphical user interface for the reactive-transport simulator PHAST

USGS Publications Warehouse

Charlton, Scott R.; Parkhurst, David L.

2013-01-01

Phast4Windows is a Windows® program for developing and running groundwater-flow and reactive-transport models with the PHAST simulator. This graphical user interface allows definition of grid-independent spatial distributions of model properties—the porous media properties, the initial head and chemistry conditions, boundary conditions, and locations of wells, rivers, drains, and accounting zones—and other parameters necessary for a simulation. Spatial data can be defined without reference to a grid by drawing, by point-by-point definitions, or by importing files, including ArcInfo® shape and raster files. All definitions can be inspected, edited, deleted, moved, copied, and switched from hidden to visible through the data tree of the interface. Model features are visualized in the main panel of the interface, so that it is possible to zoom, pan, and rotate features in three dimensions (3D). PHAST simulates single phase, constant density, saturated groundwater flow under confined or unconfined conditions. Reactions among multiple solutes include mineral equilibria, cation exchange, surface complexation, solid solutions, and general kinetic reactions. The interface can be used to develop and run simple or complex models, and is ideal for use in the classroom, for analysis of laboratory column experiments, and for development of field-scale simulations of geochemical processes and contaminant transport.

CoNNeCT Baseband Processor Module Boot Code SoftWare (BCSW)

NASA Technical Reports Server (NTRS)

Yamamoto, Clifford K.; Orozco, David S.; Byrne, D. J.; Allen, Steven J.; Sahasrabudhe, Adit; Lang, Minh

2012-01-01

This software provides essential startup and initialization routines for the CoNNeCT baseband processor module (BPM) hardware upon power-up. A command and data handling (C&DH) interface is provided via 1553 and diagnostic serial interfaces to invoke operational, reconfiguration, and test commands within the code. The BCSW has features unique to the hardware it is responsible for managing. In this case, the CoNNeCT BPM is configured with an updated CPU (Atmel AT697 SPARC processor) and a unique set of memory and I/O peripherals that require customized software to operate. These features include configuration of new AT697 registers, interfacing to a new HouseKeeper with a flash controller interface, a new dual Xilinx configuration/scrub interface, and an updated 1553 remote terminal (RT) core. The BCSW is intended to provide a "safe" mode for the BPM when initially powered on or when an unexpected trap occurs, causing the processor to reset. The BCSW allows the 1553 bus controller in the spacecraft or payload controller to operate the BPM over 1553 to upload code; upload Xilinx bit files; perform rudimentary tests; read, write, and copy the non-volatile flash memory; and configure the Xilinx interface. Commands also exist over 1553 to cause the CPU to jump or call a specified address to begin execution of user-supplied code. This may be in the form of a real-time operating system, test routine, or specific application code to run on the BPM.

Observer's Interface for Solar System Target Specification

NASA Astrophysics Data System (ADS)

Roman, Anthony; Link, Miranda; Moriarty, Christopher; Stansberry, John A.

2016-10-01

When observing an asteroid or comet with HST, it has been necessary for the observer to manually enter the target's orbital elements into the Astronomer's Proposal Tool (APT). This allowed possible copy/paste transcription errors from the observer's source of orbital elements data. In order to address this issue, APT has now been improved with the capability to identify targets in and then download orbital elements from JPL Horizons. The observer will first use a target name resolver to choose the intended target from the Horizons database, and then download the orbital elements from Horizons directly into APT. A manual entry option is also still retained if the observer does not wish to use elements from Horizons. This new capability is available for HST observing, and it will also be supported for JWST observing. The poster shows examples of this new interface.

Observer's Interface for Solar System Target Specification

NASA Astrophysics Data System (ADS)

Roman, Anthony; Link, Miranda; Moriarty, Christopher; Stansberry, John A.

2016-01-01

When observing an asteroid or comet with HST, it has been necessary for the observer to manually enter the target's orbital elements into the Astronomer's Proposal Tool (APT). This allowed possible copy/paste transcription errors from the observer's source of orbital elements data. In order to address this issue, APT has now been improved with the capability to identify targets in and then download orbital elements from JPL Horizons. The observer will first use a target name resolver to choose the intended target from the Horizons database, and then download the orbital elements from Horizons directly into APT. A manual entry option is also still retained if the observer does not wish to use elements from Horizons. This new capability is available for HST observing, and it will also be supported for JWST observing. The poster shows examples of this new interface.

Phast4Windows: a 3D graphical user interface for the reactive-transport simulator PHAST.

PubMed

Charlton, Scott R; Parkhurst, David L

2013-01-01

Phast4Windows is a Windows® program for developing and running groundwater-flow and reactive-transport models with the PHAST simulator. This graphical user interface allows definition of grid-independent spatial distributions of model properties-the porous media properties, the initial head and chemistry conditions, boundary conditions, and locations of wells, rivers, drains, and accounting zones-and other parameters necessary for a simulation. Spatial data can be defined without reference to a grid by drawing, by point-by-point definitions, or by importing files, including ArcInfo® shape and raster files. All definitions can be inspected, edited, deleted, moved, copied, and switched from hidden to visible through the data tree of the interface. Model features are visualized in the main panel of the interface, so that it is possible to zoom, pan, and rotate features in three dimensions (3D). PHAST simulates single phase, constant density, saturated groundwater flow under confined or unconfined conditions. Reactions among multiple solutes include mineral equilibria, cation exchange, surface complexation, solid solutions, and general kinetic reactions. The interface can be used to develop and run simple or complex models, and is ideal for use in the classroom, for analysis of laboratory column experiments, and for development of field-scale simulations of geochemical processes and contaminant transport. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation

PubMed Central

Veal, Colin D.; Xu, Hang; Reekie, Katherine; Free, Robert; Hardwick, Robert J.; McVey, David; Brookes, Anthony J.; Hollox, Edward J.; Talbot, Christopher J.

2013-01-01

Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design. Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT. Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org). Contact: cjt14@le.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23742985

Genome-wide identification of significant aberrations in cancer genome.

PubMed

Yuan, Xiguo; Yu, Guoqiang; Hou, Xuchu; Shih, Ie-Ming; Clarke, Robert; Zhang, Junying; Hoffman, Eric P; Wang, Roger R; Zhang, Zhen; Wang, Yue

2012-07-27

Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC), a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1) exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2) performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3) iteratively detecting Significant Copy Number Aberrations (SCAs) and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS) on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma). When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC) or tumor suppressor genes (e.g., CDKN2A/B). Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes. Open-source and platform-independent SAIC software is implemented using C++, together with R scripts for data formatting and Perl scripts for user interfacing, and it is easy to install and efficient to use. The source code and documentation are freely available at http://www.cbil.ece.vt.edu/software.htm.

Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.

PubMed

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2009-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present "Entrez Neuron", a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the 'HCLS knowledgebase' developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrate how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup.

Databases for LDEF results

NASA Technical Reports Server (NTRS)

Bohnhoff-Hlavacek, Gail

1992-01-01

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

Potential-sensing electrochemical atomic force microscopy for in operando analysis of water-splitting catalysts and interfaces

NASA Astrophysics Data System (ADS)

Nellist, Michael R.; Laskowski, Forrest A. L.; Qiu, Jingjing; Hajibabaei, Hamed; Sivula, Kevin; Hamann, Thomas W.; Boettcher, Shannon W.

2018-01-01

Heterogeneous electrochemical phenomena, such as (photo)electrochemical water splitting to generate hydrogen using semiconductors and/or electrocatalysts, are driven by the accumulated charge carriers and thus the interfacial electrochemical potential gradients that promote charge transfer. However, measurements of the "surface" electrochemical potential during operation are not generally possible using conventional electrochemical techniques, which measure/control the potential of a conducting electrode substrate. Here we show that the nanoscale conducting tip of an atomic force microscope cantilever can sense the surface electrochemical potential of electrocatalysts in operando. To demonstrate utility, we measure the potential-dependent and thickness-dependent electronic properties of cobalt (oxy)hydroxide phosphate (CoPi). We then show that CoPi, when deposited on illuminated haematite (α-Fe2O3) photoelectrodes, acts as both a hole collector and an oxygen evolution catalyst. We demonstrate the versatility of the technique by comparing surface potentials of CoPi-decorated planar and mesoporous haematite and discuss viability for broader application in the study of electrochemical phenomena.

Title V Interface Issues

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Policy and Guidance Database available at www2.epa.gov/title-v-operating-permits/title-v-operating-permit-policy-and-guidance-document-index. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Scalable Unix tools on parallel processors

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

Gropp, W.; Lusk, E.

1994-12-31

The introduction of parallel processors that run a separate copy of Unix on each process has introduced new problems in managing the user`s environment. This paper discusses some generalizations of common Unix commands for managing files (e.g. 1s) and processes (e.g. ps) that are convenient and scalable. These basic tools, just like their Unix counterparts, are text-based. We also discuss a way to use these with a graphical user interface (GUI). Some notes on the implementation are provided. Prototypes of these commands are publicly available.

Title IV-Title V Interface Guidance for States

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Policy and Guidance Database available at www2.epa.gov/title-v-operating-permits/title-v-operating-permit-policy-and-guidance-document-index. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Development of Network Interface Cards for TRIDAQ systems with the NaNet framework

NASA Astrophysics Data System (ADS)

Ammendola, R.; Biagioni, A.; Cretaro, P.; Di Lorenzo, S.; Fiorini, M.; Frezza, O.; Lamanna, G.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Neri, I.; Paolucci, P. S.; Pastorelli, E.; Piandani, R.; Pontisso, L.; Rossetti, D.; Simula, F.; Sozzi, M.; Valente, P.; Vicini, P.

2017-03-01

NaNet is a framework for the development of FPGA-based PCI Express (PCIe) Network Interface Cards (NICs) with real-time data transport architecture that can be effectively employed in TRIDAQ systems. Key features of the architecture are the flexibility in the configuration of the number and kind of the I/O channels, the hardware offloading of the network protocol stack, the stream processing capability, and the zero-copy CPU and GPU Remote Direct Memory Access (RDMA). Three NIC designs have been developed with the NaNet framework: NaNet-1 and NaNet-10 for the CERN NA62 low level trigger and NaNet3 for the KM3NeT-IT underwater neutrino telescope DAQ system. We will focus our description on the NaNet-10 design, as it is the most complete of the three in terms of capabilities and integrated IPs of the framework.

A Design for Composing and Extending Vehicle Models

NASA Technical Reports Server (NTRS)

Madden, Michael M.; Neuhaus, Jason R.

2003-01-01

The Systems Development Branch (SDB) at NASA Langley Research Center (LaRC) creates simulation software products for research. Each product consists of an aircraft model with experiment extensions. SDB treats its aircraft models as reusable components, upon which experiments can be built. SDB has evolved aircraft model design with the following goals: 1. Avoid polluting the aircraft model with experiment code. 2. Discourage the copy and tailor method of reuse. The current evolution of that architecture accomplishes these goals by reducing experiment creation to extend and compose. The architecture mechanizes the operational concerns of the model's subsystems and encapsulates them in an interface inherited by all subsystems. Generic operational code exercises the subsystems through the shared interface. An experiment is thus defined by the collection of subsystems that it creates ("compose"). Teams can modify the aircraft subsystems for the experiment using inheritance and polymorphism to create variants ("extend").

Ancient origin of placental expression in the growth hormone genes of anthropoid primates

PubMed Central

Papper, Zack; Jameson, Natalie M.; Romero, Roberto; Weckle, Amy L.; Mittal, Pooja; Benirschke, Kurt; Santolaya-Forgas, Joaquin; Uddin, Monica; Haig, David; Goodman, Morris; Wildman, Derek E.

2009-01-01

In anthropoid primates, growth hormone (GH) genes have undergone at least 2 independent locus expansions, one in platyrrhines (New World monkeys) and another in catarrhines (Old World monkeys and apes). In catarrhines, the GH cluster has a pituitary-expressed gene called GH1; the remaining GH genes include placental GHs and placental lactogens. Here, we provide cDNA sequence evidence that the platyrrhine GH cluster also includes at least 3 placenta expressed genes and phylogenetic evidence that placenta expressed anthropoid GH genes have undergone strong adaptive evolution, whereas pituitary-expressed GH genes have faced strict functional constraint. Our phylogenetic evidence also points to lineage-specific gene gain and loss in early placental mammalian evolution, with at least three copies of the GH gene present at the time of the last common ancestor (LCA) of primates, rodents, and laurasiatherians. Anthropoid primates and laurasiatherians share gene descendants of one of these three copies, whereas rodents and strepsirrhine primates each maintain a separate copy. Eight of the amino-acid replacements that occurred on the lineage leading to the LCA of extant anthropoids have been implicated in GH signaling at the maternal-fetal interface. Thus, placental expression of GH may have preceded the separate series of GH gene duplications that occurred in catarrhines and platyrrhines (i.e., the roles played by placenta-expressed GHs in human pregnancy may have a longer evolutionary history than previously appreciated). PMID:19805162

Ancient origin of placental expression in the growth hormone genes of anthropoid primates.

PubMed

Papper, Zack; Jameson, Natalie M; Romero, Roberto; Weckle, Amy L; Mittal, Pooja; Benirschke, Kurt; Santolaya-Forgas, Joaquin; Uddin, Monica; Haig, David; Goodman, Morris; Wildman, Derek E

2009-10-06

In anthropoid primates, growth hormone (GH) genes have undergone at least 2 independent locus expansions, one in platyrrhines (New World monkeys) and another in catarrhines (Old World monkeys and apes). In catarrhines, the GH cluster has a pituitary-expressed gene called GH1; the remaining GH genes include placental GHs and placental lactogens. Here, we provide cDNA sequence evidence that the platyrrhine GH cluster also includes at least 3 placenta expressed genes and phylogenetic evidence that placenta expressed anthropoid GH genes have undergone strong adaptive evolution, whereas pituitary-expressed GH genes have faced strict functional constraint. Our phylogenetic evidence also points to lineage-specific gene gain and loss in early placental mammalian evolution, with at least three copies of the GH gene present at the time of the last common ancestor (LCA) of primates, rodents, and laurasiatherians. Anthropoid primates and laurasiatherians share gene descendants of one of these three copies, whereas rodents and strepsirrhine primates each maintain a separate copy. Eight of the amino-acid replacements that occurred on the lineage leading to the LCA of extant anthropoids have been implicated in GH signaling at the maternal-fetal interface. Thus, placental expression of GH may have preceded the separate series of GH gene duplications that occurred in catarrhines and platyrrhines (i.e., the roles played by placenta-expressed GHs in human pregnancy may have a longer evolutionary history than previously appreciated).

CNVinspector: a web-based tool for the interactive evaluation of copy number variations in single patients and in cohorts.

PubMed

Knierim, Ellen; Schwarz, Jana Marie; Schuelke, Markus; Seelow, Dominik

2013-08-01

Many genetic disorders are caused by copy number variations (CNVs) in the human genome. However, the large number of benign CNV polymorphisms makes it difficult to delineate causative variants for a certain disease phenotype. Hence, we set out to create software that accumulates and visualises locus-specific knowledge and enables clinicians to study their own CNVs in the context of known polymorphisms and disease variants. CNV data from healthy cohorts (Database of Genomic Variants) and from disease-related databases (DECIPHER) were integrated into a joint resource. Data are presented in an interactive web-based application that allows inspection, evaluation and filtering of CNVs in single individuals or in entire cohorts. CNVinspector provides simple interfaces to upload CNV data, compare them with own or published control data and visualise the results in graphical interfaces. Beyond choosing control data from different public studies, platforms and methods, dedicated filter options allow the detection of CNVs that are either enriched in patients or depleted in controls. Alternatively, a search can be restricted to those CNVs that appear in individuals of similar clinical phenotype. For each gene of interest within a CNV, we provide a link to NCBI, ENSEMBL and the GeneDistiller search engine to browse for potential disease-associated genes. With its user-friendly handling, the integration of control data and the filtering options, CNVinspector will facilitate the daily work of clinical geneticists and accelerate the delineation of new syndromes and gene functions. CNVinspector is freely accessible under http://www.cnvinspector.org.

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

PubMed

Zhang, Junjun; Baran, Joachim; Cros, A; Guberman, Jonathan M; Haider, Syed; Hsu, Jack; Liang, Yong; Rivkin, Elena; Wang, Jianxin; Whitty, Brett; Wong-Erasmus, Marie; Yao, Long; Kasprzyk, Arek

2011-01-01

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research

PubMed Central

Samwald, Matthias; Lim, Ernest; Masiar, Peter; Marenco, Luis; Chen, Huajun; Morse, Thomas; Mutalik, Pradeep; Shepherd, Gordon; Miller, Perry; Cheung, Kei-Hoi

2013-01-01

The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present “Entrez Neuron”, a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the ‘HCLS knowledgebase’ developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrates how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup. PMID:19745321

User's manual for the HYPGEN hyperbolic grid generator and the HGUI graphical user interface

NASA Technical Reports Server (NTRS)

Chan, William M.; Chiu, Ing-Tsau; Buning, Pieter G.

1993-01-01

The HYPGEN program is used to generate a 3-D volume grid over a user-supplied single-block surface grid. This is accomplished by solving the 3-D hyperbolic grid generation equations consisting of two orthogonality relations and one cell volume constraint. In this user manual, the required input files and parameters and output files are described. Guidelines on how to select the input parameters are given. Illustrated examples are provided showing a variety of topologies and geometries that can be treated. HYPGEN can be used in stand-alone mode as a batch program or it can be called from within a graphical user interface HGUI that runs on Silicon Graphics workstations. This user manual provides a description of the menus, buttons, sliders, and typein fields in HGUI for users to enter the parameters needed to run HYPGEN. Instructions are given on how to configure the interface to allow HYPGEN to run either locally or on a faster remote machine through the use of shell scripts on UNIX operating systems. The volume grid generated is copied back to the local machine for visualization using a built-in hook to PLOT3D.

Cross-language Babel structs—making scientific interfaces more efficient

NASA Astrophysics Data System (ADS)

Prantl, Adrian; Ebner, Dietmar; Epperly, Thomas G. W.

2013-01-01

Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture, it is employed in a wide range of scientific applications where it is used to connect components written in different programming languages. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in (mono-lingual) scientific application programming interfaces (APIs); they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific codes can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++, Fortran 2003/2008 and Chapel, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90/95, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data to compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods. A case study shows how structs can help simplify the interfaces of scientific codes significantly.

EBR-II and TREAT Digitization Project

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

Griffith, George W.; Rabiti, Cristian

2015-09-01

Digitizing the technical drawings for EBR-II and TREAT provides multiple benefits. Moving the scanned or hard copy drawings to modern 3-D CAD (Computer Aided Drawing) format saves data that could be lost over time. The 3-D drawings produce models that can interface with other drawings to make complex assemblies. The 3-D CAD format can also include detailed material properties and parametric coding that can tie critical dimensions together allowing easier modification. Creating the new files from the old drawings has found multiple inconsistencies that are being flagged or corrected improving understanding of the reactor(s).

Bedmap2; Mapping, visualizing and communicating the Antarctic sub-glacial environment.

NASA Astrophysics Data System (ADS)

Fretwell, Peter; Pritchard, Hamish

2013-04-01

Bedmap2; Mapping, visualizing and communicating the Antarctic sub-glacial environment. The Bedmap2 project has been a large cooperative effort to compile, model, map and visualize the ice-rock interface beneath the Antarctic ice sheet. Here we present the final output of that project; the Bedmap2 printed map. The map is an A1, double sided print, showing 2d and 3d visualizations of the dataset. It includes scientific interpretations, cross sections and comparisons with other areas. Paper copies of the colour double sided map will be freely distributed at this session.

Interactive comparison and remediation of collections of macromolecular structures.

PubMed

Moriarty, Nigel W; Liebschner, Dorothee; Klei, Herbert E; Echols, Nathaniel; Afonine, Pavel V; Headd, Jeffrey J; Poon, Billy K; Adams, Paul D

2018-01-01

Often similar structures need to be compared to reveal local differences throughout the entire model or between related copies within the model. Therefore, a program to compare multiple structures and enable correction any differences not supported by the density map was written within the Phenix framework (Adams et al., Acta Cryst 2010; D66:213-221). This program, called Structure Comparison, can also be used for structures with multiple copies of the same protein chain in the asymmetric unit, that is, as a result of non-crystallographic symmetry (NCS). Structure Comparison was designed to interface with Coot(Emsley et al., Acta Cryst 2010; D66:486-501) and PyMOL(DeLano, PyMOL 0.99; 2002) to facilitate comparison of large numbers of related structures. Structure Comparison analyzes collections of protein structures using several metrics, such as the rotamer conformation of equivalent residues, displays the results in tabular form and allows superimposed protein chains and density maps to be quickly inspected and edited (via the tools in Coot) for consistency, completeness and correctness. © 2017 The Protein Society.

Soft-copy sonography: cost reduction sensitivity analysis in a pediatric hospital.

PubMed

Don, S; Albertina, M J; Ammann, D

1998-03-01

Our objective was to determine whether interpreting sonograms of pediatric patients using soft-copy (computer workstation) instead of laser-printed film could reduce costs for a pediatric radiology department. We used theoretic models of growth to analyze costs. The costs of a sonographic picture archiving and communication system (three interface devices, two workstations, a network server, maintenance expenses, and storage media costs) were compared with the potential savings of eliminating film and increasing technologist efficiency or reducing the number of technologists. The model was based on historic trends and future capitation estimates that will reduce fee-for-service reimbursement. The effects of varying the study volume and reducing technologists' work hours were analyzed. By converting to soft-copy interpretation, we saved 6 min 32 sec per examination by eliminating film processing waiting time, thus reducing examination time from 30 min to 24 min. During an average day of 27 examinations, 176 min were saved. However, 33 min a day were spent retrieving prior studies from long-term storage; thus, 143 extra minutes a day were available for scanning. This improved efficiency could result in five more sonograms a day obtained by converting to soft-copy interpretation, using existing staff and equipment. Alternatively, five examinations a day would equate to one half of a full-time equivalent technologists position. Our analysis of costs considered that the hospital's anticipated growth of sonography and the depreciation of equipment during 5 years resulted in a savings of more than $606,000. Increasing the examinations by just 200 sonograms in the first year and no further growth resulted in a savings of more than $96,000. If the number of sonograms stayed constant, elimination of film printing alone resulted in a loss of approximately $157,000; reduction of one half of a full-time equivalent technologist's position would recuperate approximately $134,000 of that loss. Soft-copy sonography can save money through improved technologist efficiency, thereby increasing the number of sonograms obtained and revenue generated. If the number of sonograms does not increase, elimination of printing costs and reduction of staff technologists will not result in a savings.

Exploratory analysis of the copy number alterations in glioblastoma multiforme.

PubMed

Freire, Pablo; Vilela, Marco; Deus, Helena; Kim, Yong-Wan; Koul, Dimpy; Colman, Howard; Aldape, Kenneth D; Bogler, Oliver; Yung, W K Alfred; Coombes, Kevin; Mills, Gordon B; Vasconcelos, Ana T; Almeida, Jonas S

2008-01-01

The Cancer Genome Atlas project (TCGA) has initiated the analysis of multiple samples of a variety of tumor types, starting with glioblastoma multiforme. The analytical methods encompass genomic and transcriptomic information, as well as demographic and clinical data about the sample donors. The data create the opportunity for a systematic screening of the components of the molecular machinery for features that may be associated with tumor formation. The wealth of existing mechanistic information about cancer cell biology provides a natural reference for the exploratory exercise. Glioblastoma multiforme DNA copy number data was generated by The Cancer Genome Atlas project for 167 patients using 227 aCGH experiments, and was analyzed to build a catalog of aberrant regions. Genome screening was performed using an information theory approach in order to quantify aberration as a deviation from a centrality without the bias of untested assumptions about its parametric nature. A novel Cancer Genome Browser software application was developed and is made public to provide a user-friendly graphical interface in which the reported results can be reproduced. The application source code and stand alone executable are available at (http://code.google.com/p/cancergenome) and (http://bioinformaticstation.org), respectively. The most important known copy number alterations for glioblastoma were correctly recovered using entropy as a measure of aberration. Additional alterations were identified in different pathways, such as cell proliferation, cell junctions and neural development. Moreover, novel candidates for oncogenes and tumor suppressors were also detected. A detailed map of aberrant regions is provided.

Interface cloning and sharing: Interaction designs for conserving labor and maintaining state across 24X7 sensor operations teams

NASA Astrophysics Data System (ADS)

Ganter, John H.; Reeves, Paul C.

2017-05-01

Processing remote sensing data is the epitome of computation, yet real-time collection systems remain human-labor intensive. Operator labor is consumed by both overhead tasks (cost) and value-added production (benefit). In effect, labor is taxed and then lost. When an operator comes on-shift, they typically duplicate setup work that their teammates have already performed many times. "Pass down" of state information can be difficult if security restrictions require total logouts and blank screens - hours or even days of valuable history and context are lost. As work proceeds, duplicative effort is common because it is typically easier for operators to "do it over" rather than share what others have already done. As we begin a major new system version, we are refactoring the user interface to reduce time and motion losses. Working with users, we are developing "click budgets" to streamline interface use. One basic function is shared clipboards to reduce the use of sticky notes and verbal communication of data strings. We illustrate two additional designs to share work: window copying and window sharing. Copying (technically, shallow or deep object cloning) allows any system user to duplicate a window and configuration for themselves or another to use. Sharing allows a window to have multiple users: shareholders with read-write functionality and viewers with read-only. These solutions would allow windows to persist across multiple shifts, with a rotating cast of shareholders and viewers. Windows thus become durable objects of shared effort and persistent state. While these are low-tech functions, the cumulative labor savings in a 24X7 crew position (525,000 minutes/year spread over multiple individuals) would be significant. New design and implementation is never free and these investments typically do not appeal to government acquisition officers with short-term acquisition-cost concerns rather than a long-term O and M (operations and maintenance) perspective. We share some successes in educating some officers, in collaboration with system users, about the human capital involved in operating the systems they are acquiring.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set.

PubMed

Alvare, Graham Gm; Roche-Lima, Abiel; Fristensky, Brian

2012-11-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces.

A Upgrade of the Aeroheating Software "MINIVER"

NASA Technical Reports Server (NTRS)

Louderback, Pierce

2013-01-01

Many software packages assist engineers with performing flight vehicle analysis, but some of these packages have gone many years without updates or significant improvements to their workflows. One such software package, known as MINIVER, is a powerful yet lightweight tool used for aeroheating analyses. However, it is an aging program that has not seen major improvements within the past decade. As part of a collaborative effort with the Florida Institute of Technology, MINIVER has received a major user interface overhaul, a change in program language, and will be continually receiving updates to improve its capabilities. The user interface update includes a migration from a command-line interface to that of a graphical user interface supported in the Windows operating system. The organizational structure of the pre-processor has been transformed to clearly defined categories to provide ease of data entry. Helpful tools have been incorporated, including the ability to copy sections of cases as well as a generalized importer which aids in bulk data entry. A visual trajectory editor has been included, as well as a CAD Editor which allows the user to input simplified geometries in order to generate MINIVER cases in bulk. To demonstrate its continued effectiveness, a case involving the JAXA OREX flight vehicle will be included, providing comparisons to captured flight data as well as other computational solutions. The most recent upgrade effort incorporated the use of the CAD Editor, and current efforts are investigating methods to link MINIVER projects with SINDA/Fluint and Thermal Desktop.

An Upgrade of the Aeroheating Software "MINIVER"

NASA Technical Reports Server (NTRS)

Louderback, Pierce M.

2013-01-01

Many software packages assist engineers with performing flight vehicle analysis, but some of these packages have gone many years without updates or significant improvements to their workflows. One such software, known as MINIVER, is a powerful yet lightweight tool that is used for aeroheating analyses. However, it is an aging program that has not seen major improvements within the past decade. As part of a collaborative effort with Florida Institute of Technology, MINIVER has received a major user interface overhaul, a change in program language, and will be continually receiving updates to improve its capabilities. The user interface update includes a migration from a command-line interface to that of a graphical user interface supported in the Windows operating system. The organizational structure of the preprocessor has been transformed to clearly defined categories to provide ease of data entry. Helpful tools have been incorporated, including the ability to copy sections of cases as well as a generalized importer which aids in bulk data entry. A visual trajectory editor has been included, as well as a CAD Editor which allows the user to input simplified geometries in order to generate MINIVER cases in bulk. To demonstrate its continued effectiveness, a case involving the JAXA OREX flight vehicle will be included, providing comparisons to captured flight data as well as other computational solutions. The most recent upgrade effort incorporated the use of the CAD Editor, and current efforts are investigating methods to link MINIVER projects with SINDA/Fluint and Thermal Desktop.

Structure of a phage display-derived variant of human growth hormone complexed to two copies of the extracellular domain of its receptor: evidence for strong structural coupling between receptor binding sites.

PubMed

Schiffer, Celia; Ultsch, Mark; Walsh, Scott; Somers, William; de Vos, Abraham M; Kossiakoff, Anthony

2002-02-15

The structure of the ternary complex between the phage display- optimized, high-affinity Site 1 variant of human growth hormone (hGH) and two copies of the extracellular domain (ECD) of the hGH receptor (hGHR) has been determined at 2.6 A resolution. There are widespread and significant structural differences compared to the wild-type ternary hGH hGHR complex. The hGH variant (hGH(v)) contains 15 Site 1 mutations and binds>10(2) tighter to the hGHR ECD (hGH(R1)) at Site 1. It is biologically active and specific to hGHR. The hGH(v) Site 1 interface is somewhat smaller and 20% more hydrophobic compared to the wild-type (wt) counterpart. Of the ten hormone-receptor H-bonds in the site, only one is the same as in the wt complex. Additionally, several regions of hGH(v) structure move up to 9A in forming the interface. The contacts between the C-terminal domains of two receptor ECDs (hGH(R1)- hGH(R2)) are conserved; however, the large changes in Site 1 appear to cause global changes in the domains of hGH(R1) that affect the hGH(v)-hGH(R2) interface indirectly. This coupling is manifested by large changes in the conformation of groups participating in the Site 2 interaction and results in a structure for the site that is reorganized extensively. The hGH(v)- hGH(R2) interface contains seven H-bonds, only one of which is found in the wt complex. Several groups on hGH(v) and hGH(R2) undergo conformational changes of up to 8 A. Asp116 of hGH(v) plays a central role in the reorganization of Site 2 by forming two new H-bonds to the side-chains of Trp104(R2) and Trp169(R2), which are the key binding determinants of the receptor. The fact that a different binding solution is possible for Site 2, where there were no mutations or binding selection pressures, indicates that the structural elements found in these molecules possess an inherent functional plasticity that enables them to bind to a wide variety of binding surfaces. Copyright 2002 Elsevier Science Ltd.

Numerical simulation of nonlinear feedback model of saccade generation circuit implemented in the LabView graphical programming language.

PubMed

Jackson, M E; Gnadt, J W

1999-03-01

The object-oriented graphical programming language LabView was used to implement the numerical solution to a computational model of saccade generation in primates. The computational model simulates the activity and connectivity of anatomical strictures known to be involved in saccadic eye movements. The LabView program provides a graphical user interface to the model that makes it easy to observe and modify the behavior of each element of the model. Essential elements of the source code of the LabView program are presented and explained. A copy of the model is available for download from the internet.

Analysis of Carbon Fiber’s X-Ray Microscopic Structure

DTIC Science & Technology

1989-08-16

this translation were extracted from the best quality copy available. Aecesslem For icr: S SRA&I1 STIC TAB Una-oun ced Just Ifleatlo By D st ri lutI am...22, No. 5, 1968 FagES Tra1;slatez: 20-2"- r - r r,. s f-~ 1~ 2022’-D(( S -EE~3 Lec Kanner Associates V~.Bcx 517 s:c: d Citv C.A 9 4 0’ ANALYSIS OF...diffraction for fac_ (002) is es eciallv intense, with th, inter-face distance equal to 1/2 Je th carbmn fiber’s lattice constan. Becau2 iz - s

Amplitude-dependent topological edge states in nonlinear phononic lattices

NASA Astrophysics Data System (ADS)

Pal, Raj Kumar; Vila, Javier; Leamy, Michael; Ruzzene, Massimo

2018-03-01

This work investigates the effect of nonlinearities on topologically protected edge states in one- and two-dimensional phononic lattices. We first show that localized modes arise at the interface between two spring-mass chains that are inverted copies of each other. Explicit expressions derived for the frequencies of the localized modes guide the study of the effect of cubic nonlinearities on the resonant characteristics of the interface, which are shown to be described by a Duffing-like equation. Nonlinearities produce amplitude-dependent frequency shifts, which in the case of a softening nonlinearity cause the localized mode to migrate to the bulk spectrum. The case of a hexagonal lattice implementing a phononic analog of a crystal exhibiting the quantum spin Hall effect is also investigated in the presence of weakly nonlinear cubic springs. An asymptotic analysis provides estimates of the amplitude dependence of the localized modes, while numerical simulations illustrate how the lattice response transitions from bulk-to-edge mode-dominated by varying the excitation amplitude. In contrast with the interface mode of the first example studies, this occurs both for hardening and softening springs. The results of this study provide a theoretical framework for the investigation of nonlinear effects that induce and control topologically protected wave modes through nonlinear interactions and amplitude tuning.

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.

PubMed

Bharat, Tanmay A M; Murshudov, Garib N; Sachse, Carsten; Löwe, Jan

2015-07-02

Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

PubMed

Chaudhary, Ruchi; Fernández-Baca, David; Burleigh, John Gordon

2015-02-01

MulRF is a platform-independent software package for phylogenetic analysis using multi-copy gene trees. It seeks the species tree that minimizes the Robinson-Foulds (RF) distance to the input trees using a generalization of the RF distance to multi-labeled trees. The underlying generic tree distance measure and fast running time make MulRF useful for inferring phylogenies from large collections of gene trees, in which multiple evolutionary processes as well as phylogenetic error may contribute to gene tree discord. MulRF implements several features for customizing the species tree search and assessing the results, and it provides a user-friendly graphical user interface (GUI) with tree visualization. The species tree search is implemented in C++ and the GUI in Java Swing. MulRF's executable as well as sample datasets and manual are available at http://genome.cs.iastate.edu/CBL/MulRF/, and the source code is available at https://github.com/ruchiherself/MulRFRepo. ruchic@ufl.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

Multivariable Control Laws for the AFTI/F-16

DTIC Science & Technology

1983-07-01

file prior to entering TOTAL. 296 CREATE, AKEY, COPY, AMAT, rIMATi COPY, HMAT, BMAT , 741 COPY, CMAT, BMAT , COPY, JMAT, AMATi 72, COPY, CMAT, NMAT...COPY, MMAT, AfIAT, COPY, IMAT, BMAT , 74, COPY, CMAT, BMAT , COPY, LMAT, AMAT, 72, COPY, CMAT, OMAT, BKEY CREATE, BKEY, COPY, OMAT, AMAT, 75, COPY, CMAT...AMAT, COPY, NMAT, BMAT , 74, COPY, CMAT, BMAT , COPY, IMAT, AMAT, 74, COPY, CMATi BMAT , COPY, HMAT, AMAT, 73,1 COPY, CMAT, AMAT, 71, COPY, AMAT, EMAT

Assembling the Tat protein translocase

PubMed Central

Alcock, Felicity; Stansfeld, Phillip J; Basit, Hajra; Habersetzer, Johann; Baker, Matthew AB; Palmer, Tracy; Wallace, Mark I; Berks, Ben C

2016-01-01

The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues. Unexpectedly, we find that TatA also associates with TatC at the polar cluster site. Our data provide a structural model for assembly of the active Tat translocase in which substrate binding triggers replacement of TatB by TatA at the polar cluster site. Our work demonstrates the power of co-evolution analysis to predict protein interfaces in multi-subunit complexes. DOI: http://dx.doi.org/10.7554/eLife.20718.001 PMID:27914200

Phosphorylation at the Homotypic Interface Regulates Nucleoprotein Oligomerization and Assembly of the Influenza Virus Replication Machinery

PubMed Central

Mondal, Arindam; Potts, Gregory K.; Dawson, Anthony R.; Coon, Joshua J.; Mehle, Andrew

2015-01-01

Negative-sense RNA viruses assemble large ribonucleoprotein (RNP) complexes that direct replication and transcription of the viral genome. Influenza virus RNPs contain the polymerase, genomic RNA and multiple copies of nucleoprotein (NP). During RNP assembly, monomeric NP oligomerizes along the length of the genomic RNA. Regulated assembly of the RNP is essential for virus replication, but how NP is maintained as a monomer that subsequently oligomerizes to form RNPs is poorly understood. Here we elucidate a mechanism whereby NP phosphorylation regulates oligomerization. We identified new evolutionarily conserved phosphorylation sites on NP and demonstrated that phosphorylation of NP decreased formation of higher-order complexes. Two phosphorylation sites were located on opposite sides of the NP:NP interface. In both influenza A and B virus, mutating or mimicking phosphorylation at these residues blocked homotypic interactions and drove NP towards a monomeric form. Highlighting the central role of this process during infection, these mutations impaired RNP formation, polymerase activity and virus replication. Thus, dynamic phosphorylation of NP regulates RNP assembly and modulates progression through the viral life cycle. PMID:25867750

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

Analysis of performance improvements for host and GPU interface of the APENet+ 3D Torus network

NASA Astrophysics Data System (ADS)

Ammendola A, R.; Biagioni, A.; Frezza, O.; Lo Cicero, F.; Lonardo, A.; Paolucci, P. S.; Rossetti, D.; Simula, F.; Tosoratto, L.; Vicini, P.

2014-06-01

APEnet+ is an INFN (Italian Institute for Nuclear Physics) project aiming to develop a custom 3-Dimensional torus interconnect network optimized for hybrid clusters CPU-GPU dedicated to High Performance scientific Computing. The APEnet+ interconnect fabric is built on a FPGA-based PCI-express board with 6 bi-directional off-board links showing 34 Gbps of raw bandwidth per direction, and leverages upon peer-to-peer capabilities of Fermi and Kepler-class NVIDIA GPUs to obtain real zero-copy, GPU-to-GPU low latency transfers. The minimization of APEnet+ transfer latency is achieved through the adoption of RDMA protocol implemented in FPGA with specialized hardware blocks tightly coupled with embedded microprocessor. This architecture provides a high performance low latency offload engine for both trasmit and receive side of data transactions: preliminary results are encouraging, showing 50% of bandwidth increase for large packet size transfers. In this paper we describe the APEnet+ architecture, detailing the hardware implementation and discuss the impact of such RDMA specialized hardware on host interface latency and bandwidth.

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set

PubMed Central

Alvare, Graham GM; Roche-Lima, Abiel; Fristensky, Brian

2016-01-01

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level nonterminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces. PMID:27818582

Mechanisms and Dynamics of Abiotic and Biotic Interactions at Environmental Interfaces

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

Roso, Kevin M.

The Stanford EMSI (SEMSI) was established in 2004 through joint funding by the National Science Foundation and the OBER-ERSD. It encompasses a number of universities and national laboratories. The PNNL component of the SEMSI is funded by ERSD and is the focus of this report. This component has the objective of providing theory support to the SEMSI by bringing computational capabilities and expertise to bear on important electron transfer problems at mineral/water and mineral/microbe interfaces. PNNL staff member Dr. Kevin Rosso, who is also ''matrixed'' into the Environmental Molecular Sciences Laboratory (EMSL) at PNNL, is a co-PI on the SEMSImore » project and the PNNL lead. The EMSL computational facilities being applied to the SEMSI project include the 11.8 teraflop massively-parallel supercomputer. Science goals of this EMSL/SEMSI partnership include advancing our understanding of: (1) The kinetics of U(VI) and Cr(VI) reduction by aqueous and solid-phase Fe(II), (2) The structure of mineral surfaces in equilibrium with solution, and (3) Mechanisms of bacterial electron transfer to iron oxide surfaces via outer-membrane cytochromes.« less

Beam director design report

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

Younger, F.C.

1986-08-01

A design and fabrication effort for a beam director is documented. The conceptual design provides for the beam to pass first through a bending and focusing system (or ''achromat''), through a second achromat, through an air-to-vacuum interface (the ''beam window''), and finally through the vernier steering system. Following an initial concept study for a beam director, a prototype permanent magnet 30/sup 0/ beam-bending achromat and prototype vernier steering magnet were designed and built. In volume II, copies are included of the funding instruments, requests for quotations, purchase orders, a complete set of as-built drawings, magnetic measurement reports, the concept designmore » report, and the final report on the design and fabrication project. (LEW)« less

Accessing Data Federations with CVMFS

DOE PAGES

Weitzel, Derek; Bockelman, Brian; Dykstra, Dave; ...

2017-11-23

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the datamore » scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. Here, we will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.« less

Accessing Data Federations with CVMFS

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

Weitzel, Derek; Bockelman, Brian; Dykstra, Dave

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the datamore » scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. Here, we will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.« less

Hardware and Software Design of FPGA-based PCIe Gen3 interface for APEnet+ network interconnect system

NASA Astrophysics Data System (ADS)

Ammendola, R.; Biagioni, A.; Frezza, O.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Paolucci, P. S.; Pastorelli, E.; Rossetti, D.; Simula, F.; Tosoratto, L.; Vicini, P.

2015-12-01

In the attempt to develop an interconnection architecture optimized for hybrid HPC systems dedicated to scientific computing, we designed APEnet+, a point-to-point, low-latency and high-performance network controller supporting 6 fully bidirectional off-board links over a 3D torus topology. The first release of APEnet+ (named V4) was a board based on a 40 nm Altera FPGA, integrating 6 channels at 34 Gbps of raw bandwidth per direction and a PCIe Gen2 x8 host interface. It has been the first-of-its-kind device to implement an RDMA protocol to directly read/write data from/to Fermi and Kepler NVIDIA GPUs using NVIDIA peer-to-peer and GPUDirect RDMA protocols, obtaining real zero-copy GPU-to-GPU transfers over the network. The latest generation of APEnet+ systems (now named V5) implements a PCIe Gen3 x8 host interface on a 28 nm Altera Stratix V FPGA, with multi-standard fast transceivers (up to 14.4 Gbps) and an increased amount of configurable internal resources and hardware IP cores to support main interconnection standard protocols. Herein we present the APEnet+ V5 architecture, the status of its hardware and its system software design. Both its Linux Device Driver and the low-level libraries have been redeveloped to support the PCIe Gen3 protocol, introducing optimizations and solutions based on hardware/software co-design.

Accessing Data Federations with CVMFS

NASA Astrophysics Data System (ADS)

Weitzel, Derek; Bockelman, Brian; Dykstra, Dave; Blomer, Jakob; Meusel, Ren

2017-10-01

Data federations have become an increasingly common tool for large collaborations such as CMS and Atlas to efficiently distribute large data files. Unfortunately, these typically are implemented with weak namespace semantics and a non-POSIX API. On the other hand, CVMFS has provided a POSIX-compliant read-only interface for use cases with a small working set size (such as software distribution). The metadata required for the CVMFS POSIX interface is distributed through a caching hierarchy, allowing it to scale to the level of about a hundred thousand hosts. In this paper, we will describe our contributions to CVMFS that merges the data scalability of XRootD-based data federations (such as AAA) with metadata scalability and POSIX interface of CVMFS. We modified CVMFS so it can serve unmodified files without copying them to the repository server. CVMFS 2.2.0 is also able to redirect requests for data files to servers outside of the CVMFS content distribution network. Finally, we added the ability to manage authorization and authentication using security credentials such as X509 proxy certificates. We combined these modifications with the OSGs StashCache regional XRootD caching infrastructure to create a cached data distribution network. We will show performance metrics accessing the data federation through CVMFS compared to direct data federation access. Additionally, we will discuss the improved user experience of providing access to a data federation through a POSIX filesystem.

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

PubMed

Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

2017-01-06

The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements.

Altools: a user friendly NGS data analyser.

PubMed

Camiolo, Salvatore; Sablok, Gaurav; Porceddu, Andrea

2016-02-17

Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to address geographical population genomics of several model species. To access core SNPs and insertion/deletion polymorphisms (indels), and to infer the phyletic patterns of speciation, most such approaches map short reads to the reference genome. Variant calling is important to establish patterns of genome-wide association studies (GWAS) for quantitative trait loci (QTLs), and to determine the population and haplotype structure based on SNPs, thus allowing content-dependent trait and evolutionary analysis. Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions. The programs available for this purpose have different strengths (e.g. accuracy, sensitivity and specificity) and weaknesses (e.g. low computation speed, complex installation procedure and absence of a user-friendly interface). Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations. Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. It also uses insert size information from the alignment of paired-end reads and detects potential large deletions. A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms. Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of positive predictive values, sensitivity, the identification of large deletion breakpoints and copy number detection. Altools is fast, reliable and easy to use for the mining of NGS data. The software package also attempts to link identified polymorphisms and structural variants to their biological functions thus providing more valuable information than similar tools.

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice

NASA Astrophysics Data System (ADS)

Liu, Jingna; Xu, Heshui; Jiang, Ying; Zhang, Kai; Hu, Yuegao; Zeng, Zhaohai

2017-01-01

Azolla caroliniana Willd. is widely used as a green manure accompanying rice, but its ecological importance remains unclear, except for its ability to fix nitrogen in association with cyanobacteria. To investigate the impacts of Azolla cultivation on methane emissions and environmental variables in paddy fields, we performed this study on the plain of Dongting Lake, China, in 2014. The results showed that the dual cropping of Azolla significantly suppressed the methane emissions from paddies, likely due to the increase in redox potential in the root region and dissolved oxygen concentration at the soil-water interface. Furthermore, the floodwater pH decreased in association with Azolla cultivation, which is also a factor significantly correlated with the decrease in methane emissions. An increase in methanotrophic bacteria population (pmoA gene copies) and a reduction in methanogenic archaea (16S rRNA gene copies) were observed in association with Azolla growth. During rice cultivation period, dual cropping of Azolla also intensified increasing trend of 1/Simpson of methanogens and significantly decreased species richness (Chao 1) and species diversity (1/Simpson, 1/D) of methanotrophs. These results clearly demonstrate the suppression of CH4 emissions by culturing Azolla and show the environmental and microbial responses in paddy soil under Azolla cultivation.

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

PubMed Central

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H.; Lau, Ching C.; Behl, Sanjiv; Man, Tsz-Kwong

2007-01-01

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License. PMID:19936083

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

PubMed

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

2007-10-06

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice.

PubMed

Liu, Jingna; Xu, Heshui; Jiang, Ying; Zhang, Kai; Hu, Yuegao; Zeng, Zhaohai

2017-01-17

Azolla caroliniana Willd. is widely used as a green manure accompanying rice, but its ecological importance remains unclear, except for its ability to fix nitrogen in association with cyanobacteria. To investigate the impacts of Azolla cultivation on methane emissions and environmental variables in paddy fields, we performed this study on the plain of Dongting Lake, China, in 2014. The results showed that the dual cropping of Azolla significantly suppressed the methane emissions from paddies, likely due to the increase in redox potential in the root region and dissolved oxygen concentration at the soil-water interface. Furthermore, the floodwater pH decreased in association with Azolla cultivation, which is also a factor significantly correlated with the decrease in methane emissions. An increase in methanotrophic bacteria population (pmoA gene copies) and a reduction in methanogenic archaea (16S rRNA gene copies) were observed in association with Azolla growth. During rice cultivation period, dual cropping of Azolla also intensified increasing trend of 1/Simpson of methanogens and significantly decreased species richness (Chao 1) and species diversity (1/Simpson, 1/D) of methanotrophs. These results clearly demonstrate the suppression of CH 4 emissions by culturing Azolla and show the environmental and microbial responses in paddy soil under Azolla cultivation.

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice

PubMed Central

Liu, Jingna; Xu, Heshui; Jiang, Ying; Zhang, Kai; Hu, Yuegao; Zeng, Zhaohai

2017-01-01

Azolla caroliniana Willd. is widely used as a green manure accompanying rice, but its ecological importance remains unclear, except for its ability to fix nitrogen in association with cyanobacteria. To investigate the impacts of Azolla cultivation on methane emissions and environmental variables in paddy fields, we performed this study on the plain of Dongting Lake, China, in 2014. The results showed that the dual cropping of Azolla significantly suppressed the methane emissions from paddies, likely due to the increase in redox potential in the root region and dissolved oxygen concentration at the soil-water interface. Furthermore, the floodwater pH decreased in association with Azolla cultivation, which is also a factor significantly correlated with the decrease in methane emissions. An increase in methanotrophic bacteria population (pmoA gene copies) and a reduction in methanogenic archaea (16S rRNA gene copies) were observed in association with Azolla growth. During rice cultivation period, dual cropping of Azolla also intensified increasing trend of 1/Simpson of methanogens and significantly decreased species richness (Chao 1) and species diversity (1/Simpson, 1/D) of methanotrophs. These results clearly demonstrate the suppression of CH4 emissions by culturing Azolla and show the environmental and microbial responses in paddy soil under Azolla cultivation. PMID:28094773

CBM First-level Event Selector Input Interface Demonstrator

NASA Astrophysics Data System (ADS)

Hutter, Dirk; de Cuveland, Jan; Lindenstruth, Volker

2017-10-01

CBM is a heavy-ion experiment at the future FAIR facility in Darmstadt, Germany. Featuring self-triggered front-end electronics and free-streaming read-out, event selection will exclusively be done by the First Level Event Selector (FLES). Designed as an HPC cluster with several hundred nodes its task is an online analysis and selection of the physics data at a total input data rate exceeding 1 TByte/s. To allow efficient event selection, the FLES performs timeslice building, which combines the data from all given input links to self-contained, potentially overlapping processing intervals and distributes them to compute nodes. Partitioning the input data streams into specialized containers allows performing this task very efficiently. The FLES Input Interface defines the linkage between the FEE and the FLES data transport framework. A custom FPGA PCIe board, the FLES Interface Board (FLIB), is used to receive data via optical links and transfer them via DMA to the host’s memory. The current prototype of the FLIB features a Kintex-7 FPGA and provides up to eight 10 GBit/s optical links. A custom FPGA design has been developed for this board. DMA transfers and data structures are optimized for subsequent timeslice building. Index tables generated by the FPGA enable fast random access to the written data containers. In addition the DMA target buffers can directly serve as InfiniBand RDMA source buffers without copying the data. The usage of POSIX shared memory for these buffers allows data access from multiple processes. An accompanying HDL module has been developed to integrate the FLES link into the front-end FPGA designs. It implements the front-end logic interface as well as the link protocol. Prototypes of all Input Interface components have been implemented and integrated into the FLES test framework. This allows the implementation and evaluation of the foreseen CBM read-out chain.

Heat Resisting Metals for Gas Turbine Parts (N-102) - Chromium- Base Alloys

DTIC Science & Technology

1945-11-28

Copy No, 69 - a. F. Killer Cory No. 68 - 71 . L. B-dgor Copy No. 70 - N. U t’.ochol Members of tho flor Uotdtoirgy Coroitteo Copy Copy Ccpy...Copy Cory Copy Copy Copy Copy Copy Cory Copy Copy Cory Nc. 71 - Ctrl Broor No. 72 t Lyaen J. Briggs Nc. 73 - J. HOB H« C*itchott No, 74...Col, R.S.A. •Dcugh&rty No, 75 - Rudolph Furrer- < Nc. : 5 - H< 71 « Glllett No. 6 - S. D, Horen No. 76 - R. P. Houor • • < Nc. 7 - Zry Jeffries Nc

VidCat: an image and video analysis service for personal media management

NASA Astrophysics Data System (ADS)

Begeja, Lee; Zavesky, Eric; Liu, Zhu; Gibbon, David; Gopalan, Raghuraman; Shahraray, Behzad

2013-03-01

Cloud-based storage and consumption of personal photos and videos provides increased accessibility, functionality, and satisfaction for mobile users. One cloud service frontier that is recently growing is that of personal media management. This work presents a system called VidCat that assists users in the tagging, organization, and retrieval of their personal media by faces and visual content similarity, time, and date information. Evaluations for the effectiveness of the copy detection and face recognition algorithms on standard datasets are also discussed. Finally, the system includes a set of application programming interfaces (API's) allowing content to be uploaded, analyzed, and retrieved on any client with simple HTTP-based methods as demonstrated with a prototype developed on the iOS and Android mobile platforms.

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

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

Yoginath, Srikanth B.; Perumalla, Kalyan S.

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

eXtended CASA Line Analysis Software Suite (XCLASS)

NASA Astrophysics Data System (ADS)

Möller, T.; Endres, C.; Schilke, P.

2017-02-01

The eXtended CASA Line Analysis Software Suite (XCLASS) is a toolbox for the Common Astronomy Software Applications package (CASA) containing new functions for modeling interferometric and single dish data. Among the tools is the myXCLASS program which calculates synthetic spectra by solving the radiative transfer equation for an isothermal object in one dimension, whereas the finite source size and dust attenuation are considered as well. Molecular data required by the myXCLASS program are taken from an embedded SQLite3 database containing entries from the Cologne Database for Molecular Spectroscopy (CDMS) and JPL using the Virtual Atomic and Molecular Data Center (VAMDC) portal. Additionally, the toolbox provides an interface for the model optimizer package Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX), which helps to find the best description of observational data using myXCLASS (or another external model program), that is, finding the parameter set that most closely reproduces the data. http://www.astro.uni-koeln.de/projects/schilke/myXCLASSInterface A copy of the code is available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/598/A7

Motivation modulates the P300 amplitude during brain-computer interface use.

PubMed

Kleih, S C; Nijboer, F; Halder, S; Kübler, A

2010-07-01

This study examined the effect of motivation as a possible psychological influencing variable on P300 amplitude and performance in a brain-computer interface (BCI) controlled by event-related potentials (ERP). Participants were instructed to copy spell a sentence by attending to cells of a randomly flashing 7*7 matrix. Motivation was manipulated by monetary reward. In two experimental groups participants received 25 (N=11) or 50 (N=11) Euro cent for each correctly selected character; the control group (N=11) was not rewarded. BCI performance was defined as the overall percentage of correctly selected characters (correct response rate=CRR). Participants performed at an average of 99%. At electrode location Cz the P300 amplitude was positively correlated to self-rated motivation. The P300 amplitude of the most motivated participants was significantly higher than that of the least motivated participants. Highly motivated participants were able to communicate correctly faster with the ERP-BCI than less motivated participants. Motivation modulates the P300 amplitude in an ERP-BCI. Motivation may contribute to variance in BCI performance and should be monitored in BCI settings. Copyright 2010 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

DOE PAGES

Yoginath, Srikanth B.; Perumalla, Kalyan S.

2018-01-31

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

Optical Sound Generation and Amplification

DTIC Science & Technology

1983-01-15

acoustic cavitation threshold of water with concentration of the polymer additives polyethylene oxide and guar gum . It was found that small amounts of...Technical Library 2800 Powder Mill Road Adelphi, Maryland 20783 1 copy 3 copies 1 copy 1 copy 1 copy 1 copy 1 copy Naval Air Development Center

Beyond Copying: A Comparison of Multi-Component Interventions on Chinese Early Literacy Skills

ERIC Educational Resources Information Center

Wang, Ying; McBride, Catherine

2017-01-01

This study assessed the effects of three intervention programs for Chinese literacy development in kindergartners: the copying (Copy) program; a combined program of copying and Pinyin knowledge (Copy + Pinyin); and a combined program of copying and morphological awareness (Copy + MA). Ninety-seven kindergarteners aged 5-7 years in mainland China…

40 CFR 51.103 - Submission of plans, preliminary review of plans.

Code of Federal Regulations, 2011 CFR

2011-07-01

... State delivers five hard copies or at least two hard copies with an electronic version of the hard copy... an exact duplicate of the hard copy. (b) Upon request of a State, the Administrator will provide... hard copies or at least two hard copies with an electronic version of the hard copy (unless otherwise...

40 CFR 51.103 - Submission of plans, preliminary review of plans.

Code of Federal Regulations, 2014 CFR

2014-07-01

... State delivers five hard copies or at least two hard copies with an electronic version of the hard copy... an exact duplicate of the hard copy. (b) Upon request of a State, the Administrator will provide... hard copies or at least two hard copies with an electronic version of the hard copy (unless otherwise...

40 CFR 51.103 - Submission of plans, preliminary review of plans.

Code of Federal Regulations, 2013 CFR

2013-07-01

... State delivers five hard copies or at least two hard copies with an electronic version of the hard copy... an exact duplicate of the hard copy. (b) Upon request of a State, the Administrator will provide... hard copies or at least two hard copies with an electronic version of the hard copy (unless otherwise...

40 CFR 51.103 - Submission of plans, preliminary review of plans.

Code of Federal Regulations, 2012 CFR

2012-07-01

... State delivers five hard copies or at least two hard copies with an electronic version of the hard copy... an exact duplicate of the hard copy. (b) Upon request of a State, the Administrator will provide... hard copies or at least two hard copies with an electronic version of the hard copy (unless otherwise...

40 CFR 51.103 - Submission of plans, preliminary review of plans.

Code of Federal Regulations, 2010 CFR

2010-07-01

... State delivers five hard copies or at least two hard copies with an electronic version of the hard copy... an exact duplicate of the hard copy. (b) Upon request of a State, the Administrator will provide... hard copies or at least two hard copies with an electronic version of the hard copy (unless otherwise...

CD-based image archival and management on a hybrid radiology intranet.

PubMed

Cox, R D; Henri, C J; Bret, P M

1997-08-01

This article describes the design and implementation of a low-cost image archival and management solution on a radiology network consisting of UNIX, IBM personal computer-compatible (IBM, Purchase, NY) and Macintosh (Apple Computer, Cupertino, CA) workstations. The picture archiving and communications system (PACS) is modular, scaleable and conforms to the Digital Imaging and Communications in Medicine (DICOM) 3.0 standard for image transfer, storage and retrieval. Image data is made available on soft-copy reporting workstations by a work-flow management scheme and on desktop computers through a World Wide Web (WWW) interface. Data archival is based on recordable compact disc (CD) technology and is automated. The project has allowed the radiology department to eliminate the use of film in magnetic resonance (MR) imaging, computed tomography (CT) and ultrasonography.

Fifth NASA Goddard Conference on Mass Storage Systems and Technologies.. Volume 1

NASA Technical Reports Server (NTRS)

Kobler, Benjamin (Editor); Hariharan, P. C. (Editor)

1996-01-01

This document contains copies of those technical papers received in time for publication prior to the Fifth Goddard Conference on Mass Storage Systems and Technologies. As one of an ongoing series, this conference continues to serve as a unique medium for the exchange of information on topics relating to the ingestion and management of substantial amounts of data and the attendant problems involved. This year's discussion topics include storage architecture, database management, data distribution, file system performance and modeling, and optical recording technology. There will also be a paper on Application Programming Interfaces (API) for a Physical Volume Repository (PVR) defined in Version 5 of the Institute of Electrical and Electronics Engineers (IEEE) Reference Model (RM). In addition, there are papers on specific archives and storage products.

Interaction surface and topology of Get3-Get4-Get5 protein complex, involved in targeting tail-anchored proteins to endoplasmic reticulum.

PubMed

Chang, Yi-Wei; Lin, Tai-Wen; Li, Yi-Chuan; Huang, Yu-Shan; Sun, Yuh-Ju; Hsiao, Chwan-Deng

2012-02-10

Recent work has uncovered the "GET system," which is responsible for endoplasmic reticulum targeting of tail-anchored proteins. Although structural information and the individual roles of most components of this system have been defined, the interactions and interplay between them remain to be elucidated. Here, we investigated the interactions between Get3 and the Get4-Get5 complex from Saccharomyces cerevisiae. We show that Get3 interacts with Get4-Get5 via an interface dominated by electrostatic forces. Using isothermal titration calorimetry and small-angle x-ray scattering, we further demonstrate that the Get3 homodimer interacts with two copies of the Get4-Get5 complex to form an extended conformation in solution.

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

PubMed

Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simão, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M

2015-01-01

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.

PubMed

Povysil, Gundula; Tzika, Antigoni; Vogt, Julia; Haunschmid, Verena; Messiaen, Ludwine; Zschocke, Johannes; Klambauer, Günter; Hochreiter, Sepp; Wimmer, Katharina

2017-07-01

Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy-number variations (CNVs) in addition to single-nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics. © 2017 The Authors. Human Mutation published by Wiley Periodicals, Inc.

Advanced transportation system studies. Technical area 2: Heavy lift launch vehicle development. Volume 2; Technical Results

NASA Technical Reports Server (NTRS)

1995-01-01

Sections 10 to 13 of the Advanced Transportation System Studies final report are included in this volume. Section 10 contains a copy of an executive summary that was prepared by Lockheed Space Operations Company (LSOC) to document their support to the TA-2 contract during the first-year period of performance of the contract, May 1992 through May 1993. LSOC participated on the TA-2 contract as part of the concurrent engineering launch system definition team, and provided outstanding heavy lift launch vehicle (HLLV) ground operations requirements and concept assessments for Lockheed Missiles and Space Company (LMSC) through an intercompany work transfer as well as providing specific HLLV ground operations assessments at the direction of NASA KSC through KSC funding that was routed to the TA-2 contract. Section 11 contains a copy of a vehicle-independent, launch system health management requirements assessment. The purpose of the assessment was to define both health management requirements and the associated interfaces between a generic advanced transportation system launch vehicle and all related elements of the entire transportation system, including the ground segment. Section 12 presents the major TA-2 presentations provided to summarize the significant results and conclusions that were developed over the course of the contract. Finally, Section 13 presents the design and assessment report on the first lunar outpost heavy lift launch vehicle.

CONAN: copy number variation analysis software for genome-wide association studies

PubMed Central

2010-01-01

Background Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) promise to shed additional light on the genetic basis of monogenic as well as complex diseases and phenotypes. Indeed, the number of detected associations between CNVs and certain phenotypes are constantly increasing. However, while several software packages support the determination of CNVs from SNP chip data, the downstream statistical inference of CNV-phenotype associations is still subject to complicated and inefficient in-house solutions, thus strongly limiting the performance of GWAS based on CNVs. Results CONAN is a freely available client-server software solution which provides an intuitive graphical user interface for categorizing, analyzing and associating CNVs with phenotypes. Moreover, CONAN assists the evaluation process by visualizing detected associations via Manhattan plots in order to enable a rapid identification of genome-wide significant CNV regions. Various file formats including the information on CNVs in population samples are supported as input data. Conclusions CONAN facilitates the performance of GWAS based on CNVs and the visual analysis of calculated results. CONAN provides a rapid, valid and straightforward software solution to identify genetic variation underlying the 'missing' heritability for complex traits that remains unexplained by recent GWAS. The freely available software can be downloaded at http://genepi-conan.i-med.ac.at. PMID:20546565

"Cloning Words": Euphemism, Neologism and Dysphemism as Literary Devices in Kazuo Ishiguro's "Never Let Me Go"

ERIC Educational Resources Information Center

Pandey, Anjali

2011-01-01

This essay examines the theme and trope of "copies" in Kazuo Ishiguro's novel "Never Let Me Go." Whatever one's final reading of the novel, the theme and thread of copy, copies, copying and copied is never far off. In a semantic sense then, the act of "copying", both as a verb and the indexing of "copies" as…

Flight Test of Advanced Digital Control Concepts.

DTIC Science & Technology

1982-03-01

34 equations, and this result is then compared against the "model" equations. OPTION :::CREATrE ,CIEY, COFPY, MAT ,AMAT, COIP-YUMAT, BMAT , 74 COPFY, CMAT...BMATY .-COPY, NMAT, AMAT ,72 ,COPY, GMAT, RMA, COP:Y, (MAT, BMA’TCOFY, MA T ,AMAT >74, COPY, CMA’TsmA, PCOPY, RMAT, BmAT , pCOPYVMiAT , AMAo.T 72...COP’Y, MAT, AMAT, >75, COPY , MAtT, BMAT , COPY, ZMAT, AMAT, 74 ,COP’Y, MAT, TMAT, COPY, VMAT, AMAT, .:COPY ,RMAiT, MAT,73,COPW GMAT, E4MAT, COP-"YTMAT

Estimating the Probability of Traditional Copying, Conditional on Answer-Copying Statistics.

PubMed

Allen, Jeff; Ghattas, Andrew

2016-06-01

Statistics for detecting copying on multiple-choice tests produce p values measuring the probability of a value at least as large as that observed, under the null hypothesis of no copying. The posterior probability of copying is arguably more relevant than the p value, but cannot be derived from Bayes' theorem unless the population probability of copying and probability distribution of the answer-copying statistic under copying are known. In this article, the authors develop an estimator for the posterior probability of copying that is based on estimable quantities and can be used with any answer-copying statistic. The performance of the estimator is evaluated via simulation, and the authors demonstrate how to apply the formula using actual data. Potential uses, generalizability to other types of cheating, and limitations of the approach are discussed.

High-order polygonal discontinuous Petrov-Galerkin (PolyDPG) methods using ultraweak formulations

NASA Astrophysics Data System (ADS)

Vaziri Astaneh, Ali; Fuentes, Federico; Mora, Jaime; Demkowicz, Leszek

2018-04-01

This work represents the first endeavor in using ultraweak formulations to implement high-order polygonal finite element methods via the discontinuous Petrov-Galerkin (DPG) methodology. Ultraweak variational formulations are nonstandard in that all the weight of the derivatives lies in the test space, while most of the trial space can be chosen as copies of $L^2$-discretizations that have no need to be continuous across adjacent elements. Additionally, the test spaces are broken along the mesh interfaces. This allows one to construct conforming polygonal finite element methods, termed here as PolyDPG methods, by defining most spaces by restriction of a bounding triangle or box to the polygonal element. The only variables that require nontrivial compatibility across elements are the so-called interface or skeleton variables, which can be defined directly on the element boundaries. Unlike other high-order polygonal methods, PolyDPG methods do not require ad hoc stabilization terms thanks to the crafted stability of the DPG methodology. A proof of convergence of the form $h^p$ is provided and corroborated through several illustrative numerical examples. These include polygonal meshes with $n$-sided convex elements and with highly distorted concave elements, as well as the modeling of discontinuous material properties along an arbitrary interface that cuts a uniform grid. Since PolyDPG methods have a natural a posteriori error estimator a polygonal adaptive strategy is developed and compared to standard adaptivity schemes based on constrained hanging nodes. This work is also accompanied by an open-source $\\texttt{PolyDPG}$ software supporting polygonal and conventional elements.

CCL3L1 copy number and susceptibility to malaria

PubMed Central

Carpenter, Danielle; Färnert, Anna; Rooth, Ingegerd; Armour, John A.L.; Shaw, Marie-Anne

2012-01-01

Copy number variation can contribute to the variation observed in susceptibility to complex diseases. Here we present the first study to investigate copy number variation of the chemokine gene CCL3L1 with susceptibility to malaria. We present a family-based genetic analysis of a Tanzanian population (n = 922), using parasite load, mean number of clinical infections of malaria and haemoglobin levels as phenotypes. Copy number of CCL3L1 was measured using the paralogue ratio test (PRT) and the dataset exhibited copy numbers ranging between 1 and 10 copies per diploid genome (pdg). Association between copy number and phenotypes was assessed. Furthermore, we were able to identify copy number haplotypes in some families, using microsatellites within the copy variable region, for transmission disequilibrium testing. We identified a high level of copy number haplotype diversity and find some evidence for an association of low CCL3L1 copy number with protection from anaemia. PMID:22484763

CCL3L1 copy number and susceptibility to malaria.

PubMed

Carpenter, Danielle; Färnert, Anna; Rooth, Ingegerd; Armour, John A L; Shaw, Marie-Anne

2012-07-01

Copy number variation can contribute to the variation observed in susceptibility to complex diseases. Here we present the first study to investigate copy number variation of the chemokine gene CCL3L1 with susceptibility to malaria. We present a family-based genetic analysis of a Tanzanian population (n=922), using parasite load, mean number of clinical infections of malaria and haemoglobin levels as phenotypes. Copy number of CCL3L1 was measured using the paralogue ratio test (PRT) and the dataset exhibited copy numbers ranging between 1 and 10 copies per diploid genome (pdg). Association between copy number and phenotypes was assessed. Furthermore, we were able to identify copy number haplotypes in some families, using microsatellites within the copy variable region, for transmission disequilibrium testing. We identified a high level of copy number haplotype diversity and find some evidence for an association of low CCL3L1 copy number with protection from anaemia. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparison of medical students' learning approaches between electronic and hard copy team-based learning.

PubMed

Sharaf, Fawzy; Alnohair, Sultan

2017-01-01

To compare the students' perception of team-based learning (TBL): The paper (hard copy) compared with the e-copy (electronic copy) in the family medicine course of the fifth year medical students, Qassim University College of Medicine. A cross-sectional study was conducted during the family medicine course in 2015-2016 to compare the hard copy and the e-copy TBL sessions. We used Google drive to distribute, collect and analyze the questionnaire. The results of the e-copy TBL are shown and displayed directly with each session to the students, which was not the same as practiced with hard copy. We used also SPSS (version 17 for Windows) for more statistical analysis. The total number of respondents of students in each was 96; a phase of TBL phase 1 (hard copy) and phase 2 (e-copy). Male were 64 (66.7%) and females 32 (33.3%). The first three knowledge questions showed no difference between the mean score between paper and e-copy TBL, but of the perception questions showed a significant difference between the paper and e-copy TBL. The results of the survey showed that the students prefer e-copy TBL as a course format, as it was an attraction for most of the students and making them even more successful in the key exam and e-copy TBL develop the skills needed to work productively in task-groups.

Buyer-seller watermarking protocol based on amplitude modulation and the El Gamal Public Key Crypto System

NASA Astrophysics Data System (ADS)

Memon, Nasir D.; Wong, Ping W.

1999-04-01

Digital watermarks have recently been proposed for the purposes of copy protection and copy deterrence for multimedia content. In copy deterrence, a content owner (seller) inserts a unique watermark into a copy of the content before it is sold to a buyer. If the buyer resells unauthorized copies of the watermarked content, then these copies can be traced to the unlawful reseller (original buyer) using a watermark detection algorithm. One problem with such an approach is that the original buyer whose watermark has been found on unauthorized copies can claim that the unauthorized copy was created or caused (for example, by a security breach) by the original seller. In this paper we propose an interactive buyer-seller protocol for invisible watermarking in which the seller does not get to know the exact watermarked copy that the buyer receives. Hence the seller cannot create copies of the original content containing the buyer's watermark. In cases where the seller finds an unauthorized copy, the seller can identify the buyer from a watermark in the unauthorized copy, and furthermore the seller can prove this fact to a third party using a dispute resolution protocol. This prevents the buyer from claiming that an unauthorized copy may have originated from the seller.

COPI selectively drives maturation of the early Golgi

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

Papanikou, Effrosyni; Day, Kasey J.; Austin, II, Jotham

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generatemore » partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Lastly, our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins.« less

COPI selectively drives maturation of the early Golgi

DOE PAGES

Papanikou, Effrosyni; Day, Kasey J.; Austin, II, Jotham; ...

2015-12-28

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generatemore » partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Lastly, our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins.« less

Beam Requirements for Light-Ion-Driven Inertial-Confinement Fusion.

DTIC Science & Technology

1980-11-27

NN 8711S Attn: J. R. Freenan I copy General Electric Company S. Hmphries 1 copy Space Division o. J. Johnson I copy Valley Forge Space Center G. W...for 3141 Sandia RPT Coll I copy Attn: J. C. Penden VFSC. PA. 4230M 1 copy AVCO Iesearch ard Systems Sroup General Electric Company 201 Lowell Street...copy Attn: P. Sub 1 copy Beeing Company . The Institute for Defense Analyses P. 0. Box 3707 400 Army-Navy Drive Seattle. VA 9蕌 Arlington, VA 22202 Attn

Reporting requirements for skeletal digital radiography: comparison of soft-copy and hard-copy presentation.

PubMed

O'Connor, P J; Davies, A G; Fowler, R C; Lintott, D J; Bury, R F; Parkin, G J; Martinez, D; Saifuddin, A; Cowen, A R

1998-04-01

To assess diagnostic performance and reader preference when reporting results from digital hard-copy and two soft-copy formats of skeletal digital radiography. The data comprised hand radiographs of patients undergoing renal dialysis. Normal hand radiographs obtained in trauma patients were assessed as control images. One hundred fifteen images acquired with a photostimulable-phosphor computed radiography system were analyzed. Image selection and initial assessment were by consensus of two experienced radiologists, who graded the radiographic changes of hyperparathyroidism with the Ritz scoring system. The images were then presented to four readers in three formats: hard-copy output and soft-copy presentations at 2K2 and 1K2 resolutions. These readers scored pathologic change and image preference. The results were analyzed with the receiver operating characteristic technique. There was a significant improvement in diagnostic performance for both soft-copy formats relative to the hard-copy format (P < .001). No significant difference in diagnostic performance was found between the two soft-copy formats. There was a significant preference for both soft-copy formats relative to the hard-copy format (P < .01), with the 2K2 soft-copy images preferred to the 1K2 images (P < .01). Soft-copy reporting can provide superior diagnostic performance even for images viewed at a modest (1K2) resolution. The lack of difference between the two soft-copy formats has important economic implications with respect to departmental hardware requirements.

Runtime and Architecture Support for Efficient Data Exchange in Multi-Accelerator Applications.

PubMed

Cabezas, Javier; Gelado, Isaac; Stone, John E; Navarro, Nacho; Kirk, David B; Hwu, Wen-Mei

2015-05-01

Heterogeneous parallel computing applications often process large data sets that require multiple GPUs to jointly meet their needs for physical memory capacity and compute throughput. However, the lack of high-level abstractions in previous heterogeneous parallel programming models force programmers to resort to multiple code versions, complex data copy steps and synchronization schemes when exchanging data between multiple GPU devices, which results in high software development cost, poor maintainability, and even poor performance. This paper describes the HPE runtime system, and the associated architecture support, which enables a simple, efficient programming interface for exchanging data between multiple GPUs through either interconnects or cross-node network interfaces. The runtime and architecture support presented in this paper can also be used to support other types of accelerators. We show that the simplified programming interface reduces programming complexity. The research presented in this paper started in 2009. It has been implemented and tested extensively in several generations of HPE runtime systems as well as adopted into the NVIDIA GPU hardware and drivers for CUDA 4.0 and beyond since 2011. The availability of real hardware that support key HPE features gives rise to a rare opportunity for studying the effectiveness of the hardware support by running important benchmarks on real runtime and hardware. Experimental results show that in a exemplar heterogeneous system, peer DMA and double-buffering, pinned buffers, and software techniques can improve the inter-accelerator data communication bandwidth by 2×. They can also improve the execution speed by 1.6× for a 3D finite difference, 2.5× for 1D FFT, and 1.6× for merge sort, all measured on real hardware. The proposed architecture support enables the HPE runtime to transparently deploy these optimizations under simple portable user code, allowing system designers to freely employ devices of different capabilities. We further argue that simple interfaces such as HPE are needed for most applications to benefit from advanced hardware features in practice.

Runtime and Architecture Support for Efficient Data Exchange in Multi-Accelerator Applications

PubMed Central

Cabezas, Javier; Gelado, Isaac; Stone, John E.; Navarro, Nacho; Kirk, David B.; Hwu, Wen-mei

2014-01-01

Heterogeneous parallel computing applications often process large data sets that require multiple GPUs to jointly meet their needs for physical memory capacity and compute throughput. However, the lack of high-level abstractions in previous heterogeneous parallel programming models force programmers to resort to multiple code versions, complex data copy steps and synchronization schemes when exchanging data between multiple GPU devices, which results in high software development cost, poor maintainability, and even poor performance. This paper describes the HPE runtime system, and the associated architecture support, which enables a simple, efficient programming interface for exchanging data between multiple GPUs through either interconnects or cross-node network interfaces. The runtime and architecture support presented in this paper can also be used to support other types of accelerators. We show that the simplified programming interface reduces programming complexity. The research presented in this paper started in 2009. It has been implemented and tested extensively in several generations of HPE runtime systems as well as adopted into the NVIDIA GPU hardware and drivers for CUDA 4.0 and beyond since 2011. The availability of real hardware that support key HPE features gives rise to a rare opportunity for studying the effectiveness of the hardware support by running important benchmarks on real runtime and hardware. Experimental results show that in a exemplar heterogeneous system, peer DMA and double-buffering, pinned buffers, and software techniques can improve the inter-accelerator data communication bandwidth by 2×. They can also improve the execution speed by 1.6× for a 3D finite difference, 2.5× for 1D FFT, and 1.6× for merge sort, all measured on real hardware. The proposed architecture support enables the HPE runtime to transparently deploy these optimizations under simple portable user code, allowing system designers to freely employ devices of different capabilities. We further argue that simple interfaces such as HPE are needed for most applications to benefit from advanced hardware features in practice. PMID:26180487

Structure of the dimeric RC–LH1–PufX complex from Rhodobaca bogoriensis investigated by electron microscopy

PubMed Central

Semchonok, Dmitry A.; Chauvin, Jean-Paul; Frese, Raoul N.; Jungas, Colette; Boekema, Egbert J.

2012-01-01

Electron microscopy and single-particle averaging were performed on isolated reaction centre (RC)—antenna complexes (RC–LH1–PufX complexes) of Rhodobaca bogoriensis strain LBB1, with the aim of establishing the LH1 antenna conformation, and, in particular, the structural role of the PufX protein. Projection maps of dimeric complexes were obtained at 13 Å resolution and show the positions of the 2 × 14 LH1 α- and β-subunits. This new dimeric complex displays two open, C-shaped LH1 aggregates of 13 αβ polypeptides partially surrounding the RCs plus two LH1 units forming the dimer interface in the centre. Between the interface and the two half rings are two openings on each side. Next to the openings, there are four additional densities present per dimer, considered to be occupied by four copies of PufX. The position of the RC in our model was verified by comparison with RC–LH1–PufX complexes in membranes. Our model differs from previously proposed configurations for Rhodobacter species in which the LH1 ribbon is continuous in the shape of an S, and the stoichiometry is of one PufX per RC. PMID:23148268

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

Grant, Robert

Under this grant, three significant software packages were developed or improved, all with the goal of improving the ease-of-use of HPC libraries. The first component is a Python package, named DistArray (originally named Odin), that provides a high-level interface to distributed array computing. This interface is based on the popular and widely used NumPy package and is integrated with the IPython project for enhanced interactive parallel distributed computing. The second Python package is the Distributed Array Protocol (DAP) that enables separate distributed array libraries to share arrays efficiently without copying or sending messages. If a distributed array library supports themore » DAP, it is then automatically able to communicate with any other library that also supports the protocol. This protocol allows DistArray to communicate with the Trilinos library via PyTrilinos, which was also enhanced during this project. A third package, PyTrilinos, was extended to support distributed structured arrays (in addition to the unstructured arrays of its original design), allow more flexible distributed arrays (i.e., the restriction to double precision data was lifted), and implement the DAP. DAP support includes both exporting the protocol so that external packages can use distributed Trilinos data structures, and importing the protocol so that PyTrilinos can work with distributed data from external packages.« less

The proposed monitoring system for the Fermilab D0 colliding beams detector

NASA Astrophysics Data System (ADS)

Goodwin, Robert; Florian, Robert; Johnson, Marvin; Jones, Alan; Shea, Mike

1986-06-01

The Fermilab D0 Detector is a collaborative effort that includes seventeen universities and national laboratories. The monitoring and control system for this detector will be separate from the online detector data system. A distributed, stand-alone, microprocessor-based system is being designed to allow monitoring and control functions to be available to the collaborators at their home institutions during the design, fabrication, and testing phases of the project. Individual stations are VMEbus-based 68000 systems that are networked together during installation using an ARCnet (by Datapoint Corporation) Local Area Network. One station, perhaps a MicroVAX, would have a hard disk to store a backup copy of the distributed database located in non-volatile RAM in the local stations. This station would also serve as a gateway to the online system, so that data from the control system will be available for logging with the detector data. Apple Macintosh personal computers are being developed for use as the local control consoles. Each would be interfaced to ARCnet to provide access to all control system data. Through the use of bit-mapped graphics with multiple windows and pull-down menus, a cost effective, flexible display system can be provided, taking advantage of familiar modern software tools to support the operator interface.

19 CFR 133.42 - Infringing copies or phonorecords.

Code of Federal Regulations, 2010 CFR

2010-04-01

....42 Infringing copies or phonorecords. (a) Definition. Infringing copies or phonorecords are “piratical” articles, i.e., copies or phonorecords which are unlawfully made (without the authorization of... chapter. Lawfully made copies are not subject to seizure and forfeiture by Customs. (d) Disclosure. When...

COPI selectively drives maturation of the early Golgi

PubMed Central

Papanikou, Effrosyni; Day, Kasey J; Austin, Jotham; Glick, Benjamin S

2015-01-01

COPI coated vesicles carry material between Golgi compartments, but the role of COPI in the secretory pathway has been ambiguous. Previous studies of thermosensitive yeast COPI mutants yielded the surprising conclusion that COPI was dispensable both for the secretion of certain proteins and for Golgi cisternal maturation. To revisit these issues, we optimized the anchor-away method, which allows peripheral membrane proteins such as COPI to be sequestered rapidly by adding rapamycin. Video fluorescence microscopy revealed that COPI inactivation causes an early Golgi protein to remain in place while late Golgi proteins undergo cycles of arrival and departure. These dynamics generate partially functional hybrid Golgi structures that contain both early and late Golgi proteins, explaining how secretion can persist when COPI has been inactivated. Our findings suggest that cisternal maturation involves a COPI-dependent pathway that recycles early Golgi proteins, followed by multiple COPI-independent pathways that recycle late Golgi proteins. DOI: http://dx.doi.org/10.7554/eLife.13232.001 PMID:26709839

The role of fretting corrosion and fretting fatigue in aircraft rivet hole cracking

NASA Technical Reports Server (NTRS)

Elliott, Charles B., III; Moesser, Mark; Hoeppner, David W.

1994-01-01

Personnel in the Quality and Integrity Design Engineering Center (QIDEC) at the University of Utah are working under a two year grant from the FAA to better understand the role of fretting corrosion and fretting fatigue in aircraft rivet hole cracking. The current program follows a one year grant program which was completed in 1993. This paper provides a status report on the results of these grant programs. Recent effort has been focused on developing basic fretting fatigue models which consider variation in the coefficient of friction with time and location within the fretting interface. This is a very important characteristic of the QIDEC model because coefficient of friction varies significantly during the fretting fatigue process. Copies of QIDEC documents discussed in this paper can be obtained by contacting the authors.

Project JOVE. [microgravity experiments and applications

NASA Technical Reports Server (NTRS)

Lyell, M. J.

1994-01-01

The goal of this project is to investigate new areas of research pertaining to free surface-interface fluids mechanics and/or microgravity which have potential commercial applications. This paper presents an introduction to ferrohydrodynamics (FHD), and discusses some applications. Also, computational methods for solving free surface flow problems are presented in detail. Both have diverse applications in industry and in microgravity fluids applications. Three different modeling schemes for FHD flows are addressed and the governing equations, including Maxwell's equations, are introduced. In the area of computational modeling of free surface flows, both Eulerian and Lagrangian schemes are discussed. The state of the art in computational methods applied to free surface flows is elucidated. In particular, adaptive grids and re-zoning methods are discussed. Additional research results are addressed and copies of the publications produced under the JOVE Project are included.

5 CFR 2638.311 - Copies of published formal advisory opinions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Copies of published formal advisory... Service § 2638.311 Copies of published formal advisory opinions. Each designated agency ethics official shall receive a copy of each published opinion. Copies will also be available to the public from the...

Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. | Office of Cancer Genomics

Cancer.gov

Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent.

[Application of rational ant colony optimization to improve the reproducibility degree of laser three-dimensional copy].

PubMed

Cui, Xiao-Yan; Huo, Zhong-Gang; Xin, Zhong-Hua; Tian, Xiao; Zhang, Xiao-Dong

2013-07-01

Three-dimensional (3D) copying of artificial ears and pistol printing are pushing laser three-dimensional copying technique to a new page. Laser three-dimensional scanning is a fresh field in laser application, and plays an irreplaceable part in three-dimensional copying. Its accuracy is the highest among all present copying techniques. Reproducibility degree marks the agreement of copied object with the original object on geometry, being the most important index property in laser three-dimensional copying technique. In the present paper, the error of laser three-dimensional copying was analyzed. The conclusion is that the data processing to the point cloud of laser scanning is the key technique to reduce the error and increase the reproducibility degree. The main innovation of this paper is as follows. On the basis of traditional ant colony optimization, rational ant colony optimization algorithm proposed by the author was applied to the laser three-dimensional copying as a new algorithm, and was put into practice. Compared with customary algorithm, rational ant colony optimization algorithm shows distinct advantages in data processing of laser three-dimensional copying, reducing the error and increasing the reproducibility degree of the copy.

Patterns, correlates, and reduction of homework copying

NASA Astrophysics Data System (ADS)

Palazzo, David J.; Lee, Young-Jin; Warnakulasooriya, Rasil; Pritchard, David E.

2010-06-01

Submissions to an online homework tutor were analyzed to determine whether they were copied. The fraction of copied submissions increased rapidly over the semester, as each weekly deadline approached and for problems later in each assignment. The majority of students, who copied less than 10% of their problems, worked steadily over the three days prior to the deadline, whereas repetitive copiers (those who copied >30% of their submitted problems) exerted little effort early. Importantly, copying homework problems that require an analytic answer correlates with a 2(σ) decline over the semester in relative score for similar problems on exams but does not significantly correlate with the amount of conceptual learning as measured by pretesting and post-testing. An anonymous survey containing questions used in many previous studies of self-reported academic dishonesty showed ˜1/3 less copying than actually was detected. The observed patterns of copying, free response questions on the survey, and interview data suggest that time pressure on students who do not start their homework in a timely fashion is the proximate cause of copying. Several measures of initial ability in math or physics correlated with copying weakly or not at all. Changes in course format and instructional practices that previous self-reported academic dishonesty surveys and/or the observed copying patterns suggested would reduce copying have been accompanied by more than a factor of 4 reduction of copying from ˜11% of all electronic problems to less than 3%. As expected (since repetitive copiers have approximately three times the chance of failing), this was accompanied by a reduction in the overall course failure rate. Survey results indicate that students copy almost twice as much written homework as online homework and show that students nationally admit to more academic dishonesty than MIT students.

Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging.

PubMed

Ridge, Perry G; Maxwell, Taylor J; Foutz, Spencer J; Bailey, Matthew H; Corcoran, Christopher D; Tschanz, JoAnn T; Norton, Maria C; Munger, Ronald G; O'Brien, Elizabeth; Kerber, Richard A; Cawthon, Richard M; Kauwe, John S K

2014-01-01

The mitochondria are essential organelles and are the location of cellular respiration, which is responsible for the majority of ATP production. Each cell contains multiple mitochondria, and each mitochondrion contains multiple copies of its own circular genome. The ratio of mitochondrial genomes to nuclear genomes is referred to as mitochondrial copy number. Decreases in mitochondrial copy number are known to occur in many tissues as people age, and in certain diseases. The regulation of mitochondrial copy number by nuclear genes has been studied extensively. While mitochondrial variation has been associated with longevity and some of the diseases known to have reduced mitochondrial copy number, the role that the mitochondrial genome itself has in regulating mitochondrial copy number remains poorly understood. We analyzed the complete mitochondrial genomes from 1007 individuals randomly selected from the Cache County Study on Memory Health and Aging utilizing the inferred evolutionary history of the mitochondrial haplotypes present in our dataset to identify sequence variation and mitochondrial haplotypes associated with changes in mitochondrial copy number. Three variants belonging to mitochondrial haplogroups U5A1 and T2 were significantly associated with higher mitochondrial copy number in our dataset. We identified three variants associated with higher mitochondrial copy number and suggest several hypotheses for how these variants influence mitochondrial copy number by interacting with known regulators of mitochondrial copy number. Our results are the first to report sequence variation in the mitochondrial genome that causes changes in mitochondrial copy number. The identification of these variants that increase mtDNA copy number has important implications in understanding the pathological processes that underlie these phenotypes.

Property and Propriety in the Digital Environment: Towards an Examination Copy License.

ERIC Educational Resources Information Center

Kahin, Brian

1988-01-01

Discussion of copyright issues involving computer software focuses on faculty examination of software for evaluation purposes. Two model examination copy licenses are proposed: one a circulating evaluation copy, for libraries and other centers where individual evaluators are not involved in copying; and one a distributable evaluation copy. (five…

48 CFR 1852.246-72 - Material inspection and receiving report.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Receiving Report (DD Form 250 series) prepared in __ [Insert number of copies, including original] copies, an original and __ copies [Insert number of copies]. (b) The Contractor shall prepare the DD Form 250 in accordance with NASA FAR Supplement 1846.6. The Contractor shall enclose the copies of the DD Form...

21 CFR 1312.14 - Distribution of copies of import permit.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the proper governmental authorities of the exporting country. (c) The quadruplet copy (Copy 4) shall... original copy (Copy 1) and the bill of lading upon arrival of the merchandise. If a discrepancy is noted... 74715, Nov. 12, 1980; 51 FR 5319, Feb. 13, 1986; 53 FR 48244, Nov. 30, 1988; 62 FR 13969, Mar. 24, 1997] ...

21 CFR 1312.14 - Distribution of copies of import permit.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the proper governmental authorities of the exporting country. (c) The quadruplet copy (Copy 4) shall... original copy (Copy 1) and the bill of lading upon arrival of the merchandise. If a discrepancy is noted... 74715, Nov. 12, 1980; 51 FR 5319, Feb. 13, 1986; 53 FR 48244, Nov. 30, 1988; 62 FR 13969, Mar. 24, 1997] ...

21 CFR 1312.14 - Distribution of copies of import permit.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the proper governmental authorities of the exporting country. (c) The quadruplet copy (Copy 4) shall... original copy (Copy 1) and the bill of lading upon arrival of the merchandise. If a discrepancy is noted... 74715, Nov. 12, 1980; 51 FR 5319, Feb. 13, 1986; 53 FR 48244, Nov. 30, 1988; 62 FR 13969, Mar. 24, 1997] ...

21 CFR 1312.14 - Distribution of copies of import permit.

Code of Federal Regulations, 2010 CFR

2010-04-01

... the proper governmental authorities of the exporting country. (c) The quadruplet copy (Copy 4) shall... original copy (Copy 1) and the bill of lading upon arrival of the merchandise. If a discrepancy is noted... 74715, Nov. 12, 1980; 51 FR 5319, Feb. 13, 1986; 53 FR 48244, Nov. 30, 1988; 62 FR 13969, Mar. 24, 1997] ...

21 CFR 1312.14 - Distribution of copies of import permit.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the proper governmental authorities of the exporting country. (c) The quadruplet copy (Copy 4) shall... original copy (Copy 1) and the bill of lading upon arrival of the merchandise. If a discrepancy is noted... 74715, Nov. 12, 1980; 51 FR 5319, Feb. 13, 1986; 53 FR 48244, Nov. 30, 1988; 62 FR 13969, Mar. 24, 1997] ...

29 CFR 1956.64 - Location of plan for inspection and copying.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 9 2010-07-01 2010-07-01 false Location of plan for inspection and copying. 1956.64... PLANS New Jersey § 1956.64 Location of plan for inspection and copying. A copy of the plan may be inspected and copied during normal business hours at the following locations: Office of State Programs, U.S...

10 CFR 26.821 - Inspections.

Code of Federal Regulations, 2010 CFR

2010-01-01

... representatives to inspect, copy, or take away copies of its records and to inspect its premises, activities, and... representatives may inspect, copy, or take away copies of any licensee's, other entity's, or C/V's documents...

JSME: a free molecule editor in JavaScript.

PubMed

Bienfait, Bruno; Ertl, Peter

2013-01-01

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

Asymmetric Assembly of Merkel Cell Polyomavirus Large T-Antigen Origin Binding Domains at the Viral Origin

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

C Harrison; G Meinke; H Kwun

2011-12-31

The double-stranded DNA polyomavirus Merkel cell polyomavirus (MCV) causes Merkel cell carcinoma, an aggressive but rare human skin cancer that most often affects immunosuppressed and elderly persons. As in other polyomaviruses, the large T-antigen of MCV recognizes the viral origin of replication by binding repeating G(A/G)GGC pentamers. The spacing, number, orientation, and necessity of repeats for viral replication differ, however, from other family members such as SV40 and murine polyomavirus. We report here the 2.9 {angstrom} crystal structure of the MCV large T-antigen origin binding domain (OBD) in complex with a DNA fragment from the MCV origin of replication. Consistentmore » with replication data showing that three of the G(A/G)GGC-like binding sites near the center of the origin are required for replication, the crystal structure contains three copies of the OBD. This stoichiometry was verified using isothermal titration calorimetry. The affinity for G(A/G)GGC-containing double-stranded DNA was found to be {approx} 740 nM, approximately 8-fold weaker than the equivalent domain in SV40 for the analogous region of the SV40 origin. The difference in affinity is partially attributable to DNA-binding residue Lys331 (Arg154 in SV40). In contrast to SV40, a small protein-protein interface is observed between MCV OBDs when bound to the central region of the origin. This protein-protein interface is reminiscent of that seen in bovine papilloma virus E1 protein. Mutational analysis indicates, however, that this interface contributes little to DNA binding energy.« less

Application of droplet digital PCR to determine copy number of endogenous genes and transgenes in sugarcane.

PubMed

Sun, Yue; Joyce, Priya Aiyar

2017-11-01

Droplet digital PCR combined with the low copy ACT allele as endogenous reference gene, makes accurate and rapid estimation of gene copy number in Q208 A and Q240 A attainable. Sugarcane is an important cultivated crop with both high polyploidy and aneuploidy in its 10 Gb genome. Without a known copy number reference gene, it is difficult to accurately estimate the copy number of any gene of interest by PCR-based methods in sugarcane. Recently, a new technology, known as droplet digital PCR (ddPCR) has been developed which can measure the absolute amount of the target DNA in a given sample. In this study, we deduced the true copy number of three endogenous genes, actin depolymerizing factor (ADF), adenine phosphoribosyltransferase (APRT) and actin (ACT) in three Australian sugarcane varieties, using ddPCR by comparing the absolute amounts of the above genes with a transgene of known copy number. A single copy of the ACT allele was detected in Q208 A , two copies in Q240 A , but was absent in Q117. Copy number variation was also observed for both APRT and ADF, and ranged from 9 to 11 in the three tested varieties. Using this newly developed ddPCR method, transgene copy number was successfully determined in 19 transgenic Q208 A and Q240 A events using ACT as the reference endogenous gene. Our study demonstrates that ddPCR can be used for high-throughput genetic analysis and is a quick, accurate and reliable alternative method for gene copy number determination in sugarcane. This discovered ACT allele would be a suitable endogenous reference gene for future gene copy number variation and dosage studies of functional genes in Q208 A and Q240 A .

Performance Characteristics of the QUANTIPLEX HIV-1 RNA 3.0 Assay for Detection and Quantitation of Human Immunodeficiency Virus Type 1 RNA in Plasma

PubMed Central

Erice, Alejo; Brambilla, Donald; Bremer, James; Jackson, J. Brooks; Kokka, Robert; Yen-Lieberman, Belinda; Coombs, Robert W.

2000-01-01

The QUANTIPLEX HIV-1 RNA assay, version 3.0 (a branched DNA, version 3.0, assay [bDNA 3.0 assay]), was evaluated by analyzing spiked and clinical plasma samples and was compared with the AMPLICOR HIV-1 MONITOR Ultrasensitive (ultrasensitive reverse transcription-PCR [US-RT-PCR]) method. A panel of spiked plasma samples that contained 0 to 750,000 copies of human immunodeficiency virus type 1 (HIV-1) RNA per ml was tested four times in each of four laboratories (1,344 assays). Negative results (<50 copies/ml) were obtained in 30 of 32 (94%) assays with seronegative samples, 66 of 128 (52%) assays with HIV-1 RNA at 50 copies/ml, and 5 of 128 (4%) assays with HIV-1 RNA at 100 copies/ml. The assay was linear from 100 to 500,000 copies/ml. The within-run standard deviation (SD) of the log10 estimated HIV-1 RNA concentration was 0.08 at 1,000 to 500,000 copies/ml, increased below 1,000 copies/ml, and was 0.17 at 100 copies/ml. Between-run reproducibility at 100 to 500 copies/ml was <0.10 log10 in most comparisons. Interlaboratory differences across runs were ≤0.10 log10 at all concentrations examined. A subset of the panel (25 to 500 copies/ml) was also analyzed by the US-RT-PCR assay. The within-run SD varied inversely with the log10 HIV-1 RNA concentration but was higher than the SD for the bDNA 3.0 assay at all concentrations. Log-log regression analysis indicated that the two methods produced very similar estimates at 100 to 500 copies/ml. In parallel testing of clinical specimens with low HIV-1 RNA levels, 80 plasma samples with <50 copies/ml by the US-RT-PCR assay had <50 copies/ml when they were retested by the bDNA 3.0 assay. In contrast, 11 of 78 (14%) plasma samples with <50 copies/ml by the bDNA 3.0 assay had ≥50 copies/ml when they were retested by the US-RT-PCR assay (median, 86 copies/ml; range, 50 to 217 copies/ml). Estimation of bDNA 3.0 values of <50 copies/ml by extending the standard curve of the assay showed that these samples with discrepant results had higher HIV-1 RNA levels than the samples with concordant results (median, 34 versus 17 copies/ml; P = 0.0051 by the Wilcoxon two-sample test). The excellent reproducibility, broad linear range, and good sensitivity of the bDNA 3.0 assay make it a very attractive method for quantitation of HIV-1 RNA levels in plasma. PMID:10921936

Beneficial effect of a high number of copies of salivary amylase AMY1 gene on obesity risk in Mexican children.

PubMed

Mejía-Benítez, María A; Bonnefond, Amélie; Yengo, Loïc; Huyvaert, Marlène; Dechaume, Aurélie; Peralta-Romero, Jesús; Klünder-Klünder, Miguel; García Mena, Jaime; El-Sayed Moustafa, Julia S; Falchi, Mario; Cruz, Miguel; Froguel, Philippe

2015-02-01

Childhood obesity is a major public health problem in Mexico, affecting one in every three children. Genome-wide association studies identified genetic variants associated with childhood obesity, but a large missing heritability remains to be elucidated. We have recently shown a strong association between a highly polymorphic copy number variant encompassing the salivary amylase gene (AMY1 also known as AMY1A) and obesity in European and Asian adults. In the present study, we aimed to evaluate the association between AMY1 copy number and obesity in Mexican children. We evaluated the number of AMY1 copies in 597 Mexican children (293 obese children and 304 normal weight controls) through highly sensitive digital PCR. The effect of AMY1 copy number on obesity status was assessed using a logistic regression model adjusted for age and sex. We identified a marked effect of AMY1 copy number on reduced risk of obesity (OR per estimated copy 0.84, with the number of copies ranging from one to 16 in this population; p = 4.25 × 10(-6)). The global association between AMY1 copy number and reduced risk of obesity seemed to be mostly driven by the contribution of the highest AMY1 copy number. Strikingly, all children with >10 AMY1 copies were normal weight controls. Salivary amylase initiates the digestion of dietary starch, which is highly consumed in Mexico. Our current study suggests putative benefits of high number of AMY1 copies (and related production of salivary amylase) on energy metabolism in Mexican children.

Multiple-copy entanglement transformation and entanglement catalysis

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

Duan Runyao; Feng Yuan; Li Xin

2005-04-01

We prove that any multiple-copy entanglement transformation [S. Bandyopadhyay, V. Roychowdhury, and U. Sen, Phys. Rev. A 65, 052315 (2002)] can be implemented by a suitable entanglement-assisted local transformation [D. Jonathan and M. B. Plenio, Phys. Rev. Lett. 83, 3566 (1999)]. Furthermore, we show that the combination of multiple-copy entanglement transformation and the entanglement-assisted one is still equivalent to the pure entanglement-assisted one. The mathematical structure of multiple-copy entanglement transformations then is carefully investigated. Many interesting properties of multiple-copy entanglement transformations are presented, which exactly coincide with those satisfied by the entanglement-assisted ones. Most interestingly, we show that an arbitrarilymore » large number of copies of state should be considered in multiple-copy entanglement transformations.« less

Low-cost soft-copy display accuracy in the detection of pulmonary nodules by single-exposure dual-energy subtraction: comparison with hard-copy viewing.

PubMed

Kido, S; Kuriyama, K; Hosomi, N; Inoue, E; Kuroda, C; Horai, T

2000-02-01

This study endeavored to clarify the usefulness of single-exposure dual-energy subtraction computed radiography (CR) of the chest and the ability of soft-copy images to detect low-contrast simulated pulmonary nodules. Conventional and bone-subtracted CR images of 25 chest phantom image sets with a low-contrast nylon nodule and 25 without a nodule were interpreted by 12 observers (6 radiologists, 6 chest physicians) who rated each on a continuous confidence scale and marked the position of the nodule if one was present. Hard-copy images were 7 x 7-inch laser-printed CR films, and soft-copy images were displayed on a 21-inch noninterlaced color CRT monitor with an optimized dynamic range. Soft-copy images were adjusted to the same size as hard-copy images and were viewed under darkened illumination in the reading room. No significant differences were found between hard- and soft-copy images. In conclusion, the soft-copy images were found to be useful in detecting low-contrast simulated pulmonary nodules.

[Dry view laser imager--a new economical photothermal imaging method].

PubMed

Weberling, R

1996-11-01

The production of hard copies is currently achieved by means of laser imagers and wet film processing in systems attached either directly in or to the laser imager or in a darkroom. Variations in image quality resulting from a not always optimal wet film development are frequent. A newly developed thermographic film developer for laser films without liquid powdered chemicals, on the other hand, is environmentally preferable and reducing operating costs. The completely dry developing process provides permanent image documentation meeting the quality and safety requirements of RöV and BAK. One of the currently available systems of this type, the DryView Laser Imager is inexpensive and easy to install. The selective connection principle of the DryView Laser Imager can be expanded as required and accepts digital and/or analog interfaces with all imaging systems (CT, MR, DR, US, NM) from the various manufactures.

Programs for generating data tables for the annual water-resources data report of the U.S. Geological Survey

USGS Publications Warehouse

Mason, R.R.; Hill, C.L.

1988-01-01

The U.S. Geological Survey has developed software that interfaces with the Automated Data Processing System to facilitate and expedite preparation of the annual water-resources data report. This software incorporates a feature that prepares daily values tables and appends them to previously edited files containing station manuscripts. Other features collate the merged files with miscellaneous sections of the report. The report is then printed as page-size, camera-ready copy. All system components reside on a minicomputer; this provides easy access and use by remote field offices. Automation of the annual report preparation process results in significant savings of labor and cost. Use of the system for producing the 1986 annual report in the North Carolina District realized a labor savings of over two man-months. A fully implemented system would produce a greater savings and speed release of the report to users.

Planar ultra thin glass seals with optical fiber interface for monitoring tamper attacks on security eminent components

NASA Astrophysics Data System (ADS)

Thiel, M.; Flachenecker, G.; Schade, W.; Gorecki, C.; Thoma, A.; Rathje, R.

2017-11-01

Optical seals consisting of waveguide Bragg grating sensor structures in ultra thin glass transparencies have been developed to cover security relevant objects for detection of unauthorized access. For generation of optical signature in the seals, femtosecond laser pulses were used. The optical seals were connected with an optical fiber to enable external read out of the seal. Different attack scenarios for getting undetected access to the object, covered by the seal, were proven and evaluated. The results presented here, verify a very high level of security. An unauthorized detaching and subsequent replacement by original or copy of the seals for tampering would be accompanied with a very high technological effort, posing a substantial barrier towards an attacker. Additionally, environmental influences like temperature effects have a strong but reproducible influence on signature, which in context of a temperature reference database increases the level of security significantly.

Making Millennial Medicine More Meta.

PubMed

Turnbaugh, Peter J

2018-01-01

Although the importance of human genetic polymorphisms in therapeutic outcomes is well established, the role of specific genotypic or copy number variants in our "second genome" (the microbiome) has been largely overlooked. In this Perspective, I will discuss three major barriers to integrating metagenomics into pharmacology, highlighting ongoing research by us and others that has begun to shed light on the mechanisms that link the human microbiome to the efficacy and toxicity of small-molecule and biological therapies. The challenges for the next 5 years and beyond are many, requiring interdisciplinary scientific teams working at the interface of chemistry and biology, and a consideration of far more variables than traditionally included in pharmacological modeling. However, the potential benefits are immense. Continued progress could enable more precise tools for predicting patient responses and the development of a new generation of therapeutics based on, or targeted at, the human microbiome.

Analysis and Exchange of Multimedia Laboratory Data Using the Brain Database

PubMed Central

Wertheim, Steven L.

1990-01-01

Two principal goals of the Brain Database are: 1) to support laboratory data collection and analysis of multimedia information about the nervous system and 2) to support exchange of these data among researchers and clinicians who may be physically distant. This has been achieved by an implementation of experimental and clinical records within a relational database. An Image Series Editor has been created that provides a graphical interface to these data for the purposes of annotation, quantification and other analyses. Cooperating laboratories each maintain their own copies of the Brain Database to which they may add private data. Although the data in a given experimental or patient record will be distributed among many tables and external image files, the user can treat each record as a unit that can be extracted from the local database and sent to a distant colleague.

The Effects of Working Memory on Brain-Computer Interface Performance

PubMed Central

Sprague, Samantha A.; McBee, Matthew; Sellers, Eric W.

2015-01-01

Objective The purpose of the present study is to evaluate the relationship between working memory and BCI performance. Methods Participants took part in two separate sessions. The first session consisted of three computerized tasks. The LSWM was used to measure working memory, the TPVT was used to measure general intelligence, and the DCCS was used to measure executive function, specifically cognitive flexibility. The second session consisted of a P300-based BCI copy-spelling task. Results The results indicate that both working memory and general intelligence are significant predictors of BCI performance. Conclusions This suggests that working memory training could be used to improve performance on a BCI task. Significance Working memory training may help to reduce a portion of the individual differences that exist in BCI performance allowing for a wider range of users to successfully operate the BCI system as well as increase the BCI performance of current users. PMID:26620822

Fifth NASA Goddard Conference on Mass Storage Systems and Technologies. Volume 2

NASA Technical Reports Server (NTRS)

Kobler, Benjamin (Editor); Hariharan, P. C. (Editor)

1996-01-01

This document contains copies of those technical papers received in time for publication prior to the Fifth Goddard Conference on Mass Storage Systems and Technologies held September 17 - 19, 1996, at the University of Maryland, University Conference Center in College Park, Maryland. As one of an ongoing series, this conference continues to serve as a unique medium for the exchange of information on topics relating to the ingestion and management of substantial amounts of data and the attendant problems involved. This year's discussion topics include storage architecture, database management, data distribution, file system performance and modeling, and optical recording technology. There will also be a paper on Application Programming Interfaces (API) for a Physical Volume Repository (PVR) defined in Version 5 of the Institute of Electrical and Electronics Engineers (IEEE) Reference Model (RM). In addition, there are papers on specific archives and storage products.

Natural supramolecular building blocks: from virus coat proteins to viral nanoparticles.

PubMed

Liu, Zhi; Qiao, Jing; Niu, Zhongwei; Wang, Qian

2012-09-21

Viruses belong to a fascinating class of natural supramolecular structures, composed of multiple copies of coat proteins (CPs) that assemble into different shapes with a variety of sizes from tens to hundreds of nanometres. Because of their advantages including simple/economic production, well-defined structural features, unique shapes and sizes, genetic programmability and robust chemistries, recently viruses and virus-like nanoparticles (VLPs) have been used widely in biomedical applications and materials synthesis. In this critical review, we highlight recent advances in the use of virus coat proteins (VCPs) and viral nanoparticles (VNPs) as building blocks in self-assembly studies and materials development. We first discuss the self-assembly of VCPs into VLPs, which can efficiently incorporate a variety of different materials as cores inside the viral protein shells. Then, the self-assembly of VNPs at surfaces or interfaces is summarized. Finally, we discuss the co-assembly of VNPs with different functional materials (178 references).

Visual Support System for Report Distinctiveness Evaluation

NASA Astrophysics Data System (ADS)

Sunayama, Wataru; Kawaguchi, Toshiaki

In recent years, as the Internet has grown, electronic reports have come to be used in educational organizations such as universities. Though reports written by hand must be evaluated by hand except for stereotype descriptions or numerical answers, electronic reports can be rated by computer. There are two major criteria in rating reports, correctness and distinctiveness. Correctness is rated by absolute criteria and distinctiveness is rated by relative criteria. Relative evaluation is difficult because raters should memorize all contents of submitted reports to provide objective rates. In addition, electronic data are easily copied or exchanged by students. This paper presents a report evaluation support system with which raters can compare each report and give objective rates for distinctiveness. This system evaluates each report by objective similarity criteria and visualizes them in a two-dimensional interface as the calculated distinctiveness order. Experimental results show the system is valid and effective for estimating associations between reports.

Investigation of the Melting Point of RDX

DTIC Science & Technology

1942-04-30

Jun 1947; OTS index dtd Jun 1947 Reproduced by AIR DOCUMENTS DIVISION t i HEADQUARTERS AIR MATERIEL COMMAND WRIGHT FIELD. DAYTON, OHIO I. I...doiWKTit contain»inform» on ."■ vti-,* ■ hvrut«**.* de ’i* i’f the I’nittd : ■..;«« «i tin the r«i nil of ’tu» «r ’lie i .• ! .ii ’.t in I...Gonoral, Piertinny Arsenal Copy No. 30 - Dr. Rogor Adams (Division B Filos ) Copy No. 31 - Copy No. 32 - Copy No. 33 - Copy No. 34 - Copy No. 35

The role of redundant information in cultural transmission and cultural stabilization.

PubMed

Acerbi, Alberto; Tennie, Claudio

2016-02-01

Redundant copying has been proposed as a manner to achieve the high-fidelity necessary to pass on and preserve complex traits in human cultural transmission. There are at least 2 ways to define redundant copying. One refers to the possibility of copying repeatedly the same trait over time, and another to the ability to exploit multiple layers of information pointing to the same trait during a single copying event. Using an individual-based model, we explore how redundant copying (defined as in the latter way) helps to achieve successful transmission. The authors show that increasing redundant copying increases the likelihood of accurately transmitting a behavior more than either augmenting the number of copying occasions across time or boosting the general accuracy of social learning. They also investigate how different cost functions, deriving, for example, from the need to invest more energy in cognitive processing, impact the evolution of redundant copying. The authors show that populations converge either to high-fitness/high-costs states (with high redundant copying and complex culturally transmitted behaviors; resembling human culture) or to low-fitness/low-costs states (with low redundant copying and simple transmitted behaviors; resembling social learning forms typical of nonhuman animals). This outcome may help to explain why cumulative culture is rare in the animal kingdom. (c) 2016 APA, all rights reserved).

The cost of copy number in a selfish genetic element: the 2-μm plasmid of Saccharomyces cerevisiae.

PubMed

Harrison, Ellie; Koufopanou, V; Burt, A; MacLean, R C

2012-11-01

Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2 μm is a multicopy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2 μm is that plasmid copy number evolves as a trade-off between selection for increased vertical transmission, favouring high copy number, and selection for decreased virulence, favouring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2 μm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (± 0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast per 2 μm associations and pave the way for future studies examining how selection can shape the cost of multicopy elements. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

48 CFR 3401.104-3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Copies. 3401.104-3 Section 3401.104-3 Federal Acquisition Regulations System DEPARTMENT OF EDUCATION ACQUISITION REGULATION GENERAL ED ACQUISITION REGULATION SYSTEM Purpose, Authority, Issuance 3401.104-3 Copies. Copies of the...

Safe Practices for Copy and Paste in the EHR

PubMed Central

Lehmann, Christoph U.; Michel, Jeremy; Solomon, Ronni; Possanza, Lorraine; Gandhi, Tejal

2017-01-01

Summary Background Copy and paste functionality can support efficiency during clinical documentation, but may promote inaccurate documentation with risks for patient safety. The Partnership for Health IT Patient Safety was formed to gather data, conduct analysis, educate, and disseminate safe practices for safer care using health information technology (IT). Objective To characterize copy and paste events in clinical care, identify safety risks, describe existing evidence, and develop implementable practice recommendations for safe reuse of information via copy and paste. Methods The Partnership 1) reviewed 12 reported safety events, 2) solicited expert input, and 3) performed a systematic literature review (2010 to January 2015) to identify publications addressing frequency, perceptions/attitudes, patient safety risks, existing guidance, and potential interventions and mitigation practices. Results The literature review identified 51 publications that were included. Overall, 66% to 90% of clinicians routinely use copy and paste. One study of diagnostic errors found that copy and paste led to 2.6% of errors in which a missed diagnosis required patients to seek additional unplanned care. Copy and paste can promote note bloat, internal inconsistencies, error propagation, and documentation in the wrong patient chart. Existing guidance identified specific responsibilities for authors, organizations, and electronic health record (EHR) developers. Analysis of 12 reported copy and paste safety events was congruent with problems identified from the literature review. Conclusion Despite regular copy and paste use, evidence regarding direct risk to patient safety remains sparse, with significant study limitations. Drawing on existing evidence, the Partnership developed four safe practice recommendations: 1) Provide a mechanism to make copy and paste material easily identifiable; 2) Ensure the provenance of copy and paste material is readily available; 3) Ensure adequate staff training and education; 4) Ensure copy and paste practices are regularly monitored, measured, and assessed. PMID:28074211

Safe Practices for Copy and Paste in the EHR. Systematic Review, Recommendations, and Novel Model for Health IT Collaboration.

PubMed

Tsou, Amy Y; Lehmann, Christoph U; Michel, Jeremy; Solomon, Ronni; Possanza, Lorraine; Gandhi, Tejal

2017-01-11

Copy and paste functionality can support efficiency during clinical documentation, but may promote inaccurate documentation with risks for patient safety. The Partnership for Health IT Patient Safety was formed to gather data, conduct analysis, educate, and disseminate safe practices for safer care using health information technology (IT). To characterize copy and paste events in clinical care, identify safety risks, describe existing evidence, and develop implementable practice recommendations for safe reuse of information via copy and paste. The Partnership 1) reviewed 12 reported safety events, 2) solicited expert input, and 3) performed a systematic literature review (2010 to January 2015) to identify publications addressing frequency, perceptions/attitudes, patient safety risks, existing guidance, and potential interventions and mitigation practices. The literature review identified 51 publications that were included. Overall, 66% to 90% of clinicians routinely use copy and paste. One study of diagnostic errors found that copy and paste led to 2.6% of errors in which a missed diagnosis required patients to seek additional unplanned care. Copy and paste can promote note bloat, internal inconsistencies, error propagation, and documentation in the wrong patient chart. Existing guidance identified specific responsibilities for authors, organizations, and electronic health record (EHR) developers. Analysis of 12 reported copy and paste safety events was congruent with problems identified from the literature review. Despite regular copy and paste use, evidence regarding direct risk to patient safety remains sparse, with significant study limitations. Drawing on existing evidence, the Partnership developed four safe practice recommendations: 1) Provide a mechanism to make copy and paste material easily identifiable; 2) Ensure the provenance of copy and paste material is readily available; 3) Ensure adequate staff training and education; 4) Ensure copy and paste practices are regularly monitored, measured, and assessed.

Very low level viraemia and risk of virological failure in treated HIV-1-infected patients.

PubMed

Teira, R; Vidal, F; Muñoz-Sánchez, P; Geijo, P; Viciana, P; Ribera, E; Domingo, P; Castaño, M; Martínez, E; Roca, B; Puig, T; Estrada, V; Deig, E; Galindo, M J; de la Fuente, B; Lozano, F; Montero, M; Muñoz-Sanz, A; Sanchez, T; Terrón, A; Romero-Palacios, A; Lacalle, J R; Garrido, M; Suárez-Lozano, I

2017-03-01

The aim of the study was to investigate whether very low level viraemia (VLLV) (20-50 HIV-1 RNA copies/mL) was associated with increased risk of virological failure (VF) as compared with persistent full suppression (< 20 copies/mL). From the VACH Cohort database, we selected those patients who started antiretroviral therapy (ART) after January 1997 and who achieved effective viral suppression [two consecutive viral loads (VLs) < 50 copies/mL] followed by full suppression (at least one VL <20 copies/mL). We carried out survival analyses to investigate whether the occurrence of VLLV rather than maintaining full suppression at < 20 copies/mL was associated with virological failure (two consecutive VLs > 200 copies/mL or one VL > 200 copies/mL followed by a change of ART regimen, administrative censoring or loss to follow-up), adjusted for nadir CD4 cell count, sex, age, ethnicity, transmission group, type of ART and time on effective suppression at < 50 copies/mL. Of 21 480 patients who started ART, 13 674 (63.7%) achieved effective suppression at < 50 copies/mL, of whom 4289 (31.4%) further achieved full suppression at < 20 copies/mL after May 2009. A total of 2623 patients (61.1%) remained fully suppressed thereafter, while 1666 had one or more episodes of VL detection > 20 copies/mL (excluding virological failure). A total of 824 patients had VLLV after suppression at < 20 copies/mL. VLLV was not associated with virological failure as compared with persistent full suppression [hazard ratio (HR) 0.67; 95% confidence interval (CI) 0.44-1.00], independently of the number of blips recorded (from one to 18). In our population of HIV-infected patients on ART who achieved viral suppression at < 20 copies/mL, the risk of virological failure was no different for patients who remained fully suppressed compared with those who experienced subsequent episodes of VLLV. © 2016 British HIV Association.

Functional effects of CCL3L1 copy number

PubMed Central

Carpenter, Danielle; McIntosh, Richard S; Pleass, Richard J; Armour, John AL

2012-01-01

Copy number variation (CNV) is becoming increasingly important as a feature of human variation in disease susceptibility studies. However, the consequences of copy number variation are not so well understood. Here we present data exploring the functional consequences of copy number variation of CCL3L1 in 55 independent UK samples with no known clinical phenotypes. Copy number of CCL3L1 was determined by the paralogue ratio test (PRT), and expression levels of MIP-1α and mRNA from stimulated monocytes were measured and analysed. The data show no statistically significant association of MIP-1α protein levels with copy number. However, there was a significant correlation between copy number and CCL3L1:CCL3 mRNA ratio. The data also provide evidence that expression of CCL3 predominates in both protein and mRNA, and therefore the observed variation of CCL3 is potentially more important biologically than that of copy number variation of CCL3L1. PMID:22476153

LADS: Optimizing Data Transfers using Layout-Aware Data Scheduling

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

Kim, Youngjae; Atchley, Scott; Vallee, Geoffroy R

While future terabit networks hold the promise of signifi- cantly improving big-data motion among geographically distributed data centers, significant challenges must be overcome even on today s 100 gigabit networks to real- ize end-to-end performance. Multiple bottlenecks exist along the end-to-end path from source to sink. Data stor- age infrastructure at both the source and sink and its in- terplay with the wide-area network are increasingly the bottleneck to achieving high performance. In this paper, we identify the issues that lead to congestion on the path of an end-to-end data transfer in the terabit network en- vironment, and we presentmore » a new bulk data movement framework called LADS for terabit networks. LADS ex- ploits the underlying storage layout at each endpoint to maximize throughput without negatively impacting the performance of shared storage resources for other users. LADS also uses the Common Communication Interface (CCI) in lieu of the sockets interface to use zero-copy, OS-bypass hardware when available. It can further im- prove data transfer performance under congestion on the end systems using buffering at the source using flash storage. With our evaluations, we show that LADS can avoid congested storage elements within the shared stor- age resource, improving I/O bandwidth, and data transfer rates across the high speed networks.« less

Structure and interactions of the Bacillus subtilis sporulation inhibitor of DNA replication, SirA, with domain I of DnaA

PubMed Central

Jameson, Katie H; Rostami, Nadia; Fogg, Mark J; Turkenburg, Johan P; Grahl, Anne; Murray, Heath; Wilkinson, Anthony J

2014-01-01

Chromosome copy number in cells is controlled so that the frequency of initiation of DNA replication matches that of cell division. In bacteria, this is achieved through regulation of the interaction between the initiator protein DnaA and specific DNA elements arrayed at the origin of replication. DnaA assembles at the origin and promotes DNA unwinding and the assembly of a replication initiation complex. SirA is a DnaA-interacting protein that inhibits initiation of replication in diploid Bacillus subtilis cells committed to the developmental pathway leading to formation of a dormant spore. Here we present the crystal structure of SirA in complex with the N-terminal domain of DnaA revealing a heterodimeric complex. The interacting surfaces of both proteins are α-helical with predominantly apolar side-chains packing in a hydrophobic interface. Site-directed mutagenesis experiments confirm the importance of this interface for the interaction of the two proteins in vitro and in vivo. Localization of GFP–SirA indicates that the protein accumulates at the replisome in sporulating cells, likely through a direct interaction with DnaA. The SirA interacting surface of DnaA corresponds closely to the HobA-interacting surface of DnaA from Helicobacter pylori even though HobA is an activator of DnaA and SirA is an inhibitor. PMID:25041308

High-volume production of single and compound emulsions in a microfluidic parallelization arrangement coupled with coaxial annular world-to-chip interfaces.

PubMed

Nisisako, Takasi; Ando, Takuya; Hatsuzawa, Takeshi

2012-09-21

This study describes a microfluidic platform with coaxial annular world-to-chip interfaces for high-throughput production of single and compound emulsion droplets, having controlled sizes and internal compositions. The production module consists of two distinct elements: a planar square chip on which many copies of a microfluidic droplet generator (MFDG) are arranged circularly, and a cubic supporting module with coaxial annular channels for supplying fluids evenly to the inlets of the mounted chip, assembled from blocks with cylinders and holes. Three-dimensional flow was simulated to evaluate the distribution of flow velocity in the coaxial multiple annular channels. By coupling a 1.5 cm × 1.5 cm microfluidic chip with parallelized 144 MFDGs and a supporting module with two annular channels, for example, we could produce simple oil-in-water (O/W) emulsion droplets having a mean diameter of 90.7 μm and a coefficient of variation (CV) of 2.2% at a throughput of 180.0 mL h(-1). Furthermore, we successfully demonstrated high-throughput production of Janus droplets, double emulsions and triple emulsions, by coupling 1.5 cm × 1.5 cm - 4.5 cm × 4.5 cm microfluidic chips with parallelized 32-128 MFDGs of various geometries and supporting modules with 3-4 annular channels.

PANEL LIBRARY AND EDITOR

NASA Technical Reports Server (NTRS)

Raible, E.

1994-01-01

The Panel Library and Editor is a graphical user interface (GUI) builder for the Silicon Graphics IRIS workstation family. The toolkit creates "widgets" which can be manipulated by the user. Its appearance is similar to that of the X-Windows System. The Panel Library is written in C and is used by programmers writing user-friendly mouse-driven applications for the IRIS. GUIs built using the Panel Library consist of "actuators" and "panels." Actuators are buttons, dials, sliders, or other mouse-driven symbols. Panels are groups of actuators that occupy separate windows on the IRIS workstation. The application user can alter variables in the graphics program, or fire off functions with a click on a button. The evolution of data values can be tracked with meters and strip charts, and dialog boxes with text processing can be built. Panels can be stored as icons when not in use. The Panel Editor is a program used to interactively create and test panel library interfaces in a simple and efficient way. The Panel Editor itself uses a panel library interface, so all actions are mouse driven. Extensive context-sensitive on-line help is provided. Programmers can graphically create and test the user interface without writing a single line of code. Once an interface is judged satisfactory, the Panel Editor will dump it out as a file of C code that can be used in an application. The Panel Library (v9.8) and Editor (v1.1) are written in C-Language (63%) and Scheme, a dialect of LISP, (37%) for Silicon Graphics 4D series workstations running IRIX 3.2 or higher. Approximately 10Mb of disk space is required once compiled. 1.5Mb of main memory is required to execute the panel editor. This program is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format for an IRIS, and includes a copy of XScheme, the public-domain Scheme interpreter used by the Panel Editor. The Panel Library Programmer's Manual is included on the distribution media. The Panel Library and Editor were released to COSMIC in 1991. Silicon Graphics, IRIS, and IRIX are trademarks of Silicon Graphics, Inc. X-Window System is a trademark of Massachusetts Institute of Technology.

Vocal copying of individually distinctive signature whistles in bottlenose dolphins

PubMed Central

King, Stephanie L.; Sayigh, Laela S.; Wells, Randall S.; Fellner, Wendi; Janik, Vincent M.

2013-01-01

Vocal learning is relatively common in birds but less so in mammals. Sexual selection and individual or group recognition have been identified as major forces in its evolution. While important in the development of vocal displays, vocal learning also allows signal copying in social interactions. Such copying can function in addressing or labelling selected conspecifics. Most examples of addressing in non-humans come from bird song, where matching occurs in an aggressive context. However, in other animals, addressing with learned signals is very much an affiliative signal. We studied the function of vocal copying in a mammal that shows vocal learning as well as complex cognitive and social behaviour, the bottlenose dolphin (Tursiops truncatus). Copying occurred almost exclusively between close associates such as mother–calf pairs and male alliances during separation and was not followed by aggression. All copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it. We found no evidence for the use of copying in aggression or deception. This use of vocal copying is similar to its use in human language, where the maintenance of social bonds appears to be more important than the immediate defence of resources. PMID:23427174

48 CFR 1301.105-3 - Copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Copies. 1301.105-3 Section 1301.105-3 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE GENERAL DEPARTMENT OF COMMERCE ACQUISITION REGULATIONS SYSTEM Purpose, Authority, Issuance 1301.105-3 Copies. (a) Copies of the CAR in...

7 CFR 1499.6 - Payments.

Code of Federal Regulations, 2010 CFR

2010-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the...); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of the...

7 CFR 1499.6 - Payments.

Code of Federal Regulations, 2011 CFR

2011-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the...); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of the...

Asymptomatic Cerebrospinal Fluid HIV-1 Viral Blips and Viral Escape During Antiretroviral Therapy: A Longitudinal Study.

PubMed

Edén, Arvid; Nilsson, Staffan; Hagberg, Lars; Fuchs, Dietmar; Zetterberg, Henrik; Svennerholm, Bo; Gisslén, Magnus

2016-12-15

We examined longitudinal cerebrospinal fluid (CSF) samples (median, 5 samples/patients; interquartile range [IQR], 3-8 samples/patient) in 75 neurologically asymptomatic human immunodeficiency virus (HIV)-infected patients receiving antiretroviral therapy. Twenty-seven patients (36%) had ≥1 CSF HIV RNA load of >20 copies/mL (23% had ≥1 load of >50 copies/mL), with a median HIV RNA load of 50 copies/mL (IQR, 32-77 copies/mL). In plasma, 42 subjects (52%) and 22 subjects (29%) had an HIV RNA load of >20 and >50 copies/mL, respectively. Two subjects had an increasing virus load in consecutive CSF samples, representing possible CSF escape. Of 418 samples, 9% had a CSF HIV RNA load of >20 copies/mL (5% had a load of >50 copies/mL) and 19% had a plasma HIV RNA load of >20 copies/mL (8% had a load of >50 copies/mL). A CSF-associated virus load of >20 copies/mL was associated with higher CSF level of neopterin. In conclusion, CSF escape was rare, and increased CSF HIV RNA loads usually represented CSF virus load blips. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Low copy number of the salivary amylase gene predisposes to obesity.

PubMed

Falchi, Mario; El-Sayed Moustafa, Julia Sarah; Takousis, Petros; Pesce, Francesco; Bonnefond, Amélie; Andersson-Assarsson, Johanna C; Sudmant, Peter H; Dorajoo, Rajkumar; Al-Shafai, Mashael Nedham; Bottolo, Leonardo; Ozdemir, Erdal; So, Hon-Cheong; Davies, Robert W; Patrice, Alexandre; Dent, Robert; Mangino, Massimo; Hysi, Pirro G; Dechaume, Aurélie; Huyvaert, Marlène; Skinner, Jane; Pigeyre, Marie; Caiazzo, Robert; Raverdy, Violeta; Vaillant, Emmanuel; Field, Sarah; Balkau, Beverley; Marre, Michel; Visvikis-Siest, Sophie; Weill, Jacques; Poulain-Godefroy, Odile; Jacobson, Peter; Sjostrom, Lars; Hammond, Christopher J; Deloukas, Panos; Sham, Pak Chung; McPherson, Ruth; Lee, Jeannette; Tai, E Shyong; Sladek, Robert; Carlsson, Lena M S; Walley, Andrew; Eichler, Evan E; Pattou, Francois; Spector, Timothy D; Froguel, Philippe

2014-05-01

Common multi-allelic copy number variants (CNVs) appear enriched for phenotypic associations compared to their biallelic counterparts. Here we investigated the influence of gene dosage effects on adiposity through a CNV association study of gene expression levels in adipose tissue. We identified significant association of a multi-allelic CNV encompassing the salivary amylase gene (AMY1) with body mass index (BMI) and obesity, and we replicated this finding in 6,200 subjects. Increased AMY1 copy number was positively associated with both amylase gene expression (P = 2.31 × 10(-14)) and serum enzyme levels (P < 2.20 × 10(-16)), whereas reduced AMY1 copy number was associated with increased BMI (change in BMI per estimated copy = -0.15 (0.02) kg/m(2); P = 6.93 × 10(-10)) and obesity risk (odds ratio (OR) per estimated copy = 1.19, 95% confidence interval (CI) = 1.13-1.26; P = 1.46 × 10(-10)). The OR value of 1.19 per copy of AMY1 translates into about an eightfold difference in risk of obesity between subjects in the top (copy number > 9) and bottom (copy number < 4) 10% of the copy number distribution. Our study provides a first genetic link between carbohydrate metabolism and BMI and demonstrates the power of integrated genomic approaches beyond genome-wide association studies.

The relationship between mitochondrial DNA copy number and stallion sperm function.

PubMed

Darr, Christa R; Moraes, Luis E; Connon, Richard E; Love, Charles C; Teague, Sheila; Varner, Dickson D; Meyers, Stuart A

2017-05-01

Mitochondrial DNA (mtDNA) copy number has been utilized as a measure of sperm quality in several species including mice, dogs, and humans, and has been suggested as a potential biomarker of fertility in stallion sperm. The results of the present study extend this recent discovery using sperm samples from American Quarter Horse stallions of varying age. By determining copy number of three mitochondrial genes, cytochrome b (CYTB), NADH dehydrogenase 1 (ND1) and NADH dehydrogenase 4 (ND4), instead of a single gene, we demonstrate an improved understanding of mtDNA fate in stallion sperm mitochondria following spermatogenesis. Sperm samples from 37 stallions ranging from 3 to 24 years old were collected at four breeding ranches in north and central Texas during the 2015 breeding season. Samples were analyzed for sperm motion characteristics, nuclear DNA denaturability and mtDNA copy number. Mitochondrial DNA content in individual sperm was determined by real-time qPCR and normalized with a single copy nuclear gene, Beta actin. Exploratory correlation analysis revealed that total motility was negatively correlated with CYTB copy number and sperm chromatin structure. Stallion age did not have a significant effect on copy number for any of the genes. Copy number differences existed between the three genes with CYTB having the greatest number of copies (20.6 ± 1.2 copies, range: 6.0 to 41.1) followed by ND4 (15.5 ± 0.8 copies, range: 6.7 to 27.8) and finally ND1 (12.0 ± 1.0 copies, range: 0.4 to 26.6) (P < 0.05). Varying copy number across mitochondrial genes is likely to be a result of mtDNA fragmentation and degradation since downregulation of sperm mtDNA occurs during spermatogenesis and may be important for normal sperm function. Beta regression analysis suggested that for every unit increase in mtDNA copy number of CYTB, there was a 4% decrease in the odds of sperm movement (P = 0.001). Influential analysis suggested that results are robust and not highly influenced by data from individual stallions despite the low number of stallions sampled with low sperm motility. Further genome sequencing is necessary to investigate if mutations or deletions are the underlying causes of inconsistent copy numbers across mitochondrial genes. In conclusion, we show, for the first time, that increased mtDNA copy number is associated with decreased total sperm motility in stallions. We therefore suggest that mtDNA copy number may be an indicator of defective spermatogenesis in stallions. Copyright © 2017 Elsevier Inc. All rights reserved.

Readability as a Factor in Magazine Ad Copy Recall.

ERIC Educational Resources Information Center

Wesson, David A.

1989-01-01

Examines the relationship between advertising copy readability and advertising effectiveness. Finds that recall is improved when the copy style is either fairly easy or fairly hard to read. Suggests the value of considering copy readability as a potential contributor, though a minor one, to the success of magazine advertising. (RS)

22 CFR 401.13 - Copies required.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Copies required. 401.13 Section 401.13 Foreign Relations INTERNATIONAL JOINT COMMISSION, UNITED STATES AND CANADA RULES OF PROCEDURE Applications § 401.13 Copies required. (a) Subject to paragraph (c) of this section, two duplicate originals and fifty copies...

9. Photographic copy enlargement from a 4x5 copy negative. (Original ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

9. Photographic copy enlargement from a 4x5 copy negative. (Original drawing located on abandoned NASA site, currently owned by the City of Downey, Downey, California). 1976 BLDGS.25, 41 SITE PLAN. - NASA Industrial Plant, Storage Facility, 12214 Lakewood Boulevard, Downey, Los Angeles County, CA

36 CFR 703.19 - Requests for authenticated copies of Library documents.

Code of Federal Regulations, 2010 CFR

2010-07-01

... copies of Library documents. 703.19 Section 703.19 Parks, Forests, and Public Property LIBRARY OF... Documents in Certain Legal Proceedings Where the Library Is Not a Party § 703.19 Requests for authenticated copies of Library documents. Requests for authenticated copies of Library documents for purposes of...

36 CFR 703.19 - Requests for authenticated copies of Library documents.

Code of Federal Regulations, 2011 CFR

2011-07-01

... copies of Library documents. 703.19 Section 703.19 Parks, Forests, and Public Property LIBRARY OF... Documents in Certain Legal Proceedings Where the Library Is Not a Party § 703.19 Requests for authenticated copies of Library documents. Requests for authenticated copies of Library documents for purposes of...

36 CFR 703.19 - Requests for authenticated copies of Library documents.

Code of Federal Regulations, 2012 CFR

2012-07-01

... copies of Library documents. 703.19 Section 703.19 Parks, Forests, and Public Property LIBRARY OF... Documents in Certain Legal Proceedings Where the Library Is Not a Party § 703.19 Requests for authenticated copies of Library documents. Requests for authenticated copies of Library documents for purposes of...

36 CFR 703.19 - Requests for authenticated copies of Library documents.

Code of Federal Regulations, 2014 CFR

2014-07-01

... copies of Library documents. 703.19 Section 703.19 Parks, Forests, and Public Property LIBRARY OF... Documents in Certain Legal Proceedings Where the Library Is Not a Party § 703.19 Requests for authenticated copies of Library documents. Requests for authenticated copies of Library documents for purposes of...

77 FR 27125 - Periodicals-Recognition of Distribution of Periodicals via Electronic Copies

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-09

... Electronic Copies AGENCY: Postal Service\\TM\\. ACTION: Final rule. SUMMARY: The Postal Service will revise the... limited reporting of electronic copies of Periodicals publications to satisfy the circulation standards...--Recognition of Distribution of Periodicals via Electronic Copies (77 FR 5470-5471) revising DMM 707.6 by...

18. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

18. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox copy of original plans, dated 1932, by Wisconsin Highway Commission. Xerox copy in possession of Westbrook Associated Engineers, Spring Green, Wisconsin. SUPERSTRUCTURE DETAILS. - Chippewa River Bridge, Spanning Chippewa River at State Highway 35, Nelson, Buffalo County, WI

16. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

16. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox copy of original plans, dated 1932, by Wisconsin Highway Commission. Xerox copy in possession of Westbrook Associated Engineers, Spring Green, Wisconsin. SUPERSTRUCTURE DETAILS. - Chippewa River Bridge, Spanning Chippewa River at State Highway 35, Nelson, Buffalo County, WI

17. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox copy of original plans, dated 1932, by Wisconsin Highway Commission. Xerox copy in possession of Westbrook Associated Engineers, Spring Green, Wisconsin. SUPERSTRUCTURE DETAILS. - Chippewa River Bridge, Spanning Chippewa River at State Highway 35, Nelson, Buffalo County, WI

7 CFR 1599.6 - Payments.

Code of Federal Regulations, 2012 CFR

2012-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the... Certificate); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... rate and signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of...

7 CFR 1599.6 - Payments.

Code of Federal Regulations, 2013 CFR

2013-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the... Certificate); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... rate and signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of...

7 CFR 1599.6 - Payments.

Code of Federal Regulations, 2010 CFR

2010-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the... Certificate); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... rate and signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of...

7 CFR 1599.6 - Payments.

Code of Federal Regulations, 2011 CFR

2011-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the... Certificate); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... rate and signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of...

7 CFR 1599.6 - Payments.

Code of Federal Regulations, 2014 CFR

2014-01-01

... containerized cargoes, a copy of the FGIS Container Condition Inspection Certificate; (5) A signed copy of the... Certificate); (ii) A signed copy of the National Cargo Bureau Certificate of Readiness (Vessel Hold Inspection... rate and signed by the originating carrier; (3) For all non-containerized cargoes: (i) A signed copy of...

1 CFR 18.1 - Original and copies required.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 1 General Provisions 1 2014-01-01 2012-01-01 true Original and copies required. 18.1 Section 18.1... PROCESSING OF DOCUMENTS PREPARATION AND TRANSMITTAL OF DOCUMENTS GENERALLY § 18.1 Original and copies... two duplicate originals or certified copies. 1 However, if the document is printed or processed on...

1 CFR 18.1 - Original and copies required.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 1 General Provisions 1 2013-01-01 2012-01-01 true Original and copies required. 18.1 Section 18.1... PROCESSING OF DOCUMENTS PREPARATION AND TRANSMITTAL OF DOCUMENTS GENERALLY § 18.1 Original and copies... two duplicate originals or certified copies. 1 However, if the document is printed or processed on...

1 CFR 18.1 - Original and copies required.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 1 General Provisions 1 2012-01-01 2012-01-01 false Original and copies required. 18.1 Section 18.1... PROCESSING OF DOCUMENTS PREPARATION AND TRANSMITTAL OF DOCUMENTS GENERALLY § 18.1 Original and copies... two duplicate originals or certified copies. 1 However, if the document is printed or processed on...

40 CFR 264.53 - Copies of contingency plan.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Copies of contingency plan. 264.53... Contingency Plan and Emergency Procedures § 264.53 Copies of contingency plan. A copy of the contingency plan... called upon to provide emergency services. [Comment: The contingency plan must be submitted to the...

Java-based remote viewing and processing of nuclear medicine images: toward "the imaging department without walls".

PubMed

Slomka, P J; Elliott, E; Driedger, A A

2000-01-01

In nuclear medicine practice, images often need to be reviewed and reports prepared from locations outside the department, usually in the form of hard copy. Although hard-copy images are simple and portable, they do not offer electronic data search and image manipulation capabilities. On the other hand, picture archiving and communication systems or dedicated workstations cannot be easily deployed at numerous locations. To solve this problem, we propose a Java-based remote viewing station (JaRViS) for the reading and reporting of nuclear medicine images using Internet browser technology. JaRViS interfaces to the clinical patient database of a nuclear medicine workstation. All JaRViS software resides on a nuclear medicine department server. The contents of the clinical database can be searched by a browser interface after providing a password. Compressed images with the Java applet and color lookup tables are downloaded on the client side. This paradigm does not require nuclear medicine software to reside on remote computers, which simplifies support and deployment of such a system. To enable versatile reporting of the images, color tables and thresholds can be interactively manipulated and images can be displayed in a variety of layouts. Image filtering, frame grouping (adding frames), and movie display are available. Tomographic mode displays are supported, including gated SPECT. The time to display 14 lung perfusion images in 128 x 128 matrix together with the Java applet and color lookup tables over a V.90 modem is <1 min. SPECT and PET slice reorientation is interactive (<1 s). JaRViS could run on a Windows 95/98/NT or a Macintosh platform with Netscape Communicator or Microsoft Intemet Explorer. The performance of Java code for bilinear interpolation, cine display, and filtering approaches that of a standard imaging workstation. It is feasible to set up a remote nuclear medicine viewing station using Java and an Internet or intranet browser. Images can be made easily and cost-effectively available to referring physicians and ambulatory clinics within and outside of the hospital, providing a convenient alternative to film media. We also find this system useful in home reporting of emergency procedures such as lung ventilation-perfusion scans or dynamic studies.

11. Photographic copy of copy of Twin Lakes Outlet Works ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

11. Photographic copy of copy of Twin Lakes Outlet Works construction drawing dated January 15, 1951. Drawn by W.A. Doe for the Twin Lakes Reservoir and Canal Co. (copy in possession of Bureau of Reclamation, location of original unknown) 'AS CONSTRUCTED' PLANS OF 1949-1950, REHABILITATION OF TWIN LAKES RESERVOIR OUTLET WORKS, DETAILS OF UPSTREAM WING WALLS. - Twin Lakes Dam & Outlet Works, Beneath Twin Lakes Reservoir, T11S, R80W, S22, Twin Lakes, Lake County, CO

12. Photographic copy of copy of Twin Lakes Outlet Works ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. Photographic copy of copy of Twin Lakes Outlet Works construction drawing dated January 15, 1951. Drawn by W.A. Doe for the Twin Lakes Reservoir and Canal Co. (copy in possession of Bureau of Reclamation, location of original unknown) 'AS CONSTRUCTED' PLANS OF 1949-50, REHABILITATION OF TWIN LAKES RESERVOIR OUTLET WORKS, DETAILS OF DISCHARGE BASIN. - Twin Lakes Dam & Outlet Works, Beneath Twin Lakes Reservoir, T11S, R80W, S22, Twin Lakes, Lake County, CO

An X-Ray Diagnostic for Light-Ion Current Measurements.

DTIC Science & Technology

1981-03-04

Company , The P. 0. Box 3707 Seattle, WA 98124 Attn: Aerospace Library 1 copy Cornell University thaca, NY 14850 tn: 0. A. H-ammer J. COPY R. N. Sudan I...CA 94303 (Fcrmnerly Aeronutronic Ford Corporation) ":tn: Library 1 copy D. q. .ciorrow M.iS G 30 1 copy Seneral Elec:ric Company S.ace Divisi-n Valley... Company Tempo-Center for Advanced Studies 316 State Street (P. 0. Drawer QQ) Santa Barbara, CA 93102 ’ttn: OASIAC 1 copy Grimman Aerospace Corporation

GASPRNG: GPU accelerated scalable parallel random number generator library

NASA Astrophysics Data System (ADS)

Gao, Shuang; Peterson, Gregory D.

2013-04-01

Graphics processors represent a promising technology for accelerating computational science applications. Many computational science applications require fast and scalable random number generation with good statistical properties, so they use the Scalable Parallel Random Number Generators library (SPRNG). We present the GPU Accelerated SPRNG library (GASPRNG) to accelerate SPRNG in GPU-based high performance computing systems. GASPRNG includes code for a host CPU and CUDA code for execution on NVIDIA graphics processing units (GPUs) along with a programming interface to support various usage models for pseudorandom numbers and computational science applications executing on the CPU, GPU, or both. This paper describes the implementation approach used to produce high performance and also describes how to use the programming interface. The programming interface allows a user to be able to use GASPRNG the same way as SPRNG on traditional serial or parallel computers as well as to develop tightly coupled programs executing primarily on the GPU. We also describe how to install GASPRNG and use it. To help illustrate linking with GASPRNG, various demonstration codes are included for the different usage models. GASPRNG on a single GPU shows up to 280x speedup over SPRNG on a single CPU core and is able to scale for larger systems in the same manner as SPRNG. Because GASPRNG generates identical streams of pseudorandom numbers as SPRNG, users can be confident about the quality of GASPRNG for scalable computational science applications. Catalogue identifier: AEOI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOI_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: UTK license. No. of lines in distributed program, including test data, etc.: 167900 No. of bytes in distributed program, including test data, etc.: 1422058 Distribution format: tar.gz Programming language: C and CUDA. Computer: Any PC or workstation with NVIDIA GPU (Tested on Fermi GTX480, Tesla C1060, Tesla M2070). Operating system: Linux with CUDA version 4.0 or later. Should also run on MacOS, Windows, or UNIX. Has the code been vectorized or parallelized?: Yes. Parallelized using MPI directives. RAM: 512 MB˜ 732 MB (main memory on host CPU, depending on the data type of random numbers.) / 512 MB (GPU global memory) Classification: 4.13, 6.5. Nature of problem: Many computational science applications are able to consume large numbers of random numbers. For example, Monte Carlo simulations are able to consume limitless random numbers for the computation as long as resources for the computing are supported. Moreover, parallel computational science applications require independent streams of random numbers to attain statistically significant results. The SPRNG library provides this capability, but at a significant computational cost. The GASPRNG library presented here accelerates the generators of independent streams of random numbers using graphical processing units (GPUs). Solution method: Multiple copies of random number generators in GPUs allow a computational science application to consume large numbers of random numbers from independent, parallel streams. GASPRNG is a random number generators library to allow a computational science application to employ multiple copies of random number generators to boost performance. Users can interface GASPRNG with software code executing on microprocessors and/or GPUs. Running time: The tests provided take a few minutes to run.

The transcription factor titration effect dictates level of gene expression.

PubMed

Brewster, Robert C; Weinert, Franz M; Garcia, Hernan G; Song, Dan; Rydenfelt, Mattias; Phillips, Rob

2014-03-13

Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle. Copyright © 2014 Elsevier Inc. All rights reserved.

Selective sweep on human amylase genes postdates the split with Neanderthals

PubMed Central

Inchley, Charlotte E.; Larbey, Cynthia D. A.; Shwan, Nzar A. A.; Pagani, Luca; Saag, Lauri; Antão, Tiago; Jacobs, Guy; Hudjashov, Georgi; Metspalu, Ene; Mitt, Mario; Eichstaedt, Christina A.; Malyarchuk, Boris; Derenko, Miroslava; Wee, Joseph; Abdullah, Syafiq; Ricaut, François-Xavier; Mormina, Maru; Mägi, Reedik; Villems, Richard; Metspalu, Mait; Jones, Martin K.; Armour, John A. L.; Kivisild, Toomas

2016-01-01

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content. PMID:27853181

Selective sweep on human amylase genes postdates the split with Neanderthals.

PubMed

Inchley, Charlotte E; Larbey, Cynthia D A; Shwan, Nzar A A; Pagani, Luca; Saag, Lauri; Antão, Tiago; Jacobs, Guy; Hudjashov, Georgi; Metspalu, Ene; Mitt, Mario; Eichstaedt, Christina A; Malyarchuk, Boris; Derenko, Miroslava; Wee, Joseph; Abdullah, Syafiq; Ricaut, François-Xavier; Mormina, Maru; Mägi, Reedik; Villems, Richard; Metspalu, Mait; Jones, Martin K; Armour, John A L; Kivisild, Toomas

2016-11-17

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

36 CFR 1290.6 - Originals and copies.

Code of Federal Regulations, 2010 CFR

2010-07-01

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17 CFR 270.8b-11 - Number of copies; signatures; binding.

Code of Federal Regulations, 2010 CFR

2010-04-01

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14 CFR 187.7 - Copies; seal.

Code of Federal Regulations, 2011 CFR

2011-01-01

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14 CFR 187.7 - Copies; seal.

Code of Federal Regulations, 2010 CFR

2010-01-01

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1 CFR 15.4 - Reproduction and certification of copies of acts and documents.

Code of Federal Regulations, 2011 CFR

2011-01-01

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15. Photographic copy englargement from a 4x5 copy negative (Original ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. Photographic copy englargement from a 4x5 copy negative (Original drawing located on abandoned NASA site, currently owned by the City of Downey, Downey, California). 1980 BLDG 10, BLDG 42 FLOOR PLAN, NASA MARCH 15 1980. - NASA Industrial Plant, Maintenance Facility, 12214 Lakewood Boulevard, Downey, Los Angeles County, CA

33 CFR 72.01-40 - Single copies.

Code of Federal Regulations, 2010 CFR

2010-07-01

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33 CFR 72.01-40 - Single copies.

Code of Federal Regulations, 2011 CFR

2011-07-01

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41 CFR 105-50.202-1 - Copies of statistical or other studies.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false Copies of statistical or... Services Administration § 105-50.202-1 Copies of statistical or other studies. This material includes a copy of any existing statistical or other studies and compilations, results of technical tests and...

5 CFR 1632.11 - Procedures for inspection and obtaining copies of transcriptions and minutes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... copies of transcriptions and minutes. 1632.11 Section 1632.11 Administrative Personnel FEDERAL RETIREMENT... inspection and obtaining copies of transcriptions and minutes. (a) Any person may inspect or copy a transcript, a recording or transcription, or minutes described in § 1632.10(c) of this part. (b) Requests for...

5 CFR 1632.11 - Procedures for inspection and obtaining copies of transcriptions and minutes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... copies of transcriptions and minutes. 1632.11 Section 1632.11 Administrative Personnel FEDERAL RETIREMENT... inspection and obtaining copies of transcriptions and minutes. (a) Any person may inspect or copy a transcript, a recording or transcription, or minutes described in § 1632.10(c) of this part. (b) Requests for...

40 CFR 264.53 - Copies of contingency plan.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 26 2014-07-01 2014-07-01 false Copies of contingency plan. 264.53... Contingency Plan and Emergency Procedures § 264.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b) Submitted to all local...

40 CFR 265.53 - Copies of contingency plan.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 26 2011-07-01 2011-07-01 false Copies of contingency plan. 265.53... DISPOSAL FACILITIES Contingency Plan and Emergency Procedures § 265.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b...

40 CFR 264.53 - Copies of contingency plan.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Copies of contingency plan. 264.53... Contingency Plan and Emergency Procedures § 264.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b) Submitted to all local...

40 CFR 264.53 - Copies of contingency plan.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 27 2012-07-01 2012-07-01 false Copies of contingency plan. 264.53... Contingency Plan and Emergency Procedures § 264.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b) Submitted to all local...

40 CFR 264.53 - Copies of contingency plan.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 26 2011-07-01 2011-07-01 false Copies of contingency plan. 264.53... Contingency Plan and Emergency Procedures § 264.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b) Submitted to all local...

40 CFR 265.53 - Copies of contingency plan.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 27 2012-07-01 2012-07-01 false Copies of contingency plan. 265.53... DISPOSAL FACILITIES Contingency Plan and Emergency Procedures § 265.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b...

40 CFR 265.53 - Copies of contingency plan.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 26 2014-07-01 2014-07-01 false Copies of contingency plan. 265.53... DISPOSAL FACILITIES Contingency Plan and Emergency Procedures § 265.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b...

40 CFR 265.53 - Copies of contingency plan.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Copies of contingency plan. 265.53... DISPOSAL FACILITIES Contingency Plan and Emergency Procedures § 265.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b...

19. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

19. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox copy of original plans, dated 1932, by Wisconsin Highway Commission. Xerox copy in possession of Westbrook Associated Engineers, Spring Green, Wisconsin. DETAILS FOR PIERS NO. 1, 2, 5 & 6. - Chippewa River Bridge, Spanning Chippewa River at State Highway 35, Nelson, Buffalo County, WI

15. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. Wayne Chandler, Photographer, August 1993 Photographic copy of Xerox copy of original plans, dated 1932, by Wisconsin Highway Commission. Xerox copy in possession of Westbrook Associated Engineers, Spring Green, Wisconsin. GENERAL PLAN AND ELEVATION OF BRIDGE. - Chippewa River Bridge, Spanning Chippewa River at State Highway 35, Nelson, Buffalo County, WI

40 CFR 262.22 - Number of copies.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 26 2011-07-01 2011-07-01 false Number of copies. 262.22 Section 262...) STANDARDS APPLICABLE TO GENERATORS OF HAZARDOUS WASTE The Manifest § 262.22 Number of copies. The manifest consists of at least the number of copies which will provide the generator, each transporter, and the owner...

40 CFR 262.22 - Number of copies.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 27 2012-07-01 2012-07-01 false Number of copies. 262.22 Section 262...) STANDARDS APPLICABLE TO GENERATORS OF HAZARDOUS WASTE The Manifest § 262.22 Number of copies. The manifest consists of at least the number of copies which will provide the generator, each transporter, and the owner...

40 CFR 262.22 - Number of copies.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Number of copies. 262.22 Section 262...) STANDARDS APPLICABLE TO GENERATORS OF HAZARDOUS WASTE The Manifest § 262.22 Number of copies. The manifest consists of at least the number of copies which will provide the generator, each transporter, and the owner...

41 CFR 105-50.202-1 - Copies of statistical or other studies.

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2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Copies of statistical or... Services Administration § 105-50.202-1 Copies of statistical or other studies. This material includes a copy of any existing statistical or other studies and compilations, results of technical tests and...

40 CFR 265.53 - Copies of contingency plan.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Copies of contingency plan. 265.53... DISPOSAL FACILITIES Contingency Plan and Emergency Procedures § 265.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b...

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

PubMed

Castle, John C; Biery, Matthew; Bouzek, Heather; Xie, Tao; Chen, Ronghua; Misura, Kira; Jackson, Stuart; Armour, Christopher D; Johnson, Jason M; Rohl, Carol A; Raymond, Christopher K

2010-04-16

DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

PubMed Central

2010-01-01

Background DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. Results We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. Conclusion The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads. PMID:20398377

The Mars mapper science and mission planning tool

NASA Technical Reports Server (NTRS)

Lo, Martin W.

1993-01-01

The Mars Mapper Program (MOm) is an interactive tool for science and mission design developed for the Mars Observer Mission (MO). MOm is a function of the Planning and Sequencing Element of the MO Ground Data System. The primary users of MOm are members of the science and mission planning teams. Using MOm, the user can display digital maps of Mars in various projections and resolutions ranging from 1 to 256 pixels per degree squared. The user can overlay the maps with ground tracks of the MO spacecraft (S/C) and footprints and swaths of the various instruments on-board the S/C. Orbital and instrument geometric parameters can be computed on demand and displayed on the digital map or plotted in XY-plots. The parameter data can also be saved into files for other uses. MOm is divided into 3 major processes: Generator, Mapper, Plotter. The Generator Process is the main control which spawns all other processes. The processes communicate via sockets. At any one time, only 1 copy of MOm may operate on the system. However, up to 5 copies of each of the major processes may be invoked from the Generator. MOm is developed on the Sun SPARCStation 2GX with menu driven graphical user interface (GUI). The map window and its overlays are mouse-sensitized to permit on-demand calculations of various parameters along an orbit. The program is currently under testing and will be delivered to the MO Mission System Configuration Management for distribution to the MO community in 3/93.

CoNVaQ: a web tool for copy number variation-based association studies.

PubMed

Larsen, Simon Jonas; do Canto, Luisa Matos; Rogatto, Silvia Regina; Baumbach, Jan

2018-05-18

Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies. The web service allows users to upload two sets of CNV segments and search for genomic regions where the occurrence of CNVs is significantly associated with the phenotype. CoNVaQ provides two models: a simple statistical model using Fisher's exact test and a novel query-based model matching regions to user-defined queries. For each region, the method computes a global q-value statistic by repeated permutation of samples among the populations. We demonstrate our platform by using it to analyze a data set of HPV-positive and HPV-negative penile cancer patients. CoNVaQ provides a simple workflow for performing CNV-based association studies. It is made available as a web platform in order to provide a user-friendly workflow for biologists and clinicians to carry out CNV data analysis without installing any software. Through the web interface, users are also able to analyze their results to find overrepresented GO terms and pathways. In addition, our method is also available as a package for the R programming language. CoNVaQ is available at https://convaq.compbio.sdu.dk .

Sampling and detection of airborne influenza virus towards point-of-care applications.

PubMed

Ladhani, Laila; Pardon, Gaspard; Meeuws, Hanne; van Wesenbeeck, Liesbeth; Schmidt, Kristiane; Stuyver, Lieven; van der Wijngaart, Wouter

2017-01-01

Airborne transmission of the influenza virus contributes significantly to the spread of this infectious pathogen, particularly over large distances when carried by aerosol droplets with long survival times. Efficient sampling of virus-loaded aerosol in combination with a low limit of detection of the collected virus could enable rapid and early detection of airborne influenza virus at the point-of-care setting. Here, we demonstrate a successful sampling and detection of airborne influenza virus using a system specifically developed for such applications. Our system consists of a custom-made electrostatic precipitation (ESP)-based bioaerosol sampler that is coupled with downstream quantitative polymerase chain reaction (qPCR) analysis. Aerosolized viruses are sampled directly into a miniaturized collector with liquid volume of 150 μL, which constitutes a simple and direct interface with subsequent biological assays. This approach reduces sample dilution by at least one order of magnitude when compared to other liquid-based aerosol bio-samplers. Performance of our ESP-based sampler was evaluated using influenza virus-loaded sub-micron aerosols generated from both cultured and clinical samples. Despite the miniaturized collection volume, we demonstrate a collection efficiency of at least 10% and sensitive detection of a minimum of 3721 RNA copies. Furthermore, we show that an improved extraction protocol can allow viral recovery of down to 303 RNA copies and a maximum sampler collection efficiency of 47%. A device with such a performance would reduce sampling times dramatically, from a few hours with current sampling methods down to a couple of minutes with our ESP-based bioaerosol sampler.

Reliability and validity of soft copy images based on flat-panel detector in pneumoconiosis classification: comparison with the analog radiographs.

PubMed

Lee, Won-Jeong; Choi, Byung-Soon

2013-06-01

The aim of this study was to evaluate the reliability and validity of soft copy images based on flat-panel detector of digital radiography (DR-FPD soft copy images) compared to analog radiographs (ARs) in pneumoconiosis classification and diagnosis. DR-FPD soft copy images and ARs from 349 subjects were independently read by four-experienced readers according to the International Labor Organization 2000 guidelines. DR-FPD soft copy images were used to obtain consensus reading (CR) by all readers as the gold standard. Reliability and validity were evaluated by a κ and receiver operating characteristic analysis, respectively. In small opacity, overall interreader agreement of DR-FPD soft copy images was significantly higher than that of ARs, but it was not significantly different in large opacity and costophrenic angle obliteration. In small opacity, agreement of DR-FPD soft copy images with CR was significantly higher than that of ARs with CR. It was also higher than that of ARs with CR in pleural plaque and thickening. Receiver operating characteristic areas were not different significantly between DR-FPD soft copy images and ARs. DR-FPD soft copy images showed accurate and reliable results in pneumoconiosis classification and diagnosis compared to ARs. Copyright © 2013 AUR. Published by Elsevier Inc. All rights reserved.

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

PubMed Central

Maron, Lyza G.; Guimarães, Claudia T.; Kirst, Matias; Albert, Patrice S.; Birchler, James A.; Bradbury, Peter J.; Buckler, Edward S.; Coluccio, Alison E.; Danilova, Tatiana V.; Kudrna, David; Magalhaes, Jurandir V.; Piñeros, Miguel A.; Schatz, Michael C.; Wing, Rod A.; Kochian, Leon V.

2013-01-01

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world’s potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments. PMID:23479633

Gene copy number variation and its significance in cyanobacterial phylogeny

PubMed Central

2012-01-01

Background In eukaryotes, variation in gene copy numbers is often associated with deleterious effects, but may also have positive effects. For prokaryotes, studies on gene copy number variation are rare. Previous studies have suggested that high numbers of rRNA gene copies can be advantageous in environments with changing resource availability, but further association of gene copies and phenotypic traits are not documented. We used one of the morphologically most diverse prokaryotic phyla to test whether numbers of gene copies are associated with levels of cell differentiation. Results We implemented a search algorithm that identified 44 genes with highly conserved copies across 22 fully sequenced cyanobacterial taxa. For two very basal cyanobacterial species, Gloeobacter violaceus and a thermophilic Synechococcus species, distinct phylogenetic positions previously found were supported by identical protein coding gene copy numbers. Furthermore, we found that increased ribosomal gene copy numbers showed a strong correlation to cyanobacteria capable of terminal cell differentiation. Additionally, we detected extremely low variation of 16S rRNA sequence copies within the cyanobacteria. We compared our results for 16S rRNA to three other eubacterial phyla (Chroroflexi, Spirochaetes and Bacteroidetes). Based on Bayesian phylogenetic inference and the comparisons of genetic distances, we could confirm that cyanobacterial 16S rRNA paralogs and orthologs show significantly stronger conservation than found in other eubacterial phyla. Conclusions A higher number of ribosomal operons could potentially provide an advantage to terminally differentiated cyanobacteria. Furthermore, we suggest that 16S rRNA gene copies in cyanobacteria are homogenized by both concerted evolution and purifying selection. In addition, the small ribosomal subunit in cyanobacteria appears to evolve at extraordinary slow evolutionary rates, an observation that has been made previously for morphological characteristics of cyanobacteria. PMID:22894826

Dietary starch intake modifies the relation between copy number variation in the salivary amylase gene and BMI.

PubMed

Rukh, Gull; Ericson, Ulrika; Andersson-Assarsson, Johanna; Orho-Melander, Marju; Sonestedt, Emily

2017-07-01

Background: Studies have shown conflicting associations between the salivary amylase gene ( AMY1 ) copy number and obesity. Salivary amylase initiates starch digestion in the oral cavity; starch is a major source of energy in the diet. Objective: We investigated the association between AMY1 copy number and obesity traits, and the effect of the interaction between AMY1 copy number and starch intake on these obesity traits. Design: We first assessed the association between AMY1 copy number (genotyped by digital droplet polymerase chain reaction) and obesity traits in 4800 individuals without diabetes (mean age: 57 y; 60% female) from the Malmö Diet and Cancer Cohort. Then we analyzed interactions between AMY1 copy number and energy-adjusted starch intake (obtained by a modified diet history method) on body mass index (BMI) and body fat percentage. Results: AMY1 copy number was not associated with BMI ( P = 0.80) or body fat percentage ( P = 0.38). We observed a significant effect of the interaction between AMY1 copy number and starch intake on BMI ( P -interaction = 0.007) and body fat percentage ( P -interaction = 0.03). Upon stratification by dietary starch intake, BMI tended to decrease with increasing AMY1 copy numbers in the low-starch intake group ( P = 0.07) and tended to increase with increasing AMY1 copy numbers in the high-starch intake group ( P = 0.08). The lowest mean BMI was observed in the group of participants with a low AMY1 copy number and a high dietary intake of starch. Conclusions: Our findings suggest an effect of the interaction between starch intake and AMY1 copy number on obesity. Individuals with high starch intake but low genetic capacity to digest starch had the lowest BMI, potentially because larger amounts of undigested starch are transported through the gastrointestinal tract, contributing to fewer calories extracted from ingested starch. © 2017 American Society for Nutrition.

Meta-analysis of two randomized controlled trials comparing combined zidovudine and didanosine therapy with combined zidovudine, didanosine, and nevirapine therapy in patients with HIV. INCAS study team.

PubMed

Raboud, J M; Rae, S; Vella, S; Harrigan, P R; Bucciardini, R; Fragola, V; Ricciardulli, D; Montaner, J S

1999-11-01

To extend the range of CD4 counts in which a plasma viral load nadir (pVL) <20 copies/ml was known to be predictive of the duration of virologic response. To determine whether baseline pVL is predictive of virologic response during the study periods. A meta-analysis was conducted of the original individual patient data from two randomized controlled trials comparing zidovudine (ZDV)/didanosine (ddI) with ZDV/ddI/nevirapine (NVP). In total, 87 patients received ZDV/ddI and 83 received ZDV/ddI/NVP. Study subjects on triple therapy with baseline pVL <100,000 copies/ml were more likely to achieve a pVL <400 copies/ml (odds ratio [OR] = 2.49; p = .02) and <20 copies/ml (OR = 4.76; p = .001) during the trial than those with baseline pVL > 100,000 copies/ml. Among triple therapy patients, the relative risk of virologic failure was higher for patients with higher baseline pVL (rate ratio [RR] = 2.51/log10 copies/ ml; p = .01), after controlling for compliance and pVL nadir. The relative risks of virologic failure associated with pVL nadir <20 copies/ml and between 21 and 400 copies/ml were .04 (p = .0001) and .56 (p = .26), respectively, compared with patients with a pVL nadir >400 copies/ml. We have extended our earlier results that achieving a pVL nadir <20 copies/ml is important for maintaining virologic suppression. In particular, we have demonstrated that a pVL nadir <20 copies/ml is at least fivefold more protective against virologic failure than achieving a pVL nadir between 20 and 400 copies/ml. Baseline pVL is significantly associated with the probability of achieving and sustaining virologic suppression.

Epidermal growth factor receptor and AKT1 gene copy numbers by multi-gene fluorescence in situ hybridization impact on prognosis in breast cancer.

PubMed

Li, Jiao; Su, Wei; Zhang, Sheng; Hu, Yunhui; Liu, Jingjing; Zhang, Xiaobei; Bai, Jingchao; Yuan, Weiping; Hu, Linping; Cheng, Tao; Zetterberg, Anders; Lei, Zhenmin; Zhang, Jin

2015-05-01

The epidermal growth factor receptor (EGFR)/PI3K/AKT signaling pathway aberrations play significant roles in breast cancer occurrence and development. However, the status of EGFR and AKT1 gene copy numbers remains unclear. In this study, we showed that the rates of EGFR and AKT1 gene copy number alterations were associated with the prognosis of breast cancer. Among 205 patients, high EGFR and AKT1 gene copy numbers were observed in 34.6% and 27.8% of cases by multi-gene fluorescence in situ hybridization, respectively. Co-heightened EGFR/AKT1 gene copy numbers were identified in 11.7% cases. No changes were found in 49.3% of patients. Although changes in EGFR and AKT1 gene copy numbers had no correlation with patients' age, tumor stage, histological grade and the expression status of other molecular makers, high EGFR (P = 0.0002) but not AKT1 (P = 0.1177) gene copy numbers correlated with poor 5-year overall survival. The patients with co-heightened EGFR/AKT1 gene copy numbers displayed a poorer prognosis than those with tumors with only high EGFR gene copy numbers (P = 0.0383). Both Univariate (U) and COX multivariate (C) analyses revealed that high EGFR and AKT1 gene copy numbers (P = 0.000 [U], P = 0.0001 [C]), similar to histological grade (P = 0.001 [U], P = 0.012 [C]) and lymph node metastasis (P = 0.046 [U], P = 0.158 [C]), were independent prognostic indicators of 5-year overall survival. These results indicate that high EGFR and AKT1 gene copy numbers were relatively frequent in breast cancer. Co-heightened EGFR/AKT1 gene copy numbers had a worse outcome than those with only high EGFR gene copy numbers, suggesting that evaluation of these two genes together may be useful for selecting patients for anti-EGFR-targeted therapy or anti-EGFR/AKT1-targeted therapy and for predicting outcomes. © 2015 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

Dynamics in copy numbers of five plasmids of a dairy Lactococcus lactis in dairy-related conditions including near-zero growth rates.

PubMed

van Mastrigt, Oscar; Lommers, Marcel M A N; de Vries, Yorick C; Abee, Tjakko; Smid, Eddy J

2018-03-23

Lactic acid bacteria can carry multiple plasmids affecting their performance in dairy fermentations. The expression of plasmid-encoded genes and the activity of the corresponding proteins is severely affected by changes in the number of plasmid copies. We studied the impact of growth rate on dynamics of plasmid copy numbers at high growth rates in chemostat cultures and down to near-zero growth rates in retentostat cultures. Five plasmids of the dairy strain Lactococcus lactis FM03-V1 were selected which varied in size (3 to 39 kb), in replication mechanism (theta or rolling-circle) and in putative (dairy-associated) functions. Copy numbers ranged from 1.5 to 40.5 and the copy number of theta-type replicating plasmids were negatively correlated to the plasmid size. Despite the extremely wide range of growth rates (0.0003 h -1 to 0.6 h -1 ), copy numbers of the five plasmids were stable and only slightly increased at near-zero growth rates showing that the plasmid replication rate was strictly controlled. One low-copy number plasmid, carrying a large exopolysaccharide gene cluster, was segregationally unstable during retentostat cultivations reflected in complete loss of the plasmid in one of the retentostat cultures. The copy number of the five plasmids was also hardly affected by varying the pH value, nutrient limitation or presence of citrate (maximum 2.2-fold) signifying the stability in copy number of the plasmids. Importance Lactococcus lactis is extensively used in starter cultures for dairy fermentations. Important traits for growth and survival of L. lactis in dairy fermentations are encoded by genes located on plasmids, such as genes involved in lactose and citrate metabolism, protein degradation and oligopeptide uptake and bacteriophage resistance. Because the number of plasmid copies could affect the expression of plasmid-encoded genes, it is important to know the factors that influence the plasmid copy numbers. We monitored plasmid copy numbers of L. lactis at near-zero growth rates, characteristic for cheese ripening. Moreover, we analysed the effect of pH, nutrient limitation and presence of citrate. This showed that plasmid copy numbers were stable giving insight into plasmid copy number dynamics in dairy fermentations. Copyright © 2018 American Society for Microbiology.

[Copy number variation of trinucleotide repeat in dynamic mutation sites of autosomal dominant cerebellar ataxias related genes].

PubMed

Chen, Pu; Ma, Mingyi; Shang, Huifang; Su, Dan; Zhang, Sizhong; Yang, Yuan

2009-12-01

To standardize the experimental procedure of the gene test for autosomal dominant cerebellar ataxias (ADCA), and provide the basis for quantitative criteria of the dynamic mutation of spinocerebellar ataxia (SCA) genes in Chinese population. Genotyping of the dynamic mutation loci of the SCA1, SCA2, SCA3, SCA6 and SCA7 genes was performed, using florescence PCR-capillary electrophoresis followed by DNA sequencing, to investigate the variation range of copy number of CAG tandem repeat of the genes in 263 probands of ADCA pedigrees and 261 non-related normal controls. Based on the sequencing result, the bias of the CAG copy number estimation using capillary electrophoresis with different DNA controls was compared to analyze the technical detailes of the electrophresis method in testing the dynamic mutation sites. PCR products containing dynamic mutation loci of the SCA genes showed significantly higher mobility than that of molecular weigh marker with relatively balanced GC content. This was particularly obvious in the SCA2, SCA 6 and SCA7 genes whereas the deviation of copy number could be corrected to +/-1 when known CAG copy number fragments were used as controls. The mobility of PCR products was primarily related to the copy number of CAG repeat when the fragments contained normal CAG repeat. In the 263 ADCA pedigrees, 6 (2.28%) carried SCA1 gene mutation, 8 (3.04%) had SCA2 mutation and 81 (30.80%) harbored SCA3 mutation. The gene mutation of SCA6 and SCA7 was not found. The normal variation range of the CAG repeat was 17-36 copies in SCA1 gene, 13-30 copies in SCA2, 14-39 copies in SCA3, 6-16 copies in SCA6 and 6-13 copies in SCA7. The heterozygosity was 76.1%, 17.7%, 74.4%, 72.1% and 41.3%, respectively. The mutation range of the CAG repeat was 49-56 copies in SCA1 gene, 36-41 copies in SCA2, 59-81 copies in SCA3. Neither homozygous mutation of an SCA gene nor double heterozygous mutation of the SCA genes was observed in the study. The copy number of the CAG repeat in SCA genes could be calculated accurately based on the result of florescence PCR-capillary electrophoresis when limited amount of known repeat copy number controls were used. Our result supported that the notion that SCA3 gene mutation was the most common cause for ADCA, and the obtained data would be helpful for establishing quantitative criteria of the dynamic mutation of the SCA genes in Chinese.

Time to viral load suppression in antiretroviral-naive and -experienced HIV-infected pregnant women on highly active antiretroviral therapy: implications for pregnant women presenting late in gestation.

PubMed

Aziz, N; Sokoloff, A; Kornak, J; Leva, N V; Mendiola, M L; Levison, J; Feakins, C; Shannon, M; Cohan, D

2013-11-01

To compare time to achieve viral load <400 copies/ml and <1000 copies/ml in HIV-infected antiretroviral (ARV) -naive versus ARV-experienced pregnant women on highly active antiretroviral therapy (HAART). Retrospective cohort study. Three university medical centers, USA. HIV-infected pregnant women initiated or restarted on HAART during pregnancy. We calculated time to viral load <400 copies/ml and <1000 copies/ml in HIV-infected pregnant women on HAART who reported at least 50% adherence, stratifying based on previous ARV exposure history. Time to HIV viral load <400 copies/ml and <1000 copies/ml. We evaluated 138 HIV-infected pregnant women, comprising 76 ARV-naive and 62 ARV-experienced. Ninety-three percent of ARV-naive women achieved a viral load < 400 copies/ml during pregnancy compared with 92% of ARV-experienced women (P = 0.82). The median number of days to achieve a viral load < 400 copies/ml in the ARV-naive cohort was 25.0 (range 3.5-133; interquartile range 16-34) days compared with 27.0 (range 8-162.5; interquartile range 18.5-54.3) days in the ARV-experienced cohort (P = 0.02). In a multiple predictor analysis, women with higher adherence (adjusted relative hazard [aRH] per 10% increase in adherence 1.29, 95% confidence interval [CI] 1.08-1.54, P = 0.01) and receiving a non-nucleotide reverse transcriptase inhibitor (NNRTI) -based regimen (aRH 2.48, 95% CI 1.33-4.63, P = 0.01) were more likely to achieve viral load <400 copies/ml earlier. Increased baseline HIV log10 viral load was associated with a later time of achieving viral load <400 copies/ml (aRH 0.60, 95% CI 0.39-0.92, P = 0.02). In a corresponding model of time to achieve viral load <1000 copies/ml, adherence (aRH per 10% increase in adherence 1.79, 95% CI 1.34-2.39, P < 0.001), receipt of NNRTI (aRH 2.95, 95% CI 1.23-7.06, P = 0.02), and CD4 cell count (aRH per 50 count increase in CD4 1.12, 95% CI 1.03-1.22, P = 0.01) were associated with an earlier time to achieve viral load below this threshold. Increasing baseline HIV log10 viral load was associated with a longer time of achieving viral load <1000 copies/ml (aRH 0.54, 95% CI 0.34-0.86, P = 0.01). In multiple predictor models, previous ARV exposure was not significantly associated with time to achieve viral load below thresholds of <400 copies/ml and <1000 copies/ml. Pregnant women with ≥50% adherence, whether ARV-naive or ARV-experienced, on average achieve a viral load <400 copies/ml within a median of 26 days and a viral load of <1000 copies/ml within a median of 14 days of HAART initiation. Increased adherence, receipt of NNRTI-based regimen and lower baseline HIV log10 viral load were all statistically significant predictors of earlier time to achieve viral load <400 copies/ml and <1000 copies/ml. Increased CD4 count was statistically significant as a predictor of earlier time to achieve viral load <1000 copies/ml. © 2013 The Authors BJOG An International Journal of Obstetrics and Gynaecology © 2013 RCOG.

Correlates of Chinese Kindergarteners' Word Reading and Writing: The Unique Role of Copying Skills?

ERIC Educational Resources Information Center

Wang, Ying; McBride-Chang, Catherine; Chan, Shing Fong

2014-01-01

Ninety-four Mainland Chinese children in the second and third years of kindergarten (mean age = 65 months, SD = 6.94) were tested on Pinyin letter-name knowledge, invented Pinyin spelling, general copying skills of unfamiliar print (in Korean, Hebrew and Vietnamese, ultimately combined to create a pure copying factor), delayed copying of…

17 CFR 260.7a-3 - Number of copies; filing; signatures; binding.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Number of copies; filing; signatures; binding. 260.7a-3 Section 260.7a-3 Commodity and Securities Exchanges SECURITIES AND EXCHANGE... § 260.7a-3 Number of copies; filing; signatures; binding. (a) Three copies of the complete application...

17 CFR 260.4c-3 - Number of copies; filing; signatures; binding.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Number of copies; filing; signatures; binding. 260.4c-3 Section 260.4c-3 Commodity and Securities Exchanges SECURITIES AND EXCHANGE... § 260.4c-3 Number of copies; filing; signatures; binding. (a) Three copies of every application and of...

17 CFR 260.5a-3 - Number of copies; filing; signatures; binding.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Number of copies; filing; signatures; binding. 260.5a-3 Section 260.5a-3 Commodity and Securities Exchanges SECURITIES AND EXCHANGE... § 260.5a-3 Number of copies; filing; signatures; binding. (a) Three copies of each statement of...

10. Photographic copy of copy of original construction drawing, dated ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. Photographic copy of copy of original construction drawing, dated 1899?. Original in possession of Twin Lakes Reservoir and Canal Company, Ordway, Colorado. PLAN OF DAM AND HEAD GATES FOR THE TWIN LAKES RESERVOIR. - Twin Lakes Dam & Outlet Works, Beneath Twin Lakes Reservoir, T11S, R80W, S22, Twin Lakes, Lake County, CO

23. Photographic copy enlargement from a 4x5 copy negative of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

23. Photographic copy enlargement from a 4x5 copy negative of a drawing (Original drawing located on abandoned NASA site, currently owned by the City of Downey, Downey, Calfornia). JANUARY 1960 USAF PLANT 16 MASTER PLOT AND GRID PLAN. - NASA Industrial Plant, Missile Research Laboratory, 12214 Lakewood Boulevard, Downey, Los Angeles County, CA

14. Photographic copy englargement from a 4x5 copy negative (Original ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

14. Photographic copy englargement from a 4x5 copy negative (Original photograph by original photographer located on abandoned NASA site, currently owned by the City of Downey, Downey, California). AERIAL PHOTOGRAPH 1935-1936 CONSOLIDATED VULTEE AIRCRAFT CORPORATION FROM WEST TO EAST - NASA Industrial Plant, Maintenance Facility, 12214 Lakewood Boulevard, Downey, Los Angeles County, CA

22. Photographic copy enlargement from a 4x5 copy negative of ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

22. Photographic copy enlargement from a 4x5 copy negative of a print. (Original print located on abandoned NASA site, currently owned by the City of Downey, Downey, California). 1954 USAF PLANT 16 AERIAL BUILDING 41 NORTH TO SOUTH. - NASA Industrial Plant, Missile Research Laboratory, 12214 Lakewood Boulevard, Downey, Los Angeles County, CA

36 CFR § 703.19 - Requests for authenticated copies of Library documents.

Code of Federal Regulations, 2013 CFR

2013-07-01

... copies of Library documents. § 703.19 Section § 703.19 Parks, Forests, and Public Property LIBRARY OF... Documents in Certain Legal Proceedings Where the Library Is Not a Party § 703.19 Requests for authenticated copies of Library documents. Requests for authenticated copies of Library documents for purposes of...

Does Visual Attention Span Relate to Eye Movements during Reading and Copying?

ERIC Educational Resources Information Center

Bosse, Marie-Line; Kandel, Sonia; Prado, Chloé; Valdois, Sylviane

2014-01-01

This research investigated whether text reading and copying involve visual attention-processing skills. Children in grades 3 and 5 read and copied the same text. We measured eye movements while reading and the number of gaze lifts (GL) during copying. The children were also administered letter report tasks that constitute an estimation of the…

28 CFR 5.1101 - Copies of the Report of the Attorney General.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ENFORCEMENT OF FOREIGN AGENTS REGISTRATION ACT OF 1938, AS AMENDED § 5.1101 Copies of the Report of the Attorney General. Copies of the Report of the Attorney General to the Congress on the Administration of the... 28 Judicial Administration 1 2011-07-01 2011-07-01 false Copies of the Report of the Attorney...

28 CFR 5.1101 - Copies of the Report of the Attorney General.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ENFORCEMENT OF FOREIGN AGENTS REGISTRATION ACT OF 1938, AS AMENDED § 5.1101 Copies of the Report of the Attorney General. Copies of the Report of the Attorney General to the Congress on the Administration of the... 28 Judicial Administration 1 2012-07-01 2012-07-01 false Copies of the Report of the Attorney...

28 CFR 5.1101 - Copies of the Report of the Attorney General.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ENFORCEMENT OF FOREIGN AGENTS REGISTRATION ACT OF 1938, AS AMENDED § 5.1101 Copies of the Report of the Attorney General. Copies of the Report of the Attorney General to the Congress on the Administration of the... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Copies of the Report of the Attorney...

28 CFR 5.1101 - Copies of the Report of the Attorney General.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ENFORCEMENT OF FOREIGN AGENTS REGISTRATION ACT OF 1938, AS AMENDED § 5.1101 Copies of the Report of the Attorney General. Copies of the Report of the Attorney General to the Congress on the Administration of the... 28 Judicial Administration 1 2014-07-01 2014-07-01 false Copies of the Report of the Attorney...

37 CFR 1.825 - Amendments to or replacement of sequence listing and computer readable copy thereof.

Code of Federal Regulations, 2014 CFR

2014-07-01

... of sequence listing and computer readable copy thereof. 1.825 Section 1.825 Patents, Trademarks, and... Amino Acid Sequences § 1.825 Amendments to or replacement of sequence listing and computer readable copy... copy of the computer readable form (§ 1.821(e)) including all previously submitted data with the...

37 CFR 1.825 - Amendments to or replacement of sequence listing and computer readable copy thereof.

Code of Federal Regulations, 2013 CFR

2013-07-01

... of sequence listing and computer readable copy thereof. 1.825 Section 1.825 Patents, Trademarks, and... Amino Acid Sequences § 1.825 Amendments to or replacement of sequence listing and computer readable copy... copy of the computer readable form (§ 1.821(e)) including all previously submitted data with the...

37 CFR 1.825 - Amendments to or replacement of sequence listing and computer readable copy thereof.

Code of Federal Regulations, 2012 CFR

2012-07-01

... of sequence listing and computer readable copy thereof. 1.825 Section 1.825 Patents, Trademarks, and... Amino Acid Sequences § 1.825 Amendments to or replacement of sequence listing and computer readable copy... copy of the computer readable form (§ 1.821(e)) including all previously submitted data with the...

28 CFR 513.44 - Fees for copies of Inmate Central File and Medical Records.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Fees for copies of Inmate Central File... Institution for Information § 513.44 Fees for copies of Inmate Central File and Medical Records. Within a reasonable time after a request, Bureau staff are to provide an inmate personal copies of requested...

28 CFR 513.44 - Fees for copies of Inmate Central File and Medical Records.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Fees for copies of Inmate Central File... Institution for Information § 513.44 Fees for copies of Inmate Central File and Medical Records. Within a reasonable time after a request, Bureau staff are to provide an inmate personal copies of requested...

20 CFR 703.105 - Copies of forms of policies to be submitted with application.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Copies of forms of policies to be submitted... REGULATIONS Authorization of Insurance Carriers § 703.105 Copies of forms of policies to be submitted with... of the Office copies of the forms of policies which the applicant proposes to issue in writing...

39 CFR 955.23 - Copies of papers, withdrawal of exhibits.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 39 Postal Service 1 2010-07-01 2010-07-01 false Copies of papers, withdrawal of exhibits. 955.23... SERVICE BOARD OF CONTRACT APPEALS § 955.23 Copies of papers, withdrawal of exhibits. (a) When books, records, papers, or documents have been received in evidence, a true copy thereof or of such part thereof...

Second and Fourth Graders' Copying Ability: From Graphical to Linguistic Processing

ERIC Educational Resources Information Center

Grabowski, Joachim; Weinzierl, Christian; Schmitt, Markus

2010-01-01

Particularly in primary school, good performance on copy tasks is an important working technique. With respect to writing skills, copying is a very basic process on which more complex writing abilities are based. We studied the copying ability of second and fourth graders across four types of symbols which vary with respect to their semantic and…

PEER Reports

Science.gov Websites

our reports. To order b&w hard copies of 2011 PEER Reports and beyond: PEER no longer keeps copies . Reports are individually priced based on the length of the report. If you are interested in a color hard copy of any reports, contact Replica Digital Ink by email. To order b&w hard copies of PEER Reports

36 CFR 1254.76 - What procedures do I follow to copy formerly national security-classified documents?

Code of Federal Regulations, 2014 CFR

2014-07-01

... CFR 2001.24. (b) You may not remove from the research room copies of documents bearing uncancelled... individual documents, the research room staff cancels the classification markings on each page of the copy... declassification authority to the guard or research room attendant when you remove copies of documents from the...

36 CFR 1254.76 - What procedures do I follow to copy formerly national security-classified documents?

Code of Federal Regulations, 2011 CFR

2011-07-01

... CFR 2001.24. (b) You may not remove from the research room copies of documents bearing uncancelled... individual documents, the research room staff cancels the classification markings on each page of the copy... declassification authority to the guard or research room attendant when you remove copies of documents from the...

36 CFR 1254.76 - What procedures do I follow to copy formerly national security-classified documents?

Code of Federal Regulations, 2010 CFR

2010-07-01

... CFR 2001.24. (b) You may not remove from the research room copies of documents bearing uncancelled... individual documents, the research room staff cancels the classification markings on each page of the copy... declassification authority to the guard or research room attendant when you remove copies of documents from the...

36 CFR § 1254.76 - What procedures do I follow to copy formerly national security-classified documents?

Code of Federal Regulations, 2013 CFR

2013-07-01

... CFR 2001.24. (b) You may not remove from the research room copies of documents bearing uncancelled... individual documents, the research room staff cancels the classification markings on each page of the copy... declassification authority to the guard or research room attendant when you remove copies of documents from the...

36 CFR 1254.76 - What procedures do I follow to copy formerly national security-classified documents?

Code of Federal Regulations, 2012 CFR

2012-07-01

... CFR 2001.24. (b) You may not remove from the research room copies of documents bearing uncancelled... individual documents, the research room staff cancels the classification markings on each page of the copy... declassification authority to the guard or research room attendant when you remove copies of documents from the...

37 CFR 1.825 - Amendments to or replacement of sequence listing and computer readable copy thereof.

Code of Federal Regulations, 2010 CFR

2010-07-01

... of sequence listing and computer readable copy thereof. 1.825 Section 1.825 Patents, Trademarks, and... Amino Acid Sequences § 1.825 Amendments to or replacement of sequence listing and computer readable copy... copy of the computer readable form (§ 1.821(e)) including all previously submitted data with the...

37 CFR 1.825 - Amendments to or replacement of sequence listing and computer readable copy thereof.

Code of Federal Regulations, 2011 CFR

2011-07-01

... of sequence listing and computer readable copy thereof. 1.825 Section 1.825 Patents, Trademarks, and... Amino Acid Sequences § 1.825 Amendments to or replacement of sequence listing and computer readable copy... copy of the computer readable form (§ 1.821(e)) including all previously submitted data with the...

A Three-Dimensional Transonic, Potential Flow Computer Program, Its Conversion to IBM Fortran and Utilization

DTIC Science & Technology

1983-12-01

MAIN OEG=NFGVB1.3266P //COPY PEOC EILE=, MEM = // EXEC PGM=IEBGENEB //SISPRINT DD SYSOUT=A //SYSIN DC DÖMMY //SYS0T1 DD...COE*,FILE=1, MEM =FL027 // EXEC COPY,FILE=2,HEM=A411IN // EXEC COEY,FILE=3, MEM =VWIN // EXEC COPY,FILE = 4, MEM =A411A01...EXEC C0EY,FILE=5,MEä=INTERE // EXEC COPY,FILE=6, MEM =A411PS // EXEC COEY,FILE=7, MEM =A411P1 // EXEC COPY,FILE

Prediction of Response to Therapy and Clinical Outcome through a Pilot Study of Complete Genetic Assessment of Ovarian Cancer

DTIC Science & Technology

2015-12-01

Oncology program supported by this grant consented patients to 11-104. OncoPanel is a cancer genomic assay that detects somatic mutations, copy number...KMT2D, EP300, FANCD2 Sertoli Leydig cell DICER1 Copy number variants: In addition, 219 patients were analyzed for copy-number variations ( CNV ) in...OncoPanel genes. >12,000 total CNV were reported in the cohort (Figure 2). Single- copy deletions (n=5558) and copy-number gains (low amplification) (n

Different Facets of Copy Number Changes: Permanent, Transient, and Adaptive

PubMed Central

Mishra, Sweta

2016-01-01

Chromosomal copy number changes are frequently associated with harmful consequences and are thought of as an underlying mechanism for the development of diseases. However, changes in copy number are observed during development and occur during normal biological processes. In this review, we highlight the causes and consequences of copy number changes in normal physiologic processes as well as cover their associations with cancer and acquired drug resistance. We discuss the permanent and transient nature of copy number gains and relate these observations to a new mechanism driving transient site-specific copy gains (TSSGs). Finally, we discuss implications of TSSGs in generating intratumoral heterogeneity and tumor evolution and how TSSGs can influence the therapeutic response in cancer. PMID:26755558

7 CFR 97.179 - Copies and certified copies.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS..., copies of applications, certificates, or of any records, books, papers, drawings, or photographs in the...

Disintegration/dissolution profiles of copies of Fosamax (alendronate).

PubMed

Epstein, S; Cryer, B; Ragi, S; Zanchetta, J R; Walliser, J; Chow, J; Johnson, M A; Leyes, A E

2003-01-01

Poor quality has been reported for some generics and other copies of original products. We performed a pilot study to compare the disintegration/dissolution profiles of FOSAMAX (alendronate) 70 mg tablets with those of copies of FOSAMAX that were manufactured outside the United States. We used the standard United States Pharmacopeia (USP) disintegration method to evaluate FOSAMAX 70 mg tablets and 13 copies. At least 12 (n = 12) dosage units were tested for each product (except Fosmin, n = 10). The dissolution profiles of FOSAMAX and one representative copy were also compared. Nine copies (Osteomax, Defixal, Fosmin, Endronax, Osteomix, Genalmen, Fixopan, Osteoplus, and Fosval) disintegrated two- to ten-fold faster than FOSAMAX. Three other copies (Neobon, Regenesis, and Ostenan) disintegrated at least five-fold slower than FOSAMAX. Neobon is a softgel capsule, so special consideration was given to this different dosage form. One copy (Arendal) did not fall into either category but exhibited potentially large inter- and intra-lot variability. Dissolution of alendronate from Regenesis lagged behind that from FOSAMAX. Slower disintegration may reduce efficacy because bisphosphonates must be taken in the fasting state and contact with food or even certain beverages severely reduces bioavailability. Faster disintegration (or the use of gel-caps or other alterations to the drug formulation) could increase the risk of esophagitis, an adverse event associated with prolonged contact of the esophagus with bisphosphonates. These disintegration and dissolution results suggest that important differences may exist between FOSAMAX and its copies with regard to bioavailability, pharmacokinetics, and clinical efficacy and safety profiles. Additional testing is warranted to evaluate the pharmacokinetics and clinical safety of these copies.

Age-related decline in mitochondrial DNA copy number in isolated human pancreatic islets.

PubMed

Cree, L M; Patel, S K; Pyle, A; Lynn, S; Turnbull, D M; Chinnery, P F; Walker, M

2008-08-01

Pancreatic beta cell function has been shown to decline with age in man. Depletion of mitochondrial DNA (mtDNA) copy number is associated with impaired insulin secretion in pancreatic beta cell lines, and decreased mtDNA copy number has been observed with age in skeletal muscle in man. We investigated whether mtDNA copy number decreases with age in human pancreatic beta cells, which might in turn contribute to the age-related decline in insulin secretory capacity. We quantified mtDNA copy number in isolated human islet preparations from 15 pancreas donors aged between 17 and 75 years. Islets (n = 20) were individually hand-picked and pooled from each donor isolate for the quantification of mtDNA copy number and deleted mtDNA (%), which were determined using real-time PCR methods. There was a significant negative correlation between mtDNA copy number and islet donor age (r = -0.53, p = 0.044). mtDNA copy number was significantly decreased in islet preparations from donors aged > or =50 years (n = 8) compared with those aged <50 years (n = 7) (median [interquartile range]: 418 [236-503] vs 596 [554-729] mtDNA copy number/diploid genome; p = 0.032). None of the islet preparations harboured high levels of deleted mtDNA affecting the major arc. Given the correlation between mtDNA content and respiratory chain activity, the age-related decrease in mtDNA copy number that we observed in human pancreatic islet preparations may contribute to the age-dependent decline in pancreatic beta cell insulin secretory capacity.

SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR.

PubMed

Stabley, Deborah L; Harris, Ashlee W; Holbrook, Jennifer; Chubbs, Nicholas J; Lozo, Kevin W; Crawford, Thomas O; Swoboda, Kathryn J; Funanage, Vicky L; Wang, Wenlan; Mackenzie, William; Scavina, Mena; Sol-Church, Katia; Butchbach, Matthew E R

2015-07-01

Proximal spinal muscular atrophy (SMA) is an early-onset motor neuron disease characterized by loss of α-motor neurons and associated muscle atrophy. SMA is caused by deletion or other disabling mutation of survival motor neuron 1 (SMN1). In the human genome, a large duplication of the SMN-containing region gives rise to a second copy of this gene (SMN2) that is distinguishable by a single nucleotide change in exon 7. Within the SMA population, there is substantial variation in SMN2 copy number; in general, those individuals with SMA who have a high SMN2 copy number have a milder disease. Because SMN2 functions as a disease modifier, its accurate copy number determination may have clinical relevance. In this study, we describe the development of an assay to assess SMN1 and SMN2 copy numbers in DNA samples using an array-based digital PCR (dPCR) system. This dPCR assay can accurately and reliably measure the number of SMN1 and SMN2 copies in DNA samples. In a cohort of SMA patient-derived cell lines, the assay confirmed a strong inverse correlation between SMN2 copy number and disease severity. Array dPCR is a practical technique to determine, accurately and reliably, SMN1 and SMN2 copy numbers from SMA samples.

41 CFR 102-75.405 - What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy...

Code of Federal Regulations, 2014 CFR

2014-01-01

... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a copy of... responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a...

41 CFR 102-75.405 - What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy...

Code of Federal Regulations, 2012 CFR

2012-01-01

... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a copy of... responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a...

41 CFR 102-75.405 - What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy...

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a copy of... responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a...

41 CFR 102-75.405 - What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 false What responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a copy of... responsibilities does the Federal Aviation Administration (FAA) have after receiving a copy of the notice (and a...

76 FR 28027 - State Program Requirements; Application for Program Revision to the National Pollutant Discharge...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-13

... copies to Hanh Shaw, Office of Water and Watersheds, Mail Stop OWW-130, 1200 Sixth Avenue, Suite 900, Seattle, WA 98101-3140. E-mail: Send electronic copies to shaw[email protected] . Fax: Fax copies to the attention of Hanh Shaw at (206) 553-0165. Hand Delivery/Courier: Deliver copies to Hanh Shaw, Office of...

Simultaneous Use of Multiple Answer Copying Indexes to Improve Detection Rates

ERIC Educational Resources Information Center

Wollack, James A.

2006-01-01

Many of the currently available statistical indexes to detect answer copying lack sufficient power at small [alpha] levels or when the amount of copying is relatively small. Furthermore, there is no one index that is uniformly best. Depending on the type or amount of copying, certain indexes are better than others. The purpose of this article was…

39 CFR 3004.40 - Hard copy requests for records and for expedited processing.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 39 Postal Service 1 2010-07-01 2010-07-01 false Hard copy requests for records and for expedited... FREEDOM OF INFORMATION ACT § 3004.40 Hard copy requests for records and for expedited processing. (a) A hard copy request for records must: (1) Be in writing; (2) Include the name and address of the...

39 CFR 3004.40 - Hard copy requests for records and for expedited processing.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 39 Postal Service 1 2013-07-01 2013-07-01 false Hard copy requests for records and for expedited... FREEDOM OF INFORMATION ACT § 3004.40 Hard copy requests for records and for expedited processing. (a) A hard copy request for records must: (1) Be in writing; (2) Include the name and address of the...

39 CFR 3004.40 - Hard copy requests for records and for expedited processing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 39 Postal Service 1 2014-07-01 2014-07-01 false Hard copy requests for records and for expedited... FREEDOM OF INFORMATION ACT § 3004.40 Hard copy requests for records and for expedited processing. (a) A hard copy request for records must: (1) Be in writing; (2) Include the name and address of the...

39 CFR 3004.40 - Hard copy requests for records and for expedited processing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 39 Postal Service 1 2012-07-01 2012-07-01 false Hard copy requests for records and for expedited... FREEDOM OF INFORMATION ACT § 3004.40 Hard copy requests for records and for expedited processing. (a) A hard copy request for records must: (1) Be in writing; (2) Include the name and address of the...

39 CFR 3004.40 - Hard copy requests for records and for expedited processing.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 39 Postal Service 1 2011-07-01 2011-07-01 false Hard copy requests for records and for expedited... FREEDOM OF INFORMATION ACT § 3004.40 Hard copy requests for records and for expedited processing. (a) A hard copy request for records must: (1) Be in writing; (2) Include the name and address of the...

11 CFR 108.3 - Filing copies of reports and statements in connection with the campaign of any congressional...

Code of Federal Regulations, 2010 CFR

2010-01-01

... 11 Federal Elections 1 2010-01-01 2010-01-01 false Filing copies of reports and statements in... Elections FEDERAL ELECTION COMMISSION GENERAL FILING COPIES OF REPORTS AND STATEMENTS WITH STATE OFFICERS (2 U.S.C. 439) § 108.3 Filing copies of reports and statements in connection with the campaign of any...

Noble Work, but Undervalued: The Status and Value of Copy Editing in Journalism Schools.

ERIC Educational Resources Information Center

Auman, Ann E.; Fee, Frank E., Jr.; Russial, John T.

2002-01-01

Presents and discusses results of a survey of editing instructors in the United States on the status of copy editing. Provides benchmark data on the state of copy editing instruction in accredited colleges and universities. Concludes that copy editing is generally healthy and respected in most programs but that it mirrors the industry in taking a…

28 CFR 79.5 - Requirements for medical documentation, contemporaneous records, and other records or documents.

Code of Federal Regulations, 2010 CFR

2010-07-01

... copies of the originals, unless it is impossible to obtain an original or certified copy of the original. If it is impossible for a claimant to provide an original or certified copy of an original, the... setting forth the reason why it is impossible to provide an original or a certified copy of an original...

The Differential Effects of Two Self-Managed Math Instruction Procedures: Cover, Copy, and Compare versus Copy, Cover, and Compare

ERIC Educational Resources Information Center

Grafman, Joel M.; Cates, Gary L.

2010-01-01

This study compared the fluency and error rates produced when using the Cover, Copy, and Compare (CCC) and a modified CCC procedure (MCCC) called Copy, Cover, and Compare to complete subtraction math problems. Two second-grade classrooms consisting of 47 total students participated in the study. The following items were administered to…

How bio-questionable are the different recombinant human erythropoietin copy products in Thailand?

PubMed

Halim, Liem Andhyk; Brinks, Vera; Jiskoot, Wim; Romeijn, Stefan; Praditpornsilpa, Kearkiat; Assawamakin, Anunchai; Schellekens, Huub

2014-05-01

The high prevalence of pure red cell aplasia in Thailand has been associated with the sharp increase in number of recombinant human erythropoietin (rhEPO) copy products, based on a classical generic regulatory pathway, which have entered the market. This study aims to assess the quality of rhEPO copy products being used in Thailand. Twelve rhEPO copy products were purchased from pharmacies in Thailand, shipped under controlled cold chain conditions to the Netherlands and characterized using (1) high performance size-exclusion chromatography, (2) asymmetrical flow field-flow fractionation, (3) sodium dodecyl sulfate polyacrylamide gel electrophoresis in combination with (4) Western blotting and additionally tested for (5) host cell protein impurities as well as (6) endotoxin contamination. Some of the tested rhEPO copy products showed high aggregate levels and contained a substantial amount of protein fragments. Also, one of rhEPO copy products had a high endotoxin level, exceeding the FDA limit. Our observations show that some of the tested copy products on the Thai market differ significantly from the originator rhEPO product, Epogen®. This comparison study supports a link between the quality attributes of copy rhEPO products and their immunogenicity.

Imitation, Inspiration, and Creation: Cognitive Process of Creative Drawing by Copying Others' Artworks.

PubMed

Okada, Takeshi; Ishibashi, Kentaro

2017-09-01

To investigate the cognitive processes underlying creative inspiration, we tested the extent to which viewing or copying prior examples impacted creative output in art. In Experiment 1, undergraduates made drawings under three conditions: (a) copying an artist's drawing, then producing an original drawing; (b) producing an original drawing without having seen another's work; and (c) copying another artist's work, then reproducing that artist's style independently. We discovered that through copying unfamiliar abstract drawings, participants were able to produce creative drawings qualitatively different from the model drawings. Process analyses suggested that participants' cognitive constraints became relaxed, and new perspectives were formed from copying another's artwork. Experiment 2 showed that exposure to styles of artwork considered unfamiliar facilitated creativity in drawing, while styles considered familiar did not do so. Experiment 3 showed that both copying and thoroughly viewing artwork executed using an unfamiliar style facilitated creativity in drawing, whereas merely thinking about alternative styles of artistic representation did not do so. These experiments revealed that deep encounters with unfamiliar artworks-whether through copying or prolonged observation-change people's cognitive representations of the act of drawing to produce novel artwork. Copyright © 2016 Cognitive Science Society, Inc.

Allelic recombination between distinct genomic locations generates copy number diversity in human β-defensins

PubMed Central

Bakar, Suhaili Abu; Hollox, Edward J.; Armour, John A. L.

2009-01-01

β-Defensins are small secreted antimicrobial and signaling peptides involved in the innate immune response of vertebrates. In humans, a cluster of at least 7 of these genes shows extensive copy number variation, with a diploid copy number commonly ranging between 2 and 7. Using a genetic mapping approach, we show that this cluster is at not 1 but 2 distinct genomic loci ≈5 Mb apart on chromosome band 8p23.1, contradicting the most recent genome assembly. We also demonstrate that the predominant mechanism of change in β-defensin copy number is simple allelic recombination occurring in the interval between the 2 distinct genomic loci for these genes. In 416 meiotic transmissions, we observe 3 events creating a haplotype copy number not found in the parent, equivalent to a germ-line rate of copy number change of ≈0.7% per gamete. This places it among the fastest-changing copy number variants currently known. PMID:19131514

COPI Is Required for Enterovirus 71 Replication

PubMed Central

Wang, Jianmin; Wu, Zhiqiang; Jin, Qi

2012-01-01

Enterovirus 71 (EV71), a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11), is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies. PMID:22662263

Diversity of human copy number variation and multicopy genes.

PubMed

Sudmant, Peter H; Kitzman, Jacob O; Antonacci, Francesca; Alkan, Can; Malig, Maika; Tsalenko, Anya; Sampas, Nick; Bruhn, Laurakay; Shendure, Jay; Eichler, Evan E

2010-10-29

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

Comparing CNV detection methods for SNP arrays.

PubMed

Winchester, Laura; Yau, Christopher; Ragoussis, Jiannis

2009-09-01

Data from whole genome association studies can now be used for dual purposes, genotyping and copy number detection. In this review we discuss some of the methods for using SNP data to detect copy number events. We examine a number of algorithms designed to detect copy number changes through the use of signal-intensity data and consider methods to evaluate the changes found. We describe the use of several statistical models in copy number detection in germline samples. We also present a comparison of data using these methods to assess accuracy of prediction and detection of changes in copy number.

Virological failure and all-cause mortality in HIV-positive adults with low-level viremia during antiretroviral treatment.

PubMed

Elvstam, Olof; Medstrand, Patrik; Yilmaz, Aylin; Isberg, Per-Erik; Gisslén, Magnus; Björkman, Per

2017-01-01

Although most HIV-infected individuals achieve undetectable viremia during antiretroviral therapy (ART), a subset have low-level viremia (LLV) of varying duration and magnitude. The impact of LLV on treatment outcomes is unclear. We investigated the association between LLV and virological failure and/or all-cause mortality among Swedish patients receiving ART. HIV-infected patients from two Swedish HIV centers were identified from the nationwide register InfCare HIV. Subjects aged ≥15 years with triple agent ART were included at 12 months after treatment initiation if ≥2 following viral load measurements were available. Patients with 2 consecutive HIV RNA values ≥1000 copies/mL at this time point were excluded. Participants were stratified into four categories depending on viremia profiles: permanently suppressed viremia (<50 copies/mL), LLV 50-199 copies/mL, LLV 200-999 copies/mL and viremia ≥1000 copies/mL. Association between all four viremia categories and all-cause death was calculated using survival analysis with viremia as a time-varying covariate, so that patients could change viremia category during follow-up. Association between the three lower categories and virological failure (≥2 consecutive measurements ≥1000 copies/mL) was calculated in a similar manner. LLV 50-199 copies/mL was recorded in 70/1015 patients (6.9%) and LLV 200-999 copies/mL in 89 (8.8%) during 7812 person-years of follow-up (median 6.5 years). LLV 200-999 copies/mL was associated with virological failure (adjusted hazard ratio 3.14 [95% confidence interval 1.41-7.03, p<0.01]), whereas LLV 50-199 copies/mL was not (1.01 [0.34-4.31, p = 0.99]; median follow-up 4.5 years). LLV 200-999 copies/mL had an adjusted mortality hazard ratio of 2.29 (0.98-5.32, p = 0.05) and LLV 50-199 copies/mL of 2.19 (0.90-5.37, p = 0.09). In this Swedish cohort followed during ART for a median of 4.5 years, LLV 200-999 copies/mL was independently associated with virological failure. Patients with LLV had higher rates of all-cause mortality, although not statistically significant in multivariate analysis.

Historical Paintings

Science.gov Websites

copies of one print, one copy of each of five different prints, or any combination adding up to five copies of one print, or one copy of each of two different prints). Presidential Prints (One Set of 20) If you want the Presidential Prints, you may order one set of the small prints. We do not ship these

32 CFR 37.1045 - To whom must I send copies of the award document?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 1 2012-07-01 2012-07-01 false To whom must I send copies of the award document... of the Award Document § 37.1045 To whom must I send copies of the award document? You must send a copy of the award document to the: (a) Recipient. You must include on the first page of the recipient's...

32 CFR 37.1045 - To whom must I send copies of the award document?

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 1 2014-07-01 2014-07-01 false To whom must I send copies of the award document... of the Award Document § 37.1045 To whom must I send copies of the award document? You must send a copy of the award document to the: (a) Recipient. You must include on the first page of the recipient's...

32 CFR 37.1045 - To whom must I send copies of the award document?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 1 2010-07-01 2010-07-01 false To whom must I send copies of the award document... of the Award Document § 37.1045 To whom must I send copies of the award document? You must send a copy of the award document to the: (a) Recipient. You must include on the first page of the recipient's...

32 CFR 37.1045 - To whom must I send copies of the award document?

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 1 2013-07-01 2013-07-01 false To whom must I send copies of the award document... of the Award Document § 37.1045 To whom must I send copies of the award document? You must send a copy of the award document to the: (a) Recipient. You must include on the first page of the recipient's...

32 CFR 37.1045 - To whom must I send copies of the award document?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 1 2011-07-01 2011-07-01 false To whom must I send copies of the award document... of the Award Document § 37.1045 To whom must I send copies of the award document? You must send a copy of the award document to the: (a) Recipient. You must include on the first page of the recipient's...

38 CFR 1.526 - Copies of records and papers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... papers. 1.526 Section 1.526 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS... Copies of records and papers. (a) Any person desiring a copy of any record or document in the custody of... plain one-sided paper copies of a standard size (81/2″ × 11″; 81/2″ × 14″; 11″ × 14″) $0.15 per page...

38 CFR 1.526 - Copies of records and papers.

Code of Federal Regulations, 2011 CFR

2011-07-01

... papers. 1.526 Section 1.526 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS... Copies of records and papers. (a) Any person desiring a copy of any record or document in the custody of... plain one-sided paper copies of a standard size (81/2″ × 11″; 81/2″ × 14″; 11″ × 14″) $0.15 per page...

27 CFR 28.40 - Evidence of exportation: distilled spirits and wine.

Code of Federal Regulations, 2013 CFR

2013-04-01

... exportation of any shipment of distilled spirits or wine may be evidenced by: (a) A copy of the export bill of lading (§ 28.250); or (b) A copy of the railway express receipt (§ 28.251); or (c) A copy of the air express receipt (§ 28.252); or (d) A copy of the through bill of lading where exportation is to a...

27 CFR 28.40 - Evidence of exportation: distilled spirits and wine.

Code of Federal Regulations, 2014 CFR

2014-04-01

... exportation of any shipment of distilled spirits or wine may be evidenced by: (a) A copy of the export bill of lading (§ 28.250); or (b) A copy of the railway express receipt (§ 28.251); or (c) A copy of the air express receipt (§ 28.252); or (d) A copy of the through bill of lading where exportation is to a...

27 CFR 28.40 - Evidence of exportation: distilled spirits and wine.

Code of Federal Regulations, 2011 CFR

2011-04-01

... exportation of any shipment of distilled spirits or wine may be evidenced by: (a) A copy of the export bill of lading (§ 28.250); or (b) A copy of the railway express receipt (§ 28.251); or (c) A copy of the air express receipt (§ 28.252); or (d) A copy of the through bill of lading where exportation is to a...

27 CFR 28.40 - Evidence of exportation: distilled spirits and wine.

Code of Federal Regulations, 2012 CFR

2012-04-01

... exportation of any shipment of distilled spirits or wine may be evidenced by: (a) A copy of the export bill of lading (§ 28.250); or (b) A copy of the railway express receipt (§ 28.251); or (c) A copy of the air express receipt (§ 28.252); or (d) A copy of the through bill of lading where exportation is to a...

Peripheral artery disease, calf skeletal muscle mitochondrial DNA copy number, and functional performance.

PubMed

McDermott, Mary M; Peterson, Charlotte A; Sufit, Robert; Ferrucci, Luigi; Guralnik, Jack M; Kibbe, Melina R; Polonsky, Tamar S; Tian, Lu; Criqui, Michael H; Zhao, Lihui; Stein, James H; Li, Lingyu; Leeuwenburgh, Christiaan

2018-05-01

In people without lower extremity peripheral artery disease (PAD), mitochondrial DNA copy number declines with aging, and this decline is associated with declines in mitochondrial activity and functional performance. However, whether lower extremity ischemia is associated with lower mitochondrial DNA copy number and whether mitochondrial DNA copy number is associated with the degree of functional impairment in people with PAD is unknown. In people with and without PAD, age 65 years and older, we studied associations of the ankle-brachial index (ABI) with mitochondrial DNA copy number and associations of mitochondrial DNA copy number with functional impairment. Calf muscle biopsies were obtained from 34 participants with PAD (mean age: 73.5 years (SD 6.4), mean ABI: 0.67 (SD 0.15), mean 6-minute walk distance: 1191 feet (SD 223)) and 10 controls without PAD (mean age: 73.1 years (SD 4.7), mean ABI: 1.14 (SD 0.07), mean 6-minute walk distance: 1387 feet (SD 488)). Adjusting for age and sex, lower ABI values were associated with higher mitochondrial DNA copy number, measured in relative copy number (ABI<0.60: 914, ABI 0.60-0.90: 731, ABI 0.90-1.50: 593; p trend=0.016). The association of mitochondrial DNA copy number with the 6-minute walk distance and 4-meter walking velocity differed significantly between participants with versus without PAD ( p-value for interaction=0.001 and p=0.015, respectively). The correlation coefficient between mitochondrial DNA copy number and the 6-minute walk distance was 0.653 ( p=0.056) among people without PAD and -0.254 ( p=0.154) among people with PAD and ABI < 0.90. In conclusion, lower ABI values are associated with increased mitochondrial DNA copy number. Associations of mitochondrial DNA copy number with the 6-minute walk distance and 4-meter walking velocity significantly differed between people with versus without PAD, with stronger positive associations observed in people without PAD than in people with PAD. The cross-sectional and exploratory nature of the analyses precludes conclusions regarding causal inferences. ClinicalTrials.gov Identifier: NCT02246660.

HIV-1 Drug Resistance and Second-Line Treatment in Children Randomized to Switch at Low Versus Higher RNA Thresholds.

PubMed

Harrison, Linda; Melvin, Ann; Fiscus, Susan; Saidi, Yacine; Nastouli, Eleni; Harper, Lynda; Compagnucci, Alexandra; Babiker, Abdel; McKinney, Ross; Gibb, Diana; Tudor-Williams, Gareth

2015-09-01

The PENPACT-1 trial compared virologic thresholds to determine when to switch to second-line antiretroviral therapy (ART). Using PENPACT-1 data, we aimed to describe HIV-1 drug resistance accumulation on first-line ART by virologic threshold. PENPACT-1 had a 2 × 2 factorial design, randomizing HIV-infected children to start protease inhibitor (PI) versus nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART, and switch at a 1000 copies/mL versus 30,000 copies/mL threshold. Switch criteria were not achieving the threshold by week 24, confirmed rebound above the threshold thereafter, or Center for Disease Control and Prevention stage C event. Resistance tests were performed on samples ≥1000 copies/mL before switch, resuppression, and at 4-years/trial end. Sixty-seven children started PI-based ART and were randomized to switch at 1000 copies/mL (PI-1000), 64 PIs and 30,000 copies/mL (PI-30,000), 67 NNRTIs and 1000 copies/mL (NNRTI-1000), and 65 NNRTI and 30,000 copies/mL (NNRTI-30,000). Ninety-four (36%) children reached the 1000 copies/mL switch criteria during 5-year follow-up. In 30,000 copies/mL threshold arms, median time from 1000 to 30,000 copies/mL switch criteria was 58 (PI) versus 80 (NNRTI) weeks (P = 0.81). In NNRTI-30,000, more nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations accumulated than other groups. NNRTI mutations were selected before switching at 1000 copies/mL (23% NNRTI-1000, 27% NNRTI-30,000). Sixty-two children started abacavir + lamivudine, 166 lamivudine + zidovudine or stavudine, and 35 other NRTIs. The abacavir + lamivudine group acquired fewest NRTI mutations. Of 60 switched to second-line, 79% PI-1000, 63% PI-30,000, 64% NNRTI-1000, and 100% NNRTI-30,000 were <400 copies/mL 24 weeks later. Children on first-line NNRTI-based ART who were randomized to switch at a higher virologic threshold developed the most resistance, yet resuppressed on second-line. An abacavir + lamivudine NRTI combination seemed protective against development of NRTI resistance.

Glyoxalase 1 copy number variation in patients with well differentiated gastro-entero-pancreatic neuroendocrine tumours (GEP-NET)

PubMed Central

Xue, Mingzhan; Shafie, Alaa; Qaiser, Talha; Rajpoot, Nasir M.; Kaltsas, Gregory; James, Sean; Gopalakrishnan, Kishore; Fisk, Adrian; Dimitriadis, Georgios K.; Grammatopoulos, Dimitris K.; Rabbani, Naila; Thornalley, Paul J.; Weickert, Martin O.

2017-01-01

Background The glyoxalase-1 gene (GLO1) is a hotspot for copy-number variation (CNV) in human genomes. Increased GLO1 copy-number is associated with multidrug resistance in tumour chemotherapy, but prevalence of GLO1 CNV in gastro-entero-pancreatic neuroendocrine tumours (GEP-NET) is unknown. Methods GLO1 copy-number variation was measured in 39 patients with GEP-NET (midgut NET, n = 25; pancreatic NET, n = 14) after curative or debulking surgical treatment. Primary tumour tissue, surrounding healthy tissue and, where applicable, additional metastatic tumour tissue were analysed, using real time qPCR. Progression and survival following surgical treatment were monitored over 4.2 ± 0.5 years. Results In the pooled GEP-NET cohort, GLO1 copy-number in healthy tissue was 2.0 in all samples but significantly increased in primary tumour tissue in 43% of patients with pancreatic NET and in 72% of patients with midgut NET, mainly driven by significantly higher GLO1 copy-number in midgut NET. In tissue from additional metastases resection (18 midgut NET and one pancreatic NET), GLO1 copy number was also increased, compared with healthy tissue; but was not significantly different compared with primary tumour tissue. During mean 3 - 5 years follow-up, 8 patients died and 16 patients showed radiological progression. In midgut NET, a high GLO1 copy-number was associated with earlier progression. In NETs with increased GLO1 copy number, there was increased Glo1 protein expression compared to non-malignant tissue. Conclusions GLO1 copy-number was increased in a large percentage of patients with GEP-NET and correlated positively with increased Glo1 protein in tumour tissue. Analysis of GLO1 copy-number variation particularly in patients with midgut NET could be a novel prognostic marker for tumour progression. PMID:29100361

Differences in AMY1 Gene Copy Numbers Derived from Blood, Buccal Cells and Saliva Using Quantitative and Droplet Digital PCR Methods: Flagging the Pitfall.

PubMed

Ooi, Delicia Shu Qin; Tan, Verena Ming Hui; Ong, Siong Gim; Chan, Yiong Huak; Heng, Chew Kiat; Lee, Yung Seng

2017-01-01

The human salivary (AMY1) gene, encoding salivary α-amylase, has variable copy number variants (CNVs) in the human genome. We aimed to determine if real-time quantitative polymerase chain reaction (qPCR) and the more recently available Droplet Digital PCR (ddPCR) can provide a precise quantification of the AMY1 gene copy number in blood, buccal cells and saliva samples derived from the same individual. Seven participants were recruited and DNA was extracted from the blood, buccal cells and saliva samples provided by each participant. Taqman assay real-time qPCR and ddPCR were conducted to quantify AMY1 gene copy numbers. Statistical analysis was carried out to determine the difference in AMY1 gene copy number between the different biological specimens and different assay methods. We found significant within-individual difference (p<0.01) in AMY1 gene copy number between different biological samples as determined by qPCR. However, there was no significant within-individual difference in AMY1 gene copy number between different biological samples as determined by ddPCR. We also found that AMY1 gene copy number of blood samples were comparable between qPCR and ddPCR, while there is a significant difference (p<0.01) between AMY1 gene copy numbers measured by qPCR and ddPCR for both buccal swab and saliva samples. Despite buccal cells and saliva samples being possible sources of DNA, it is pertinent that ddPCR or a single biological sample, preferably blood sample, be used for determining highly polymorphic gene copy numbers like AMY1, due to the large within-individual variability between different biological samples if real time qPCR is employed.

[Relationship between mitochondrial DNA copy number, membrane potential of human embryo and embryo morphology].

PubMed

Zhao, H; Teng, X M; Li, Y F

2017-11-25

Objective: To explore the relationship between the embryo with the different morphological types in the third day and its mitochondrial copy number, the membrane potential. Methods: Totally 117 embryos with poor development after normal fertilization and were not suitable transferred in the fresh cycle and 106 frozen embryos that were discarded voluntarily by infertility patients with in vitro fertilization-embryo transfer after successful pregnancy were selected. According to evaluation of international standard in embryos, all cleavage stage embryos were divided into class Ⅰ frozen embryo group ( n= 64), class Ⅱ frozen embryo group ( n= 42) and class Ⅲ fresh embryonic group (not transplanted embryos; n= 117). Real-time PCR and confocal microscopy methods were used to detect mitochondrial DNA (mtDNA) copy number and the mitochondrial membrane potential of a single embryo. The differences between embryo quality and mtDNA copy number and membrane potential of each group were compared. Results: The copy number of mtDNA and the mitochondrial membrane potential in class Ⅲ fresh embryonic group [(1.7±1.0)×10(5) copy/μl, 1.56±0.32] were significantly lower than those in class Ⅰ frozen embryo group [(3.4±1.7)×10(5) copy/μl, 2.66±0.21] and class Ⅱ frozen embryo group [(2.6±1.2)×10(5) copy/μl, 1.80±0.32; all P< 0.05]. The copy number of mtDNA and the mitochondrial membrane potential in classⅠ frozen embryo group were significantly higher than those in classⅡ frozen embryo group (both P< 0.05). Conclusion: The mtDNA copy number and the mitochondrial membrane potential of embryos of the better quality embryo are higher.

36 CFR 1254.72 - What procedures do I follow to copy documents?

Code of Federal Regulations, 2010 CFR

2010-07-01

... RECORDS ADMINISTRATION PUBLIC AVAILABILITY AND USE USING RECORDS AND DONATED HISTORICAL MATERIALS Copying... determination of suitability if you ask. After copying is completed, you must return documents removed from...

7 CFR 1738.201 - Application submission.

Code of Federal Regulations, 2014 CFR

2014-01-01

... applications must contain two hard copies and an electronic copy of the entire application. An application is considered received upon receipt of the hard and electronic copies by the National Office. The date and time...

7 CFR 1738.201 - Application submission.

Code of Federal Regulations, 2013 CFR

2013-01-01

... applications must contain two hard copies and an electronic copy of the entire application. An application is considered received upon receipt of the hard and electronic copies by the National Office. The date and time...

7 CFR 1738.201 - Application submission.

Code of Federal Regulations, 2012 CFR

2012-01-01

... applications must contain two hard copies and an electronic copy of the entire application. An application is considered received upon receipt of the hard and electronic copies by the National Office. The date and time...

Notable Carrier Risks for Individuals Having Two Copies of SMN1 in Spinal Muscular Atrophy Families with 2-copy Alleles: Estimation Based on Chinese Meta-analysis Data.

PubMed

Wei, Xianda; Tan, Hu; Yang, Pu; Zhang, Rui; Tan, Bo; Zhang, Yue; Mei, Libin; Liang, Desheng; Wu, Lingqian

2017-02-01

Spinal muscular atrophy is an autosomal recessive neuromuscular disease mainly caused by homozygous deletion of SMN1. The 2-copy SMN1 allele may present in the families of SMA patients with homozygous deletion of SMN1, one of whose parents has two SMN1 copies. In such families, individuals having two SMN1 copies still have a chance to be "2 + 0" carriers. In this study, the risks for the parents, fetuses and other siblings having two SMN1 copies to be "2 + 0" carriers were estimated based on Chinese meta-analysis data and turned out to be rather striking. Our findings would help to optimize genetic counseling regarding spinal muscular atrophy.

Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D.

PubMed

Okamoto, Yuji; Goksungur, Meryem Tuba; Pehlivan, Davut; Beck, Christine R; Gonzaga-Jauregui, Claudia; Muzny, Donna M; Atik, Mehmed M; Carvalho, Claudia M B; Matur, Zeliha; Bayraktar, Serife; Boone, Philip M; Akyuz, Kaya; Gibbs, Richard A; Battaloglu, Esra; Parman, Yesim; Lupski, James R

2014-05-01

Copy-number variations as a mutational mechanism contribute significantly to human disease. Approximately one-half of the patients with Charcot-Marie-Tooth (CMT) disease have a 1.4 Mb duplication copy-number variation as the cause of their neuropathy. However, non-CMT1A neuropathy patients rarely have causative copy-number variations, and to date, autosomal-recessive disease has not been associated with copy-number variation as a mutational mechanism. We performed Agilent 8 × 60 K array comparative genomic hybridization on DNA from 12 recessive Turkish families with CMT disease. Additional molecular studies were conducted to detect breakpoint junctions and to evaluate gene expression levels in a family in which we detected an intragenic duplication copy-number variation. We detected an ~6.25 kb homozygous intragenic duplication in NDRG1, a gene known to be causative for recessive HMSNL/CMT4D, in three individuals from a Turkish family with CMT neuropathy. Further studies showed that this intragenic copy-number variation resulted in a homozygous duplication of exons 6-8 that caused decreased mRNA expression of NDRG1. Exon-focused high-resolution array comparative genomic hybridization enables the detection of copy-number variation carrier states in recessive genes, particularly small copy-number variations encompassing or disrupting single genes. In families for whom a molecular diagnosis has not been elucidated by conventional clinical assays, an assessment for copy-number variations in known CMT genes might be considered.

iCopyDAV: Integrated platform for copy number variations—Detection, annotation and visualization

PubMed Central

Vogeti, Sriharsha

2018-01-01

Discovery of copy number variations (CNVs), a major category of structural variations, have dramatically changed our understanding of differences between individuals and provide an alternate paradigm for the genetic basis of human diseases. CNVs include both copy gain and copy loss events and their detection genome-wide is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. However, accurate detection of CNVs from NGS data is not straightforward due to non-uniform coverage of reads resulting from various systemic biases. We have developed an integrated platform, iCopyDAV, to handle some of these issues in CNV detection in whole genome NGS data. It has a modular framework comprising five major modules: data pre-treatment, segmentation, variant calling, annotation and visualization. An important feature of iCopyDAV is the functional annotation module that enables the user to identify and prioritize CNVs encompassing various functional elements, genomic features and disease-associations. Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop. Here we show the effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs. Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths. It is an open-source integrated pipeline available at https://github.com/vogetihrsh/icopydav and as Docker’s image at http://bioinf.iiit.ac.in/icopydav/. PMID:29621297

rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants

PubMed Central

Kwan, Elizabeth X.; Wang, Xiaobin S.; Amemiya, Haley M.; Brewer, Bonita J.; Raghuraman, M. K.

2016-01-01

The Saccharomyces cerevisiae ribosomal DNA (rDNA) locus is known to exhibit greater instability relative to the rest of the genome. However, wild-type cells preferentially maintain a stable number of rDNA copies, suggesting underlying genetic control of the size of this locus. We performed a screen of a subset of the Yeast Knock-Out (YKO) single gene deletion collection to identify genetic regulators of this locus and to determine if rDNA copy number correlates with yeast replicative lifespan. While we found no correlation between replicative lifespan and rDNA size, we identified 64 candidate strains with significant rDNA copy number differences. However, in the process of validating candidate rDNA variants, we observed that independent isolates of our de novo gene deletion strains had unsolicited but significant changes in rDNA copy number. Moreover, we were not able to recapitulate rDNA phenotypes from the YKO yeast deletion collection. Instead, we found that the standard lithium acetate transformation protocol is a significant source of rDNA copy number variation, with lithium acetate exposure being the treatment causing variable rDNA copy number events after transformation. As the effects of variable rDNA copy number are being increasingly reported, our finding that rDNA is affected by lithium acetate exposure suggested that rDNA copy number variants may be influential passenger mutations in standard strain construction in S. cerevisiae. PMID:27449518

rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants.

PubMed

Kwan, Elizabeth X; Wang, Xiaobin S; Amemiya, Haley M; Brewer, Bonita J; Raghuraman, M K

2016-09-08

The Saccharomyces cerevisiae ribosomal DNA (rDNA) locus is known to exhibit greater instability relative to the rest of the genome. However, wild-type cells preferentially maintain a stable number of rDNA copies, suggesting underlying genetic control of the size of this locus. We performed a screen of a subset of the Yeast Knock-Out (YKO) single gene deletion collection to identify genetic regulators of this locus and to determine if rDNA copy number correlates with yeast replicative lifespan. While we found no correlation between replicative lifespan and rDNA size, we identified 64 candidate strains with significant rDNA copy number differences. However, in the process of validating candidate rDNA variants, we observed that independent isolates of our de novo gene deletion strains had unsolicited but significant changes in rDNA copy number. Moreover, we were not able to recapitulate rDNA phenotypes from the YKO yeast deletion collection. Instead, we found that the standard lithium acetate transformation protocol is a significant source of rDNA copy number variation, with lithium acetate exposure being the treatment causing variable rDNA copy number events after transformation. As the effects of variable rDNA copy number are being increasingly reported, our finding that rDNA is affected by lithium acetate exposure suggested that rDNA copy number variants may be influential passenger mutations in standard strain construction in S. cerevisiae. Copyright © 2016 Kwan et al.

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat.

PubMed

Würschum, Tobias; Boeven, Philipp H G; Langer, Simon M; Longin, C Friedrich H; Leiser, Willmar L

2015-07-29

Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown. Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties' region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time. In conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.

Coherent-state information concentration and purification in atomic memory

NASA Astrophysics Data System (ADS)

Herec, Jiří; Filip, Radim

2006-12-01

We propose a feasible method of coherent-state information concentration and purification utilizing quantum memory. The method allows us to optimally concentrate and purify information carried by many noisy copies of an unknown coherent state (randomly distributed in time) to a single copy. Thus nonclassical resources and operations can be saved, if we compare information processing with many noisy copies and a single copy with concentrated and purified information.

Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease.

PubMed

Aldhous, Marian C; Abu Bakar, Suhaili; Prescott, Natalie J; Palla, Raquel; Soo, Kimberley; Mansfield, John C; Mathew, Christopher G; Satsangi, Jack; Armour, John A L

2010-12-15

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case-control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case-control studies.

A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans.

PubMed

Jeon, Jae Pil; Shim, Sung Mi; Jung, Jong Sun; Nam, Hye Young; Lee, Hye Jin; Oh, Berm Seok; Kim, Kuchan; Kim, Hyung Lae; Han, Bok Ghee

2009-09-30

To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.

Real-time PCR assays for monitoring anaerobic fungal biomass and population size in the rumen.

PubMed

Lwin, Khin Ohnmar; Hayakawa, Mika; Ban-Tokuda, Tomomi; Matsui, Hiroki

2011-04-01

The relationship between copy numbers of internal transcribed spacer 1 (ITS1) and biomass or zoospore count of anaerobic fungi was studied to develop a quantitative real-time PCR-based monitoring method for fungal biomass or population in the rumen. Nine fungal strains were used to determine the relationship between ITS1 copy number and fungal biomass. Rumen fluid from three sheep and a cow were used to determine the relationship between ITS1 copy number and fungal population. ITS1 copy number was determined by real-time PCR with a specific primer set for anaerobic fungi. Freeze-dried fungal cells were weighed for fungal biomass. Zoospore counts were determined by the roll-tube method. A positive correlation was observed between both ITS1 copy number and dry weight and ITS1 copy number and zoospore counts, suggesting that the use of ITS1 copy numbers is effective for estimating fungal biomass and population density. On the basis of ITS1 copy numbers, fluctuations in the fungal population in sheep rumen showed that although the values varied among individual animals, the fungal population tended to decrease after feeding. In the present study, a culture-independent method was established that will provide a powerful tool for understanding the ecology of anaerobic fungi in the rumen.

Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease

PubMed Central

Aldhous, Marian C.; Abu Bakar, Suhaili; Prescott, Natalie J.; Palla, Raquel; Soo, Kimberley; Mansfield, John C.; Mathew, Christopher G.; Satsangi, Jack; Armour, John A.L.

2010-01-01

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case–control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case–control studies. PMID:20858604

Does testing with feedback improve adult spelling skills relative to copying and reading?

PubMed

Pan, Steven C; Rubin, Benjamin R; Rickard, Timothy C

2015-12-01

We examined testing's ability to enhance adult spelling acquisition, relative to copying and reading. Across 3 experiments in which testing with feedback was compared with copying, the spelling improvement after testing matched that following the same amount of time spent copying. A potent testing advantage, however, was observed for spelling words free-recalled. In the fourth experiment, a large testing advantage for both word free recall and spelling was observed, versus reading. Subjects also generally preferred testing and rated it as more effective than copying or reading. The equivalent performance of testing and copying for spelling contrasts with prior work involving children and suggests that retrieval practice may not be the only effective mechanism for spelling skill acquisition. Rather, we suggest that the critical learning event for spelling is focused study on phoneme-to-grapheme mappings for previously unlearned letter sequences. For adults with extensive spelling expertise, focused study is more automatic during both copying and testing with feedback than for individuals with beginning spelling skills. Reading, however, would not be expected to produce efficient focused study of phoneme-to-grapheme mappings, regardless of expertise level. Overall, adult spelling skill acquisition benefits both from testing and copying, and substantially less from reading. (c) 2015 APA, all rights reserved).

22 CFR 92.79 - Procuring copies of foreign public documents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... foreign officials copies of birth, death, and marriage certificates, or copies of other public records... assistance. Persons requesting documents for use in the preparation of family trees or in the compilation of...

22 CFR 92.79 - Procuring copies of foreign public documents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... foreign officials copies of birth, death, and marriage certificates, or copies of other public records... assistance. Persons requesting documents for use in the preparation of family trees or in the compilation of...

22 CFR 92.79 - Procuring copies of foreign public documents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... foreign officials copies of birth, death, and marriage certificates, or copies of other public records... assistance. Persons requesting documents for use in the preparation of family trees or in the compilation of...

22 CFR 92.79 - Procuring copies of foreign public documents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... foreign officials copies of birth, death, and marriage certificates, or copies of other public records... assistance. Persons requesting documents for use in the preparation of family trees or in the compilation of...

14 CFR 221.92 - Number of copies required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... PROCEEDINGS) ECONOMIC REGULATIONS TARIFFS Filing Tariff Publications With Department § 221.92 Number of copies required. Two copies of each paper tariff, tariff revision and adoption notice to be filed shall be sent to...

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies.

PubMed

Willemsen, Marjolein H; de Leeuw, Nicole; de Brouwer, Arjan P M; Pfundt, Rolph; Hehir-Kwa, Jayne Y; Yntema, Helger G; Nillesen, Willy M; de Vries, Bert B A; van Bokhoven, Hans; Kleefstra, Tjitske

2012-11-01

Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

An Essential Role for COPI in mRNA Localization to Mitochondria and Mitochondrial Function.

PubMed

Zabezhinsky, Dmitry; Slobodin, Boris; Rapaport, Doron; Gerst, Jeffrey E

2016-04-19

Nuclear-encoded mRNAs encoding mitochondrial proteins (mMPs) can localize directly to the mitochondrial surface, yet how mMPs target mitochondria and whether RNA targeting contributes to protein import into mitochondria and cellular metabolism are unknown. Here, we show that the COPI vesicle coat complex is necessary for mMP localization to mitochondria and mitochondrial function. COPI inactivation leads to reduced mMP binding to COPI itself, resulting in the dissociation of mMPs from mitochondria, a reduction in mitochondrial membrane potential, a decrease in protein import in vivo and in vitro, and severe deficiencies in mitochondrial respiration. Using a model mMP (OXA1), we observed that COPI inactivation (or mutation of the potential COPI-interaction site) led to altered mRNA localization and impaired cellular respiration. Overall, COPI-mediated mMP targeting is critical for mitochondrial protein import and function, and transcript delivery to the mitochondria or endoplasmic reticulum is regulated by cis-acting RNA sequences and trans-acting proteins. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

49 CFR 512.5 - How many copies should I submit?

Code of Federal Regulations, 2010 CFR

2010-10-01

... must send the following in hard copy or electronic format to the Chief Counsel when making a claim for... format, a copy of any special software required to review materials for which confidential treatment is...

49 CFR 10.75 - Fee schedule.

Code of Federal Regulations, 2014 CFR

2014-10-01

..., each standard size sheet (4″×6″ containing up to 65 frames) .15 (3) Apertune card to hard copy, each copy .50 (4) 16mm microfilm to hard copy: First .25 Additional .07 (g) Computerline printer output...

49 CFR 10.75 - Fee schedule.

Code of Federal Regulations, 2012 CFR

2012-10-01

..., each standard size sheet (4″×6″ containing up to 65 frames) .15 (3) Apertune card to hard copy, each copy .50 (4) 16mm microfilm to hard copy: First .25 Additional .07 (g) Computerline printer output...

49 CFR 10.75 - Fee schedule.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., each standard size sheet (4″×6″ containing up to 65 frames) .15 (3) Apertune card to hard copy, each copy .50 (4) 16mm microfilm to hard copy: First .25 Additional .07 (g) Computerline printer output...

1. Historic American Buildings Survey Charles E. Peterson, Photographer Copied ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. Historic American Buildings Survey Charles E. Peterson, Photographer Copied July 29, 1940 Copied from old photograph - Joseph R. Brown House, Sam Brown Memorial Park (moved from Dakota Territory), Browns Valley, Traverse County, MN

37. Photographic copy of architects plan, no date, (original in ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

37. Photographic copy of architects plan, no date, (original in possession of Montana State University, Bozeman, Montana.) PHOTOGRAPHIC COPY OF ORIGINAL DRAWING - Hardin City Water Works, 101 East Fourth Street, Hardin, Big Horn County, MT

Creating single-copy genetic circuits

PubMed Central

Lee, Jeong Wook; Gyorgy, Andras; Cameron, D. Ewen; Pyenson, Nora; Choi, Kyeong Rok; Way, Jeffrey C.; Silver, Pamela A.; Del Vecchio, Domitilla; Collins, James J.

2017-01-01

SUMMARY Synthetic biology is increasingly used to develop sophisticated living devices for basic and applied research. Many of these genetic devices are engineered using multi-copy plasmids, but as the field progresses from proof-of-principle demonstrations to practical applications, it is important to develop single-copy synthetic modules that minimize consumption of cellular resources and can be stably maintained as genomic integrants. Here we use empirical design, mathematical modeling and iterative construction and testing to build single-copy, bistable toggle switches with improved performance and reduced metabolic load that can be stably integrated into the host genome. Deterministic and stochastic models led us to focus on basal transcription to optimize circuit performance and helped to explain the resulting circuit robustness across a large range of component expression levels. The design parameters developed here provide important guidance for future efforts to convert functional multi-copy gene circuits into optimized single-copy circuits for practical, real-world use. PMID:27425413

Comparison of the copy numbers of bovine leukemia virus in the lymph nodes of cattle with enzootic bovine leukosis and cattle with latent infection.

PubMed

Somura, Yoshiko; Sugiyama, Emi; Fujikawa, Hiroshi; Murakami, Kenji

2014-10-01

To establish a diagnostic index for predicting enzootic bovine leukosis (EBL), proviral bovine leukemia virus (BLV) copies in whole blood, lymph nodes and spleen were examined by quantitative real-time PCR (qPCR). Cattle were divided into two groups, EBL and BLV-infected, based on meat inspection data. The number of BLV copies in all specimens of EBL cattle was significantly higher than those of BLV-infected cattle (p < 0.0001), and the number of BLV copies in the lymph nodes was particularly large. Over 70 % of the superficial cervical, medial iliac and jejunal lymph nodes from EBL cattle had more than 1,000 copies/10 ng DNA, whereas lymph nodes from BLV-infected cattle did not. These findings suggest that the cattle harboring more than 1,000 BLV copies may be diagnosed with EBL.

Protocols for Copying and Proofreading in Template-Assisted Polymerization

NASA Astrophysics Data System (ADS)

Pigolotti, Simone; Sartori, Pablo

2016-03-01

We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation pathway. In the first protocol, monomer incorporation occurs in a single stochastic transition. We then move to a more elaborate protocol in which an intermediate step can be used for error correction. Finally, we discuss the operating regimes of two kinetic proofreading protocols: one in which proofreading acts from the final copying step, and one in which it acts from an intermediate step. We review known results for these models and, in some cases, extend them to analyze all possible combinations of energetic and kinetic discrimination. We show that, in each of these protocols, only a limited number of these combinations leads to an improvement of the overall copying accuracy.

Virological failure and all-cause mortality in HIV-positive adults with low-level viremia during antiretroviral treatment

PubMed Central

Medstrand, Patrik; Yilmaz, Aylin; Isberg, Per-Erik; Gisslén, Magnus; Björkman, Per

2017-01-01

Objective Although most HIV-infected individuals achieve undetectable viremia during antiretroviral therapy (ART), a subset have low-level viremia (LLV) of varying duration and magnitude. The impact of LLV on treatment outcomes is unclear. We investigated the association between LLV and virological failure and/or all-cause mortality among Swedish patients receiving ART. Methods HIV-infected patients from two Swedish HIV centers were identified from the nationwide register InfCare HIV. Subjects aged ≥15 years with triple agent ART were included at 12 months after treatment initiation if ≥2 following viral load measurements were available. Patients with 2 consecutive HIV RNA values ≥1000 copies/mL at this time point were excluded. Participants were stratified into four categories depending on viremia profiles: permanently suppressed viremia (<50 copies/mL), LLV 50–199 copies/mL, LLV 200–999 copies/mL and viremia ≥1000 copies/mL. Association between all four viremia categories and all-cause death was calculated using survival analysis with viremia as a time-varying covariate, so that patients could change viremia category during follow-up. Association between the three lower categories and virological failure (≥2 consecutive measurements ≥1000 copies/mL) was calculated in a similar manner. Results LLV 50–199 copies/mL was recorded in 70/1015 patients (6.9%) and LLV 200–999 copies/mL in 89 (8.8%) during 7812 person-years of follow-up (median 6.5 years). LLV 200–999 copies/mL was associated with virological failure (adjusted hazard ratio 3.14 [95% confidence interval 1.41–7.03, p<0.01]), whereas LLV 50–199 copies/mL was not (1.01 [0.34–4.31, p = 0.99]; median follow-up 4.5 years). LLV 200–999 copies/mL had an adjusted mortality hazard ratio of 2.29 (0.98–5.32, p = 0.05) and LLV 50–199 copies/mL of 2.19 (0.90–5.37, p = 0.09). Conclusions In this Swedish cohort followed during ART for a median of 4.5 years, LLV 200–999 copies/mL was independently associated with virological failure. Patients with LLV had higher rates of all-cause mortality, although not statistically significant in multivariate analysis. PMID:28683128

Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia.

PubMed

Yan, Yuanlong; Yang, Xiling; Liu, Yunqiang; Shen, Ying; Tu, Wenling; Dong, Qiang; Yang, Dong; Ma, Yongyi; Yang, Yuan

2017-07-01

What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome. RBMY1 encodes an RNA-binding protein that serves as a pre-mRNA splicing regulator during spermatogenesis, and male mice deficient in Rbmy are sterile. A total of 3127 adult males were recruited from 2009 to 2016; of this group, the dosage of RBMY1 functional copy were investigated in 486 fertile males. In the remaining 2641 males with known spermatogenesis status, 1070 Y-chromosome haplogroup (Y-hg) O3* or O3e carriers without chromosomal aberration or known AZF structure mutations responsible for spermatogenic impairment, including 506 men with normozoospermia and 564 men with oligozoospermia or/and asthenozoospermia, were screened, and the RBMY1 functional copy dosage and copy conversion were determined to explore their associations with sperm phenotypes. The correlation between RBMY1 dosage and its mRNA level or RBMY1 protein level and the correlation between sperm RBMY1 level and motility were analysed in 15 testis tissue samples and eight semen samples. Ten additional semen samples were used to confirm the subcellular localization of RBMY1 in individual sperm. All the Han volunteers donating whole blood, semen and testis tissue were from southwest China. RBMY1 copy number, copy conversion, mRNA/protein amount and protein location in sperm were detected using the AccuCopy® assay method, paralog ratio test, quantitative PCR, western blotting and immunofluorescence staining methods, respectively. This study identified Y-hg-independent CNV of functional RBMY1 in the enrolled population. A difference in the distribution of RBMY1 copy number was observed between the group with normal sperm motility and the group with asthenozoospermia. A positive correlation between the RBMY1 copy dosage and sperm motility was identified, and the males with fewer than six copies of RBMY1 showed an elevated risk for asthenozoospermia relative to those with six RBMY1 copies, the most common dosage in the population. The RBMY1 copy dosage was positively correlated with its mRNA and protein level in the testis. Sperm with high motility were found to carry more RBMY1 protein than those with relatively low motility. The RBMY1 protein was confirmed to predominantly localize in the neck and mid-piece region of sperm as well as the principal piece of the sperm tail. Our population study completes a chain of evidence suggesting that RBMY1 influences the susceptibility of males to asthenozoospermia by modulating sperm motility. High sequence similarity between the RBMY1 functional copies and a large number of pseudogenes potentially reduces the accuracy of the copy number detection. The mechanism underlying the CNV in RBMY1 is still unclear, and the effect of the structural variations in the RBMY1 copy cluster on the copy dosage of other protein-coding genes located in the region cannot be excluded, which may potentially bias our observations. Asthenozoospermia is a multi-factor complex disease with a limited number of proven susceptibility genes. This study identified a novel genomic candidate independently contributing to the condition, enriching our understanding of the role of AZF-linked genes in male reproduction. Our finding provides insight into the physiological and pathological characteristics of RBMY1 in terms of sperm motility, supplies persuasive evidence of the significance of RBMY1 copy number analysis in the clinical counselling of male infertility resulting from asthenozoospermia. This work was funded by the National Natural Science Foundation of China (Nos. 81370748 and 30971598). The authors have no conflicts of interest. © The Author 2017. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The Electronic View Box: a software tool for radiation therapy treatment verification.

PubMed

Bosch, W R; Low, D A; Gerber, R L; Michalski, J M; Graham, M V; Perez, C A; Harms, W B; Purdy, J A

1995-01-01

We have developed a software tool for interactively verifying treatment plan implementation. The Electronic View Box (EVB) tool copies the paradigm of current practice but does so electronically. A portal image (online portal image or digitized port film) is displayed side by side with a prescription image (digitized simulator film or digitally reconstructed radiograph). The user can measure distances between features in prescription and portal images and "write" on the display, either to approve the image or to indicate required corrective actions. The EVB tool also provides several features not available in conventional verification practice using a light box. The EVB tool has been written in ANSI C using the X window system. The tool makes use of the Virtual Machine Platform and Foundation Library specifications of the NCI-sponsored Radiation Therapy Planning Tools Collaborative Working Group for portability into an arbitrary treatment planning system that conforms to these specifications. The present EVB tool is based on an earlier Verification Image Review tool, but with a substantial redesign of the user interface. A graphical user interface prototyping system was used in iteratively refining the tool layout to allow rapid modifications of the interface in response to user comments. Features of the EVB tool include 1) hierarchical selection of digital portal images based on physician name, patient name, and field identifier; 2) side-by-side presentation of prescription and portal images at equal magnification and orientation, and with independent grayscale controls; 3) "trace" facility for outlining anatomical structures; 4) "ruler" facility for measuring distances; 5) zoomed display of corresponding regions in both images; 6) image contrast enhancement; and 7) communication of portal image evaluation results (approval, block modification, repeat image acquisition, etc.). The EVB tool facilitates the rapid comparison of prescription and portal images and permits electronic communication of corrections in port shape and positioning.

Implementation of a patient-facing genomic test report in the electronic health record using a web-application interface.

PubMed

Williams, Marc S; Kern, Melissa S; Lerch, Virginia R; Billet, Jonathan; Williams, Janet L; Moore, Gregory J

2018-05-30

Genomic medicine is emerging into clinical care. Communication of genetic laboratory results to patients and providers is hampered by the complex technical nature of the laboratory reports. This can lead to confusion and misinterpretation of the results resulting in inappropriate care. Patients usually do not receive a copy of the report leading to further opportunities for miscommunication. To address these problems, interpretive reports were created using input from the intended end users, patients and providers. This paper describes the technical development and deployment of the first patient-facing genomic test report (PGR) within an electronic health record (EHR) ecosystem using a locally developed standards-based web-application interface. A patient-facing genomic test report with a companion provider report was configured for implementation within the EHR using a locally developed software platform, COMPASS™. COMPASS™ is designed to manage secure data exchange, as well as patient and provider access to patient reported data capture and clinical display tools. COMPASS™ is built using a Software as a Service (SaaS) approach which exposes an API that apps can interact with. An authoring tool was developed that allowed creation of patient-specific PGRs and the accompanying provider reports. These were converted to a format that allowed them to be presented in the patient portal and EHR respectively using the existing COMPASS™ interface thus allowing patients, caregivers and providers access to individual reports designed for the intended end user. The PGR as developed was shown to enhance patient and provider communication around genomic results. It is built on current standards but is designed to support integration with other tools and be compatible with emerging opportunities such as SMART on FHIR. This approach could be used to support genomic return of results as the tool is scalable and generalizable.

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events.

PubMed

Demeke, Tigst; Eng, Monika

2018-05-01

Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantification of GE canola events by ddPCR. The suitability of four endogenous reference sequences ( HMG-I/Y , FatA(A), CruA and Ccf) for absolute quantification of GE canola events by ddPCR was investigated. The effect of DNA extraction methods and DNA quality on the assessment of reference gene copy numbers was also investigated. ddPCR results were affected by the use of single vs. two copy reference genes. The single copy, FatA(A), reference gene was found to be stable and suitable for absolute quantification of GE canola events by ddPCR. For the copy numbers measured, the HMG-I/Y reference gene was less consistent than FatA(A) reference gene. The expected ddPCR values were underestimated when CruA and Ccf (two copy endogenous Cruciferin sequences) were used because of high number of copies. It is important to make an adjustment if two copy reference genes are used for ddPCR in order to obtain accurate results. On the other hand, real-time quantitative PCR results were not affected by the use of single vs. two copy reference genes.

Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders.

PubMed

Carpenter, Danielle; Walker, Susan; Prescott, Natalie; Schalkwijk, Joost; Armour, John Al

2011-08-18

Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn's disease, rheumatoid arthritis and psoriasis clinical cohorts. We evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn's disease, rheumatoid arthritis or psoriasis. Differential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion.

Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders

PubMed Central

2011-01-01

Background Copy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn's disease, rheumatoid arthritis and psoriasis clinical cohorts. Results We evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn's disease, rheumatoid arthritis or psoriasis. Conclusions Differential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion. PMID:21851606

Mitochondrial DNA copy number in peripheral blood cell and hypertension risk among mining workers: a case-control study in Chinese coal miners.

PubMed

Lei, L; Guo, J; Shi, X; Zhang, G; Kang, H; Sun, C; Huang, J; Wang, T

2017-09-01

Alteration of mitochondrial DNA (mtDNA) copy number, which reflects oxidant-induced cell damage, has been observed in a wide range of human diseases. However, whether it correlates with hypertension has not been elucidated. We aimed to explore the association between mtDNA copy number and the risk of hypertension in Chinese coal miners. A case-control study was performed with 378 hypertension patients and 325 healthy controls in a large coal mining group located in North China. Face-to-face interviews were conducted by trained staffs with necessary medical knowledge. The mtDNA copy number was measured by a quantitative real-time PCR assay using DNA extracted from peripheral blood. No significant differences in mtDNA copy number were observed between hypertension patients and healthy controls. However, in both case and control groups, the mtDNA copy number was statistically significantly lower in the elder population (≥45 years old) compared with the younger subjects (<45 years old; 7.17 vs 6.64, P=0.005 and 7.21 vs 6.84, P=0.036). A significantly higher mtDNA copy number could be found in hypertension patients consuming alcohol regularly compared with no alcohol consumption patients (7.09 vs 6.69); mtDNA copy number was also positively correlated with age and alcohol consumption. Hypertension was found significantly correlated with factors such as age, work duration, monthly family income and drinking status. Our results suggest that the mtDNA copy number is not associated with hypertension in coal miners.

Copy Number Variations of TBK1 in Australian Patients With Primary Open-Angle Glaucoma

PubMed Central

AWADALLA, MONA S.; FINGERT, JOHN H.; ROOS, BENJAMIN E.; CHEN, SIMON; HOLMES, RICHARD; GRAHAM, STUART L.; CHEHADE, MARK; GALANOPOLOUS, ANNA; RIDGE, BRONWYN; SOUZEAU, EMMANUELLE; ZHOU, TIGER; SIGGS, OWEN M.; HEWITT, ALEX W.; MACKEY, DAVID A.; BURDON, KATHRYN P.; CRAIG, JAMIE E.

2015-01-01

PURPOSE To investigate the presence of TBK1 copy number variations in a large, well-characterized Australian cohort of patients with glaucoma comprising both normal-tension glaucoma and high-tension glaucoma cases. DESIGN A retrospective cohort study. METHODS DNA samples from patients with normal-tension glaucoma and high-tension glaucoma and unaffected controls were screened for TBK1 copy number variations using real-time quantitative polymerase chain reaction. Samples with additional copies of the TBK1 gene were further tested using custom comparative genomic hybridization arrays. RESULTS Four out of 334 normal-tension glaucoma cases (1.2%) were found to carry TBK1 copy number variations using quantitative polymerase chain reaction. One extra dose of the TBK1 gene (duplication) was detected in 3 normal-tension glaucoma patients, while 2 extra doses of the gene (triplication) were detected in a fourth normal-tension glaucoma patient. The results were further confirmed by custom comparative genomic hybridization arrays. Further, the TBK1 copy number variation segregated with normal-tension glaucoma in the family members of the probands, showing an autosomal dominant pattern of inheritance. No TBK1 copy number variations were detected in 1045 Australian patients with high-tension glaucoma or in 254 unaffected controls. CONCLUSION We report the presence of TBK1 copy number variations in our Australian normal-tension glaucoma cohort, including the first example of more than 1 extra copy of this gene in glaucoma patients (gene triplication). These results confirm TBK1 to be an important cause of normal-tension glaucoma, but do not suggest common involvement in high-tension glaucoma. PMID:25284765

Amylase activity is associated with AMY2B copy numbers in dog: implications for dog domestication, diet and diabetes

PubMed Central

Arendt, Maja; Fall, Tove; Lindblad-Toh, Kerstin; Axelsson, Erik

2014-01-01

High amylase activity in dogs is associated with a drastic increase in copy numbers of the gene coding for pancreatic amylase, AMY2B, that likely allowed dogs to thrive on a relatively starch-rich diet during early dog domestication. Although most dogs thus probably digest starch more efficiently than do wolves, AMY2B copy numbers vary widely within the dog population, and it is not clear how this variation affects the individual ability to handle starch nor how it affects dog health. In humans, copy numbers of the gene coding for salivary amylase, AMY1, correlate with both salivary amylase levels and enzyme activity, and high amylase activity is related to improved glycemic homeostasis and lower frequencies of metabolic syndrome. Here, we investigate the relationship between AMY2B copy numbers and serum amylase activity in dogs and show that amylase activity correlates with AMY2B copy numbers. We then describe how AMY2B copy numbers vary in individuals from 20 dog breeds and find strong breed-dependent patterns, indicating that the ability to digest starch varies both at the breed and individual level. Finally, to test whether AMY2B copy number is strongly associated with the risk of developing diabetes mellitus, we compare copy numbers in cases and controls as well as in breeds with varying diabetes susceptibility. Although we see no such association here, future studies using larger cohorts are needed before excluding a possible link between AMY2B and diabetes mellitus. PMID:24975239

19 CFR 151.64 - Extra copy of entry summary.

Code of Federal Regulations, 2013 CFR

2013-04-01

... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.64 Extra copy of entry summary. One extra copy of the entry summary covering wool or hair subject to duty at a rate per...

19 CFR 151.64 - Extra copy of entry summary.

Code of Federal Regulations, 2012 CFR

2012-04-01

... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.64 Extra copy of entry summary. One extra copy of the entry summary covering wool or hair subject to duty at a rate per...

19 CFR 151.64 - Extra copy of entry summary.

Code of Federal Regulations, 2011 CFR

2011-04-01

... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.64 Extra copy of entry summary. One extra copy of the entry summary covering wool or hair subject to duty at a rate per...

19 CFR 151.64 - Extra copy of entry summary.

Code of Federal Regulations, 2014 CFR

2014-04-01

... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.64 Extra copy of entry summary. One extra copy of the entry summary covering wool or hair subject to duty at a rate per...

19 CFR 151.64 - Extra copy of entry summary.

Code of Federal Regulations, 2010 CFR

2010-04-01

... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.64 Extra copy of entry summary. One extra copy of the entry summary covering wool or hair subject to duty at a rate per...

76 FR 10755 - Practices and Procedures, Board Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-28

... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... transcription. (3) The Board shall maintain a complete verbatim copy of the transcript, a complete copy of the...

29 CFR 4902.8 - Fees.

Code of Federal Regulations, 2010 CFR

2010-07-01

... of record copies furnished. Where the copying fee is less than $1.50, it shall not be assessed. (b... shall provide facilities for such copying without charge between the hours of 9 a.m. and 4 p.m. on any working day. ...

A uniform approach for programming distributed heterogeneous computing systems

PubMed Central

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-01-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater’s performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations. PMID:25844015

(Development of advanced models of the MCC full expansion (quiet) engine): First quarterly report

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

Not Available

This is the first quarterly report to the Department of Energy on the progress associated with the development of advanced models of the MCC full expansion (quiet) engine. These models will be evaluated in successive steps and eventually incorporated into a lawn mower for the purpose of commercializing the engine for small wheeled lawn and garden applications. During the first three months of the program (July 1 thru Sept 30), the Phase I design was basically completed with the exception of some engine/lawn mower interface hardware which will be completed during the final stages of the development program after wemore » have selected a lawn mower deck. Rick Erickson, the design engineer for the program, completed the initial parts drawings utilizing the computer drafting system together with guidance from Fredrick Erickson, the program principal engineer and Jeff Erickson, who is in charge of manufacturing the engines. A miniature copy of these drawings is included in the appendix for your review.« less

A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers

NASA Astrophysics Data System (ADS)

Du, Yan; Hughes, Randall A.; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.; Li, Bingling

2015-06-01

Strand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20-100 copies/μl, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device.

Absence of the HLA-G*0113N allele in Amerindian populations from the Brazilian Amazon region.

PubMed

Mendes-Junior, Celso T; Castelli, Erick C; Moreau, Philippe; Simões, Aguinaldo L; Donadi, Eduardo A

2010-04-01

The HLA-G gene is predominantly expressed at the maternal-fetal interface and has been associated with maternal-fetal tolerance. The HLA-G*0113N is a null allele defined by the insertion of a premature stop codon at exon 2, observed in a single Ghanaian individual. Likewise the G*0105N allele, the occurrence of the HLA-G*0113N in a population from an area with high pathogen load suggests that the reduced HLA-G expression in G*0113N heterozygous placentas could improve the intrauterine defense against infections. The presence of the G*0113N allele here was investigated in 150 Amerindians from five isolated tribes that inhabit the Central Amazon and in 295 admixed individuals from the State of São Paulo, Southeastern Brazil, previously genotyped for HLA-G. No copy of the G*0113N null allele was found in both population samples by exon 2 sequence-based analysis, reinforcing its restricted occurrence in Africa.

Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

NASA Astrophysics Data System (ADS)

Lerner, Michael G.; Meagher, Kristin L.; Carlson, Heather A.

2008-10-01

Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.

An interactive website for analytical method comparison and bias estimation.

PubMed

Bahar, Burak; Tuncel, Ayse F; Holmes, Earle W; Holmes, Daniel T

2017-12-01

Regulatory standards mandate laboratories to perform studies to ensure accuracy and reliability of their test results. Method comparison and bias estimation are important components of these studies. We developed an interactive website for evaluating the relative performance of two analytical methods using R programming language tools. The website can be accessed at https://bahar.shinyapps.io/method_compare/. The site has an easy-to-use interface that allows both copy-pasting and manual entry of data. It also allows selection of a regression model and creation of regression and difference plots. Available regression models include Ordinary Least Squares, Weighted-Ordinary Least Squares, Deming, Weighted-Deming, Passing-Bablok and Passing-Bablok for large datasets. The server processes the data and generates downloadable reports in PDF or HTML format. Our website provides clinical laboratories a practical way to assess the relative performance of two analytical methods. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

The effects of working memory on brain-computer interface performance.

PubMed

Sprague, Samantha A; McBee, Matthew T; Sellers, Eric W

2016-02-01

The purpose of the present study is to evaluate the relationship between working memory and BCI performance. Participants took part in two separate sessions. The first session consisted of three computerized tasks. The List Sorting Working Memory Task was used to measure working memory, the Picture Vocabulary Test was used to measure general intelligence, and the Dimensional Change Card Sort Test was used to measure executive function, specifically cognitive flexibility. The second session consisted of a P300-based BCI copy-spelling task. The results indicate that both working memory and general intelligence are significant predictors of BCI performance. This suggests that working memory training could be used to improve performance on a BCI task. Working memory training may help to reduce a portion of the individual differences that exist in BCI performance allowing for a wider range of users to successfully operate the BCI system as well as increase the BCI performance of current users. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

DNA Nanostructure-based Interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA

NASA Astrophysics Data System (ADS)

Wen, Yanli; Pei, Hao; Shen, Ye; Xi, Junjie; Lin, Meihua; Lu, Na; Shen, Xizhong; Li, Jiong; Fan, Chunhai

2012-11-01

MicroRNAs (miRNAs) have been identified as promising cancer biomarkers due to their stable presence in serum. As an alternative to PCR-based homogenous assays, surface-based electrochemical biosensors offer great opportunities for low-cost, point-of-care tests (POCTs) of disease-associated miRNAs. Nevertheless, the sensitivity of miRNA sensors is often limited by mass transport and crowding effects at the water-electrode interface. To address such challenges, we herein report a DNA nanostructure-based interfacial engineering approach to enhance binding recognition at the gold electrode surface and drastically improve the detection sensitivity. By employing this novel strategy, we can directly detect as few as attomolar (<1, 000 copies) miRNAs with high single-base discrimination ability. Given that this ultrasensitive electrochemical miRNA sensor (EMRS) is highly reproducible and essentially free of prior target labeling and PCR amplification, we also demonstrate its application by analyzing miRNA expression levels in clinical samples from esophageal squamous cell carcinoma (ESCC) patients.

Flight Plasma Diagnostics for High-Power, Solar-Electric Deep-Space Spacecraft

NASA Technical Reports Server (NTRS)

Johnson, Lee; De Soria-Santacruz Pich, Maria; Conroy, David; Lobbia, Robert; Huang, Wensheng; Choi, Maria; Sekerak, Michael J.

2018-01-01

NASA's Asteroid Redirect Robotic Mission (ARRM) project plans included a set of plasma and space environment instruments, the Plasma Diagnostic Package (PDP), to fulfill ARRM requirements for technology extensibility to future missions. The PDP objectives were divided into the classes of 1) Plasma thruster dynamics, 2) Solar array-specific environmental effects, 3) Plasma environmental spacecraft effects, and 4) Energetic particle spacecraft environment. A reference design approach and interface requirements for ARRM's PDP was generated by the PDP team at JPL and GRC. The reference design consisted of redundant single-string avionics located on the ARRM spacecraft bus as well as solar array, driving and processing signals from multiple copies of several types of plasma, effects, and environments sensors distributed over the spacecraft and array. The reference design sensor types were derived in part from sensors previously developed for USAF Research Laboratory (AFRL) plasma effects campaigns such as those aboard TacSat-2 in 2007 and AEHF-2 in 2012.

A uniform approach for programming distributed heterogeneous computing systems.

PubMed

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-12-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater's performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations.

MICROPROCESSOR-BASED DATA-ACQUISITION SYSTEM FOR A BOREHOLE RADAR.

USGS Publications Warehouse

Bradley, Jerry A.; Wright, David L.

1987-01-01

An efficient microprocessor-based system is described that permits real-time acquisition, stacking, and digital recording of data generated by a borehole radar system. Although the system digitizes, stacks, and records independently of a computer, it is interfaced to a desktop computer for program control over system parameters such as sampling interval, number of samples, number of times the data are stacked prior to recording on nine-track tape, and for graphics display of the digitized data. The data can be transferred to the desktop computer during recording, or it can be played back from a tape at a latter time. Using the desktop computer, the operator observes results while recording data and generates hard-copy graphics in the field. Thus, the radar operator can immediately evaluate the quality of data being obtained, modify system parameters, study the radar logs before leaving the field, and rerun borehole logs if necessary. The system has proven to be reliable in the field and has increased productivity both in the field and in the laboratory.

Large Scale Analysis of Geospatial Data with Dask and XArray

NASA Astrophysics Data System (ADS)

Zender, C. S.; Hamman, J.; Abernathey, R.; Evans, K. J.; Rocklin, M.; Zender, C. S.; Rocklin, M.

2017-12-01

The analysis of geospatial data with high level languages has acceleratedinnovation and the impact of existing data resources. However, as datasetsgrow beyond single-machine memory, data structures within these high levellanguages can become a bottleneck. New libraries like Dask and XArray resolve some of these scalability issues,providing interactive workflows that are both familiar tohigh-level-language researchers while also scaling out to much largerdatasets. This broadens the access of researchers to larger datasets on highperformance computers and, through interactive development, reducestime-to-insight when compared to traditional parallel programming techniques(MPI). This talk describes Dask, a distributed dynamic task scheduler, Dask.array, amulti-dimensional array that copies the popular NumPy interface, and XArray,a library that wraps NumPy/Dask.array with labeled and indexes axes,implementing the CF conventions. We discuss both the basic design of theselibraries and how they change interactive analysis of geospatial data, and alsorecent benefits and challenges of distributed computing on clusters ofmachines.

Proceedings of the second SISAL users` conference

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

Feo, J T; Frerking, C; Miller, P J

1992-12-01

This report contains papers on the following topics: A sisal code for computing the fourier transform on S{sub N}; five ways to fill your knapsack; simulating material dislocation motion in sisal; candis as an interface for sisal; parallelisation and performance of the burg algorithm on a shared-memory multiprocessor; use of genetic algorithm in sisal to solve the file design problem; implementing FFT`s in sisal; programming and evaluating the performance of signal processing applications in the sisal programming environment; sisal and Von Neumann-based languages: translation and intercommunication; an IF2 code generator for ADAM architecture; program partitioning for NUMA multiprocessor computer systems;more » mapping functional parallelism on distributed memory machines; implicit array copying: prevention is better than cure ; mathematical syntax for sisal; an approach for optimizing recursive functions; implementing arrays in sisal 2.0; Fol: an object oriented extension to the sisal language; twine: a portable, extensible sisal execution kernel; and investigating the memory performance of the optimizing sisal compiler.« less

Unambiguous discrimination between linearly dependent equidistant states with multiple copies

NASA Astrophysics Data System (ADS)

Zhang, Wen-Hai; Ren, Gang

2018-07-01

Linearly independent quantum states can be unambiguously discriminated, but linearly dependent ones cannot. For linearly dependent quantum states, however, if C copies of the single states are available, then they may form linearly independent states, and can be unambiguously discriminated. We consider unambiguous discrimination among N = D + 1 linearly dependent states given that C copies are available and that the single copies span a D-dimensional space with equal inner products. The maximum unambiguous discrimination probability is derived for all C with equal a priori probabilities. For this classification of the linearly dependent equidistant states, our result shows that if C is even then adding a further copy fails to increase the maximum discrimination probability.

Video copy protection and detection framework (VPD) for e-learning systems

NASA Astrophysics Data System (ADS)

ZandI, Babak; Doustarmoghaddam, Danial; Pour, Mahsa R.

2013-03-01

This Article reviews and compares the copyright issues related to the digital video files, which can be categorized as contended based and Digital watermarking copy Detection. Then we describe how to protect a digital video by using a special Video data hiding method and algorithm. We also discuss how to detect the copy right of the file, Based on expounding Direction of the technology of the video copy detection, and Combining with the own research results, brings forward a new video protection and copy detection approach in terms of plagiarism and e-learning systems using the video data hiding technology. Finally we introduce a framework for Video protection and detection in e-learning systems (VPD Framework).

Copy Number Variation across European Populations

PubMed Central

Chen, Wanting; Hayward, Caroline; Wright, Alan F.; Hicks, Andrew A.; Vitart, Veronique; Knott, Sara; Wild, Sarah H.; Pramstaller, Peter P.; Wilson, James F.; Rudan, Igor; Porteous, David J.

2011-01-01

Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations. PMID:21829696

CALL FOR PAPERS: Optical implementation of quantum computers

NASA Astrophysics Data System (ADS)

Rarity, John; Weinfurter, Harald

2004-09-01

A topical issue of Journal of Optics B: Quantum and Semiclassical Optics will be devoted to recent advances in optical implementation of quantum computers. The topics to be covered will include, but are not limited to: bullet Linear optics quantum gates bullet Progress towards nonlinear optics quantum gates bullet Interface between optical qubits and atomic/solid state qubits bullet Novel architectures bullet Single-photon sources and detectors bullet Photonic quantum networks bullet Few-qubit applications The DEADLINE for submission of contributions is 15 January 2005 to allow the topical issue to be published in about October 2005. All contributions will be peer-reviewed in accordance with the normal refereeing procedures and standards of Journal of Optics B: Quantum and Semiclassical Optics. Submissions should preferably be in either standard LaTeX form or Microsoft Word. Advice on publishing your work in the journal may be found at www.iop.org/journals/authors/jopb. There are no page charges for publication. The corresponding author of each paper published will receive a complimentary copy of the topical issue. Contributions to the topical issue should preferably be submitted electronically at www.iop.org/journals/authors/jopb or by e-mail to jopb@iop.org. Authors unable to submit online or by e-mail may send hard copy contributions (enclosing the electronic code) to: Dr Claire Bedrock (Publisher), Journal of Optics B: Quantum and Semiclassical Optics, Institute of Physics Publishing, Dirac House, Temple Back, Bristol BS1 6BE, UK. All contributions should be accompanied by a readme file or covering letter, quoting `JOPB Topical Issue - Optical implementation of quantum computers', giving the postal and e-mail addresses for correspondence. Any subsequent change of address should be notified to the publishing office. We look forward to receiving your contribution to this topical issue.

Cryo-EM reconstruction of AlfA from Bacillus subtilis reveals the structure of a simplified actin-like filament at 3.4-Å resolution.

PubMed

Szewczak-Harris, Andrzej; Löwe, Jan

2018-03-27

Low copy-number plasmid pLS32 of Bacillus subtilis subsp. natto contains a partitioning system that ensures segregation of plasmid copies during cell division. The partitioning locus comprises actin-like protein AlfA, adaptor protein AlfB, and the centromeric sequence parN Similar to the ParMRC partitioning system from Escherichia coli plasmid R1, AlfA filaments form actin-like double helical filaments that arrange into an antiparallel bipolar spindle, which attaches its growing ends to sister plasmids through interactions with AlfB and parN Because, compared with ParM and other actin-like proteins, AlfA is highly diverged in sequence, we determined the atomic structure of nonbundling AlfA filaments to 3.4-Å resolution by cryo-EM. The structure reveals how the deletion of subdomain IIB of the canonical actin fold has been accommodated by unique longitudinal and lateral contacts, while still enabling formation of left-handed, double helical, polar and staggered filaments that are architecturally similar to ParM. Through cryo-EM reconstruction of bundling AlfA filaments, we obtained a pseudoatomic model of AlfA doublets: the assembly of two filaments. The filaments are antiparallel, as required by the segregation mechanism, and exactly antiphasic with near eightfold helical symmetry, to enable efficient doublet formation. The structure of AlfA filaments and doublets shows, in atomic detail, how deletion of an entire domain of the actin fold is compensated by changes to all interfaces so that the required properties of polymerization, nucleotide hydrolysis, and antiparallel doublet formation are retained to fulfill the system's biological raison d'être.

Multiple copies of genes coding for electron transport proteins in the bacterium Nitrosomonas europaea.

PubMed

McTavish, H; LaQuier, F; Arciero, D; Logan, M; Mundfrom, G; Fuchs, J A; Hooper, A B

1993-04-01

The genome of Nitrosomonas europaea contains at least three copies each of the genes coding for hydroxylamine oxidoreductase (HAO) and cytochrome c554. A copy of an HAO gene is always located within 2.7 kb of a copy of a cytochrome c554 gene. Cytochrome P-460, a protein that shares very unusual spectral features with HAO, was found to be encoded by a gene separate from the HAO genes.

Survival differences of CIMP subtypes integrated with CNA information in human breast cancer.

PubMed

Wang, Huihan; Yan, Weili; Zhang, Shumei; Gu, Yue; Wang, Yihan; Wei, Yanjun; Liu, Hongbo; Wang, Fang; Wu, Qiong; Zhang, Yan

2017-07-25

CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation. The gene panel identified two groups corresponding to distinct copy number profiles. In status of mere-loss copy number, patients were faced with a greater risk if they presented a higher CpG islands methylation pattern in biomarker panels. But for samples presenting merely-gained copy number, higher methylation level of CpG islands was associated with improved viability. In all, the integration of copy number alteration and methylation information enhanced the classification power on prognosis. Moreover, we found the molecular subtypes of breast cancer presented different distributions in two CpG island methylation phenotypes. Generated by the same set of human methylation 450K data, additional copy number information could provide insights into survival prediction of cancers with less heterogeneity and might help to determine the biomarkers for diagnosis and treatment for breast cancer patients in a more personalized approach.

Survival differences of CIMP subtypes integrated with CNA information in human breast cancer

PubMed Central

Wang, Huihan; Yan, Weili; Zhang, Shumei; Gu, Yue; Wang, Yihan; Wei, Yanjun; Liu, Hongbo; Wang, Fang; Wu, Qiong; Zhang, Yan

2017-01-01

CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation. The gene panel identified two groups corresponding to distinct copy number profiles. In status of mere-loss copy number, patients were faced with a greater risk if they presented a higher CpG islands methylation pattern in biomarker panels. But for samples presenting merely-gained copy number, higher methylation level of CpG islands was associated with improved viability. In all, the integration of copy number alteration and methylation information enhanced the classification power on prognosis. Moreover, we found the molecular subtypes of breast cancer presented different distributions in two CpG island methylation phenotypes. Generated by the same set of human methylation 450K data, additional copy number information could provide insights into survival prediction of cancers with less heterogeneity and might help to determine the biomarkers for diagnosis and treatment for breast cancer patients in a more personalized approach. PMID:28415743

Cognitive profile of patients with rotated drawing at copy or recall: a controlled group study.

PubMed

Molteni, Federica; Traficante, Debora; Ferri, Francesca; Isella, Valeria

2014-03-01

When copying or recalling a figure from memory, some patient with dementia or focal brain lesions may rotate the drawing through ±90° or 180°. We have tried to clarify the nature of this phenomenon by investigating the cognitive profile of 22 patients who rotated the copy of the Rey-Osterrieth Complex Figure and 27 who rotated (only) the recall, and two control groups of cases with the same neuropsychiatric diagnoses, but no misorientation deficit. Brain MRI and FDG-PET images were also analysed. Predictor of rotation at the copy versus rotation at the recall was visuospatial impairment as measured by the copy of the Rey Figure; predictors of rotation at the copy versus no rotation were, again, visuospatial deficits, in addition to an abnormal performance at the task of selective attention. No specific profile of cognitive impairment distinguished patients with and without rotation at the recall. Disproportionate temporo-parieto-occipital atrophy or hypometabolism were evident in cases with misorientation of the copy, while predominant frontal abnormalities were found in cases of rotated recall. Based on these findings, rotated drawing at the copy is interpreted as a dorsal visual stream deficit, whose occurrence is more probable when attentional control is impaired. Rotation at recall seems to have a distinct, more anterior, neural substrate, but its dysexecutive nature has yet to be demonstrated. Copyright © 2014 Elsevier Inc. All rights reserved.

Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR.

PubMed

Plotka, Magdalena; Wozniak, Mateusz; Kaczorowski, Tadeusz

2017-01-01

Bacteria can be considered as biological nanofactories that manufacture a cornucopia of bioproducts most notably recombinant proteins. As such, they must perfectly match with appropriate plasmid vectors to ensure successful overexpression of target genes. Among many parameters that correlate positively with protein productivity plasmid copy number plays pivotal role. Therefore, development of new and more accurate methods to assess this critical parameter will result in optimization of expression of plasmid-encoded genes. In this study, we present a simple and highly accurate method for quantifying plasmid copy number utilizing an EvaGreen single colour, droplet digital PCR. We demonstrate the effectiveness of this method by examining the copy number of the pBR322 vector within Escherichia coli DH5α cells. The obtained results were successfully validated by real-time PCR. However, we observed a strong dependency of the plasmid copy number on the method chosen for isolation of the total DNA. We found that application of silica-membrane-based columns for DNA purification or DNA isolation with use of bead-beating, a mechanical cell disruption lead to determination of an average of 20.5 or 7.3 plasmid copies per chromosome, respectively. We found that recovery of the chromosomal DNA from purification columns was less efficient than plasmid DNA (46.5 ± 1.9% and 87.4 ± 5.5%, respectively) which may lead to observed differences in plasmid copy number. Besides, the plasmid copy number variations dependent on DNA template isolation method, we found that droplet digital PCR is a very convenient method for measuring bacterial plasmid content. Careful determination of plasmid copy number is essential for better understanding and optimization of recombinant proteins production process. Droplet digital PCR is a very precise method that allows performing thousands of individual PCR reactions in a single tube. The ddPCR does not depend on running standard curves and is a straightforward and reliable method to quantify the plasmid copy number. Therefore we believe that the ddPCR designed in this study will be widely used for any plasmid copy number calculation in the future.

Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR

PubMed Central

Plotka, Magdalena; Wozniak, Mateusz; Kaczorowski, Tadeusz

2017-01-01

Bacteria can be considered as biological nanofactories that manufacture a cornucopia of bioproducts most notably recombinant proteins. As such, they must perfectly match with appropriate plasmid vectors to ensure successful overexpression of target genes. Among many parameters that correlate positively with protein productivity plasmid copy number plays pivotal role. Therefore, development of new and more accurate methods to assess this critical parameter will result in optimization of expression of plasmid-encoded genes. In this study, we present a simple and highly accurate method for quantifying plasmid copy number utilizing an EvaGreen single colour, droplet digital PCR. We demonstrate the effectiveness of this method by examining the copy number of the pBR322 vector within Escherichia coli DH5α cells. The obtained results were successfully validated by real-time PCR. However, we observed a strong dependency of the plasmid copy number on the method chosen for isolation of the total DNA. We found that application of silica-membrane-based columns for DNA purification or DNA isolation with use of bead-beating, a mechanical cell disruption lead to determination of an average of 20.5 or 7.3 plasmid copies per chromosome, respectively. We found that recovery of the chromosomal DNA from purification columns was less efficient than plasmid DNA (46.5 ± 1.9% and 87.4 ± 5.5%, respectively) which may lead to observed differences in plasmid copy number. Besides, the plasmid copy number variations dependent on DNA template isolation method, we found that droplet digital PCR is a very convenient method for measuring bacterial plasmid content. Careful determination of plasmid copy number is essential for better understanding and optimization of recombinant proteins production process. Droplet digital PCR is a very precise method that allows performing thousands of individual PCR reactions in a single tube. The ddPCR does not depend on running standard curves and is a straightforward and reliable method to quantify the plasmid copy number. Therefore we believe that the ddPCR designed in this study will be widely used for any plasmid copy number calculation in the future. PMID:28085908

Statistical tools for transgene copy number estimation based on real-time PCR.

PubMed

Yuan, Joshua S; Burris, Jason; Stewart, Nathan R; Mentewab, Ayalew; Stewart, C Neal

2007-11-01

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination. Three experimental designs and four data quality control integrated statistical models are presented. For the first method, external calibration curves are established for the transgene based on serially-diluted templates. The Ct number from a control transgenic event and putative transgenic event are compared to derive the transgene copy number or zygosity estimation. Simple linear regression and two group T-test procedures were combined to model the data from this design. For the second experimental design, standard curves were generated for both an internal reference gene and the transgene, and the copy number of transgene was compared with that of internal reference gene. Multiple regression models and ANOVA models can be employed to analyze the data and perform quality control for this approach. In the third experimental design, transgene copy number is compared with reference gene without a standard curve, but rather, is based directly on fluorescence data. Two different multiple regression models were proposed to analyze the data based on two different approaches of amplification efficiency integration. Our results highlight the importance of proper statistical treatment and quality control integration in real-time PCR-based transgene copy number determination. These statistical methods allow the real-time PCR-based transgene copy number estimation to be more reliable and precise with a proper statistical estimation. Proper confidence intervals are necessary for unambiguous prediction of trangene copy number. The four different statistical methods are compared for their advantages and disadvantages. Moreover, the statistical methods can also be applied for other real-time PCR-based quantification assays including transfection efficiency analysis and pathogen quantification.

47 CFR 1.734 - Specifications as to pleadings, briefs, and other documents; subscription.

Code of Federal Regulations, 2010 CFR

2010-10-01

... submitted both as hard copies and on computer disk formatted to be compatible with the Commission's computer... copies of tariffs or reports with their hard copies need not include such tariffs or reports on the disk...

A Simulation Model for Purchasing Duplicate Copies in a Library

ERIC Educational Resources Information Center

Arms, W. Y.; Walter, T. P.

1974-01-01

A method of estimating the number of duplicate copies of books needed based on a computer simulation which takes into account number of copies available, number of loans, total underlying demand, satisfaction level, percentage time on shelf. (LS)

12 CFR 516.30 - What information must I provide with my application?

Code of Federal Regulations, 2010 CFR

2010-01-01

... on OTS's web page at www.ots.treas.gov. (b) Captions and exhibits. You must caption the original... signatures on copies if you include a copy of the signed signature page or the copy otherwise indicates that...

ACTG A5353: A Pilot Study of Dolutegravir Plus Lamivudine for Initial Treatment of Human Immunodeficiency Virus-1 (HIV-1)-infected Participants With HIV-1 RNA <500000 Copies/mL.

PubMed

Taiwo, Babafemi O; Zheng, Lu; Stefanescu, Andrei; Nyaku, Amesika; Bezins, Baiba; Wallis, Carole L; Godfrey, Catherine; Sax, Paul E; Acosta, Edward; Haas, David; Smith, Kimberly Y; Sha, Beverly; Van Dam, Cornelius; Gulick, Roy M

2018-05-17

Limited data exist on initial human immunodeficiency virus type 1 (HIV-1) treatment with dolutegravir plus lamivudine. A5353 is a phase 2, single-arm, pilot study of once-daily dolutegravir (50 mg) plus lamivudine (300 mg) in treatment-naive participants with HIV-1 RNA ≥1000 and <500000 copies/mL. Exclusion criteria included active hepatitis B or major protease, reverse transcriptase, or integrase resistance. The primary efficacy measure was the proportion with HIV-1 RNA <50 copies/mL (FDA [US Food and Drug Administration] Snapshot) at week 24. Virologic failure (VF) was confirmed HIV-1 RNA >400 copies/mL at week 16/20 or >200 copies/mL at or after week 24. Dolutegravir levels and drug resistance testing were performed at VF. One hundred and twenty participants (87% male, median age 30 years, 37 (31%) HIV-1 RNA >100000 copies/mL) initiated study treatment. Median entry HIV-1 RNA and CD4 count were 4.61 log10 copies/mL and 387 cells/mm3. Virologic efficacy at week 24 was 108/120 (90%, confidence interval [83%, 95%]), with comparable results in the >100000 copies/mL and ≤100000 copies/mL strata, that is, 89% (75%, 97%) and 90% (82%, 96%), respectively. Three participants with VF, had undetected plasma dolutegravir at ≥1 time points; the M184V and R263R/K mutations developed in 1 participant. Two participants experienced grade 3 possible/probable treatment-related adverse events; none discontinued treatment due to adverse events. Dolutegravir plus lamivudine demonstrated efficacy in individuals with pretreatment HIV-1 RNA up to 500000 copies/mL in this pilot trial, but a participant developed resistance mutations. NCT02582684.

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

PubMed

Black, Holly A; Khan, Fayeza F; Tyson, Jess; Al Armour, John

2014-07-21

The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile.

PubMed

Huang, Yen-Tsung; Hsu, Thomas; Christiani, David C

2014-01-01

The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X (2) distributions that can be obtained using permutation with scaled X (2) approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (<2.8 × 10(-5)), including the PTEN pathway (7.8 × 10(-7)), the gene set up-regulated under heat shock (3.6 × 10(-6)), the gene sets involved in the immune profile for rejection of kidney transplantation (9.2 × 10(-6)) and for transcriptional control of leukocytes (2.2 × 10(-5)), and the ganglioside biosynthesis pathway (2.7 × 10(-5)). In conclusion, we present a new method for pathway analyses of copy number data, and causal mechanisms of the five pathways require further study.

Development of a high-copy plasmid for enhanced production of recombinant proteins in Leuconostoc citreum.

PubMed

Son, Yeon Jeong; Ryu, Ae Jin; Li, Ling; Han, Nam Soo; Jeong, Ki Jun

2016-01-15

Leuconostoc is a hetero-fermentative lactic acid bacteria, and its importance is widely recognized in the dairy industry. However, due to limited genetic tools including plasmids for Leuconostoc, there has not been much extensive research on the genetics and engineering of Leuconostoc yet. Thus, there is a big demand for high-copy-number plasmids for useful gene manipulation and overproduction of recombinant proteins in Leuconostoc. Using an existing low-copy plasmid, the copy number of plasmid was increased by random mutagenesis followed by FACS-based high-throughput screening. First, a random library of plasmids was constructed by randomizing the region responsible for replication in Leuconostoc citreum; additionally, a superfolder green fluorescent protein (sfGFP) was used as a reporter protein. With a high-speed FACS sorter, highly fluorescent cells were enriched, and after two rounds of sorting, single clone exhibiting the highest level of sfGFP was isolated. The copy number of the isolated plasmid (pCB4270) was determined by quantitative PCR (qPCR). It was found that the isolated plasmid has approximately a 30-fold higher copy number (approx. 70 copies per cell) than that of the original plasmid. From the sequence analysis, a single mutation (C→T) at position 4690 was found, and we confirmed that this single mutation was responsible for the increased plasmid copy number. The effectiveness of the isolated high-copy-number plasmid for the overproduction of recombinant proteins was successfully demonstrated with two protein models Glutathione-S-transferase (GST) and α-amylase. The high-copy number plasmid was successfully isolated by FACS-based high-throughput screening of a plasmid library in L. citreum. The isolated plasmid could be a useful genetic tool for high-level gene expression in Leuconostoc, and for extending the applications of this useful bacteria to various areas in the dairy and pharmaceutical industries.

Performance characteristics of finger-stick dried blood spots (DBS) on the determination of human immunodeficiency virus (HIV) treatment failure in a pediatric population in Mozambique

PubMed Central

Chang, Joy; de Sousa, Amina; Sabatier, Jennifer; Assane, Mariamo; Zhang, Guoqing; Bila, Dulce; Vaz, Paula; Alfredo, Charity; Cossa, Loide; Bhatt, Nilesh; Koumans, Emilia H.; Yang, Chunfu; Rivadeneira, Emilia; Jani, Ilesh; Houston, James C.

2017-01-01

Quantitative plasma viral load (VL) at 1000 copies /mL was recommended as the threshold to confirm antiretroviral therapy (ART) failure by the World Health Organization (WHO). Because of ongoing challenges of using plasma for VL testing in resource-limited settings (RLS), especially for children, this study collected 717 DBS and paired plasma samples from children receiving ART ≥1 year in Mozambique and compared the performance of DBS using Abbott’s VL test with a paired plasma sample using Roche’s VL test. At a cut-off of 1000 copies/mL, sensitivity of DBS using Abbott DBS VL test was 79.9%, better than 71.0% and 63.9% at 3000 and 5000 copies/mL, respectively. Specificities were 97.6%, 98.8%, 99.3% at 1000, 3000, and 5000 copies/mL, respectively. The Kappa value at 1000 copies/mL, 0.80 (95% CI: 0.73, 0.87), was higher than 0.73 (95% CI: 0.66, 0.80) and 0.66 (95% CI: 0.59, 0.73) at 3000, 5000 copies/mL, respectively, also indicating better agreement. The mean difference between the DBS and plasma VL tests with 95% limits of agreement by Bland-Altman was 0.311 (-0.908, 1.530). Among 73 children with plasma VL between 1000 to 5000 copies/mL, the DBS results were undetectable in 53 at the 1000 copies/mL threshold. While one DBS sample in the Abbott DBS VL test may be an alternative method to confirm ART failure at 1000 copies/mL threshold when a plasma sample is not an option for treatment monitoring, because of sensitivity concerns between 1,000 and 5,000 copies/ml, two DBS samples may be preferred accompanied by careful patient monitoring and repeat testing. PMID:28704560

Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes.

PubMed

Ziemons, Sandra; Koutsantas, Katerina; Becker, Kordula; Dahlmann, Tim; Kück, Ulrich

2017-02-16

Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster. We performed pulsed-field gel electrophoresis (PFGE), quantitative qRT-PCR, and penicillin bioassays to investigate production, deletion and overexpression strains generated in the P. chrysogenum P2niaD18 background, in order to determine the copy number of the penicillin biosynthesis gene cluster, and study the expression of one penicillin biosynthesis gene, and the penicillin titer. Analysis of production and recombinant strain showed that the enhanced penicillin titer did not depend on the copy number of the penicillin gene cluster. Our assumption was strengthened by results with a penicillin null strain lacking pcbC encoding isopenicillin N synthase. Reintroduction of one or two copies of the cluster into the pcbC deletion strain restored transcriptional high expression of the pcbC gene, but recombinant strains showed no significantly different penicillin titer compared to parental strains. Here we present a molecular genetic analysis of production and recombinant strains in the P2niaD18 background carrying different copy numbers of the penicillin biosynthesis gene cluster. Our analysis shows that the enhanced penicillin titer does not strictly depend on the copy number of the cluster. Based on these overall findings, we hypothesize that instead, complex regulatory mechanisms are prominently implicated in increased penicillin biosynthesis in production strains.

Cognitive predictors of copying and drawing from memory of the Rey-Osterrieth complex figure in 7- to 10-year-old children.

PubMed

Senese, Vincenzo Paolo; De Lucia, Natascia; Conson, Massimiliano

2015-01-01

Cognitive models of drawing are mainly based on assessment of copying performance of adults, whereas only a few studies have verified these models in young children. Moreover, developmental investigations have only rarely performed a systematic examination of the contribution of perceptual and representational visuo-spatial processes to copying and drawing from memory. In this study we investigated the role of visual perception and mental representation in both copying and drawing from memory skills in a sample of 227 typically developing children (53% females) aged 7-10 years. Participants underwent a neuropsychological assessment and the Rey-Osterrieth Complex Figure (ROCF). The fit and invariance of the predictive model considering visuo-spatial abilities, working memory, and executive functions were tested by means of hierarchical regressions and path analysis. Results showed that, in a gender invariant way, visual perception abilities and spatial mental representation had a direct effect on copying performance, whereas copying performance was the only specific predictor for drawing from memory. These effects were independent from age and socioeconomic status, and showed that cognitive models of drawing built up for adults could be considered for predicting copying and drawing from memory in children.

Interpreting aCGH-defined karyotypic changes in gliomas using copy number status, loss of heterozygosity and allelic ratios

PubMed Central

Cowell, John K; Lo, Ken C; Luce, Jesse; Hawthorn, Lesleyann

2009-01-01

We have used SNP mapping arrays to simultaneously record copy number changes, loss of heterozygosity and allele ratios (ploidy) in a series of 13 gliomas. This combined analysis has defined novel amplification events in this tumor type involving chr1:241544532-243005121 and chr18:54716681-54917277 which contain the AKT3 and ZNF532 genes respectively. The high resolution of this analysis has also identified homozygous deletions involving chr17:25600031-26490848 and Chr19:53883612-55061878. Throughout the karyotypes of these tumors, the combined analysis revealed counter intuitive relationships between copy number and LOH that requires reinterpretation of the significance of copy number gains and losses. It was not uncommon to observe copy number gains that were associated with loss of heterozygosity as well as copy number losses that were not. These events appeared to be related to ploidy status in the tumors as determined using allelic ratio calculations. Overall, this analysis of gliomas provides evidence for the need to perform more comprehensive interpretation of the CGH data beyond copy number analysis alone to evaluate the significance of individual events in the karyotypes. PMID:19818351

Association of Higher Defensin β-4 Genomic Copy Numbers with Behçet's Disease in Iraqi Patients.

PubMed

Hameed, Ammar F; Jaradat, Sameh; Al-Musawi, Bassam M; Sharquie, Khalifa; Ibrahim, Mazin J; Hayani, Raafa K; Norgauer, Johannes

2015-11-01

Behçet's disease (BD) is an immune-mediated small vessel systemic vasculitis. Human β-defensins are antimicrobial peptides associated with many inflammatory diseases and are encoded by the β-defensin family of multiple-copy genes. However, their role in BD necessitates further investigation. The aim of the present study was to investigate the possible association of BD in its various clinical forms with defensin β-4 (DEFB4) genomic copy numbers. This case-control study was conducted from January to September 2011 and included 50 control subjects and 27 unrelated Iraqi BD patients registered at Baghdad Teaching Hospital, Bagdad, Iraq. Copy numbers of the DEFB4 gene were determined using the comparative cycle threshold method by duplex real-time polymerase chain reaction technology at the Department of Dermatology of Jena University Hospital, Jena, Germany. DEFB4 genomic copy numbers were significantly higher in the BD group compared to the control group (P = 0.010). However, no statistically significant association was found between copy numbers and clinical variables within the BD group. The DEFB4 copy number polymorphism may be associated with BD; however, it is not associated with different clinical manifestations of the disease.

Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors.

PubMed

Martin-Trujillo, Alex; Vidal, Enrique; Monteagudo-Sa Nchez, Ana; Sanchez-Delgado, Marta; Moran, Sebastian; Hernandez Mora, Jose Ramon; Heyn, Holger; Guitart, Miriam; Esteller, Manel; Monk, David

2017-09-07

It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.Altered genomic imprinting is frequently reported in cancer. Here, the authors analyze copy number and methylation in cancer cell lines and primary tumors to show that imprinted methylation profiles represent the accumulation of copy number alteration, rather than epigenetic alterations.

7 CFR 1780.83 - Bond transcript documents.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Copies of general incumbency certificate; (c) Certified copies of minutes or excerpts from all meetings... statutory requirements incident to calling and holding a favorable bond election, if one is necessary; (e..., with any attached coupons; (h) Attorney's no-litigation certificate; (i) Certified copies of...

44 CFR 5.85 - Authentication and attestation of copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Authentication and attestation of copies. 5.85 Section 5.85 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT... Authentication and attestation of copies. The Administrator, Deputy Administrators, Regional Administrators...

48 CFR 201.105-3 - Copies.

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2010-10-01

... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Copies. 201.105-3 Section 201.105-3 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE GENERAL FEDERAL ACQUISITION REGULATIONS SYSTEM Purpose, Authority, Issuance 201.105-3 Copies. The...

40. Photographic copy of original construction drawing, dated June 1911 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

40. Photographic copy of original construction drawing, dated June 1911 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). ROOF PLAN. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

38. Photographic copy of original construction drawing, dated June 1911 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

38. Photographic copy of original construction drawing, dated June 1911 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). FIRST FLOOR PLAN. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

37. Photographic copy of original construction drawing, dated June 1911 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

37. Photographic copy of original construction drawing, dated June 1911 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). BASEMENT PLAN. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

39. Photographic copy of original construction drawing, dated June 1911 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

39. Photographic copy of original construction drawing, dated June 1911 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). SECOND FLOOR PLAN. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

45. Photographic copy of original construction drawing, dated 16 February ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

45. Photographic copy of original construction drawing, dated 16 February 1916 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). LOT SURVEY. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

41. Photographic copy of original construction drawing, dated June 1911 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

41. Photographic copy of original construction drawing, dated June 1911 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). CROSS SECTIONS. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

16 CFR 4.2 - Requirements as to form, and filing of documents other than correspondence.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Administrative Law Judge) or twelve (12) paper copies (if before the Commission), and an electronic copy in Adobe... an electronic copy on a compact disc (CD) or digital video disc (DVD) in Adobe portable document...

16 CFR 4.2 - Requirements as to form, and filing of documents other than correspondence.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Administrative Law Judge) or twelve (12) paper copies (if before the Commission), and an electronic copy in Adobe... an electronic copy on a compact disc (CD) or digital video disc (DVD) in Adobe portable document...

47 CFR 3.25 - Number of copies.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL AUTHORIZATION AND ADMINISTRATION OF ACCOUNTING... copies. One original and one copy of FCC Form 44, “Application For Certification As An Accounting... commencement of settlement activities to allow time for the Commission to review the application and to allow...

Human-Compatible Animal Models for Preclinical Research on Hormones in Breast Cancer

DTIC Science & Technology

2012-09-01

Hormone/Prolactin Family in Biology and Disease” in July, 2012. Several participants inquired as to whether we had determined the number of copies of...in situ hybridization) analysis of both lines to determine the copy number of the transgene. We found that the BAC-h8 line has a single copy of the...transgene and the BAC-h30 line has two copies (Figure 5). Breeding of the hPRL+ mice onto an immunodeficient background: As discussed in last

DNA Copy Number Signature to Predict Recurrence in Early Stage Ovarian Cancer

DTIC Science & Technology

2016-08-01

AWARD NUMBER: W81XWH-14-1-0194 TITLE: DNA Copy Number Signature to Predict Recurrence in Early-Stage Ovarian Cancer PRINCIPAL INVESTIGATOR...SUBTITLE 5a. CONTRACT NUMBER DNA Copy Number Signature to Predict Recurrence in Early-Stage Ovarian Cancer 5b. GRANT NUMBER W81XWH-14-1-0194 5c. PROGRAM...determine the copy number gain and loss for early stage high grade ovarian cancers through IlluminaHumanOmniExpress-FFPE BeadChip system • Subtask 1 DNA

Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas.

PubMed

Etemadmoghadam, Dariush; deFazio, Anna; Beroukhim, Rameen; Mermel, Craig; George, Joshy; Getz, Gad; Tothill, Richard; Okamoto, Aikou; Raeder, Maria B; Harnett, Paul; Lade, Stephen; Akslen, Lars A; Tinker, Anna V; Locandro, Bianca; Alsop, Kathryn; Chiew, Yoke-Eng; Traficante, Nadia; Fereday, Sian; Johnson, Daryl; Fox, Stephen; Sellers, William; Urashima, Mitsuyoshi; Salvesen, Helga B; Meyerson, Matthew; Bowtell, David

2009-02-15

A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-based treatment. We analyzed somatic DNA copy number variation and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers. Genome-wide copy number variation was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate copy number variation to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of 12 candidate genes as independent validation of previously reported associations with clinical outcome. Likely copy number variation targets and tumor molecular subtypes were further characterized by gene expression profiling. Amplification of 19q12, containing cyclin E (CCNE1), and 20q11.22-q13.12, mapping immediately adjacent to the steroid receptor coactivator NCOA3, was significantly associated with poor response to primary treatment. Other genes previously associated with copy number variation and clinical outcome in ovarian cancer were not associated with primary treatment resistance. Chemoresistant tumors with high CCNE1 copy number and protein expression were associated with increased cellular proliferation but so too was a subset of treatment-responsive patients, suggesting a cell-cycle independent role for CCNE1 in modulating chemoresponse. Patients with a poor clinical outcome without CCNE1 amplification overexpressed genes involved in extracellular matrix deposition. We have identified two distinct mechanisms of primary treatment failure in serous ovarian cancer, involving CCNE1 amplification and enhanced extracellular matrix deposition. CCNE1 copy number is validated as a dominant marker of patient outcome in ovarian cancer.

DUF1220 copy number is linearly associated with increased cognitive function as measured by total IQ and mathematical aptitude scores

PubMed Central

Davis, Jonathon M.; Searles, Veronica B.; Anderson, Nathan; Keeney, Jonathon; Raznahan, Armin; Horwood, L. John; Fergusson, David M.; Kennedy, Martin A.; Giedd, Jay

2014-01-01

DUF1220 protein domains exhibit the greatest human lineage-specific copy number expansion of any protein-coding sequence in the genome, and variation in DUF1220 copy number has been linked to both brain size in humans and brain evolution among primates. Given these findings, we examined associations between DUF1220 subtypes CON1 and CON2 and cognitive aptitude. We identified a linear association between CON2 copy number and cognitive function in two independent populations of European descent. In North American males, an increase in CON2 copy number corresponded with an increase in WISC IQ (R2 = 0.13, p = 0.02), which may be driven by males aged 6–11 (R2 = 0.42, p = 0.003). We utilized ddPCR in a subset as a confirmatory measurement. This group had 26–33 copies of CON2 with a mean of 29, and each copy increase of CON2 was associated with a 3.3-point increase in WISC IQ (R2 = 0.22, p = 0.045). In individuals from New Zealand, an increase in CON2 copy number was associated with an increase in math aptitude ability (R2 = 0.10 p = 0.018). These were not confounded by brain size. To our knowledge, this is the first study to report a replicated association between copy number of a gene coding sequence and cognitive aptitude. Remarkably, dosage variations involving DUF1220 sequences have now been linked to human brain expansion, autism severity and cognitive aptitude, suggesting that such processes may be genetically and mechanistically inter-related. The findings presented here warrant expanded investigations in larger, well-characterized cohorts. PMID:25287832

The effect of input DNA copy number on genotype call and characterising SNP markers in the humpback whale genome using a nanofluidic array.

PubMed

Bhat, Somanath; Polanowski, Andrea M; Double, Mike C; Jarman, Simon N; Emslie, Kerry R

2012-01-01

Recent advances in nanofluidic technologies have enabled the use of Integrated Fluidic Circuits (IFCs) for high-throughput Single Nucleotide Polymorphism (SNP) genotyping (GT). In this study, we implemented and validated a relatively low cost nanofluidic system for SNP-GT with and without Specific Target Amplification (STA). As proof of principle, we first validated the effect of input DNA copy number on genotype call rate using well characterised, digital PCR (dPCR) quantified human genomic DNA samples and then implemented the validated method to genotype 45 SNPs in the humpback whale, Megaptera novaeangliae, nuclear genome. When STA was not incorporated, for a homozygous human DNA sample, reaction chambers containing, on average 9 to 97 copies, showed 100% call rate and accuracy. Below 9 copies, the call rate decreased, and at one copy it was 40%. For a heterozygous human DNA sample, the call rate decreased from 100% to 21% when predicted copies per reaction chamber decreased from 38 copies to one copy. The tightness of genotype clusters on a scatter plot also decreased. In contrast, when the same samples were subjected to STA prior to genotyping a call rate and a call accuracy of 100% were achieved. Our results demonstrate that low input DNA copy number affects the quality of data generated, in particular for a heterozygous sample. Similar to human genomic DNA, a call rate and a call accuracy of 100% was achieved with whale genomic DNA samples following multiplex STA using either 15 or 45 SNP-GT assays. These calls were 100% concordant with their true genotypes determined by an independent method, suggesting that the nanofluidic system is a reliable platform for executing call rates with high accuracy and concordance in genomic sequences derived from biological tissue.

Amylase activity is associated with AMY2B copy numbers in dog: implications for dog domestication, diet and diabetes.

PubMed

Arendt, Maja; Fall, Tove; Lindblad-Toh, Kerstin; Axelsson, Erik

2014-10-01

High amylase activity in dogs is associated with a drastic increase in copy numbers of the gene coding for pancreatic amylase, AMY2B, that likely allowed dogs to thrive on a relatively starch-rich diet during early dog domestication. Although most dogs thus probably digest starch more efficiently than do wolves, AMY2B copy numbers vary widely within the dog population, and it is not clear how this variation affects the individual ability to handle starch nor how it affects dog health. In humans, copy numbers of the gene coding for salivary amylase, AMY1, correlate with both salivary amylase levels and enzyme activity, and high amylase activity is related to improved glycemic homeostasis and lower frequencies of metabolic syndrome. Here, we investigate the relationship between AMY2B copy numbers and serum amylase activity in dogs and show that amylase activity correlates with AMY2B copy numbers. We then describe how AMY2B copy numbers vary in individuals from 20 dog breeds and find strong breed-dependent patterns, indicating that the ability to digest starch varies both at the breed and individual level. Finally, to test whether AMY2B copy number is strongly associated with the risk of developing diabetes mellitus, we compare copy numbers in cases and controls as well as in breeds with varying diabetes susceptibility. Although we see no such association here, future studies using larger cohorts are needed before excluding a possible link between AMY2B and diabetes mellitus. © 2014 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

Reduced mtDNA copy number increases the sensitivity of tumor cells to chemotherapeutic drugs.

PubMed

Mei, H; Sun, S; Bai, Y; Chen, Y; Chai, R; Li, H

2015-04-02

Many cancer drugs are toxic to cells by activating apoptotic pathways. Previous studies have shown that mitochondria have key roles in apoptosis in mammalian cells, but the role of mitochondrial DNA (mtDNA) copy number variation in the pathogenesis of tumor cell apoptosis remains largely unknown. We used the HEp-2, HNE2, and A549 tumor cell lines to explore the relationship between mtDNA copy number variation and cell apoptosis. We first induced apoptosis in three tumor cell lines and one normal adult human skin fibroblast cell line (HSF) with cisplatin (DDP) or doxorubicin (DOX) treatment and found that the mtDNA copy number significantly increased in apoptotic tumor cells, but not in HSF cells. We then downregulated the mtDNA copy number by transfection with shRNA-TFAM plasmids or treatment with ethidium bromide and found that the sensitivity of tumor cells to DDP or DOX was significantly increased. Furthermore, we observed that levels of reactive oxygen species (ROS) increased significantly in tumor cells with lower mtDNA copy numbers, and this might be related to a low level of antioxidant gene expression. Finally, we rescued the increase of ROS in tumor cells with lipoic acid or N-acetyl-L-cysteine and found that the apoptosis rate decreased. Our studies suggest that the increase of mtDNA copy number is a self-protective mechanism of tumor cells to prevent apoptosis and that reduced mtDNA copy number increases ROS levels in tumor cells, increases the tumor cells' sensitivity to chemotherapeutic drugs, and increases the rate of apoptosis. This research provides evidence that mtDNA copy number variation might be a promising new therapeutic target for the clinical treatment of tumors.

ALK gene copy number gain and immunohistochemical expression status using three antibodies in neuroblastoma.

PubMed

Kim, Eun Kyung; Kim, Sewha

2016-03-17

Anaplastic lymphoma kinase (ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones). ALK amplification and copy number gain were observed in 10% (3/30) and 53.3% (16/30) of the cohort, respectively. There were positive correlations between ALK copy number and IHC positive rate in ALK1 and 5A4 antibodies (p= < 0.001 and 0.019, respectively). ALK1, D5F3, and 5A4 antibodies equally showed 100% sensitivity in detecting ALK amplification. However, the sensitivity for detecting copy number gain differed among the three antibodies, with 75% sensitivity in D5F3 and 0% sensitivity in ALK1. ALK-amplified NBs were correlated with synchronous MYCN amplification and chromosome 1p deletion. ALK IHC positivity was frequently observed in INSS stage IV and high-risk group patients. In conclusion, this study identified that an increase in the ALK copy number is a frequent genetic alteration in poorly differentiated NB. ALK-amplified NBs showed consistent ALK IHC positivity with all kinds of antibodies. In contrast, the detection performance of ALK copy number gain was antibody dependent, with the D5F3 antibody showing the best sensitivity.

ALK Gene Copy Number Gain and Immunohistochemical Expression Status Using Three Antibodies in Neuroblastoma.

PubMed

Kim, Eun Kyung; Kim, Sewha

2017-01-01

Anaplastic lymphoma kinase ( ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones). ALK amplification and copy number gain were observed in 10% (3/30) and 53.3% (16/30) of the cohort, respectively. There were positive correlations between ALK copy number and IHC-positive rate in ALK1 and 5A4 antibodies ( P < 0.001 and P = 0.019, respectively). ALK1, D5F3, and 5A4 antibodies equally showed 100% sensitivity in detecting ALK amplification. However, the sensitivity for detecting copy number gain differed among the three antibodies, with 75% sensitivity in D5F3 and 0% sensitivity in ALK1. ALK-amplified NBs were correlated with synchronous MYCN amplification and chromosome 1p deletion. ALK IHC positivity was frequently observed in INSS stage IV and high-risk group patients. In conclusion, this study identified that an increase in the ALK copy number is a frequent genetic alteration in poorly differentiated NB. ALK-amplified NBs showed consistent ALK IHC positivity with all kinds of antibodies. In contrast, the detection performance of ALK copy number gain was antibody dependent, with the D5F3 antibody showing the best sensitivity.

Association of mitochondrial DNA in peripheral blood with depression, anxiety and stress- and adjustment disorders in primary health care patients.

PubMed

Wang, Xiao; Sundquist, Kristina; Rastkhani, Hamideh; Palmér, Karolina; Memon, Ashfaque A; Sundquist, Jan

2017-08-01

Mitochondrial dysfunction may result in a variety of diseases. The objectives here were to examine possible differences in mtDNA copy number between healthy controls and patients with depression, anxiety or stress- and adjustment disorders; the association between mtDNA copy number and disease severity at baseline; and the association between mtDNA copy number and response after an 8-week treatment (mindfulness, cognitive based therapy). A total of 179 patients in primary health care (age 20-64 years) with depression, anxiety and stress- and adjustment disorders, and 320 healthy controls (aged 19-70 years) were included in the study. Relative mtDNA copy number was measured using quantitative real-time PCR on peripheral blood samples. We found that the mean mtDNA copy number was significantly higher in patients compared to controls (84.9 vs 75.9, p<0.0001) at baseline. The difference in mtDNA copy number between patients and controls remained significant after controlling for age and sex (ß=8.13, p<0.0001; linear regression analysis). The mtDNA copy number was significantly associated with Patient Health Questionnaire (PHQ-9) scores (β=0.57, p=0.02) at baseline. After treatment, the change in mtDNA copy number was significantly associated with the treatment response, i.e., change in Hospital Anxiety and Depression Scale (HADS-D) and PHQ-9 scores (ß=1.00, p=0.03 and ß=0.65, p=0.04, respectively), after controlling for baseline scores, age, sex, BMI, smoking status, alcohol drinking and medication. Our findings show that mtDNA copy number is associated with symptoms of depression, anxiety and stress- and adjustment disorders and treatment response in these disorders. Copyright © 2017 Elsevier B.V. and ECNP. All rights reserved.

Mitochondrial DNA Copy Number in Sleep Duration Discordant Monozygotic Twins.

PubMed

Wrede, Joanna E; Mengel-From, Jonas; Buchwald, Dedra; Vitiello, Michael V; Bamshad, Michael; Noonan, Carolyn; Christiansen, Lene; Christensen, Kaare; Watson, Nathaniel F

2015-10-01

Mitochondrial DNA (mtDNA) copy number is an important component of mitochondrial function and varies with age, disease, and environmental factors. We aimed to determine whether mtDNA copy number varies with habitual differences in sleep duration within pairs of monozygotic twins. Academic clinical research center. 15 sleep duration discordant monozygotic twin pairs (30 twins, 80% female; mean age 42.1 years [SD 15.0]). Sleep duration was phenotyped with wrist actigraphy. Each twin pair included a "normal" (7-9 h/24) and "short" (< 7 h/24) sleeping twin. Fasting peripheral blood leukocyte DNA was assessed for mtDNA copy number via the n-fold difference between qPCR measured mtDNA and nuclear DNA creating an mtDNA measure without absolute units. We used generalized estimating equation linear regression models accounting for the correlated data structure to assess within-pair effects of sleep duration on mtDNA copy number. Mean within-pair sleep duration difference per 24 hours was 94.3 minutes (SD 62.6 min). We found reduced sleep duration (β = 0.06; 95% CI 0.004, 0.12; P < 0.05) and sleep efficiency (β = 0.51; 95% CI 0.06, 0.95; P < 0.05) were significantly associated with reduced mtDNA copy number within twin pairs. Thus every 1-minute decrease in actigraphy-defined sleep duration was associated with a decrease in mtDNA copy number of 0.06. Likewise, a 1% decrease in actigraphy-defined sleep efficiency was associated with a decrease in mtDNA copy number of 0.51. Reduced sleep duration and sleep efficiency were associated with reduced mitochondrial DNA copy number in sleep duration discordant monozygotic twins offering a potential mechanism whereby short sleep impairs health and longevity through mitochondrial stress. © 2015 Associated Professional Sleep Societies, LLC.

DNA replication stress restricts ribosomal DNA copy number.

PubMed

Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

2017-09-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

Pneumocystis jirovecii (Pj) quantitative PCR to differentiate Pj pneumonia from Pj colonization in immunocompromised patients.

PubMed

Maillet, M; Maubon, D; Brion, J P; François, P; Molina, L; Stahl, J P; Epaulard, O; Bosseray, A; Pavese, P

2014-03-01

Conventional polymerase chain reaction (PCR) in respiratory samples does not differentiate between Pneumocystis pneumonia (PCP) and Pneumocystis jirovecii (Pj) colonization. We used Pj real-time quantitative PCR (qPCR) with the objective to discriminate PCP from Pj colonization in immunocompromised patients. All positive Pj qPCR [targeting the major surface glycoprotein (MSG) gene] obtained in respiratory samples from immunocompromised patients presenting pneumonia at the Grenoble University Hospital, France, were collected between August 2009 and April 2011. Diagnoses were retrospectively determined by a multidisciplinary group of experts blinded to the Pj qPCR results. Thirty-one bronchoalveolar lavages and four broncho aspirations positive for the Pj qPCR were obtained from 35 immunocompromised patients. Diagnoses of definite, probable, and possible PCP, and pneumonia from another etiology were retrospectively made for 7, 4, 5, and 19 patients, respectively. Copy numbers were significantly higher in the "definite group" (median 465,000 copies/ml) than in the "probable group" (median 38,600 copies/ml), the "possible group" (median 1,032 copies/ml), and the "other diagnosis group" (median 390 copies/ml). With the value of 3,160 copies/ml, the sensitivity and specificity of qPCR for the diagnosis of PCP were 100 % and 70 %, respectively. With the value of 31,600 copies/ml, the sensitivity and specificity were 80 % and 100 %, respectively. The positive predictive value was 100 % for results with more than 31,600 copies/ml and the negative predictive value was 100 % for results with fewer than 3,160 copies/ml. qPCR targeting the MSG gene can be helpful to discriminate PCP from Pj colonization in immunocompromised patients, using two cut-off values, with a gray zone between them.

The copy of the Essays of Jean Rey, used by Bayen and Gobet, at the BIU Sante, pole Pharmacie.

PubMed

Lafont, Olivier

2016-06-01

The copy of the innovative book written by Jean Rey in 1630, entitied : The Essays on the reasons why the weight of stain and lead increased when they were burnt, which is nowadays kept in the BIU Sante, pole Pharmacie, proved to be the authentic copy which had been used by Pierre Bayer when he rediscovered Jean Rey's Works. It was also the same copy that Gobey used when he real- ized his new edition of the Essays in 1777. This copy first belonged to M. de Villars from La Rochelle, and then was acquired by M. de Villiers, who accepted to lend it to Bayen. The probes for this identification were detailed in the article.

Detection of Copy-Rotate-Move Forgery Using Zernike Moments

NASA Astrophysics Data System (ADS)

Ryu, Seung-Jin; Lee, Min-Jeong; Lee, Heung-Kyu

As forgeries have become popular, the importance of forgery detection is much increased. Copy-move forgery, one of the most commonly used methods, copies a part of the image and pastes it into another part of the the image. In this paper, we propose a detection method of copy-move forgery that localizes duplicated regions using Zernike moments. Since the magnitude of Zernike moments is algebraically invariant against rotation, the proposed method can detect a forged region even though it is rotated. Our scheme is also resilient to the intentional distortions such as additive white Gaussian noise, JPEG compression, and blurring. Experimental results demonstrate that the proposed scheme is appropriate to identify the forged region by copy-rotate-move forgery.

System of and method for transparent management of data objects in containers across distributed heterogenous resources

DOEpatents

Moore, Reagan W.; Rajasekar, Arcot; Wan, Michael Y.

2004-01-13

A system of and method for maintaining data objects in containers across a network of distributed heterogeneous resources in a manner which is transparent to a client. A client request pertaining to containers is resolved by querying meta data for the container, processing the request through one or more copies of the container maintained on the system, updating the meta data for the container to reflect any changes made to the container as a result processing the request, and, if a copy of the container has changed, changing the status of the copy to indicate dirty status or synchronizing the copy to one or more other copies that may be present on the system.

System of and method for transparent management of data objects in containers across distributed heterogenous resources

DOEpatents

Moore, Reagan W [San Diego, CA; Rajasekar, Arcot [Del Mar, CA; Wan, Michael Y [San Diego, CA

2007-09-11

A system of and method for maintaining data objects in containers across a network of distributed heterogeneous resources in a manner which is transparent to a client. A client request pertaining to containers is resolved by querying meta data for the container, processing the request through one or more copies of the container maintained on the system, updating the meta data for the container to reflect any changes made to the container as a result processing the re quest, and, if a copy of the container has changed, changing the status of the copy to indicate dirty status or synchronizing the copy to one or more other copies that may be present on the system.

System of and method for transparent management of data objects in containers across distributed heterogenous resources

DOEpatents

Moore, Reagan W.; Rajasekar, Arcot; Wan, Michael Y.

2010-09-21

A system of and method for maintaining data objects in containers across a network of distributed heterogeneous resources in a manner which is transparent to a client. A client request pertaining to containers is resolved by querying meta data for the container, processing the request through one or more copies of the container maintained on the system, updating the meta data for the container to reflect any changes made to the container as a result processing the request, and, if a copy of the container has changed, changing the status of the copy to indicate dirty status or synchronizing the copy to one or more other copies that may be present on the system.

44. Photographic copy of original construction drawing, dated August 1911 ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

44. Photographic copy of original construction drawing, dated August 1911 (from paper-copy of aperture-card negative at Bureau of Reclamation, Pacific Northwest Regional Office, Boise, ID). PLANS AND SECTIONS OF VAULTS. - Boise Project, Boise Project Office, 214 Broadway, Boise, Ada County, ID

Hacking DNA copy number for circuit engineering.

PubMed

Wu, Feilun; You, Lingchong

2017-07-27

DNA copy number represents an essential parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered. A new study demonstrates how dynamic control of DNA copy number can serve as an effective strategy to program robust oscillations in gene expression circuits.

14 CFR 1206.700 - Schedule of fees.

Code of Federal Regulations, 2013 CFR

2013-01-01

... copies include the time spent in duplicating the documents. For copies of computer disks, still photographs, blueprints, videotapes, engineering drawings, hard copies of aperture cards, etc., the fee... records. Because of the diversity in the types and configurations of computers which may be required in...

14 CFR 1206.700 - Schedule of fees.

Code of Federal Regulations, 2011 CFR

2011-01-01

... copies include the time spent in duplicating the documents. For copies of computer disks, still photographs, blueprints, videotapes, engineering drawings, hard copies of aperture cards, etc., the fee... records. Because of the diversity in the types and configurations of computers which may be required in...

14 CFR 1206.700 - Schedule of fees.

Code of Federal Regulations, 2012 CFR

2012-01-01

... copies include the time spent in duplicating the documents. For copies of computer disks, still photographs, blueprints, videotapes, engineering drawings, hard copies of aperture cards, etc., the fee... records. Because of the diversity in the types and configurations of computers which may be required in...

22 CFR 1413.7 - Transcripts, recordings or minutes of closed meeting; public availability; retention.

Code of Federal Regulations, 2011 CFR

2011-04-01

... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... transcription. (c) The agency shall maintain a complete verbatim copy of the transcript, a complete copy of the...

22 CFR 1413.7 - Transcripts, recordings or minutes of closed meeting; public availability; retention.

Code of Federal Regulations, 2010 CFR

2010-04-01

... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... transcription. (c) The agency shall maintain a complete verbatim copy of the transcript, a complete copy of the...

78 FR 21160 - Paperwork Reduction Act; 30-Day Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-09

... concepts (OMB 3201-0011), pre-broadcast quantitative (or ``copy'') testing of developed advertising (OMB... Research--Focus groups; OMB 3201-0006--Copy testing--15-minute online interviews; OMB 3201-0010--Tracking...--Qualitative Research--Quarterly; OMB 3201-0006--Copy testing--Quarterly; OMB 3201-0010--Tracking Study...

22 CFR 1429.25 - Number of copies.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Number of copies. 1429.25 Section 1429.25 Foreign Relations FOREIGN SERVICE LABOR RELATIONS BOARD; FEDERAL LABOR RELATIONS AUTHORITY; GENERAL... AND GENERAL REQUIREMENTS General Requirements § 1429.25 Number of copies. Unless otherwise provided by...

[Study on analysis of copy paper by Fourier transform infrared spectroscopy].

PubMed

Li, Ji-Min; Wang, Yan-Ji; Wang, Jing-Han; Yao, Li-Juan; Zhang, Biao

2009-06-01

A new method of fast identification of copy papers by Fourier transform infrared spectroscopy (FTIR) was developed. The kinds of filler and the cellulosic degree of crystallinity were analyzed by FTIR, and the ageing curves of cellulosic paper were studied with heating and ultraviolet light. The cellulosic degree of crystallinity was showed by the ratio of absorbance at 1 429 cm(-1) to that at 893 cm(-1), the standard deviation of different brands of copy papers was 0.010 7-0.016 0, and the standard deviation of the same brands of copy papers was 0.014 8. The kinds of filler and the cellulosic degree of crystallinity were different in copy papers from different brands of different manufacturing plants, different brands of same manufacturing plants and different manufacturing times of the same brands from the same manufacturing plants, and the curves of ageing were different with heating and ultraviolet light. The results of fast identification of copy papers by FTIR are satisfactory.

Determining Complementary Properties with Quantum Clones.

PubMed

Thekkadath, G S; Saaltink, R Y; Giner, L; Lundeen, J S

2017-08-04

In a classical world, simultaneous measurements of complementary properties (e.g., position and momentum) give a system's state. In quantum mechanics, measurement-induced disturbance is largest for complementary properties and, hence, limits the precision with which such properties can be determined simultaneously. It is tempting to try to sidestep this disturbance by copying the system and measuring each complementary property on a separate copy. However, perfect copying is physically impossible in quantum mechanics. Here, we investigate using the closest quantum analog to this copying strategy, optimal cloning. The coherent portion of the generated clones' state corresponds to "twins" of the input system. Like perfect copies, both twins faithfully reproduce the properties of the input system. Unlike perfect copies, the twins are entangled. As such, a measurement on both twins is equivalent to a simultaneous measurement on the input system. For complementary observables, this joint measurement gives the system's state, just as in the classical case. We demonstrate this experimentally using polarized single photons.

Determining Complementary Properties with Quantum Clones

NASA Astrophysics Data System (ADS)

Thekkadath, G. S.; Saaltink, R. Y.; Giner, L.; Lundeen, J. S.

2017-08-01

In a classical world, simultaneous measurements of complementary properties (e.g., position and momentum) give a system's state. In quantum mechanics, measurement-induced disturbance is largest for complementary properties and, hence, limits the precision with which such properties can be determined simultaneously. It is tempting to try to sidestep this disturbance by copying the system and measuring each complementary property on a separate copy. However, perfect copying is physically impossible in quantum mechanics. Here, we investigate using the closest quantum analog to this copying strategy, optimal cloning. The coherent portion of the generated clones' state corresponds to "twins" of the input system. Like perfect copies, both twins faithfully reproduce the properties of the input system. Unlike perfect copies, the twins are entangled. As such, a measurement on both twins is equivalent to a simultaneous measurement on the input system. For complementary observables, this joint measurement gives the system's state, just as in the classical case. We demonstrate this experimentally using polarized single photons.

Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny.

PubMed

Urrutia, Eugene; Chen, Hao; Zhou, Zilu; Zhang, Nancy R; Jiang, Yuchao

2018-06-15

Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies. In cancer genomics, detection of somatic copy number changes and profiling of allele-specific copy number (ASCN) are complicated by experimental biases and artifacts as well as normal cell contamination and cancer subclone admixture. Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. Here we describe a flexible computational pipeline, MARATHON, which integrates multiple related statistical software for copy number profiling and downstream analyses in disease genetic studies. MARATHON is publicly available at https://github.com/yuchaojiang/MARATHON. Supplementary data are available at Bioinformatics online.

Social learning strategies.

PubMed

Laland, Kevin N

2004-02-01

In most studies of social learning in animals, no attempt has been made to examine the nature of the strategy adopted by animals when they copy others. Researchers have expended considerable effort in exploring the psychological processes that underlie social learning and amassed extensive data banks recording purported social learning in the field, but the contexts under which animals copy others remain unexplored. Yet, theoretical models used to investigate the adaptive advantages of social learning lead to the conclusion that social learning cannot be indiscriminate and that individuals should adopt strategies that dictate the circumstances under which they copy others and from whom they learn. In this article, I discuss a number of possible strategies that are predicted by theoretical analyses, including copy when uncertain, copy the majority, and copy if better, and consider the empirical evidence in support of each, drawing from both the animal and human social learning literature. Reliance on social learning strategies may be organized hierarchically, their being employed by animals when unlearned and asocially learned strategies prove ineffective but before animals take recourse in innovation.

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer

PubMed Central

Mamlouk, Soulafa; Childs, Liam Harold; Aust, Daniela; Heim, Daniel; Melching, Friederike; Oliveira, Cristiano; Wolf, Thomas; Durek, Pawel; Schumacher, Dirk; Bläker, Hendrik; von Winterfeld, Moritz; Gastl, Bastian; Möhr, Kerstin; Menne, Andrea; Zeugner, Silke; Redmer, Torben; Lenze, Dido; Tierling, Sascha; Möbs, Markus; Weichert, Wilko; Folprecht, Gunnar; Blanc, Eric; Beule, Dieter; Schäfer, Reinhold; Morkel, Markus; Klauschen, Frederick; Leser, Ulf; Sers, Christine

2017-01-01

Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal–distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC. PMID:28120820

TTT and PIKK Complex Genes Reverted to Single Copy Following Polyploidization and Retain Function Despite Massive Retrotransposition in Maize.

PubMed

Garcia, Nelson; Messing, Joachim

2017-01-01

The TEL2, TTI1, and TTI2 proteins are co-chaperones for heat shock protein 90 (HSP90) to regulate the protein folding and maturation of phosphatidylinositol 3-kinase-related kinases (PIKKs). Referred to as the TTT complex, the genes that encode them are highly conserved from man to maize. TTT complex and PIKK genes exist mostly as single copy genes in organisms where they have been characterized. Members of this interacting protein network in maize were identified and synteny analyses were performed to study their evolution. Similar to other species, there is only one copy of each of these genes in maize which was due to a loss of the duplicated copy created by ancient allotetraploidy. Moreover, the retained copies of the TTT complex and the PIKK genes tolerated extensive retrotransposon insertion in their introns that resulted in increased gene lengths and gene body methylation, without apparent effect in normal gene expression and function. The results raise an interesting question on whether the reversion to single copy was due to selection against deleterious unbalanced gene duplications between members of the complex as predicted by the gene balance hypothesis, or due to neutral loss of extra copies. Uneven alteration of dosage either by adding extra copies or modulating gene expression of complex members is being proposed as a means to investigate whether the data supports the gene balance hypothesis or not.

Untrained Chimpanzees (Pan troglodytes schweinfurthii) Fail to Imitate Novel Actions

PubMed Central

Tennie, Claudio; Call, Josep; Tomasello, Michael

2012-01-01

Background Social learning research in apes has focused on social learning in the technical (problem solving) domain - an approach that confounds action and physical information. Successful subjects in such studies may have been able to perform target actions not as a result of imitation learning but because they had learnt some technical aspect, for example, copying the movements of an apparatus (i.e., different forms of emulation learning). Methods Here we present data on action copying by non-enculturated and untrained chimpanzees when physical information is removed from demonstrations. To date, only one such study (on gesture copying in a begging context) has been conducted – with negative results. Here we have improved this methodology and have also added non-begging test situations (a possible confound of the earlier study). Both familiar and novel actions were used as targets. Prior to testing, a trained conspecific demonstrator was rewarded for performing target actions in view of observers. All but one of the tested chimpanzees already failed to copy familiar actions. When retested with a novel target action, also the previously successful subject failed to copy – and he did so across several contexts. Conclusion Chimpanzees do not seem to copy novel actions, and only some ever copy familiar ones. Due to our having tested only non-enculturated and untrained chimpanzees, the performance of our test subjects speak more than most other studies of the general (dis-)ability of chimpanzees to copy actions, and especially novel actions. PMID:22905102

A spatial haplotype copying model with applications to genotype imputation.

PubMed

Yang, Wen-Yun; Hormozdiari, Farhad; Eskin, Eleazar; Pasaniuc, Bogdan

2015-05-01

Ever since its introduction, the haplotype copy model has proven to be one of the most successful approaches for modeling genetic variation in human populations, with applications ranging from ancestry inference to genotype phasing and imputation. Motivated by coalescent theory, this approach assumes that any chromosome (haplotype) can be modeled as a mosaic of segments copied from a set of chromosomes sampled from the same population. At the core of the model is the assumption that any chromosome from the sample is equally likely to contribute a priori to the copying process. Motivated by recent works that model genetic variation in a geographic continuum, we propose a new spatial-aware haplotype copy model that jointly models geography and the haplotype copying process. We extend hidden Markov models of haplotype diversity such that at any given location, haplotypes that are closest in the genetic-geographic continuum map are a priori more likely to contribute to the copying process than distant ones. Through simulations starting from the 1000 Genomes data, we show that our model achieves superior accuracy in genotype imputation over the standard spatial-unaware haplotype copy model. In addition, we show the utility of our model in selecting a small personalized reference panel for imputation that leads to both improved accuracy as well as to a lower computational runtime than the standard approach. Finally, we show our proposed model can be used to localize individuals on the genetic-geographical map on the basis of their genotype data.

4 CFR 28.56 - Hearing procedures, conduct and copies of exhibits.

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Accurate measure of transgene copy number in crop plants using droplet digital PCR

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Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy numb...

37. Photographic copy of the original construction drawing, 1934, by ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

37. Photographic copy of the original construction drawing, 1934, by Sverdrup and Parcel, Consulting Engineers, from microfilm copy at Bridge Division, Missouri Highway and Transportation Department. Stress sheet, continuous span - Mark Twain Memorial Bridge, Spanning Mississippi River at US Route 36, Hannibal, Marion County, MO

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10 CFR 34.81 - Copies of operating and emergency procedures.

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14 CFR 221.92 - Number of copies required.

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75 FR 78265 - Notice of Submission of Proposed Information Collection to OMB HUD Conditional Commitment/Direct...

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46 CFR Sec. 5 - Responsibility for duplicating copies of NSA-WORKSMALREP Contract.

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75 FR 32341 - Import Administration IA ACCESS Pilot Program

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