PERLE. Powerful energy recovery linac for experiments. Conceptual design report

NASA Astrophysics Data System (ADS)

Angal-Kalinin, D.; Arduini, G.; Auchmann, B.; Bernauer, J.; Bogacz, A.; Bordry, F.; Bousson, S.; Bracco, C.; Brüning, O.; Calaga, R.; Cassou, K.; Chetvertkova, V.; Cormier, E.; Daly, E.; Douglas, D.; Dupraz, K.; Goddard, B.; Henry, J.; Hutton, A.; Jensen, E.; Kaabi, W.; Klein, M.; Kostka, P.; Lasheras, N.; Levichev, E.; Marhauser, F.; Martens, A.; Milanese, A.; Militsyn, B.; Peinaud, Y.; Pellegrini, D.; Pietralla, N.; Pupkov, Y.; Rimmer, R.; Schirm, K.; Schulte, D.; Smith, S.; Stocchi, A.; Valloni, A.; Welsch, C.; Willering, G.; Wollmann, D.; Zimmermann, F.; Zomer, F.

2018-06-01

A conceptual design is presented of a novel energy-recovering linac (ERL) facility for the development and application of the energy recovery technique to linear electron accelerators in the multi-turn, large current and large energy regime. The main characteristics of the powerful energy recovery linac experiment facility (PERLE) are derived from the design of the Large Hadron electron Collider, an electron beam upgrade under study for the LHC, for which it would be the key demonstrator. PERLE is thus projected as a facility to investigate efficient, high current (HC) (>10 mA) ERL operation with three re-circulation passages through newly designed SCRF cavities, at 801.58 MHz frequency, and following deceleration over another three re-circulations. In its fully equipped configuration, PERLE provides an electron beam of approximately 1 GeV energy. A physics programme possibly associated with PERLE is sketched, consisting of high precision elastic electron–proton scattering experiments, as well as photo-nuclear reactions of unprecedented intensities with up to 30 MeV photon beam energy as may be obtained using Fabry–Perot cavities. The facility has further applications as a general technology test bed that can investigate and validate novel superconducting magnets (beam induced quench tests) and superconducting RF structures (structure tests with HC beams, beam loading and transients). Besides a chapter on operation aspects, the report contains detailed considerations on the choices for the SCRF structure, optics and lattice design, solutions for arc magnets, source and injector and on further essential components. A suitable configuration derived from the here presented design concept may next be moved forward to a technical design and possibly be built by an international collaboration which is being established.

Counselors' Evaluation of Rogers-Perls-Ellis's Relationship Skills

ERIC Educational Resources Information Center

Woodward, Wallace S.; And Others

1975-01-01

Participants (12 employment counselors and 10 counselor supervisors) attending a three-week workshop on enhancing relationship skills, evaluated the Rogers, Perls, Ellis film, Three Approaches to Psychotherapy, on 15 skills. Results indicate there was general agreement between the counselors and the supervisors when judging levels of therapist…

PeRL: a circum-Arctic Permafrost Region Pond and Lake database

NASA Astrophysics Data System (ADS)

Muster, Sina; Roth, Kurt; Langer, Moritz; Lange, Stephan; Cresto Aleina, Fabio; Bartsch, Annett; Morgenstern, Anne; Grosse, Guido; Jones, Benjamin; Sannel, A. Britta K.; Sjöberg, Ylva; Günther, Frank; Andresen, Christian; Veremeeva, Alexandra; Lindgren, Prajna R.; Bouchard, Frédéric; Lara, Mark J.; Fortier, Daniel; Charbonneau, Simon; Virtanen, Tarmo A.; Hugelius, Gustaf; Palmtag, Juri; Siewert, Matthias B.; Riley, William J.; Koven, Charles D.; Boike, Julia

2017-06-01

Ponds and lakes are abundant in Arctic permafrost lowlands. They play an important role in Arctic wetland ecosystems by regulating carbon, water, and energy fluxes and providing freshwater habitats. However, ponds, i.e., waterbodies with surface areas smaller than 1. 0 × 104 m2, have not been inventoried on global and regional scales. The Permafrost Region Pond and Lake (PeRL) database presents the results of a circum-Arctic effort to map ponds and lakes from modern (2002-2013) high-resolution aerial and satellite imagery with a resolution of 5 m or better. The database also includes historical imagery from 1948 to 1965 with a resolution of 6 m or better. PeRL includes 69 maps covering a wide range of environmental conditions from tundra to boreal regions and from continuous to discontinuous permafrost zones. Waterbody maps are linked to regional permafrost landscape maps which provide information on permafrost extent, ground ice volume, geology, and lithology. This paper describes waterbody classification and accuracy, and presents statistics of waterbody distribution for each site. Maps of permafrost landscapes in Alaska, Canada, and Russia are used to extrapolate waterbody statistics from the site level to regional landscape units. PeRL presents pond and lake estimates for a total area of 1. 4 × 106 km2 across the Arctic, about 17 % of the Arctic lowland ( < 300 m a.s.l.) land surface area. PeRL waterbodies with sizes of 1. 0 × 106 m2 down to 1. 0 × 102 m2 contributed up to 21 % to the total water fraction. Waterbody density ranged from 1. 0 × 10 to 9. 4 × 101 km-2. Ponds are the dominant waterbody type by number in all landscapes representing 45-99 % of the total waterbody number. The implementation of PeRL size distributions in land surface models will greatly improve the investigation and projection of surface inundation and carbon fluxes in permafrost lowlands. Waterbody maps, study area boundaries, and maps of regional permafrost landscapes including

A Taxonomic Approach to the Gestalt Theory of Perls

ERIC Educational Resources Information Center

Raming, Henry E.; Frey, David H.

1974-01-01

This study applied content analysis and cluster analysis to the ideas of Fritz Perls to develop a taxonomy of Gestalt processes and goals. Summaries of the typal groups or clusters were written and the implications of taxonomic research in counseling discussed. (Author)

Study of different thermal processes on boron-doped PERL cells

NASA Astrophysics Data System (ADS)

Li, Wenjia; Wang, Zhenjiao; Han, Peiyu; Lu, Hongyan; Yang, Jian; Guo, Ying; Shi, Zhengrong; Li, Guohua

2014-08-01

In this paper, three kinds of thermal processes for boron-doped PERL cells were investigated. These are the forming gas annealing (FGA), the rapid thermal (RTP) and the low temperature annealing processes. FGA was introduced after laser ablation and doping in order to increase minority carrier lifetime by hydrogenating the trapping centers. Subsequent evaluation revealed considerable enhancement of minority carrier lifetime (from 150 μs to 240 μs) and the implied Voc (from 660 mV to 675 mV). After aluminum sputtering, three actual peak temperatures (370 °C, 600 °C and 810 °C) of RTP (as it occurs in the compressed air environment used in our experiment) were utilized to form a contact between the metal and the semi-conductor. It is concluded that only low temperature (lower than 600 °C) firing could create boron back surface field and high quality rear reflector. Lastly, a method of improving the performance of finished PERL cells which did not experience high temperature (over 800 °C) firing was investigated. Finished cells undergone low temperature annealing in N2 atmosphere at 150 °C for 15 min produced 0.44% absolute increase in PERL cells. The enhancement of low temperature annealing originally comes from the activation of passivated boron which is deactivated during FGA.

PeRL: A circum-Arctic Permafrost Region Pond and Lake database

USGS Publications Warehouse

Muster, Sina; Roth, Kurt; Langer, Moritz; Lange, Stephan; Cresto Aleina, Fabio; Bartsch, Annett; Morgenstern, Anne; Grosse, Guido; Jones, Benjamin M.; Sannel, A.B.K.; Sjoberg, Ylva; Gunther, Frank; Andresen, Christian; Veremeeva, Alexandra; Lindgren, Prajna R.; Bouchard, Frédéric; Lara, Mark J.; Fortier, Daniel; Charbonneau, Simon; Virtanen, Tarmo A.; Hugelius, Gustaf; Palmtag, J.; Siewert, Matthias B.; Riley, William J.; Koven, Charles; Boike, Julia

2017-01-01

Ponds and lakes are abundant in Arctic permafrost lowlands. They play an important role in Arctic wetland ecosystems by regulating carbon, water, and energy fluxes and providing freshwater habitats. However, ponds, i.e., waterbodies with surface areas smaller than 1. 0 × 104 m2, have not been inventoried on global and regional scales. The Permafrost Region Pond and Lake (PeRL) database presents the results of a circum-Arctic effort to map ponds and lakes from modern (2002–2013) high-resolution aerial and satellite imagery with a resolution of 5 m or better. The database also includes historical imagery from 1948 to 1965 with a resolution of 6 m or better. PeRL includes 69 maps covering a wide range of environmental conditions from tundra to boreal regions and from continuous to discontinuous permafrost zones. Waterbody maps are linked to regional permafrost landscape maps which provide information on permafrost extent, ground ice volume, geology, and lithology. This paper describes waterbody classification and accuracy, and presents statistics of waterbody distribution for each site. Maps of permafrost landscapes in Alaska, Canada, and Russia are used to extrapolate waterbody statistics from the site level to regional landscape units. PeRL presents pond and lake estimates for a total area of 1. 4 × 106 km2 across the Arctic, about 17 % of the Arctic lowland ( <  300 m a.s.l.) land surface area. PeRL waterbodies with sizes of 1. 0 × 106 m2 down to 1. 0 × 102 m2 contributed up to 21 % to the total water fraction. Waterbody density ranged from 1. 0 × 10 to 9. 4 × 101 km−2. Ponds are the dominant waterbody type by number in all landscapes representing 45–99 % of the total waterbody number. The implementation of PeRL size distributions in land surface models will greatly improve the investigation and projection of surface inundation and carbon fluxes in permafrost lowlands. Waterbody maps

PACCE: Perl Algorithm to Compute Continuum and Equivalent Widths

NASA Astrophysics Data System (ADS)

Riffel, Rogério; Borges Vale, Tibério

2011-05-01

PACCE (Perl Algorithm to Compute continuum and Equivalent Widths) computes continuum and equivalent widths. PACCE is able to determine mean continuum and continuum at line center values, which are helpful in stellar population studies, and is also able to compute the uncertainties in the equivalent widths using photon statistics.

BioC implementations in Go, Perl, Python and Ruby

PubMed Central

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W. John; Comeau, Donald C.

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ PMID:24961236

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines.

PubMed

Hernández, Yözen; Bernstein, Rocky; Pagan, Pedro; Vargas, Levy; McCaig, William; Ramrattan, Girish; Akther, Saymon; Larracuente, Amanda; Di, Lia; Vieira, Filipe G; Qiu, Wei-Gang

2018-03-02

Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl ( http://bioperl.org ) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users. Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of the most popular BioPerl modules readily accessible on the command line to novice as well as to experienced bioinformatics practitioners. The initial release of BpWrapper includes four utilities with concise command-line user interfaces, bioseq, bioaln, biotree, and biopop, specialized for manipulation of molecular sequences, sequence alignments, phylogenetic trees, and DNA polymorphisms, respectively. Over a hundred methods are currently available as command-line options and new methods are easily incorporated. Performance of BpWrapper utilities lags that of precompiled utilities while equivalent to that of other utilities based on BioPerl. BpWrapper has been tested on BioPerl Release 1.6, Perl versions 5.10.1 to 5.25.10, and operating systems including Apple macOS, Microsoft Windows, and GNU/Linux. Release code is available from the Comprehensive Perl Archive Network (CPAN) at https://metacpan.org/pod/Bio::BPWrapper . Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper . BpWrapper improves on existing sequence utilities by following the design principles of Unix text utilities such including a concise user interface, extensive command-line options, and standard input/output for serialized operations. Further, dozens of novel methods for

PeRL: a circum-Arctic Permafrost Region Pond and Lake database

DOE PAGES

Muster, Sina; Roth, Kurt; Langer, Moritz; ...

2017-06-06

Ponds and lakes are abundant in Arctic permafrost lowlands. They play an important role in Arctic wetland ecosystems by regulating carbon, water, and energy fluxes and providing freshwater habitats. However, ponds, i.e., waterbodies with surface areas smaller than 1.0 × 10 4 m 2, have not been inventoried on global and regional scales. The Permafrost Region Pond and Lake (PeRL) database presents the results of a circum-Arctic effort to map ponds and lakes from modern (2002–2013) high-resolution aerial and satellite imagery with a resolution of 5 m or better. The database also includes historical imagery from 1948 to 1965 withmore » a resolution of 6 m or better. PeRL includes 69 maps covering a wide range of environmental conditions from tundra to boreal regions and from continuous to discontinuous permafrost zones. Waterbody maps are linked to regional permafrost landscape maps which provide information on permafrost extent, ground ice volume, geology, and lithology. This paper describes waterbody classification and accuracy, and presents statistics of waterbody distribution for each site. Maps of permafrost landscapes in Alaska, Canada, and Russia are used to extrapolate waterbody statistics from the site level to regional landscape units. PeRL presents pond and lake estimates for a total area of 1.4 × 10 6 km 2 across the Arctic, about 17 % of the Arctic lowland ( < 300 m a.s.l.) land surface area. PeRL waterbodies with sizes of 1.0 ×10 6 m 2 down to 1.0 ×10 2 m 2 contributed up to 21 % to the total water fraction. Waterbody density ranged from 1.0 ×10 to 9.4 × 10 1 km –2. Ponds are the dominant waterbody type by number in all landscapes representing 45–99 % of the total waterbody number. In conclusion, the implementation of PeRL size distributions in land surface models will greatly improve the investigation and projection of surface inundation and carbon fluxes in permafrost lowlands.« less

PeRL: a circum-Arctic Permafrost Region Pond and Lake database

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

Muster, Sina; Roth, Kurt; Langer, Moritz

Ponds and lakes are abundant in Arctic permafrost lowlands. They play an important role in Arctic wetland ecosystems by regulating carbon, water, and energy fluxes and providing freshwater habitats. However, ponds, i.e., waterbodies with surface areas smaller than 1.0 × 10 4 m 2, have not been inventoried on global and regional scales. The Permafrost Region Pond and Lake (PeRL) database presents the results of a circum-Arctic effort to map ponds and lakes from modern (2002–2013) high-resolution aerial and satellite imagery with a resolution of 5 m or better. The database also includes historical imagery from 1948 to 1965 withmore » a resolution of 6 m or better. PeRL includes 69 maps covering a wide range of environmental conditions from tundra to boreal regions and from continuous to discontinuous permafrost zones. Waterbody maps are linked to regional permafrost landscape maps which provide information on permafrost extent, ground ice volume, geology, and lithology. This paper describes waterbody classification and accuracy, and presents statistics of waterbody distribution for each site. Maps of permafrost landscapes in Alaska, Canada, and Russia are used to extrapolate waterbody statistics from the site level to regional landscape units. PeRL presents pond and lake estimates for a total area of 1.4 × 10 6 km 2 across the Arctic, about 17 % of the Arctic lowland ( < 300 m a.s.l.) land surface area. PeRL waterbodies with sizes of 1.0 ×10 6 m 2 down to 1.0 ×10 2 m 2 contributed up to 21 % to the total water fraction. Waterbody density ranged from 1.0 ×10 to 9.4 × 10 1 km –2. Ponds are the dominant waterbody type by number in all landscapes representing 45–99 % of the total waterbody number. In conclusion, the implementation of PeRL size distributions in land surface models will greatly improve the investigation and projection of surface inundation and carbon fluxes in permafrost lowlands.« less

BioC implementations in Go, Perl, Python and Ruby.

PubMed

Liu, Wanli; Islamaj Doğan, Rezarta; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W John; Comeau, Donald C

2014-01-01

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/ Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Values in Fritz Perls's Gestalt Therapy: On the Dangers of Half-Truths.

ERIC Educational Resources Information Center

Cadwallader, Eva H.

1984-01-01

Examines some of the values in Perls's theory of psychotherapy, which his Gestalt Prayer epitomizes. Argues that at least five of the major value claims presupposed by his psychotherapeutic theory and practice are in fact dangerous half-truths. (JAC)

UPIC: Perl scripts to determine the number of SSR markers to run

USDA-ARS?s Scientific Manuscript database

We have developed Perl Scripts for the cost-effective planning of fingerprinting and genotyping experiments. The UPIC scripts detect the best combination of polymorphic simple sequence repeat (SSR) markers and provide coefficients of the amount of information obtainable (number of alleles of patter...

Earth Observations taken by Expedition 38 crewmember

NASA Image and Video Library

2014-01-28

ISS038-E-036501 (28 Jan. 2014) --- This wide field-of-view image photographed by an Expedition 38 crew member on the International Space Station shows an east-west swath of the southwestern Indian Ocean. Two remote islands, part of the French Southern and Antarctic Lands, appear in the center of the image. Possession Island (right center) and East Island (center) are both only 18 kilometers long. A smaller island, Ile aux Cochons (Pigs Island), lies 100 kilometers to the west. Each island has set up V-shaped trains of waves, like bow waves, as the air flows over the islands from the west (right to left). The bow-wave patterns are overlaid on the low regional stratus (blanket) cloud that is so common in the southern Indian Ocean at 50 degrees south latitude. This view was taken from more than 400 kilometers above the sea surface and reveals relationships that could not be readily understood by someone standing on one of the islands. For example, larger and higher islands produce larger waves. So the largest are being generated by Possession Island (934 meters above sea level at the highest point), and East Island, versus much smaller waves developed downwind of the tiny Ile de Pingouins (340 meters above sea level high, invisible below the cloud deck). Other patterns also can be detected. Waves in an upper layer can be seen casting shadows onto a lower layer (lower left). In the top half of the image the waves are making thicker and thinner zones in the clouds of the lower layer. Wave trains from Possession Island and Ile aux Cochons are interacting in a cross-hatch pattern (center).

Good Moments in Gestalt Therapy: A Descriptive Analysis of Two Perls Sessions.

ERIC Educational Resources Information Center

Boulet, Donald; And Others

1993-01-01

Analyzed two Gestalt therapy sessions conducted by Fritz Perls using category system for identifying in-session client behaviors valued by Gestalt therapists. Four judges independently rated 210 client statements. Found common pattern of therapeutic movement: initial phase dominated by building block good moments and second phase characterized by…

22.7% efficient PERL silicon solar cell module with a textured front surface

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

Zhao, J.; Wang, A.; Campbell, P.

1997-12-31

This paper describes a solar cell module efficiency of 22.7% independently measured at Sandia National Laboratories. This is the highest ever confirmed efficiency for a photovoltaic module of this size achieved by cells made from any material. This 778-cm{sup 2} module used 40 large-area double layer antireflection coated PERL (passivated emitter, rear locally-diffused) silicon cells of average efficiency of 23.1%. A textured front module surface considerably improve the module efficiency. Also reported is an independently confirmed efficiency of 23.7% for a 21.6 cm{sup 2} cell of the type used in the module. Using these PERL cells in the 1996 Worldmore » Solar Challenge solar car race from Darwin to Adelaide across Australia, Honda`s Dream and Aisin Seiki`s Aisol III were placed first and third, respectively. Honda also set a new record by reaching Adelaide in four days with an average speed of 90km/h over the 3010 km course.« less

AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis

USDA-ARS?s Scientific Manuscript database

A useful biological interpretation of diploid heterozygotes is in terms of the dose of the common allele (0, 1 or 2 copies). We have developed a PERL script that converts FASTA files into coded spreadsheets suitable for Principal Component Analysis (PCA). In combination with R and R Commander, two- ...

Thermoreception and Nociception of the Skin: A Classic Paper of Bessou and Perl and Analyses of Thermal Sensitivity during a Student Laboratory Exercise

ERIC Educational Resources Information Center

Kuhtz-Buschbeck, Johann P.; Andresen, Wiebke; Gobel, Stephan; Gilster, Rene; Stick, Carsten

2010-01-01

About four decades ago, Perl and collaborators were the first ones who unambiguously identified specifically nociceptive neurons in the periphery. In their classic work, they recorded action potentials from single C-fibers of a cutaneous nerve in cats while applying carefully graded stimuli to the skin (Bessou P, Perl ER. Response of cutaneous…

Comparison of Rogers, Perls, and Ellis on the Hill Counselor Verbal Response Category System.

ERIC Educational Resources Information Center

Hill, Clara E.; And Others

1979-01-01

Analyzes transcripts of films of Rogers, Perls, and Ellis counseling the same client, according to the Hill Counselor Verbal Response Category System. The system described verbal behaviors of the three counselors and detected behavioral differences reflective of their differing theoretical orientations. (Author)

Using Perls Staining to Trace the Iron Uptake Pathway in Leaves of a Prunus Rootstock Treated with Iron Foliar Fertilizers

PubMed Central

Rios, Juan J.; Carrasco-Gil, Sandra; Abadía, Anunciación; Abadía, Javier

2016-01-01

The aim of this study was to trace the Fe uptake pathway in leaves of Prunus rootstock (GF 677; Prunus dulcis × Prunus persica) plants treated with foliar Fe compounds using the Perls blue method, which detects labile Fe pools. Young expanded leaves of Fe-deficient plants grown in nutrient solution were treated with Fe-compounds using a brush. Iron compounds used were the ferrous salt FeSO4, the ferric salts Fe2(SO4)3 and FeCl3, and the chelate Fe(III)-EDTA, all of them at concentrations of 9 mM Fe. Leaf Fe concentration increases were measured at 30, 60, 90 min, and 24 h, and 70 μm-thick leaf transversal sections were obtained with a vibrating microtome and stained with Perls blue. In vitro results show that the Perls blue method is a good tool to trace the Fe uptake pathway in leaves when using Fe salts, but is not sensitive enough when using synthetic Fe(III)-chelates such as Fe(III)-EDTA and Fe(III)-IDHA. Foliar Fe fertilization increased leaf Fe concentrations with all Fe compounds used, with inorganic Fe salts causing larger leaf Fe concentration increases than Fe(III)-EDTA. Results show that Perls blue stain appeared within 30 min in the stomatal areas, indicating that Fe applied as inorganic salts was taken up rapidly via stomata. In the case of using FeSO4 a progression of the stain was seen with time toward vascular areas in the leaf blade and the central vein, whereas in the case of Fe(III) salts the stain mainly remained in the stomatal areas. Perls stain was never observed in the mesophyll areas, possibly due to the low concentration of labile Fe pools. PMID:27446123

The Evaluation of Filmed Excerpts of Rogers, Perls, and Ellis by Beginning Counselor Trainees

ERIC Educational Resources Information Center

Kelly, F. Donald; Byrne, Thomas P.

1977-01-01

Students (N=29) viewed three stimulus films and rated therapeutic effectiveness of the therapists. Students were subsequently rank-ordered on the basis of skill development and assigned to one of three groups (high, middle, or low.) Results revealed an overall higher evaluation for Rogers as compared to either Perls or Ellis. (Author)

SCTE: An open-source Perl framework for testing equipment control and data acquisition

NASA Astrophysics Data System (ADS)

Mostaço-Guidolin, Luiz C.; Frigori, Rafael B.; Ruchko, Leonid; Galvão, Ricardo M. O.

2012-07-01

SCTE intends to provide a simple, yet powerful, framework for building data acquisition and equipment control systems for experimental Physics, and correlated areas. Via its SCTE::Instrument module, RS-232, USB, and LAN buses are supported, and the intricacies of hardware communication are encapsulated underneath an object oriented abstraction layer. Written in Perl, and using the SCPI protocol, enabled instruments can be easily programmed to perform a wide variety of tasks. While this work presents general aspects of the development of data acquisition systems using the SCTE framework, it is illustrated by particular applications designed for the calibration of several in-house developed devices for power measurement in the tokamak TCABR Alfvén Waves Excitement System. Catalogue identifier: AELZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AELZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License Version 3 No. of lines in distributed program, including test data, etc.: 13 811 No. of bytes in distributed program, including test data, etc.: 743 709 Distribution format: tar.gz Programming language: Perl version 5.10.0 or higher. Computer: PC. SCPI capable digital oscilloscope, with RS-232, USB, or LAN communication ports, null modem, USB, or Ethernet cables Operating system: GNU/Linux (2.6.28-11), should also work on any Unix-based operational system Classification: 4.14 External routines: Perl modules: Device::SerialPort, Term::ANSIColor, Math::GSL, Net::HTTP. Gnuplot 4.0 or higher Nature of problem: Automation of experiments and data acquisition often requires expensive equipment and in-house development of software applications. Nowadays personal computers and test equipment come with fast and easy-to-use communication ports. Instrument vendors often supply application programs capable of controlling such devices, but are very restricted in terms of

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Transition to a Unified System: Using Perl To Drive Library Databases and Enhance Web Site Functionality.

ERIC Educational Resources Information Center

Fagan, Judy Condit

2001-01-01

Discusses the need for libraries to routinely redesign their Web sites, and presents a case study that describes how a Perl-driven database at Southern Illinois University's library improved Web site organization and patron access, simplified revisions, and allowed staff unfamiliar with HTML to update content. (Contains 56 references.) (Author/LRW)

Learning SAS’s Perl Regular Expression Matching the Easy Way: By Doing

DTIC Science & Technology

2015-01-12

Doing 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Paul Genovesi 5d. PROJECT NUMBER 5e. TASK NUMBER 5f...regex_learning_tool allows both beginner and expert to efficiently practice PRX matching by selecting and processing only the match records that the user is interested...perl regular expression and/or source string. The regex_learning_tool allows both beginner and expert to efficiently practice PRX matching by

Uric acid lowering to prevent kidney function loss in diabetes: the preventing early renal function loss (PERL) allopurinol study.

PubMed

Maahs, David M; Caramori, Luiza; Cherney, David Z I; Galecki, Andrzej T; Gao, Chuanyun; Jalal, Diana; Perkins, Bruce A; Pop-Busui, Rodica; Rossing, Peter; Mauer, Michael; Doria, Alessandro

2013-08-01

Diabetic kidney disease causes significant morbidity and mortality among people with type 1 diabetes (T1D). Intensive glucose and blood pressure control have thus far failed to adequately curb this problem and therefore a major need for novel treatment approaches exists. Multiple observations link serum uric acid levels to kidney disease development and progression in diabetes and strongly argue that uric acid lowering should be tested as one such novel intervention. A pilot of such a trial, using allopurinol, is currently being conducted by the Preventing Early Renal Function Loss (PERL) Consortium. Although the PERL trial targets T1D individuals at highest risk of kidney function decline, the use of allopurinol as a renoprotective agent may also be relevant to a larger segment of the population with diabetes. As allopurinol is inexpensive and safe, it could be cost-effective even for relatively low-risk patients, pending the completion of appropriate trials at earlier stages.

pacce: Perl algorithm to compute continuum and equivalent widths

NASA Astrophysics Data System (ADS)

Riffel, Rogério; Borges Vale, Tibério

2011-08-01

We present Perl Algorithm to Compute continuum and Equivalent Widths ( pacce). We describe the methods used in the computations and the requirements for its usage. We compare the measurements made with pacce and "manual" ones made using iraf splot task. These tests show that for synthetic simple stellar population (SSP) models the equivalent widths strengths are very similar (differences ≲0.2 Å) for both measurements. In real stellar spectra, the correlation between both values is still very good, but with differences of up to 0.5 Å. pacce is also able to determine mean continuum and continuum at line center values, which are helpful in stellar population studies. In addition, it is also able to compute the uncertainties in the equivalent widths using photon statistics. The code is made available for the community through the web at http://www.if.ufrgs.br/~riffel/software.html .

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

PubMed

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

2016-02-01

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

L'Anse Aux Meadows, Newfoundland

NASA Technical Reports Server (NTRS)

2008-01-01

L'Anse aux Meadows is a site on the northernmost tip of the island of Newfoundland, located in the Province of Newfoundland and Labrador, Canada, where the remains of a Viking village were discovered in 1960 by the Norwegians Helge and Anne Ingstad. The only authenticated Viking settlement in North America outside Greenland, it was the site of a multi-year archaeological dig that found dwellings, tools and implements that verified its time frame. The settlement, dating more than five hundred years before Christopher Columbus, contains the earliest European structures in North America. Named a World Heritage site by UNESCO, it is thought by many to be the semi-legendary 'Vinland' settlement of explorer Leif Ericson around AD 1000. The settlement at L'Anse aux Meadows consisted of at least eight buildings, including a forge and smelter, and a lumber yard that supported a shipyard. The largest house measured 28.8 by 15.6 m and consisted of several rooms. Sewing and knitting tools found at the site indicate women were present at L'Anse aux Meadows

The image was acquired on September 14, 2007, covers an area of 14.2 x 14.6 km, and is located at 51.5 degrees north latitude, 55.6 degrees west longitude.

The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

Solar-energy-system-performance evaluation: Perl-Mack Enterprises, Inc. , single-family residence, Denver, Colorado, April 1978-March 1979

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

Walker, R.V.

1979-01-01

The Perl-Mack Enterprises, Inc. site is a single-family dwelling whose solar heating system is designed to provide approximately 68% of the annual space heating and hot water requirements. The system consists of an array of flat plate collectors using a water-propylene glycol solution, a concrete water storage tank, and an auxiliary gas burner. The system is described, and its performance is analyzed using a system energy balance technique. (LEW)

OsAUX1 controls lateral root initiation in rice (Oryza sativa L.).

PubMed

Zhao, Heming; Ma, Tengfei; Wang, Xin; Deng, Yingtian; Ma, Haoli; Zhang, Rongsheng; Zhao, Jie

2015-11-01

Polar auxin transport, mediated by influx and efflux transporters, controls many aspects of plant growth and development. The auxin influx carriers in Arabidopsis have been shown to control lateral root development and gravitropism, but little is known about these proteins in rice. This paper reports on the functional characterization of OsAUX1. Three OsAUX1 T-DNA insertion mutants and RNAi knockdown transgenic plants reduced lateral root initiation compared with wild-type (WT) plants. OsAUX1 overexpression plants exhibited increased lateral root initiation and OsAUX1 was highly expressed in lateral roots and lateral root primordia. Similarly, the auxin reporter, DR5-GUS, was expressed at lower levels in osaux1 than in the WT plants, which indicated that the auxin levels in the mutant roots had decreased. Exogenous 1-naphthylacetic acid (NAA) treatment rescued the defective phenotype in osaux1-1 plants, whereas indole-3-acetic acid (IAA) and 2,4-D could not, which suggested that OsAUX1 was a putative auxin influx carrier. The transcript levels of several auxin signalling genes and cell cycle genes significantly declined in osaux1, hinting that the regulatory role of OsAUX1 may be mediated by auxin signalling and cell cycle genes. Overall, our results indicated that OsAUX1 was involved in polar auxin transport and functioned to control auxin-mediated lateral root initiation in rice. © 2014 John Wiley & Sons Ltd.

AUX: a scripting language for auditory signal processing and software packages for psychoacoustic experiments and education.

PubMed

Kwon, Bomjun J

2012-06-01

This article introduces AUX (AUditory syntaX), a scripting syntax specifically designed to describe auditory signals and processing, to the members of the behavioral research community. The syntax is based on descriptive function names and intuitive operators suitable for researchers and students without substantial training in programming, who wish to generate and examine sound signals using a written script. In this article, the essence of AUX is discussed and practical examples of AUX scripts specifying various signals are illustrated. Additionally, two accompanying Windows-based programs and development libraries are described. AUX Viewer is a program that generates, visualizes, and plays sounds specified in AUX. AUX Viewer can also be used for class demonstrations or presentations. Another program, Psycon, allows a wide range of sound signals to be used as stimuli in common psychophysical testing paradigms, such as the adaptive procedure, the method of constant stimuli, and the method of adjustment. AUX Library is also provided, so that researchers can develop their own programs utilizing AUX. The philosophical basis of AUX is to separate signal generation from the user interface needed for experiments. AUX scripts are portable and reusable; they can be shared by other researchers, regardless of differences in actual AUX-based programs, and reused for future experiments. In short, the use of AUX can be potentially beneficial to all members of the research community-both those with programming backgrounds and those without.

Sequence stratigraphy of the Aux Vases Sandstone: A major oil producer in the Illinois basin

USGS Publications Warehouse

Leetaru, H.E.

2000-01-01

The Aux Vases Sandstone (Mississippian) has contributed between 10 and 25% of all the oil produced in Illinois. The Aux Vases is not only an important oil reservoir but is also an important source of groundwater, quarrying stone, and fluorspar. Using sequence stratigraphy, a more accurate stratigraphic interpretation of this economically important formation can be discerned and thereby enable more effective exploration for the resources contained therein. Previous studies have assumed that the underlying Spar Mountain, Karnak, and Joppa formations interfingered with the Aux Vases, as did the overlying Renault Limestone. This study demonstrates that these formations instead are separated by sequence boundaries; therefore, they are not genetically related to each other. A result of this sequence stratigraphic approach is the identification of incised valleys, paleotopography, and potential new hydrocarbon reservoirs in the Spar Mountain and Aux Vases. In eastern Illinois, the Aux Vases is bounded by sequence boundaries with 20 ft (6 m) of relief. The Aux Vases oil reservoir facies was deposited as a tidally influenced siliciclastic wedge that prograded over underlying carbonate-rich sediments. The Aux Vases sedimentary succession consists of offshore sediment overlain by intertidal and supratidal sediments. Low-permeability shales and carbonates typically surround the Aux Vases reservoir sandstone and thereby form numerous bypassed compartments from which additional oil can be recovered. The potential for new significant oil fields within the Aux Vases is great, as is the potential for undrained reservoir compartments within existing Aux Vases fields.

Les soins aux enfants et aux adolescents des familles des militaires canadiens : les considérations particulières

PubMed Central

Rowan-Legg, Anne

2017-01-01

Résumé Les familles des militaires font face à de nombreux facteurs de stress, tels que les réinstallations fréquentes, les longues pério des de séparation familiale, l’isolement géographique du réseau de soutien de la famille élargie et le déploiement en zones très dangereuses. Les enfants et les adolescents des familles des militaires vivent les mêmes trajectoires développementales et motivationnelles que leurs homologues civils, mais ils sont également aux prises avec des pressions et des facteurs de stress liés à leur développement qui sont inhabituels et qui leur sont imposés par les exigences de la vie militaire. Les effets de la vie militaire sur les familles et les enfants commencent à être admis et mieux caractérisés. Il est essentiel de comprendre les préoccupations propres aux enfants et aux adolescents des familles des militaires et de mobiliser les ressources nécessaires pour les soutenir afin de répondre à leurs besoins en matière de santé.

Perl One-Liners: Bridging the Gap Between Large Data Sets and Analysis Tools.

PubMed

Hokamp, Karsten

2015-01-01

Computational analyses of biological data are becoming increasingly powerful, and researchers intending on carrying out their own analyses can often choose from a wide array of tools and resources. However, their application might be obstructed by the wide variety of different data formats that are in use, from standard, commonly used formats to output files from high-throughput analysis platforms. The latter are often too large to be opened, viewed, or edited by standard programs, potentially leading to a bottleneck in the analysis. Perl one-liners provide a simple solution to quickly reformat, filter, and merge data sets in preparation for downstream analyses. This chapter presents example code that can be easily adjusted to meet individual requirements. An online version is available at http://bioinf.gen.tcd.ie/pol.

Martin L. Perl (1927-2014): A Biographical Memoir

NASA Astrophysics Data System (ADS)

Feldman, Gary; Jaros, John; Schindler, Rafe H.

2017-10-01

Particle physicist Martin Lewis Perl was recognized worldwide for his discovery of the τ (tau) lepton. For that achievement he received the 1982 Wolf Prize and shared the 1995 Nobel Prize in Physics. He was also a Fellow of the American Physical Society and a member of the National Academy of Sciences (elected 1981). Martin's distinctive approach to scientific investigation had its origins in his upbringing and in the influence of I. I. Rabi, his graduate advisor at Columbia University. After coming to Stanford University in 1963, Martin sought to understand why there should be two and only two families of leptons: the electron and its associated neutrino; and the muon and the muon neutrino. His discovery of the τ provided evidence for a third family of fundamental leptons. The bottom quark was discovered shortly afterward at the Fermi National Accelerator Laboratory, providing evidence for a third family of quarks. Direct evidence for the τ neutrino came later, thereby completing the third lepton generation, while the discovery of the top quark in 1995 completed the third generation of quarks. These achievements established leptons and quarks as fundamental constituents of matter and, along with the fundamental forces, provided the experimental basis of the "Standard Model," our picture of how all matter is made up and how its components interact. Why there are three and only three families of leptons and quarks remains an unsolved mystery to this day.

Structural basis for the auxin-induced transcriptional regulation by Aux/IAA17.

PubMed

Han, Mookyoung; Park, Yangshin; Kim, Iktae; Kim, Eun-Hee; Yu, Tae-Kyung; Rhee, Sangkee; Suh, Jeong-Yong

2014-12-30

Auxin is the central hormone that regulates plant growth and organ development. Transcriptional regulation by auxin is mediated by the auxin response factor (ARF) and the repressor, AUX/IAA. Aux/IAA associates with ARF via domain III-IV for transcriptional repression that is reversed by auxin-induced Aux/IAA degradation. It has been known that Aux/IAA and ARF form homo- and hetero-oligomers for the transcriptional regulation, but what determines their association states is poorly understood. Here we report, to our knowledge, the first solution structure of domain III-IV of Aux/IAA17 (IAA17), and characterize molecular interactions underlying the homotypic and heterotypic oligomerization. The structure exhibits a compact β-grasp fold with a highly dynamic insert helix that is unique in Aux/IAA family proteins. IAA17 associates to form a heterogeneous ensemble of front-to-back oligomers in a concentration-dependent manner. IAA17 and ARF5 associate to form homo- or hetero-oligomers using a common scaffold and binding interfaces, but their affinities vary significantly. The equilibrium dissociation constants (KD) for homo-oligomerization are 6.6 μM and 0.87 μM for IAA17 and ARF5, respectively, whereas hetero-oligomerization reveals a ∼ 10- to ∼ 100-fold greater affinity (KD = 73 nM). Thus, individual homo-oligomers of IAA17 and ARF5 spontaneously exchange their subunits to form alternating hetero-oligomers for transcriptional repression. Oligomerization is mainly driven by electrostatic interactions, so that charge complementarity at the interface determines the binding affinity. Variable binding affinity by surface charge modulation may effectively regulate the complex interaction network between Aux/IAA and ARF family proteins required for the transcriptional control of auxin-response genes.

Adding EUNIS and VAULT rocket data to the VSO with Modern Perl frameworks

NASA Astrophysics Data System (ADS)

Mansky, Edmund

2017-08-01

A new Perl code is described, that uses the modern Object-oriented Moose framework, to add EUNIS and VAULT rocket data to the Virtual Solar Observatory website. The code permits the easy fixing of FITS header fields in the case where some FITS fields that are required are missing from the original data files. The code makes novel use of the Moose extensions “before” and “after” to build in dependencies so that database creation of tables occurs before the loading of data, and that the validation of file-dependent tables occurs after the loading is completed. Also described is the computation and loading of the deferred FITS field CHECKSUM into the database following the loading and validation of the file-dependent tables. The loading of the EUNIS 2006 and 2007 flight data, and the VAULT 2.0 flight data is described in detail as illustrative examples.

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales.

PubMed

Riccardi, Demian; Parks, Jerry M; Johs, Alexander; Smith, Jeremy C

2015-04-27

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. The core is well-tested, well-documented, and easy to install across computational platforms. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

Interdire aux enfants et aux adolescents de moins de 18 ans l’accès aux établissements commerciaux de bronzage

PubMed Central

Taddeo, Danielle; Stanwick, Richard

2012-01-01

RÉSUMÉ Le nombre de mélanomes cutanés malins a plus que triplé depuis 35 ans. Puisque les dommages sont cumulatifs, l’exposition aux rayonnements ultraviolets tôt dans la vie accroît le risque, qui augmente davantage avec l’utilisation de sources artificielles de rayonnements ultraviolets. Il peut falloir des années pour évaluer les répercussions et l’étendue complètes des dommages causés par le bronzage artificiel à longueur d’année, compte tenu de la longue période de latence de la plupart des cancers de la peau. Les adolescents fréquentent souvent les salons de bronzage, les filles s’y rendant davantage et de manière soutenue. L’industrie du bronzage conteste la classification de cancérigène physique de groupe 1 qu’attribuent au bronzage artificiel l’Organisation mondiale de la santé et le Centre international de recherche sur le cancer. Les salons de bronzage cherchent à établir et à maintenir une clientèle chez les adolescents. Par conséquent, la Société canadienne de pédiatrie s’ajoute à d’autres organismes de santé réputés pour appuyer l’interdiction des établissements commerciaux de bronzage aux enfants et adolescents de moins de 18 ans.

Evidence supporting an intentional Neandertal burial at La Chapelle-aux-Saints.

PubMed

Rendu, William; Beauval, Cédric; Crevecoeur, Isabelle; Bayle, Priscilla; Balzeau, Antoine; Bismuth, Thierry; Bourguignon, Laurence; Delfour, Géraldine; Faivre, Jean-Philippe; Lacrampe-Cuyaubère, François; Tavormina, Carlotta; Todisco, Dominique; Turq, Alain; Maureille, Bruno

2014-01-07

The bouffia Bonneval at La Chapelle-aux-Saints is well known for the discovery of the first secure Neandertal burial in the early 20th century. However, the intentionality of the burial remains an issue of some debate. Here, we present the results of a 12-y fieldwork project, along with a taphonomic analysis of the human remains, designed to assess the funerary context of the La Chapelle-aux-Saints Neandertal. We have established the anthropogenic nature of the burial pit and underlined the taphonomic evidence of a rapid burial of the body. These multiple lines of evidence support the hypothesis of an intentional burial. Finally, the discovery of skeletal elements belonging to the original La Chapelle aux Saints 1 individual, two additional young individuals, and a second adult in the bouffia Bonneval highlights a more complex site-formation history than previously proposed.

Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals.

PubMed

Wu, Wentao; Liu, Yaxue; Wang, Yuqian; Li, Huimin; Liu, Jiaxi; Tan, Jiaxin; He, Jiadai; Bai, Jingwen; Ma, Haoli

2017-10-08

The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three ( Physcomitrella patens ) to 63 ( Glycine max ). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.

Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals

PubMed Central

Wu, Wentao; Liu, Yaxue; Wang, Yuqian; Li, Huimin; Liu, Jiaxi; Tan, Jiaxin; He, Jiadai; Bai, Jingwen

2017-01-01

The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution. PMID:28991190

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

DOE PAGES

Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander; ...

2015-03-20

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, anmore » abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.« less

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

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

Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, anmore » abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.« less

AUX1 regulates root gravitropism in Arabidopsis by facilitating auxin uptake within root apical tissues.

PubMed Central

Marchant, A; Kargul, J; May, S T; Muller, P; Delbarre, A; Perrot-Rechenmann, C; Bennett, M J

1999-01-01

Plants employ a specialized transport system composed of separate influx and efflux carriers to mobilize the plant hormone auxin between its site(s) of synthesis and action. Mutations within the permease-like AUX1 protein significantly reduce the rate of carrier-mediated auxin uptake within Arabidopsis roots, conferring an agravitropic phenotype. We are able to bypass the defect within auxin uptake and restore the gravitropic root phenotype of aux1 by growing mutant seedlings in the presence of the membrane-permeable synthetic auxin, 1-naphthaleneacetic acid. We illustrate that AUX1 expression overlaps that previously described for the auxin efflux carrier, AtPIN2, using transgenic lines expressing an AUX1 promoter::uidA (GUS) gene. Finally, we demonstrate that AUX1 regulates gravitropic curvature by acting in unison with the auxin efflux carrier to co-ordinate the localized redistribution of auxin within the Arabidopsis root apex. Our results provide the first example of a developmental role for the auxin influx carrier within higher plants and supply new insight into the molecular basis of gravitropic signalling. PMID:10205161

Possible quantum valence criticality in CeCu6-xAux

NASA Astrophysics Data System (ADS)

Shiino, Takayuki; Nobe, Kohei; Imura, Keiichiro; Deguchi, Kazuhiko; Sato, Noriaki K.

2018-05-01

CeCu6-xAux is known as a heavy fermion compound that exhibits antiferromagnetism for x ≳ 0 . 1 and non-Fermi-liquid (NFL) behavior around the critical concentration xc ≈ 0 . 1. Although this material has been studied by means of a lot of experiments, the origin of its NFL is still veiled in mystery. In this study, we examine the magnetic properties of CeCu6-xAux for various values of x (0 ≤ x ≤ 0.8), and discuss the possibility that the quantum valence criticality might be responsible for the low-temperature magnetic properties.

Solar project description for Perl-Mack Enterprises' single family residences, Denver, Colorado

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

Not Available

1979-08-21

The Perl-Mack Enterprises Co. solar energy system(s) are installed in a total of 25 single family dwellings located in Denver, Colorado. The 25 dwellings are of three different configurations. Two of the twenty-five dwellings have been fully instrumented for performance monitoring and evaluation since September 1977. All the solar systems are designed to provide approximately 69 percent of the space heating and energy requirements for each dwelling. Solar energy is collected by an array of flat plate collectors having a gross area of 470 square feet. A water-glycol mixture is used as the medium for delivering solar heat from themore » collection to the storage tank. The storage tank has a total capacity of 945 gallons. A liquid-to-liquid heat exchanger, within the storage tank, transfers the stored heat from the transfer medium to the domestic hot water tank of the house. Space heating demands are met by circulating heated water/glycol mixture from the storage tank through the heat exchanger coil installed downstream from the auxiliary furnace blower. The auxiliary gas-fired furnace is activated whenever room thermostat demands heat.« less

MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites.

PubMed

Olarerin-George, Anthony O; Jaffrey, Samie R

2017-05-15

An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots. The code and associated tutorial are available at https://github.com/olarerin/metaPlotR . srj2003@med.cornell.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Identification and Analyses of AUX-IAA target genes controlling multiple pathways in developing fiber cells of Gossypium hirsutum L

PubMed Central

Nigam, Deepti; Sawant, Samir V

2013-01-01

Technological development led to an increased interest in systems biological approaches in plants to characterize developmental mechanism and candidate genes relevant to specific tissue or cell morphology. AUX-IAA proteins are important plant-specific putative transcription factors. There are several reports on physiological response of this family in Arabidopsis but in cotton fiber the transcriptional network through which AUX-IAA regulated its target genes is still unknown. in-silico modelling of cotton fiber development specific gene expression data (108 microarrays and 22,737 genes) using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) reveals 3690 putative AUX-IAA target genes of which 139 genes were known to be AUX-IAA co-regulated within Arabidopsis. Further AUX-IAA targeted gene regulatory network (GRN) had substantial impact on the transcriptional dynamics of cotton fiber, as showed by, altered TF networks, and Gene Ontology (GO) biological processes and metabolic pathway associated with its target genes. Analysis of the AUX-IAA-correlated gene network reveals multiple functions for AUX-IAA target genes such as unidimensional cell growth, cellular nitrogen compound metabolic process, nucleosome organization, DNA-protein complex and process related to cell wall. These candidate networks/pathways have a variety of profound impacts on such cellular functions as stress response, cell proliferation, and cell differentiation. While these functions are fairly broad, their underlying TF networks may provide a global view of AUX-IAA regulated gene expression and a GRN that guides future studies in understanding role of AUX-IAA box protein and its targets regulating fiber development. PMID:24497725

Ti1-xAux Alloys: Hard Biocompatible Metals and Their Possible Applications

NASA Astrophysics Data System (ADS)

Svanidze, Eteri; Besara, Tiglet; Ozaydin, M. Fevzi; Xin, Yan; Han, Ke; Liang, Hong; Siegrist, Theo; Morosan, Emilia

2015-03-01

The search for new hard materials is often challenging from both theoretical and experimental points of view. Furthermore, using materials for biomedical applications calls for alloys with high biocompatibility which are even more sparse. The Ti1-xAux (0 . 22 <= x <= 0 . 8) exhibit extreme hardness and strength values, elevated melting temperatures (compared to those of constituent elements), reduced density compared to Au, high malleability, bulk metallicity, high biocompatibility, low wear, reduced friction, potentially high radio opacity, as well as osseointegration. All these properties render the Ti1-xAux alloys particularly useful for orthopedic, dental, and prosthetic applications, where they could be used as both permanent and temporary components. Additionally, the ability of Ti1-xAux alloys to adhere to ceramic parts could reduce the weight and cost of these components. The work at Rice was supported by NSF DMR 0847681 (E.M. and E.S.).

Pastoral Group Counselling at a High Security Prison in Israel: Integrating Pierre Janet's Psychological Analysis with Fritz Perls' Gestalt Therapy.

PubMed

Brown, Paul; Brown, Marta

2015-03-01

This is a report of a short-term, pastoral counselling group conducted with Jewish internees in a high security prison in Israel. It was held as an adjunct to daily secular individual and group counselling and rehabilitation run by the Department of Social Work. Pastoral counselling employed spiritual and psychosocial methodologies to reduce anger, improve prisoner frustration tolerance, and develop a sense of self-efficacy and communal identity. It combined semi-didactic scriptural input with Pierre Janet's personality model, Fritz Perls' gestalt therapy, and analysis of the group process. © The Author(s) 2015 Reprints and permissions:sagepub.co.uk/journalsPermissions.nav.

The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A.

PubMed

Xie, Rangjin; Pang, Shaoping; Ma, Yanyan; Deng, Lie; He, Shaolan; Yi, Shilai; Lv, Qiang; Zheng, Yongqiang

2015-12-01

Completion of the whole genome sequencing of citrus enabled us to perform genome-wide identification and functional analysis of the gene families involved in agronomic traits and morphological diversity of citrus. In this study, 22 CitARF, 11 CitGH3 and 26 CitAUX/IAA genes were identified in citrus, respectively. Phylogenetic analysis revealed that all the genes of each gene family could be subdivided into three groups and showed strong evolutionary conservation. The GH3 and AUX/IAA gene families shrank and ARF gene family was highly conserved in the citrus genome after speciation from Arabidopsis thaliana. Tissue-specific expression profiles revealed that 54 genes were expressed in at least one tissue while just 5 genes including CitARF07, CitARF20, CitGH3.04, CitAUX/IAA25 and CitAUX/IAA26 with very low expression level in all tissues tested, suggesting that the CitARF, CitGH3 and CitAUX/IAA gene families played important roles in the development of citrus organs. In addition, our data found that the expression of 2 CitARF, 4 CitGH3 and 4 AUX/IAA genes was affected by IAA treatment, and 7 genes including, CitGH3.04, CitGH3.07, CitAUX/IAA03, CitAUX/IAA04, CitAUX/IAA18, CitAUX/IAA19 and CitAUX/IAA23 were related to fruitlet abscission. This study provides a foundation for future studies on elucidating the precise role of citrus ARF, GH3 and AUX/IAA genes in early steps of auxin signal transduction and open up a new opportunity to uncover the molecular mechanism underlying citrus fruitlet abscission.

Disruptions in AUX1-dependent auxin influx alter hypocotyl phototropism in Arabidopsis.

PubMed

Stone, Bethany B; Stowe-Evans, Emily L; Harper, Reneé M; Celaya, R Brandon; Ljung, Karin; Sandberg, Göran; Liscum, Emmanuel

2008-01-01

Phototropism represents a differential growth response by which plant organs can respond adaptively to changes in the direction of incident light to optimize leaf/stem positioning for photosynthetic light capture and root growth orientation for water/nutrient acquisition. Studies over the past few years have identified a number of components in the signaling pathway(s) leading to development of phototropic curvatures in hypocotyls. These include the phototropin photoreceptors (phot1 and phot2) that perceive directional blue-light (BL) cues and then stimulate signaling, leading to relocalization of the plant hormone auxin, as well as the auxin response factor NPH4/ARF7 that responds to changes in local auxin concentrations to directly mediate expression of genes likely encoding proteins necessary for development of phototropic curvatures. While null mutations in NPH4/ARF7 condition an aphototropic response to unidirectional BL, seedlings carrying the same mutations recover BL-dependent phototropic responsiveness if co-irradiated with red light (RL) or pre-treated with either ethylene. In the present study, we identify second-site enhancer mutations in the nph4 background that abrogate these recovery responses. One of these mutations--map1 (modifier of arf7 phenotypes 1)--was found to represent a missense allele of AUX1--a gene encoding a high-affinity auxin influx carrier previously associated with a number of root responses. Pharmacological studies and analyses of additional aux1 mutants confirmed that AUX1 functions as a modulator of hypocotyl phototropism. Moreover, we have found that the strength of dependence of hypocotyl phototropism on AUX1-mediated auxin influx is directly related to the auxin responsiveness of the seedling in question.

Maladies reliées aux loisirs aquatiques

PubMed Central

Sanborn, Margaret; Takaro, Tim

2013-01-01

Résumé Objectif Passer en revue les facteurs de risque, la prise en charge et la prévention des maladies reliées aux loisirs aquatiques en pratique familiale. Sources des données Des articles originaux et de synthèse entre janvier 1998 et février 2012 ont été identifiés à l’aide de PubMed et des expressions de recherche en anglais water-related illness, recreational water illness et swimmer illness. Message principal Il y a un risque de 3 % à 8 % de maladies gastrointestinales (MGI) après la baignade. Les groupes à risque élevé de MGI sont les enfants de moins de 5 ans, surtout s’ils n’ont pas été vaccinés contre le rotavirus, les personnes âgées et les patients immunodéficients. Les enfants sont à plus grand risque parce qu’ils avalent plus d’eau quand ils nagent, restent dans l’eau plus longtemps et jouent dans l’eau peu profonde et le sable qui sont plus contaminés. Les adeptes des sports dans lesquels le contact avec l’eau est abondant comme le triathlon et le surf cerf-volant sont aussi à risque élevé et même ceux qui s’adonnent à des activités impliquant un contact partiel avec l’eau comme la navigation de plaisance et la pêche ont un risque de 40 % à 50 % fois plus grand de MGI par rapport à ceux qui ne pratiquent pas de sports aquatiques. Il y a lieu de faire une culture des selles quand on soupçonne une maladie reliée aux loisirs aquatiques et l’échelle clinique de la déshydratation est utile pour l’évaluation des besoins de traitement chez les enfants affectés. Conclusion Les maladies reliées aux loisirs aquatiques est la principale cause de MGI durant la saison des baignades. La reconnaissance que la baignade est une source importante de maladies peut aider à prévenir les cas récurrents et secondaires. On recommande fortement le vaccin contre le rotavirus chez les enfants qui se baignent souvent.

The aux1 gene of the Ri plasmid is sufficient to confer auxin autotrophy in tobacco BY-2 cells.

PubMed

Nemoto, Keiichirou; Hara, Masamitsu; Goto, Shingo; Kasai, Kouji; Seki, Hikaru; Suzuki, Masashi; Oka, Atsuhiro; Muranaka, Toshiya; Mano, Yoshihiro

2009-05-01

Tobacco (Nicotiana tabacum) Bright Yellow-2 (BY-2) cells are rapidly proliferating meristematic cells that require auxin for culture in vitro. We have established several transgenic BY-2 cell lines that carry the T-DNA of Agrobacterium rhizogenes 15834, which harbors an agropine-type root-inducing (Ri) plasmid. Two of these lines, BYHR-3 and BYHR-7, were used to test the role of auxin in the proliferation of plant cells. The lines grew rapidly in Linsmaier-Skoog (LS) medium lacking auxin and other phytohormones. The TR-DNA, containing the aux1 (tryptophan monooxygenase) and aux2 (indoleacetamide hydrolase) genes, was present in the genomes of both transgenic lines, whereas the TL-DNA, containing the rolA, B, C and D genes, was present in the genome of BYHR-7 but not BYHR-3. Since the introduction of the rolABCD genes alone did not affect the auxin requirement of BY-2 cells, the aux1 and aux2 genes, but not the rolABCD genes, appear to be relevant to the auxin autotrophy of these transgenic lines. Furthermore, the overexpression of aux1 allowed BY-2 cells to grow rapidly in the absence of auxin, suggesting the existence in plant cells of an unidentified gene whose product is functionally equivalent or similar to that of aux2 of the Ri plasmid.

Thermoreception and nociception of the skin: a classic paper of Bessou and Perl and analyses of thermal sensitivity during a student laboratory exercise.

PubMed

Kuhtz-Buschbeck, Johann P; Andresen, Wiebke; Göbel, Stephan; Gilster, René; Stick, Carsten

2010-06-01

About four decades ago, Perl and collaborators were the first ones who unambiguously identified specifically nociceptive neurons in the periphery. In their classic work, they recorded action potentials from single C-fibers of a cutaneous nerve in cats while applying carefully graded stimuli to the skin (Bessou P, Perl ER. Response of cutaneous sensory units with unmyelinated fibers to noxious stimuli. J Neurophysiol 32: 1025-1043, 1969). They discovered polymodal nociceptors, which responded to mechanical, thermal, and chemical stimuli in the noxious range, and differentiated them from low-threshold thermoreceptors. Their classic findings form the basis of the present method that undergraduate medical students experience during laboratory exercises of sensory physiology, namely, quantitative testing of the thermal detection and pain thresholds. This diagnostic method examines the function of thin afferent nerve fibers. We collected data from nearly 300 students that showed that 1) women are more sensitive to thermal detection and thermal pain at the thenar than men, 2) habituation shifts thermal pain thresholds during repetititve testing, 3) the cold pain threshold is rather variable and lower when tested after heat pain than in the reverse case (order effect), and 4) ratings of pain intensity on a visual analog scale are correlated with the threshold temperature for heat pain but not for cold pain. Median group results could be reproduced in a retest. Quantitative sensory testing of thermal thresholds is feasible and instructive in the setting of a laboratory exercise and is appreciated by the students as a relevant and interesting technique.

Pathology and the posture of the La Chapelle-aux-Saints Neandertal.

PubMed

Trinkaus, E

1985-05-01

The depiction of the Neandertals as incompletely erect was based primarily on Boule's (1911, 1912a, 1913) analysis of the La Chapelle-aux-Saints 1 partial skeleton. The inaccurate aspects of Boule's postural reconstruction were corrected during the 1950s. However, it has come to be believed, following Straus and Cave (1957), that Boule's errors of reconstruction were due to the diseased condition of the La Chapelle-aux-Saints 1 remains, rather than to Boule's misinterpretation of morphology. The abnormalities on the La Chapelle-aux-Saints 1 postcranium include: lower cervical, upper thoracic, and lower thoracic intervertebral degenerative joint disease (DJD), a distal fracture of a mid-thoracic rib, extensive DJD of the left hip, DJD of the right fifth proximal interphalangeal articulation, bilateral humeral head eburnation, and minor exostosis formation on the right humerus, ulna, and radius. These were associated with extensive alveolar inflammation including apical abscesses and antemortem tooth loss, some temporomandibular DJD, bilateral auditory exostoses, and minimal occipital condyle DJD. None of these abnormalities significantly affected Boule's Neandertal postural reconstruction, and a review of his analysis indicates that early twentieth century interpretations of skeletal morphology (primarily of the cranium, cervical vertebrae, lumbar and sacral vertebrae, proximal femora and tibiae, posterior tarsals, and hallucial tarsometatarsal joint), combined with Boule's evolutionary preconceptions, were responsible for his mistaken view of Neandertal posture.

First-principles study of the structural and elastic properties of AuxV1-x and AuxNb1-x alloys

NASA Astrophysics Data System (ADS)

Al-Zoubi, N.

2018-04-01

Ab initio total energy calculations, based on the Exact Muffin-Tin Orbitals (EMTO) method in combination with the coherent potential approximation (CPA), are used to calculate the total energy of AuxV1-x and AuxNb1-x random alloys along the Bain path that connects the body-centred cubic (bcc) and face-centred cubic (fcc) structures as a function of composition x (0 ≤ x ≤ 1). The equilibrium Wigner-Seitz radius and the elastic properties of both systems are determined as a function of composition. Our theoretical prediction in case of pure elements (x = 0 or x = 1) are in good agreement with the available experimental data. For the Au-V system, the equilibrium Wigner-Seitz radius increase as x increases, while for the Au-Nb system, the equilibrium Wigner-Seitz radius is almost constant. The bulk modulus B and C44 for both alloys exhibit nearly parabolic trend. On the other hand, the tetragonal shear elastic constant C‧ decreases as x increases and correlates reasonably well with the structural energy difference between fcc and bcc structures. Our results offer a consistent starting point for further theoretical and experimental studies of the elastic and micromechanical properties of Au-V and Au-Nb systems.

Molecular adsorption properties of CO and H2O on Au-, Cu-, and AuxCuy-doped MoS2 monolayer

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Gökoğlu, Gökhan; Üzengi Aktürk, Olcay

2017-12-01

In this study, we investigate the adsorption properties of Au, Cu, and AuxCuy nanoclusters on MoS2 sheet and the interactions of the adsorbed systems with CO and H2O molecules by using first principles calculations. Results indicate that Au, Cu, or AuxCuy strongly binds to MoS2 monolayer resulting in enhanced chemical activity and sensitivity toward CO and H2O molecules compared to bare MoS2 monolayer. Although both CO and H2O molecules bind weakly to pristine MoS2 monolayer, CO strongly binds to MoS2 sheet in the presence of Au, Cu atoms or AuxCuy clusters. Semiconductor MoS2 monolayer turns into metal upon Au or Cu adsorption. AuxCuy nanocluster adsorption decreases the band gap of MoS2 monolayer acting as a n-type dopant. AuxCuy-doped MoS2 systems have improved adsorption properties for CO and H2O molecules, so the conclusions provided in this study can be useful as a guide for next generation device modeling.

Identification of ARF and AUX/IAA gene families in Rafflesia cantleyi

NASA Astrophysics Data System (ADS)

Elias, Nur Atiqah Mohd; Goh, Hoe-Han; Isa, Nurulhikma Md; Wan, Kiew-Lian

2016-11-01

Rafflesia is a unique plant that produces the largest flowers in the world. It has a short blooming period of 6 to 7 days. Due to its rarity and limited accessibility, little is known about the growth and developmental process in the Rafflesia plant. In all plant species, auxin is the key hormone that is involved in growth and development. The auxin signal transduction involves members of the ARF transcription factor and AUX/IAA regulator families, which activate or inhibit the regulation of auxin response genes, thereby control the developmental process in plants. To gain a better understanding of molecular regulations in the Rafflesia plant development during flowering, members of the ARF and AUX/IAA gene families were identified from the transcriptome data of flower blooming stages in Rafflesia cantleyi. Based on Rafflesia unique transcripts (UTs) against the Arabidopsis TAIR database using BLASTX search, a total of nine UTs were identified as ARF transcription factors, while another seven UTs were identified as AUX/IAA regulators. These genes were found to be expressed in all three R. cantleyi flower stages i.e. days 1 (F1), 3 (F2), and 5 (F3). Gene expression analysis identified three genes that are differentially expressed in stage F1 vs. F2 i.e. IAA4 is upregulated while IAA8 and ARF3 are downregulated. These genes may be involved in the activation and/or inhibition of the auxin signal transduction pathway. Further analysis of these genes may unravel their function in the phenotypic development of the Rafflesia plant.

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees.

PubMed

Sauvage, Thomas; Plouviez, Sophie; Schmidt, William E; Fredericq, Suzanne

2018-03-05

The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.

Accounting Data to Web Interface Using PERL

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

Hargeaves, C

2001-08-13

This document will explain the process to create a web interface for the accounting information generated by the High Performance Storage Systems (HPSS) accounting report feature. The accounting report contains useful data but it is not easily accessed in a meaningful way. The accounting report is the only way to see summarized storage usage information. The first step is to take the accounting data, make it meaningful and store the modified data in persistent databases. The second step is to generate the various user interfaces, HTML pages, that will be used to access the data. The third step is tomore » transfer all required files to the web server. The web pages pass parameters to Common Gateway Interface (CGI) scripts that generate dynamic web pages and graphs. The end result is a web page with specific information presented in text with or without graphs. The accounting report has a specific format that allows the use of regular expressions to verify if a line is storage data. Each storage data line is stored in a detailed database file with a name that includes the run date. The detailed database is used to create a summarized database file that also uses run date in its name. The summarized database is used to create the group.html web page that includes a list of all storage users. Scripts that query the database folder to build a list of available databases generate two additional web pages. A master script that is run monthly as part of a cron job, after the accounting report has completed, manages all of these individual scripts. All scripts are written in the PERL programming language. Whenever possible data manipulation scripts are written as filters. All scripts are written to be single source, which means they will function properly on both the open and closed networks at LLNL. The master script handles the command line inputs for all scripts, file transfers to the web server and records run information in a log file. The rest of the scripts

Genome-wide analysis and characterization of Aux/IAA family genes related to fruit ripening in papaya (Carica papaya L.).

PubMed

Liu, Kaidong; Yuan, Changchun; Feng, Shaoxian; Zhong, Shuting; Li, Haili; Zhong, Jundi; Shen, Chenjia; Liu, Jinxiang

2017-05-05

Auxin/indole-3-acetic acid (Aux/IAA) family genes encode short-lived nuclear proteins that mediate the responses of auxin-related genes and are involved in several plant developmental and growth processes. However, how Aux/IAA genes function in the fruit development and ripening of papaya (Carica papaya L.) is largely unknown. In this study, a comprehensive identification and a distinctive expression analysis of 18 C. papaya Aux/IAA (CpIAA) genes were performed using newly updated papaya reference genome data. The Aux/IAA gene family in papaya is slightly smaller than that in Arabidopsis, but all of the phylogenetic subfamilies are represented. Most of the CpIAA genes are responsive to various phytohormones and expressed in a tissues-specific manner. To understand the putative biological functions of the CpIAA genes involved in fruit development and ripening, quantitative real-time PCR was used to test the expression profiling of CpIAA genes at different stages. Furthermore, an IAA treatment significantly delayed the ripening process in papaya fruit at the early stages. The expression changes of CpIAA genes in ACC and 1-MCP treatments suggested a crosstalk between auxin and ethylene during the fruit ripening process of papaya. Our study provided comprehensive information on the Aux/IAA family in papaya, including gene structures, phylogenetic relationships and expression profiles. The involvement of CpIAA gene expression changes in fruit development and ripening gives us an opportunity to understand the roles of auxin signaling in the maturation of papaya reproductive organs.

Genome-wide survey of Aux/IAA gene family members in potato (Solanum tuberosum): Identification, expression analysis, and evaluation of their roles in tuber development.

PubMed

Gao, Junpeng; Cao, Xiaoli; Shi, Shandang; Ma, Yuling; Wang, Kai; Liu, Shengjie; Chen, Dan; Chen, Qin; Ma, Haoli

2016-03-04

The Auxin/indole-3-acetic acid (Aux/IAA) genes encode short-lived nuclear proteins that are known to be involved in the primary cellular responses to auxin. To date, systematic analysis of the Aux/IAA genes in potato (Solanum tuberosum) has not been conducted. In this study, a total of 26 potato Aux/IAA genes were identified (designated from StIAA1 to StIAA26), and the distribution of four conserved domains shared by the StIAAs were analyzed based on multiple sequence alignment and a motif-based sequence analysis. A phylogenetic analysis of the Aux/IAA gene families of potato and Arabidopsis was also conducted. In order to assess the roles of StIAA genes in tuber development, the results of RNA-seq studies were reformatted to analyze the expression patterns of StIAA genes, and then verified by quantitative real-time PCR. A large number of StIAA genes (12 genes) were highly expressed in stolon organs and in during the tuber initiation and expansion developmental stages, and most of these genes were responsive to indoleacetic acid treatment. Our results suggested that StIAA genes were involved in the process of tuber development and provided insights into functional roles of potato Aux/IAA genes. Copyright © 2016 Elsevier Inc. All rights reserved.

Localized Iron Supply Triggers Lateral Root Elongation in Arabidopsis by Altering the AUX1-Mediated Auxin Distribution[C][W][OA

PubMed Central

Giehl, Ricardo F.H.; Lima, Joni E.; von Wirén, Nicolaus

2012-01-01

Root system architecture depends on nutrient availability, which shapes primary and lateral root development in a nutrient-specific manner. To better understand how nutrient signals are integrated into root developmental programs, we investigated the morphological response of Arabidopsis thaliana roots to iron (Fe). Relative to a homogeneous supply, localized Fe supply in horizontally separated agar plates doubled lateral root length without having a differential effect on lateral root number. In the Fe uptake-defective mutant iron-regulated transporter1 (irt1), lateral root development was severely repressed, but a requirement for IRT1 could be circumvented by Fe application to shoots, indicating that symplastic Fe triggered the local elongation of lateral roots. The Fe-stimulated emergence of lateral root primordia and root cell elongation depended on the rootward auxin stream and was accompanied by a higher activity of the auxin reporter DR5-β-glucuronidase in lateral root apices. A crucial role of the auxin transporter AUXIN RESISTANT1 (AUX1) in Fe-triggered lateral root elongation was indicated by Fe-responsive AUX1 promoter activities in lateral root apices and by the failure of the aux1-T mutant to elongate lateral roots into Fe-enriched agar patches. We conclude that a local symplastic Fe gradient in lateral roots upregulates AUX1 to accumulate auxin in lateral root apices as a prerequisite for lateral root elongation. PMID:22234997

Arabidopsis SHR and SCR transcription factors and AUX1 auxin influx carrier control the switch between adventitious rooting and xylogenesis in planta and in in vitro cultured thin cell layers.

PubMed

Della Rovere, F; Fattorini, L; D'Angeli, S; Veloccia, A; Del Duca, S; Cai, G; Falasca, G; Altamura, M M

2015-03-01

Adventitious roots (ARs) are essential for vegetative propagation. The Arabidopsis thaliana transcription factors SHORT ROOT (SHR) and SCARECROW (SCR) affect primary/lateral root development, but their involvement in AR formation is uncertain. LAX3 and AUX1 auxin influx carriers contribute to primary/lateral root development. LAX3 expression is regulated by SHR, and LAX3 contributes to AR tip auxin maximum. In contrast, AUX1 involvement in AR development is unknown. Xylogenesis is induced by auxin plus cytokinin as is AR formation, but the genes involved are largely unknown. Stem thin cell layers (TCLs) form ARs and undergo xylogenesis under the same auxin plus cytokinin input. The aim of this research was to investigate SHR, SCR, AUX1 and LAX3 involvement in AR formation and xylogenesis in intact hypocotyls and stem TCLs in arabidopsis. Hypocotyls of scr-1, shr-1, lax3, aux1-21 and lax3/aux1-21 Arabidopsis thaliana null mutant seedlings grown with or without auxin plus cytokinin were examined histologically, as were stem TCLs cultured with auxin plus cytokinin. SCR and AUX1 expression was monitored using pSCR::GFP and AUX1::GUS lines, and LAX3 expression and auxin localization during xylogenesis were monitored by using LAX3::GUS and DR5::GUS lines. AR formation was inhibited in all mutants, except lax3. SCR was expressed in pericycle anticlinally derived AR-forming cells of intact hypocotyls, and in cell clumps forming AR meristemoids of TCLs. The apex was anomalous in shr and scr ARs. In all mutant hypocotyls, the pericycle divided periclinally to produce xylogenesis. Xylary element maturation was favoured by auxin plus cytokinin in shr and aux1-21. Xylogenesis was enhanced in TCLs, and in aux1-21 and shr in particular. AUX1 was expressed before LAX3, i.e. in the early derivatives leading to either ARs or xylogenesis. AR formation and xylogenesis are developmental programmes that are inversely related, but they involve fine-tuning by the same proteins, namely SHR

Alternatives to Anti-Personnel Landmines (Solutions de remplacement aux mines antipersonnel)

DTIC Science & Technology

2003-05-01

remplacement ont un prix : elles sont plus pesantes sur le plan logistique et impliquent des risques opérationnels pour les forces de l’OTAN. En...très importante, de l’interopérabilité dans le transfert de secteurs qui ont été minés par un pays non-signataire de la Convention d’Ottawa. Le...SEINE CEDEX, FRANCE RTO TECHNICAL REPORT 40(I) Alternatives to Anti-Personnel Landmines (Solutions de remplacement aux mines antipersonnel) Military

Approche aux soins en milieu communautaire à des adultes ayant une déficience développementale

PubMed Central

Osmun, W.E.; Chan, Nelson; Solomon, Robert

2015-01-01

Résumé Objectif Passer en revue les obligations d’ordre médical, éthique et juridique dans les soins aux adultes ayant une déficience développementale (DD) qui vivent dans la communauté. Sources des données Des recherches ont été faites dans Google et MEDLINE à l’aide des mots disabled, disability, vulnerable et community. Les lois pertinentes ont fait l’objet d’un examen. Message principal Le traitement d’un patient ayant une DD varie en fonction de facteurs comme la pathogenèse du problème actuel du patient, ses affections concomitantes, la gravité de ses déficiences et ses soutiens sociaux habituels. Bien que l’on s’entende sur les bienfaits du transfert des soins institutionnels vers des soins communautaires pour les patients ayant une DD, il s’est révélé difficile de leur dispenser des soins de grande qualité en milieu communautaire. Par ailleurs, il existe peu de travaux de recherche sur les façons d’offrir efficacement des soins aux adultes ayant une DD. En tant que professionnels des soins primaires, les médecins de famille sont souvent le premier point de contact pour les patients et sont à la fois responsables de la coordination et de la continuité des soins. Compte tenu de l’importance accrue accordée aux soins préventifs et à la détection précoce des maladies, la participation active du patient revêt aussi une grande importance. Les valeurs et les objectifs du patient sont des éléments essentiels à prendre en compte, même s’ils vont à l’encontre de la bonne santé du patient ou des propres valeurs du clinicien. Les lois s’appliquant aux personnes vulnérables varient d’une province à l’autre. Par conséquent, l’obligation de signaler des mauvais traitements suspectés pourrait différer selon que la personne vulnérable habite dans un centre de soins ou la communauté, que la personne qui soupçonne le comportement abusif est un fournisseur de services ou un professionnel de la santé ou

Soins primaires aux adultes ayant une déficience développementale

PubMed Central

Sullivan, William F.; Berg, Joseph M.; Bradley, Elspeth; Cheetham, Tom; Denton, Richard; Heng, John; Hennen, Brian; Joyce, David; Kelly, Maureen; Korossy, Marika; Lunsky, Yona; McMillan, Shirley

2011-01-01

Résumé Objectif Mettre à jour les lignes directrices canadiennes de 2006 sur les soins primaires aux adultes ayant une déficience développementale (DD) et présenter des recommandations pratiques fondées sur les connaissances actuelles pour traiter des problèmes de santé particuliers chez des adultes ayant une DD. Qualité des preuves Des professionnels de la santé expérimentés participant à un colloque et un groupe de travail subséquent ont discuté et convenu des révisions aux lignes directrices de 2006 en se fondant sur une recherche documentaire exhaustive, la rétroaction obtenue des utilisateurs du guide de pratique et les expériences cliniques personnelles. La plupart des preuves disponibles dans ce domaine viennent de l’opinion d’experts ou de déclarations consensuelles publiées (niveau III). Message principal Les adultes ayant une DD ont des problèmes de santé complexes, dont plusieurs diffèrent de ceux de la population en général. De bons soins primaires permettent d’identifier les problèmes de santé particuliers dont souffrent les adultes ayant une DD pour améliorer leur qualité de vie et leur accès aux soins de santé et prévenir la morbidité et le décès prématuré. Ces lignes directrices résument les problèmes de santé générale, physique, comportementale et mentale des adultes ayant une DD que devraient connaître les professionnels des soins primaires et présentent des recommandations pour le dépistage et la prise en charge en se basant sur les connaissances actuelles que les cliniciens peuvent mettre en pratique. En raison de l’interaction des facteurs biologiques, psychoaffectifs et sociaux qui contribuent à la santé et au bien-être des adultes ayant une DD, ces lignes directrices insistent sur la participation des aidants, l’adaptation des interventions, au besoin, et la consultation auprès de divers professionnels de la santé quand ils sont accessibles. Elles mettent aussi en évidence la

Chemical composition and geologic history of saline waters in Aux Vases and Cypress Formations, Illinois Basin

USGS Publications Warehouse

Demir, I.; Seyler, B.

1999-01-01

Seventy-six samples of formation waters were collected from oil wells producing from the Aux Vases or Cypress Formations in the Illinois Basin. Forty core samples of the reservoir rocks were also collected from the two formations. Analyses of the samples indicated that the total dissolved solids content (TDS) of the waters ranged from 43,300 to 151,400 mg/L, far exceeding the 35,400 mg/mL of TDS found in typical seawater. Cl-Br relations suggested that high salinities in the Aux Vases and Cypress formation waters resulted from the evaporation of original seawater and subsequent mixing of the evaporated seawater with concentrated halite solutions. Mixing with the halite solutions increased Na and Cl concentrations and diluted the concentration of other ions in the formation waters. The elemental concentrations were influenced further by diagenetic reactions with silicate and carbonate minerals. Diagenetic signatures revealed by fluid chemistry and rock mineralogy delineated the water-rock interactions that took place in the Aux Vases and Cypress sandstones. Dissolution of K-feldspar released K into the solution, leading to the formation of authigenic illite and mixed-layered illite/smectite. Some Mg was removed from the solution by the formation of authigenic chlorite and dolomite. Dolomitization, calcite recrystallization, and contribution from clay minerals raised Sr levels significantly in the formation waters. The trend of increasing TDS of the saline formation waters with depth can be explained with density stratification. But, it is difficult to explain the combination of the increasing TDS and increasing Ca/Na ratio with depth without invoking the controversial 'ion filtration' mechanism.

The auxin transporter, OsAUX1, is involved in primary root and root hair elongation and in Cd stress responses in rice (Oryza sativa L.).

PubMed

Yu, ChenLiang; Sun, ChenDong; Shen, Chenjia; Wang, Suikang; Liu, Fang; Liu, Yan; Chen, YunLong; Li, Chuanyou; Qian, Qian; Aryal, Bibek; Geisler, Markus; Jiang, De An; Qi, YanHua

2015-09-01

Auxin and cadmium (Cd) stress play critical roles during root development. There are only a few reports on the mechanisms by which Cd stress influences auxin homeostasis and affects primary root (PR) and lateral root (LR) development, and almost nothing is known about how auxin and Cd interfere with root hair (RH) development. Here, we characterize rice osaux1 mutants that have a longer PR and shorter RHs in hydroponic culture, and that are more sensitive to Cd stress compared to wild-type (Dongjin). OsAUX1 expression in root hair cells is different from that of its paralogous gene, AtAUX1, which is expressed in non-hair cells. However, OsAUX1, like AtAUX1, localizes at the plasma membrane and appears to function as an auxin tranporter. Decreased auxin distribution and contents in the osaux1 mutant result in reduction of OsCyCB1;1 expression and shortened PRs, LRs and RHs under Cd stress, but may be rescued by treatment with the membrane-permeable auxin 1-naphthalene acetic acid. Treatment with the auxin transport inhibitors 1-naphthoxyacetic acid and N-1-naphthylphthalamic acid increased the Cd sensitivity of WT rice. Cd contents in the osaux1 mutant were not altered, but reactive oxygen species-mediated damage was enhanced, further increasing the sensitivity of the osaux1 mutant to Cd stress. Taken together, our results indicate that OsAUX1 plays an important role in root development and in responses to Cd stress. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Conséquences comportementales de la violence faite aux enfants

PubMed Central

Al Odhayani, Abdulaziz; Watson, William J.; Watson, Lindsay

2013-01-01

Résumé Objectif Discuter des répercussions de la violence sur le développement comportemental durant l’enfance, mettre en évidence certains signes comportementaux susceptibles d’alerter les médecins à la présence d’une maltraitance continue d’un enfant et explorer le rôle précis du médecin de famille dans une telle situation clinique. Sources des données Une recension systématique a servi à examiner la recherche pertinente, les articles de révision clinique et les sites web des organismes de protection de la jeunesse. Message principal Le comportement d’un enfant est une manifestation extériorisée de sa stabilité et de sa sécurité intérieures. C’est une lentille au travers de laquelle le médecin de famille peut observer le développement de l’enfant pendant toute sa vie. Tous les genres de violence sont dommageables pour les enfants, qu’elle soit physique, affective ou psychologique, et peuvent causer des problèmes à long terme dans le développement du comportement et de la santé mentale. Les médecins de famille doivent connaître les indices de maltraitance et de négligence envers les enfants et être aux aguets de ces derniers afin d’entreprendre les interventions appropriées et améliorer les résultats pour ces enfants. Conclusion La violence faite aux enfants peut causer un développement psychologique désordonné et des problèmes de comportement. Les médecins de famille exercent un rôle important dans la reconnaissance des signes comportementaux laissant présager une maltraitance, ainsi que pour offrir de l’aide afin de protéger les enfants.

Self-assembly of bimetallic AuxPd1-x alloy nanoparticles via dewetting of bilayers through the systematic control of temperature, thickness, composition and stacking sequence

NASA Astrophysics Data System (ADS)

Kunwar, Sundar; Pandey, Puran; Sui, Mao; Bastola, Sushil; Lee, Jihoon

2018-03-01

Bimetallic alloy nanoparticles (NPs) are attractive materials for various applications with their morphology and elemental composition dependent optical, electronic, magnetic and catalytic properties. This work demonstrates the evolution of AuxPd1-x alloy nanostructures by the solid-state dewetting of sequentially deposited bilayers of Au and Pd on sapphire (0001). Various shape, size and configuration of AuxPd1‑x alloy NPs are fabricated by the systematic control of annealing temperature, deposition thickness, composition as well as stacking sequence. The evolution of alloy nanostructures is attributed to the surface diffusion, interface diffusion between bilayers, surface and interface energy minimization, Volmer-Weber growth model and equilibrium configuration. Depending upon the temperature, the surface morphologies evolve with the formation of pits, grains and voids and gradually develop into isolated semi-spherical alloy NPs by the expansion of voids and agglomeration of Au and Pd adatoms. On the other hand, small isolated to enlarged elongated and over-grown layer-like alloy nanostructures are fabricated due to the coalescence, partial diffusion and inter-diffusion with the increased bilayer thickness. In addition, the composition and stacking sequence of bilayers remarkably affect the final geometry of AuxPd1‑x nanostructures due to the variation in the dewetting process. The optical analysis based on the UV–vis-NIR reflectance spectra reveals the surface morphology dependent plasmonic resonance, scattering, reflection and absorption properties of AuxPd1‑x alloy nanostructures.

Periodicity, Electronic Structures, and Bonding of Gold Tetrahalides [AuX4](-) (X = F, CI, Br, I, At, Uus)

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

Li, Wan-Lu; Li, Yong; Xu, Congqiao

2015-12-07

Systematic theoretical and experimental investigations have been performed to understand the periodicity and electronic structures of trivalent-gold halides using gold tetrahalides [AuX4]⁻ anions (X = F, Cl, Br, I, At, Uus). The [AuX4]⁻ (X = Cl, Br, I) anions were produced in gas phase and their negative-ion photoelectron spectra were obtained, which exhibited rich and well-resolved spectral peaks. We calculated the adiabatic as well as vertical electron detachment energies using density functional methods with scalar and spin-orbit coupling relativistic effects. The simulated photoelectron spectra based on these calculations are in good agreement with the experimental spectra. Our results show thatmore » the trivalent Au(III) oxidation state becomes progressively less stable while Au(I) is preferred when the halides become heavier along the Period Table. This trend reveals that the oxidation state of metals in complexes can be manipulated through ligand design« less

Des furoncles résistants aux antibiotiques: penser à la myiase !!

PubMed Central

Ajili, Faida; Abid, Rim; Bousseta, Najeh; Mrabet, Ali; Karoui, Ghazi; Louzir, Bassem; Battikh, Riadh; Othmani, Salah

2013-01-01

Les myiases sont des infections parasitaires par des larves de mouches. La localisation cutanée doit être évoquée de retour d'un pays tropical devant une évolution inhabituelle de lésions cutanées. Nous rapportons une observation d'un militaire tunisien, ayant séjourné en République Démocratique du Congo. Il était atteint de myiase cutanée simulatrice d'une furonculose résistante aux antibiotiques. L'intérêt de cette observation est de souligner l'importance d’évoquer la myiase dont le traitement est simple et rapide chez un patient de retour de zone d'endémie. PMID:24106569

Le recours aux modeles dans l'enseignement de la biologie au secondaire : Conceptions d'enseignantes et d'enseignants et modes d'utilisation

NASA Astrophysics Data System (ADS)

Varlet, Madeleine

Le recours aux modeles et a la modelisation est mentionne dans la documentation scientifique comme un moyen de favoriser la mise en oeuvre de pratiques d'enseignement-apprentissage constructivistes pour pallier les difficultes d'apprentissage en sciences. L'etude prealable du rapport des enseignantes et des enseignants aux modeles et a la modelisation est alors pertinente pour comprendre leurs pratiques d'enseignement et identifier des elements dont la prise en compte dans les formations initiale et disciplinaire peut contribuer au developpement d'un enseignement constructiviste des sciences. Plusieurs recherches ont porte sur ces conceptions sans faire de distinction selon les matieres enseignees, telles la physique, la chimie ou la biologie, alors que les modeles ne sont pas forcement utilises ou compris de la meme maniere dans ces differentes disciplines. Notre recherche s'est interessee aux conceptions d'enseignantes et d'enseignants de biologie au secondaire au sujet des modeles scientifiques, de quelques formes de representations de ces modeles ainsi que de leurs modes d'utilisation en classe. Les resultats, que nous avons obtenus au moyen d'une serie d'entrevues semi-dirigees, indiquent que globalement leurs conceptions au sujet des modeles sont compatibles avec celle scientifiquement admise, mais varient quant aux formes de representations des modeles. L'examen de ces conceptions temoigne d'une connaissance limitee des modeles et variable selon la matiere enseignee. Le niveau d'etudes, la formation prealable, l'experience en enseignement et un possible cloisonnement des matieres pourraient expliquer les differentes conceptions identifiees. En outre, des difficultes temporelles, conceptuelles et techniques peuvent freiner leurs tentatives de modelisation avec les eleves. Toutefois, nos resultats accreditent l'hypothese que les conceptions des enseignantes et des enseignants eux-memes au sujet des modeles, de leurs formes de representation et de leur approche

Gestion des ressources hydriques adaptee aux changements climatiques pour la production optimale d'hydroelectricite. Etude de cas: Bassin versant de la riviere Manicouagan

NASA Astrophysics Data System (ADS)

Haguma, Didier

Il est dorenavant etabli que les changements climatiques auront des repercussions sur les ressources en eau. La situation est preoccupante pour le secteur de production d'energie hydroelectrique, car l'eau constitue le moteur pour generer cette forme d'energie. Il sera important d'adapter les regles de gestion et/ou les installations des systemes hydriques, afin de minimiser les impacts negatifs et/ou pour capitaliser sur les retombees positives que les changements climatiques pourront apporter. Les travaux de la presente recherche s'interessent au developpement d'une methode de gestion des systemes hydriques qui tient compte des projections climatiques pour mieux anticiper les impacts de l'evolution du climat sur la production d'hydroelectricite et d'etablir des strategies d'adaptation aux changements climatiques. Le domaine d'etude est le bassin versant de la riviere Manicouagan situe dans la partie centrale du Quebec. Une nouvelle approche d'optimisation des ressources hydriques dans le contexte des changements climatiques est proposee. L'approche traite le probleme de la saisonnalite et de la non-stationnarite du climat d'une maniere explicite pour representer l'incertitude rattachee a un ensemble des projections climatiques. Cette approche permet d'integrer les projections climatiques dans le probleme d'optimisation des ressources en eau pour une gestion a long terme des systemes hydriques et de developper des strategies d'adaptation de ces systemes aux changements climatiques. Les resultats montrent que les impacts des changements climatiques sur le regime hydrologique du bassin de la riviere Manicouagan seraient le devancement et l'attenuation de la crue printaniere et l'augmentation du volume annuel d'apports. L'adaptation des regles de gestion du systeme hydrique engendrerait une hausse de la production hydroelectrique. Neanmoins, une perte de la performance des installations existantes du systeme hydrique serait observee a cause de l'augmentation des

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

PubMed Central

2014-01-01

Background Of the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by the RepeatMasker program. RepeatMasker generates several output files, including the .out file, which provides annotations for all detected repeats in a query sequence. However, a remaining challenge consists of identifying the different copies of TEs that correspond to the identified hits. This step is essential for any evolutionary/comparative analysis of the different copies within a family. Different possibilities can lead to multiple hits corresponding to a unique copy of an element, such as the presence of large deletions/insertions or undetermined bases, and distinct consensus corresponding to a single full-length sequence (like for long terminal repeat (LTR)-retrotransposons). These possibilities must be taken into account to determine the exact number of TE copies. Results We have developed a perl tool that parses the RepeatMasker .out file to better determine the number and positions of TE copies in the query sequence, in addition to computing quantitative information for the different families. To determine the accuracy of the program, we tested it on several RepeatMasker .out files corresponding to two organisms (Drosophila melanogaster and Homo sapiens) for which the TE content has already been largely described and which present great differences in genome size, TE content, and TE families. Conclusions Our tool provides access to detailed information concerning the TE content in a genome at the family level from the .out file of RepeatMasker. This information includes the exact position and orientation of each copy, its proportion in the query sequence, and its quality compared to the reference element. In addition, our tool allows a user to directly retrieve the sequence of each copy and obtain the same detailed information at the family level when a local

The Evolution of Minehunting in France (L’Evolution de la Chasse aux Mines en France),

DTIC Science & Technology

1983-07-13

The Necessity of Minehunting in France And why are the French , Ohl such a small number of experts, interested in minehunting? The coasts of France are...AD-A132 532 THE EVOLUTION OF MINEHUNTING IN FRANCE IL’EVOLUTION DE I/1 LA CHASSE AUX MINES EN FRANCE )(U) NAVAL INTELLIGENCE SUPPORT CENTER WASHINGTON...MINEHUNTING IN FRANCE AUTHOR: DE DREZIGUE TRANSLATEO gY: LCDR ROBERT AUGELLI, USNR-R NISC TRANSLATION UNIT 0166 eei o DTIC MI’S OR&I DfIC T ELECTE Ja~tinoati

Largely enhanced photocatalytic activity of Au/XS2/Au (X = Re, Mo) antenna-reactor hybrids: charge and energy transfer.

PubMed

Chen, Kai; Ding, Si-Jing; Luo, Zhi-Jun; Pan, Gui-Ming; Wang, Jia-Hong; Liu, Jia; Zhou, Li; Wang, Qu-Quan

2018-02-22

An antenna-reactor hybrid coupling plasmonic antenna with catalytic nanoparticles is a new strategy to optimize photocatalytic activity. Herein, we have rationally proposed a Au/XS 2 /Au (X = Re, Mo) antenna reactor, which has a large Au core as the antenna and small satellite Au nanoparticles as the reactor separated by an ultrathin two-dimensional transition-metal dichalcogenide XS 2 shell (∼2.6 nm). Due to efficient charge transfer across the XS 2 shell as well as energy transfer via coupling of the Au antenna and Au reactor, the photocatalytic activity has been largely enhanced: Au/ReS 2 /Au exhibits a 3.59-fold enhancement, whereas Au/MoS 2 /Au exhibits a 2.66-fold enhancement as compared to that of the sum of the three individual components. The different enhancement in the Au/ReS 2 /Au and Au/MoS 2 /Au antenna-reactor hybrid is related to the competition and cooperation of charge and energy transfer. These results indicate the great potential of the Au/XS 2 /Au antenna-reactor hybrid for the development of highly efficient plasmonic photocatalysts.

Complex facies relationships and regional stratigraphy of the Mississippian Ste. Genevieve, Paoli, and Aux Vases Formations, Illinois basin: A major hydrocarbon-producing interval

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

Cole, R.D.; Nelson, W.J.

1993-03-01

The Mississippian Ste. Genevieve and Paoli Limestones and sandstones of the Aux Vases Formation are lateral facies of one another. This interpretation is based on comprehensive investigations of outcrops, and selected cores, samples of well cuttings, and geophysical logs conducted over a period of four years. Both units exhibit similar sedimentological characteristics and represent open marine, shallow subtidal, and intertidal environments. The presence of low-angle cross-laminae, ripple- and plane-laminae, climbing ripples, and ooid shoals suggest most deposition occurred under low energy conditions. Lenticular, channel-like scour and fill structures that contain both fine-grained quartz sand and abraded, disarticulated fossil fragments indicatemore » localized higher energy deposition. The authors studies indicate that siliciclastic vs. carbonate deposition was controlled strictly by available sediment, and not by regressive (siliciclastic) and transgressive (carbonate) events, as inferred by previous workers. This conclusion is based on lateral facies relationships, and the supplanting of carbonates by clastics occurring in the upper part of the Ste. Genevieve through the middle part of the Paoli. The Aux Vases is thickest, coarsest, and least mature in the northwestern part of the Illinois Basin, and pinches out to the southeast. This implies a northwesterly source for clastics, perhaps the Transcontinental Arch. After early Chesterian time, the Transcontinental Arch apparently supplied little or no sediment to any flanking basin. The Ste. Genevieve, Paoli, and Aux Vases are major oil-producing units in the Illinois Basin. New understanding of regional relationships should enhance exploratory success and improve recovery from established fields.« less

Evaluation des indicateurs d’alerte précoce de la résistance du VIH aux ARV en Côte d’Ivoire en 2011

PubMed Central

Yao, Kouadio Jean; Damey, Néto Florence; Konan, Diby Jean Paul; Aka, Joseph; Aka-Konan, Sandrine; Ani, Alex; Bonle, Marguerite Te; Kouassi, Dinard

2016-01-01

Introduction En 2001, l'Organisation des Nations Unies recommandait de rendre disponible les médicaments antirétroviraux dans les pays à ressources limitées. Cependant, l'utilisation de ces médicaments à grande échelle s'accompagne du développement de résistance du virus. En Côte d'Ivoire, plusieurs sites prescrivent les antirétroviraux. Cette étude avait pour objectif d'évaluer les facteurs programmatiques associés à un risque élevé d'émergence de résistance du VIH aux antirétroviraux. Méthodes Il s'agit d'une cohorte rétrospective sur 20 sites de prise en charge des personnes vivant avec le VIH. La population d'étude était constituée des personnes ayant initié leur traitement antirétroviral sur les sites en 2008-2009. L'estimation de la taille de l'échantillon a été faite à partir de la stratégie d'échantillonnage de l'OMS. Résultats Sur 20 sites, 98% des prescriptions initiales étaient conformes aux directives nationales et 20% des sites avaient 100% de prescriptions conformes. Au total, 33% des patients étaient perdus de vue au cours des 12 premiers mois de traitement antirétroviral et 20% des sites avaient moins de 20% de perdus de vue. A 12 mois, 51% des patients demeuraient sous traitement de première intention approprié et 11% des sites ont atteint le seuil d'au moins 70% de patients sous traitement de première intention approprié. Un seul site n'a pas connu de rupture d'antirétroviraux sur les 12 mois. Conclusion Des insuffisances relevées dans la prise en charge des personnes vivant avec le VIH traduisent l'existence d'un risque important de résistance du virus aux antirétroviraux en 2008-2009. Pour minimiser ce risque les pratiques de prescription devraient être améliorées, un système de recherche des absents aux rendez-vous devrait être mis en place et la disponibilité constante des antirétroviraux devraient être assurée. PMID:28250876

Modelisation de la diffusion sur les surfaces metalliques: De l'adatome aux processus de croissance

NASA Astrophysics Data System (ADS)

Boisvert, Ghyslain

Cette these est consacree a l'etude des processus de diffusion en surface dans le but ultime de comprendre, et de modeliser, la croissance d'une couche mince. L'importance de bien mai triser la croissance est primordiale compte tenu de son role dans la miniaturisation des circuits electroniques. Nous etudions ici les surface des metaux nobles et de ceux de la fin de la serie de transition. Dans un premier temps, nous nous interessons a la diffusion d'un simple adatome sur une surface metallique. Nous avons, entre autres, mis en evidence l'apparition d'une correlation entre evenements successifs lorsque la temperature est comparable a la barriere de diffusion, i.e., la diffusion ne peut pas etre associee a une marche aleatoire. Nous proposons un modele phenomenologique simple qui reproduit bien les resultats des simulations. Ces calculs nous ont aussi permis de montrer que la diffusion obeit a la loi de Meyer-Neldel. Cette loi stipule que, pour un processus active, le prefacteur augmente exponentiellement avec la barriere. En plus, ce travail permet de clarifier l'origine physique de cette loi. En comparant les resultats dynamiques aux resultats statiques, on se rend compte que la barriere extraite des calculs dynamiques est essentiellement la meme que celle obtenue par une approche statique, beaucoup plus simple. On peut donc obtenir cette barriere a l'aide de methodes plus precises, i.e., ab initio, comme la theorie de la fonctionnelle de la densite, qui sont aussi malheureusement beaucoup plus lourdes. C'est ce que nous avons fait pour plusieurs systemes metalliques. Nos resultats avec cette derniere approche se comparent tres bien aux resultats experimentaux. Nous nous sommes attardes plus longuement a la surface (111) du platine. Cette surface regorge de particularites interessantes, comme la forme d'equilibre non-hexagonale des i lots et deux sites d'adsorption differents pour l'adatome. De plus, des calculs ab initio precedents n'ont pas reussi a confirmer la

Paternité des articles et intérêts concurrents : une analyse des recommandations aux auteurs des journaux traitant de pratique pharmaceutique

PubMed Central

Courbon, Ève; Tanguay, Cynthia; Lebel, Denis; Bussières, Jean-François

2014-01-01

RÉSUMÉ Contexte : La présence d’auteurs honorifiques et fantômes ainsi que les intérêts concurrents représentent des difficultés bien documentées, liées à la publication d’articles scientifiques. Il existe des lignes directrices encadrant la rédaction et la publication de manuscrits scientifiques, notamment celles de l’International Committee of Medical Journal Editors (ICMJE). Objectifs : L’objectif principal de cette étude descriptive et transversale visait à recenser les instructions portant sur la paternité des articles et les intérêts concurrents provenant des recommandations aux auteurs des journaux traitant de pratique pharmaceutique. L’objectif secondaire visait à déterminer des mesures correctrices pour une paternité des articles plus transparente. Méthode : La recherche a débuté par l’identification des journaux traitant de pratique pharmaceutique. La consultation des instructions aux auteurs des journaux a permis ensuite de recenser les recommandations destinées à éviter les problèmes de paternité des articles et d’intérêts concurrents. Finalement, les membres de l’équipe de recherche se sont consultés afin de définir des mesures correctrices possibles à l’intention des chercheurs. Résultats : Des 232 journaux traitant de pharmacie, 33 ont été définis comme traitant de pratique pharmaceutique. Un total de 24 (73 %) journaux mentionnaient suivre la politique de l’ICMJE, 14 (42 %) demandaient aux auteurs de remplir un formulaire de déclaration d’intérêts concurrents au moment de la soumission de l’article, 17 (52 %) présentaient une définition de la qualité d’auteur et 5 (15 %) demandaient de détailler les contributions de chaque auteur. Une grille de 40 critères a été élaborée pour définir l’attribution du statut d’auteur. Conclusion : Moins de la moitié des journaux demandait aux auteurs de transmettre un formulaire de déclaration des intérêts concurrents au moment de la

Symetries et integrabilite des equations aux differences finies

NASA Astrophysics Data System (ADS)

Lafortune, Stephane

2000-09-01

La présente thèse porte sur l'étude des symétries et des propriétés d'intégrabilité des équations aux différences finies. Dans le chapitre 1, le groupe de symétrie ponctuelle d'un système couplé à deux équations différentielles aux différences est étudié. On montre que dans certains cas, la dimension du groupe peut être infinie. Les équations peuvent décrire l'interaction de deux longues chaînes moléculaires, chacune étant composée d'atomes d'un même type. Dans le chapitre 2, une classe de théories de champs avec interaction exponentielle est introduite. L'interaction dépend de deux matrices de ``couplage'' et est suffisamment générale pour inclure toutes les théories de champs de Toda existant dans la littérature. Les symétries de Lie ponctuelles sont obtenues pour les cas où l'on a un nombre fini, infini ou semi-infini de champs. Une attention spéciale est accordée à la présence de l'invariance conforme. Dans le chapitre 3, nous procédons à la classification et à l'étude d'équations linéarisables. Nous examinons tout d'abord l'équation de Gambier continue qui contient, comme réductions, toutes les équations de deuxième ordre intégrables par linéarisation. Nous introduisons par la suite la forme discrète de cette équation et obtenons les conditions d'intégrabilité à l'aide du confinement des singularités. Nous étudions aussi les différentes réductions du cas discret. De plus, nous obtenons des transformations de Schlesinger pour les équations de Gambier discrète et continue. Dans la dernière partie du chapitre, nous étudions une famille d'équations discrètes du deuxième ordre incluant des équations résolubles par linéarisation. Plusieurs cas intégrables sont obtenus. Dans le cas discret, l'étude de l'intégrabilité est faite à l'aide du confinement des singularités. Dans le chapitre 4, nous étudions un autre critère d'intégrabilité: l'entropie algébrique. Nous montrons que les r

Conception, elaboration et mise a l'essai d'un simulateur interactif permettant une approche modelisante: Application aux lois de la genetique mendelienne

NASA Astrophysics Data System (ADS)

Lasri, Abdel-Halim

Dans cette recherche-developpement, nous avons concu, developpe et mis a l'essai un simulateur interactif pour favoriser l'apprentissage des lois probabilistes impliqees dans la genetique mendelienne. Cet environnement informatise devra permettre aux etudiants de mener des experiences simulees, utilisant les statistiques et les probebilites comme outils mathematiques pour modeliser le phenomene de la transmission des caracteres hereditaires. L'approche didactique est essentiellement orientee vers l'utilisation des methodes quantitatives impliquees dans l'experimentation des facteurs hereditaires. En incorporant au simulateur le principe de la "Lunette cognitive" de Nonnon (1986), l'etudiant fut place dans une situation ou il a pu synchroniser la perception de la representation iconique (concrete) et symbolique (abstraite) des lois probabilistes de Mendel. A l'aide de cet environnement, nous avons amene l'etudiant a identifier le(s) caractere(s) hereditaire(s) des parents a croiser, a predire les frequences phenotypiques probables de la descendance issue du croisement, a observer les resultats statistiques et leur fluctuation au niveau de l'histogramme des frequences, a comparer ces resultats aux predictions anticipees, a interpreter les donnees et a selectionner en consequence d'autres experiences a realiser. Les etapes de l'approche inductive sont privilegiees du debut a la fin des activites proposees. L'elaboration, du simulateur et des documents d'accompagnement, a ete concue a partir d'une vingtaine de principes directeurs et d'un modele d'action. Ces principes directeurs et le modele d'action decoulent de considerations theoriques psychologiques, didactiques et technologiques. La recherche decrit la structure des differentes parties composant le simulateur. L'architecture de celui-ci est construite autour d'une unite centrale, la "Principale", dont les liens et les ramifications avec les autres unites confere a l'ensemble du simulateur sa souplesse et sa

Soins primaires aux adultes ayant des déficiences intellectuelles et développementales

PubMed Central

Sullivan, William F.; Diepstra, Heidi; Heng, John; Ally, Shara; Bradley, Elspeth; Casson, Ian; Hennen, Brian; Kelly, Maureen; Korossy, Marika; McNeil, Karen; Abells, Dara; Amaria, Khush; Boyd, Kerry; Gemmill, Meg; Grier, Elizabeth; Kennie-Kaulbach, Natalie; Ketchell, Mackenzie; Ladouceur, Jessica; Lepp, Amanda; Lunsky, Yona; McMillan, Shirley; Niel, Ullanda; Sacks, Samantha; Shea, Sarah; Stringer, Katherine; Sue, Kyle; Witherbee, Sandra

2018-01-01

Résumé Objectif Mettre à jour les Lignes directrices consensuelles canadiennes 2011 en matière de soins primaires aux adultes ayant une déficience développementale. Méthodes Des médecins de famille et d’autres professionnels de la santé expérimentés dans les soins aux personnes ayant des DID ont examiné et synthétisé les récentes connaissances empiriques, d’écosystèmes, expertes et expérientielles. Un système a été conçu pour catégoriser la qualité des recommandations. Recommandations Les adultes ayant des DID sont un groupe hétérogène de patients qui présentent des affections médicales et des facteurs qui influent sur leur santé, qui diffèrent de ceux qui touchent les autres membres de la communauté de par leur nature, leurs manifestations, leur gravité ou leur complexité. Ces personnes nécessitent une approche de soins et des interventions adaptées à leurs besoins. Les présentes lignes directrices offrent des conseils en matière de normes de soins. Nous avons incorporé des références à des outils cliniques et à d’autres ressources pratiques. Les approches de soins décrites ici s’appliquent aussi à d’autres groupes de patients ayant un déficit cognitif ou de la communication, ou d’autres déficits des fonctions adaptatives. Conclusion À titre de fournisseurs de soins de première ligne, les médecins de famille jouent un rôle vital de promotion de la santé et de bien-être auprès des adultes ayant des DID. Ces lignes directrices peuvent les aider à prendre des décisions avec les patients et les aidants naturels. PMID:29650617

Myles A. Steiner | NREL

Science.gov Websites

; Emmett E. Perl, John Simon, Daniel J. Friedman, Nikhil Jain, Paul Sharps, Claiborne McPheeters, Yukun Sun , Kevin L. Schulte, Ryan M. France, William E. McMahon, Emmett E. Perl, Daniel J. Friedman, Journal of ; E.E. Perl, D. Kuciauskas, J. Simon, D.J. Friedman, M.A. Steiner, Journal of Applied Physics, 122

Distribution of enteric bacteria in Antarctic seawater surrounding the Port-aux-Français permanent station (Kerguelen Island).

PubMed

Delille, D; Gleizon, F

2003-09-01

Untreated sewage has been released from Port-aux Français station, Kerguelen Island, into the Southern Ocean for more than 50 years. We investigated the spatial distribution of faecal bacteria indicators during a one-year survey conducted in seawater off Morbihan Bay near the French permanent station of the Kerguelen Island (49 degrees 21(')S, 70 degrees 30(')E). Seawater samples were taken bimonthly from nine stations evenly distributed around the sewage outfalls of the station. Escherichia coli and enterococci were estimated using specific microplates (Miniaturized method for the enumeration of E. coli or enterococci in surface and waste waters, "MU/EC or MU/SF methods", BIO-RAD( Copyright)). In order to evaluate the role of seasonal changes of environmental parameters on the survival of enteric bacteria, total and saprophytic bacterial abundances were also estimated in all seawater samples. High densities of faecal bacteria (maximum 10(4) cells 100 ml(-1)) were found in seawater surrounding the sewage outfall. However, enteric bacterial counts decreased rapidly with increasing distance from the outfall. In all samples collected further than 2 km from the outfall, the bacterial indicators were absent or present in small numbers (<10 cells 100 ml(-1)). Faecal coliforms were not detected in samples collected at pristine sites located 10 km from Port-aux-Français. Despite these low contamination levels, faecal bacteria were always detected in the vicinity of the sewage outfall during the seasonal survey. The concentration of faecal bacteria may be related to the number of people inhabiting the station.

Fundamentals and Special Problems of Synthetic Aperture Radar (SAR) (Les Aspects Fondamentaux et les Problemes Specifiques aux Radars a Ouverture Synthetique (SAR)

DTIC Science & Technology

1992-08-01

limits of these topics will be included. Digital SAR processing is for SAR indispensible. Theories and special algorithms will be given along with basic...traitement num~rique est indispensable aux SAP,. Des theories et des algorithmes sp~cifiques; seront proposes, ainsi que des configurations de processeur...equation If N independent pixel values are added than fol- lows from the laws of probability theory that the ra mean value of the sum is identical with

Diversification and Expression of the PIN, AUX/LAX, and ABCB Families of Putative Auxin Transporters in Populus

PubMed Central

Carraro, Nicola; Tisdale-Orr, Tracy Eizabeth; Clouse, Ronald Matthew; Knöller, Anne Sophie; Spicer, Rachel

2012-01-01

Intercellular transport of the plant hormone auxin is mediated by three families of membrane-bound protein carriers, with the PIN and ABCB families coding primarily for efflux proteins and the AUX/LAX family coding for influx proteins. In the last decade our understanding of gene and protein function for these transporters in Arabidopsis has expanded rapidly but very little is known about their role in woody plant development. Here we present a comprehensive account of all three families in the model woody species Populus, including chromosome distribution, protein structure, quantitative gene expression, and evolutionary relationships. The PIN and AUX/LAX gene families in Populus comprise 16 and 8 members respectively and show evidence for the retention of paralogs following a relatively recent whole genome duplication. There is also differential expression across tissues within many gene pairs. The ABCB family is previously undescribed in Populus and includes 20 members, showing a much deeper evolutionary history, including both tandem and whole genome duplication as well as probable gene loss. A striking number of these transporters are expressed in developing Populus stems and we suggest that evolutionary and structural relationships with known auxin transporters in Arabidopsis can point toward candidate genes for further study in Populus. This is especially important for the ABCBs, which is a large family and includes members in Arabidopsis that are able to transport other substrates in addition to auxin. Protein modeling, sequence alignment and expression data all point to ABCB1.1 as a likely auxin transport protein in Populus. Given that basipetal auxin flow through the cambial zone shapes the development of woody stems, it is important that we identify the full complement of genes involved in this process. This work should lay the foundation for studies targeting specific proteins for functional characterization and in situ localization. PMID:22645571

Analytic reconstruction of magnetic resonance imaging signal obtained from a periodic encoding field.

PubMed

Rybicki, F J; Hrovat, M I; Patz, S

2000-09-01

We have proposed a two-dimensional PERiodic-Linear (PERL) magnetic encoding field geometry B(x,y) = g(y)y cos(q(x)x) and a magnetic resonance imaging pulse sequence which incorporates two fields to image a two-dimensional spin density: a standard linear gradient in the x dimension, and the PERL field. Because of its periodicity, the PERL field produces a signal where the phase of the two dimensions is functionally different. The x dimension is encoded linearly, but the y dimension appears as the argument of a sinusoidal phase term. Thus, the time-domain signal and image spin density are not related by a two-dimensional Fourier transform. They are related by a one-dimensional Fourier transform in the x dimension and a new Bessel function integral transform (the PERL transform) in the y dimension. The inverse of the PERL transform provides a reconstruction algorithm for the y dimension of the spin density from the signal space. To date, the inverse transform has been computed numerically by a Bessel function expansion over its basis functions. This numerical solution used a finite sum to approximate an infinite summation and thus introduced a truncation error. This work analytically determines the basis functions for the PERL transform and incorporates them into the reconstruction algorithm. The improved algorithm is demonstrated by (1) direct comparison between the numerically and analytically computed basis functions, and (2) reconstruction of a known spin density. The new solution for the basis functions also lends proof of the system function for the PERL transform under specific conditions.

"PERLE bedside-examination-course for candidates in state examination" - Developing a training program for the third part of medical state examination (oral examination with practical skills).

PubMed

Karthaus, Anne; Schmidt, Anita

2016-01-01

In preparation for the state examination, many students have open questions and a need for advice. Tutors of the Skills Lab PERLE-"Praxis ERfahren und Lernen" (experiencing and learning practical skills) have developed a new course concept to provide support and practical assistance for the examinees. The course aims to familiarize the students with the exam situation in order to gain more confidence. This enables the students to experience a confrontation with the specific situation of the exam in a protected environment. Furthermore, soft skills are utilized and trained. Concept of the course: The course was inspired by the OSCE-model (Objective Structured Clinical Examination), an example for case-based learning and controlling. Acquired knowledge can be revised and extended through the case studies. Experienced tutors provide assistance in discipline-specific competencies, and help in organizational issues such as dress code and behaviour. Evaluation of the course: An evaluation was conducted by the attending participants after every course. Based on this assessment, the course is constantly being developed. In March, April and October 2015 six courses, with a total of 84 participants, took place. Overall 76 completed questionnaires (91%) were analysed. Strengths of the course are a good tutor-participants-ratio with 1:4 (1 Tutor provides guidance for 4 participants), the interactivity of the course, and the high flexibility in responding to the group's needs. Weaknesses are the tight schedule, and the currently not yet performed evaluation before and after the course. In terms of "best practise", this article shows an example of how to offer low-cost and low-threshold preparation for the state examination.

Occurrence des traumatismes alvéolo-dentaires aux cliniques universitaires de Kinshasa: deuxième partie, étude préliminaire de 93 cas

PubMed Central

Foche, Adelin Nzudjom; Bushabu, Fidele Nyimi; Mana, Charles Mfutu; Haruna, Ramazani; Masin, Steve Sekele; Nsudila, Monique; Alifi, Paul Bobe; Muinamiyi, Pierre Muyembi; Burley, Jean Paul Sekele Isourady

2018-01-01

Introduction L'objectif de cette étude était d'analyser les caractéristiques épidémiologiques cliniques des fractures alvéolo-dentaires aux cliniques universitaires de Kinshasa/RDC. Méthodes Étude transversale de 7 ans, réalisée dans le département d'odontostomatologie, service de stomatologie et de chirurgie maxillo-faciale/cliniques universitaires de Kinshasa de Janvier 2007 à Décembre 2014. Résultats Sur les 93 dossiers colligés, le sexe masculin était prédominant (66,7%) et l'âge le plus prévalent se situait entre 20 ans et 29 ans. Les causes les plus fréquentes ont été les agressions/rixes (52,7%) et la luxation dentaire a été le type des lésions la plus fréquente avec 52,7%. La RX retro-alvéolaire été réalisée dans 75,7%, et le blocage mono-maxillaire fut le type de traitement le plus réalisé (60,2%). Conclusion L'analyse de profil clinique des traumatismes alvéolo-dentaires aux cliniques universitaires de Kinshasa est celui d'un adulte jeune de sexe masculin, présentant des luxations dentaires des maxillaires dont les causes sont les agressions/rixes. PMID:29875931

The Geoinformatica free and open source software stack

NASA Astrophysics Data System (ADS)

Jolma, A.

2012-04-01

The Geoinformatica free and open source software (FOSS) stack is based mainly on three established FOSS components, namely GDAL, GTK+, and Perl. GDAL provides access to a very large selection of geospatial data formats and data sources, a generic geospatial data model, and a large collection of geospatial analytical and processing functionality. GTK+ and the Cairo graphics library provide generic graphics and graphical user interface capabilities. Perl is a programming language, for which there is a very large set of FOSS modules for a wide range of purposes and which can be used as an integrative tool for building applications. In the Geoinformatica stack, data storages such as FOSS RDBMS PostgreSQL with its geospatial extension PostGIS can be used below the three above mentioned components. The top layer of Geoinformatica consists of a C library and several Perl modules. The C library comprises a general purpose raster algebra library, hydrological terrain analysis functions, and visualization code. The Perl modules define a generic visualized geospatial data layer and subclasses for raster and vector data and graphs. The hydrological terrain functions are already rather old and they suffer for example from the requirement of in-memory rasters. Newer research conducted using the platform include basic geospatial simulation modeling, visualization of ecological data, linking with a Bayesian network engine for spatial risk assessment in coastal areas, and developing standards-based distributed water resources information systems in Internet. The Geoinformatica stack constitutes a platform for geospatial research, which is targeted towards custom analytical tools, prototyping and linking with external libraries. Writing custom analytical tools is supported by the Perl language and the large collection of tools that are available especially in GDAL and Perl modules. Prototyping is supported by the GTK+ library, the GUI tools, and the support for object

Low-temperature thermoelectric, galvanomagnetic, and thermodynamic properties of the type-I clathrate Ba8AuxSi46-x

NASA Astrophysics Data System (ADS)

Aydemir, U.; Candolfi, C.; Ormeci, A.; Oztan, Y.; Baitinger, M.; Oeschler, N.; Steglich, F.; Grin, Yu.

2011-11-01

Polycrystalline samples of the clathrate Ba8AuxSi46-x were synthesized for 0.2 ⩽ x ⩽ 10. The homogeneity range of the type-I clathrate phase was determined to be 3.63 ⩽ x ⩽ 6.10 after annealing at 900 °C, while a lower Au concentration (x ≈ 2.2) was obtained by steel-quenching. Quasisingle phase materials were obtained for 4.10 ⩽ x ⩽ 6.10. In this composition range, thermoelectric properties, including electrical resistivity, thermopower, and thermal conductivity, were investigated between 2 and 350 K. These experiments were complemented by low-temperature specific heat and Hall-effect measurements (2-300 K). First-principles calculations were carried out to determine the evolution of the electronic structure as a function of x. Both theoretical and experimental results evidence a progressive evolution, with the Au content, from a metallic-like behavior towards a highly doped semiconducting state which develops around x = 5.43. At this concentration, a crossover from n- to p-type conduction occurs, suggesting that the present system satisfies the Zintl-Klemm concept, which predicts a transition at x = 5.33. This crossover is traced by Hall-effect data indicating a dominant electronlike response for x ⩽ 5.43, which turns into a holelike signal at higher x values. Analysis of the data based on a single-parabolic-band model under the assumption of a single scattering mechanism of the charge carriers proved to adequately describe the transport properties in the compositional range investigated. Interestingly, the temperature dependence of the lattice thermal conductivity is strongly influenced by the Au concentration: the typical behavior of crystalline insulators in the n-type compounds evolves into a glasslike dependence in the p-type samples. The series Ba8AuxSi46-x thus provides an excellent testing ground for the interplay between crystal structure, electronic properties, and lattice thermal conductivity in type-I clathrates.

IRACproc: IRAC Post-BCD Processing

NASA Astrophysics Data System (ADS)

Schuster, Mike; Marengo, Massimo; Patten, Brian

2012-09-01

IRACproc is a software suite that facilitates the co-addition of dithered or mapped Spitzer/IRAC data to make them ready for further analysis with application to a wide variety of IRAC observing programs. The software runs within PDL, a numeric extension for Perl available from pdl.perl.org, and as stand alone perl scripts. In acting as a wrapper for the Spitzer Science Center's MOPEX software, IRACproc improves the rejection of cosmic rays and other transients in the co-added data. In addition, IRACproc performs (optional) Point Spread Function (PSF) fitting, subtraction, and masking of saturated stars.

Exceptional collections in surface-like categories

NASA Astrophysics Data System (ADS)

Kuznetsov, A. G.

2017-09-01

We provide a categorical framework for recent results of Markus Perling's on the combinatorics of exceptional collections on numerically rational surfaces. Using it we simplify and generalize some of Perling's results as well as Vial's criterion for the existence of a numerical exceptional collection. Bibliography: 18 titles.

A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

Differential effects of NAA and 2,4-D in reducing floret abscission in cestrum (Cestrum elegans) cut flowers are associated with their differential activation of Aux/IAA homologous genes.

PubMed

Abebie, Bekele; Lers, Amnon; Philosoph-Hadas, Sonia; Goren, Raphael; Riov, Joseph; Meir, Shimon

2008-01-01

A previous study showed that the relative effectiveness of 2,4-dichlorophenoxyacetic acid (2,4-D) compared with that of 1-naphthaleneacetic acid (NAA) in reducing floret bud abscission in cestrum (Cestrum elegans) cut flowers was due to its acropetal transport. The aim of the present study was to examine if the differential effect of these auxins on floret abscission is reflected in the expression of Aux/IAA genes in the floret abscission zone (AZ). cDNAs were isolated by PCR-based cloning from the floret AZ of auxin-treated cut flowers. The expression patterns of the cDNAs in various tissues and the effect of indole-3-acetic acid (IAA), applied with or without cycloheximide, on their expression in the floret AZ were examined by northern blot analysis. The regulation of transcript accumulation in the floret AZ in response to NAA or 2,4-D was measured by real-time PCR during auxin pulsing of cut flowers and vase life, concomitantly with floret abscission. Six isolated cDNAs were identified to represent Aux/IAA homologous genes, designated as Cestrum elegans (Ce)-IAA1 to Ce-IAA6. Four Ce-IAA genes were characterized as early auxin-responsive genes (ARGs), and two (Ce-IAA1 and Ce-IAA5) as late ARGs. Only Ce-IAA5 was AZ-specific in floret buds. A temporal regulation of Ce-IAA transcript levels in the floret AZ was found, with 2,4-D inducing higher expression levels than NAA in floret buds. These Ce-IAA expression levels were negatively correlated with floret abscission. The differential transport characteristics of NAA and 2,4-D in cestrum cut flowers were reflected in differential activation of the Ce-IAA genes identified in the floret AZ. Therefore, Aux/IAA genes can be used as molecular markers to measure auxin activity, which reflects free auxin level in the AZ. Two of the identified genes, Ce-IAA1 and Ce-IAA5, may also have a regulatory role in abscission.

“PERLE bedside-examination-course for candidates in state examination” – Developing a training program for the third part of medical state examination (oral examination with practical skills)

PubMed Central

Karthaus, Anne; Schmidt, Anita

2016-01-01

Introduction: In preparation for the state examination, many students have open questions and a need for advice. Tutors of the Skills Lab PERLE-„Praxis ERfahren und Lernen“ (experiencing and learning practical skills) have developed a new course concept to provide support and practical assistance for the examinees. Objectives: The course aims to familiarize the students with the exam situation in order to gain more confidence. This enables the students to experience a confrontation with the specific situation of the exam in a protected environment. Furthermore, soft skills are utilized and trained. Concept of the course: The course was inspired by the OSCE-model (Objective Structured Clinical Examination), an example for case-based learning and controlling. Acquired knowledge can be revised and extended through the case studies. Experienced tutors provide assistance in discipline-specific competencies, and help in organizational issues such as dress code and behaviour. Evaluation of the course: An evaluation was conducted by the attending participants after every course. Based on this assessment, the course is constantly being developed. In March, April and October 2015 six courses, with a total of 84 participants, took place. Overall 76 completed questionnaires (91%) were analysed. Discussion: Strengths of the course are a good tutor-participants-ratio with 1:4 (1 Tutor provides guidance for 4 participants), the interactivity of the course, and the high flexibility in responding to the group's needs. Weaknesses are the tight schedule, and the currently not yet performed evaluation before and after the course. Conclusion: In terms of “best practise”, this article shows an example of how to offer low-cost and low-threshold preparation for the state examination. PMID:27579355

Production code control system for hydrodynamics simulations

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

Slone, D.M.

1997-08-18

We describe how the Production Code Control System (pCCS), written in Perl, has been used to control and monitor the execution of a large hydrodynamics simulation code in a production environment. We have been able to integrate new, disparate, and often independent, applications into the PCCS framework without the need to modify any of our existing application codes. Both users and code developers see a consistent interface to the simulation code and associated applications regardless of the physical platform, whether an MPP, SMP, server, or desktop workstation. We will also describe our use of Perl to develop a configuration managementmore » system for the simulation code, as well as a code usage database and report generator. We used Perl to write a backplane that allows us plug in preprocessors, the hydrocode, postprocessors, visualization tools, persistent storage requests, and other codes. We need only teach PCCS a minimal amount about any new tool or code to essentially plug it in and make it usable to the hydrocode. PCCS has made it easier to link together disparate codes, since using Perl has removed the need to learn the idiosyncrasies of system or RPC programming. The text handling in Perl makes it easy to teach PCCS about new codes, or changes to existing codes.« less

How transformational learning promotes caring, consultation and creativity, and ultimately contributes to sustainable development: Lessons from the Partnership for Education and Research about Responsible Living (PERL) network

NASA Astrophysics Data System (ADS)

Thoresen, Victoria Wyszynski

2017-12-01

Oases of learning which are transformative and lead to significant behavioural change can be found around the globe. Transformational learning has helped learners not only to understand what they have been taught but also to re-conceptualise and re-apply this understanding to their daily lives. Unfortunately, as many global reports indicate, inspirational transformational learning approaches for sustainable development are rare and have yet to become the norm - despite calls for such approaches by several outstanding educators and organisations. This article examines three learning approaches developed by the network of the Partnership for Education and Research about Responsible Living (PERL). These approaches are structured around core elements of transformative learning for sustainable development, yet focus particularly on the ability to care, consult with others and be creative. They seem to depend on the learners' ability to articulate their perceptions of sustainable development in relation to their own values and to identify how these are actualised in their daily life. Together with other core elements of transformative learning, an almost magical (not precisely measurable) synergy then emerges. The intensity of this synergy appears to be directly related to the individual learner's understanding of the contradictions, interlinkages and interdependencies of modern society. The impact of this synergy seems to be concurrent with the extent to which the learner engages in a continual learning process with those with whom he/she has contact. The findings of this study suggest that mainstreaming transformational learning for sustainable development in ways that release the "magic synergy of creative caring" can result in the emergence of individuals who are willing and able to move from "business as usual" towards more socially just, economically equitable, and environmentally sensitive behaviour.

Strategies for single-point diamond machining a large format germanium blazed immersion grating

NASA Astrophysics Data System (ADS)

Montesanti, R. C.; Little, S. L.; Kuzmenko, P. J.; Bixler, J. V.; Jackson, J. L.; Lown, J. G.; Priest, R. E.; Yoxall, B. E.

2016-07-01

A large format germanium immersion grating was flycut with a single-point diamond tool on the Precision Engineering Research Lathe (PERL) at the Lawrence Livermore National Laboratory (LLNL) in November - December 2015. The grating, referred to as 002u, has an area of 59 mm x 67 mm (along-groove and cross-groove directions), line pitch of 88 line/mm, and blaze angle of 32 degree. Based on total groove length, the 002u grating is five times larger than the previous largest grating (ZnSe) cut on PERL, and forty-five times larger than the previous largest germanium grating cut on PERL. The key risks associated with cutting the 002u grating were tool wear and keeping the PERL machine running uninterrupted in a stable machining environment. This paper presents the strategies employed to mitigate these risks, introduces pre-machining of the as-etched grating substrate to produce a smooth, flat, damage-free surface into which the grooves are cut, and reports on trade-offs that drove decisions and experimental results.

Phénomènes aux parois dans un mélange binaire critique

NASA Astrophysics Data System (ADS)

Fisher, Michael E.; de Gennes, Pierre-Gilles

Au contact d'un mélange binaire critique, une plaque solide perturbe les concentrations sur une épaisseur de corrélation ξ(T). Aux distances z < ξ, la perturbation décroit comme z-β/ν, ou β et ν sont deux exposants critiques (β/ν 1/2). Deux plaques identiques immergées dans le mélange, séparées par une épaisseur D < ξ, doivent s'attirer avec une énergie par centimètre carrè proportionnelle à 1/D2. Cette attraction s'ajoute à celle de van der Waals, et pourrait jouer un rôle dans la stabilité de certains colloïdes. In a near critical binary liquid mixture, the concentrations near a wall are perturbed over a distance of the order of the correlation length (ξ(T). At distances z smaller than ξ, the perturbation decreases, like z-β/ν. where β and ν are critical exponents (β/ν 1/2). Two identical plates in a mixture, separated by a thickness D < ξ, Should attract each other, the interaction decreasing as in 1/D2. This attraction is superimposed on the van der Waals forces, and may play a role in the stability of certain colloids.

DET/MPS - THE GSFC ENERGY BALANCE PROGRAM, DIRECT ENERGY TRANSFER/MULTIMISSION SPACECRAFT MODULAR POWER SYSTEM (MACINTOSH A/UX VERSION)

NASA Technical Reports Server (NTRS)

Jagielski, J. M.

1994-01-01

The DET/MPS programs model and simulate the Direct Energy Transfer and Multimission Spacecraft Modular Power System in order to aid both in design and in analysis of orbital energy balance. Typically, the DET power system has the solar array directly to the spacecraft bus, and the central building block of MPS is the Standard Power Regulator Unit. DET/MPS allows a minute-by-minute simulation of the power system's performance as it responds to various orbital parameters, focusing its output on solar array output and battery characteristics. While this package is limited in terms of orbital mechanics, it is sufficient to calculate eclipse and solar array data for circular or non-circular orbits. DET/MPS can be adjusted to run one or sequential orbits up to about one week, simulated time. These programs have been used on a variety of Goddard Space Flight Center spacecraft projects. DET/MPS is written in FORTRAN 77 with some VAX-type extensions. Any FORTRAN 77 compiler that includes VAX extensions should be able to compile and run the program with little or no modifications. The compiler must at least support free-form (or tab-delineated) source format and 'do do-while end-do' control structures. DET/MPS is available for three platforms: GSC-13374, for DEC VAX series computers running VMS, is available in DEC VAX Backup format on a 9-track 1600 BPI tape (standard distribution) or TK50 tape cartridge; GSC-13443, for UNIX-based computers, is available on a .25 inch streaming magnetic tape cartridge in UNIX tar format; and GSC-13444, for Macintosh computers running AU/X with either the NKR FORTRAN or AbSoft MacFORTRAN II compilers, is available on a 3.5 inch 800K Macintosh format diskette. Source code and test data are supplied. The UNIX version of DET requires 90K of main memory for execution. DET/MPS was developed in 1990. A/UX and Macintosh are registered trademarks of Apple Computer, Inc. VMS, DEC VAX and TK50 are trademarks of Digital Equipment Corporation. UNIX is a

The Fundamental Issues Study within the British BMD Review

DTIC Science & Technology

1998-02-01

also be considered. Nevertheless, how formidable a challenge is posed by the ascent release of submunitions is acknowledged by Richard Garwin on the...Arguably, the crunch came in February 1987 when Richard Perle, visiting London as US Assistant Secretary for Defense, extolled a strong SDI as the...resignation of Richard Perle. That year was also to see the departure from political office in the Pentagon of four other SDI stalwarts: Frank

Tilt and strain deformation induced by hydrologically active natural fractures: application to the tiltmeters installed in Sainte-Croix-aux-Mines observatory (France)

NASA Astrophysics Data System (ADS)

Longuevergne, Laurent; Florsch, Nicolas; Boudin, Frédéric; Oudin, Ludovic; Camerlynck, Christian

2009-08-01

We investigate the deformation induced by water pressure variations in hydrologically active natural fractures, and recorded by tiltmeters and strainmeters. The deformation associated with a single fracture is derived using finite-element modelling (FEM). A range in fracture geometries is explored, first to highlight the sensitivity of each geometrical parameter to the deformation, and secondly to allow transfer to observation sites. Water level variations in the fracture are then derived from a hydrological model, driven by observed rainfall, and calibrated on fracture water flow measurements. The modelling results are explicitly applied to constrain the local hydrological contribution to observations with the 100-m-long hydrostatic tiltmeter installed at Sainte-Croix-aux-Mines (France). Our study shows that well-founded physical modelling of local hydrological effect allows a substantial correction of records in observatories.

FAST: FAST Analysis of Sequences Toolbox

PubMed Central

Lawrence, Travis J.; Kauffman, Kyle T.; Amrine, Katherine C. H.; Carper, Dana L.; Lee, Raymond S.; Becich, Peter J.; Canales, Claudia J.; Ardell, David H.

2015-01-01

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought. PMID:26042145

Initiated Protocol Telephony Feasibility for the US Navy, Embedded Proof-of-Concept

DTIC Science & Technology

2011-03-01

2.1 Generating Certificates Using Open SSL 1. OpenSSL can be used to generate certificates. There are a number of helper scripts written in Perl that...help with the creation and maintenance of the certificate and keys. OpenSSL is available from a number of sites, i.e., slproweb.com. The default...installation is adequate although it may be useful to add the OpenSSL \\bin directory to the system environment variable PATH. Perl is also available

Pollution Atmosphérique et Santé: Corrélation ou Causalité? Le Cas de la Relation entre l'Exposition aux Particules et la Mortalité Cardio-pulmonaire.

PubMed

Dab, William; Ségala, Claire; Dor, Frédéric; Festy, Bernard; Lameloise, Philippe; Moullec, Yvon Le; Tertre, Alain Le; Médina, Sylvia; Quénel, Philippe; Wallaert, Benoît; Zmirou, Et Denis

2001-02-01

De nombreuses études épidémiologiques ont observé dans des contextes différents une faible relation à court terme entre les particules et la mortalité cardio-pulmonaire, même quand les normes de qualité de l'air n'étaient pas dépassées. La causalité de cette relation est un enjeu de santé publique en raison de l'importance de la population exposée. Notre objectif est de faire l'inventaire critique des arguments utilisés dans 15 revues de la littérature publiées. Nous expliquons l'importance de distinguer la validité de la causalité et analysons de façon systématique les différents critères de jugement dans le contexte des études écologiques temporelles. Notre conclusion est que la relation observée est valide et que la plupart des critères de causalité sont respectés. Diminuer le niveau d'exposition des populations aux particules est souhaitable. En Europe, en agissant à la source, notamment sur les émissions Diesel, on diminuera aussi d'autres polluants qui peuvent jouer un rôle sanitaire. Aux États-Unis, la situation est plus complexe car les particules sont surtout secondaires. Il est également indispensable de poursuivre les recherches pour mieux connaître les déterminants des expositions globales des individus et mieux comprendre le rôle toxique des différents facteurs physico-chimiques des particules.

Mutations in the Circadian Gene period Alter Behavioral and Biochemical Responses to Ethanol in Drosophila

PubMed Central

Liao, Jennifer; Seggio, Joseph A.; Ahmad, S. Tariq

2016-01-01

Clock genes, such as period, which maintain an organism’s circadian rhythm, can have profound effects on metabolic activity, including ethanol metabolism. In turn, ethanol exposure has been shown in Drosophila and mammals to cause disruptions of the circadian rhythm. Previous studies from our labs have shown that larval ethanol exposure disrupted the free-running period and period expression of Drosophila. In addition, a recent study has shown that arrhythmic flies show no tolerance to ethanol exposure. As such, Drosophila period mutants, which have either a shorter than wild-type free-running period (perS) or a longer one (perL), may also exhibit altered responses to ethanol due to their intrinsic circadian differences. In this study, we tested the initial sensitivity and tolerance of ethanol exposure on Canton-S, perS, and perL, and then measured their Alcohol Dehydrogenase (ADH) and body ethanol levels. We showed that perL flies had slower sedation rate, longer recovery from ethanol sedation, and generated higher tolerance for sedation upon repeated ethanol exposure compared to Canton-S wild-type flies. Furthermore, perL flies had lower ADH activity and had a slower ethanol clearance compared to wild-type flies. The findings of this study suggest that period mutations influence ethanol induced behavior and ethanol metabolism in Drosophila and that flies with longer circadian periods are more sensitive to ethanol exposure. PMID:26802726

Identification de lois constitutives et de lois de frottement adaptées aux grandes vitesses de sollicitation

NASA Astrophysics Data System (ADS)

Dalverny, O.; Capéraa, S.; Pantalé, O.; Sattouf, C.

2002-12-01

Cet article présente une méthodologie d'identification de lois constitutives et de lois de contact adaptées aux matériaux métalliques sous chargement dynamique à grande vitesse de déformation. Les essais sont effectués à partir de montages expérimentaux adaptés à un lanceur à gaz permettant d'obtenir une vitesse de projectile de l'ordre de 350m/s pour une masse totale de 30gr. Le premier essai consiste en un impact de Taylor correspondant à un chargement mécanique de type compression. Le second essai de type “extrusion conique" permet la détermination des lois de frottement à grande vitesse. La procédure générale d'identification des lois de comportement à partir d'essais dynamiques se fait au moyen d'une analyse post-mortem des échantillons et de la corrélation entre ces résultats expérimentaux et un modèle numérique des essais. Pour les deux cas précédemment cités, nous présentons la configuration optimale d'essai ainsi que les résultats obtenus à partir d'un algorithme d'optimisation de type Levenberg-Marquard.

Rear surface effects in high efficiency silicon solar cells

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

Wenham, S.R.; Robinson, S.J.; Dai, X.

1994-12-31

Rear surface effects in PERL solar cells can lead not only to degradation in the short circuit current and open circuit voltage, but also fill factor. Three mechanisms capable of changing the effective rear surface recombination velocity with injection level are identified, two associated with oxidized p-type surfaces, and the third with two dimensional effects associated with a rear floating junction. Each of these will degrade the fill factor if the range of junction biases corresponding to the rear surface transition, coincides with the maximum power point. Despite the identified non idealities, PERL cells with rear floating junctions (PERF cells)more » have achieved record open circuit voltages for silicon solar cells, while simultaneously achieving fill factor improvements relative to standard PERL solar cells. Without optimization, a record efficiency of 22% has been demonstrated for a cell with a rear floating junction. The results of both theoretical and experimental studies are provided.« less

Three Psychotherapies Examined: Ellis, Rogers, Perls

ERIC Educational Resources Information Center

Stoten, J.; Goos, W.

1974-01-01

This study uses Bales' Interaction Process Analysis (I. P. A.) to identify significant process elements in counselling and psychotherapy. For this purpose, the film "Three Approaches to Psychotherapy" was analysed. (Editor)

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

Aspects épidémiologiques des accidents vasculaires cérébraux (AVC) aux urgences de l'institut de cardiologie d'Abidjan (ICA)

PubMed Central

N'goran, Yves N'da Kouakou; Traore, Fatou; Tano, Micesse; Kramoh, Kouadio Euloge; Kakou, Jean-Baptiste Anzouan; Konin, Christophe; Kakou, Maurice Guikahue

2015-01-01

Introduction L'objectif de notre étude était de décrire les caractéristiques sociodémographiques et les Facteurs de Risque cardio-Vasculaires (FRV) des patients admis pour accidents vasculaires cérébraux (AVC) dans un service autre que celui de la neurologie. Méthodes Étude transversale rétrospective sur une période de 2 ans (janv. 2010 et déc. 2011), réalisée aux urgences de l'institut de cardiologie d'Abidjan. Résultats Il s'agissait de 176 adultes avec un âge moyen de 60 ans, une prédominance féminine. Les facteurs de risque majeurs retrouvés étaient l'hypertension artérielle dans 86,4% des cas, le diabète dans 11,4% des cas, le tabagisme dans 2,2% des cas. Les motifs de consultation étaient la perte de connaissance dans 36,4% des cas, l'hémiplégie dans 31,8% des cas, les céphalées dans 17,4% des cas, les vertiges dans 10,9% et les palpitations dans 2,2% des cas. La tension artérielle systolique moyenne était à 174 mmHg, la tension artérielle diastolique moyenne était à 105 mmHg et la pression pulsée moyenne était à 70 mmHg. Les AVC étaient associés à une arythmie complète par fibrillation auriculaire dans 11,4% des cas. Les AVC ischémiques représentaient 84,1%. L’évolution aux urgences a été marquée par un décès dans 17% (30) des cas. Conclusion Les AVC constituent un problème majeur de santé publique. Malgré sa prédominance féminine, ils (AVC) touchaient 44% des hommes dans notre étude lorsqu'on sait qu'en Afrique l'activité sociale repose sur les hommes. Ils restent une pathologie grave par la forte létalité. PMID:26327997

Perl Tools for Automating Satellite Ground Systems

NASA Technical Reports Server (NTRS)

McLean, David; Haar, Therese; McDonald, James

2000-01-01

The freeware scripting language Pert offers many opportunities for automating satellite ground systems for new satellites as well as older, in situ systems. This paper describes a toolkit that has evolved from of the experiences gained by using Pert to automate the ground system for the Compton Gamma Ray Observatory (CGRO) and for automating some of the elements in the Earth Observing System Data and Operations System (EDOS) ground system at Goddard Space Flight Center (GSFC). CGRO is an older ground system that was forced to automate because of fund cuts. Three 8 hour shifts were cut back to one 8 hour shift, 7 days per week. EDOS supports a new mission called Terra, launched December 1999 that requires distribution and tracking of mission-critical reports throughout the world. Both of these ground systems use Pert scripts to process data and display it on the Internet as well as scripts to coordinate many of the other systems that make these ground systems work as a coherent whole. Another task called Automated Multimodal Trend Analysis System (AMTAS) is looking at technology for isolation and recovery of spacecraft problems. This effort has led to prototypes that seek to evaluate various tools and technology that meet at least some of the AMTAS goals. The tools, experiences, and lessons learned by implementing these systems are described here.

JEnsembl: a version-aware Java API to Ensembl data systems.

PubMed

Paterson, Trevor; Law, Andy

2012-11-01

The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

J. M. Despréaux' lichens from the Canary Islands and West Africa: an account of a 19th century collection found in an English archive.

PubMed

Aguirre-Hudson, Begoña; Whitworth, Isabella; Spooner, Brian M

2011-01-01

This is an historical and descriptive account of 28 herbarium specimens, 27 lichens and an alga, found in the archives of Charles Chalcraft, a descendant of the Bedford family, who were dye manufacturers in Leeds, England, in the 19th century. The lichens comprise 13 different morphotypes collected in the Canary Islands and West Africa by the French botanist J. M. Despréaux between 1833 and 1839. The collections include samples of "Roccella fuciformis", "R. phycopsis" and "R. tinctoria" (including the fertile morphotype "R. canariensis"), "Ramalina crispatula" and "R. cupularis", two distinct morphotypes of "Sticta", "S. canariensis" and "S. dufouri", "Physconia enteroxantha", "Pseudevernia furfuracea var. ceratea" and "Pseudocyphellaria argyracea". The herbarium also includes authentic material of "Parmotrema tinctorum" and a probable syntype of "Seirophora scorigena". Most of these species are known as a source of the purple dye orchil, which was used to dye silk and wool.

Yaxx: Yet another X-ray extractor

NASA Astrophysics Data System (ADS)

Aldcroft, Tom

2013-06-01

Yaxx is a Perl script that facilitates batch data processing using Perl open source software and commonly available software such as CIAO/Sherpa, S-lang, SAS, and FTOOLS. For Chandra and XMM analysis it includes automated spectral extraction, fitting, and report generation. Yaxx can be run without climbing an extensive learning curve; even so, yaxx is highly configurable and can be customized to support complex analysis. yaxx uses template files and takes full advantage of the unique Sherpa / S-lang environment to make much of the processing user configurable. Although originally developed with an emphasis on X-ray data analysis, yaxx evolved to be a general-purpose pipeline scripting package.

Séroprévalence et facteurs associés au VIH et aux hépatites virales B et C dans la ville de Bafoussam au Cameroun

PubMed Central

Mbopi-Keou, Francois-Xavier; Nkala, Isabelle Vanessa Monthe; Kalla, Ginette Claude Mireille; Nguefack-Tsague, Georges; Kamga, Hortense Gonsu; Noubom, Michel; Mvogo, Côme Ebana; Sosso, Maurice Aurelien

2015-01-01

Introduction L'objectif de ce travail était de déterminer la séroprévalence et les facteurs associés au VIH et aux hépatites virales B et C dans la ville de Bafoussam au Cameroun. Méthodes Il s'agissait d'une étude descriptive et analytique réalisée de février 2012 à Juin 2012 dans la ville de Bafoussam au Cameroun. Pour cette étude, nous avons obtenu une clairance éthique. Résultats Au total, 982 personnes ont été dépistées pour le VIH et les hépatites virales B et C. Les femmes représentaient 56,3% des personnes dépistées. La tranche d’âge la plus représentée était celle des 20 à 24 ans. L’âge médian était de 34,5 ans. Les prévalences du VIH, de l'AgHBs, et de l'Ac anti HCV étaient respectivement de 6,0%, 4,1%, et 0,4%. La prévalence du VIH était 2 fois plus élevée parmi les femmes que les hommes avec 8,1% contre 3,5% (p=0,01). Les prévalences les plus élevées ont été observées chez les personnes de 30 à 34 ans, 40 à 44 ans avec 15,0% et 11,5% (p=0,01), les personnes sans emploi avec 11,1% (p<0,001) et les personnes en union libre avec 17,9% (p=0,000). La prévalence du VIH n’était pas directement liée aux comportements et pratiques sexuels de la population de l’étude. On enregistrait une prévalence élevée de 29,3% chez les individus ayant déclaré avoir au moins une infection sexuellement transmissible (p=0,000). Conclusion Il apparait urgent de mettre en place des stratégies de prévention contre le VIH, les hépatites virales et les facteurs associés au Cameroun. PMID:26113899

Limiting loss mechanisms in 23% efficient silicon solar cells

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

Aberle, A.G.; Altermatt, P.P.; Heiser, G.

1995-04-01

The ``passivated emitter and rear locally diffused`` (PERL) silicon solar cell structure presently demonstrates the highest terrestrial performance of any silicon-based solar cell. This paper presents a detailed investigation of the limiting loss mechanisms in PERL cells exhibiting independently confirmed 1-sun efficiencies of up to 23.0%. Optical, resistive, and recombinative losses are all analyzed under the full range of solar cell operating conditions with the aid of two-dimensional (2D) device simulations. The analysis is based on measurements of the reflectance, quantum efficiency, dark and illuminated current--voltage ({ital I}--{ital V}) characteristics, and properties of the Si--SiO{sub 2} interfaces employed on thesemore » cells for surface passivation. Through the use of the 2D simulations, particular attention has been paid to the magnitudes of the spatially resolved recombination losses in these cells. It is shown that approximately 50% of the recombination losses at the 1-sun maximum power point occur in the base of the cells, followed by recombination losses at the rear and front oxidized surfaces (25% and {lt}25%, respectively). The relatively low fill factors of PERL cells are principally a result of resistive losses; however, the recombination behavior in the base and at the rear surface also contributes. This work predicts that the efficiency of 23% PERL cells could be increased by about 0.7% absolute if ohmic losses were eliminated, a further 1.1% absolute if there were no reflection losses at the nonmetallized front surface regions, about 2.0% by introducing ideal light trapping and eliminating shading losses due to the front metallization, and by about 3.7% absolute if the device had no defect-related recombination losses. New design rules for future efficiency improvements, evident from this analysis, are also presented. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.« less

A Ruby API to query the Ensembl database for genomic features.

PubMed

Strozzi, Francesco; Aerts, Jan

2011-04-01

The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases. Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.

Negative phototropism is seen in Arabidopsis inflorescences when auxin signaling is reduced to a minimal level by an Aux/IAA dominant mutation, axr2.

PubMed

Sato, Atsuko; Sasaki, Shu; Matsuzaki, Jun; Yamamoto, Kotaro T

2015-01-01

Inflorescences of a dominant mutant of Arabidopsis Aux/IAA7, axr2, showed negative phototropism with a similar fluence response curve to the positive phototropism of wild-type stems. Application of a synthetic auxin, NAA, and an inhibitor of polar auxin transport, NPA, increased and decreased respectively the magnitude of the phototropic response in the wild type, while in axr2 application of NAA reduced the negative phototropic response and NPA had no effect. Decapitation of the apex induced a small negative phototropism in wild-type stems, and had no effect in axr2 plants. Inflorescences of the double mutants of auxin transporters, pgp1 pgp19, showed no phototropic response, while decapitation resulted in a negative phototropic response. These results suggest that negative phototropism can occur when the level of auxin or of auxin signaling is reduced to a minimal level, and that in plant axial organs the default phototropic response to unilateral blue light may be negative. Expression of axr2 protein by an endodermis-specific promoter resulted in agravitropism of inflorescences in a similar way to that of axr2, but phototropism was normal, confirming that the endodermis does not play a critical role in phototropism.

Speech-rhythm characteristics of client-centered, Gestalt, and rational-emotive therapy interviews.

PubMed

Chen, C L

1981-07-01

The aim of this study was to discover whether client-centered, Gestalt, and rational-emotive psychotherapy interviews could be described and differentiated on the basis of quantitative measurement of their speech rhythms. These measures were taken from the sound portion of a film showing interviews by Carl Rogers, Frederick Perls, and Albert Ellis. The variables used were total session and percentage of speaking times, speaking turns, vocalizations, interruptions, inside and switching pauses, and speaking rates. The three types of interview had very distinctive patterns of speech-rhythm variables. These patterns suggested that Rogers's Client-centered therapy interview was patient dominated, that Ellis's rational-emotive therapy interview was therapist dominated, and that Perls's Gestalt therapy interview was neither therapist nor patient dominated.

JEnsembl: a version-aware Java API to Ensembl data systems

PubMed Central

Paterson, Trevor; Law, Andy

2012-01-01

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact: jensembl-develop@lists.sf.net, andy.law@roslin.ed.ac.uk, trevor.paterson@roslin.ed.ac.uk PMID:22945789

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectropscopy using IFEFFIT

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

Ravel, B.; Newville, M.; UC)

2010-07-20

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demandsmore » of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.« less

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

PubMed

Holt, Kathryn E; Teo, Yik Y; Li, Heng; Nair, Satheesh; Dougan, Gordon; Wain, John; Parkhill, Julian

2009-08-15

Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded > or =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x. The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.

The Potential of CGI: Using Pre-Built CGI Scripts to Make Interactive Web Pages.

ERIC Educational Resources Information Center

Nackerud, Shane A.

1998-01-01

Describes CGI (Common Gateway Interface) scripts that are available on the Web and explains how librarians can use them to make Web pages more interactive. Topics include CGI security; Perl scripts; UNIX; and HTML. (LRW)

Negative phototropism is seen in Arabidopsis inflorescences when auxin signaling is reduced to a minimal level by an Aux/IAA dominant mutation, axr2

PubMed Central

Sato, Atsuko; Sasaki, Shu; Matsuzaki, Jun; Yamamoto, Kotaro T.

2015-01-01

Inflorescences of a dominant mutant of Arabidopsis Aux/IAA7, axr2, showed negative phototropism with a similar fluence response curve to the positive phototropism of wild-type stems. Application of a synthetic auxin, NAA, and an inhibitor of polar auxin transport, NPA, increased and decreased respectively the magnitude of the phototropic response in the wild type, while in axr2 application of NAA reduced the negative phototropic response and NPA had no effect. Decapitation of the apex induced a small negative phototropism in wild-type stems, and had no effect in axr2 plants. Inflorescences of the double mutants of auxin transporters, pgp1 pgp19, showed no phototropic response, while decapitation resulted in a negative phototropic response. These results suggest that negative phototropism can occur when the level of auxin or of auxin signaling is reduced to a minimal level, and that in plant axial organs the default phototropic response to unilateral blue light may be negative. Expression of axr2 protein by an endodermis-specific promoter resulted in agravitropism of inflorescences in a similar way to that of axr2, but phototropism was normal, confirming that the endodermis does not play a critical role in phototropism. PMID:25738325

Personal Change and Intervention Style

ERIC Educational Resources Information Center

Andrews, John D. W.

1977-01-01

Presents a theory of personal change and analyzes growth-producing interventions using examples from the film, "Three Approaches to Psychotherapy". Compares the styles of Carl Rogers, Frttz Perls, and Albert Ellis to illustrate the theory. (Editor/RK)

Gestalt Workshops: Suggested In-Service Training for Teachers.

ERIC Educational Resources Information Center

Fiordo, Richard

1981-01-01

Fritz Perls' Gestalt Workshops are explained and recommended for inservice training for teachers. Since Gestalt Workshops increase their participants' growth, awareness, and integration personally and environmentally, their benefit to classroom teachers would be direct and dramatic. (Author)

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.

PubMed

Sand, Olivier; Thomas-Chollier, Morgane; Vervisch, Eric; van Helden, Jacques

2008-01-01

This protocol shows how to access the Regulatory Sequence Analysis Tools (RSAT) via a programmatic interface in order to automate the analysis of multiple data sets. We describe the steps for writing a Perl client that connects to the RSAT Web services and implements a workflow to discover putative cis-acting elements in promoters of gene clusters. In the presented example, we apply this workflow to lists of transcription factor target genes resulting from ChIP-chip experiments. For each factor, the protocol predicts the binding motifs by detecting significantly overrepresented hexanucleotides in the target promoters and generates a feature map that displays the positions of putative binding sites along the promoter sequences. This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is approximately 6 min on the example data set.

The clathrin-binding motif and the J-domain of Drosophila Auxilin are essential for facilitating Notch ligand endocytosis

PubMed Central

Kandachar, Vasundhara; Bai, Ting; Chang, Henry C

2008-01-01

Background Ligand endocytosis plays a critical role in regulating the activity of the Notch pathway. The Drosophila homolog of auxilin (dAux), a J-domain-containing protein best known for its role in the disassembly of clathrin coats from clathrin-coated vesicles, has recently been implicated in Notch signaling, although its exact mechanism remains poorly understood. Results To understand the role of auxilin in Notch ligand endocytosis, we have analyzed several point mutations affecting specific domains of dAux. In agreement with previous work, analysis using these stronger dAux alleles shows that dAux is required for several Notch-dependent processes, and its function during Notch signaling is required in the signaling cells. In support of the genetic evidences, the level of Delta appears elevated in dAux deficient cells, suggesting that the endocytosis of Notch ligand is disrupted. Deletion analysis shows that the clathrin-binding motif and the J-domain, when over-expressed, are sufficient for rescuing dAux phenotypes, implying that the recruitment of Hsc70 to clathrin is a critical role for dAux. However, surface labeling experiment shows that, in dAux mutant cells, Delta accumulates at the cell surface. In dAux mutant cells, clathrin appears to form large aggregates, although Delta is not enriched in these aberrant clathrin-positive structures. Conclusion Our data suggest that dAux mutations inhibit Notch ligand internalization at an early step during clathrin-mediated endocytosis, before the disassembly of clathrin-coated vesicles. Further, the inhibition of ligand endocytosis in dAux mutant cells possibly occurs due to depletion of cytosolic pools of clathrin via the formation of clathrin aggregates. Together, our observations argue that ligand endocytosis is critical for Notch signaling and auxilin participates in Notch signaling by facilitating ligand internalization. PMID:18466624

Molecular cloning and characterization of the genes encoding an auxin efflux carrier and the auxin influx carriers associated with the adventitious root formation in mango (Mangifera indica L.) cotyledon segments.

PubMed

Li, Yun-He; Zou, Ming-Hong; Feng, Bi-Hong; Huang, Xia; Zhang, Zhi; Sun, Guang-Ming

2012-06-01

Polar auxin transport (PAT) plays an important role in the adventitious root formation of mango cotyledon segments, but the molecular mechanism remains unclear. In this study, we cloned a gene encoding an auxin efflux carrier (designated as MiPIN1), and we cloned four genes encoding auxin influx carriers (designated as MiAUX1, MiAUX2, MiAUX3 and MiAUX4). The results of a phylogenetic tree analysis indicated that MiPIN1 and the MiAUXs belong to plant PIN and AUXs/LAXs groups. Quantitative real-time PCR indicated that the expression of MiPIN1 and the MiAUXs was lowest at 0 days but sharply increased on and after day 4. During the root formation in the mango cotyledon segments, the MiPIN1 expression in the distal cut surface (DCS) was always higher than the expression in the proximal cut surface (PCS) whereas the expression of the MiAUXs in the PCS was usually higher than in the DCS. This expression pattern might be result in the PAT from the DCS to the PCS, which is essential for the adventitious root formation in the PCS. Our previous study indicated that a pre-treatment of embryos with indole-3-butyric acid (IBA) significantly promoted adventitious rooting in PCS whereas a pre-treatment with 2,3,5-triiodobenzoic acid (TIBA) completely inhibited this rooting. In this study, however, IBA and TIBA pre-treatments slightly changed the expression of MiPIN1. In contrast, while the MiAUX3 and MiAUX4 expression levels were significantly up-regulated by the IBA pre-treatment, the expression levels were down-regulated by the TIBA pre-treatment. These findings imply that MiAUX3 and MiAUX4 are more sensitive to the IBA and TIBA treatments and that they might play important roles during adventitious root formation in mango cotyledon segments. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Person-Centered Gestalt Therapy: A Synthesis.

ERIC Educational Resources Information Center

Herlihy, Barbara

1985-01-01

Highlights the similarities between the person-centered approach to counseling of Carl Rogers and the Gestalt therapy of Fritz Perls. Discusses implementation of the two approaches and suggests they may be synthesized into a person-centered Gestalt therapy. (MCF)

MOCASSIN-prot software

USDA-ARS?s Scientific Manuscript database

MOCASSIN-prot is a software, implemented in Perl and Matlab, for constructing protein similarity networks to classify proteins. Both domain composition and quantitative sequence similarity information are utilized in constructing the directed protein similarity networks. For each reference protein i...

Advantages of Application of Electronic Commerce in Procurement for the Armed Forces of Brazil and South Korea

DTIC Science & Technology

2001-12-01

Northern Europe.”, Ecommerce Times, [http://www.ecommercetimes.com/perl/story/3546.html], June 2001. Mc Gregor, Don, “Encryption”, [http...sans.org/infosecFAQ/ ecommerce /fraud.htm], September 2001. Schneider, Gary P. and James T. Perry, “Electronic Commerce”, Course Technology, 2001

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.

PubMed

Simillion, Cedric; Janssens, Koen; Sterck, Lieven; Van de Peer, Yves

2008-01-01

i-ADHoRe is a software tool that combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. The new version offers, besides a significant increase in performance, several optimizations to the algorithm, most importantly to the profile alignment routine. As a result, the annotations of multiple genomes, or parts thereof, can be fed simultaneously into the program, after which it will report all regions of homology, both within and between genomes. The i-ADHoRe 2.0 package contains the C++ source code for the main program as well as various Perl scripts and a fully documented Perl API to facilitate post-processing. The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http://bioinformatics.psb.ugent.be/

A RESTful Service Oriented Architecture for Science Data Processing

NASA Astrophysics Data System (ADS)

Duggan, B.; Tilmes, C.; Durbin, P.; Masuoka, E.

2012-12-01

The Atmospheric Composition Processing System is an implementation of a RESTful Service Oriented Architecture which handles incoming data from the Ozone Monitoring Instrument and the Ozone Monitoring and Profiler Suite aboard the Aura and NPP spacecrafts respectively. The system has been built entirely from open source components, such as Postgres, Perl, and SQLite and has leveraged the vast resources of the Comprehensive Perl Archive Network (CPAN). The modular design of the system also allows for many of the components to be easily released and integrated into the CPAN ecosystem and reused independently. At minimal expense, the CPAN infrastructure and community provide peer review, feedback and continuous testing in a wide variety of environments and architectures. A well defined set of conventions also facilitates dependency management, packaging, and distribution of code. Test driven development also provides a way to ensure stability despite a continuously changing base of dependencies.

Light-dependent gravitropism and negative phototropism of inflorescence stems in a dominant Aux/IAA mutant of Arabidopsis thaliana, axr2.

PubMed

Sato, Atsuko; Sasaki, Shu; Matsuzaki, Jun; Yamamoto, Kotaro T

2014-09-01

Gravitropism and phototropism of the primary inflorescence stems were examined in a dominant Aux/IAA mutant of Arabidopsis, axr2/iaa7, which did not display either tropism in hypocotyls. axr2-1 stems completely lacked gravitropism in the dark but slowly regained it in light condition. Though wild-type stems showed positive phototropism, axr2 stems displayed negative phototropism with essentially the same light fluence-response curve as the wild type (WT). Application of 1-naphthaleneacetic acid-containing lanolin to the stem tips enhanced the positive phototropism of WT, and reduced the negative phototropism of axr2. Decapitation of stems caused a small negative phototropism in WT, but did not affect the negative phototropism of axr2. p-glycoprotein 1 (pgp1) pgp19 double mutants showed no phototropism, while decapitated double mutants exhibited negative phototropism. Expression of auxin-responsive IAA14/SLR, IAA19/MSG2 and SAUR50 genes was reduced in axr2 and pgp1 pgp19 stems relative to that of WT. These suggest that the phototropic response of stem is proportional to the auxin supply from the shoot apex, and that negative phototropism may be a basal response to unilateral blue-light irradiation when the levels of auxin or auxin signaling are reduced to the minimal level in the primary stems. In contrast, all of these treatments reduced or did not affect gravitropism in wild-type or axr2 stems. Tropic responses of the transgenic lines that expressed axr2-1 protein by the endodermis-specific promoter suggest that AXR2-dependent auxin response in the endodermis plays a more crucial role in gravitropism than in phototropism in stems but no significant roles in either tropism in hypocotyls.

The Maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID Gene Family: Phylogeny, Synteny, and Unique Root-Type and Tissue-Specific Expression Patterns during Development

PubMed Central

Ludwig, Yvonne; Zhang, Yanxiang; Hochholdinger, Frank

2013-01-01

The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues. PMID:24223858

The maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID gene family: phylogeny, synteny, and unique root-type and tissue-specific expression patterns during development.

PubMed

Ludwig, Yvonne; Zhang, Yanxiang; Hochholdinger, Frank

2013-01-01

The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

U. S. Atlantic Fleet, Eighth Amphibious Force. Operation Plan Number 2-44

DTIC Science & Technology

1944-01-01

distributed with this Operation Order. (c) Panoramic Bench Sketches No. P-l for Boach 259 and No. P~3 for Loach 26l (South) givo viator level...To indicate tank or ID targets. (g) Green Cluster, White Cluster - Lift Artillery fire. Page 32 of 33. ANNEX KENS . GTMFIRS SUPPORT PLAN. TABLE VI...AURORA . SFCP 5 AUX GROUND SPOT - LIVERMORS SFCP 6 AUX GROUND SPOT - LA GLOIRE SFCP 7 AUX GROUND -SPOT ~ TERM- ERIC SFCP 8 AUX GROUND SPOT - ORION-KEAR

Climate Prediction Center - Reanalysis: Atmospheric Data

Science.gov Websites

files; i.e., wgrib for GRIB-2 files wgrib2mv,wgrib2ms parallel processing with wgrib2 grb1to2.pl perl US government, DOC, NWS, NCEP or CPC. All spelling errors are property of the finder. comments

Neuro-Linguistic Programming: The New Eclectic Therapy.

ERIC Educational Resources Information Center

Betts, Nicoletta C.

Richard Bandler and John Grinder developed neuro-linguisitc programming (NLP) after observing "the magical skills of potent psychotherapists" Frederick Perls, Virginia Satir, and Milton Erikson. They compiled the most effective techniques for building rapport, gathering data, and influencing change in psychotherapy, offering them only as…

Development and Evaluation of a Thai Learning System on the Web Using Natural Language Processing.

ERIC Educational Resources Information Center

Dansuwan, Suyada; Nishina, Kikuko; Akahori, Kanji; Shimizu, Yasutaka

2001-01-01

Describes the Thai Learning System, which is designed to help learners acquire the Thai word order system. The system facilitates the lessons on the Web using HyperText Markup Language and Perl programming, which interfaces with natural language processing by means of Prolog. (Author/VWL)

Applied Computational Chemistry for the Blind and Visually Impaired

ERIC Educational Resources Information Center

Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

2012-01-01

We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

The Surrogate Self

ERIC Educational Resources Information Center

Gunnison, Hugh

1976-01-01

The use of the "surrogate self" in counseling is a simple Gestalt-like role-playing technique (Perls 1969) that can be especially effective when the client has begun to see the counselor as a trusted, caring, and understanding person. The role-playing is described. (Author/EJT)

The HEASARC Swift Gamma-Ray Burst Archive: The Pipeline and the Catalog

NASA Technical Reports Server (NTRS)

Donato, Davide; Angelini, Lorella; Padgett, C.A.; Reichard, T.; Gehrels, Neil; Marshall, Francis E.; Sakamoto, Takanori

2012-01-01

Since its launch in late 2004, the Swift satellite triggered or observed an average of one gamma-ray burst (GRB) every 3 days, for a total of 771 GRBs by 2012 January. Here, we report the development of a pipeline that semi automatically performs the data-reduction and data-analysis processes for the three instruments on board Swift (BAT, XRT, UVOT). The pipeline is written in Perl, and it uses only HEAsoft tools and can be used to perform the analysis of a majority of the point-like objects (e.g., GRBs, active galactic nuclei, pulsars) observed by Swift. We run the pipeline on the GRBs, and we present a database containing the screened data, the output products, and the results of our ongoing analysis. Furthermore, we created a catalog summarizing some GRB information, collected either by running the pipeline or from the literature. The Perl script, the database, and the catalog are available for downloading and querying at the HEASARC Web site.

Pressure Ratio to Thermal Environments

NASA Technical Reports Server (NTRS)

Lopez, Pedro; Wang, Winston

2012-01-01

A pressure ratio to thermal environments (PRatTlE.pl) program is a Perl language code that estimates heating at requested body point locations by scaling the heating at a reference location times a pressure ratio factor. The pressure ratio factor is the ratio of the local pressure at the reference point and the requested point from CFD (computational fluid dynamics) solutions. This innovation provides pressure ratio-based thermal environments in an automated and traceable method. Previously, the pressure ratio methodology was implemented via a Microsoft Excel spreadsheet and macro scripts. PRatTlE is able to calculate heating environments for 150 body points in less than two minutes. PRatTlE is coded in Perl programming language, is command-line-driven, and has been successfully executed on both the HP and Linux platforms. It supports multiple concurrent runs. PRatTlE contains error trapping and input file format verification, which allows clear visibility into the input data structure and intermediate calculations.

Laser doping of boron-doped Si paste for high-efficiency silicon solar cells

NASA Astrophysics Data System (ADS)

Tomizawa, Yuka; Imamura, Tetsuya; Soeda, Masaya; Ikeda, Yoshinori; Shiro, Takashi

2015-08-01

Boron laser doping (LD) is a promising technology for high-efficiency solar cells such as p-type passivated locally diffused solar cells and n-type Si-wafer-based solar cells. We produced a printable phosphorus- or boron-doped Si paste (NanoGram® Si paste/ink) for use as a diffuser in the LD process. We used the boron LD process to fabricate high-efficiency passivated emitter and rear locally diffused (PERL) solar cells. PERL solar cells on Czochralski Si (Cz-Si) wafers yielded a maximum efficiency of 19.7%, whereas the efficiency of a reference cell was 18.5%. Fill factors above 79% and open circuit voltages above 655 mV were measured. We found that the boron-doped area effectively performs as a local boron back surface field (BSF). The characteristics of the solar cell formed using NanoGram® Si paste/ink were better than those of the reference cell.

The HEASARC Swift Gamma-Ray Burst Archive: The Pipeline and the Catalog

NASA Astrophysics Data System (ADS)

Donato, D.; Angelini, L.; Padgett, C. A.; Reichard, T.; Gehrels, N.; Marshall, F. E.; Sakamoto, T.

2012-11-01

Since its launch in late 2004, the Swift satellite triggered or observed an average of one gamma-ray burst (GRB) every 3 days, for a total of 771 GRBs by 2012 January. Here, we report the development of a pipeline that semi-automatically performs the data-reduction and data-analysis processes for the three instruments on board Swift (BAT, XRT, UVOT). The pipeline is written in Perl, and it uses only HEAsoft tools and can be used to perform the analysis of a majority of the point-like objects (e.g., GRBs, active galactic nuclei, pulsars) observed by Swift. We run the pipeline on the GRBs, and we present a database containing the screened data, the output products, and the results of our ongoing analysis. Furthermore, we created a catalog summarizing some GRB information, collected either by running the pipeline or from the literature. The Perl script, the database, and the catalog are available for downloading and querying at the HEASARC Web site.

The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation.

PubMed

Miguel-Arribas, Andrés; Hao, Jian-An; Luque-Ortega, Juan R; Ramachandran, Gayetri; Val-Calvo, Jorge; Gago-Córdoba, César; González-Álvarez, Daniel; Abia, David; Alfonso, Carlos; Wu, Ling J; Meijer, Wilfried J J

2017-01-01

Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer ( oriT ), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis . We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1 LS20 and aux2 LS20 , and which we show are essential for conjugation. Both Aux1 LS20 and Aux2 LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1 LS20 and Aux2 LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriT LS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1 LS20 and/or Aux2 LS20 are located upstream of almost 400 relaxase genes of the Rel LS20 family (MOB L ) of relaxases. Thus, Aux1 LS20 and Aux2 LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.

Perspectives on the energy landscape of Au-Cl binary systems from the structural phase diagram of AuxCly (x + y = 20).

PubMed

Tian, Zhimei; Cheng, Longjiu

2015-05-28

Ligand-protected gold (Au-L) nanoclusters have attracted much attention, where the reported electronic and geometric structures show great diversity. To give a direct and overall view of the energy landscape of Au-L binary systems, the AuxCly (x + y = 20) system is taken as a test case. By intensive global search of the potential energy surface at the level of density functional theory, a diverse set of global minima and low-lying isomers are found at each composition, and the structural phase diagram is obtained. The unbiased global search is carried out using the method combining the genetic algorithm with the TPSS functional. At x = 10 with the stoichiometric ratio of Au and Cl (1 : 1), the cluster presents a catenane structure. When x is in the range of 11-20, the clusters are Au-rich, and the Au-Cl system can be viewed as Cl-protected gold nanoclusters, where the gold cores consist of superatoms, superatom networks, or superatomic molecules in electronic structures. At x = 11-15, the gold cores consist of Au3, Au4 and Au5 2e-superatoms protected by staple motifs. At x = 16-20, the clusters are pyramidal superatomic molecules with one Au16 superatom core bonding with the four vertical atoms (Au or Cl). When x is in the scope of 9-5, the clusters are Cl-rich, and the 5d electrons of Au participate in bonding, resulting in high multiplicities. The Au-Cl binary system shows great diversity and flexibility in electronic and geometric structures, and there are corresponding structures to most of the experimentally produced Au-L nanoclusters in our structural phase diagram. We believe that the structural phase diagram gives an overall perspective on the universe of Au-L nanoclusters.

ICCE/ICCAI 2000 Full & Short Papers (Intelligent Tutoring Systems).

ERIC Educational Resources Information Center

2000

This document contains the full and short papers on intelligent tutoring systems (ITS) from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction) covering the following topics: a framework for Internet-based distributed learning; a fuzzy-based assessment for the Perl tutoring…

Multidimensional Perception of Counselor Behavior

ERIC Educational Resources Information Center

Barak, Azy; LaCrosse, Michael B.

1975-01-01

Investigated Strong's prediction of the existence of three dimensions of perceived counselor behavior--expertness, attractiveness, and trustworthiness. Films of interviews given by Rogers, Ellis, and Perls were watched by 202 subjects, who rated each counselor on 36 bipolar scales. Results supported the existence of the hypothesized dimensions for…

Client Good Moments: An Intensive Analysis of a Single Session.

ERIC Educational Resources Information Center

Stalikas, Anastassios; Fitzpatrick, Marilyn

1995-01-01

An intensive analysis of a single counseling session conducted by Fritz Perls was carried out to examine relationships among client experiencing level, client strength of feeling, counselor interventions, and client good moments. The possibility that positive therapeutic outcome is related to the accretion of good moments is discussed. (JBJ)

A Model of RHIC Using the Unified Accelerator Libraries

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

Pilat, F.; Tepikian, S.; Trahern, C. G.

1998-01-01

The Unified Accelerator Library (UAL) is an object oriented and modular software environment for accelerator physics which comprises an accelerator object model for the description of the machine (SMF, for Standard Machine Format), a collection of Physics Libraries, and a Perl inte,face that provides a homo­geneous shell for integrating and managing these components. Currently available physics libraries include TEAPOT++, a collection of C++ physics modules conceptually derived from TEAPOT, and DNZLIB, a differential algebra package for map generation. This software environment has been used to build a flat model of RHIC which retains the hierarchical lat­tice description while assigning specificmore » characteristics to individual elements, such as measured field har­monics. A first application of the model and of the simulation capabilities of UAL has been the study of RHIC stability in the presence of siberian snakes and spin rotators. The building blocks of RHIC snakes and rotators are helical dipoles, unconventional devices that can not be modeled by traditional accelerator phys­ics codes and have been implemented in UAL as Taylor maps. Section 2 describes the RHIC data stores, Section 3 the RHIC SMF format and Section 4 the RHIC spe­cific Perl interface (RHIC Shell). Section 5 explains how the RHIC SMF and UAL have been used to study the RHIC dynamic behavior and presents detuning and dynamic aperture results. If the reader is not familiar with the motivation and characteristics of UAL, we include in the Appendix an useful overview paper. An example of a complete set of Perl Scripts for RHIC simulation can also be found in the Appendix.« less

Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies.

PubMed

Prins, Pjotr; Goto, Naohisa; Yates, Andrew; Gautier, Laurent; Willis, Scooter; Fields, Christopher; Katayama, Toshiaki

2012-01-01

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the Java Virtual Machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, BioJava, and BioRuby implementations, and with call stack bindings to BioJava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on VirtualBox-supported operating systems, including Windows, OSX, and Linux.

Higher prices in Jamaica.

PubMed

1982-03-01

Price increases in the Jamaica CSM program went into effect on August 31, 1981. The program began in 1975. While the need for higher prices has been under discussion for the past 3 years, this is the 1st time the requisite approval from the Jamaica Price Commission has been obtained. The Jamaica National Family Planning Board (JNFPB) reports that the Panther 3-pack (condom) is up US$0.15 to US$0.30. Each Perle package (oral contraceptive) was increased by US$0.20. Single cycle Perle now sells for US$0.50, and 3-pack Perle sells for US$1.10. The 6-year price stagnation experienced by the CSM program resulted in a decreasing operational budget as program costs continued to rise. Marketing costs alone during this period escalated by 100-300%. For example, Panther pop-up display cartons cost the project US 16U each in 1975. By 1979 the same product cost US 49U. Newspaper advertisements have increased from the 1975 cost of US$68.00 to nearly $200.00 per placement. The overall inflation rate in Jamaica during the last 5 years has averaged more than 20% annually. In the face of these rising costs, outlet expansion for Perle has been prevented, wholesaler margins have been unavailable, and new retailer training has been discontinued. It is projected that the new prices will result in an annual increased revenues of US$80,000 which will be used to reinstate these essential marketing activities. The JNFPB is also planning to introduce a Panther 12-pack and Panther strips to the CSM product line. According to Marketing Manager Aston Evans, "We believe the public is now ready for this type of packaging" which is scheduled to be available soon. Panther is presently only available in a 3-pack, but annual sales have been steady. The new 12-pack will be stocked on supermarket shelves to provide higher product visibility and wider distribution. The selling price has been set as US$1.20 and is expected to yield a 25% increase in sales during the 1st year. A complete sales promotion

Jamaica: a middle-aged program searches for new horizons.

PubMed

1984-01-01

The advertising and marketing consultant for Jamaica's Commercial Distribution of Contraceptives (JCDC) program, states that the program has reached a state of maturity that has resulted in some inertia. Although still the leader among contraceptive social marketing (CSM) programs in reaching the greatest percentage of its target market, product sales are no longer on an upswing, and retail outlets are not increasing in number. The project is hoping that the introduction of a new thin condom can help, but more than 1 new product may be needed to recapture momentum. The JCDC began in 1974 when Westinghouse Health Systems won a 3 year Agency for International Development (AID) award to create a Jamaican CSM program. Challenges facing the new social marketing project included: oral contraceptives (OCs) were sold only by prescription; most pharmacies were located in urban areas; many consumers associated condoms with prostitution and disease; and retailers were reluctant to carry contraceptives and ignorant of OC side effects. The 1st breakthrough came when Westinghouse obtained government permission to sell a project pill without prescription. After market research, project managers chose the name "Perle" for the JCDC's pill, manufactured in the US by Syntex as Noriday. "Panther" became the project's condom. Prices were set at US17 cents for a Panther 3-pack and 34 cents for a Perle cycle. Advertising messages appeared on television, radio, bus shelters, cinema screens, billboards, and point of purchase displays. By the end of the 1st year's sales, a soft goods manufacturer had asked permission to produce Panther T-shirts and a Reggae composer had popularized songs about the product. Such promotional tactics boosted sales of all contraceptives on the island. About 690,000 Panther condoms and 450,000 other brands were sold in 1976; 195,000 Perle cycles were purchased compared with 135,000 cycles for all other brands combined. By 1977, Westinghouse was reducing

Research as a Recursive Process: Reconsidering "The Composing Processes of Unskilled College Writers" 35 Years Later

ERIC Educational Resources Information Center

Perl, Sondra

2014-01-01

This article describes Sondra Perl's retrospective review of the composing processes of unskilled college writers and whether her assumptions and values in the designing of research projects have changed over her long teaching career. She uses her college dissertation "Five Writers Writing" as the basis to reflect on the authors and…

Prise en charge hospitalière de la malnutrition aigue sévère chez l'enfant avec des préparations locales alternatives aux F-75 et F-100: résultats et défis

PubMed Central

Nguefack, Félicitée; Adjahoung, Chritoph Akazong; Keugoung, Basile; Kamgaing, Nelly; Dongmo, Roger

2015-01-01

Introduction La mise en œuvre des directives de l'OMS permettrait de réduire significativement la mortalité hospitalière due à la malnutrition sévère. Cependant, elle n'est pas effective et la pénurie en aliments thérapeutiques est l'une des principales causes. L’étude décrit notre expérience sur la prise en charge hospitalière de la malnutrition aigue sévère avec des laits alternatifs aux F75 et F100 composés localement. Méthodes Il s'agissait d'un essai clinique non randomisé. La prise en charge des patients utilisait les laits composés localement et une évaluation quotidienne du gain pondéral était faite. Résultats L’étude a porté sur 41 sujets âgés de 6 à 59 mois. Au total, 73,2% avaient le kwashiorkor-marasmique, 17,0% le kwashiorkor, 9,8% le marasme et 41,5% étaient infectés par le VIH. Nous avons noté une prise progressive du poids d'environ 10 g/kg/jour vers le 7ème jour et de 15 à 20 g/kg/jour en fin d'hospitalisation. Le taux de mortalité était de 21,9% soit une réduction de 8,4% des chiffres antérieurs. Conclusion Malgré les obstacles financiers liés au coût des ingrédients, les préparations lactées alternatives aux standards F75 et F100, sont adaptables dans notre contexte. En l'absence des formules standards de l'OMS et lorsque la référence vers une structure qui en disposent n'est pas possible, les préparations locales permettraient de réhabiliter efficacement les patients. D'autres recherches pointues permettraient de tirer les ingrédients uniquement de notre environnement. Elles contribueraient ainsi à minimiser les couts des préparations et de favoriser la pérennisation des laits thérapeutiques locaux. PMID:26587175

Les recommandations relatives aux vaccins antigrippaux administrés aux enfants et aux adolescents pour la saison 2017-2018.

PubMed

Moore, Dorothy L

2018-02-01

La Société canadienne de pédiatrie continue d'encourager la vaccination antigrippale annuelle de TOUS les enfants et les adolescents, dès l'âge de six mois. Les recommandations du Comité consultatif national de l'immunisation (CCNI) pour la saison 2017-2018 n'ont pas subi de changements importants par rapport à la saison précédente. Le CCNI a analysé toutes les données sur l'efficacité du vaccin vivant atténué contre l'influenza (VVAI) sur le marché et conclut qu'elles en appuient l'utilisation au Canada, même si les États-Unis ne le recommandent pas en raison de doutes quant à son efficacité.

CONCLUSIONS ET RECOMMANDATIONS À L’ISSUE DE LA CONSULTATION DE L’OMS SUR LA LUTTE CONTRE LA CARENCE MARTIALE CHEZ LE NOURRISSON ET LE JEUNE ENFANT DANS LES PAYS D’ENDÉMIE PALUSTRE

PubMed Central

Allen, L.; Black, R.E.; Brandes, N.; Brittenham, G.; Chazot, G.; Chunming, C.; Crawley, J.; de Benoist, B.; Dalmiya, N.; Darnton-Hill, I.; Dewey, K.; El-Arifeen, S.; Fontaine, O.; Geissler, C.; Haberle, H.; Harvey, P.; Hasler, J.; Hershko, C.; Hurrell, R.; Juma, M.A.; Lönnerdal, B.; Lozoff, B.; Lynch, S.; Salgado, H. Martines; McLean, E.; Metz, J.; Oppenheimer, S.; Premji, Z.; Prentice, A.; Ramsan, M.; Ratledge, C.; Stoltzfus, R.; Tielsch, J.; Winachagoon, P.

2011-01-01

Cet article présentent les résultats d'une Consultation d'Experts dont l'objectif était d'évaluer l'efficacité et l'innocuité des suppléments de fer administrés aux nourrissons et aux jeunes enfants dans les zones d’endémie palustre, ainsi que les conséquences d’une telle mesure pour la santé publique. Les participants à cette Consultation, qui s’est déroulée à Lyon (France) les 12–14 juin 2006, se sont entendus sur plusieurs questions importantes concernant l’administration d’une supplémentation martiale aux nourrissons et aux jeunes enfants dans les zones d’endémie palustre. Les conclusions du présent rapport s’appliquent plus particulièrement aux pays où le paludisme est endémique. PMID:18630054

What's new in the Atmospheric Model Evaluation Tool (AMET) version 1.3

EPA Science Inventory

A new version of the Atmospheric Model Evaluation Tool (AMET) has been released. The new version of AMET, version 1.3 (AMETv1.3), contains a number of updates and changes from the previous of version of AMET (v1.2) released in 2012. First, the Perl scripts used in the previous ve...

Categories of Counselors Behavior as Defined from Cross-Validated Factoral Descriptions.

ERIC Educational Resources Information Center

Zimmer, Jules M.; And Others

The intent of the study was to explore and categorize counselor responses. Three separate filmed presentations were shown. Participating with the same client were Albert Ellis, Frederick Perls, and Carl Rogers. At the beginning of each counselor statement, a number was inserted in sequence and remained on the videotape until completion of that…

Disabling Fictions: Institutionalized Delimitations of Revision.

ERIC Educational Resources Information Center

Carroll, Jeffrey

1989-01-01

Examines three contemporary taxonomies of revision as proposed by Wallace Hildick, Lester Faigley and Stephen Witte, and Sondra Perl. Uses literary and cultural theory to bridge the gap between these theories and students' revision practices. Argues that while revision may be prescriptive, it must also be subordinate to the writer's intentions and…

A Comprehensive Reasoning Framework for Information Survivability (User Intent Encapsulation and Reasoning About Intrusion: Implementation and Performance Assessment)

DTIC Science & Technology

2006-08-01

obvious and apparent attacks such as transferring the /etc/ passwd file from one host to another, password-cracking by comparing the entries in the /etc... passwd file to entries in another file, using a dictionary file for the same, and exploiting the vulnerabilities such as rdist, perl 5.0.1, etc. The

67 FR 24495 - United States v. Microsoft Corporation; Public Comments; Notice (MTC-00003461 - MTC-00007629)

Federal Register 2010, 2011, 2012, 2013, 2014

2002-05-03

... (web-serving software), Linux, Perl, and those who are building a compatible & free version of MS`s..., Argument from Design Argument from Design-Web & Multimedia [email protected] http://www.ardes.com MTC-00003464... organization could be a good target for this effort. Their web address is http:// www.gnu.org/. This effort...

GenomeVista

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

Poliakov, Alexander; Couronne, Olivier

2002-11-04

Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program tomore » find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

Multiple Objective Evaluation and Choicemaking under Risk with partial Preference Information.

DTIC Science & Technology

1981-02-01

6I. PERlORUl, O RG n. REP[IORT NUMOIER Chelsea C./White," t.. 4-0 -C,6542 ~-Andrew P ,/Sage S. PERFORMING ORGANIZATION NAME ANO ADORES$ 10, POGAM...Vickson, R. G., "Theoretical Foundations of Stochastic Dominance," Chapter 2 in Whitmore , G. A., and Findlay, M. C. (eds), Stochastic Dominance: An

Isozyme variation in lychee (Litchi chinensis Sonn.)

USDA-ARS?s Scientific Manuscript database

A genetic diversity analysis involving 49 lychee (Litchi chinensis SOM.) accessions using eight enzyme systems encoding 12 loci (Zdh-I, Zdh-2, Mdh-2, Per-l, Pgi-2, Pgm-1, Pgm-2, Sk& Tpi-1, Tpi-2, Ugpp-1, and Ugpp-2) revealed moderate to high levels of genetic variability. Cluster analysis of the iso...

An Investigation of How ESL Students Write.

ERIC Educational Resources Information Center

Raimes, Ann

A study is described which investigated the differences between English-as-a-second-language (ESL) writers and native-English-speaking writers and examined closely a range of ESL writers and their composing processes. The procedures used were those used by Sondra Perl in a study of the composing processes of unskilled college writers (1979).…

Looking for One's Shadow at Noon: Vol. II. Finding the Self in School and Community.

ERIC Educational Resources Information Center

Leue, Mary M.

This volume contains a collection of essays, reflections, and other writings (many of which originally appeared in several journals) on the relations among self and school and community. The first selection is an obituary of Fritz Perls, a leader of Gestalt therapy. The second essay, "A Social and Political Reassessment of the Work of Wilhelm…

Relentless Verity: Education for Being-Becoming-Belonging.

ERIC Educational Resources Information Center

Kidd, James Robbins

The dynamic relationship of the concepts of being, becoming, and belonging is and must be the heart and central goal of adult education. The concept can be understood most readily by examination of the writings of humanist psychologists such as Carl Rogers, Fritz Perls, Gordon Allport, and Abraham Maslow. Some characteristics or dimensions of an…

Leading System-Wide Improvement

ERIC Educational Resources Information Center

Harris, Alma

2012-01-01

Around the world there is a preoccupation with improving the performance of schools and school systems. Comparisons made between countries through PISA and PERLs have led to a preoccupation, and in some cases, an obsession, with securing a high position in the international league tables. The minds of policy-makers and politicians alike are…

Dynamic Subcellular Localization of Iron during Embryo Development in Brassicaceae Seeds

PubMed Central

Ibeas, Miguel A.; Grant-Grant, Susana; Navarro, Nathalia; Perez, M. F.; Roschzttardtz, Hannetz

2017-01-01

Iron is an essential micronutrient for plants. Little is know about how iron is loaded in embryo during seed development. In this article we used Perls/DAB staining in order to reveal iron localization at the cellular and subcellular levels in different Brassicaceae seed species. In dry seeds of Brassica napus, Nasturtium officinale, Lepidium sativum, Camelina sativa, and Brassica oleracea iron localizes in vacuoles of cells surrounding provasculature in cotyledons and hypocotyl. Using B. napus and N. officinale as model plants we determined where iron localizes during seed development. Our results indicate that iron is not detectable by Perls/DAB staining in heart stage embryo cells. Interestingly, at torpedo development stage iron localizes in nuclei of different cells type, including integument, free cell endosperm and almost all embryo cells. Later, iron is detected in cytoplasmic structures in different embryo cell types. Our results indicate that iron accumulates in nuclei in specific stages of embryo maturation before to be localized in vacuoles of cells surrounding provasculature in mature seeds. PMID:29312417

Comparison of effects of glass fibre and glass powder on guinea-pig lungs

PubMed Central

Botham, Susan K.; Holt, P. F.

1973-01-01

Botham, Susan K., and Holt, P. F. (1973).British Journal of Industrial Medicine,30, 232-236. Comparison of effects of glass fibre and glass powder on guinea-pig lungs. Following 24 hours inhalation by guinea-pigs of powdered glass dust, the pulmonary effects over the succeeding month differed from those previously observed to follow inhalation of glass fibre in that (1) fewer erythrocytes escaped from the capillaries, (2) very few giant cells were produced, (3) erythrocytes and intracellular glass particles were cleared more readily because junctions between respiratory and terminal bronchioles were not blocked by giant cells, (4) intracellular granules containing Perls-positive material did not appreciably increase in number or intensity of staining during the month, and (5) particles were not coated with Perls-positive material during the time that pseudo-asbestos bodies would be formed from glass fibres. The difference between the effects of chemically similar glass powder and fibre during a month in a guinea-pig lung is considered to be due to the morphology of the inhaled particle. Images PMID:4124978

Open source clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.

PubMed

Zhang, Yanxiang; Paschold, Anja; Marcon, Caroline; Liu, Sanzhen; Tai, Huanhuan; Nestler, Josefine; Yeh, Cheng-Ting; Opitz, Nina; Lanz, Christa; Schnable, Patrick S; Hochholdinger, Frank

2014-09-01

The maize (Zea mays L.) Aux/IAA protein RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEMS 1) controls seminal and lateral root initiation. To identify RUM1-dependent gene expression patterns, RNA-Seq of the differentiation zone of primary roots of rum1 mutants and the wild type was performed in four biological replicates. In total, 2 801 high-confidence maize genes displayed differential gene expression with Fc ≥2 and FDR ≤1%. The auxin signalling-related genes rum1, like-auxin1 (lax1), lax2, (nam ataf cuc 1 nac1), the plethora genes plt1 (plethora 1), bbm1 (baby boom 1), and hscf1 (heat shock complementing factor 1) and the auxin response factors arf8 and arf37 were down-regulated in the mutant rum1. All of these genes except nac1 were auxin-inducible. The maize arf8 and arf37 genes are orthologues of Arabidopsis MP/ARF5 (MONOPTEROS/ARF5), which controls the differentiation of vascular cells. Histological analyses of mutant rum1 roots revealed defects in xylem organization and the differentiation of pith cells around the xylem. Moreover, histochemical staining of enlarged pith cells surrounding late metaxylem elements demonstrated that their thickened cell walls displayed excessive lignin deposition. In line with this phenotype, rum1-dependent mis-expression of several lignin biosynthesis genes was observed. In summary, RNA-Seq of RUM1-dependent gene expression in maize primary roots, in combination with histological and histochemical analyses, revealed the specific regulation of auxin signal transduction components by RUM1 and novel functions of RUM1 in vascular development. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

IT Resources - Betty Petersen Memorial Library

Science.gov Websites

Available NOAA-wide. Note: This link takes you to a nonfederal website. Guide for usage Apress.com Free eBooks Free eBooks available through Apress publishers. Topics include PHP, Perl, and programming VB .Net . Note: This link takes you to a nonfederal website. Online Programming Books Free programming books

Web-Based Search and Plot System for Nuclear Reaction Data

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

Otuka, N.; Nakagawa, T.; Fukahori, T.

2005-05-24

A web-based search and plot system for nuclear reaction data has been developed, covering experimental data in EXFOR format and evaluated data in ENDF format. The system is implemented for Linux OS, with Perl and MySQL used for CGI scripts and the database manager, respectively. Two prototypes for experimental and evaluated data are presented.

Nonhuman Primates are Protected from Smallpox Virus or Monkeypox Virus Challenges by the Antiviral Drug ST-246

DTIC Science & Technology

2009-06-01

Drug ST-246 John Huggins,1 Arthur Goff,1 Lisa Hensley,1 Eric Mucker,1 Josh Shamblin,1 Carly Wlazlowski,1 Wendy Johnson,1 Jennifer Chapman,1 Tom Larsen...Hauer, M. Layton , J. McDade, M. T. Osterholm, T. O’Toole, G. Parker, T. Perl, P. K. Russell, K. Tonat, and the Working Group on Civilian Biodefense

Gravistimulation changes expression of genes encoding putative carrier proteins of auxin polar transport in etiolated pea epicotyls

NASA Astrophysics Data System (ADS)

Hoshino, T.; Hitotsubashi, R.; Miyamoto, K.; Tanimoto, E.; Ueda, J.

STS-95 space experiment has showed that auxin polar transport in etiolated epicotyls of pea (Pisum sativum L. cv. Alaska) seedlings is controlled by gravistimulation. In Arabidopsis thaliana auxin polar transport has considered to be regulated by efflux and influx carrier proteins in plasma membranes, AtPIN1 and AtAUX1, respectively. In order to know how gravistimuli control auxin polar transport in etiolated pea epicotyls at molecular levels, strenuous efforts have been made, resulting in successful isolation of full-length cDNAs of a putative auxin efflux and influx carriers, PsPIN2 and PsAUX1, respectively. Significantly high levels in homology were found on nucleotide and deduced amino acid sequences among PsPIN2, PsPIN1 (accession no. AY222857, Chawla and DeMason, 2003) and AtPINs, and also among PsAUX1, AtAUX1 and their related genes. Phylogenetic analyses based on the deduced amino acid sequences revealed that PsPIN2 belonged to a subclade including AtPIN3, AtPIN4 relating to lateral transport of auxin, while PsPIN1 belonged to the same clade as AtPIN1 relating to auxin polar transport. In the present study, we examined the effects of gravistimuli on the expression of PsPINs and PsAUX1 in etiolated pea seedlings by northern blot analysis. Expression of PsPIN1, PsPIN2 and PsAUX1 in hook region of 3.5-d-old etiolated pea seedlings grown under simulated microgravity conditions on a 3-D clinostat increased as compared with that of the seedlings grown under 1 g conditions. On the other hand, that of PsPIN1 and PsAUX1 in the 1st internode region under simulated microgravity conditions on a 3-D clinostat also increased, while that of PsPIN2 was affected little. These results suggest that expression of PsPIN1, PsPIN2 and PsAUX1 regulating polar/lateral transport of auxin is substantially under the control of gravity. A possible role of PsPINs and PsAUX1 of auxin polar transport in etiolated pea seedlings will also be discussed.

Foreign Language Analysis and Recognition (FLARe) Initial Progress

DTIC Science & Technology

2012-11-29

University Language Modeling ToolKit CoMMA Count Mediated Morphological Analysis CRUD Create, Read , Update & Delete CPAN Comprehensive Perl Archive...DATES COVERED (From - To) 1 October 2010 – 30 September 2012 4. TITLE AND SUBTITLE Foreign Language Analysis and Recognition (FLARe) Initial Progress...AFRL-RH-WP-TR-2012-0165 FOREIGN LANGUAGE ANALYSIS AND RECOGNITION (FLARE) INITIAL PROGRESS Brian M. Ore

Storytelling as Scholarship: A Writerly Approach to Research

ERIC Educational Resources Information Center

Perl, Sondra; Counihan, Beth; McCormack, Tim; Schnee, Emily

2007-01-01

What does it mean to take a writerly approach to research? Sondra Perl and her co-authors have pondered this question over the past five years as they have each worked with her to design and draft dissertations that combine their work as literacy researchers with their love of writing. Each of them has moved toward storytelling as a compelling and…

Data Reduction of Jittered Infrared Images Using the ORAC Pipeline

NASA Astrophysics Data System (ADS)

Currie, Malcolm; Wright, Gillian; Bridger, Alan; Economou, Frossie

We relate our experiences using the ORAC data reduction pipeline for jittered images of stars and galaxies. The reduction recipes currently combine applications from several Starlink packages with intelligent Perl recipes to cater to UKIRT data. We describe the recipes and some of the algorithms used, and compare the quality of the resultant mosaics and photometry with the existing facilities.

Analytical Solutions for Predicting Underwater Explosion Gas Bubble Behaviour

DTIC Science & Technology

2010-11-01

donne les meilleures prévisions comparativement aux ajustements avec les données expérimentales. Le modèle à fluide incompressible exige d’utiliser une...couplage des mouvements radial et migratoire. L’étude montre que, comparativement aux résultats d’expérience, la réduction du rayon de la bulle... comparativement aux ajustements avec les données expérimentales. Le modèle à fluide incompressible exige d’utiliser une fonction empirique de perte d’énergie

Web-based biobank system infrastructure monitoring using Python, Perl, and PHP.

PubMed

Norling, Martin; Kihara, Absolomon; Kemp, Steve

2013-12-01

The establishment and maintenance of biobanks is only as worthwhile as the security and logging of the biobank contents. We have designed a monitoring system that continuously measures temperature and gas content, records the movement of samples in and out of the biobank, and also records the opening and closing of the freezers-storing the results and images in a database. We have also incorporated an early warning feature that sends out alerts, via SMS and email, to responsible persons if any measurement is recorded outside the acceptable limits, guaranteeing the integrity of biobanked samples, as well as reagents used in sample analysis. A surveillance system like this increases the value for any biobank as the initial investment is small and the value of having trustworthy samples for future research is high.

Comparison of Three Commercial Systems for Identification of Yeasts Commonly Isolated in the Clinical Microbiology Laboratory

PubMed Central

Wadlin, Jill K.; Hanko, Gayle; Stewart, Rebecca; Pape, John; Nachamkin, Irving

1999-01-01

We evaluated three commercial systems (RapID Yeast Plus System; Innovative Diagnostic Systems, Norcross, Ga.; API 20C Aux; bioMerieux-Vitek, Hazelwood, Mo.; and Vitek Yeast Biochemical Card, bioMerieux-Vitek) against an auxinographic and microscopic morphologic reference method for the ability to identify yeasts commonly isolated in our clinical microbiology laboratory. Two-hundred one yeast isolates were compared in the study. The RapID Yeast Plus System was significantly better than either API 20C Aux (193 versus 167 correct identifications; P < 0.0001) or the Vitek Yeast Biochemical Card (193 versus 173 correct identifications; P = 0.003) for obtaining correct identifications to the species level without additional testing. There was no significant difference between results obtained with API 20C Aux and the Vitek Yeast Biochemical Card system (P = 0.39). The API 20C Aux system did not correctly identify any of the Candida krusei isolates (n = 23) without supplemental testing and accounted for the major differences between the API 20C Aux and RapID Yeast Plus systems. Overall, the RapID Yeast Plus System was easy to use and is a good system for the routine identification of clinically relevant yeasts. PMID:10325356

A comparison of common programming languages used in bioinformatics.

PubMed

Fourment, Mathieu; Gillings, Michael R

2008-02-05

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

A comparison of common programming languages used in bioinformatics

PubMed Central

Fourment, Mathieu; Gillings, Michael R

2008-01-01

Background The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Results Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from Conclusion This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language. PMID:18251993

LavaNet—Neural network development environment in a general mine planning package

NASA Astrophysics Data System (ADS)

Kapageridis, Ioannis Konstantinou; Triantafyllou, A. G.

2011-04-01

LavaNet is a series of scripts written in Perl that gives access to a neural network simulation environment inside a general mine planning package. A well known and a very popular neural network development environment, the Stuttgart Neural Network Simulator, is used as the base for the development of neural networks. LavaNet runs inside VULCAN™—a complete mine planning package with advanced database, modelling and visualisation capabilities. LavaNet is taking advantage of VULCAN's Perl based scripting environment, Lava, to bring all the benefits of neural network development and application to geologists, mining engineers and other users of the specific mine planning package. LavaNet enables easy development of neural network training data sets using information from any of the data and model structures available, such as block models and drillhole databases. Neural networks can be trained inside VULCAN™ and the results be used to generate new models that can be visualised in 3D. Direct comparison of developed neural network models with conventional and geostatistical techniques is now possible within the same mine planning software package. LavaNet supports Radial Basis Function networks, Multi-Layer Perceptrons and Self-Organised Maps.

BiDiBlast: comparative genomics pipeline for the PC.

PubMed

de Almeida, João M G C F

2010-06-01

Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license. Copyright 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Tapir: A web interface for transit/eclipse observability

NASA Astrophysics Data System (ADS)

Jensen, Eric

2013-06-01

Tapir is a set of tools, written in Perl, that provides a web interface for showing the observability of periodic astronomical events, such as exoplanet transits or eclipsing binaries. The package provides tools for creating finding charts for each target and airmass plots for each event. The code can access target lists that are stored on-line in a Google spreadsheet or in a local text file.

VAC: Versatile Advection Code

NASA Astrophysics Data System (ADS)

Tóth, Gábor; Keppens, Rony

2012-07-01

The Versatile Advection Code (VAC) is a freely available general hydrodynamic and magnetohydrodynamic simulation software that works in 1, 2 or 3 dimensions on Cartesian and logically Cartesian grids. VAC runs on any Unix/Linux system with a Fortran 90 (or 77) compiler and Perl interpreter. VAC can run on parallel machines using either the Message Passing Interface (MPI) library or a High Performance Fortran (HPF) compiler.

A Disk-Based System for Producing and Distributing Science Products from MODIS

NASA Technical Reports Server (NTRS)

Masuoka, Edward; Wolfe, Robert; Sinno, Scott; Ye Gang; Teague, Michael

2007-01-01

Since beginning operations in 1999, the MODIS Adaptive Processing System (MODAPS) has evolved to take advantage of trends in information technology, such as the falling cost of computing cycles and disk storage and the availability of high quality open-source software (Linux, Apache and Perl), to achieve substantial gains in processing and distribution capacity and throughput while driving down the cost of system operations.

An Ontology for Insider Threat Indicators Development and Applications

DTIC Science & Technology

2014-11-01

An Ontology for Insider Threat Indicators Development and Applications Daniel L. Costa , Matthew L. Collins, Samuel J. Perl, Michael J. Albrethsen...services, commit fraud against an organization, steal intellectual property, or conduct national security espionage, sabotaging systems and data, as...engineering plans from the victim organization’s computer systems to his new employer.  The insider accessed a web server with an administrator account

Study of Tools for Network Discovery and Network Mapping

DTIC Science & Technology

2003-11-01

connected to the switch. iv. Accessibility of historical data and event data In general, network discovery tools keep a history of the collected...has the following software dependencies: - Java Virtual machine 76 - Perl modules - RRD Tool - TomCat - PostgreSQL STRENGTHS AND...systems - provide a simple view of the current network status - generate alarms on status change - generate history of status change VISUAL MAP

DefEX: Hands-On Cyber Defense Exercise for Undergraduate Students

DTIC Science & Technology

2011-07-01

Injection, and 4) File Upload. Next, the students patched the associated flawed Perl and PHP Hypertext Preprocessor ( PHP ) code. Finally, students...underlying script. The Zora XSS vulnerability existed in a PHP file that echoed unfiltered user input back to the screen. To eliminate the...vulnerability, students filtered the input using the PHP htmlentities function and retested the code. The htmlentities function translates certain ambiguous

Caracterisation de la propagation sans-fil dans les avions commerciaux pour une transmission dediee aux services aux passagers et aux systemes avioniques

NASA Astrophysics Data System (ADS)

Saghir, Hassane

Aircraft systems are interconnected by cable bundles that may represent a hundred kilometres. Those wirings penalize the aircraft weight. Cable bundles favour electromagnetic interference on board aircraft and routing a new cable for integrating new equipment boxes in a sustained aircraft requires a lot of retrofit work. Consequently, the aviation industry and aerospace community are working in the scope of different projects on new alternatives that will better fit to the future generation of aircrafts and help to reduce interconnecting wires on board. Wireless technologies represent a coveted solution that could make significant improvements and benefits to new generations of aircrafts. This research work focuses on the study of the wireless propagation over some frequency bands inside commercial aircrafts. The main objective is to provide conclusions and recommendations on criteria that may help optimizing the wireless communication without impacting the existent systems. Targeted applications are the inflight entertainment (IFE) service and wireless sensing systems. This work was conducted in collaboration with Bombardier-Aerospace based in Montreal (QC) in the frame of AVIO-402 project under the grant of CRIAQ (http://www.criaq.aero/). In this study, an experimental characterization of the propagation channel in the ISM band around 2.4 GHz frequency 5.8 GHz has been performed in a CRJ700 aircraft from Bombardier Aerospace. This characterization allowed to extract the parameters needed to analyze the channel behavior. The measurements results have shown that the propagation characteristics are close to those of both typical indoor medium in terms of the delay spread and a tunnel in terms of path loss. Then, a 3D channel modeling and simulation have been achieved with an RF prediction software (Wireless Insite Remcom). The simulations also consider the millimeter band around 60 GHz. The simulations yielded to analytical models of radio coverage which were subsequently used to evaluate wireless link interference scenarios and performance metrics. Finally, these models were used to design a TDL (Tapped Delay Line) channel model with the goal of an implementation under Matlab in a wireless transmission chain.

Visit CD

ScienceCinema

None

2017-12-09

Le DG H.Schopper souhaite la bienvenue aux ambassadeurs des pays membres et aux représentants des pays avec lesquels le Cern entretient des relations proches et fait un exposé sur les activités au Cern

A Non-Invasive Technique which Demonstrates the Iron in the Buccal Mucosa of Sickle Cell Anaemia and Thalassaemia Patients who Undergo Repeated Blood Transfusions.

PubMed

Chittamsetty, Harika; Sekhar, M S Muni; Ahmed, Syed Afroz; Suri, Charu; Palla, Sridevi; Venkatesh, S Muni; Tanveer, Shahela

2013-06-01

Iron is vital for all the living organisms. However, excess iron is hazardous because it produces free radical formation. Therefore, the iron absorption is carefully regulated to maintain an equilibrium between the absorption and the body loss of iron. Considering the lack of specific excretory pathways for iron in humans, an iron overload in the tissues is frequently encountered. It can be precipitated by a variety of conditions such as increased iron absorption, as is seen in haemochromatosis or a frequent parenteral iron administration, as is seen in thalassaemia and sickle cell anaemia patients (a transfusional overload). To demonstrate the iron overload at an early stage by oral exfoliative cytology in the oral mucosal cells of thalassaemia and sickle cell anaemia patients and to compare the presence of iron in the exfoliated oral epithelial cells with that of the serum ferritin levels in those patients. The present study comprised of 40 β- thalassaemia major and 20 sickle cell anaemia patients who were undergoing repeated blood transfusions of a minimum of 15/more, along with 60 clinically healthy individuals. Scrapings were obtained from the buccal mucosa and they were smeared onto glass slides. Then the slides were stained with a Perl's Prussian staining kit and they were examined under a light microscope. 72.5% of the thalassaemia patients and 35% of the sickle cell anaemia patients revealed a positivity for the Perl's Prussian blue reaction and none of the controls showed this positivity. It was also observed that as the serum ferritin levels increased, the iron overload in the oral mucosal cells of the thalassaemia patients also increased, which was not statistically significant, whereas it was statistically significant in case of the sickle cell anemia patients. Since the exfoliative cytology is a simple, painless, non-invasive and a quick procedure to perform, a lot of research should be carried out on the correlation of the Perl's Prussian blue

New insights into Fe localization in plant tissues

PubMed Central

Roschzttardtz, Hannetz; Conéjéro, Geneviève; Divol, Fanchon; Alcon, Carine; Verdeil, Jean-Luc; Curie, Catherine; Mari, Stéphane

2013-01-01

Deciphering cellular iron (Fe) homeostasis requires having access to both quantitative and qualitative information on the subcellular pools of Fe in tissues and their dynamics within the cells. We have taken advantage of the Perls/DAB Fe staining procedure to perform a systematic analysis of Fe distribution in roots, leaves and reproductive organs of the model plant Arabidopsis thaliana, using wild-type and mutant genotypes affected in iron transport and storage. Roots of soil-grown plants accumulate iron in the apoplast of the central cylinder, a pattern that is strongly intensified when the citrate effluxer FRD3 is not functional, thus stressing the importance of citrate in the apoplastic movement of Fe. In leaves, Fe level is low and only detected in and around vascular tissues. In contrast, Fe staining in leaves of iron-treated plants extends in the surrounding mesophyll cells where Fe deposits, likely corresponding to Fe-ferritin complexes, accumulate in the chloroplasts. The loss of ferritins in the fer1,3,4 triple mutant provoked a massive accumulation of Fe in the apoplastic space, suggesting that in the absence of iron buffering in the chloroplast, cells activate iron efflux and/or repress iron influx to limit the amount of iron in the cell. In flowers, Perls/DAB staining has revealed a major sink for Fe in the anthers. In particular, developing pollen grains accumulate detectable amounts of Fe in small-size intracellular bodies that aggregate around the vegetative nucleus at the binuclear stage and that were identified as amyloplasts. In conclusion, using the Perls/DAB procedure combined to selected mutant genotypes, this study has established a reliable atlas of Fe distribution in the main Arabidopsis organs, proving and refining long-assumed intracellular locations and uncovering new ones. This “iron map” of Arabidopsis will serve as a basis for future studies of possible actors of iron movement in plant tissues and cell compartments. PMID:24046774

Regional strategy tested in Caribbean.

PubMed

1984-01-01

Barbados, St. Vincent, and St. Lucia have joined forces in the world's 1st regional Contraceptive Social Marketing (CSM) effort -- the Caribbean CSM. The Barbados Family Planning Association (BFPS) is overseeing the operation, which begins selling 2 contraceptive pills and a condom in early February. Costs and start-up times were shaved by adopting brand names and advertising materials from Jamaica's highly successful CSM project. Jamaica's popular "Panther" condom and "Perle" oral contraceptive (OC) are being used by the Caribbean CSM project. Perle's 9-year-old package has been redesigned and the Caribbean CSM project also is selling a 2nd, low-dose version called "Perle-LD." The products are manufactured in the US by Syntex as Noriday and Norminest, respectively. But the regional approach's financial gains also had a debit side, most notably a tripling of bureaucratic procedures. Part of project difficulties stem from differences among the 3 Caribbean countries. While sharing a common cultural heritage, St. Lucians speak a patois dialect in addition to the English prevalent on the other islands. The biggest hurdle was overcoming an economic disparity between Barbados and its less affluent neighbors, St. Vincent and St. Lucia. The CSM project decided to try a 2-tier product pricing strategy. In US currency, prices run $1.75 per cycle for both OCs on Barbados, but $1.26 on St. Vincent and St. Lucia. A Panther 3-pack costs 75 cents on Barbados and 42 cents on the othe 2 islands. The project is being promoted with generic family planning media advertisements. The project also has held physician orientation seminars on each island. The pilot program will be accompanied by retailer training seminars. In addition the project may introduce a spermicidal foaming tablet, once the US Food and Drug Administration approvs a new American-made product. The unique Caribbean CSM project may spread an idea as potent as the family planning message. Its success could transmit the

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

Gao, Junpeng; Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi 712100; Cao, Xiaoli

The Auxin/indole-3-acetic acid (Aux/IAA) genes encode short-lived nuclear proteins that are known to be involved in the primary cellular responses to auxin. To date, systematic analysis of the Aux/IAA genes in potato (Solanum tuberosum) has not been conducted. In this study, a total of 26 potato Aux/IAA genes were identified (designated from StIAA1 to StIAA26), and the distribution of four conserved domains shared by the StIAAs were analyzed based on multiple sequence alignment and a motif-based sequence analysis. A phylogenetic analysis of the Aux/IAA gene families of potato and Arabidopsis was also conducted. In order to assess the roles ofmore » StIAA genes in tuber development, the results of RNA-seq studies were reformatted to analyze the expression patterns of StIAA genes, and then verified by quantitative real-time PCR. A large number of StIAA genes (12 genes) were highly expressed in stolon organs and in during the tuber initiation and expansion developmental stages, and most of these genes were responsive to indoleacetic acid treatment. Our results suggested that StIAA genes were involved in the process of tuber development and provided insights into functional roles of potato Aux/IAA genes. - Highlights: • A systematic analysis of the potato AUX/IAA gene family were performed. • StIAA genes were related to auxin perception and signal transduction. • Candidate StIAA genes likely related to tuber initiation and expansion were screened.« less

Surveillance urinaire des professionnels de la santé exposés aux antinéoplasiques dans le cadre de leur travail: revue de la littérature de 2010 à 2015

PubMed Central

Poupeau, Céline; Roland, Christel; Bussières, Jean-François

2016-01-01

RÉSUMÉ Contexte Il existe de plus en plus de données sur la présence de traces de médicaments dangereux dans l’urine des professionnels de la santé exposés à ces médicaments. Objectif Présenter une revue de la littérature scientifique concernant la surveillance urinaire de professionnels de la santé exposés aux anti-néoplasiques dans le cadre de leur travail. Sources de données Recherche sur PubMed avec les Medical Subject Headings (MeSH) « occupational exposure » et « antineoplastic agents » ainsi que sur Google Scholar avec les termes « antineoplastic », « urine » et « occupational exposure ». Sélection des études et extraction des données L’examen a porté sur tous les articles en anglais et en français ayant trait aux professionnels de la santé exposés à des médicaments dangereux dans le cadre de leur travail, publiés entre le 1er janvier 2010 et le 31 décembre 2015. Les articles ne comportant pas de résultats urinaires et ceux concernant les vétérinaires ainsi que les revues de littérature, les éditoriaux, les lettres à la rédaction et les résumés de congrès ont été exclus. Synthèse des données Vingt-quatre articles ont été retenus. Les études ont été menées dans 52 établissements de santé provenant de sept pays. Elles regroupaient 826 travailleurs exposés à des médicaments dangereux et 175 témoins, notamment des infirmiers (n = 16 études), des pharmaciens (n = 10), des assistants techniques en pharmacie (n = 8), des médecins (n = 7), des aides-soignants (n = 2) et autres (n = 8). Différentes méthodes analytiques ont été utilisées pour quantifier la présence de 13 médicaments dangereux, principalement le cyclophosphamide (n = 16 études), les platines (n = 7) et l’alpha-fluoro-béta-alanine, un métabolite urinaire du 5-fluorouracile (n = 3). La proportion de travailleurs qui ont étés déclarés positifs s’étendait de 0 % (n = 10 études) à 100 % (n = 4). Si l’on ne retient que

Analysis of the Impact of Data Normalization on Cyber Event Correlation Query Performance

DTIC Science & Technology

2012-03-01

2003). Organizations use it in planning, target marketing , decision-making, data analysis, and customer services (Shin, 2003). Organizations that...Following this IP address is a router message sequence number. This is a globally unique number for each router terminal and can range from...Appendix G, invokes the PERL parser for the log files from a particular USAF base, and invokes the CTL file that loads the resultant CSV file into the

Some Effects of Compressibility on the Flow Through Fans and Turbines

DTIC Science & Technology

1945-08-01

conditions, or the velocity diagram, for the cascade of airfoils representing a fan or a turbine - blade arrangement (fig. 1). The conservation laws...Compressibility on the Flow Through Fans and Turbines AUTHOR(S); Perl. W.j Epstein, H.T. ORIGINATING AGENCY: Aircraft Engine Research Lab., Cleveland, O... turbine blading . It appears, however, that use of a suitable polytropic exponent n?^7 allows direct application in many cases.) Substitution of

A Multi Agent System for Flow-Based Intrusion Detection

DTIC Science & Technology

2013-03-01

Student t-test, as it is less likely to spuriously indicate significance because of the presence of outliers [128]. We use the MATLAB ranksum function [77...effectiveness of self-organization and “ entangled hierarchies” for accomplishing scenario objectives. One of the interesting features of SOMAS is the ability...cross-validation and automatic model selection. It has interfaces for Java, Python, R, Splus, MATLAB , Perl, Ruby, and LabVIEW. Kernels: linear

Absolute NMR shielding scales and nuclear spin–rotation constants in {sup 175}LuX and {sup 197}AuX (X = {sup 19}F, {sup 35}Cl, {sup 79}Br and {sup 127}I)

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

Demissie, Taye B., E-mail: taye.b.demissie@uit.no; Komorovsky, Stanislav; Repisky, Michal

2015-10-28

We present nuclear spin–rotation constants, absolute nuclear magnetic resonance (NMR) shielding constants, and shielding spans of all the nuclei in {sup 175}LuX and {sup 197}AuX (X = {sup 19}F, {sup 35}Cl, {sup 79}Br, {sup 127}I), calculated using coupled-cluster singles-and-doubles with a perturbative triples (CCSD(T)) correction theory, four-component relativistic density functional theory (relativistic DFT), and non-relativistic DFT. The total nuclear spin–rotation constants determined by adding the relativistic corrections obtained from DFT calculations to the CCSD(T) values are in general in agreement with available experimental data, indicating that the computational approach followed in this study allows us to predict reliable results formore » the unknown spin–rotation constants in these molecules. The total NMR absolute shielding constants are determined for all the nuclei following the same approach as that applied for the nuclear spin–rotation constants. In most of the molecules, relativistic effects significantly change the computed shielding constants, demonstrating that straightforward application of the non-relativistic formula relating the electronic contribution to the nuclear spin–rotation constants and the paramagnetic contribution to the shielding constants does not yield correct results. We also analyze the origin of the unusually large absolute shielding constant and its relativistic correction of gold in AuF compared to the other gold monohalides.« less

Open-source framework for documentation of scientific software written on MATLAB-compatible programming languages

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

Numerical simulators for adaptive optics systems have become an essential tool for the research and development of the future advanced astronomical instruments. However, growing software code of the numerical simulator makes it difficult to continue to support the code itself. The problem of adequate documentation of the astronomical software for adaptive optics simulators may complicate the development since the documentation must contain up-to-date schemes and mathematical descriptions implemented in the software code. Although most modern programming environments like MATLAB or Octave have in-built documentation abilities, they are often insufficient for the description of a typical adaptive optics simulator code. This paper describes a general cross-platform framework for the documentation of scientific software using open-source tools such as LATEX, mercurial, Doxygen, and Perl. Using the Perl script that translates M-files MATLAB comments into C-like, one can use Doxygen to generate and update the documentation for the scientific source code. The documentation generated by this framework contains the current code description with mathematical formulas, images, and bibliographical references. A detailed description of the framework components is presented as well as the guidelines for the framework deployment. Examples of the code documentation for the scripts and functions of a MATLAB-based adaptive optics simulator are provided.

Enzyme-Linked Immunosorbant Assays for Identification of Biological Agents in Sample Unknowns: NATO SIBCA. Exercise 5

DTIC Science & Technology

2004-12-01

avantage comme Brucella spp par ex. De plus, chaque ELISA d’agent devrait &tre test~e avec un agent vivant pour confirmer la sensibilit6 du biotest aux...materiaux vivants . A plus long terme, i1 serait souhaitable d𔄀tudier des solutions de rechange qui seraient plus sensibles aux techniques

Gestalt Therapy: Student Perceptions of Fritz Perls in "Three Approaches to Psychotherapy"

ERIC Educational Resources Information Center

Reilly, Joe; Jacobus, Veronica

2009-01-01

The "Three Approaches to Psychotherapy" ("TAP") videotape series introduces students to three major schools of psychotherapy: client-centered therapy, Gestalt therapy, and rational-emotive therapy. A sample of undergraduate students viewed the "TAP" series. The students were surveyed about their observations of…

Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin.

PubMed

Nag, Ronita; Maity, Manas Kanti; Dasgupta, Maitrayee

2005-11-01

The ABA responsive ABI3 and the auxin responsive ARF family of transcription factors bind the CATGCATG (Sph) and TGTCTC core motifs in ABA and auxin response elements (ABRE and AuxRE), respectively. Several evidences indicate ABI3s to act downstream to auxin too. Because DNA binding domain of ABI3s shows significant overlap with ARFs we enquired whether auxin responsiveness through ABI3s could be mediated by their binding to canonical AuxREs. Investigations were undertaken through in vitro gel mobility shift assays (GMSA) using the DNA binding domain B3 of PvAlf (Phaseolus vulgaris ABI3 like factor) and upstream regions of auxin responsive gene GH3 (-267 to -141) and ABA responsive gene Em (-316 to -146) harboring AuxRE and ABRE, respectively. We demonstrate that B3 domain of PvAlf could bind AuxRE only when B3 was associated with its flanking domain B2 (B2B3). Such strict requirement of B2 domain was not observed with ABRE, where B3 could bind with or without being associated with B2. This dual specificity in DNA binding of ABI3s was also demonstrated with nuclear extracts of cultured cells of Arachis hypogea. Supershift analysis of ABRE and AuxRE bound nuclear proteins with antibodies raised against B2B3 domains of PvAlf revealed that ABI3 associated complexes were detectable in association with both cis elements. Competition GMSA confirmed the same complexes to bind ABRE and AuxRE. This dual specificity of ABI3 like factors in DNA binding targeted to natural promoters responsive to ABA and auxin suggests them to have a potential role in conferring crosstalk between these two phytohormones.

Trust Restoration in International Military Missions

DTIC Science & Technology

2010-11-01

confiance comparativement aux scénarios sans bris de confiance (groupe témoin). ii DRDC Toronto TR 2010-151 This page intentionally left...restauration de la confiance comparativement aux scénarios sans bris de confiance (groupe témoin). Nos observations concordent avec celles d’études...11 Figure 2: Design Overview

Open Scenario Study, Phase II Report: Assessment and Development of Approaches for Satisfying Unclassified Scenario Needs

DTIC Science & Technology

2010-01-01

interface, another providing the application logic (a program used to manipulate the data), and a server running Microsoft SQL Server or Oracle RDBMS... Oracle ) • Mysql (Open Source) • Other What application server software will be needed? • Application Server • CGI PHP/Perl (Open Source...are used throughout DoD and serve a variety of functions. While DoD has a codified and institutionalized process for the development of a common set

PAL: A Positional Astronomy Library

NASA Astrophysics Data System (ADS)

Jenness, T.; Berry, D. S.

2013-10-01

PAL is a new positional astronomy library written in C that attempts to retain the SLALIB API but is distributed with an open source GPL license. The library depends on the IAU SOFA library wherever a SOFA routine exists and uses the most recent nutation and precession models. Currently about 100 of the 200 SLALIB routines are available. Interfaces are also available from Perl and Python. PAL is freely available via github.

An Airlift Hub-and-Spoke Location-Routing Model with Time Windows: Case Study of the CONUS-to-Korea Airlift Problem

DTIC Science & Technology

1998-03-01

a point of embarkation to a point of debarkation. This study develops an alternative hub-and-spoke combined location-routing integer linear...programming prototype model, and uses this model to determine what advantages a hub-and-spoke system offers, and in which scenarios it is better-suited than the...extension on the following works: the hierarchical model of Perl and Daskin (1983), time windows features of Chan (1991), combining subtour-breaking and range

Playing Detective: Reconstructing Software Architecture from Available Evidence

DTIC Science & Technology

1997-10-01

information • PostgreSQL (based on POSTGRES [Stonebraker 90]) for model storage • IAPR [Kazman 96c], RMTool [Murphy 95], and Perl for analysis and...720-741. Stonebraker, M.; Rowe, L; & Hirohama, M. ’The Implementation of POSTGRES ." IEEE Transactions on Knowledge and Data Engineering 2,1 (March...Engineering 19,7 (July 1993): 720-741. Stonebraker, M.; Rowe, L; & Hirohama, M. "The Implementation of POSTGRES ." IEEE Transactions on Knowledge and

A Public/Private Extension of Conway's Accessor Model

NASA Technical Reports Server (NTRS)

McCann, Karen M.; Yarrow, Maurice

2000-01-01

We present a new object-oriented model for a Perl package, based on Damien Conway's 'accessor' model. Our model includes both public and private data; it uses strategies to reduce a package namespace, but still maintains a robust and error-trapped approach. With this extended model we can make any package data or functions 'private', as well as 'public'. (Note: 'namespace' in this context means all the names, variables and subs, associated with a package.)

The American History of PTSD: Civil War -- Vietnam

DTIC Science & Technology

2011-03-21

ABSTRACTION FROM, OR REPRODUCTION OF ALL OR ANY PART OF TillS DOCUI\\1ENT IS PERl\\flTTED PROVIDED PROPER ACKNOWLEDGEI\\1ENT IS MADE. Acknowledgments I would...treatment procedure for "shell shock" involved administering a hypnotic therapy designed to restore the victim’s memory through the trancelike repetition and...of the most effective methods of ensuring long lasting recovery. However, the negative cmmotations associated with hypnotism ensured that only a

La santé des Premières nations, des Inuits et des Métis: les facteurs que doivent envisager les leaders en santé canadiens dans la foulée du rapport de la Commission de vérité et réconciliation du Canada.

PubMed

McNally, Mary; Martin, Debbie

2017-03-01

Les peuples des Premières nations, inuits et métis qui habitent au Canada sont aux prises avec de profondes disparités en matière de santé par rapport aux Canadiens non autochtones, et ce, dans presque toutes les mesures liées à la santé et au bien-être. Pour faire progresser les services de santé auprès des peuples autochtones, il faut passer à l'action dans tous les ordres de prestation des soins et des politiques en santé. Il est donc essentiel que les leaders et les prestataires des établissements, des systèmes et des installations de santé du Canada comprennent et prennent en main les déterminants de la santé propres aux peuples autochtones, y compris l'héritage du colonialisme et le racisme ancien et actuel. La Commission de vérité et réconciliation du Canada est le point de départ pour réagir de manière positive aux injustices.

Low Temperature Quartz Crystal Oscillator Fast Warm-Up Saw Oscillator.

DTIC Science & Technology

1981-07-01

TASK_Q Centre National de la Recherche ScientifiqueARA&WKLI k Laboratoire de Physique et Metrologie des!2 Oscillateurs - 50 Bsnon-F 2 3 32 av. o l...propri6t6s non lin6aires des ondes Alastiques de sur- face : applications aux oscillateurs et aux capteurs A quartz", Thse Besanqon, 1979. (6) D. Hauden, G

L’évaluation et le traitement du nourrisson exposé au virus d’immunodéficience humaine de type 1

PubMed Central

2004-01-01

RÉSUMÉ Dans les pays industrialisés, des soins et un traitement sont offerts aux femmes enceintes et aux nourrissons, afin de faire chuter à 2 % ou moins le taux d’infection périnatale au virus d’immunodéficience humaine de type 1 (VIH-1). Le pédiatre joue un rôle de premier plan dans la prévention de la transmission du VIH-1 de la mère à l’enfant par le dépistage des nourrissons exposés au VIH dont l’infection au VIH de la mère n’a pas été diagnostiquée avant l’accouchement. Il prescrit une prophylaxie antirétrovirale à ces nourrissons, afin de réduire le risque d’acquisition de l’infection au VIH-1 et d’en éviter le plus possible la transmission par le lait maternel. De plus, le pédiatre peut soigner les nourrissons exposés au VIH-1 en les surveillant pour obtenir un dépistage précoce de l’infection au VIH-1 et évaluer les toxicités à court et à long terme de l’exposition aux antirétroviraux, assurer une chimioprophylaxie de la pneumonie à Pneumocystis et soutenir les familles qui vivent avec une infection au VIH-1, grâce à des conseils thérapeutiques aux parents ou aux soignants.

Resources for comparing the speed and performance of medical autocoders.

PubMed

Berman, Jules J

2004-06-15

Concept indexing is a popular method for characterizing medical text, and is one of the most important early steps in many data mining efforts. Concept indexing differs from simple word or phrase indexing because concepts are typically represented by a nomenclature code that binds a medical concept to all equivalent representations. A concept search on the term renal cell carcinoma would be expected to find occurrences of hypernephroma, and renal carcinoma (concept equivalents). The purpose of this study is to provide freely available resources to compare speed and performance among different autocoders. These tools consist of: 1) a public domain autocoder written in Perl (a free and open source programming language that installs on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text. A simple lexical autocoder was written that parses plain-text into a listing of all 1,2,3, and 4-word strings contained in text, assigning a nomenclature code for text strings that match terms in the nomenclature. The nomenclature used is the unencumbered subset of the 2003 Unified Medical Language System (UMLS). The unencumbered subset of UMLS was reduced to exclude homonymous one-word terms and proper names, resulting in a term/code data dictionary containing about a half million medical terms. The Online Mendelian Inheritance in Man (OMIM), a 92+ Megabyte publicly available medical opus, was used as sample medical text for the autocoder. The autocoding Perl script is remarkably short, consisting of just 38 command lines. The 92+ Megabyte OMIM file was completely autocoded in 869 seconds on a 2.4 GHz processor (less than 10 seconds per Megabyte of text). The autocoded output file (9,540,442 bytes) contains 367,963 coded terms from OMIM and is distributed with this manuscript. A public domain Perl script is

Mesozoic fault reactivation along the St. Lawrence Rift System as constrained by (U-Th/He) thermochronology

NASA Astrophysics Data System (ADS)

Bouvier, L.; Pinti, D. L.; Tremblay, A.; Minarik, W. G.; Roden-Tice, M. K.; Pik, R.

2011-12-01

mass spectrometer in CRPG-Nancy and duplicates using a quadrupole mass spectrometer at GEOTOP-UQAM. 4He was measured against internal He gas standards and Durango apatite, with the reference U-Th/He age of 31.13 ± 1.01 Ma. U and Th contents were determined at CRPG-Nancy and duplicated at McGill University by ICP-MS. Preliminary results of U-Th/He on St.-Laurent fault yield an age of 137±12 Ma for the hanging wall, at Sault-au-Cochon and 118±10 Ma for a sample from the footwall, at Cap-aux-oies. Previous Apatite Fission Track (AFT) performed for the two locations gave expected older ages at 149±16 Ma and 196±19 Ma for the hanging wall and the footwall, respectively. These preliminary U-Th/He results are consistent with AFT ages of the area (i.e. as expected, U-Th/He ages are younger than AFT ages) but do not yet provide new constraints for the structural evolution of the St. Lawrence rift system. We are determining further U-Th/He ages and these ages will constrain an exhumation model of the region.

Automated Alerting for Black Hole Routing

DTIC Science & Technology

2007-09-01

Beginners or Learning Bro). Reply: Just the documentation that comes with it and is available from the wiki. Question 4: Is Bro compatible with...other scripts written in Python , Java, or Perl? Reply: It can call arbitrary programs but doesn’t link directly into other interpreters. Question 5...need to write that daemon? (C) What kind of scripts does Spunk support…and are Python and C part of them or not? 88 Reply: Puri, the answers to all

Software Assurance Measurement -- State of the Practice

DTIC Science & Technology

2013-11-01

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

Image

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

Marsh, Amber; Harsch, Tim; Pitt, Julie

2007-08-31

The computer side of the IMAGE project consists of a collection of Perl scripts that perform a variety of tasks; scripts are available to insert, update and delete data from the underlying Oracle database, download data from NCBI's Genbank and other sources, and generate data files for download by interested parties. Web scripts make up the tracking interface, and various tools available on the project web-site (image.llnl.gov) that provide a search interface to the database.

Simple Ontology Format (SOFT)

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

Sorokine, Alexandre

2011-10-01

Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

Tools for automating spacecraft ground systems: The Intelligent Command and Control (ICC) approach

NASA Technical Reports Server (NTRS)

Stoffel, A. William; Mclean, David

1996-01-01

The practical application of scripting languages and World Wide Web tools to the support of spacecraft ground system automation, is reported on. The mission activities and the automation tools used at the Goddard Space Flight Center (MD) are reviewed. The use of the Tool Command Language (TCL) and the Practical Extraction and Report Language (PERL) scripting tools for automating mission operations is discussed together with the application of different tools for the Compton Gamma Ray Observatory ground system.

Comparison of Vitek Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Versus Conventional Methods in Candida Identification.

PubMed

Keçeli, Sema Aşkın; Dündar, Devrim; Tamer, Gülden Sönmez

2016-02-01

Candida species are generally identified by conventional methods such as germ tube or morphological appearance on corn meal agar, biochemical methods using API kits and molecular biological methods. Alternative to these methods, rapid and accurate identification methods of microorganisms called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDİ-TOF MS) has recently been described. In this study, Candida identification results by API Candida kit, API 20C AUX kit and identifications on corn meal agar (CMA) are compared with the results obtained on Vitek-MS. All results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Totally, 97 Candida strains were identified by germ tube test, CMA, API and Vitek-MS. Vitek-MS results were compatible with 74.2 % of API 20C AUX and 81.4 % of CMA results. The difference between the results of API Candida and API 20C AUX was detected. The ratio of discrepancy between Vitek-MS and API 20C AUX was 25.8 %. Candida species mostly identified as C. famata or C. tropicalis by and not compatible with API kits were identified as C. albicans by Vitek-MS. Sixteen Candida species having discrepant results with Vitek-MS, API or CMA were randomly chosen, and ITS sequence analysis was performed. The results of sequencing were compatible 56.2 % with API 20C AUX, 50 % with CMA and 93.7 % with Vitek-MS. When compared with conventional identification methods, MS results are more reliable and rapid for Candida identification. MS system may be used as routine identification method in clinical microbiology laboratories.

X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.

PubMed

Barr, Ian; Stich, Troy A; Gizzi, Anthony S; Grove, Tyler L; Bonanno, Jeffrey B; Latham, John A; Chung, Tyler; Wilmot, Carrie M; Britt, R David; Almo, Steven C; Klinman, Judith P

2018-02-27

The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.

Spiders and Camels and Sybase! Oh, My!

NASA Astrophysics Data System (ADS)

Barg, Irene; Ferro, Anthony J.; Stobie, Elizabeth

The Hubble Space Telescope NICMOS Guaranteed Time Observers (GTOs) requested a means of sharing point spread function (PSF) observations. Because of the specifics of the instrument, these PSFs are very useful in the analysis of observations and can vary with the conditions on the telescope. The GTOs are geographically diverse, so a centralized processing solution would not work. The individual PSF observations were reduced by different people, at different institutions, using different reduction software. These varied observations had to be combined into a single database and linked to other information as well. The NICMOS software group at the University of Arizona developed a solution based on a World Wide Web (WWW) interface, using Perl/CGI forms to query the submitter about the PSF data to be entered. After some semi-automated sanity checks, using the FTOOLS package, the metadata are then entered into a Sybase relational database system. A user of the system can then query the database, again through a WWW interface, to locate and retrieve PSFs which may match their observations, as well as determine other information regarding the telescope conditions at the time of the observations (e.g., the breathing parameter). This presentation discusses some of the driving forces in the design, problems encountered, and the choices made. The tools used, including Sybase, Perl, FTOOLS, and WWW elements are also discussed.

Quality assessment of protein model-structures using evolutionary conservation.

PubMed

Kalman, Matan; Ben-Tal, Nir

2010-05-15

Programs that evaluate the quality of a protein structural model are important both for validating the structure determination procedure and for guiding the model-building process. Such programs are based on properties of native structures that are generally not expected for faulty models. One such property, which is rarely used for automatic structure quality assessment, is the tendency for conserved residues to be located at the structural core and for variable residues to be located at the surface. We present ConQuass, a novel quality assessment program based on the consistency between the model structure and the protein's conservation pattern. We show that it can identify problematic structural models, and that the scores it assigns to the server models in CASP8 correlate with the similarity of the models to the native structure. We also show that when the conservation information is reliable, the method's performance is comparable and complementary to that of the other single-structure quality assessment methods that participated in CASP8 and that do not use additional structural information from homologs. A perl implementation of the method, as well as the various perl and R scripts used for the analysis are available at http://bental.tau.ac.il/ConQuass/. nirb@tauex.tau.ac.il Supplementary data are available at Bioinformatics online.

Automated radiotherapy treatment plan integrity verification

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

Yang Deshan; Moore, Kevin L.

2012-03-15

Purpose: In our clinic, physicists spend from 15 to 60 min to verify the physical and dosimetric integrity of radiotherapy plans before presentation to radiation oncology physicians for approval. The purpose of this study was to design and implement a framework to automate as many elements of this quality control (QC) step as possible. Methods: A comprehensive computer application was developed to carry out a majority of these verification tasks in the Philips PINNACLE treatment planning system (TPS). This QC tool functions based on both PINNACLE scripting elements and PERL sub-routines. The core of this technique is the method ofmore » dynamic scripting, which involves a PERL programming module that is flexible and powerful for treatment plan data handling. Run-time plan data are collected, saved into temporary files, and analyzed against standard values and predefined logical rules. The results were summarized in a hypertext markup language (HTML) report that is displayed to the user. Results: This tool has been in clinical use for over a year. The occurrence frequency of technical problems, which would cause delays and suboptimal plans, has been reduced since clinical implementation. Conclusions: In addition to drastically reducing the set of human-driven logical comparisons, this QC tool also accomplished some tasks that are otherwise either quite laborious or impractical for humans to verify, e.g., identifying conflicts amongst IMRT optimization objectives.« less

Longitudinal noninvasive magnetic resonance imaging of brain microhemorrhages in BACE inhibitor-treated APP transgenic mice.

PubMed

Beckmann, Nicolau; Doelemeyer, Arno; Zurbruegg, Stefan; Bigot, Karine; Theil, Diethilde; Frieauff, Wilfried; Kolly, Carine; Moulin, Pierre; Neddermann, Daniel; Kreutzer, Robert; Perrot, Ludovic; Brzak, Irena; Jacobson, Laura H; Staufenbiel, Matthias; Neumann, Ulf; Shimshek, Derya R

2016-09-01

Currently, several immunotherapies and BACE (Beta Site APP Cleaving Enzyme) inhibitor approaches are being tested in the clinic for the treatment of Alzheimer's disease. A crucial mechanism-related safety concern is the exacerbation of microhemorrhages, which are already present in the majority of Alzheimer patients. To investigate potential safety liabilities of long-term BACE inhibitor therapy, we used aged amyloid precursor protein (APP) transgenic mice (APP23), which robustly develop cerebral amyloid angiopathy. T2*-weighted magnetic resonance imaging (MRI), a translational method applicable in preclinical and clinical studies, was used for the detection of microhemorrhages throughout the entire brain, with subsequent histological validation. Three-dimensional reconstruction based on in vivo MRI and serial Perls' stained sections demonstrated a one-to-one matching of the lesions thus allowing for their histopathological characterization. MRI detected small Perls' positive areas with a high spatial resolution. Our data demonstrate that volumetric assessment by noninvasive MRI is well suited to monitor cerebral microhemorrhages in vivo. Furthermore, 3 months treatment of aged APP23 with the potent BACE-inhibitor NB-360 did not exacerbate microhemorrhages in contrast to Aβ-antibody β1. These results substantiate the safe use of BACE inhibitors regarding microhemorrhages in long-term clinical studies for the treatment of Alzheimer's disease. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion.

PubMed

Santillán, Orlando; Ramírez-Romero, Miguel A; Dávila, Guillermo

2017-06-25

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI). CAPRRESI benefits from many strengths of the original plasmid recovery method and introduces restriction enzyme digestion to ease DNA ligation reactions (required for chimera assembly). For this protocol, users clone wildtype genes into the same plasmid (pUC18 or pUC19). After the in silico selection of amino acid sequence regions where chimeras should be assembled, users obtain all the synonym DNA sequences that encode them. Ad hoc Perl scripts enable users to determine all synonym DNA sequences. After this step, another Perl script searches for restriction enzyme sites on all synonym DNA sequences. This in silico analysis is also performed using the ampicillin resistance gene (ampR) found on pUC18/19 plasmids. Users design oligonucleotides inside synonym regions to disrupt wildtype and ampR genes by PCR. After obtaining and purifying complementary DNA fragments, restriction enzyme digestion is accomplished. Chimera assembly is achieved by ligating appropriate complementary DNA fragments. pUC18/19 vectors are selected for CAPRRESI because they offer technical advantages, such as small size (2,686 base pairs), high copy number, advantageous sequencing reaction features, and commercial availability. The usage of restriction enzymes for chimera assembly eliminates the need for DNA polymerases yielding blunt-ended products. CAPRRESI is a fast and low-cost method for fusing protein-coding genes.

"Le Cochon", a Washed up Mermaid, and Soldier's Bread: Three Generations of Acadian Women at the Intersection of Museums and Fiction

ERIC Educational Resources Information Center

Taber, Nancy

2018-01-01

In this autoethnographic narrative article, I apply a feminist antimilitarist lens to discuss how the critical learning that museums can facilitate can provide a powerful pedagogic lens into the past and present, particularly when connected to self. These sites can illuminate the strength of women as they encounter/ed individual and societal…

Evaluation d'un scenario d'apprentissage favorisant la mobilisation des habiletes reliees au processus d'enquete

NASA Astrophysics Data System (ADS)

Blanchard, Samuel F. J.

Les resultats au Programme international pour le suivi des acquis des eleves (PISA) demontrent que les jeunes neobrunswickois francophones se classent b un niveau significativement inferieur comparaiivement aux eleves anglophones du Nouveau-Brunswick, aux eleves des autres provinces canadiennes et se classent sous la moyenne internationale de tous les pays participants quant b la culture scientifique. L'evaluation de cette culture scientifique est basee sur une serie de savoirs, de savoir-faire et de savoir-etre reliee au processus d'enquete scolaire. Le processus d'enquete scolaire est une approche b l'apprentissage ou les eleves effectuent des recherches d'informations, discutent d'idees et entreprennent des investigations pour augmenter leur comprehension d'un probleme ou d'un sujet. Les recherches demontrent que le processus d'enquete scolaire est rarement une composante pedagogique importante de la salle de classe et les recherches portant sur l'implantation du processus d'enquete scolaire recommandent de rendre ce dernier plus accessible aux enseignantes et aux enseignants. Afin de rendre le processus d'enquete plus accessible aux enseignantes et aux enseignants, notre recherche porte sur l'evaluation de la valeur pedagogique d'un scenario d'apprentissage (PhaRoboS) concu specialement pour creer un environnement dans lequel les eleves auront plusieurs occasions a mobiliser les habiletes reliees au processus d'enquete. Les retombees de cette evaluation nous permettront d'offrir des pistes de remediations afin d'aider plus d'enseignantes et d'enseignants b creer un environnement dans lequel les eleves auront plusieurs occasions b mobiliser les habiletes reliees au processus d'enquete. Cette evaluation s'est faite a partir d'une methodologie inspiree de l'evaluation pour fin d'amelioration d'un objet pedagogique. L'analyse des donnees qualitatives recueillies aupres des eleves et de leur enseignante d'une ecole francophone du Nouveau-Brunswick semble montrer que

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

Introduction to Python for CMF Authority Users

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

Pritchett-Sheats, Lori A.

This talk is a very broad over view of Python that highlights key features in the language used in the Common Model Framework (CMF). I assume that the audience has some programming experience in a shell scripting language (C shell, Bash, PERL) or other high level language (C/C++/ Fortran). The talk will cover Python data types, classes (objects) and basic programming constructs. The talk concludes with slides describing how I developed the basic classes for a TITANS homework assignment.

Modeling of Impact Properties of Auxetic Materials: Phase 1

DTIC Science & Technology

2013-08-01

avantages marqués comparativement aux matériaux techniques classiques. La présente étude avait pour objectifs de mieux comprendre le comportement des...possible benefits of incorporating auxetic materials into lightweight armour designs . New armour designs incorporating novel auxetic materials may...Poisson négatif et ils offriraient, pour certaines applications, des avantages marqués comparativement aux matériaux techniques classiques. La présente

Relapsed chronic lymphocytic leukemia retreated with rituximab: interim results of the PERLE study.

PubMed

Chaoui, Driss; Choquet, Sylvain; Sanhes, Laurence; Mahé, Béatrice; Hacini, Maya; Fitoussi, Olivier; Arkam, Yazid; Orfeuvre, Hubert; Dilhuydy, Marie-Sarah; Barry, Marly; Jourdan, Eric; Dreyfus, Brigitte; Tempescul, Adrian; Leprêtre, Stéphane; Bardet, Aurélie; Leconte, Pierre; Maynadié, Marc; Delmer, Alain

2017-06-01

This prospective non-interventional study assessed the management of relapsed/refractory CLL after one or two treatments with rituximab, and retreatment with a rituximab-based regimen. An interim analysis was performed at the end of the induction period in 192 evaluable patients. Median age was 72 years [35-89], first relapse (55%), and second relapse (45%). Rituximab administered during first (68%), second (92%), or both treatment lines (20%). R-bendamustine administered in 56% of patients, R-purine analogs (21%), and R-alkylating agents (19%). The overall response rate (ORR) was 74.6%, in favor of R-purine analogs (90%), R-bendamustine (75%), and R-alkylating agents (69%). Lower ORR in Del 17p patients (43%) and third time rituximab (31%). Most frequent adverse events were hematological (23% patients) including neutropenia (11%) and infections (12%); grade 3/4 AEs (23% patients), mainly hematological (18%); death during induction treatment (7%). This first large study focusing on relapsed/refractory CLL patients retreated with rituximab-based regimens is still ongoing.

Glutathione-capped gold nanoclusters as photosensitizers. Visible light-induced hydrogen generation in neutral water.

PubMed

Chen, Yong-Siou; Kamat, Prashant V

2014-04-23

Glutathione-capped metal nanoclusters (Aux-GSH NCs) which exhibit molecular-like properties are employed as a photosensitizer for hydrogen generation in a photoelectrochemical cell (PEC) and a photocatalytic slurry reactor. The reversible reduction (E(0) = -0.63 V vs RHE) and oxidation (E(0) = 0.97 and 1.51 V vs RHE) potentials of these metal nanoclusters make them suitable for driving the water-splitting reaction. When a mesoscopic TiO2 film sensitized by Aux-GSH NCs is used as the photoanode with a Pt counter electrode in aqueous buffer solution (pH = 7), we observe significant photocurrent activity under visible light (400-500 nm) excitation. Additionally, sensitizing Pt/TiO2 nanoparticles with Aux-GSH NCs in an aqueous slurry system and irradiating with visible light produce H2 at a rate of 0.3 mmol of hydrogen/h/g of Aux-GSH NCs. The rate of H2 evolution is significantly enhanced (∼5 times) when a sacrificial donor, such as EDTA, is introduced into the system. Using metal nanoclusters as a photosensitizer for hydrogen generation lays the foundation for the future exploration of other metal nanoclusters with well-controlled numbers of metal atoms and capping ligands.

Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana

PubMed Central

Siligato, Riccardo; Alonso, Jose M.; Swarup, Ranjan; Bennett, Malcolm J.; Mähönen, Ari Pekka; Caño-Delgado, Ana I.; Ibañes, Marta

2015-01-01

Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants. PMID:25922946

Teaching resources. Model of the TIR1 pathway for auxin-mediated gene expression.

PubMed

Laskowski, Marta

2006-02-14

Auxin mediates numerous plant responses, some of which have been shown to require transcriptional regulation. One auxin response pathway, which depends on the relief of transcriptional repression, is mediated by TIR1 (transport inhibitor response protein 1). TIR1 is an auxin receptor and also a subunit of an SCF-type ubiquitin ligase. In the presence of a low concentration of auxin in the nucleus, members of the Aux/IAA family of transcriptional repressors bind to ARF proteins and inhibit the transcription of specific auxin response genes. Increased nuclear concentrations of auxin promote auxin binding to TIR1, causing the Aux/IAA proteins to associate with TIR1 and leading to their degradation by a proteasome-mediated pathway. This decreases the concentration of Aux/IAA proteins in the nucleus and thereby enables the expression of certain auxin response genes.

AGARD/SMP Review Damage Tolerance for Engine Structures. 3. Component Behaviour and Life Management

DTIC Science & Technology

1990-06-01

Life Management (Revue AGARD/SMP - ToIrance aux Dommages pour les Composants de Moteurs 3. Le Comportement des Composants et la Gestion %𔄀 de Leur Dur...Structures 3. Component Behaviour and Life Management . (Revue AGARD/SMP - ToI~rance aux Dommages pour les Compos ants de Moteurs 3. Le Comportement...engine parts. The present report includes the papers presented during Workshop Ill which was devoted to Component Behaviour and Life Management . It also

SNS Proton Beam Window Disposal

NASA Astrophysics Data System (ADS)

Popova, Irina; Gallmeier, Franz X.; Trotter, Steven

2017-09-01

In order to support the disposal of the proton beam window assembly of the Spallation Neutron Source beamline to the target station, waste classification analyses are performed. The window has a limited life-time due to radiation-induced material damage. Analyses include calculation of the radionuclide inventory and shielding analyses for the transport package/container to ensure that the container is compliant with the transportation and waste management regulations. In order to automate this procedure and minimize manual work a script in Perl language was written.

Web-based data acquisition and management system for GOSAT validation Lidar data analysis

NASA Astrophysics Data System (ADS)

Okumura, Hiroshi; Takubo, Shoichiro; Kawasaki, Takeru; Abdullah, Indra N.; Uchino, Osamu; Morino, Isamu; Yokota, Tatsuya; Nagai, Tomohiro; Sakai, Tetsu; Maki, Takashi; Arai, Kohei

2012-11-01

An web-base data acquisition and management system for GOSAT (Greenhouse gases Observation SATellite) validation lidar data analysis is developed. The system consists of data acquisition sub-system (DAS) and data management sub-system (DMS). DAS written in Perl language acquires AMeDAS ground-level meteorological data, Rawinsonde upper-air meteorological data, ground-level oxidant data, skyradiometer data, skyview camera images, meteorological satellite IR image data and GOSAT validation lidar data. DMS written in PHP language demonstrates satellite-pass date and all acquired data.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor

Reengineering Workflow for Curation of DICOM Datasets.

PubMed

Bennett, William; Smith, Kirk; Jarosz, Quasar; Nolan, Tracy; Bosch, Walter

2018-06-15

Reusable, publicly available data is a pillar of open science and rapid advancement of cancer imaging research. Sharing data from completed research studies not only saves research dollars required to collect data, but also helps insure that studies are both replicable and reproducible. The Cancer Imaging Archive (TCIA) is a global shared repository for imaging data related to cancer. Insuring the consistency, scientific utility, and anonymity of data stored in TCIA is of utmost importance. As the rate of submission to TCIA has been increasing, both in volume and complexity of DICOM objects stored, the process of curation of collections has become a bottleneck in acquisition of data. In order to increase the rate of curation of image sets, improve the quality of the curation, and better track the provenance of changes made to submitted DICOM image sets, a custom set of tools was developed, using novel methods for the analysis of DICOM data sets. These tools are written in the programming language perl, use the open-source database PostgreSQL, make use of the perl DICOM routines in the open-source package Posda, and incorporate DICOM diagnostic tools from other open-source packages, such as dicom3tools. These tools are referred to as the "Posda Tools." The Posda Tools are open source and available via git at https://github.com/UAMS-DBMI/PosdaTools . In this paper, we briefly describe the Posda Tools and discuss the novel methods employed by these tools to facilitate rapid analysis of DICOM data, including the following: (1) use a database schema which is more permissive, and differently normalized from traditional DICOM databases; (2) perform integrity checks automatically on a bulk basis; (3) apply revisions to DICOM datasets on an bulk basis, either through a web-based interface or via command line executable perl scripts; (4) all such edits are tracked in a revision tracker and may be rolled back; (5) a UI is provided to inspect the results of such edits, to

DISCOURS QUI RÉSISTENT À L’OBJECTIVATION : QUE PEUT-ON EN TIRER POUR L’ÉVALUATION?

PubMed Central

Brousselle, Astrid

2013-01-01

Résumé L’évaluateur doit porter attention aux distorsions qu’il contribue à créer lorsqu’il utilise l’entrevue comme méthode de collecte de données. L’évaluation est un exercice politique qui, placé dans un contexte politique, peut favoriser l’émergence de discours de résistance à l’objectivation. À partir des entrevues que nous avons effectuées lors de l’évaluation du processus d’implantation de l’initiative ONUSIDA d’accès aux médicaments au Chili, nous illustrons différentes tactiques que les acteurs utilisent et qui peuvent soit attirer la sympathie de l’évaluateur, soit faire obstacle à son besoin d’information. Nous présentons une méthode d’analyse que l’évaluateur peut utiliser pour redonner du sens aux discours de résistance. PMID:23997421

The Cascading Impacts of Technology Selection: Incorporating Ruby on Rails into ECHO

NASA Astrophysics Data System (ADS)

Pilone, D.; Cechini, M.

2010-12-01

NASA’s Earth Observing System (EOS) ClearingHOuse (ECHO) is a SOA based Earth Science Data search and order system implemented in Java with one significant exception: the web client used by 98% of our users is written in Perl. After several decades of maintenance the Perl based application had reached the end of its serviceable life and ECHO was tasked with implementing a replacement. Despite a broad investment in Java, the ECHO team conducted a survey of modern development technologies including Flex, Python/Django, JSF2/Spring and Ruby on Rails. The team ultimately chose Ruby on Rails (RoR) with Cucumber for testing due to its perceived applicability to web application development and corresponding development efficiency gains. Both positive and negative impacts on the entire ECHO team, including our stakeholders, were immediate and sometimes subtle. The technology selection caused shifts in our architecture and design, development and deployment procedures, requirement definition approach, testing approach, and, somewhat surprisingly, our project team structure and software process. This presentation discusses our experiences, including technical, process, and psychological, using RoR on a production system. During this session we will discuss: - Real impacts of introducing a dynamic language to a Java team - Real and perceived efficiency advantages - Impediments to adoption and effectiveness - Impacts of transition from Test Driven Development to Behavior Driven Development - Leveraging Cucumber to provide fully executable requirement documents - Impacts on team structure and roles

Ultraviolet photography of the in vivo human cornea unmasks the Hudson-Stähli line and physiologic vortex patterns.

PubMed

Every, Sean G; Leader, John P; Molteno, Anthony C B; Bevin, Tui H; Sanderson, Gordon

2005-10-01

To perform ultraviolet (UV) macrophotography of the normal in vivo human cornea, establishing biometric data of the major component of UV absorption for comparison with the Hudson-Stähli (HS) line, the distribution of iron demonstrated by Perl stain, and cases of typical amiodarone keratopathy. Nonrandomized comparative case series of UV photographs of 76 normal corneas (group 1) and 16 corneas with typical amiodarone keratopathy (group 2). Image-analysis software was used to grade the major component of UV absorption for slope and the coordinates of its points of intersection with the vertical corneal meridian and inflection. In group 1 the major component had a mean slope of 5.8 degrees, sloping down from nasal to temporal cornea. The mean coordinates of points of intersection with the vertical corneal meridian and inflection were (0, 0.30) and (0.02, 0.31), respectively. No significant differences between groups 1 and 2 were found for slope (P = 0.155), intersection with the vertical corneal meridian (P = 0.517), and point of inflection (P = 0.344). The major component of UV absorption was consistent with published characteristics of the HS line, and coincidence of UV absorption and Perl-stained iron was demonstrated in one corneal button. A vortex pattern of UV absorption was observed in all corneas. UV photography demonstrates subclinical corneal iron, confirming its deposition in an integrated HS line/vortex pattern. Coincident iron and amiodarone deposition occurs in amiodarone keratopathy.

Development and Implementation of Dynamic Scripts to Execute Cycled WRF/GSI Forecasts

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Berndt, Emily; Li, Quanli; Watson, Leela

2014-01-01

Automating the coupling of data assimilation (DA) and modeling systems is a unique challenge in the numerical weather prediction (NWP) research community. In recent years, the Development Testbed Center (DTC) has released well-documented tools such as the Weather Research and Forecasting (WRF) model and the Gridpoint Statistical Interpolation (GSI) DA system that can be easily downloaded, installed, and run by researchers on their local systems. However, developing a coupled system in which the various preprocessing, DA, model, and postprocessing capabilities are all integrated can be labor-intensive if one has little experience with any of these individual systems. Additionally, operational modeling entities generally have specific coupling methodologies that can take time to understand and develop code to implement properly. To better enable collaborating researchers to perform modeling and DA experiments with GSI, the Short-term Prediction Research and Transition (SPoRT) Center has developed a set of Perl scripts that couple GSI and WRF in a cycling methodology consistent with the use of real-time, regional observation data from the National Centers for Environmental Prediction (NCEP)/Environmental Modeling Center (EMC). Because Perl is open source, the code can be easily downloaded and executed regardless of the user's native shell environment. This paper will provide a description of this open-source code and descriptions of a number of the use cases that have been performed by SPoRT collaborators using the scripts on different computing systems.

Recommandations pour le dépistage de l’hypertension chez les adultes canadiens

PubMed Central

Lindsay, Patrice; Gorber, Sarah Connor; Joffres, Michel; Birtwhistle, Richard; McKay, Donald; Cloutier, Lyne

2013-01-01

Résumé Objectif Présenter des recommandations concernant le dépistage de l’hypertension chez les adultes de 18 ans et plus qui n’ont pas reçu antérieurement de diagnostic d’hypertension. Qualité des données Les données probantes sont tirées d’une recension systématique dans MEDLINE, EMBASE et la base de données des synthèses systématiques de la Collaboration Cochrane (EBM Reviews), de janvier 1985 à septembre 2011. Les types d’études retenues se limitaient aux études randomisées contrôlées, aux synthèses systématiques et aux études observationnelles avec groupes témoins. Message principal Trois fortes recommandations se sont dégagées de données probantes de qualité modérée. Il est recommandé de mesurer la pression artérielle à toutes les consultations appropriées en soins primaires, conformément aux techniques actuelles décrites dans les recommandations du Programme éducatif canadien sur l’hypertension pour la mesure de la pression artérielle en cabinet et en soins ambulatoires. Les critères du Programme éducatif canadien sur l’hypertension pour l’évaluation et le diagnostic de l’hypertension devraient s’appliquer aux personnes chez qui on observe une pression artérielle élevée. Conclusion À la suite d’un examen des plus récentes données probantes, le Groupe d’étude canadien sur les soins de santé préventifs continue de recommander la mesure de la pression artérielle lors des consultations périodiques auprès du médecin.

Automation Framework for Flight Dynamics Products Generation

NASA Technical Reports Server (NTRS)

Wiegand, Robert E.; Esposito, Timothy C.; Watson, John S.; Jun, Linda; Shoan, Wendy; Matusow, Carla

2010-01-01

XFDS provides an easily adaptable automation platform. To date it has been used to support flight dynamics operations. It coordinates the execution of other applications such as Satellite TookKit, FreeFlyer, MATLAB, and Perl code. It provides a mechanism for passing messages among a collection of XFDS processes, and allows sending and receiving of GMSEC messages. A unified and consistent graphical user interface (GUI) is used for the various tools. Its automation configuration is stored in text files, and can be edited either directly or using the GUI.

Ion tracking in photocathode rf guns

NASA Astrophysics Data System (ADS)

Lewellen, John W.

2002-02-01

Projected next-generation linac-based light sources, such as PERL or the TESLA free-electron laser, generally assume, as essential components of their injector complexes, long-pulse photocathode rf electron guns. These guns, due to their design rf pulse durations of many milliseconds to continuous wave, may be more susceptible to ion bombardment damage of their cathodes than conventional rf guns, which typically use rf pulses of microsecond duration. This paper explores this possibility in terms of ion propagation within the gun, and presents a basis for future study of the subject.

Querying and Computing with BioCyc Databases

PubMed Central

Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas; Yan, Thomas; Karp, Peter D.

2006-01-01

Summary We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml PMID:15961440

Refractive Surgery: New Techniques and Usability for Military Personnel (La chirurgie refractive: Nouvelles techniques et leur application pour le personnel militaire)

DTIC Science & Technology

2012-11-01

de loin sans correction, la chirurgie réfractive permet aux jeunes recrues ou militaires du rang de satisfaire aux normes de vision sans...correction exigées pour le métier militaire de leur choix, d’où une augmentation du nombre de candidats et la possibilité pour les individus...réfractive risquent d’engendrer des handicaps visuels et d’écourter des carrières militaires. Pour cette raison, la qualité du service fourni

Major Events Coordinated Security Solutions Technical Report Closeout (MECSS): The Application of Science and Technology to Reduce Risk for V2010 and G8/G20 Summits

DTIC Science & Technology

2010-12-01

CBRNE), aux infrastructures essentielles, à la surveillance, à la sécurité physique, à la cybernétique et à la socio- psychologie . Le présent rapport...la socio- psychologie . Dans le cadre du projet SCSGE, on a produit plus de 195 rapports scientifiques, fruit des efforts, du dévouement et du...aux infrastructures essentielles, à la surveillance, à la sécurité physique, à la cybernétique et à la socio- psychologie . Le présent rapport

High-Level Operations in Nonprocedural Programming Languages.

DTIC Science & Technology

1983-12-01

defining type specific operators. Abstract data type has been applied to the nonprocedural language NOPAL [Sang8O]. It was primarily used as a tool...level operation is transformed using the integral operation MATINV as follows: 1 GA IS GROUP, 2 GRA(*) IS GROUP, 3 AUX(*) IS FIELD (DEC FLOAT); I GI...IS GROUP, 2 GRI(*) IS GROUP, 3 INV(*) IS FIELD (DEC FLOAT); AUX = A; GI = MATINV( GA ); C = INV; In code generation, the assertion GI=MATINV( GA ) is

Et pourquoi pas une education aux sciences qui aborde la participation des acteurs sociaux aux controverses sociotechniques?

ERIC Educational Resources Information Center

Pouliot, Chantal

2012-01-01

In this article we discuss research that was conducted as part of a project on citizen science education. We present the research and some of the results, and then take a position on the pertinence of examining, in science classes, questions on citizen participation in socio-technical debates and the roles and capacities of the social actors…

Down-regulation of SlIAA15 in tomato altered stem xylem development and production of volatile compounds in leaf exudates.

PubMed

Deng, Wei; Yan, Fang; Liu, Minchun; Wang, Xinyu; Li, Zhengguo

2012-08-01

The Aux/IAA family genes encode short-lived nuclear proteins that function as transcriptional regulators in auxin signal transduction. Aux/IAA genes have been reported to control many processes of plant development. Our recent study showed that down-regulation of SlIAA15 in tomato reduced apical dominance, altered pattern of axillary shoot development, increased lateral root formation and leaves thickness. The SlIAA15 suppressed lines display strong reduction of trichome density, suggesting that SlIAA15 is involved in trichome formation. Here, we reported that SlIAA15-suppressed transgenic lines display increased number of xylem cells compared to wild-type plants. Moreover, the monoterpene content in trichome exudates are significantly reduced in SlIAA15 down-regulated leaves. The results provide the roles of SlIAA15 in production of volatile compounds in leaf exudates and xylem development, clearly indicating that members of the Aux/IAA gene family can play distinct and specific functions. 

Ampleur et impact des évènements indésirables graves liés aux soins: étude d'incidence dans un hôpital du Centre-Est tunisien

PubMed Central

Bouafia, Nabiha; Bougmiza, Iheb; Bahri, Fathi; Letaief, Mondher; Astagneau, Pascal; Njah, Mansour

2013-01-01

Introduction La prévention des événements indésirables représente une priorité de santé du fait de leur fréquence et de leur gravité potentielle. Ce travail a été mené afin d'avoir un diagnostic de la situation épidémiologique relative aux événements indésirables survenant dans notre hôpital. Méthodes Une étude prospective a été menée auprès de tous les patients qui ont été hospitalisés au CHU Farhat Hached - Sousse (Tunisie) sur une période d'un mois dans quatorze services de l'hôpital. La détection d'évènement indésirable grave (EIG) était basée sur les critères adoptés dans différentes études. Les tests T et Chi 2 ont été utilisés pour identifier les facteurs contribuant à l'apparition d'évènements indésirables. Résultats Au total, 162 EIG ont été identifiés pendant la période. 45% de ces évènements étaient des infections nosocomiales. Ces EIG ont eu comme conséquences un décès chez 9,2% des patients, la mise en jeu du pronostic vital de 26% des patients et la prolongation de la durée de séjour chez 61,7% d'entre eux. L'admission dans des circonstances particulières et l'exposition à des soins invasifs étaient identifiés comme des facteurs de risque potentiels EIG. Conclusion Le renforcement de la stratégie de gestion des risques sanitaires en ciblant préférentiellement le risque infectieux constitue une étape fondamentale dans l'amélioration de la sécurité des patients au sein de notre établissement de santé. PMID:24711868

Lignes directrices canadiennes sur l’utilisation sécuritaire et efficace des opioïdes pour la douleur chronique non cancéreuse

PubMed Central

Kahan, Meldon; Wilson, Lynn; Mailis-Gagnon, Angela; Srivastava, Anita

2011-01-01

Résumé Objectif Présenter aux médecins de famille un résumé clinique pratique sur la prescription d’opioïdes à des populations particulières en se fondant sur les recommandations faites dans les lignes directrices canadiennes sur l’utilisation sécuritaire et efficace des opioïdes pour la douleur chronique non cancéreuse. Qualité des données Pour produire les lignes directrices, les chercheurs ont effectué une synthèse critique de la littérature médicale en insistant plus précisément sur les études de l’efficacité et de la sécurité des opioïdes dans des populations particulières. Message principal Les médecins de famille peuvent atténuer les risques de surdose, de sédation, d’usage abusif et de dépendance grâce à des stratégies adaptées à l’âge et à l’état de santé des patients. Dans le cas de patients à risque de dépendance, on devrait réserver les opioïdes aux douleurs nociceptives ou neuropathiques bien définies qui n’ont pas répondu aux traitements de première intention. Il faut procéder lentement au titrage des opioïdes, avec des dispensations fréquentes et une étroite surveillance pour dépister tout signe d’usage abusif. Une dépendance aux opioïdes suspectée est prise en charge au moyen d’une thérapie structurée aux opioïdes, d’un traitement à la méthadone ou à la buprénorphine ou encore d’un traitement fondé sur l’abstinence. Les patients souffrant de troubles de l’humeur ou d’anxiété ont tendance à avoir une réponse analgésique atténuée aux opioïdes, sont à risque plus élevé d’usage abusif et prennent souvent des sédatifs qui interagissent défavorablement avec les opioïdes. Il faut prendre des précautions semblables à celles utilisées avec d’autres patients à risque élevé. Il faut faire un sevrage progressif si la douleur du patient demeure sévère même avec un essai adéquat de thérapie aux opioïdes. Chez les personnes âgées, la s

A Web-based database for pathology faculty effort reporting.

PubMed

Dee, Fred R; Haugen, Thomas H; Wynn, Philip A; Leaven, Timothy C; Kemp, John D; Cohen, Michael B

2008-04-01

To ensure appropriate mission-based budgeting and equitable distribution of funds for faculty salaries, our compensation committee developed a pathology-specific effort reporting database. Principles included the following: (1) measurement should be done by web-based databases; (2) most entry should be done by departmental administration or be relational to other databases; (3) data entry categories should be aligned with funding streams; and (4) units of effort should be equal across categories of effort (service, teaching, research). MySQL was used for all data transactions (http://dev.mysql.com/downloads), and scripts were constructed using PERL (http://www.perl.org). Data are accessed with forms that correspond to fields in the database. The committee's work resulted in a novel database using pathology value units (PVUs) as a standard quantitative measure of effort for activities in an academic pathology department. The most common calculation was to estimate the number of hours required for a specific task, divide by 2080 hours (a Medicare year) and then multiply by 100. Other methods included assigning a baseline PVU for program, laboratory, or course directorship with an increment for each student or staff in that unit. With these methods, a faculty member should acquire approximately 100 PVUs. Some outcomes include (1) plotting PVUs versus salary to identify outliers for salary correction, (2) quantifying effort in activities outside the department, (3) documenting salary expenditure for unfunded research, (4) evaluating salary equity by plotting PVUs versus salary by sex, and (5) aggregating data by category of effort for mission-based budgeting and long-term planning.

CD1 Mouse Retina Is Shielded From Iron Overload Caused by a High Iron Diet

PubMed Central

Bhoiwala, Devang L.; Song, Ying; Cwanger, Alyssa; Clark, Esther; Zhao, Liang-liang; Wang, Chenguang; Li, Yafeng; Song, Delu; Dunaief, Joshua L.

2015-01-01

Purpose High RPE iron levels have been associated with age-related macular degeneration. Mutation of the ferroxidase ceruloplasmin leads to RPE iron accumulation and degeneration in patients with aceruloplasminemia; mice lacking ceruloplasmin and its homolog hephaestin have a similar RPE degeneration. To determine whether a high iron diet (HID) could cause RPE iron accumulation, possibly contributing to RPE oxidative stress in AMD, we tested the effect of dietary iron on mouse RPE iron. Methods Male CD1 strain mice were fed either a standard iron diet (SID) or the same diet with extra iron added (HID) for either 3 months or 10 months. Mice were analyzed with immunofluorescence and Perls' histochemical iron stain to assess iron levels. Levels of ferritin, transferrin receptor, and oxidative stress gene mRNAs were measured by quantitative PCR (qPCR) in neural retina (NR) and isolated RPE. Morphology was assessed in plastic sections. Results Ferritin immunoreactivity demonstrated a modest increase in the RPE in 10-month HID mice. Analysis by qPCR showed changes in mRNA levels of iron-responsive genes, indicating moderately increased iron in the RPE of 10-month HID mice. However, even by age 18 months, there was no Perls' signal in the retina or RPE and no retinal degeneration. Conclusions These findings indicate that iron absorbed from the diet can modestly increase the level of iron deposition in the wild-type mouse RPE without causing RPE or retinal degeneration. This suggests regulation of retinal iron uptake at the blood-retinal barriers. PMID:26275132

Identification des risques professionnels dans l'industrie textile en République Démocratique du Congo

PubMed Central

Kitronza, Panda Lukongo

2014-01-01

Introduction Le but de cette étude est de mettre en évidence les facteurs de risques professionnels liés aux conditions de travail. Méthodes Cette étude qualitative basée sur les entretiens de groupe a été réalisée par une équipe pluridisciplinaire dans l'industrie textile de la région du Est de la RDC; comprenant un médecin de travail, un médecin de santé publique, un toxicologue, deux infirmiers du centre hospitalier de l'usine, un représentant du comité d'hygiène et un technicien de prévention. La démarche méthodologique a consisté en des entretiens en groupe, des observations et visites guidées de lieux de travail de l'entreprise. Résultats Dans la culture du coton, les effets d'une forte exposition aux pesticides peuvent entraîner des intoxications aiguës, chroniques et voire le décès. Les autres risques sont les accidents de travail, les maladies professionnelles, les troubles psychologiques. Dans l'industrie, les travailleurs sont exposés aux risques liés à l'empoussiérage des fibres de coton, aux facteurs des risques traumatiques, physiques (bruits, vibration) et chimiques (acides forts, bases fortes, solvants et colorants minéraux), ainsi qu'aux risques psychosociaux. La pollution de l'environnement et l’écotoxicité inhérente à ces activités restent l'effet de l'usage des grandes quantités d'intrants agricoles, engrais et produits phytosanitaires. Conclusion Cette étude a permis de mettre en évidence les différents facteurs de risques auxquelles sont soumis les travailleurs textiles; ainsi que les risques environnementaux liés à cette activité. Cela est de nature à permettre la mise sur pied d'une stratégie efficace de prévention et de protection des travailleurs. PMID:25977736

Reconnaissance invariante d'objets 3-D et correlation SONG

NASA Astrophysics Data System (ADS)

Roy, Sebastien

Cette these propose des solutions a deux problemes de la reconnaissance automatique de formes: la reconnaissance invariante d'objets tridimensionnels a partir d'images d'intensite et la reconnaissance robuste a la presence de bruit disjoint. Un systeme utilisant le balayage angulaire des images et un classificateur par trajectoires d'espace des caracteristiques permet d'obtenir la reconnaissance invariante d'objets tridimensionnels. La reconnaissance robuste a la presence de bruit disjoint est realisee au moyen de la correlation SONG. Nous avons realise la reconnaissance invariante aux translations, rotations et changements d'echelle d'objets tridimensionnels a partir d'images d'intensite segmentees. Nous utilisons le balayage angulaire et un classificateur a trajectoires d'espace des caracteris tiques. Afin d'obtenir l'invariance aux translations, le centre de balayage angulaire coincide avec le centre geometrique de l'image. Le balayage angulaire produit un vecteur de caracteristiques invariant aux changements d'echelle de l'image et il transforme en translations du signal les rotations autour d'un axe parallele a la ligne de visee. Le classificateur par trajectoires d'espace des caracteristiques represente une rotation autour d'un axe perpendiculaire a la ligne de visee par une courbe dans l'espace. La classification se fait par la mesure de la distance du vecteur de caracteristiques de l'image a reconnaitre aux trajectoires stockees dans l'espace. Nos resultats numeriques montrent un taux de classement atteignant 98% sur une banque d'images composee de 5 vehicules militaires. La correlation non-lineaire generalisee en tranches orthogonales (SONG) traite independamment les niveaux de gris presents dans une image. Elle somme les correlations lineaires des images binaires ayant le meme niveau de gris. Cette correlation est equivalente a compter le nombre de pixels situes aux memes positions relatives et ayant les memes intensites sur deux images. Nous presentons

FAMA: Fast Automatic MOOG Analysis

NASA Astrophysics Data System (ADS)

Magrini, Laura; Randich, Sofia; Friel, Eileen; Spina, Lorenzo; Jacobson, Heather; Cantat-Gaudin, Tristan; Donati, Paolo; Baglioni, Roberto; Maiorca, Enrico; Bragaglia, Angela; Sordo, Rosanna; Vallenari, Antonella

2014-02-01

FAMA (Fast Automatic MOOG Analysis), written in Perl, computes the atmospheric parameters and abundances of a large number of stars using measurements of equivalent widths (EWs) automatically and independently of any subjective approach. Based on the widely-used MOOG code, it simultaneously searches for three equilibria, excitation equilibrium, ionization balance, and the relationship between logn(FeI) and the reduced EWs. FAMA also evaluates the statistical errors on individual element abundances and errors due to the uncertainties in the stellar parameters. Convergence criteria are not fixed "a priori" but instead are based on the quality of the spectra.

GPC: General Polygon Clipper library

NASA Astrophysics Data System (ADS)

Murta, Alan

2015-12-01

The University of Manchester GPC library is a flexible and highly robust polygon set operations library for use with C, C#, Delphi, Java, Perl, Python, Haskell, Lua, VB.Net and other applications. It supports difference, intersection, exclusive-or and union clip operations, and polygons may be comprised of multiple disjoint contours. Contour vertices may be given in any order - clockwise or anticlockwise, and contours may be convex, concave or self-intersecting, and may be nested (i.e. polygons may have holes). Output may take the form of either polygon contours or tristrips, and hole and external contours are differentiated in the result.

mpiGraph

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

Moody, Adam

2007-05-22

MpiGraph consists of an MPI application called mpiGraph written in C to measure message bandwidth and an associated crunch_mpiGraph script written in Perl to process the application output into an HTMO report. The mpiGraph application is designed to inspect the health and scalability of a high-performance interconnect while under heavy load. This is useful to detect hardware and software problems in a system, such as slow nodes, links, switches, or contention in switch routing. It is also useful to characterize how interconnect performance changes with different settings or how one interconnect type compares to another.

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

PubMed

Sobreira, Tiago José P; Durham, Alan M; Gruber, Arthur

2006-02-01

TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

Decrease in artificial tanning by French teenagers: 2011-2016.

PubMed

Say, Matthieu; Beauchet, Alain; Vouldoukis, Ioannis; Beauchet, Pascale; Boudet, Monique; Tella, Emilie; Mahé, Emmanuel

2018-03-13

The major risk factor for skin cancers is exposure to solar and artificial ultraviolet radiation, in particular during childhood and adolescence. In France, a law was restricted for tanning-bed access to adults (≥18 years) since 1997. To evaluate teenagers' artificial tanning behaviour in 2016 and to compare results with those obtained in a similar survey performed in 2011. The SOLADO 2011 and 2016 surveys were conducted in a general school in Antony and a technical school in Fontenay-aux-Roses (Paris suburb). In 2016, 630 teenagers (mean age: 14.2 ± 1.9 y: Males/Females: 301/329) completed the questionnaire, 1.3% of teenagers reported using tanning beds, 1.1% tanning pills and 8.9% tanning creams. Between 2011 and 2016, the use of tanning beds decreased from 1.4% to 0.7% in Antony (P = .26) and from 9.5% to 4.8% in Fontenay-aux-Roses (P = .01), and the use of tanning creams from 39.8% to 17.6% in Fontenay-aux-Rose (P = .0007). The incidence of sunburn decreased from 60.5% to 54.0% in Antony (P = .02) and from 55.4% to 42.4% in Fontenay-aux-Roses (P = .05). As compared to 2011, teenagers used artificial tanning methods less frequently in 2016. In particular, they used tanning beds less frequently, suggesting that the new stricter legislation has been effective. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Engine Fluid Leakage Detection: A Feasibility Study

DTIC Science & Technology

2011-07-01

2011 © Sa Majesté la Reine (en droit du Canada), telle que représentée par le ministre de la Défense nationale, 2011 DRDC Atlantic TM 2011-050 i... de détecter tout problème possible lié à la sécurité ou aux performances des moteurs à turbine à gaz d’aéronefs. Le signalement immédiat d’une fuite...carburant ou d’huile moteur nuisent non seulement aux performances d’un moteur, mais elles représentent également une menace réelle pour la sécurité de

Swell Across the Continental Shelf

DTIC Science & Technology

2001-09-01

Arlington, VA The views expressed in this thesis are those of the author and do not reflect the official policy or position of the Department of Defense ...le terme de source, tandis que les effets de la réfraction et du levage causés par les variations de profondeur aux échelles sous-maille sont...précisement pris en compte grâce aux rayons pré- calculés. Ainsi ce modèle peut être appliqué à de vastes zones côtières avec des maillages

Post-Deployment Reintegration Experiences of AF Personnel: Implications for Scale Development

DTIC Science & Technology

2006-09-01

peuvent également présenter des avantages, notamment une amélioration aux points de vue suivants : confiance en soi , tolérance à l’égard de soi...notamment une amélioration aux points de vue suivants : confiance en soi , tolérance à l’égard de soi, compréhension politique et compétence militaire... confiance en soi , tolérance à l’égard de soi, compréhension politique et compétence militaire. À ce jour, les études sur l’expérience de réinsertion

Formation Stellaire Aux Échelles Des Galaxies

NASA Astrophysics Data System (ADS)

Boissier, S.

2012-12-01

Star Formation is at the very core of the evolution of galaxies. From their gas reservoir (filled by infall or fusions), stars form at the "Star Formation Rate" (SFR), with an enormous impact on many aspects of the evolution of galaxies. This HDR presents first the formalism concerning star formation (SFR, IMF), some theoretical suggestions on physical processes that may affect star formation on various galactic scales, and the methods used to determine the SFR from observations. A large part is dedicated to the "Star Formation Laws" (e.g. Schmidt law) on various scales (local, radial, and global law). Finally, the last part concerns the largest scales (evolution of the "cosmic" SFR and effect of the environment).

The WORM site: worm.csirc.net

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

Jones, T.

2000-07-01

The Write One, Run Many (WORM) site (worm.csirc.net) is the on-line home of the WORM language and is hosted by the Criticality Safety Information Resource Center (CSIRC) (www.csirc.net). The purpose of this web site is to create an on-line community for WORM users to gather, share, and archive WORM-related information. WORM is an embedded, functional, programming language designed to facilitate the creation of input decks for computer codes that take standard ASCII text files as input. A functional programming language is one that emphasizes the evaluation of expressions, rather than execution of commands. The simplest and perhaps most common examplemore » of a functional language is a spreadsheet such as Microsoft Excel. The spreadsheet user specifies expressions to be evaluated, while the spreadsheet itself determines the commands to execute, as well as the order of execution/evaluation. WORM functions in a similar fashion and, as a result, is very simple to use and easy to learn. WORM improves the efficiency of today's criticality safety analyst by allowing: (1) input decks for parameter studies to be created quickly and easily; (2) calculations and variables to be embedded into any input deck, thus allowing for meaningful parameter specifications; (3) problems to be specified using any combination of units; and (4) complex mathematically defined models to be created. WORM is completely written in Perl. Running on all variants of UNIX, Windows, MS-DOS, MacOS, and many other operating systems, Perl is one of the most portable programming languages available. As such, WORM works on practically any computer platform.« less

Maladie des vibrations

PubMed Central

Shen, Shixin (Cindy); House, Ronald A.

2017-01-01

Résumé Objectif Permettre aux médecins de famille de comprendre l’épidémiologie, la pathogenèse, les symptômes, le diagnostic et la prise en charge de la maladie des vibrations, une maladie professionnelle importante et courante au Canada. Sources d’information Une recherche a été effectuée sur MEDLINE afin de relever les recherches et comptes rendus portant sur la maladie des vibrations. Une recherche a été effectuée sur Google dans le but d’obtenir la littérature grise qui convient au contexte canadien. D’autres références ont été tirées des articles relevés. Message principal La maladie des vibrations est une maladie professionnelle répandue touchant les travailleurs de diverses industries qui utilisent des outils vibrants. La maladie est cependant sous-diagnostiquée au Canada. Elle compte 3 éléments : vasculaire, sous la forme d’un phénomène de Raynaud secondaire; neurosensoriel; et musculosquelettique. Aux stades les plus avancés, la maladie des vibrations entraîne une invalidité importante et une piètre qualité de vie. Son diagnostic exige une anamnèse minutieuse, en particulier des antécédents professionnels, un examen physique, des analyses de laboratoire afin d’éliminer les autres diagnostics, et la recommandation en médecine du travail aux fins d’investigations plus poussées. La prise en charge consiste à réduire l’exposition aux vibrations, éviter les températures froides, abandonner le tabac et administrer des médicaments. Conclusion Pour assurer un diagnostic rapide de la maladie des vibrations et améliorer le pronostic et la qualité de vie, les médecins de famille devraient connaître cette maladie professionnelle courante, et pouvoir obtenir les détails pertinents durant l’anamnèse, recommander les patients aux cliniques de médecine du travail et débuter les demandes d’indemnisation de manière appropriée. PMID:28292812

SlLAX1 is Required for Normal Leaf Development Mediated by Balanced Adaxial and Abaxial Pavement Cell Growth in Tomato.

PubMed

Pulungan, Sri Imriani; Yano, Ryoichi; Okabe, Yoshihiro; Ichino, Takuji; Kojima, Mikiko; Takebayashi, Yumiko; Sakakibara, Hitoshi; Ariizumi, Tohru; Ezura, Hiroshi

2018-06-01

Leaves are the major plant organs with a primary function for photosynthesis. Auxin controls various aspects of plant growth and development, including leaf initiation, expansion and differentiation. Unique and intriguing auxin features include its polar transport, which is mainly controlled by the AUX1/LAX and PIN gene families as influx and efflux carriers, respectively. The role of AUX1/LAX genes in root development is well documented, but the role of these genes in leaf morphogenesis remains unclear. Moreover, most studies have been conducted in the plant model Arabidopsis thaliana, while studies in tomato are still scarce. In this study, we isolated six lines of the allelic curly leaf phenotype 'curl' mutants from a γ-ray and EMS (ethyl methanesulfonate) mutagenized population. Using a map-based cloning strategy combined with exome sequencing, we observed that a mutation occurred in the SlLAX1 gene (Solyc09g014380), which is homologous to an Arabidopsis auxin influx carrier gene, AUX1 (AtAUX1). Characterization of six alleles of single curl mutants revealed the pivotal role of SlLAX1 in controlling tomato leaf flatness by balancing adaxial and abaxial pavement cell growth, which has not been reported in tomato. Using TILLING (Targeting Induced Local Lesions IN Genome) technology, we isolated an additional mutant allele of the SlLAX1 gene and this mutant showed a curled leaf phenotype similar to other curl mutants, suggesting that Solyc09g014380 is responsible for the curl phenotype. These results showed that SlLAX1 is required for normal leaf development mediated by balanced adaxial and abaxial pavement cell growth in tomato.

Exotic species with explicit noble metal-noble gas-noble metal linkages.

PubMed

Moreno, Norberto; Restrepo, Albeiro; Hadad, C Z

2018-02-14

We present a study of the isoelectronic Pt 2 Ng 2 F 4 and [Au 2 Ng 2 F 4 ] 2+ species with noble gas atoms (Ng = Kr, Xe, Rn) acting as links bridging the two noble metal atoms. The stability of the species is investigated using several thermodynamic, kinetic and reactivity indicators. The results are compared against [AuXe 4 ] 2+ , which is thermodynamically unstable in the gas phase but is stabilized in the solid state to the point that it has been experimentally detected as [AuXe 4 ](Sb 2 F 11 ) 2 (S. Seidel and K. Seppelt, Science, 2000, 290, 117-118). Our results indicate that improving upon [AuXe 4 ] 2+ , these exotic combinations between the a priori non-reactive noble metals and noble gases lead to metastable species, and, therefore, they have the possibility of existing in the solid state under adequate conditions. Our calculations include accurate energies and geometries at both the CCSD/SDDALL and MP2/SDDALL levels. We offer a detailed description of the nature of the bonding interactions using orbital and density-based analyses. The computational evidence suggests partially covalent and ionic interactions as the stabilization factors.

Consensus formalisé: recommandations de pratiques cliniques pour la prise en charge de la migraine du patient adulte africain

PubMed Central

Ahmed, Mahmoud Ait Kaci; Haddad, Monia; Kouassi, Beugré; Ouhabi, Hamid; Serrie, Alain

2016-01-01

La migraine est une céphalée primaire (selon les derniers critères de l'International Headache Society) qui affecte environ 8% de la population africaine. Les femmes sont plus fréquemment touchées que les hommes et les crises apparaissent le plus souvent avant l’âge de 40 ans. Bien qu'un certain nombre de traitements, de mesure hygiéno-diététiques, et d'autres méthodes non pharmacologiques permettent de limiter l'intensité et la fréquence des crises, la prise en charge médicamenteuse de la crise de migraine est très souvent nécessaire. La disponibilité des traitements et l'accès aux soins diffèrent sur le continent africain et ont conduit à la réalisation du 1er consensus d'experts pour la prise en charge du patient adulte africain. Destiné aux praticiens, ce travail collaboratif multinational a pour objectif de fournir 16 recommandations de pratiques cliniques simples, fondées sur les preuves, et adaptées aux conditions de l'exercice médical en Afrique. PMID:27642420

Consensus formalisé: recommandations de pratiques cliniques pour la prise en charge de la lombalgie aiguë du patient africain

PubMed Central

Elleuch, Mohamed; El Maghraoui, Abdellah; Griene, Brahim; Nejmi, Mati; Ndongo, Souhaibou; Serrie, Alain

2015-01-01

La lombalgie aiguë est la pathologie rhumatismale la plus fréquente en Afrique. L’épidémiologie et la présentation clinique ne diffèrent pas de celles observées sur les autres continents. En revanche, les aspects psycho-sociaux, la disponibilité des traitements, l'accès aux soins et le poids culturel des médecines traditionnelles sont autant de spécificités qui ont conduit à la réalisation du 1er consensus d'experts en rhumatologie pour la prise en charge du patient africain. Destiné aux praticiens, ce travail collaboratif multinational a pour objectif de fournir 11 recommandations de pratiques cliniques simples, fondées sur les preuves, et adaptées aux conditions de l'exercice médical en Afrique. Leur ambition est d'améliorer la prise en charge de la lombalgie aigue par une évaluation initiale clinique pertinente, une diminution des examens radiologiques inutiles, une prescription médicamenteuse adéquate et l'abandon de procédures invasives inappropriées. PMID:26955427

featsel: A framework for benchmarking of feature selection algorithms and cost functions

NASA Astrophysics Data System (ADS)

Reis, Marcelo S.; Estrela, Gustavo; Ferreira, Carlos Eduardo; Barrera, Junior

In this paper, we introduce featsel, a framework for benchmarking of feature selection algorithms and cost functions. This framework allows the user to deal with the search space as a Boolean lattice and has its core coded in C++ for computational efficiency purposes. Moreover, featsel includes Perl scripts to add new algorithms and/or cost functions, generate random instances, plot graphs and organize results into tables. Besides, this framework already comes with dozens of algorithms and cost functions for benchmarking experiments. We also provide illustrative examples, in which featsel outperforms the popular Weka workbench in feature selection procedures on data sets from the UCI Machine Learning Repository.

AST: World Coordinate Systems in Astronomy

NASA Astrophysics Data System (ADS)

Berry, David S.; Warren-Smith, Rodney F.

2014-04-01

The AST library provides a comprehensive range of facilities for attaching world coordinate systems to astronomical data, for retrieving and interpreting that information in a variety of formats, including FITS-WCS, and for generating graphical output based on it. Core projection algorithms are provided by WCSLIB (ascl:1108.003) and astrometry is provided by the PAL (ascl:1606.002) and SOFA (ascl:1403.026) libraries. AST bindings are available in Python (pyast), Java (JNIAST) and Perl (Starlink::AST). AST is used as the plotting and astrometry library in DS9 and GAIA, and is distributed separately and as part of the Starlink software collection.

Detecting distant homologies on protozoans metabolic pathways using scientific workflows.

PubMed

da Cruz, Sérgio Manuel Serra; Batista, Vanessa; Silva, Edno; Tosta, Frederico; Vilela, Clarissa; Cuadrat, Rafael; Tschoeke, Diogo; Dávila, Alberto M R; Campos, Maria Luiza Machado; Mattoso, Marta

2010-01-01

Bioinformatics experiments are typically composed of programs in pipelines manipulating an enormous quantity of data. An interesting approach for managing those experiments is through workflow management systems (WfMS). In this work we discuss WfMS features to support genome homology workflows and present some relevant issues for typical genomic experiments. Our evaluation used Kepler WfMS to manage a real genomic pipeline, named OrthoSearch, originally defined as a Perl script. We show a case study detecting distant homologies on trypanomatids metabolic pathways. Our results reinforce the benefits of WfMS over script languages and point out challenges to WfMS in distributed environments.

Accessing SDO data in a pipeline environment using the VSO WSDL/SOAP interface

NASA Astrophysics Data System (ADS)

Suarez Sola, F. I.; Hourcle, J. A.; Amezcua, A.; Bogart, R.; Davey, A. R.; Gurman, J. B.; Hill, F.; Hughitt, V. K.; Martens, P. C.; Spencer, J.; Vso Team

2010-12-01

As part of the Virtual Solar Observatory (VSO) effort to support the Solar Dynamics Observatory (SDO) data, the VSO has worked on bringing up to date its WSDL document and SOAP interface to make it compatible with most widely used web services core engines. (E.g. axis2, jws, etc.) In this presentation we will explore the possibilities available for searching and/or fetching data within pipeline code. We will explain some of the WSDL/VSO-SDO interface intricacies and show how the vast amount of data that is available via the VSO can be tapped via IDL, Java, Perl or C in an uncomplicated way.

[Two cases of skin pigmentation in association with minocycline therapy (author's transl)].

PubMed

Leroy, J P; Dorval, J C; Dewitte, J D; Guillerm, D; Volant, A; Masse, R

1981-01-01

Report of two cases of skin pigmentation during minocycline therapy. Examination showed confluent blue-gray oval patches on the anterior part of the legs, occurring after ingestion of respectively 12 g and 100 g of minocycline. Microscopic examination of each case was identical and showed two lesions: increase in the amount of melanine deposition in the basal layer of the epidermis; presence of brown-black pigment at all the level of the dermis but specially near the sweet glands. This pigment was strongly positive with Perls' stain. Electron microscopic examination showed a finely granular pigment exclusively intracellular in dermis fibroblast and macrophage. This pigment seemed to contain mainly hemodiderine.

Comparative XAFS studies of some Cobalt complexes of (3-N- phenyl -thiourea-pentanone-2)

NASA Astrophysics Data System (ADS)

soni, Namrata; Parsai, Neetu; Mishra, Ashutosh

2016-10-01

XAFS spectroscopy is a useful method for determining the local structure around a specific atom in disordered systems. XAFS study of some cobalt complexes of (3-N-phenyle- thiourea-pentanon-2) is carried out using the latest XAFS analysis software Demeter with Strawberry Perl. The same study is also carried out theoretically using Mathcad software. It is found that the thiourea has significant influence in the spectra and the results obtained experimentally and theoretically are in agreement. Fourier transform of the experimental and theoretically generated XAFS have been taken to obtain first shell radial distance. The values so obtained are in agreement with each other.

Study of XAFS of some Fe compounds and determination of first shell radial distance

NASA Astrophysics Data System (ADS)

Parsai, Neetu; Mishra, Ashutosh

2017-05-01

X-ray absorption fine structure (XAFS) of some Fe compounds have been studied using the latest XAFS analysis software Demeter with Strawberry Perl. The processed XAFS data of the Fe compounds have been taken from available model compound library. The XAFS data have been processed to plot the µ(E) verses E spectra. These spectra have been converted into K-space, R-space and q-space. R-space spectra have been used to obtain first shell radial distance in Fe compounds. Structural parameters like first shell radial distance is useful in determination of bond length in Fe compounds. Hence the study play important role in biological applications.

The variant call format and VCFtools.

PubMed

Danecek, Petr; Auton, Adam; Abecasis, Goncalo; Albers, Cornelis A; Banks, Eric; DePristo, Mark A; Handsaker, Robert E; Lunter, Gerton; Marth, Gabor T; Sherry, Stephen T; McVean, Gilean; Durbin, Richard

2011-08-01

The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. http://vcftools.sourceforge.net

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

Révision systématique des effets de la fréquence des repas en famille sur les résultats psychosociaux chez les jeunes

PubMed Central

Harrison, Megan E.; Norris, Mark L.; Obeid, Nicole; Fu, Maeghan; Weinstangel, Hannah; Sampson, Margaret

2015-01-01

Résumé Objectif Effectuer une révision systématique des effets de repas en famille fréquents sur les résultats psychosociaux chez les enfants et les adolescents et examiner s’il existe des différences dans les résultats selon le sexe. Sources des données Des études ont été cernées à la suite d’une recherche dans MEDLINE (de 1948 à la dernière semaine de juin 2011) et dans PsycINFO (de 1806 à la première semaine de juillet 2011) à l’aide de l’interface Ovide. Les expressions et mots clés MeSH utilisés seuls ou en combinaisons étaient les suivants : family, meal, food intake, nutrition, diets, body weight, adolescent attitudes, eating behaviour, feeding behaviour et eating disorders. Les bibliographies des articles jugés pertinents ont aussi été passées en revus. Sélection des études La recherche initiale a produit 1783 articles. Pour être incluses dans l’analyse, les études devaient répondre aux critères suivants : être publiées en anglais dans une revue révisée par des pairs; porter sur des enfants ou des adolescents; traiter de l’influence des repas en famille sur les paramètres psychosociaux (p. ex. consommation de drogues et autres substances, troubles de l’alimentation, dépression) chez les enfants ou les adolescents; avoir une conception d’étude appropriée, notamment des méthodes statistiques acceptables pour l’analyse des paramètres. Quatorze articles satisfaisaient aux critères d’inclusion. Deux examinateurs indépendants ont étudié et analysé les articles. Synthèse Dans l’ensemble, les résultats font valoir que la fréquence des repas en famille est inversement proportionnelle aux troubles de l’alimentation, à la consommation d’alcool et de drogues, aux comportements violents, aux sentiments de dépression ou aux pensées suicidaires chez les adolescents. Il existe une relation positive entre de fréquents repas en famille, une bonne estime de soi et la réussite scolaire. Les �

Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts

NASA Astrophysics Data System (ADS)

Li, Zhen; Lee, Hee Sun; Darve, Eric; Karniadakis, George Em

2017-01-01

Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function.

Anthocyanin biosynthesis is differentially regulated by light in the skin and flesh of white-fleshed and teinturier grape berries.

PubMed

Guan, Le; Dai, Zhanwu; Wu, Ben-Hong; Wu, Jing; Merlin, Isabelle; Hilbert, Ghislaine; Renaud, Christel; Gomès, Eric; Edwards, Everard; Li, Shao-Hua; Delrot, Serge

2016-01-01

Light exclusion reduces the concentration and modifies the composition of grape anthocyanins, by altering the expression of genes involved in anthocyanin biosynthesis and transport, in a cultivar- and tissue-specific manner. Unlike most grapes, teinturier grapes accumulate anthocyanins both in skin and flesh. However, the concentration and composition of anthocyanins in both tissues differ, providing a valuable system to study tissue-specific regulation of anthocyanin synthesis. Furthermore, little is known about the mechanisms controlling the sensitivity of anthocyanin accumulation to light. Here, light was excluded from Gamay (white-fleshed) and Gamay Fréaux (teinturier mutant) berries throughout berry development. Under light-exposed conditions, the skin of Gamay Fréaux accumulated the highest level of anthocyanins, followed by the skin of Gamay, while the pulp of Gamay Fréaux had much lower anthocyanins than the skins. Network analysis revealed the same order on the number of significant correlations among metabolites and transcripts in the three colored tissues, indicating a higher connectivity that reflects a higher efficiency of the anthocyanin pathway. Compared to light conditions, light exclusion reduced the total amount of anthocyanins, most severely in the skin of Gamay and to a lesser extent in the flesh and skin of Gamay Fréaux. Coordinated decrease in the transcript abundance of structural, regulatory and transporter genes by light exclusion correlated with the reduced anthocyanin concentration in a cultivar- and tissue-specific manner. Moreover, light exclusion increased the ratio of dihydroxylated to trihydroxylated anthocyanins, in parallel with F3'H and F3'5'H transcript amounts. Sugars and ABA only play a limited role in the control of anthocyanin synthesis in the berries, in contrast with what has been described in cell suspensions. This study provides novel insights into the regulation of anthocyanin in wild type and teinturier cultivars.

L'Apport de la Greffe de Peau Totale dans le Traitement des Sequelles des Brulures de la Main: a Propos de 14 Cas

PubMed Central

Ettalbi, S.; Ibnouzahir, M.; Rachid, M.; Bahaichar, N.; Boukind, H.

2007-01-01

Summary La main est fréquemment exposée aux brûlures, ce qui entraîne des séquelles cutanées. A partir d'une série de 14 patients suivis dans notre service sur une année, nous avons essayé d'établir la simplicité, l'efficacité et le rôle de la greffe de peau totale dans le traitement de ces séquelles (les organes nobles ne sont pas mis à nu). La greffe de peau totale associée à une rééducation efficace permet aux patients de reprendre la mobilité des mains dans les brefs délais. PMID:21991094

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

PubMed

Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Thomsen, Martin Christen Frølund; Friis, Carsten; Rasmussen, Simon; Aarestrup, Frank M

2012-01-01

The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script.The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evaluation results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/.

Informatics Technology Mimics Ecology: Dense, Mutualistic Collaboration Networks Are Associated with Higher Publication Rates

PubMed Central

Sorani, Marco D.

2012-01-01

Information technology (IT) adoption enables biomedical research. Publications are an accepted measure of research output, and network models can describe the collaborative nature of publication. In particular, ecological networks can serve as analogies for publication and technology adoption. We constructed network models of adoption of bioinformatics programming languages and health IT (HIT) from the literature. We selected seven programming languages and four types of HIT. We performed PubMed searches to identify publications since 2001. We calculated summary statistics and analyzed spatiotemporal relationships. Then, we assessed ecological models of specialization, cooperativity, competition, evolution, biodiversity, and stability associated with publications. Adoption of HIT has been variable, while scripting languages have experienced rapid adoption. Hospital systems had the largest HIT research corpus, while Perl had the largest language corpus. Scripting languages represented the largest connected network components. The relationship between edges and nodes was linear, though Bioconductor had more edges than expected and Perl had fewer. Spatiotemporal relationships were weak. Most languages shared a bioinformatics specialization and appeared mutualistic or competitive. HIT specializations varied. Specialization was highest for Bioconductor and radiology systems. Specialization and cooperativity were positively correlated among languages but negatively correlated among HIT. Rates of language evolution were similar. Biodiversity among languages grew in the first half of the decade and stabilized, while diversity among HIT was variable but flat. Compared with publications in 2001, correlation with publications one year later was positive while correlation after ten years was weak and negative. Adoption of new technologies can be unpredictable. Spatiotemporal relationships facilitate adoption but are not sufficient. As with ecosystems, dense, mutualistic

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

PubMed

Thakur, Shalabh; Guttman, David S

2016-06-30

Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .

Passive stiffness of monoarticular lower leg muscles is influenced by knee joint angle.

PubMed

Ateş, Filiz; Andrade, Ricardo J; Freitas, Sandro R; Hug, François; Lacourpaille, Lilian; Gross, Raphael; Yucesoy, Can A; Nordez, Antoine

2018-03-01

While several studies demonstrated the occurrence of intermuscular mechanical interactions, the physiological significance of these interactions remains a matter of debate. The purpose of this study was to quantify the localized changes in the shear modulus of the gastrocnemius lateralis (GL), monoarticular dorsi- and plantar-flexor muscles induced by a change in knee angle. Participants underwent slow passive ankle rotations at the following two knee positions: knee flexed at 90° and knee fully extended. Ultrasound shear wave elastography was used to assess the muscle shear modulus of the GL, soleus [both proximally (SOL-proximal) and distally (SOL distal)], peroneus longus (PERL), and tibialis anterior (TA). This was performed during two experimental sessions (experiment I: n = 11; experiment II: n = 10). The shear modulus of each muscle was compared between the two knee positions. The shear modulus was significantly higher when the knee was fully extended than when the knee was flexed (P < 0.001) for the GL (averaged increase on the whole range of motion: + 5.8 ± 1.3 kPa), SOL distal (+ 4.5 ± 1.5 kPa), PERL (+ 1.1 ± 0.7 kPa), and TA (+ 1.6 ± 1.0 kPa). In contrast, a lower SOL-proximal shear modulus (P < 0.001, - 5.9 ± 1.0 kPa) was observed. As the muscle shear modulus is linearly related to passive muscle force, these results provide evidence of a non-negligible intermuscular mechanical interaction between the human lower leg muscles during passive ankle rotations. The role of these interactions in the production of coordinated movements requires further investigation.

Implementation of a Shared Resource Financial Management System

PubMed Central

Caldwell, T.; Gerlach, R.; Israel, M.; Bobin, S.

2010-01-01

CF-6 Norris Cotton Cancer Center (NCCC), an NCI-designated Comprehensive Cancer Center at Dartmouth Medical School, administers 12 Life Sciences Shared Resources. These resources are diverse and offer multiple products and services. Previous methods for tracking resource use, billing, and financial management were time consuming, error prone and lacked appropriate financial management tools. To address these problems, we developed and implemented a web-based application with a built-in authorization system that uses Perl, ModPerl, Apache2, and Oracle as the software infrastructure. The application uses a role-based system to differentiate administrative users with those requesting services and includes many features requested by users and administrators. To begin development, we chose a resource that had an uncomplicated service, a large number of users, and required the use of all of the applications features. The Molecular Biology Core Facility at NCCC fit these requirements and was used as a model for developing and testing the application. After model development, institution wide deployment followed a three-stage process. The first stage was to interview the resource manager and staff to understand day-to-day operations. At the second stage, we generated and tested customized forms defining resource services. During the third stage, we added new resource users and administrators to the system before final deployment. Twelve months after deployment, resource administrators reported that the new system performed well for internal and external billing and tracking resource utilization. Users preferred the application's web-based system for distribution of DNA sequencing and other data. The sample tracking features have enhanced day-to-day resource operations, and an on-line scheduling module for shared instruments has proven a much-needed utility. Principal investigators now are able to restrict user spending to specific accounts and have final approval of the

OOSTethys - Open Source Software for the Global Earth Observing Systems of Systems

NASA Astrophysics Data System (ADS)

Bridger, E.; Bermudez, L. E.; Maskey, M.; Rueda, C.; Babin, B. L.; Blair, R.

2009-12-01

An open source software project is much more than just picking the right license, hosting modular code and providing effective documentation. Success in advancing in an open collaborative way requires that the process match the expected code functionality to the developer's personal expertise and organizational needs as well as having an enthusiastic and responsive core lead group. We will present the lessons learned fromOOSTethys , which is a community of software developers and marine scientists who develop open source tools, in multiple languages, to integrate ocean observing systems into an Integrated Ocean Observing System (IOOS). OOSTethys' goal is to dramatically reduce the time it takes to install, adopt and update standards-compliant web services. OOSTethys has developed servers, clients and a registry. Open source PERL, PYTHON, JAVA and ASP tool kits and reference implementations are helping the marine community publish near real-time observation data in interoperable standard formats. In some cases publishing an OpenGeospatial Consortium (OGC), Sensor Observation Service (SOS) from NetCDF files or a database or even CSV text files could take only minutes depending on the skills of the developer. OOSTethys is also developing an OGC standard registry, Catalog Service for Web (CSW). This open source CSW registry was implemented to easily register and discover SOSs using ISO 19139 service metadata. A web interface layer over the CSW registry simplifies the registration process by harvesting metadata describing the observations and sensors from the “GetCapabilities” response of SOS. OPENIOOS is the web client, developed in PERL to visualize the sensors in the SOS services. While the number of OOSTethys software developers is small, currently about 10 around the world, the number of OOSTethys toolkit implementers is larger and growing and the ease of use has played a large role in spreading the use of interoperable standards compliant web services widely

Informatics technology mimics ecology: dense, mutualistic collaboration networks are associated with higher publication rates.

PubMed

Sorani, Marco D

2012-01-01

Information technology (IT) adoption enables biomedical research. Publications are an accepted measure of research output, and network models can describe the collaborative nature of publication. In particular, ecological networks can serve as analogies for publication and technology adoption. We constructed network models of adoption of bioinformatics programming languages and health IT (HIT) from the literature.We selected seven programming languages and four types of HIT. We performed PubMed searches to identify publications since 2001. We calculated summary statistics and analyzed spatiotemporal relationships. Then, we assessed ecological models of specialization, cooperativity, competition, evolution, biodiversity, and stability associated with publications.Adoption of HIT has been variable, while scripting languages have experienced rapid adoption. Hospital systems had the largest HIT research corpus, while Perl had the largest language corpus. Scripting languages represented the largest connected network components. The relationship between edges and nodes was linear, though Bioconductor had more edges than expected and Perl had fewer. Spatiotemporal relationships were weak. Most languages shared a bioinformatics specialization and appeared mutualistic or competitive. HIT specializations varied. Specialization was highest for Bioconductor and radiology systems. Specialization and cooperativity were positively correlated among languages but negatively correlated among HIT. Rates of language evolution were similar. Biodiversity among languages grew in the first half of the decade and stabilized, while diversity among HIT was variable but flat. Compared with publications in 2001, correlation with publications one year later was positive while correlation after ten years was weak and negative.Adoption of new technologies can be unpredictable. Spatiotemporal relationships facilitate adoption but are not sufficient. As with ecosystems, dense, mutualistic

In Vivo Iron-Chelating Activity and Phenolic Profiles of the Angel's Wings Mushroom, Pleurotus porrigens (Higher Basidiomycetes).

PubMed

Khalili, Masoumeh; Ebrahimzadeh, Mohammad Ali; Kosaryan, Mehrnoush

2015-01-01

Pleurotus porrigens is an culinary-medicinal mushroom. It is locally called sadafi and is found in the northern regions of Iran, especially in Mazandaran. This mushroom is used to prepare a variety of local and specialty foods. Because of the phenol and flavonoid contents and the strong iron-chelating activity of this mushroom, it was selected for an assay of in vivo iron-chelating activity. Methanolic extract was administered intraperitoneally to iron-overloaded mice at two dosages (200 and 400 mg/kg/24 hours) for a total of 20 days, with a frequency of 5 times a week for 4 successive weeks. The total iron content was determined by atomic absorption spectroscopy. Plasma Fe3+ content was determined using a kit. Liver sections were stained by hematoxylin and eosin and Perls stain. A significant decrease in the plasma concentration of iron was observed in mice treated with extracts (P < 0.001). The animals showed a dramatic decrease in plasma Fe3+ content when compared with the control group (P < 0.001). Also, Perls stain improved the smaller amount of deposited iron in the liver of iron-overloaded mice treated with the extract. Liver sections revealed a marked reduction in the extent of necrotic hepatocytes, fibrous tissues, and pseudo-lobules. A high-performance liquid chromatography method was developed to simultaneously separate 7 phenolic acids in extract. Rutin (1.784 ± 0.052 mg g(-1) of extract) and p-coumaric acid (1.026 ± 0.043 mg g(-1) of extract) were detected as the main flavonoid and phenolic acids in extract, respectively. The extract exhibited satisfactory potency to chelate excessive iron in mice, potentially offering new natural alternatives to treat patients with iron overload. More studies are needed to determine which compounds are responsible for these biological activities.

Investigating Plasma Motion of Magnetic Clouds at 1 AU through a Velocity-modified Cylindrical Force-free Flux Rope Model

NASA Astrophysics Data System (ADS)

Wang, Y.; Shen, C.; Liu, R.; Zhou, Z.

2014-12-01

Magnetic clouds (MCs) are the interplanetary counterparts of coronal mass ejections (CMEs). Due to the very low value of Can't connect to bucket.int.confex.com:4201 (Connection refused) LWP::Protocol::http::Socket: connect: Connection refused at /usr/local/lib/perl5/site_perl/5.8.8/LWP/Protocol/http.pm line 51. in MCs, they are believed to be in a nearly force-free state and therefore are able to be modeled by a cylindrical force-free flux rope. However, the force-free state only describes the magnetic field topology but not the plasma motion of a MC. For a MC propagating in interplanetary space, the global plasma motion has three possible components: linear propagating motion of a MC away from the Sun, expanding motion and circular motion with respect to the axis of the MC. By assuming the quasi-steady evolution and self-similar expansion, we introduced the three-component motion into the cylindrical force-free flux rope model, and developed a velocity-modified model. Then we applied the model to 73 MCs observed by Wind spacecraft to investigate the properties of the plasma motion of MCs. It is found that (1) some MCs did not propagate along the Sun-Earth line, suggesting the direct evidence of the CME's deflected propagation and/or rotation in interplanetary space, (2) the expansion speed is correlated with the radial propagation speed and 62%/17% of MCs underwent a under/over-expansion at 1 AU, and (3) the circular motion does exists though it is only on the order of 10 km s-1. These findings advance our understanding of the MC's properties at 1 AU as well as the dynamic evolution of CMEs from the Sun to interplanetary space.

Automated Job Controller for Clouds and the Earth's Radiant Energy System (CERES) Production Processing

NASA Astrophysics Data System (ADS)

Gleason, J. L.; Hillyer, T. N.

2011-12-01

Clouds and the Earth's Radiant Energy System (CERES) is one of NASA's highest priority Earth Observing System (EOS) scientific instruments. The CERES science team will integrate data from the CERES Flight Model 5 (FM5) on the NPOESS Preparatory Project (NPP) in addition to the four CERES scanning instrument on Terra and Aqua. The CERES production system consists of over 75 Product Generation Executives (PGEs) maintained by twelve subsystem groups. The processing chain fuses CERES instrument observations with data from 19 other unique sources. The addition of FM5 to over 22 instrument years of data to be reprocessed from flight models 1-4 creates a need for an optimized production processing approach. This poster discusses a new approach, using JBoss and Perl to manage job scheduling and interdependencies between PGEs and external data sources. The new optimized approach uses JBoss to serve handler servlets which regulate PGE-level job interdependencies and job completion notifications. Additional servlets are used to regulate all job submissions from the handlers and to interact with the operator. Perl submission scripts are used to build Process Control Files and to interact directly with the operating system and cluster scheduler. The result is a reduced burden on the operator by algorithmically enforcing a set of rules that determine the optimal time to produce data products with the highest integrity. These rules are designed on a per PGE basis and periodically change. This design provides the means to dynamically update PGE rules at run time and increases the processing throughput by using an event driven controller. The immediate notification of a PGE's completion (an event) allows successor PGEs to launch at the proper time with minimal start up latency, thereby increasing computer system utilization.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

Development and Implementation of Dynamic Scripts to Support Local Model Verification at National Weather Service Weather Forecast Offices

NASA Technical Reports Server (NTRS)

Zavordsky, Bradley; Case, Jonathan L.; Gotway, John H.; White, Kristopher; Medlin, Jeffrey; Wood, Lance; Radell, Dave

2014-01-01

Local modeling with a customized configuration is conducted at National Weather Service (NWS) Weather Forecast Offices (WFOs) to produce high-resolution numerical forecasts that can better simulate local weather phenomena and complement larger scale global and regional models. The advent of the Environmental Modeling System (EMS), which provides a pre-compiled version of the Weather Research and Forecasting (WRF) model and wrapper Perl scripts, has enabled forecasters to easily configure and execute the WRF model on local workstations. NWS WFOs often use EMS output to help in forecasting highly localized, mesoscale features such as convective initiation, the timing and inland extent of lake effect snow bands, lake and sea breezes, and topographically-modified winds. However, quantitatively evaluating model performance to determine errors and biases still proves to be one of the challenges in running a local model. Developed at the National Center for Atmospheric Research (NCAR), the Model Evaluation Tools (MET) verification software makes performing these types of quantitative analyses easier, but operational forecasters do not generally have time to familiarize themselves with navigating the sometimes complex configurations associated with the MET tools. To assist forecasters in running a subset of MET programs and capabilities, the Short-term Prediction Research and Transition (SPoRT) Center has developed and transitioned a set of dynamic, easily configurable Perl scripts to collaborating NWS WFOs. The objective of these scripts is to provide SPoRT collaborating partners in the NWS with the ability to evaluate the skill of their local EMS model runs in near real time with little prior knowledge of the MET package. The ultimate goal is to make these verification scripts available to the broader NWS community in a future version of the EMS software. This paper provides an overview of the SPoRT MET scripts, instructions for how the scripts are run, and example use

Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna

PubMed Central

Bollinedi, Haritha; S., Gopala Krishnan; Prabhu, Kumble Vinod; Singh, Nagendra Kumar; Mishra, Sushma; Khurana, Jitendra P.; Singh, Ashok Kumar

2017-01-01

Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB) using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm) but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI) driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis. PMID:28068433

Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna.

PubMed

Bollinedi, Haritha; S, Gopala Krishnan; Prabhu, Kumble Vinod; Singh, Nagendra Kumar; Mishra, Sushma; Khurana, Jitendra P; Singh, Ashok Kumar

2017-01-01

Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB) using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm) but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI) driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis.

Suivi après le traitement du cancer du sein

PubMed Central

Sisler, Jeffrey; Chaput, Geneviève; Sussman, Jonathan; Ozokwelu, Emmanuel

2016-01-01

Résumé Objectif Offrir aux médecins de famille un résumé des recommandations fondées sur les données probantes pour guider les soins aux survivantes traitées pour le cancer du sein. Qualité des données Une recherche documentaire a été effectuée dans MEDLINE entre 2000 et 2016 à l’aide des mots-clés anglais suivants : breast cancer, survivorship, follow-up care, aftercare, guidelines et survivorship care plans, en se concentrant sur la revue des lignes directrices publiées récemment par les organismes nationaux de cancérologie. Les données étaient de niveaux I à III. Message principal Les soins aux survivantes comportent 4 facettes : surveillance et dépistage, prise en charge des effets à long terme, promotion de la santé et coordination des soins. La surveillance des récidives ne se traduit que par une mammographie annuelle, et le dépistage d’autres cancers doit suivre les lignes directrices basées sur la population. La prise en charge des effets à long terme du cancer et de son traitement aborde des problèmes courants tels la douleur, la fatigue, le lymphœdème, la détresse et les effets indésirables des médicaments, de même que les préoccupations à long terme comme la santé du cœur et des os. La promotion de la santé met en relief les bienfaits de l’activité chez les survivantes du cancer, avec l’accent mis sur l’activité physique. Les soins aux survivantes sont de meilleure qualité lorsque divers services et professionnels de la santé participent aux soins, et le médecin de famille joue un rôle important dans la coordination des soins. Conclusion Les médecins de famille sont de plus en plus souvent les principaux fournisseurs de soins de suivi après le traitement du cancer du sein. Le cancer du sein doit être considéré comme une affection médicale chronique, même chez les femmes en rémission, et les patientes profitent de la même approche que celle utilisée pour les autres affections chroniques en

Finding, Browsing and Getting Data Easily Using SPDF Web Services

NASA Technical Reports Server (NTRS)

Candey, R.; Chimiak, R.; Harris, B.; Johnson, R.; Kovalick, T.; Lal, N.; Leckner, H.; Liu, M.; McGuire, R.; Papitashvili, N.;

Charming Users into Scripting CIAO with Python

NASA Astrophysics Data System (ADS)

Burke, D. J.

2011-07-01

The Science Data Systems group of the Chandra X-ray Center provides a number of scripts and Python modules that extend the capabilities of CIAO. Experience in converting the existing scripts—written in a variety of languages such as bash, csh/tcsh, Perl and S-Lang—to Python, and conversations with users, led to the development of the ciao_contrib.runtool module. This allows users to easily run CIAO tools from Python scripts, and utilizes the metadata provided by the parameter-file system to create an API that provides the flexibility and safety guarantees of the command-line. The module is provided to the user community and is being used within our group to create new scripts.

PRay - A graphical user interface for interactive visualization and modification of rayinvr models

NASA Astrophysics Data System (ADS)

Fromm, T.

2016-01-01

PRay is a graphical user interface for interactive displaying and editing of velocity models for seismic refraction. It is optimized for editing rayinvr models but can also be used as a dynamic viewer for ray tracing results from other software. The main features are the graphical editing of nodes and fast adjusting of the display (stations and phases). It can be extended by user-defined shell scripts and links to phase picking software. PRay is open source software written in the scripting language Perl, runs on Unix-like operating systems including Mac OS X and provides a version controlled source code repository for community development (https://sourceforge.net/projects/pray-plot-rayinvr/).

JLIFE: THE JEFFERSON LAB INTERACTIVE FRONT END FOR THE OPTICAL PROPAGATION CODE

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

Watson, Anne M.; Shinn, Michelle D.

2013-08-01

We present details on a graphical interface for the open source software program Optical Propagation Code, or OPC. This interface, written in Java, allows a user with no knowledge of OPC to create an optical system, with lenses, mirrors, apertures, etc. and the appropriate drifts between them. The Java code creates the appropriate Perl script that serves as the input for OPC. The mode profile is then output at each optical element. The display can be either an intensity profile along the x axis, or as an isometric 3D plot which can be tilted and rotated. These profiles can bemore » saved. Examples of the input and output will be presented.« less

Distributed run of a one-dimensional model in a regional application using SOAP-based web services

NASA Astrophysics Data System (ADS)

Smiatek, Gerhard

This article describes the setup of a distributed computing system in Perl. It facilitates the parallel run of a one-dimensional environmental model on a number of simple network PC hosts. The system uses Simple Object Access Protocol (SOAP) driven web services offering the model run on remote hosts and a multi-thread environment distributing the work and accessing the web services. Its application is demonstrated in a regional run of a process-oriented biogenic emission model for the area of Germany. Within a network consisting of up to seven web services implemented on Linux and MS-Windows hosts, a performance increase of approximately 400% has been reached compared to a model run on the fastest single host.

ConoDictor: a tool for prediction of conopeptide superfamilies.

PubMed

Koua, Dominique; Brauer, Age; Laht, Silja; Kaplinski, Lauris; Favreau, Philippe; Remm, Maido; Lisacek, Frédérique; Stöcklin, Reto

2012-07-01

ConoDictor is a tool that enables fast and accurate classification of conopeptides into superfamilies based on their amino acid sequence. ConoDictor combines predictions from two complementary approaches-profile hidden Markov models and generalized profiles. Results appear in a browser as tables that can be downloaded in various formats. This application is particularly valuable in view of the exponentially increasing number of conopeptides that are being identified. ConoDictor was written in Perl using the common gateway interface module with a php submission page. Sequence matching is performed with hmmsearch from HMMER 3 and ps_scan.pl from the pftools 2.3 package. ConoDictor is freely accessible at http://conco.ebc.ee.

EST databases and web tools for EST projects.

PubMed

Shen, Yao-Qing; O'Brien, Emmet; Koski, Liisa; Lang, B Franz; Burger, Gertraud

2009-01-01

This chapter outlines key considerations for constructing and implementing an EST database. Instead of showing the technological details step by step, emphasis is put on the design of an EST database suited to the specific needs of EST projects and how to choose the most suitable tools. Using TBestDB as an example, we illustrate the essential factors to be considered for database construction and the steps for data population and annotation. This process employs technologies such as PostgreSQL, Perl, and PHP to build the database and interface, and tools such as AutoFACT for data processing and annotation. We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices.

Intoxications aigues aux organophosphores chez la femme enceinte

PubMed Central

Barhoumi, Mohamed Hafed; Bannour, Badra; Barhoumi, Tarek; Jouini, Rami; Marwene, Nadia; Fatnassi, Mohamed Ridha

2016-01-01

Les intoxications aiguës par les pesticides organophosphorés (OP) au cours de la grossesse sont des événements rares, peu décrites dans la littérature. A travers cette étude rétrospective, nous rapportons les résultats de sept cas d’ingestion suicidaire d’OP chez des femmes enceintes. Cette intoxication était le plus souvent grave. En effet, cinq des sept parturientes avaient un Glasgow initial < 9 et le POP score était ≥ 3 chez toutes les parturientes. Cinq patientes avaient nécessité une ventilation mécanique de durée moyenne de 3,4 jours. L’évolution était favorable pour toutes les patientes mais dans plus de la moitié des cas elle était défavorable pour le fœtus (mort fœtal in utéro). Deux mécanismes peuvent expliquer ces complications fœtales. Le premier est l’hypoxie fœtale associée ou non à un état de choc qui peuvent se traduire au niveau du RCF par une tachycardie ou des décélérations et aboutir ainsi à un décès in utero. Le deuxième mécanisme est le passage de ces pesticides à travers la barrière placentaire, ce qui pose un risque potentiel pour le fœtus par altération des systèmes enzymatiques des microsomes. PMID:28293343

Lésions concomitantes aux genoux flottants et gravite

PubMed Central

Eone, Daniel Handy; Lamah, Léopold; Bayiha, Jean Emile; Ondoa, Danielle Larissa Essomba; Nonga, Bernadette Ngo; Ibrahima, Farikou; Bahebeck, Jean

2016-01-01

Le genou flottant est issu d’un traumatisme de haute énergie, dont la genèse suggère de vaste dégâts aussi bien sur le plan locorégional que général. Faisant référence au polytaumatisme. Le but de notre étude était de recenser toutes les lésions concomitantes au genou flottant dans notre milieu de pratique et d’évaluer la sévérité. Nous avons mené une étude descriptive et rétrospective couvrant une période de 14 ans et 9 mois. Sur un échantillon de 75 genoux flottants, avec une moyenne d’âge de 35 ans. Soixante six patients avaient obtenu un score d’ISS supérieur ou égal à 16 donc qualifié de polytraumatisé. Les traumatismes crâniens, les lésions thoraciques et abdominales retrouvés en même temps que le genou flottant exigent une réanimation adéquate. PMID:28292046

Contrôle du marché informel à l’heure de la mondialisation des échanges. Le cas des antirétroviraux au Chili

PubMed Central

Brousselle, Astrid; Morales, Cristián

2013-01-01

Résumé Les nouveaux médicaments pour le VIH/sida ont créé des besoins d’accessibilité aux traitements que les gouvernements n’ont pas toujours réussi à couvrir. Il en résulte l’émergence d’un marché informel des ARV. Par l’analyse de la situation au Chili, nous traitons des différents créneaux d’approvisionnement, des conséquences de l’existence d’un tel marché, ainsi que des moyens envisageables pour réduire les effets indésirables. Les aspects tant microéconomiques que macroéconomiques concernant le marché et l’accessibilité aux médicaments sont abordés. PMID:23997580

Formulation, caracterisation, modelisation et prevision du comportement thermomecanique des pieces plastiques et composites de fibres de bois : Application aux engrenages =

NASA Astrophysics Data System (ADS)

Mijiyawa, Faycal

Cette etude permet d'adapter des materiaux composites thermoplastiques a fibres de bois aux engrenages, de fabriquer de nouvelles generations d'engrenages et de predire le comportement thermique de ces engrenages. Apres une large revue de la litterature sur les materiaux thermoplastiques (polyethylene et polypropylene) renforces par les fibres de bois (bouleau et tremble), sur la formulation et l'etude du comportement thermomecanique des engrenages en plastique-composite; une relation a ete etablie avec notre presente these de doctorat. En effet, beaucoup d'etudes sur la formulation et la caracterisation des materiaux composites a fibres de bois ont ete deja realisees, mais aucune ne s'est interessee a la fabrication des engrenages. Les differentes techniques de formulation tirees de la litterature ont facilite l'obtention d'un materiau composite ayant presque les memes proprietes que les materiaux plastiques (nylon, acetal...) utilises dans la conception des engrenages. La formulation des materiaux thermoplastiques renforces par les fibres de bois a ete effectuee au Centre de recherche en materiaux lignocellulosiques (CRML) de l'Universite du Quebec a Trois-Rivieres (UQTR), en collaboration avec le departement de Genie Mecanique, en melangeant les composites avec deux rouleaux sur une machine de type Thermotron-C.W. Brabender (modele T-303, Allemand) ; puis des pieces ont ete fabriquees par thermocompression. Les thermoplastiques utilises dans le cadre de cette these sont le polypropylene (PP) et le polyethylene haute densite (HDPE), avec comme renfort des fibres de bouleau et de tremble. A cause de l'incompatibilite entre la fibre de bois et le thermoplastique, un traitement chimique a l'aide d'un agent de couplage a ete realise pour augmenter les proprietes mecaniques des materiaux composites. Pour les composites polypropylene/bois : (1) Les modules elastiques et les contraintes a la rupture en traction des composites PP/bouleau et PP/tremble evoluent

Final Determination - signed October 16, 1985

EPA Pesticide Factsheets

Fianl Determination of the U.S. EPA's Assistant Administrator for External Affairs concerning the Bayou Aux Carpes site in Jefferson Parish, Louisiana pursuant to Section 404(c) of the Clean Water Act.

A Feminist Intervention That Hurt Women: Biological Differences, Ergonomics, and Occupational Health: Une intervention féministe qui a nui aux femmes: différences biologiques, égalité, ergonomie et santé au travail.

PubMed

Messing, Karen

2017-11-01

éministes aux solutions pour le milieu de travail, ainsi que des pistes de recherche.

Clathrin-Mediated Auxin Efflux and Maxima Regulate Hypocotyl Hook Formation and Light-Stimulated Hook Opening in Arabidopsis.

PubMed

Yu, Qinqin; Zhang, Ying; Wang, Juan; Yan, Xu; Wang, Chao; Xu, Jian; Pan, Jianwei

2016-01-04

The establishment of auxin maxima by PIN-FORMED 3 (PIN3)- and AUXIN RESISTANT 1/LIKE AUX1 (LAX) 3 (AUX1/LAX3)-mediated auxin transport is essential for hook formation in Arabidopsis hypocotyls. Until now, however, the underlying regulatory mechanism has remained poorly understood. Here, we show that loss of function of clathrin light chain CLC2 and CLC3 genes enhanced auxin maxima and thereby hook curvature, alleviated the inhibitory effect of auxin overproduction on auxin maxima and hook curvature, and delayed blue light-stimulated auxin maxima reduction and hook opening. Moreover, pharmacological experiments revealed that auxin maxima formation and hook curvature in clc2 clc3 were sensitive to auxin efflux inhibitors 1-naphthylphthalamic acid and 2,3,5-triiodobenzoic acid but not to the auxin influx inhibitor 1-naphthoxyacetic acid. Live-cell imaging analysis further uncovered that loss of CLC2 and CLC3 function impaired PIN3 endocytosis and promoted its lateralization in the cortical cells but did not affect AUX1 localization. Taken together, these results suggest that clathrin regulates auxin maxima and thereby hook formation through modulating PIN3 localization and auxin efflux, providing a novel mechanism that integrates developmental signals and environmental cues to regulate plant skotomorphogenesis and photomorphogenesis. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Role of auxin during intercellular infection of Discaria trinervis by Frankia

PubMed Central

Imanishi, Leandro; Perrine-Walker, Francine M.; Ndour, Adama; Vayssières, Alice; Conejero, Genevieve; Lucas, Mikaël; Champion, Antony; Laplaze, Laurent; Wall, Luis; Svistoonoff, Sergio

2014-01-01

Nitrogen-fixing nodules induced by Frankia in the actinorhizal plant Discaria trinervis result from a primitive intercellular root invasion pathway that does not involve root hair deformation and infection threads. Here, we analyzed the role of auxin in this intercellular infection pathway at the molecular level and compared it with our previous work in the intracellular infected actinorhizal plant Casuarina glauca. Immunolocalisation experiments showed that auxin accumulated in Frankia-infected cells in both systems. We then characterized the expression of auxin transporters in D. trinervis nodules. No activation of the heterologous CgAUX1 promoter was detected in infected cells in D. trinervis. These results were confirmed with the endogenous D. trinervis gene, DtAUX1. However, DtAUX1 was expressed in the nodule meristem. Consistently, transgenic D. trinervis plants containing the auxin response marker DR5:VENUS showed expression of the reporter gene in the meristem. Immunolocalisation experiments using an antibody against the auxin efflux carrier PIN1, revealed the presence of this transporter in the plasma membrane of infected cells. Finally, we used in silico cellular models to analyse auxin fluxes in D. trinervis nodules. Our results point to the existence of divergent roles of auxin in intercellularly- and intracellularly-infected actinorhizal plants, an ancestral infection pathways leading to root nodule symbioses. PMID:25191330

L'astronomie des Anciens

NASA Astrophysics Data System (ADS)

Nazé, Yaël

2009-04-01

Quelle que soit la civilisation à laquelle il appartient, l'être humain cherche dans le ciel des réponses aux questions qu'il se pose sur son origine, son avenir et sa finalité. Le premier mérite de ce livre est de nous rappeler que l'astronomie a commencé ainsi à travers les mythes célestes imaginés par les Anciens pour expliquer l'ordre du monde et la place qu'ils y occupaient. Mais les savoirs astronomiques passés étaient loin d'être négligeables et certainement pas limités aux seuls travaux des Grecs : c'est ce que l'auteur montre à travers une passionnante enquête, de Stonehenge à Gizeh en passant par Pékin et Mexico, fondée sur l'étude des monuments anciens et des sources écrites encore accessibles. Les tablettes mésopotamiennes, les annales chinoises, les chroniques médiévales, etc. sont en outre d'une singulière utilité pour les astronomes modernes : comment sinon remonter aux variations de la durée du jour au cours des siècles, ou percer la nature de l'explosion qui a frappé tant d'observateurs en 1054 ? Ce livre offre un voyage magnifiquement illustré à travers les âges, entre astronomie et archéologie.

La prise en charge des morsures de chien chez les enfants

PubMed Central

Sabhaney, Vikram; Goldman, Ran D.

2012-01-01

Résumé Question Une fillette de 4 ans jouait avec le chien de ses voisins. Le chien s’est excité et a mordu la jeune fille à l’avant-bras, y laissant une plaie punctiforme. À cause cette blessure, elle s’est présentée à mon bureau. Devrais-je la traiter avec des antibiotiques? Quel antibiotique faut-il utiliser et pendant combien de temps? Réponse L’administration d’antibiotiques prophylactiques est indiquée lorsqu’on a procédé à une suture primitive de la morsure, que la plaie est de gravité modérée à sévère, qu’elle est punctiforme (particulièrement s’il y a eu pénétration de l’os, de la gaine tendineuse ou de l’articulation), pour les morsures au visage, aux mains, aux pieds ou aux parties génitales ou lorsque les victimes sont immunodéprimées ou souffrent d’asplénisme. L’antibiotique de première intention est l’amoxicilline-clavulanate. La prophylaxie appropriée antitétanique et contre la rage devrait faire partie des soins chez un patient qui a été mordu par un chien, tout comme le débridement local et le nettoyage complet de la plaie.

Les agressions sexuelles des jeunes ayant une incapacité ou une maladie chronique

PubMed Central

Kaufman, M

2011-01-01

Pour diverses raisons, les enfants et les adolescents ayant une incapacité ou une maladie chronique sont plus vulnérables aux agressions sexuelles. Les dispensateurs de soins, de même que les parents et les éducateurs, doivent se méfier davantage de la possibilité d’agression sexuelle au sein de cette population. Les médecins, tout particulièrement, doivent prôner des politiques pour prévenir ou déceler les agressions dans les hôpitaux, les écoles et autres établissements. Ces politiques incluent le dépistage détaillé et la surveillance étroite des employés et des bénévoles, la présence d’un chaperon aux examens physiques et aux interventions thérapeutiques, la supervision des sorties et une culture qui favorise la vie privée du patient en établissement. De plus, les médecins doivent favoriser la conscience de soi et l’habilitation des patients et leur donner très tôt des conseils préventifs au sujet de la sexualité, de l’habilitation personnelle et des risques d’agression. Le présent document de principes remplace celui que la Société canadienne de pédiatrie a publié en 1997.

Nouvelles morphologies de fibres electrofilees de polymere thermosensible =

NASA Astrophysics Data System (ADS)

Sta, Marwa

Ce memoire presente une etude sur la possibilite d'obtenir des membranes a base de polymeres thermosensibles avec differentes morphologies pour des applications d'administration de medicaments. Ces membranes ont ete obtenues par electrofilage du Poly (N vinylcaprolactame) (PNVCL), un polymere thermosensible, soit seul ou en melange avec du Polycaprolactone (PCL), un polymere biodegradable. Les parametres de procede ainsi que les proprietes de la solution a electrofiler ont ete optimises dans le but de creer des fibres de PNVCL lisses, continues et sans perles. Des solutions du melange (PNVCL) / (PCL) ont ete ensuite preparees en suivant quatre methodes differentes de preparation. Ces methodes se basent sur l'emploi de solvants distincts, eau distillee et chloroforme, avec differentes concentrations de polymere, 42wt% et 30wt% respectivement. Ces solutions ont ete electrofilees en utilisant les parametres de procede qui correspondaient aux meilleures conditions pour l'electrofilage du PNVCL. Ensuite, le ketophofene, un medicament hydrophobe, a ete ajoute au PNVCL et au melange PNVCL/PCL avant l'electrofilage afin d'etudier la capacite des fibres de PNVCL et de melanges de retenir le medicament hydrophobe et a en faire sa liberation. Enfin, des fibres noyau-enveloppes ont ete obtenues par electrofilage coaxial, en utilisant une solution aqueuse du melange PNVCL/PCL (42 wt%) pour l'enveloppe et une solution aqueuse du PEG (30 wt%) pour le noyau. Les morphologies des membranes resultantes et de leurs fibres ont ete caracterisees par microscopie electronique a balayage (MEB). La temperature de solution critique inferieure (LCST) de ces fibres, qui est la temperature en dessous de laquelle le polymere est soluble dans l'eau et au-dessus duquel il precipite, a ete evaluee par calorimetrie differentielle a balayage (DSC). L'efficacite d'encapsulation (EE) et la liberation du medicament ont ete evaluees en utilisant la technique de spectrophotometrie UV-visible. Des coupes

Effets de la pollution de l’air sur la santé

PubMed Central

Abelsohn, Alan; Stieb, Dave M.

2011-01-01

Résumé Objectif Faire connaître aux médecins de famille les effets de la pollution atmosphérique sur la santé et indiquer quels conseils donner aux patients vulnérables pour qu’ils soient moins exposés. Sources de l’information On a consulté MEDLINE à l’aide des termes relatifs à la pollution atmosphérique et à ses effets indésirables. On a révisé les articles en anglais publiés entre janvier 2008 et décembre 2009. La plupart des études contenaient des preuves de niveau II. Principal message Au Canada, la pollution de l’air extérieur cause une morbidité et une mortalité importantes. Elle peut affecter le système respiratoire (exacerbation de l’asthme et de la maladie pulmonaire obstructive chronique) et le système cardiovasculaire (déclencher l’arythmie, l’insuffisance cardiaque et les AVC). La cote air santé (CAS) est un nouvel outil de communication mis au point par Santé Canada et Environnement Canada qui indique sur une échelle de 1 à 10, le risque pour la santé causé par la pollution atmosphérique. La CAS est largement diffusée dans les médias et cet outil pourrait être utile au médecin de famille pour inciter les patients à haut risque (comme ceux qui souffrent d’asthme, de maladie pulmonaire obstructive chronique ou d’insuffisance cardiaque) à réduire leur exposition à la pollution atmosphérique. Conclusion Le médecin de famille peut se servir de la CAS et de ses messages sur la santé pour enseigner aux asthmatiques et aux autres patients à risque élevé la façon de réduire les risques pour la santé causés par la pollution atmosphérique.

L’expérience d’une patiente qui reçoit des soins pour la démence

PubMed Central

Frank, Christopher; Forbes, Rev Faye

2017-01-01

Résumé Objectif Permettre aux médecins de famille de comprendre « l’expérience vécue » de la démence de la bouche d’une personne atteinte de démence—Faye Forbes, ministre anglicane de 64 ans atteinte de la maladie d’Alzheimer, qui donne son point de vue sur comment vivre avec la démence—et utiliser cette information pour améliorer les soins et les résultats. Sources d’information Une recherche a été effectuée dans MEDLINE sur Ovid entre janvier 2005 et février 2015, à l’aide des mots-clés anglais suivants : dementia, caregiver, perspectives et quality of health care. Les articles qui s’adressaient aux médecins de famille ont été sélectionnés. Des revues pertinentes et des articles de recherche originaux ont été utilisés, le cas échéant, s’ils s’appliquaient aux personnes atteintes de démence et à leurs soignants. Message principal Plusieurs cadres de référence organisent les principales expériences décrites par les patients et leurs soignants. Nous avons utilisé une revue de la littérature qualitative pour fournir un cadre de référence résumant l’expérience de Faye, en fonction des thèmes suivants : tenter d’obtenir un diagnostic, accéder au soutien et aux services, besoins en matière d’information, prise en charge de la maladie, et communication et attitudes. Conclusion Les médecins doivent tenir compte de ces thèmes lorsqu’ils planifient la prise en charge des personnes atteintes de démence. Il importe de tenter de comprendre l’expérience et le point de vue des personnes atteintes de démence et de leurs soignants afin de pouvoir dispenser des soins optimaux. PMID:28115451

Les recommandations de prise en charge des complications métaboliques associées aux antipsychotiques de deuxième génération chez les enfants et les adolescents

PubMed Central

Ho, Josephine; Panagiotopoulos, Constadina; McCrindle, Brian; Grisaru, Silviu; Pringsheim, Tamara

2012-01-01

HISTORIQUE : Les antipsychotiques de deuxième génération s’associent souvent à des complications métaboliques. Ces médicaments sont utilisés plus souvent pour le traitement des troubles de santé mentale chez les enfants, ce qui a requis l’élaboration de lignes directrices officielles sur la surveillance de leur innocuité et de leur efficacité. Des lignes directrices ont déjà été élaborées pour surveiller les complications métaboliques et neurologiques. Afin d’aider les praticiens qui effectuent ces interventions de surveillance, une série de recommandations thérapeutiques complémentaires a été élaborée pour les cas où l’on observe des mesures ou des résultats anormaux. OBJECTIF : Créer des recommandations probantes afin de contribuer à la prise en charge des complications métaboliques chez les enfants traités au moyen d’antipsychotiques de deuxième génération. MÉTHODOLOGIE : Les auteurs ont procédé à une analyse systématique des publications sur les complications métaboliques des antipsychotiques de deuxième génération chez les enfants. Les membres du groupe consensuel ont évalué l’information recueillie grâce à l’analyse bibliographique systématique et ont fait appel à un processus de groupe nominal pour parvenir à un consensus à l’égard de recommandations thérapeutiques. Dans la mesure du possible, ils se sont reportés aux lignes directrices existantes sur l’évaluation et le traitement des anomalies métaboliques chez les enfants. RÉSULTATS : Des recommandations probantes sont présentées pour contribuer à la prise en charge des complications métaboliques, y compris la prise de poids, l’augmentation du tour de taille, l’élévation des taux de prolactine, de cholestérol, de triglycérides et de glucose, les épreuves de fonction hépatique anormales et les études thyroïdiennes anormales. CONCLUSION : Il faut recourir à des mesures de surveillance convenables lorsqu’on prescrit

Perturbation of auxin homeostasis by overexpression of wild-type IAA15 results in impaired stem cell differentiation and gravitropism in roots.

PubMed

Yan, Da-Wei; Wang, Jing; Yuan, Ting-Ting; Hong, Li-Wei; Gao, Xiang; Lu, Ying-Tang

2013-01-01

Aux/IAAs interact with auxin response factors (ARFs) to repress their transcriptional activity in the auxin signaling pathway. Previous studies have focused on gain-of-function mutations of domain II and little is known about whether the expression level of wild-type Aux/IAAs can modulate auxin homeostasis. Here we examined the perturbation of auxin homeostasis by ectopic expression of wild-type IAA15. Root gravitropism and stem cell differentiation were also analyzed. The transgenic lines were less sensitive to exogenous auxin and exhibited low-auxin phenotypes including failures in gravity response and defects in stem cell differentiation. Overexpression lines also showed an increase in auxin concentration and reduced polar auxin transport. These results demonstrate that an alteration in the expression of wild-type IAA15 can disrupt auxin homeostasis.

Responses to auxin signals: an operating principle for dynamical sensitivity yet high resilience

PubMed Central

Bravi, B.; Martin, O. C.

2018-01-01

Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signalling network involves a negative feedback on Aux/IAA proteins which mediate the influence of auxin (the signal) on the auxin response factor (ARF) transcription factors (the drivers of the response). To probe the role of this feedback, we consider alternative in silico signalling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative feedback allows the system to have a far larger sensitivity in its dynamical response to auxin and that this sensitivity does not prevent the system from being highly resilient. Given this insight, we build a new biomolecular signalling model for quantitatively describing such Aux/IAA and ARF responses. PMID:29410878

BOREAS TE-6 NPP For The Tower Flux, Carbon Evaluation, and Auxiliary Sites

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Gower, Stith T.; Vogel, Jason G.

2000-01-01

The BOREAS TE-6 team collected several data sets to examine the influence of vegetation, climate, and their interactions on the major carbon fluxes for boreal forest species. This data set contains estimates of the biomass produced by the plant species at the TF, CEV, and AUX sites in the SSA and NSA for a given year. Temporally, the data cover the years of 1985 to 1995. The plant biomass production (i.e., aboveground, belowground, understory, litterfall), spatial coverage, and temporal nature of measurements varied between the TF, CEV, and AUX sites as deemed necessary by BOREAS principal investigators. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distrobuted Activity Archive Center (DAAC).

Neutron Radiation Affects the Expression of Genes Involved in the Response to Auxin, Senescence and Oxidative Stress in Arabidopsis

NASA Astrophysics Data System (ADS)

Fortunati, A.; Tassone, P.; Migliaccio, F.

2008-06-01

Researches were conducted on the effect of neutron radiation on the expression of genes auxin activated or connected with the process of senescence in Arabidopsis plants. The research was done by applying the real-time polymerase chain reaction (PCR) technique. The results indicated that the auxin response factors (ARFs) genes are clearly downregulated, whereas the indolacetic acid-induced (Aux/IAAs) genes in some cases were upregulated. By contrast in the mutants for auxin transport aux1 and eir1 the ARFs genes were upregulated. In addition, both in the wildtype and mutants, some already known genes activated by stress and senescence were significantly upregulated. On the basis of these researches we conclude that the process of senescence induced by irradiation is, at least in part, controlled by the physiology of the hormone auxin.

NOAO observing proposal processing system

NASA Astrophysics Data System (ADS)

Bell, David J.; Gasson, David; Hartman, Mia

2002-12-01

Since going electronic in 1994, NOAO has continued to refine and enhance its observing proposal handling system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form or via Gemini's downloadable Phase-I Tool. NOAO staff can use online interfaces for administrative tasks, technical reviews, telescope scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available online. The system, now known as ANDES, is designed as a thin-client architecture (web pages are now used for almost all database functions) built using open source tools (FreeBSD, Apache, MySQL, Perl, PHP) to process descriptively-marked (LaTeX, XML) proposal documents.

The Ensembl Web Site: Mechanics of a Genome Browser

PubMed Central

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V.

2004-01-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species. PMID:15123591

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

PubMed Central

Wolfinger, Michael T.; Fallmann, Jörg; Eggenhofer, Florian; Amman, Fabian

2015-01-01

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools. PMID:26236465

MK3TOOLS & NetCDF - storing VLBI data in a machine independent array oriented data format

NASA Astrophysics Data System (ADS)

Hobiger, T.; Koyama, Y.; Kondo, T.

2007-07-01

In the beginning of 2002 the International VLBI Service (IVS) has agreed to introduce a Platform-independent VLBI exchange format (PIVEX) which permits the exchange of observational data and stimulates the research across different analysis groups. Unfortunately PIVEX has never been implemented and many analysis software packages are still depending on prior processing (e.g. ambiguity resolution and computation of ionosphere corrections) done by CALC/SOLVE. Thus MK3TOOLS which handles MK3 databases without CALC/SOLVE being installed has been developed. It uses the NetCDF format to store the data and since interfaces exist for a variety of programming languages (FORTRAN, C/C++, JAVA, Perl, Python) it can be easily incorporated in existing and upcoming analysis software packages.

Calculation of streamflow statistics for Ontario and the Great Lakes states

USGS Publications Warehouse

Piggott, Andrew R.; Neff, Brian P.

2005-01-01

Basic, flow-duration, and n-day frequency statistics were calculated for 779 current and historical streamflow gages in Ontario and 3,157 streamflow gages in the Great Lakes states with length-of-record daily mean streamflow data ending on December 31, 2000 and September 30, 2001, respectively. The statistics were determined using the U.S. Geological Survey’s SWSTAT and IOWDM, ANNIE, and LIBANNE software and Linux shell and PERL programming that enabled the mass processing of the data and calculation of the statistics. Verification exercises were performed to assess the accuracy of the processing and calculations. The statistics and descriptions, longitudes and latitudes, and drainage areas for each of the streamflow gages are summarized in ASCII text files and ESRI shapefiles.

The Ensembl Web site: mechanics of a genome browser.

PubMed

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V

2004-05-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules

PubMed Central

Hussain, A. S. Z.; Kumar, Ch. Kiran; Rajesh, C. K.; Sheik, S. S.; Sekar, K.

2003-01-01

SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows the users to save the three-dimensional atomic coordinates of the symmetry equivalent molecules in the local machine. The widely recognized graphics program RasMol has been deployed to visualize the reference (input atomic coordinates) and the symmetry equivalent molecules. This program is written using CGI/Perl scripts and has been interfaced with all the three-dimensional structures (solved using X-ray crystallography) available in the Protein Data Bank. The program, SEM, can be accessed over the World Wide Web interface at http://dicsoft2.physics.iisc.ernet.in/sem/ or http://144.16.71.11/sem/. PMID:12824326

Automated Sequence Processor: Something Old, Something New

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Schrock, Mitchell; Fisher, Forest; Himes, Terry

2012-01-01

High productivity required for operations teams to meet schedules Risk must be minimized. Scripting used to automate processes. Scripts perform essential operations functions. Automated Sequence Processor (ASP) was a grass-roots task built to automate the command uplink process System engineering task for ASP revitalization organized. ASP is a set of approximately 200 scripts written in Perl, C Shell, AWK and other scripting languages.. ASP processes/checks/packages non-interactive commands automatically.. Non-interactive commands are guaranteed to be safe and have been checked by hardware or software simulators.. ASP checks that commands are non-interactive.. ASP processes the commands through a command. simulator and then packages them if there are no errors.. ASP must be active 24 hours/day, 7 days/week..

Development of a Response Planner using the UCT Algorithm for Cyber Defense

DTIC Science & Technology

2013-03-01

writer2l, guess passwd r2l, imap r2l, ipsweep probe, land dos, loadmodule u2r, multihop r2l, neptune dos, nmap probe, perl u2r, phf r2l, pod dos, portsweep...2646 10 pod 201 11 back 956 12 guess passwd 53 Item Type Count 13 ftp write 8 14 multihop 7 15 rootkit 10 16 buffer overflow 30 17 imap 11 18...pod 0 0 0 87 6 11 0 0 64 33 0 0 0 0 k = back 908 0 0 0 0 0 0 0 0 0 47 0 1 0 l = guess passwd 0 0 0 42 3 0 1 0 0 0 0 5 1 0 m = buffer overflow 0 0 17

Gromita: a fully integrated graphical user interface to gromacs 4.

PubMed

Sellis, Diamantis; Vlachakis, Dimitrios; Vlassi, Metaxia

2009-09-07

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/.

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

HippDB: a database of readily targeted helical protein-protein interactions.

PubMed

Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

2013-11-01

HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases.

PubMed

Khan, Mohd Shoaib; Gupta, Amit Kumar; Kumar, Manoj

2016-01-01

To develop a computational resource for viral epigenomic methylation profiles from diverse diseases. Methylation patterns of Epstein-Barr virus and hepatitis B virus genomic regions are provided as web platform developed using open source Linux-Apache-MySQL-PHP (LAMP) bundle: programming and scripting languages, that is, HTML, JavaScript and PERL. A comprehensive and integrated web resource ViralEpi v1.0 is developed providing well-organized compendium of methylation events and statistical analysis associated with several diseases. Additionally, it also facilitates 'Viral EpiGenome Browser' for user-affable browsing experience using JavaScript-based JBrowse. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.

GENOME-ENABLED DISCOVERY OF CARBON SEQUESTRATION GENES IN POPLAR

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

DAVIS J M

2007-10-11

Plants utilize carbon by partitioning the reduced carbon obtained through photosynthesis into different compartments and into different chemistries within a cell and subsequently allocating such carbon to sink tissues throughout the plant. Since the phytohormones auxin and cytokinin are known to influence sink strength in tissues such as roots (Skoog & Miller 1957, Nordstrom et al. 2004), we hypothesized that altering the expression of genes that regulate auxin-mediated (e.g., AUX/IAA or ARF transcription factors) or cytokinin-mediated (e.g., RR transcription factors) control of root growth and development would impact carbon allocation and partitioning belowground (Fig. 1 - Renewal Proposal). Specifically, themore » ARF, AUX/IAA and RR transcription factor gene families mediate the effects of the growth regulators auxin and cytokinin on cell expansion, cell division and differentiation into root primordia. Invertases (IVR), whose transcript abundance is enhanced by both auxin and cytokinin, are critical components of carbon movement and therefore of carbon allocation. Thus, we initiated comparative genomic studies to identify the AUX/IAA, ARF, RR and IVR gene families in the Populus genome that could impact carbon allocation and partitioning. Bioinformatics searches using Arabidopsis gene sequences as queries identified regions with high degrees of sequence similarities in the Populus genome. These Populus sequences formed the basis of our transgenic experiments. Transgenic modification of gene expression involving members of these gene families was hypothesized to have profound effects on carbon allocation and partitioning.« less

Electromagnetics and Electrothermal Approach to Evaluate Failures in Microelectronic Devices Caused by Electrostatic Discharges: Stochastical Aspects of the Device Reliability.

DTIC Science & Technology

1987-08-01

C C CALL THE ELSV SUBROUTINE TO INVERT THE MATRIX. EPO .1D-09 . CALL ELSV(Z,AUX1,AUX2,tN, DE ,EP) WRITE(93,118) DE 118 FORMAT(5X,’ DE -,1E) C C MULTIPLY...IFCABS(W).LT.EP)GO TO 17 DO 13 I=1,N Y’=A( I,K)/W DO 13 J=1,N 13 AC I,J)=A(I,J)-B(J)*Y DE =O.DO DO.15 J=1,N B(J)0O.DO DO 16 I=1,N 16 B(J)=B(J)+A(I,J...15 DE - DE +C(J)*B(J) RETURN 1. DE -1.DO RETURN -18- IMPLICIT COMPLEX*16 (C) IMPLICIT REAL*8 (A-B,E-H,P-z) C C C THIS PROGRAM GIVES THE POTENTIAL AND THE

Conference B.Bettelheim

ScienceCinema

None

2017-12-09

Le Dr.Bruno Bettelheim, psychologue américain, d'origine viennoise, a passé son doctorat en psychologie à l'université de Vienne. Il émigra aux Etats-Unis et enseigna la psychologie au Rockford College en Illinois et la psychologie de l'éducation à L'université de Chicago, où il dirigea également l'institut orthogénique Sonia-Shankman pour le traitement des enfants psychotiques. Cet homme a bouleversé la compréhension des relations parents et enfants en y introduisant la psychanalyse. Basé sur ses expériences aux Etats-Unis,il nous parle des changements dans la structure de la famille et ses conséquences pour la relation entre enfants et parents.

The Live Access Server Scientific Product Generation Through Workflow Orchestration

NASA Astrophysics Data System (ADS)

Hankin, S.; Calahan, J.; Li, J.; Manke, A.; O'Brien, K.; Schweitzer, R.

2006-12-01

The Live Access Server (LAS) is a well-established Web-application for display and analysis of geo-science data sets. The software, which can be downloaded and installed by anyone, gives data providers an easy way to establish services for their on-line data holdings, so their users can make plots; create and download data sub-sets; compare (difference) fields; and perform simple analyses. Now at version 7.0, LAS has been in operation since 1994. The current "Armstrong" release of LAS V7 consists of three components in a tiered architecture: user interface, workflow orchestration and Web Services. The LAS user interface (UI) communicates with the LAS Product Server via an XML protocol embedded in an HTTP "get" URL. Libraries (APIs) have been developed in Java, JavaScript and perl that can readily generate this URL. As a result of this flexibility it is common to find LAS user interfaces of radically different character, tailored to the nature of specific datasets or the mindset of specific users. When a request is received by the LAS Product Server (LPS -- the workflow orchestration component), business logic converts this request into a series of Web Service requests invoked via SOAP. These "back- end" Web services perform data access and generate products (visualizations, data subsets, analyses, etc.). LPS then packages these outputs into final products (typically HTML pages) via Jakarta Velocity templates for delivery to the end user. "Fine grained" data access is performed by back-end services that may utilize JDBC for data base access; the OPeNDAP "DAPPER" protocol; or (in principle) the OGC WFS protocol. Back-end visualization services are commonly legacy science applications wrapped in Java or Python (or perl) classes and deployed as Web Services accessible via SOAP. Ferret is the default visualization application used by LAS, though other applications such as Matlab, CDAT, and GrADS can also be used. Other back-end services may include generation of Google

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

PubMed

Hallin, Peter F; Ussery, David W

2004-12-12

Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues. A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase.

Differentiation between Trichophyton mentagrophytes and T. rubrum by sorbitol assimilation.

PubMed Central

Rezusta, A; Rubio, M C; Alejandre, M C

1991-01-01

Trichophyton rubrum was easily differentiated from T. mentagrophytes by its ability to assimilate sorbitol with an API 20C AUX strip. One hundred percent of 36 T. rubrum strains and none of 147 T. mentagrophytes strains assimilated sorbitol. PMID:1993760

Supplémentation préconceptionnelle en acide folique / multivitamines pour la prévention primaire et secondaire des anomalies du tube neural et d'autres anomalies congénitales sensibles à l'acide folique.

PubMed

Wilson, R Douglas

2016-12-01

Offrir des renseignements à jour sur l'utilisation pré et postconceptionnelle d'acide folique par voie orale, avec ou sans supplément de multivitamines / micronutriments, aux fins de la prévention des anomalies du tube neural et d'autres anomalies congénitales. Ces renseignements aideront les médecins, les sages-femmes, les infirmières et les autres professionnels de la santé à contribuer aux efforts de sensibilisation des femmes quant à l'utilisation et aux posologies adéquates de la supplémentation en acide folique / multivitamines, avant et pendant la grossesse. RéSULTATS: La littérature publiée a été récupérée par l'intermédiaire de recherches menées dans PubMed, Medline, CINAHL et la Cochrane Library en janvier 2011 au moyen d'un vocabulaire contrôlé et de mots clés appropriés (p. ex. « folic acid », « prenatal multivitamins », « folate sensitive birth defects », « congenital anomaly risk reduction », « pre-conception counselling »). Les résultats ont été restreints aux analyses systématiques, aux études observationnelles et aux essais comparatifs randomisés / essais cliniques comparatifs publiés en anglais entre 1985 et juin 2014. Les recherches ont été mises à jour de façon régulière et intégrées à la directive clinique jusqu'en juin 2014. La littérature grise (non publiée) a été identifiée par l'intermédiaire de recherches menées dans les sites Web d'organismes s'intéressant à l'évaluation des technologies dans le domaine de la santé et d'organismes connexes, dans des collections de directives cliniques, dans des registres d'essais cliniques, et auprès de sociétés de spécialité médicale nationales et internationales. COûTS, RISQUES ET AVANTAGES: Les coûts financiers sont ceux de la supplémentation quotidienne en vitamines et de la consommation d'un régime alimentaire santé enrichi en folate. Les risques sont ceux qui sont liés à une association signalée entre la suppl

Les recommandations thérapeutiques relatives aux effets secondaires extrapyramidaux associés à l’utilisation d’antipsychotiques de deuxième génération chez les enfants et les adolescents

PubMed Central

Pringsheim, Tamara; Doja, Asif; Belanger, Stacey; Patten, Scott

2012-01-01

HISTORIQUE ET OBJECTIF : L’utilisation d’antipsychotiques augmente chez les enfants. Le présent article visait à orienter les cliniciens quant à la prise en charge clinique des effets secondaires extrapyramidaux des antipsychotiques de deuxième génération. MÉTHODOLOGIE : Les publications, les entrevues avec des informateurs clés et des échanges avec les membres d’un groupe de discussion et les partenaires ont permis de déterminer les principaux secteurs cliniques d’orientation et les préférences quant à la structure des présentes recommandations. Les membres responsables des lignes directrices ont reçu le projet de recommandations, ont évalué l’information recueillie grâce à une analyse bibliographique systématique et ont utilisé un processus de groupe nominal pour parvenir à un consensus quant aux recommandations thérapeutiques. Les lignes directrices contiennent une description des anomalies neurologiques souvent observées avec l’utilisation d’antipsychotiques ainsi que les recommandations sur le moyen d’examiner et de quantifier ces anomalies. Une démarche séquentielle sur la prise en charge des anomalies neurologiques est présentée. RÉSULTATS : On peut observer plusieurs types de symptômes extrapyramidaux attribuables à l’utilisation d’antipsychotiques chez les enfants, y compris la dystonie aiguë, l’akathisie, le parkinsonisme et la dyskinésie tardive, toutes induites par les neuroleptiques, de même que la dystonie tardive, l’akathisie tardive et les dyskinésies de sevrage. La forte majorité des données probantes sur le traitement des troubles du mouvement induits par les antipsychotiques proviennent de patients adultes atteints de schizophrénie. Étant donné le peu de données pédiatriques, les recommandations découlent de publications portant tant sur des adultes que sur des enfants. Compte tenu des limites de généralisation des données provenant de sujets adultes pour des enfants, il

Prise en charge en cabinet des lésions cérébrales traumatiques légères chez les enfants et les adolescents

PubMed Central

Garcia-Rodriguez, Juan Antonio; Thomas, Roger E.

2014-01-01

Résumé Objectif Fournir aux médecins de famille de l’information à jour, pratique et factuelle sur les lésions cérébrales traumatiques légères et les commotions cérébrales dans la population pédiatrique. Sources d’information Une recherche a été effectuée dans MEDLINE (de 1950 à février 2013), la base de données des revues systématiques Cochrane (de 2005 à 2013), le registre central Cochrane des essais contrôlés (de 2005 à 2013) et DARE (2005 à 2013) à l’aide de mots-clés liés aux commotions cérébrales et aux traumatismes crâniens. Des lignes directrices, énoncés de position, articles et rapports de recherche originaux pertinents aux lésions cérébrales traumatiques légères ont été sélectionnés. Message principal Le traumatisme est la cause principale de décès chez les enfants de plus d’un an et, dans ce groupe, le traumatisme crânien est la cause la plus fréquente d’incapacité et de décès. Neuf pour cent des blessures sportives rapportées chez les élèves du secondaire sont associées à une lésion cérébrale traumatique légère. Les médecins de famille doivent effectuer une anamnèse ciblée et un examen physique et neurologique, utiliser les instruments d’évaluation standardisés (Échelle de Glasgow; Outil d’évaluation des commotions cérébrales dans le sport, version 3; version pédiatrique de l’Outil d’évaluation des commotions cérébrales dans le sport; et échelle BESS [Balance Error Scoring System]), expliquer aux parents comment surveiller leurs enfants, décider des circonstances où les soignants ne sont pas une ressource dûment responsable, faire un suivi prompt auprès des patients, guider le retour sécuritaire au jeu ou à l’école et décider dans quelles circonstances un test neuropsychologique est nécessaire au suivi à long terme. Conclusion La prise en charge par le médecin de famille des lésions cérébrales traumatiques légères chez les enfants repose sur une

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

PubMed Central

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H.A.; Hlavacek, William S.; Posner, Richard G.

2016-01-01

Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary information: Supplementary data are available at Bioinformatics online. Contact: bionetgen.help@gmail.com PMID:26556387

New Directions in the NOAO Observing Proposal System

NASA Astrophysics Data System (ADS)

Gasson, David; Bell, Dave

For the past eight years NOAO has been refining its on-line observing proposal system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form, or via the Gemini Phase I Tool. NOAO staff can use the system to do administrative tasks, scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available on-line, including the proposals themselves (in HTML, PDF and PostScript) and technical comments. Grades and TAC comments are entered and edited through web forms, and can be sorted and filtered according to specified criteria. Current developments include a move away from proprietary solutions, toward open standards such as SQL (in the form of the MySQL relational database system), Perl, PHP and XML.

New strategic directions for Caribbean CSM project.

PubMed

1986-01-01

Recent changes in the strategy of the Caribbean Contraceptive Social Marketing Project emphasize the condom, under the brand name, Panther. Since 1984, CCSMP began marketing their Perle rand of oral contraceptive, since dropped, in Barbados, St. Vincent and St. Lucia. Now wider commercial connections are envisioned, with support by CCSMP to promote generic brands. The Panther condom campaign will include an array of mass media, point-of-purchase and sporting event advertising. Pharmacies report that Panther is selling as well as the leading commercial brand. CCSMP is looking to introduce an ultra-thin condom and a vaginal foaming tablet. Market research, involving physicians and users as well as retail audits, indicates that although population in numbers alone is not a serious problem in the Caribbean, early pregnancy is a concern in the area.

ParTIES: a toolbox for Paramecium interspersed DNA elimination studies.

PubMed

Denby Wilkes, Cyril; Arnaiz, Olivier; Sperling, Linda

2016-02-15

Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available. We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms. ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Generating and Executing Complex Natural Language Queries across Linked Data.

PubMed

Hamon, Thierry; Mougin, Fleur; Grabar, Natalia

2015-01-01

With the recent and intensive research in the biomedical area, the knowledge accumulated is disseminated through various knowledge bases. Links between these knowledge bases are needed in order to use them jointly. Linked Data, SPARQL language, and interfaces in Natural Language question-answering provide interesting solutions for querying such knowledge bases. We propose a method for translating natural language questions in SPARQL queries. We use Natural Language Processing tools, semantic resources, and the RDF triples description. The method is designed on 50 questions over 3 biomedical knowledge bases, and evaluated on 27 questions. It achieves 0.78 F-measure on the test set. The method for translating natural language questions into SPARQL queries is implemented as Perl module available at http://search.cpan.org/ thhamon/RDF-NLP-SPARQLQuery.

Chado controller: advanced annotation management with a community annotation system.

PubMed

Guignon, Valentin; Droc, Gaëtan; Alaux, Michael; Baurens, Franc-Christophe; Garsmeur, Olivier; Poiron, Claire; Carver, Tim; Rouard, Mathieu; Bocs, Stéphanie

2012-04-01

We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr Supplementary data are available at Bioinformatics online.

CancerNet redistribution via WWW.

PubMed

Quade, G; Püschel, N; Far, F

1996-01-01

CancerNet from the National Cancer Institute contains nearly 500 ASCII-files, updated monthly, with up-to-date information about cancer and the "Golden Standard" in tumor therapy. Perl scripts are used to convert these files to HTML-documents. A complex algorithm, using regular expression matching and extensive exception handling, detects headlines, listings and other constructs of the original ASCII-text and converts them into their HTML-counterparts. A table of contents is also created during the process. The resulting files are indexed for full-text search via WAIS. Building the complete CancerNet WWW redistribution takes less than two hours with a minimum of manual work. For 26,000 requests of information from our service per month the average costs for the worldwide delivery of one document is about 19 cents.

Report on IVS-WG4

NASA Astrophysics Data System (ADS)

Gipson, John

2011-07-01

I describe the proposed data structure for storing, archiving and processing VLBI data. In this scheme, most VLBI data is stored in NetCDF files. NetCDF has the advantage that there are interfaces to most common computer languages including Fortran, Fortran-90, C, C++, Perl, etc, and the most common operating systems including linux, Windows and Mac. The data files for a particular session are organized by special ASCII "wrapper" files which contain pointers to the data files. This allows great flexibility in the processing and analysis of VLBI data, and also allows for extending the types of data used, e.g., source maps. I discuss the use of the new format in calc/solve and other VLBI analysis packages. I also discuss plans for transitioning to the new structure.

Accessing near real-time Antarctic meteorological data through an OGC Sensor Observation Service (SOS)

NASA Astrophysics Data System (ADS)

Kirsch, Peter; Breen, Paul

2013-04-01

We wish to highlight outputs of a project conceived from a science requirement to improve discovery and access to Antarctic meteorological data in near real-time. Given that the data was distributed in both spatial and temporal domains and is to be accessed across several science disciplines, the creation of an interoperable, OGC compliant web service was deemed the most appropriate approach. We will demonstrate an implementation of the OGC SOS Interface Standard to discover, browse, and access Antarctic meteorological data-sets. A selection of programmatic (R, Perl) and web client interfaces utilizing open technologies ( e.g. jQuery, Flot, openLayers ) will be demonstrated. In addition we will show how high level abstractions can be constructed to allow the users flexible and straightforward access to SOS retrieved data.

A new Information Architecture, Website and Services for the CMS Experiment

NASA Astrophysics Data System (ADS)

Taylor, Lucas; Rusack, Eleanor; Zemleris, Vidmantas

2012-12-01

The age and size of the CMS collaboration at the LHC means it now has many hundreds of inhomogeneous web sites and services, and hundreds of thousands of documents. We describe a major initiative to create a single coherent CMS internal and public web site. This uses the Drupal web Content Management System (now supported by CERN/IT) on top of a standard LAMP stack (Linux, Apache, MySQL, and php/perl). The new navigation, content and search services are coherently integrated with numerous existing CERN services (CDS, EDMS, Indico, phonebook, Twiki) as well as many CMS internal Web services. We describe the information architecture; the system design, implementation and monitoring; the document and content database; security aspects; and our deployment strategy, which ensured continual smooth operation of all systems at all times.

CommServer: A Communications Manager For Remote Data Sites

NASA Astrophysics Data System (ADS)

Irving, K.; Kane, D. L.

2012-12-01

CommServer is a software system that manages making connections to remote data-gathering stations, providing a simple network interface to client applications. The client requests a connection to a site by name, and the server establishes the connection, providing a bidirectional channel between the client and the target site if successful. CommServer was developed to manage networks of FreeWave serial data radios with multiple data sites, repeaters, and network-accessed base stations, and has been in continuous operational use for several years. Support for Iridium modems using RUDICS will be added soon, and no changes to the application interface are anticipated. CommServer is implemented on Linux using programs written in bash shell, Python, Perl, AWK, under a set of conventions we refer to as ThinObject.

System for NIS Forecasting Based on Ensembles Analysis

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

2014-01-02

BMA-NIS is a package/library designed to be called by a script (e.g. Perl or Python). The software itself is written in the language of R. The software assists electric power delivery systems in planning resource availability and demand, based on historical data and current data variables. Net Interchange Schedule (NIS) is the algebraic sum of all energy scheduled to flow into or out of a balancing area during any interval. Accurate forecasts for NIS are important so that the Area Control Error (ACE) stays within an acceptable limit. To date, there are many approaches for forecasting NIS but all nonemore » of these are based on single models that can be sensitive to time of day and day of week effects.« less

ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.

PubMed

Lou, Shao-Ke; Ni, Bing; Lo, Leung-Yau; Tsui, Stephen Kwok-Wing; Chan, Ting-Fung; Leung, Kwong-Sak

2011-02-01

Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are neither designed for reads that span across splice junctions nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here, we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature. The software is freely available at: http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.

Anomalous dielectric relaxation in lithium-potassium tantalate crystals

NASA Astrophysics Data System (ADS)

Doussineau, P.; Farssi, Y.; Frénois, C.; Levelut, A.; Toulouse, J.; Ziolkiewicz, S.

1994-08-01

In order to describe the unusual dielectric properties observed in Ki{1-χ}Li{χ}TaO3. crystals a new approchh is proposed. The dynamical Glauber theory, previously applied to spinglasses, is modifiéd by the introduction of the spectral distribution of the random interactions between the dipoles associated with the Li+ ions. Moreover, the dipole corrélations are taken into account by the Onsager réaction field. As a result, the calculated dielectric constant reproduces well the unusual features of the Argand diagrams and, in particular, their finite slope at low frequencies and infinite slope at high frequencies (strophoidal shape). The temperature dépendance of some parameters shows, however, the limits of a spin-glass type model in describing the collective behaviour of randomly distributed dipoles in a highly polarizable medium. Une nouvelle approche est présentée qui permet de décrire les propriétés diélectriques particulières de cristaux mixtes de Ki{1-χ}Li{χ}TaO3. Elle s'appuie sur la théorie dynamique de Glauber, déjà utilisée pour les verres de spins, et modifiée par l'introduction d'une distribution spectrale spécifique aux interactions aléatoires des dipôles électriques associés aux ions Li+. En outre, les corrélations entre dipôles sont prises en compte par le champ de réaction d'Onsager. II s'ensuit que la constante diélectrique complexe ainsi calculée reproduit fidèlement les particularités des diagrammes d'Argand, telles que la pente finie aux basses fréquences et la pente infinie aux hautes fréquences (forme strophoïdale). La dépendance en température de certains paramètres déterminés par le calcul montre les limites de l'analogie avec les verres de spins et met en évidence le rôle d'un réseau très polarisable dans le comportement collectif d'une assemblée de dipôles électriques.

Conduite automobile et démence

PubMed Central

Lee, Linda; Molnar, Frank

2017-01-01

Résumé Objectif Fournir aux médecins de première ligne une approche relative aux préoccupations de sécurité au volant lorsque les personnes âgées présentent des troubles de mémoire. Sources d’information L’approche est fondée sur un programme de formation agréé des cliniques de la mémoire, élaboré par la clinique de la mémoire du Centre for Family Medicine. Message principal L’un des aspects les plus difficiles des soins aux personnes atteintes de démence est l’évaluation de la sécurité au volant. Les conducteurs atteints de démence présentent un risque plus élevé de collisions, quoique de nombreux conducteurs dont l’atteinte est légère soient aptes à conduire pendant encore plusieurs années. Puisque l’aptitude à conduire dépend de multiples compétences cognitives et fonctionnelles, de nombreux facteurs entrent en jeu lorsque les cliniciens déterminent si les sujets de préoccupation en matière de cognition se répercutent sur l’aptitude à conduire. Les observations spécifiques tirées de l’anamnèse corroborée et des tests cognitifs effectués en cabinet pourraient aider le médecin à décider s’il doit recommander le patient à un examen pratique complet et aviser les autorités provinciales du transport, conformément aux exigences en matière de déclarations. La communication doit être axée sur le patient et menée avec tact. Conclusion Les médecins de première ligne doivent tenir compte de plusieurs facteurs lorsqu’ils déterminent si les sujets de leurs préoccupations en matière de cognition pourraient se répercuter sur l’aptitude des conducteurs âgés à prendre le volant. PMID:28115452

morphogen: Translation into Morphologically Rich Languages with Synthetic Phrases

DTIC Science & Technology

2013-10-01

specific trans - lation phrases. These “synthetic phrases” augment the standard translation grammars and decoding proceeds normally with a standard...Genitive case grandparent(poss) Hebrew Suffix ים ( masculine plural) parent=NNS after=NNS Prefix א (first person sing. + future) child(nsubj)=I child(aux

BOREAS TE-10 Leaf Optical Properties

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Papagno, Andrea (Editor); Chan, Stephen S.; Middleton, Elizabeth

2000-01-01

The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-10 (Terrestrial Ecology) team collected several data sets in support of its efforts to characterize and interpret information on the reflectance, transmittance, gas exchange, oxygen evolution, and biochemical properties of boreal vegetation. This data set describes the spectral optical properties (reflectance and transmittance) of boreal forest conifers and broadleaf tree leaves as measured with a Spectron Engineering SE590 spectroradiometer at the Southern Study Area Old Black Spruce (SSA OBS), Old Jack Pine (OJP), Young Jack Pine (YJP), Old Aspen (OA), Old Aspen Auxiliary (OA-AUX), Young Aspen Auxiliary (YA-AUX), and Young Aspen (YA) sites. The data were collected during the growing seasons of 1994 and 1996 and are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Dégénérescence Maculaire Liée à l' âge et Risque d' Accident Vasculaire Cérébral

PubMed Central

Biousse, Valérie; Bousser, Marie-Germaine; Gaudric, Alain

2010-01-01

La dégénérescence maculaire liée à l' âge (DMLA) et les accidents vasculaires cérébraux (AVC) affectent un nombre important de sujets de plus de 40 ans à travers le monde et contribuent largement aux dépenses de la santé. Les causes de la DMLA restent mystérieuses et de nombreuses études épidémiologiques ont suggéré une association entre DMLA et facteurs de risque cardio-vasculaire associés aux AVC. Il a également été suggéré que les patients atteints de DMLA ont un risque plus important d' AVC que la population générale du même âge. Les arguments en faveur de cette association entre DMLA et AVC sont résumés dans cet article. PMID:18401309

Comprehensive Analysis of the Soybean (Glycine max) GmLAX Auxin Transporter Gene Family

PubMed Central

Chai, Chenglin; Wang, Yongqin; Valliyodan, Babu; Nguyen, Henry T.

2016-01-01

The phytohormone auxin plays a critical role in regulation of plant growth and development as well as plant responses to abiotic stresses. This is mainly achieved through its uneven distribution in plant via a polar auxin transport process. Auxin transporters are major players in polar auxin transport. The AUXIN RESISTENT 1/LIKE AUX1 (AUX/LAX) auxin influx carriers belong to the amino acid permease family of proton-driven transporters and function in the uptake of indole-3-acetic acid (IAA). In this study, genome-wide comprehensive analysis of the soybean AUX/LAX (GmLAX) gene family, including phylogenic relationships, chromosome localization, and gene structure, was carried out. A total of 15 GmLAX genes, including seven duplicated gene pairs, were identified in the soybean genome. They were distributed on 10 chromosomes. Despite their higher percentage identities at the protein level, GmLAXs exhibited versatile tissue-specific expression patterns, indicating coordinated functioning during plant growth and development. Most GmLAXs were responsive to drought and dehydration stresses and auxin and abscisic acid (ABA) stimuli, in a tissue- and/or time point- sensitive mode. Several GmLAX members were involved in responding to salt stress. Sequence analysis revealed that promoters of GmLAXs contained different combinations of stress-related cis-regulatory elements. These studies suggest that the soybean GmLAXs were under control of a very complex regulatory network, responding to various internal and external signals. This study helps to identity candidate GmLAXs for further analysis of their roles in soybean development and adaption to adverse environments. PMID:27014306

Microscopie par rayons X dans la fenêtre de l'eau : faisabilité et intérêt pour la biologie d'un instrument de laboratoire

NASA Astrophysics Data System (ADS)

Adam, J. F.; Moy, J. P.

2005-06-01

La biologie étudie des structures ou des phénomènes sub-cellulaires. Pour cela la microscopie est la technique d'observation privilégiée. La résolution spatiale de la microscopie optique s'avère bien souvent insuffisante pour de telles observations. Les techniques plus résolvantes, comme la microscopie électronique par transmission sont souvent destructrices et d'une complexité peu adaptée aux besoins des biologistes. La microscopie par rayons X dans la fenêtre de l'eau permet l'imagerie rapide de cellules dans leur milieu naturel, nécessite peu de préparation et offre des résolutions de quelques dizaines de nanomètres. De plus, il existe un bon contraste naturel entre les structures carbonées (protéines, lipides) et l'eau. Actuellement cette technique est limitée aux centres de rayonnement synchrotron, ce qui impose une planification et des déplacements incompatibles avec les besoins de la biologie. Un tel microscope fonctionnant avec uns source de laboratoire serait d'une grande utilité. Ce document présente un état de l'art de la microscopie par rayons X dans la fenêtre de l'eau. Un cahier des charges détaillé pour un appareil de laboratoire ayant les performances optiques requises par les biologistes est présenté et confronté aux microscopes X de laboratoire déjà existants. Des solutions concernant la source et les optiques sont également discutées.

Profil comparatif et évolutif des personnes infectées par le virus de l'immunodéficience humaine traitées aux antirétroviraux à Kinshasa, République Démocratique du Congo

PubMed Central

Koy, Tshingani; Mukumbi, Henri; Malandala, Ghislain Lubangi Muteba; Donnen, Philippe; Wilmet–Dramaix, Michèle

2014-01-01

Introduction A trithérapie (ARV) introduite en R.D.Congo en 1996, a permis l′amélioration substantielle de la qualité de vie des PVVIH et a réduit la morbimortalité liée au sida en R.D. Congo. L'objectif de cette étude est de présenter le profil épidémiologique comparatif, clinique, ainsi que l’évolution anthropométrique des PVVIH sous ARV à Kinshasa. Méthodes Etude de cohorte sur 438 PVVIH, de 18 ans et plus, suivies entre mai 2010 à 2011 à Amo Congo à Kinshasa. Une comparaison a été faite entre les patients suivis pendant un an et ceux perdus de vue. Le Chi carré de Mc Nemar et l'analyse de variance pour mesures répétées ont été appliqués pour étudier l’évolution. Résultats Près 12 mois de suivi, 11,4% de patients ont été perdus de vue. Parmi eux, on observait des proportions significativement plus élevées de personnes de niveau socioéconomique bas, d'indice de masse corporelle (IMC) bas, présentant de l'anorexie, des affections opportunistes. Les proportions de patients aux stades OMS 3 & 4 et naïfs étaient également significativement plus élevées et la durée sous ARV plus courte. Les gains moyens des paramètres anthropométriques au 12ème mois, étaient importants: de 3,6 [3,2 - 4,0] kg pour le poids, 1,8 (1,4 - 2,3) cm pour le périmètre abdominal, 0,9 (0,8 - 1,2) cm pour le périmètre brachial, 1,4 (1,2 - 1,5) kg/m2 pour l'IMC. La proportion de patients avec un IMC <18,5 kg/m2 a significativement plus baissé entre l'admission et le 12ème mois parmi les patients sans stomatite que parmi ceux avec stomatite. L'IMC moyen évoluait significativement différemment entre l'admission et le 12ème mois selon l’âge et la taille de ménage. Conclusion Les facteurs fragilisant la rétention des patients sous antirétroviraux et une évolution progressive de l’état nutritionnel ont été observés. PMID:25995784

30 CFR Appendix to Part 553 - List of U.S. Geological Survey Topographic Maps

Code of Federal Regulations, 2013 CFR

2013-07-01

...; Three Mile Bay; Tigre Lagoon; Timbalier Island; Triumph; Venice; Weeks; West of Johnson Bayou; Western... Islands; Tivoli SE; Turtle Bay; Umbrella Point; Virginia Point; West of Johnson Bayou; Whites Ranch...; Hollingers Island; Isle Aux Herbes; Kreole; Lillian; Little Dauphin Island; Little Point Clear; Magnolia...

30 CFR Appendix to Part 553 - List of U.S. Geological Survey Topographic Maps

Code of Federal Regulations, 2012 CFR

2012-07-01

...; Three Mile Bay; Tigre Lagoon; Timbalier Island; Triumph; Venice; Weeks; West of Johnson Bayou; Western... Islands; Tivoli SE; Turtle Bay; Umbrella Point; Virginia Point; West of Johnson Bayou; Whites Ranch...; Hollingers Island; Isle Aux Herbes; Kreole; Lillian; Little Dauphin Island; Little Point Clear; Magnolia...

30 CFR Appendix to Part 553 - List of U.S. Geological Survey Topographic Maps

Code of Federal Regulations, 2014 CFR

2014-07-01

...; Three Mile Bay; Tigre Lagoon; Timbalier Island; Triumph; Venice; Weeks; West of Johnson Bayou; Western... Islands; Tivoli SE; Turtle Bay; Umbrella Point; Virginia Point; West of Johnson Bayou; Whites Ranch...; Hollingers Island; Isle Aux Herbes; Kreole; Lillian; Little Dauphin Island; Little Point Clear; Magnolia...

Cluster shading modifies amino acids in grape (Vitis vinifera L.) berries in a genotype- and tissue-dependent manner.

PubMed

Guan, Le; Wu, Benhong; Hilbert, Ghislaine; Li, Shaohua; Gomès, Eric; Delrot, Serge; Dai, Zhanwu

2017-08-01

Amino acid composition of the grape berry at harvest is important for wine making. The present study investigates the complex interplay between tissue, cultivar and light conditions that determine berry amino acid content. Twenty amino acids were assessed in the berry skin and pulp of two grape cultivars (Gamay Noir and Gamay Fréaux), grown under either light exposure or cluster shading conditions. In all samples, cluster shading significantly reduced most amino acids, except gamma-aminobutyric acid (GABA) and phenylalanine. However, the magnitude of the decrease was stronger in the skin (67.0% decrease) than in the pulp (30.4%) and stronger in cv. Gamay Noir (69.7%) than in Gamay Fréaux (30.7%). Cluster shading also significantly modified amino acid composition by decreasing the proline content while increasing the GABA content. These results are of oenological interest for shaping the amino acid composition of the must and improving wine quality. Copyright © 2017 Elsevier Ltd. All rights reserved.

Innovative Technology for Teaching Introductory Astronomy

NASA Astrophysics Data System (ADS)

Guidry, Mike

The application of state-of-the-art technology (primarily Java and Flash MX Actionscript on the client side and Java PHP PERL XML and SQL databasing on the server side) to the teaching of introductory astronomy will be discussed. A completely online syllabus in introductory astronomy built around more than 350 interactive animations called ""Online Journey through Astronomy"" and a new set of 20 online virtual laboratories in astronomy that we are currently developing will be used as illustration. In addition to demonstration of the technology our experience using these technologies to teach introductory astronomy to thousands of students in settings ranging from traditional classrooms to full distance learning will be summarized. Recent experiments using Java and vector graphics programming of handheld devices (Personal Digital Assistants and cell phones) with wireless wide-area connectivity for applications in astronomy education will also be described.

Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.

PubMed

Zakrzewski, Martha; Proietti, Carla; Ellis, Jonathan J; Hasan, Shihab; Brion, Marie-Jo; Berger, Bernard; Krause, Lutz

2017-03-01

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo ( https://zenodo.org/record/50931 ). The software is freely available for non-commercial users. l.krause@uq.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Trends in surface ozone concentrations at Arosa (Switzerland)

NASA Astrophysics Data System (ADS)

Staehelin, Johannes; Thudium, Juerg; Buehler, Ralph; Volz-Thomas, Andreas; Graber, Werner

During the years 1989-1991, ozone was measured at four sites around Arosa (Switzerland). One of these sites was identical with that, where surface ozone was measured in the 1950s (Götz and Volz, 1951; Perl, 1965). Comparison of both old and recent data indicates that surface ozone concentrations at Arosa have increased by a factor of approximately 2.2. The increase shows a seasonal variation with a relative increase of more than a factor of three in December and January. The results are discussed in the context of measurements made at other times, locations and altitudes. The comparison indicates that the increase in ozone levels at Arosa has most likely occured between the fifties and today. The measurements additionally suggest that photochemical ozone production in the free troposphere has significantly contributed to the observed ozone trends in winter.

Aerobraking Maneuver (ABM) Report Generator

NASA Technical Reports Server (NTRS)

Fisher, Forrest; Gladden, Roy; Khanampornpan, Teerapat

2008-01-01

abmREPORT Version 3.1 is a Perl script that extracts vital summarization information from the Mars Reconnaissance Orbiter (MRO) aerobraking ABM build process. This information facilitates sequence reviews, and provides a high-level summarization of the sequence for mission management. The script extracts information from the ENV, SSF, FRF, SCMFmax, and OPTG files and burn magnitude configuration files and presents them in a single, easy-to-check report that provides the majority of the parameters necessary for cross check and verification during the sequence review process. This means that needed information, formerly spread across a number of different files and each in a different format, is all available in this one application. This program is built on the capabilities developed in dragReport and then the scripts evolved as the two tools continued to be developed in parallel.

A new information architecture, website and services for the CMS experiment

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

Taylor, Lucas; Rusack, Eleanor; Zemleris, Vidmantas

2012-01-01

The age and size of the CMS collaboration at the LHC means it now has many hundreds of inhomogeneous web sites and services, and hundreds of thousands of documents. We describe a major initiative to create a single coherent CMS internal and public web site. This uses the Drupal web Content Management System (now supported by CERN/IT) on top of a standard LAMP stack (Linux, Apache, MySQL, and php/perl). The new navigation, content and search services are coherently integrated with numerous existing CERN services (CDS, EDMS, Indico, phonebook, Twiki) as well as many CMS internal Web services. We describe themore » information architecture, the system design, implementation and monitoring, the document and content database, security aspects, and our deployment strategy, which ensured continual smooth operation of all systems at all times.« less

GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes

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

Kyrpides, Nikos C.; Ivanova, Natalia N.; Pati, Amrita

2010-07-08

GenePRIMP (Gene Prediction Improvement Pipeline, Http://geneprimp.jgi-psf.org), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missing genes, and split genes. We show that manual curation of gene models using the anomaly reports generated by GenePRIMP improves their quality and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome sequencing and annotation technologies. Keywords in context: Gene model, Quality Control, Translation start sites, Automatic correction. Hardware requirements; PC, MAC; Operating System: UNIX/LINUX; Compiler/Version: Perl 5.8.5 or higher; Special requirements: NCBI Blast and nr installation; File Types:more » Source Code, Executable module(s), Sample problem input data; installation instructions other; programmer documentation. Location/transmission: http://geneprimp.jgi-psf.org/gp.tar.gz« less

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

[The development and evaluation of software to verify diagnostic accuracy].

PubMed

Jensen, Rodrigo; de Moraes Lopes, Maria Helena Baena; Silveira, Paulo Sérgio Panse; Ortega, Neli Regina Siqueira

2012-02-01

This article describes the development and evaluation of software that verifies the accuracy of diagnoses made by nursing students. The software was based on a model that uses fuzzy logic concepts, including PERL, the MySQL database for Internet accessibility, and the NANDA-I 2007-2008 classification system. The software was evaluated in terms of its technical quality and usability through specific instruments. The activity proposed in the software involves four stages in which students establish the relationship values between nursing diagnoses, defining characteristics/risk factors and clinical cases. The relationship values determined by students are compared to those of specialists, generating performance scores for the students. In the evaluation, the software demonstrated satisfactory outcomes regarding the technical quality and, according to the students, helped in their learning and may become an educational tool to teach the process of nursing diagnosis.

Chado Controller: advanced annotation management with a community annotation system

PubMed Central

Guignon, Valentin; Droc, Gaëtan; Alaux, Michael; Baurens, Franc-Christophe; Garsmeur, Olivier; Poiron, Claire; Carver, Tim; Rouard, Mathieu; Bocs, Stéphanie

2012-01-01

Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form Contact: valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22285827

Prediction of novel pre-microRNAs with high accuracy through boosting and SVM.

PubMed

Zhang, Yuanwei; Yang, Yifan; Zhang, Huan; Jiang, Xiaohua; Xu, Bo; Xue, Yu; Cao, Yunxia; Zhai, Qian; Zhai, Yong; Xu, Mingqing; Cooke, Howard J; Shi, Qinghua

2011-05-15

High-throughput deep-sequencing technology has generated an unprecedented number of expressed short sequence reads, presenting not only an opportunity but also a challenge for prediction of novel microRNAs. To verify the existence of candidate microRNAs, we have to show that these short sequences can be processed from candidate pre-microRNAs. However, it is laborious and time consuming to verify these using existing experimental techniques. Therefore, here, we describe a new method, miRD, which is constructed using two feature selection strategies based on support vector machines (SVMs) and boosting method. It is a high-efficiency tool for novel pre-microRNA prediction with accuracy up to 94.0% among different species. miRD is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/rpg/mird/mird.php.

Development of a High Level Architecture Federation of Ship Replenishment at Sea

DTIC Science & Technology

2011-10-01

utiliser une infrastructure de simulation appelée architecture de haut niveau (HLA) afin de fournir des environne - ments de simulation interarmées...fournir un environnement de simulation qui modélise l’interactions entre les divers composants afin de simuler les conditions qui mènent aux

The Communicative Computer Compares: A CALL Design Project for Elementary French.

ERIC Educational Resources Information Center

Kyle, Patricia J.

A computer lesson entitled "Aux Jeux Olympiques" (To the Olympic Games) simulates an ongoing situational dialog between the French student and the PLATO computer system. It offers an international setting for functional learning exercises focusing on students' understanding and use of comparative constructions, selected verbs, and other linguistic…

A role for the gene regulatory module microRNA172/TARGET OF EARLY ACTIVATION TAGGED 1/FLOWERING LOCUS T (miRNA172/TOE1/FT) in the feeding sites induced by Meloidogyne javanica in Arabidopsis thaliana.

PubMed

Díaz-Manzano, Fernando E; Cabrera, Javier; Ripoll, Juan-José; Del Olmo, Iván; Andrés, Mari Fe; Silva, Ana Cláudia; Barcala, Marta; Sánchez, María; Ruíz-Ferrer, Virginia; de Almeida-Engler, Janice; Yanofsky, Martin F; Piñeiro, Manuel; Jarillo, Jose Antonio; Fenoll, Carmen; Escobar, Carolina

2018-01-01

Root knot nematodes (RKNs) penetrate into the root vascular cylinder, triggering morphogenetic changes to induce galls, de novo formed 'pseudo-organs' containing several giant cells (GCs). Distinctive gene repression events observed in early gall/GCs development are thought to be mediated by post-transcriptional silencing via microRNAs (miRNAs), a process that is far from being fully characterized. Arabidopsis thaliana backgrounds with altered activities based on target 35S::MIMICRY172 (MIM172), 35S::TARGET OF EARLY ACTIVATION TAGGED 1 (TOE1)-miR172-resistant (35S::TOE1 R ) and mutant (flowering locus T-10 (ft-10)) lines were used for functional analysis of nematode infective and reproductive parameters. The GUS-reporter lines, MIR172A-E::GUS, treated with auxin (IAA) and an auxin-inhibitor (a-(phenyl ethyl-2-one)-indole-3-acetic acid (PEO-IAA)), together with the MIR172C AuxRE::GUS line with two mutated auxin responsive elements (AuxREs), were assayed for nematode-dependent gene expression. Arabidopsis thaliana backgrounds with altered expression of miRNA172, TOE1 or FT showed lower susceptibility to the RKNs and smaller galls and GCs. MIR172C-D::GUS showed restricted promoter activity in galls/GCs that was regulated by auxins through auxin-responsive factors. IAA induced their activity in galls while PEO-IAA treatment and mutations in AuxRe motifs abolished it. The results showed that the regulatory module miRNA172/TOE1/FT plays an important role in correct GCs and gall development, where miRNA172 is modulated by auxins. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

[Graviresponse in higher plants and its regulation in molecular bases: relevance to growth and development, and auxin polar transport in etiolated pea seedlings].

PubMed

Ueda, Junichi; Miyamoto, Kensuke

2003-08-01

We review the graviresponse under true and simulated microgravity conditions on a clinostat in higher plants, and its regulation in molecular bases, especially on the aspect of auxin polar transport in etiolated pea (Pisum sativum L. cv. Alaska) seedlings which were the plant materials subjected to STS-95 space experiments. True and simulated microgravity conditions substantially affected growth and development in etiolated pea seedlings, especially the direction of growth of stems and roots, resulting in automorphosis. In etiolated pea seedlings grown in space, epicotyls were the most oriented toward the direction far from the cotyledons, and roots grew toward the aerial space of Plant Growth Chamber. Automorphosis observed in space were well simulated by a clinorotation on a 3-dimensional clinostat and also phenocopied by the application of auxin polar transport inhibitors of 2,3,5-triiodobenzoic acid, N-(1-naphtyl)phthalamic acid and 9-hydroxyfluorene-9-carboxylic acid. Judging from the results described above together with the fact that activities of auxin polar transport in epicotyls of etiolated pea seedlings grown in space substantially were reduced, auxin polar transport seems to be closely related to automorphosis. Strenuous efforts to learn in molecular levels how gravity contributes to the auxin polar transport in etiolated pea epicotyls resulted in successful identification of PsPIN2 and PsAUX1 genes located in plasma membrane which products are considered to be putative efflux and influx carriers of auxin, respectively. Based on the results of expression of PsPIN2 and PsAUX1 genes under various gravistimulations, a possible role of PsPIN2 and PsAUX1 genes for auxin polar transport in etiolated pea seedlings will be discussed.

Validation materielle d'une architecture generique de reseaux avioniques basee sur une gestion modulaire de la redondance

NASA Astrophysics Data System (ADS)

Tremblay, Jose-Philippe

Les systemes avioniques ne cessent d'evoluer depuis l'apparition des technologies numeriques au tournant des annees 60. Apres le passage par plusieurs paradigmes de developpement, ces systemes suivent maintenant l'approche " Integrated Modular Avionics " (IMA) depuis le debut des annees 2000. Contrairement aux methodes anterieures, cette approche est basee sur une conception modulaire, un partage de ressources generiques entre plusieurs systemes et l'utilisation plus poussee de bus multiplexes. La plupart des concepts utilises par l'architecture IMA, bien que deja connus dans le domaine de l'informatique distribuee, constituent un changement marque par rapport aux modeles anterieurs dans le monde avionique. Ceux-ci viennent s'ajouter aux contraintes importantes de l'avionique classique telles que le determinisme, le temps reel, la certification et les cibles elevees de fiabilite. L'adoption de l'approche IMA a declenche une revision de plusieurs aspects de la conception, de la certification et de l'implementation d'un systeme IMA afin d'en tirer profit. Cette revision, ralentie par les contraintes avioniques, est toujours en cours, et offre encore l'opportunite de developpement de nouveaux outils, methodes et modeles a tous les niveaux du processus d'implementation d?un systeme IMA. Dans un contexte de proposition et de validation d'une nouvelle architecture IMA pour un reseau generique de capteurs a bord d?un avion, nous avons identifie quelques aspects des differentes approches traditionnelles pour la realisation de ce type d?architecture pouvant etre ameliores. Afin de remedier a certaines des differentes lacunes identifiees, nous avons propose une approche de validation basee sur une plateforme materielle reconfigurable ainsi qu'une nouvelle approche de gestion de la redondance pour l'atteinte des cibles de fiabilite. Contrairement aux outils statiques plus limites satisfaisant les besoins pour la conception d'une architecture federee, notre approche de

Parasitémie asymptomatique chez les enfants de moins de 5 ans, enfants en âge scolaire et prise en charge des épisodes fébriles dans les ménages de Lubumbashi, République Démocratique du Congo

PubMed Central

Mukomena, Sompwe Eric; Philipe, Cilundika Mulenga; Désiré, Mashinda Kulimba; Pascal, Lutumba Tshindele; Ali, Mapatano Mala; Oscar, Luboya Numbi

2016-01-01

Introduction longtemps négligé, le paludisme asymptomatique est actuellement reconnu comme potentielle menace et frein au contrôle du paludisme. En RD Congo, la prévalence de cette parasitémie est peu documentée. L'objectif de cette étude était de déterminer la prévalence de la parasitémie asymptomatique aussi bien chez les enfants de moins de 5 ans que ceux âgés de plus de cinq ans aux regards des interventions de masse en cours (MILDS). Méthodes il s'agit d'une étude transversale menée chez les écoliers et chez les enfants de moins de cinq ans dans les ménages de Lubumbashi. Les écoles, les écoliers et les enfants de moins de 5 ans avaient été sélectionnés aléatoirement. Les frottis, gouttes épaisses et les tests rapides avaient été prélevés et lues. Résultats sur 350 écoliers examinés, 43 soit une prévalence de 12,3%, IC 95% (9,14-16,04) avaient une goutte épaisse positive. Dans tous les 43 cas, seul le Plasmodium falciparum a été identifié.314 ménages, soit 90,5% ont déclaré avoir recouru aux antipaludéens pour soigner la fièvre de leurs enfants à domicile. Plus d'1/3 des enfants dans les ménages, soit 39,9% des interviewés avait avoué avoir recouru aux antipyrétiques pour soulager la fièvre de leurs enfants, 19,7% à la quinine et seulement moins de 2% aux ACT à base de Lumefantrine. En considérant l'utilisation des TDR, la prévalence due à la parasitémie asymptomatique est de 3% IC 95% (2,075-4,44), mais quand on considère la microscopie comme le gold standard, cette prévalence est de 1,9%, IC 95% (1,13-3,01). Conclusion le paludisme asymptomatique n'est pas exempt de toute conséquence sur la santé, il est donc important de mener des enquêtes pareilles pour identifier les nouvelles stratégies de contrôle du paludisme. PMID:27642433

Insuffisance cervicale et cerclage cervical.

PubMed

Brown, Richard; Gagnon, Robert; Delisle, Marie-France

2016-12-01

La présente directive clinique a pour but de fournir un cadre de référence que les cliniciens pourront utiliser pour identifier les femmes qui sont exposées aux plus grands risques de connaître une insuffisance cervicale, ainsi que pour déterminer les circonstances en présence desquelles la mise en place d'un cerclage pourrait s'avérer souhaitable. RéSULTATS: La littérature publiée a été récupérée par l'intermédiaire de recherches menées dans PubMed ou MEDLINE, CINAHL et The Cochrane Library en 2012 au moyen d'un vocabulaire contrôlé (p. ex. « uterine cervical incompetence ») et de mots clés appropriés (p. ex. « cervical insufficiency », « cerclage », « Shirodkar », « cerclage », « MacDonald », « cerclage », « abdominal », « cervical length », « mid-trimester pregnancy loss »). Les résultats ont été restreints aux analyses systématiques, aux essais comparatifs randomisés / essais cliniques comparatifs et aux études observationnelles. Aucune restriction n'a été appliquée en matière de date ou de langue. Les recherches ont été mises à jour de façon régulière et intégrées à la directive clinique jusqu'en janvier 2011. La littérature grise (non publiée) a été identifiée par l'intermédiaire de recherches menées dans les sites Web d'organismes s'intéressant à l'évaluation des technologies dans le domaine de la santé et d'organismes connexes, dans des collections de directives cliniques, dans des registres d'essais cliniques et auprès de sociétés de spécialité médicale nationales et internationales. La qualité des résultats est évaluée au moyen des critères décrits dans le rapport du Groupe d'étude canadien sur les soins de santé préventifs (Tableau). RECOMMANDATIONS. Copyright © 2016. Published by Elsevier Inc.

La contribution des astronomes aux mesures de précision.

NASA Astrophysics Data System (ADS)

Debarbat, S.

The system for astronomical constants includes the astronomical unit, the velocity of light and the light-time for the unit distance in the metric system. In France, at least from the 17th century, scientists had in mind to unify the units. But it is not before the time of the French Revolution that it was succeeded to adopt a unified system based on the metre. Measurements were made of an arc of meridian, from Dunkirk to Barcelona to determine the new unit as the fraction of 1 over 107 of a quarter of any part of the Earth from the north pole to the equator. On the occasion of the bicentenary of the nomenclature of the metric system (1795), the Paris Observatory has presented during more than six months in 1995, mostly for students, manuscripts, documents related to the subject, in its galeries on the first floor of the Perrault building. The exhibition ended with the 1960 and 1983 definitions of the meter to which the Paris Observatory has contributed. For astronomers it was recalled the reason for which the Angström had to be considered as not more usable, being only close to the fraction 1/1010 of the meter.

Loi constitutive chimioplastique pour le beton expose aux hautes temperatures

NASA Astrophysics Data System (ADS)

Hammoud, Rabah

Concrete is the most widely used construction material in the world. Even though it has been used for several centuries, its behavior to high temperature remains to be understood. In the light of recent extreme events, including accidents, and arson, special attention has been focused on the performance of concrete in the fire safety assessment of buildings and tunnels. Fire represents one of the most severe conditions encountered during the life-time of a structure. Concrete exposed to high temperature can significantly jeopardize the structural integrity and load bearing capacity of the structure. Spalling of concrete remains one of the main issues to be addressed in the case of fire in buildings and tunnels. Successful modeling of this phenomenon depends not only on the accurate prediction of the temperature distribution through structural concrete but also on its mechanical response to the heating and boundaries restrains conditions and the migration of moisture and associated pore pressures. Therefore, it is necessary to develop a reliable formulation of concrete with all required information to understand its behavior during and after exposure to elevated temperature. It is also necessary to properly assess the effects of thermal degradation in order to develop predictive tools and validate design codes. Many structural problems can be adequately worthy by an elastoplastic model. The ultimate goal of this study is the development of a new constitutive model under a chemoplastic framework. To do this, an experimental program is carried out. The purpose of this program is twofold. First, it is essential to calibrate the proposed constitutive law that will be developed, and, second, for defining an inverse a problem. Usually, uniaxial and triaxial tests, conducted with confining pressure varied between 1.3 and 24 MPa and a temperature up to 700°C, allow us to identify the constitutive law parameters. This law reproduces the reduced field strength due to degradation of exothermic origin. This experimental program puts emphasis on the fragile nature of the preheated concrete and demonstrates the non-applicability of two failure criteria often used in engineering calculation. An alternative is proposed and well-tested. Indeed, exposing the concrete to high temperature results in irreversible loss of stiffness as well as a loss of decohesion strength. These losses are, typically, expressed through semi-empirical relationships of the mechanical properties with temperature. Unfortunately, these relationships are inadequate because the direct impact of this degradation, on the macroscopic scale, can result in a dependency relationship between the elastic properties and the hydrates mass. Therefore, unlike traditional methods using conventional elasto-plastic models and adjusting certain parameters with local temperature, the proposed constitutive law that incorporates a function of dehydration similar to the softening index in chemo-plastics gives good results. An Etse and Willam similar criterion is used and modified for the occasion. Hardening and softening mechanisms are then needed to expand and contract the loading surface for defining the strength of the concrete on a wide range of dehydration processes. The direction and magnitude of a permanent deformation, core of the inelastic domain, are defined through the development of non-associated chemoplastic potential and new curve of ductility. The influence of hydrostatic pressure (dilatancy) and dehydration on the concrete behavior are taken into account in our model. The model is implemented in the Matlab(c) code. Strains and stresses generated in the concrete are now accurately predicted. To illustrate the capabilities of the developed model to predict the complex behavior of concrete exposed to high temperature, simulations are performed through numerical loading paths scenarios. The model is able to accurately reproduce all the experimental data.

IFLA General Conference 1991. Division of Regional Activities: Section of Africa; Section of Asia and Oceania; Section of Latin America and the Carribean. Booklet 8.

ERIC Educational Resources Information Center

International Federation of Library Associations and Institutions, The Hague (Netherlands).

The six papers in this collection were presented at three sections of the Division of Regional Activities: (1) "A la recherche d'Approches adaptees aux Besoins en Documentation des Africains (In Search of an Approach Adapted to the Information Needs of Africans)" (Touria Temsamani Haji, Morocco); (2) "People's Libraries: An African…

Pulse combustion engineering research laboratory for indirect heating applications (PERL-IH). Final report, October 1, 1989-June 30, 1992

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

Belles, F.E.

1993-01-01

Uncontrolled NOx emissions from a variety of pulse combustors were measured. The implementation of flue-gas recirculation to reduce NOx was studied. A flexible workstation for parametric testing was built and used to study the phasing between pressure and heat release, and effects of fuel/air mixing on performance. Exhaust-pipe heat transfer was analyzed. An acoustic model of pulse combustion was developed. Technical support was provided to manufacturers on noise, ignition and condensation. A computerized bibliographic database on pulse combustion was created.

Whole-Body Diffusion-weighted MR Imaging of Iron Deposits in Hodgkin, Follicular, and Diffuse Large B-Cell Lymphoma.

PubMed

Cottereau, Anne-Ségolène; Mulé, Sébastien; Lin, Chieh; Belhadj, Karim; Vignaud, Alexandre; Copie-Bergman, Christiane; Boyez, Alice; Zerbib, Pierre; Tacher, Vania; Scherman, Elodie; Haioun, Corinne; Luciani, Alain; Itti, Emmanuel; Rahmouni, Alain

2018-02-01

Purpose To analyze the frequency and distribution of low-signal-intensity regions (LSIRs) in lymphoma lesions and to compare these to fluorodeoxyglucose (FDG) uptake and biologic markers of inflammation. Materials and Methods The authors analyzed 61 untreated patients with a bulky lymphoma (at least one tumor mass ≥7 cm in diameter). When a LSIR within tumor lesions was detected on diffusion-weighted images obtained with a b value of 50 sec/mm 2 , a T2-weighted gradient-echo (GRE) sequence was performed and calcifications were searched for with computed tomography (CT). In two patients, Perls staining was performed on tissue samples from the LSIR. LSIRs were compared with biologic inflammatory parameters and baseline FDG positon emission tomography (PET)/CT parameters (maximum standardized uptake value [SUV max ], total metabolic tumor volume [TMTV]). Results LSIRs were detected in 22 patients and corresponded to signal void on GRE images; one LSIR was due to calcifications, and three LSIRS were due to a recent biopsy. In 18 patients, LSIRs appeared to be related to focal iron deposits; this was proven with Perls staining in two patients. The LSIRs presumed to be due to iron deposits were found mostly in patients with aggressive lymphoma (nine of 26 patients with Hodgkin lymphoma and eight of 20 patients with diffuse large B-cell lymphoma vs one of 15 patients with follicular lymphoma; P = .047) and with advanced stage disease (15 of 18 patients). LSIRS were observed in spleen (n = 14), liver (n = 3), and nodal (n = 8) lesions and corresponded to foci FDG uptake, with mean SUV max of 9.8, 6.7, and 16.2, respectively. These patients had significantly higher serum levels of C-reactive protein, α 1 -globulin, and α 2 -globulin and more frequently had microcytic anemia than those without such deposits (P = .0072, P = .003, P = .0068, and P < .0001, respectively). They also had a significantly higher TMTV (P = .0055) and higher levels of spleen involvement (P

Morpho-histology of head kidney of female catfish Heteropneustes fossilis: seasonal variations in melano-macrophage centers, melanin contents and effects of lipopolysaccharide and dexamethasone on melanins.

PubMed

Kumar, Ravi; Joy, K P; Singh, S M

2016-10-01

In the catfish Heteropneustes fossilis, the anterior kidney is a hemopoietic tissue which surrounds the adrenal homologues, interrenal (IR) and chromaffin tissues corresponding to the adrenal cortical and adrenal medulla of higher mammals. The IR tissue is arranged in cell cords around the posterior cardinal vein (PCV) and its tributaries and secretes corticosteroids. The chromaffin tissue is scattered singly or in nests of one or more cells around the epithelial lining of the PCV or blood capillaries within the IR tissue. They are ferric ferricyanide-positive. Leukemia-inhibitory factor (LIF)-like reactivity was noticed in the lining of the epithelium of the IR cell cords and around the wall of the PCV and blood capillaries. No staining was observed in the hemopoietic cells. IL-1β- and TNF-α-like immunoreactivity was seen in certain cells in the hemopoietic tissue but not in the IR region. Macrophages were identified with mammalian macrophage-specific MAC387 antibodies and are present in the hemopoietic mass but not in the IR tissue. Pigments accumulate in the hemopoietic mass as melano-macrophage centers (MMCs) and are PAS-, Schmorl's- and Perls'-positive. The pigments contain melanin (black), hemosiderin (blue) and lipofuscin/ceroid (oxidized lipid, yellowish tan), as evident from the Perls' reaction. The MMCs were TUNEL-positive as evident from FITC fluorescence, indicating their apoptotic nature. The MMCs showed significant seasonal variation with their density increasing to the peak in the postspawning phase. Melanins were characterized spectrophotometrically for the first time in fish anterior kidney. The predominant form is pheomelanin (PM), followed by eumelanin (EM) and alkali-soluble melanin (ASM). Melanins showed significant seasonal variations with the level low in the resting phase and increasing to the peak in the postspawning phase. Under in vitro conditions, lipopolysaccharide (10 µg/mL) treatment increased significantly the levels of PM and EM

The School Car: Bringing the Three R's to Newfoundland's Remote Railway Settlements (1936-1942).

ERIC Educational Resources Information Center

Noseworthy, Randy P.

During the mid-1930s, the main line of the Newfoundland (Canada) Railway stretched 547 miles from St. John's to Port aux Basques, and railway workers and their families lived along the line in small isolated settlements. The provincial department of education, the Newfoundland Railway, and the Anglo-Newfoundland Development Company devised an…

Detailed Maintenance Planning for Military Systems with Random Lead Times and Cannibalization

DTIC Science & Technology

2014-12-01

relativement aux systèmes d’entretien. Prendre les meilleures décisions possible signifie ici de trouver un équilibre entre les coûts d’exploitation et la...Multistage Stochastic Programming: A Scenario Tree Based Approach to Planning under Uncertainty, In Sucar, L. E., Morales , E. F., and Hoey, J

A new approach for annotation of transposable elements using small RNA mapping

PubMed Central

El Baidouri, Moaine; Kim, Kyung Do; Abernathy, Brian; Arikit, Siwaret; Maumus, Florian; Panaud, Olivier; Meyers, Blake C.; Jackson, Scott A.

2015-01-01

Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants. Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/ PMID:25813049

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

PubMed

Thomas, Brandon R; Chylek, Lily A; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H A; Hlavacek, William S; Posner, Richard G

2016-03-01

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary data are available at Bioinformatics online. bionetgen.help@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Webmail: an Automated Web Publishing System

NASA Astrophysics Data System (ADS)

Bell, David

A system for publishing frequently updated information to the World Wide Web will be described. Many documents now hosted by the NOAO Web server require timely posting and frequent updates, but need only minor changes in markup or are in a standard format requiring only conversion to HTML. These include information from outside the organization, such as electronic bulletins, and a number of internal reports, both human and machine generated. Webmail uses procmail and Perl scripts to process incoming email messages in a variety of ways. This processing may include wrapping or conversion to HTML, posting to the Web or internal newsgroups, updating search indices or links on related pages, and sending email notification of the new pages to interested parties. The Webmail system has been in use at NOAO since early 1997 and has steadily grown to include fourteen recipes that together handle about fifty messages per week.

Installing the Unix Starlink Software

NASA Astrophysics Data System (ADS)

Bly, M. J.

This note is the release note and installation instructions for the DEC Alpha AXP / Digital UNIX, Sun Sparc / Solaris v2.x, and Sun Sparc / SunOS 4.1.x versions of the Starlink Software Collection (USSC). You will be supplied with pre-built (and installed) versions on tape and will just need to copy the tape to disk to have a working version. The tapes (where appropriate) will contain in addition, copies of the NAG and MEMSYS libraries, and Tcl, Tk, Expect, Mosaic, TeX, Pine, Perl, Jed, Ispell, Ghostscript, LaXeX2html and Ftnchek for the relevant system. The Sun Sparc SunOS 4.1.x version of the USSC was frozen at USSC111 and no further updates are available. The instructions for installing the main section of the USSC may continue to be used for installing Sun Sparc SunOS 4.1.x version.

Production Experiences with the Cray-Enabled TORQUE Resource Manager

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

Ezell, Matthew A; Maxwell, Don E; Beer, David

High performance computing resources utilize batch systems to manage the user workload. Cray systems are uniquely different from typical clusters due to Cray s Application Level Placement Scheduler (ALPS). ALPS manages binary transfer, job launch and monitoring, and error handling. Batch systems require special support to integrate with ALPS using an XML protocol called BASIL. Previous versions of Adaptive Computing s TORQUE and Moab batch suite integrated with ALPS from within Moab, using PERL scripts to interface with BASIL. This would occasionally lead to problems when all the components would become unsynchronized. Version 4.1 of the TORQUE Resource Manager introducedmore » new features that allow it to directly integrate with ALPS using BASIL. This paper describes production experiences at Oak Ridge National Laboratory using the new TORQUE software versions, as well as ongoing and future work to improve TORQUE.« less

nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

PubMed Central

Alharbi, Bader A.; Alshammari, Thamir H.; Felton, Nathan L.; Zhurkin, Victor B.; Cui, Feng

2014-01-01

Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site. PMID:25220945

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

PubMed

Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

2014-02-01

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

Barg, M. I.; Stobie, E. B.; Ferro, A. J.; O'Neil, E. J.

In the spring of 2000, at the request of the ADASS Program Organizing Committee (POC), we began organizing information from previous ADASS conferences in an effort to create a centralized database. The beginnings of this database originated from data (invited speakers, participants, papers, etc.) extracted from HyperText Markup Language (HTML) documents from past ADASS host sites. Unfortunately, not all HTML documents are well formed and parsing them proved to be an iterative process. It was evident at the beginning that if these Web documents were organized in a standardized way, such as XML (Extensible Markup Language), the processing of this information across the Web could be automated, more efficient, and less error prone. This paper will briefly review the many programming tools available for processing XML, including Java, Perl and Python, and will explore the mapping of relational data from our MySQL database to XML.

Documenting AUTOGEN and APGEN Model Files

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Khanampompan, Teerapat; Fisher, Forest W.; DelGuericio, Chris c.

2008-01-01

A computer program called "autogen hypertext map generator" satisfies a need for documenting and assisting in visualization of, and navigation through, model files used in the AUTOGEN and APGEN software mentioned in the two immediately preceding articles. This program parses autogen script files, autogen model files, PERL scripts, and apgen activity-definition files and produces a hypertext map of the files to aid in the navigation of the model. This program also provides a facility for adding notes and descriptions, beyond what is in the source model represented by the hypertext map. Further, this program provides access to a summary of the model through variable, function, sub routine, activity and resource declarations as well as providing full access to the source model and source code. The use of the tool enables easy access to the declarations and the ability to traverse routines and calls while analyzing the model.

Ferrenberg Swendsen Analysis of LLNL and NYBlue BG/L p4rhms Data

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

Soltz, R

2007-12-05

These results are from the continuing Lattice Quantum Chromodynamics runs on BG/L. These results are from the Ferrenberg-Swendsen analysis [?] of the combined data from LLNL and NYBlue BG/L runs for 32{sup 3} x 8 runs with the p4rhmc v2.0 QMP-MPI.X (semi-optimized p4 code using qmp over mpi). The jobs include beta values ranging from 3.525 to 3.535 with an alternate analysis extending to 3.540. The NYBlue data sets are from 9k trajectories from Oct 2007, and the LLNL data are from two independent streams of {approx}5k each, taking from the July 2007 runs. The following outputs are produced bymore » the fs-2+1-chiub.c program. All outputs have had checksums produced by addCks.pl and checked by the checkCks.pl perl script after scanning.« less

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

Thomas, Gregory S.; Nickless, William K.; Thiede, David R.

Enterprise level cyber security requires the deployment, operation, and monitoring of many sensors across geographically dispersed sites. Communicating with the sensors to gather data and control behavior is a challenging task when the number of sensors is rapidly growing. This paper describes the system requirements, design, and implementation of T3, the third generation of our transport software that performs this task. T3 relies on open source software and open Internet standards. Data is encoded in MIME format messages and transported via NNTP, which provides scalability. OpenSSL and public key cryptography are used to secure the data. Robustness and ease ofmore » development are increased by defining an internal cryptographic API, implemented by modules in C, Perl, and Python. We are currently using T3 in a production environment. It is freely available to download and use for other projects.« less

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

PubMed

Perycz, Malgorzata; Krwawicz, Joanna; Bochtler, Matthias

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

RNA-Seq-Based Transcript Structure Analysis with TrBorderExt.

PubMed

Wang, Yejun; Sun, Ming-An; White, Aaron P

2018-01-01

RNA-Seq has become a routine strategy for genome-wide gene expression comparisons in bacteria. Despite lower resolution in transcript border parsing compared with dRNA-Seq, TSS-EMOTE, Cappable-seq, Term-seq, and others, directional RNA-Seq still illustrates its advantages: low cost, quantification and transcript border analysis with a medium resolution (±10-20 nt). To facilitate mining of directional RNA-Seq datasets especially with respect to transcript structure analysis, we developed a tool, TrBorderExt, which can parse transcript start sites and termination sites accurately in bacteria. A detailed protocol is described in this chapter for how to use the software package step by step to identify bacterial transcript borders from raw RNA-Seq data. The package was developed with Perl and R programming languages, and is accessible freely through the website: http://www.szu-bioinf.org/TrBorderExt .

An in silico pipeline to filter the Toxoplasma gondii proteome for proteins that could traffic to the host cell nucleus and influence host cell epigenetic regulation.

PubMed

Syn, Genevieve; Blackwell, Jenefer M; Jamieson, Sarra E; Francis, Richard W

2018-01-01

Toxoplasma gondii uses epigenetic mechanisms to regulate both endogenous and host cell gene expression. To identify genes with putative epigenetic functions, we developed an in silico pipeline to interrogate the T. gondii proteome of 8313 proteins. Step 1 employs PredictNLS and NucPred to identify genes predicted to target eukaryotic nuclei. Step 2 uses GOLink to identify proteins of epigenetic function based on Gene Ontology terms. This resulted in 611 putative nuclear localised proteins with predicted epigenetic functions. Step 3 filtered for secretory proteins using SignalP, SecretomeP, and experimental data. This identified 57 of the 611 putative epigenetic proteins as likely to be secreted. The pipeline is freely available online, uses open access tools and software with user-friendly Perl scripts to automate and manage the results, and is readily adaptable to undertake any such in silico search for genes contributing to particular functions.

The cotton transcription factor TCP14 functions in auxin-mediated epidermal cell differentiation and elongation.

PubMed

Wang, Miao-Ying; Zhao, Pi-Ming; Cheng, Huan-Qing; Han, Li-Bo; Wu, Xiao-Min; Gao, Peng; Wang, Hai-Yun; Yang, Chun-Lin; Zhong, Nai-Qin; Zuo, Jian-Ru; Xia, Gui-Xian

2013-07-01

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play crucial roles in development, but their functional mechanisms remain largely unknown. Here, we characterized the cellular functions of the class I TCP transcription factor GhTCP14 from upland cotton (Gossypium hirsutum). GhTCP14 is expressed predominantly in fiber cells, especially at the initiation and elongation stages of development, and its expression increased in response to exogenous auxin. Induced heterologous overexpression of GhTCP14 in Arabidopsis (Arabidopsis thaliana) enhanced initiation and elongation of trichomes and root hairs. In addition, root gravitropism was severely affected, similar to mutant of the auxin efflux carrier PIN-FORMED2 (PIN2) gene. Examination of auxin distribution in GhTCP14-expressing Arabidopsis by observation of auxin-responsive reporters revealed substantial alterations in auxin distribution in sepal trichomes and root cortical regions. Consistent with these changes, expression of the auxin uptake carrier AUXIN1 (AUX1) was up-regulated and PIN2 expression was down-regulated in the GhTCP14-expressing plants. The association of GhTCP14 with auxin responses was also evidenced by the enhanced expression of auxin response gene IAA3, a gene in the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) family. Electrophoretic mobility shift assays showed that GhTCP14 bound the promoters of PIN2, IAA3, and AUX1, and transactivation assays indicated that GhTCP14 had transcription activation activity. Taken together, these results demonstrate that GhTCP14 is a dual-function transcription factor able to positively or negatively regulate expression of auxin response and transporter genes, thus potentially acting as a crucial regulator in auxin-mediated differentiation and elongation of cotton fiber cells.

The Cotton Transcription Factor TCP14 Functions in Auxin-Mediated Epidermal Cell Differentiation and Elongation1[C][W

PubMed Central

Wang, Miao-Ying; Zhao, Pi-Ming; Cheng, Huan-Qing; Han, Li-Bo; Wu, Xiao-Min; Gao, Peng; Wang, Hai-Yun; Yang, Chun-Lin; Zhong, Nai-Qin; Zuo, Jian-Ru; Xia, Gui-Xian

2013-01-01

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play crucial roles in development, but their functional mechanisms remain largely unknown. Here, we characterized the cellular functions of the class I TCP transcription factor GhTCP14 from upland cotton (Gossypium hirsutum). GhTCP14 is expressed predominantly in fiber cells, especially at the initiation and elongation stages of development, and its expression increased in response to exogenous auxin. Induced heterologous overexpression of GhTCP14 in Arabidopsis (Arabidopsis thaliana) enhanced initiation and elongation of trichomes and root hairs. In addition, root gravitropism was severely affected, similar to mutant of the auxin efflux carrier PIN-FORMED2 (PIN2) gene. Examination of auxin distribution in GhTCP14-expressing Arabidopsis by observation of auxin-responsive reporters revealed substantial alterations in auxin distribution in sepal trichomes and root cortical regions. Consistent with these changes, expression of the auxin uptake carrier AUXIN1 (AUX1) was up-regulated and PIN2 expression was down-regulated in the GhTCP14-expressing plants. The association of GhTCP14 with auxin responses was also evidenced by the enhanced expression of auxin response gene IAA3, a gene in the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) family. Electrophoretic mobility shift assays showed that GhTCP14 bound the promoters of PIN2, IAA3, and AUX1, and transactivation assays indicated that GhTCP14 had transcription activation activity. Taken together, these results demonstrate that GhTCP14 is a dual-function transcription factor able to positively or negatively regulate expression of auxin response and transporter genes, thus potentially acting as a crucial regulator in auxin-mediated differentiation and elongation of cotton fiber cells. PMID:23715527

Lithofacies variation across the Mammoth Cave-Pope Megagroup boundary -- a sequence stratigraphic approach

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

McDonald, T.A.; Tabor, E.; Marzolf, J.E.

1994-04-01

Regional stratigraphic relations in southern Illinois suggest a major unconformity near the top of the St. Genevieve Limestone. Large exposures below the unconformity within the Anna quarries display a retrogradational parasequence-stacking pattern. Eight to 12 m-thick parasequences comprise thinning-upward marine bioclastic wackestone overlain by oolitic and bioclastic thickening-upward eolian( ) grainstone. An eolian origin for the bioclastic grainstones is supported by large scale cross stratification (0.5 to 2 m-thick sets), reworked character of rounded, coated bioclasts, and preserved duneforms. At the quarries, the unconformity is directly overlain by mudstones and sandstones. Thinning-upward mudstones interbedded with very thin (1 to 3more » cm thick) intraclastic packstone tempestites crop out in a roadcut about 500 m NE of the quarries. Small-scale ripples and absence of trace fossils in lower mudstone units suggest an estuarine or lagoonal, brackish-waver environment. The trace fossil Conostichus and horizontal burrows appear abruptly in the upper, thin mudstone units. Highly bioturbated green and red shales overlying a 1 to 4 m-thick covered interval in a roadcut 610 m farther north are interbedded with tidally deposited, medium- to coarse-grained, bioclastic grainstones. The shale-draped, medium cross-bedded grainstones document ten or more tidal bundles. The cross-bedded grainstone is overlain by wavy- to flaser-bedded very fine-grained sandstone suggestive of sand flat origin. These sandstones are overlain by the Aux Vases Sandstone. Numerous low-angle bounding surfaces within the Aux Vases enclose low-angle, wedge-planar cross-bedding. A single irregular surface coated by a few centimeters of poorly sorted unstratified sandstone defines a ravinement surface near the base of the Aux Vases Sandstone.« less

Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes.

PubMed

Wang, Yijun; Deng, Dexiang; Shi, Yating; Miao, Nan; Bian, Yunlong; Yin, Zhitong

2012-03-01

Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

The novel cyst nematode effector protein 19C07 interacts with the Arabidopsis auxin influx transporter LAX3 to control feeding site development.

PubMed

Lee, Chris; Chronis, Demosthenis; Kenning, Charlotte; Peret, Benjamin; Hewezi, Tarek; Davis, Eric L; Baum, Thomas J; Hussey, Richard; Bennett, Malcolm; Mitchum, Melissa G

2011-02-01

Plant-parasitic cyst nematodes penetrate plant roots and transform cells near the vasculature into specialized feeding sites called syncytia. Syncytia form by incorporating neighboring cells into a single fused cell by cell wall dissolution. This process is initiated via injection of esophageal gland cell effector proteins from the nematode stylet into the host cell. Once inside the cell, these proteins may interact with host proteins that regulate the phytohormone auxin, as cellular concentrations of auxin increase in developing syncytia. Soybean cyst nematode (Heterodera glycines) Hg19C07 is a novel effector protein expressed specifically in the dorsal gland cell during nematode parasitism. Here, we describe its ortholog in the beet cyst nematode (Heterodera schachtii), Hs19C07. We demonstrate that Hs19C07 interacts with the Arabidopsis (Arabidopsis thaliana) auxin influx transporter LAX3. LAX3 is expressed in cells overlying lateral root primordia, providing auxin signaling that triggers the expression of cell wall-modifying enzymes, allowing lateral roots to emerge. We found that LAX3 and polygalacturonase, a LAX3-induced cell wall-modifying enzyme, are expressed in the developing syncytium and in cells to be incorporated into the syncytium. We observed no decrease in H. schachtii infectivity in aux1 and lax3 single mutants. However, a decrease was observed in both the aux1lax3 double mutant and the aux1lax1lax2lax3 quadruple mutant. In addition, ectopic expression of 19C07 was found to speed up lateral root emergence. We propose that Hs19C07 most likely increases LAX3-mediated auxin influx and may provide a mechanism for cyst nematodes to modulate auxin flow into root cells, stimulating cell wall hydrolysis for syncytium development.

Extraction of water and solutes from argillaceous rocks for geochemical characterisation: Methods, processes and current understanding

NASA Astrophysics Data System (ADS)

Sacchi, Elisa; Michelot, Jean-Luc; Pitsch, Helmut; Lalieux, Philippe; Aranyossy, Jean-François

2001-01-01

This paper summarises the results of a comprehensive critical review, initiated by the OECD/NEA "Clay Club," of the extraction techniques available to obtain water and solutes from argillaceous rocks. The paper focuses on the mechanisms involved in the extraction processes, the consequences on the isotopic and chemical composition of the extracted pore water and the attempts made to reconstruct its original composition. Finally, it provides some examples of reliable techniques and information, as a function of the purpose of the geochemical study. Résumé. Cet article résume les résultats d'une synthèse critique d'ensemble, lancée par le OECD/NEA "Clay Club", sur les techniques d'extraction disponibles pour obtenir l'eau et les solutés de roches argileuses. L'article est consacré aux mécanismes impliqués dans les processus d'extraction, aux conséquences sur la composition isotopique et chimique de l'eau porale extraite et aux tentatives faites pour reconstituer sa composition originelle. Finalement, il donne quelques exemples de techniques fiables et d'informations, en fonction du but de l'étude géochimique. Resúmen. Este artículo resume los resultados de una revisión crítica exhaustiva (iniciada por el "Clay Club" OECD/NEA) de las técnicas de extracción disponibles para obtener agua y solutos en rocas arcillosas. El artículo se centra en los mecanismos involucrados en los procesos extractivos, las consecuencias en la composición isotópica y química del agua intersticial extraída, y en los intentos realizados para reconstruir su composición original. Finalmente, se presentan algunos ejemplos de técnicas fiables e información, en función del propósito del estudio geoquímico.

Cation-Dependent Gold Recovery with α-Cyclodextrin Facilitated by Second-Sphere Coordination.

PubMed

Liu, Zhichang; Samanta, Avik; Lei, Juying; Sun, Junling; Wang, Yuping; Stoddart, J Fraser

2016-09-14

Herein, we report an alkali metal cation-dependent approach to gold recovery, facilitated by second-sphere coordination with eco-friendly α-cyclodextrin (α-CD). Upon mixing eight salts composed of Na(+), K(+), Rb(+), or Cs(+) cations and [AuX4](-) (X = Cl/Br) anions with α-, β-, or γ-CD in water, co-precipitates form selectively from the three (out of 24) aqueous solutions containing α-CD with KAuBr4, RbAuBr4, and CsAuBr4, from which the combination of α-CD and KAuBr4 affords the highest yield. Single-crystal X-ray analyses reveal that in 20 of the 24 adducts CD and [AuX4](-) anions form 2:1 sandwich-type second-sphere adducts driven partially by [C-H···X-Au] interactions between [AuX4](-) anions and the primary faces of two neighboring CDs. In the adduct formed between α-CD and KAuBr4, a [K(OH2)6](+) cation is encapsulated inside the cavity between the secondary faces of two α-CDs, leading to highly efficient precipitation owing to the formation of a cation/anion alternating ion wire residing inside a continuous α-CD nanotube. By contrast, in the other 19 adducts, the cations are coordinated by OH groups and glucopyranosyl ring O atoms in CDs. The strong coordination of Rb(+) and Cs(+) cations by these ligands, in conjunction with the stereoelectronically favorable binding of [AuBr4](-) anions with two α-CDs, facilitates the co-precipitation of the two adducts formed between α-CD with RbAuBr4 and CsAuBr4. In order to develop an efficient process for green gold recovery, the co-precipitation yield of α-CD and KAuBr4 has been optimized regarding both the temperature and the molar ratio of α-CD to KAuBr4.

Experiences in porting NASTRAN (R) to non-traditional platforms

NASA Technical Reports Server (NTRS)

Davis, Gregory L.; Norton, Robert L.

1991-01-01

The 1990 UNIX version of NASTRAN was ported to two new platforms that are not supported by COSMIC: the Sun SPARC workstation and the Apple Macintosh using the A/UX version of UNIX. The experiences of the authers in porting NASTRAN is summarized here. Suggestions for users who might attempt similar ports are given.

Properties of Organic Superconductors.

DTIC Science & Technology

1983-09-01

fBEDrrrF) 4 (ReO 4 ) 2 , devient supraconducteur pour des pressions suptrseures A 4 kbar avec une temperature de transition aol environs dce 2 K. A plus...coupl6es aux 6lectrons. Ces experiences sont incompatibles avec linterpr~tation expliquant lorigine /I/ du pic A 29 cm- 1 par un pseudogap supraconducteur

La prévention des blessures chez les enfants et les adolescents : une démarche de santé publique

PubMed Central

Yanchar, Natalie L; Warda, Lynne J; Fuselli, Pamela

2012-01-01

RÉSUMÉ La majorité des blessures dont sont victimes les enfants et les adolescents sont évitables. Le présent document de principes contient des renseignements généraux, des conseils et une déclaration d’engagement à l’égard de la prévention des blessures au Canada. Il sert de base sur laquelle construire en s’attardant d’abord aux définitions, à l’étendue et aux priorités en matière de prévention des blessures. Il contient également une description du fardeau et du profil des blessures non intentionnelles, de même que les principes d’interventions de prévention efficaces. La version intégrale renferme une liste de ressources en vue d’obtenir des données et de l’information probante (www.cps.ca). Enfin, le présent document de principes peut être utilisé pour la défense généralisée de la prévention des blessures.

Brassinosteroid control of shoot gravitropism interacts with ethylene and depends on auxin signaling components.

PubMed

Vandenbussche, Filip; Callebert, Pieter; Zadnikova, Petra; Benkova, Eva; Van Der Straeten, Dominique

2013-01-01

To reach favorable conditions for photosynthesis, seedlings grow upward when deprived of light upon underground germination. To direct their growth, they use their negative gravitropic capacity. Negative gravitropism is under tight control of multiple hormones. By counting the number of standing plants in a population or by real time monitoring of the reorientation of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis of transcriptomic data on AUX/IAA genes was gathered, and subsequent mutant analysis was performed. Ethylene and BR have opposite effects in regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in 2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX/IAA genes. BRs regulate a wider range of auxin signaling components than ethylene. Upward growth in seedlings depends strongly on the internal hormonal balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism in a manner that depends on the function of different, yet overlapping sets of auxin signaling components.

Emotional and behavioural reactions to moral transgressions: cross-cultural and individual variations in India and Britain.

PubMed

Laham, Simon M; Chopra, Sonavi; Lalljee, Mansur; Parkinson, Brian

2010-02-01

Reactions to moral transgressions are subject to influence at both the cultural and individual levels. Transgressions against an individual's rights or against social conventions of hierarchy may elicit different reactions in individualistic and collectivistic cultures. In the current study, affective and behavioural reactions to transgressions of autonomy (rights) and community (hierarchy) were examined in India and Britain. Results revealed that although reactions to autonomy transgressions are similar in India and Britain, Indian participants express more moral outrage than do Britons in response to transgressions of community. Results also supported the contention of emotion-specificity in affective moral reaction: Participants in both India and Britain reported anger in response to autonomy transgressions, but contempt in response to violations of community. Importantly, these results extend previous research by demonstrating the importance of emotion specificity in moral reactions, as opposed to categorization or dilemma resolution. In addition, an individual difference measure of respect for persons was shown to moderate reactions to moral transgressions. Specifically, participants with high respect for persons were less negative to violators of the community ethic, but not the autonomy ethic. These findings highlight the importance of examining emotion-specific responses in the moral domain and introduce a significant individual difference variable, respect for persons, into the psychology of morality. Les réactions aux transgressions morales sont susceptibles d'influence à la fois aux niveaux culturel et individuel. Les transgressions contre les droits d'un individu ou contre les conventions sociales d'hiérarchie peuvent susciter de différentes réactions dans les cultures individualiste et collectiviste. Dans la présente étude, les réactions affective et comportementale aux transgressions de l'autonomie (droits) et de la communauté (hi

EC 92: Implications for United States Trade Policy

DTIC Science & Technology

1990-04-09

38. 8. Veronique Maurus, "Le Maroc : le Nouveau Dragon aux Portes d’Europe," Le Monde (Paris), 03 November 1989, p. 9. 9. Carl Hamilton...Marx, Bernard. "What 1992 Has in Store for Europe." World Marxist Review, Vol. 32, January 1989, pp. 78-82. 33. Maurus, Veronique. "Le Maroc : le Nouveau

Software Description for the O’Hare Runway Configuration Management System. Volume II. Low-Level Pseudocode,

DTIC Science & Technology

1982-10-01

BACK_ GVRATON; (geserate log me"ses from wather and wind planning log screenJ PERFORN AIPORT.PLANNIG LOGISSA ORItATION; (eSamrate log message from...ISSAGN H31.TAL(COUNT) .26 -kAUX imesase is constructed with wather imforimetiom ad stated) IF(VILO.TAM(J).DIl A(S)’ ’)1 (VXLOG.TABL(J).VU.(S)’ THEN

Characterisation of Fibre Reinforced Titanium Matrix Composites. (La Caracterisation des Materiaux Composites a Matrice de Titane Renforces par Fibres)

DTIC Science & Technology

1994-02-01

devait servir de forum pour un 6change d’informations sur ce sujet important. Dans ce cas. [a caracterisation se ref~re A l’analyse du comportement des...phases de d~veloppement et de mise a l’echelle. mais aussi aux activites de caracterisation et de demonstration des composants. Dans le cas des materiaux

Granger Causality and National Procurement Spending: Applications to the CC130 Hercules Fleet Performance

DTIC Science & Technology

2011-09-01

intentionally left blank. ii DRDC CORA TM 2011-154 Dr aft Co py Executive summary Granger Causality and National Procurement Spending David W...à croire que la chaîne d’approvisionnement sous jacente est optimale - la résistance aux chocs de dépenses peut simplement s’expliquer par des stocks...i Executive summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii Sommaire

L'enseignement d'une langue (non-maternelle ou maternelle) aux apprenants en difficulté et aux enfants issus de milieux socialement défavorisés

NASA Astrophysics Data System (ADS)

Wambach, Michel

1986-06-01

Official statistics reveal a high percentage of school failure at primary-school level in Belgium, notably among children from socially disadvantaged backgrounds, be they francophone or foreign. Furthermore, the percentage of adult illiteracy is rising. These situations share a common root: the methodology of the mother tongue at school and the approach to the written language in particular. After defining the psychological objective of a language course the present study proposes a methodology, a synthesis of up-to-date psycho-pedagogical, linguistic and (neuro) biological trends. The data from this research make it possible to verify the working hypotheses which have been elaborated and revised over the last twenty years. Within the recommended methodology, the libération de la parole (`liberation of speech') occupies an important place. This initial stage increases and reinforces the creative dispositions in the child and prepares for real language activities. These help the child to communicate and enable a functional learning of the language. The methodology of reading takes into account research conducted on the operation of the memory and the selective activity of the brain. A first evaluation of the methodology has verified the working hypotheses. Moreover, the pupils in the experimental classes obtained markedly higher grades in tests such as reading comprehension, elaborating texts and in those tests calling for imagination and creativity.

Le role du phytoplancton de petite taille (<20 mum) dans les variations des proprietes optiques des eaux du Saint-Laurent

NASA Astrophysics Data System (ADS)

Mas, Sebastien

Les mesures satellitaires de couleur des oceans sont largement determinees par les proprietes optiques inherentes (IOPs) des eaux de surface. D'autre part, le phytoplancton de petite taille (<20 mum) est le plus souvent dominant dans les oceans, et peut donc etre une source importante de variation des IOPs dans les oceans. Dans ce contexte, le but principal de ce doctorat etait de definir l'impact du phytoplancton (<20 mum) sur les variations des proprietes optiques de l'Estuaire et du Golfe du Saint-Laurent (Canada). Afin d'atteindre cet objectif, il etait necessaire de determiner en milieu controle les facteurs de variabilite des proprietes optiques cellulaires et des IOPs du phytoplancton (<20 mum) des eaux du Saint-Laurent, et d'evaluer la contribution du phytoplancton (<20 mum) aux proprietes optiques totales des eaux du Saint-Laurent. Des experiences en laboratoire ont montre que les variations des proprietes optiques des cellules phytoplanctoniques soumises a un cycle jour-nuit, ainsi qu'a des changements concomitants d'intensite lumineuse, peuvent contribuer significativement a la variabilite des proprietes optiques observee en milieu naturel. D'autres experiences ont, quant a elles, mis en evidence que les variations des proprietes optiques des cellules phytoplanctoniques dues aux phases de croissance peuvent alterer les IOPs des oceans, particulierement pendant les periodes de floraison. De plus, la presence de bacteries et de particules detritiques peut egalement affecter la variabilite des IOPs totales, notamment la diffusion. Au printemps, dans l'Estuaire et le Golfe du Saint-Laurent, la contribution du phytoplancton <20 mum aux IOPs presentait des differences regionales evidentes pour les proprietes d'absorption et de diffusion. En plus de la variabilite spatiale, les proprietes optiques cellulaires presentaient des variations journalieres, et ce particulierement pour le picophytoplancton. Enfin, la plupart des differences observees dans les

Caracterisation environnementale des emissions atmospheriques d'une source fixe et creation d'un outil de gestion dynamique =

NASA Astrophysics Data System (ADS)

Fournier, Marie-Claude

Une caracterisation des emissions atmospheriques provenant des sources fixes en operation, alimentees au gaz et a l'huile legere, a ete conduite aux installations visees des sites no.1 et no.2. La caracterisation et les calculs theoriques des emissions atmospheriques aux installations des sites no.1 et no.2 presentent des resultats qui sont en dessous des valeurs reglementaires pour des conditions d'operation normales en periode hivernale et par consequent, a de plus fortes demandes energetiques. Ainsi, pour une demande energetique plus basse, le taux de contaminants dans les emissions atmospheriques pourrait egalement etre en dessous des reglementations municipales et provinciales en vigueur. Dans la perspective d'une nouvelle reglementation provinciale, dont les termes sont discutes depuis 2005, il serait souhaitable que le proprietaire des infrastructures visees participe aux echanges avec le Ministere du Developpement Durable, de l'Environnement et des Parcs (MDDEP) du Quebec. En effet, meme si le principe de droit acquis permettrait d'eviter d'etre assujetti a la nouvelle reglementation, l'application de ce type de principe ne s'inscrit pas dans ceux d'un developpement durable. L'âge avance des installations etudiees implique la planification d'un entretien rigoureux afin d'assurer les conditions optimales de combustion en fonction du type de combustible. Des tests de combustion sur une base reguliere sont donc recommandes. Afin de supporter le processus de suivi et d'evaluation de la performance environnementale des sources fixes, un outil d'aide a la gestion de l'information environnementale a ete developpe. Dans ce contexte, la poursuite du developpement d'un outil d'aide a la gestion de l'information environnementale faciliterait non seulement le travail des personnes affectees aux inventaires annuels mais egalement le processus de communication entre les differents acteurs concernes tant intra- qu'inter-etablissement. Cet outil serait egalement un bon

Vulvovaginite : Dépistage et prise en charge de la trichomonase, de la candidose vulvovaginale et de la vaginose bactérienne.

PubMed

van Schalkwyk, Julie; Yudin, Mark H

2016-12-01

Analyser les données probantes et formuler des recommandations quant au dépistage et à la prise en charge de la candidose vulvovaginale, de la trichomonase et de la vaginose bactérienne. Parmi les issues évaluées, on trouve l'efficacité de l'antibiothérapie, les taux de guérison en ce qui concerne les infections simples et compliquées, et les implications de ces pathologies pendant la grossesse. RéSULTATS: La littérature publiée a été récupérée par l'intermédiaire de recherches menées dans MEDLINE, EMBASE, CINAHL et The Cochrane Library en juin 2013 au moyen d'un vocabulaire contrôlé (p. ex. « vaginitis », « trichomoniasis », « vaginal candidiasis ») et de mots clés (p. ex. « bacterial vaginosis », « yeast », « candidiasis », « trichomonas vaginalis », « trichomoniasis », « vaginitis », « treatment ») appropriés. Les résultats ont été restreints aux analyses systématiques, aux essais comparatifs randomisés / essais cliniques comparatifs et aux études observationnelles. Aucune restriction n'a été appliquée en matière de date, mais les résultats ont été limités aux documents rédigés en anglais ou en français. Les recherches ont été mises à jour de façon régulière et intégrées à la directive clinique jusqu'en mai 2014. La littérature grise (non publiée) a été identifiée par l'intermédiaire de recherches menées dans les sites Web d'organismes s'intéressant à l'évaluation des technologies dans le domaine de la santé et d'organismes connexes, dans des collections de directives cliniques et auprès de sociétés de spécialité médicale nationales et internationales. La qualité des résultats est évaluée au moyen des critères décrits par le Groupe d'étude canadien sur les soins de santé préventifs (Tableau 1). DéCLARATIONS SOMMAIRES: RECOMMANDATIONS. Copyright © 2016. Published by Elsevier Inc.

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.

PubMed

McKain, Michael R; Hartsock, Ryan H; Wohl, Molly M; Kellogg, Elizabeth A

2017-01-01

Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/ It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. mrmckain@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

ABACAS: algorithm-based automatic contiguation of assembled sequences

PubMed Central

Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

2009-01-01

Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

Geospatial Authentication

NASA Technical Reports Server (NTRS)

Lyle, Stacey D.

2009-01-01

A software package that has been designed to allow authentication for determining if the rover(s) is/are within a set of boundaries or a specific area to access critical geospatial information by using GPS signal structures as a means to authenticate mobile devices into a network wirelessly and in real-time has been developed. The advantage lies in that the system only allows those with designated geospatial boundaries or areas into the server. The Geospatial Authentication software has two parts Server and Client. The server software is a virtual private network (VPN) developed in Linux operating system using Perl programming language. The server can be a stand-alone VPN server or can be combined with other applications and services. The client software is a GUI Windows CE software, or Mobile Graphical Software, that allows users to authenticate into a network. The purpose of the client software is to pass the needed satellite information to the server for authentication.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

A Reliability Comparison of Classical and Stochastic Thickness Margin Approaches to Address Material Property Uncertainties for the Orion Heat Shield

NASA Technical Reports Server (NTRS)

Sepka, Steven A.; McGuire, Mary Kathleen; Vander Kam, Jeremy C.

2018-01-01

The Orion Thermal Protection System (TPS) margin process uses a root-sum-square approach with branches addressing trajectory, aerothermodynamics, and material response uncertainties in ablator thickness design. The material response branch applies a bondline temperature reduction between the Avcoat ablator and EA9394 adhesive by 60 C (108 F) from its peak allowed value of 260 C (500 F). This process is known as the Bond Line Temperature Material Margin (BTMM) and is intended to cover material property and performance uncertainties. The value of 60 C (108 F) is a constant, applied at any spacecraft body location and for any trajectory. By varying only material properties in a random (monte carlo) manner, the perl-based script mcCHAR is used to investigate the confidence interval provided by the BTMM. In particular, this study will look at various locations on the Orion heat shield forebody for a guided and an abort (ballistic) trajectory.

Does Altered Uric Acid Metabolism Contribute to Diabetic Kidney Disease Pathophysiology?

PubMed

Gul, Ambreen; Zager, Philip

2018-03-01

Multiple experimental and clinical studies have identified pathways by which uric acid may facilitate the development and progression of chronic kidney disease (CKD) in people with diabetes. However, it remains uncertain if the association of uric acid with CKD represents a pathogenic effect or merely reflects renal impairment. In contrast to many published reports, a recent Mendelian randomization study did not identify a causal link between uric acid and CKD in people with type 1 diabetes. Two recent multicenter randomized control trials, Preventing Early Renal Function Loss in Diabetes (PERL) and FEbuxostat versus placebo rAndomized controlled Trial regarding reduced renal function in patients with Hyperuricemia complicated by chRonic kidney disease stage 3 (FEATHER), were recently designed to assess if uric acid lowering slows progression of CKD. We review the evidence supporting a role for uric acid in the pathogenesis of CKD in people with diabetes and the putative benefits of uric acid lowering.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

PubMed

Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin

2014-07-01

The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu. © The Author 2014. Published by Oxford University Press.

Assessment of morphological and functional changes in organs of rats after intramuscular introduction of iron nanoparticles and their agglomerates.

PubMed

Sizova, Elena; Miroshnikov, Sergey; Yausheva, Elena; Polyakova, Valentina

2015-01-01

The research was performed on male Wistar rats based on assumptions that new microelement preparations containing metal nanoparticles and their agglomerates had potential. Morphological and functional changes in tissues in the injection site and dynamics of chemical element metabolism (25 indicators) in body were assessed after repeated intramuscular injections (total, 7) with preparation containing agglomerate of iron nanoparticles. As a result, iron depot was formed in myosymplasts of injection sites. The quantity of muscle fibers having positive Perls' stain increased with increasing number of injections. However, the concentration of the most chemical elements and iron significantly decreased in the whole skeletal muscle system (injection sites are not included). Consequently, it increased up to the control level after the sixth and the seventh injections. Among the studied organs (liver, kidneys, and spleen), Caspase-3 expression was revealed only in spleen. The expression had a direct dependence on the number of injections. Processes of iron elimination from preparation containing nanoparticles and their agglomerates had different intensity.

Assessment of Morphological and Functional Changes in Organs of Rats after Intramuscular Introduction of Iron Nanoparticles and Their Agglomerates

PubMed Central

Sizova, Elena; Miroshnikov, Sergey; Yausheva, Elena; Polyakova, Valentina

2015-01-01

The research was performed on male Wistar rats based on assumptions that new microelement preparations containing metal nanoparticles and their agglomerates had potential. Morphological and functional changes in tissues in the injection site and dynamics of chemical element metabolism (25 indicators) in body were assessed after repeated intramuscular injections (total, 7) with preparation containing agglomerate of iron nanoparticles. As a result, iron depot was formed in myosymplasts of injection sites. The quantity of muscle fibers having positive Perls' stain increased with increasing number of injections. However, the concentration of the most chemical elements and iron significantly decreased in the whole skeletal muscle system (injection sites are not included). Consequently, it increased up to the control level after the sixth and the seventh injections. Among the studied organs (liver, kidneys, and spleen), Caspase-3 expression was revealed only in spleen. The expression had a direct dependence on the number of injections. Processes of iron elimination from preparation containing nanoparticles and their agglomerates had different intensity. PMID:25789310

nuMap: a web platform for accurate prediction of nucleosome positioning.

PubMed

Alharbi, Bader A; Alshammari, Thamir H; Felton, Nathan L; Zhurkin, Victor B; Cui, Feng

2014-10-01

Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site. Copyright © 2014 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

SeqDepot: streamlined database of biological sequences and precomputed features.

PubMed

Ulrich, Luke E; Zhulin, Igor B

2014-01-15

Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot-a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to >28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines. Freely available on the web at http://seqdepot.net/. RESTaccess via http://seqdepot.net/api/v1. Database files and scripts maybe downloaded from http://seqdepot.net/download.

EasyModeller: A graphical interface to MODELLER

PubMed Central

2010-01-01

Background MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. Findings The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way. Conclusion EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system. PMID:20712861

Suggestions for Improvement of User Access to GOCE L2 Data

NASA Astrophysics Data System (ADS)

Tscherning, C. C.

2011-07-01

ESA's has required that most GOCE L2 products are delivered in XML format. This creates difficulties for the users because a Parser written in Perl is needed to convert the files to files without XML tags. However several products, such as the coefficients of spherical harmonic coefficients are made available on standard form through the International Center for Global Gravity Field Models. The variance-covariance information for the gravity field models is only available without XML tags. It is suggested that all XML products are made available in the Virtual Data Archive as files without tags. This will besides making the data directly usable by a FORTRAN program also reduce the size (storage requirements) of the product to about 30 %. A further reduction of used storage should be made by tuning the number of digits for the individual quantities in the products, so that it corresponds to the actual number of significant digits.

Replacement Sequence of Events Generator

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladden, Daniel Wenkert Roy; Khanampompan, Teerpat

2008-01-01

The soeWINDOW program automates the generation of an ITAR (International Traffic in Arms Regulations)-compliant sub-RSOE (Replacement Sequence of Events) by extracting a specified temporal window from an RSOE while maintaining page header information. RSOEs contain a significant amount of information that is not ITAR-compliant, yet that foreign partners need to see for command details to their instrument, as well as the surrounding commands that provide context for validation. soeWINDOW can serve as an example of how command support products can be made ITAR-compliant for future missions. This software is a Perl script intended for use in the mission operations UNIX environment. It is designed for use to support the MRO (Mars Reconnaissance Orbiter) instrument team. The tool also provides automated DOM (Distributed Object Manager) storage into the special ITAR-okay DOM collection, and can be used for creating focused RSOEs for product review by any of the MRO teams.

Improvement of web-based data acquisition and management system for GOSAT validation lidar data analysis

NASA Astrophysics Data System (ADS)

Okumura, Hiroshi; Takubo, Shoichiro; Kawasaki, Takeru; Abdullah, Indra Nugraha; Uchino, Osamu; Morino, Isamu; Yokota, Tatsuya; Nagai, Tomohiro; Sakai, Tetsu; Maki, Takashi; Arai, Kohei

2013-01-01

A web-base data acquisition and management system for GOSAT (Greenhouse gases Observation SATellite) validation lidar data-analysis has been developed. The system consists of data acquisition sub-system (DAS) and data management sub-system (DMS). DAS written in Perl language acquires AMeDAS (Automated Meteorological Data Acquisition System) ground-level local meteorological data, GPS Radiosonde upper-air meteorological data, ground-level oxidant data, skyradiometer data, skyview camera images, meteorological satellite IR image data and GOSAT validation lidar data. DMS written in PHP language demonstrates satellite-pass date and all acquired data. In this article, we briefly describe some improvement for higher performance and higher data usability. GPS Radiosonde upper-air meteorological data and U.S. standard atmospheric model in DAS automatically calculate molecule number density profiles. Predicted ozone density prole images above Saga city are also calculated by using Meteorological Research Institute (MRI) chemistry-climate model version 2 for comparison to actual ozone DIAL data.

IMCAT: Image and Catalogue Manipulation Software

NASA Astrophysics Data System (ADS)

Kaiser, Nick

2011-08-01

The IMCAT software was developed initially to do faint galaxy photometry for weak lensing studies, and provides a fairly complete set of tools for this kind of work. Unlike most packages for doing data analysis, the tools are standalone unix commands which you can invoke from the shell, via shell scripts or from perl scripts. The tools are arranges in a tree of directories. One main branch is the ’imtools’. These deal only with fits files. The most important imtool is the ’image calculator’ ’ic’ which allows one to do rather general operations on fits images. A second branch is the ’catools’ which operate only on catalogues. The key cattool is ’lc’; this effectively defines the format of IMCAT catalogues, and allows one to do very general operations on and filtering of such catalogues. A third branch is the ’imcattools’. These tend to be much more specialised than the cattools and imcattools and are focussed on faint galaxy photometry.

Assessment of the systemic distribution of a bioconjugated anti-Her2 magnetic nanoparticle in a breast cancer model by means of magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Huerta-Núñez, L. F. E.; Villanueva-Lopez, G. Cleva; Morales-Guadarrama, A.; Soto, S.; López, J.; Silva, J. G.; Perez-Vielma, N.; Sacristán, E.; Gudiño-Zayas, Marco E.; González, C. A.

2016-09-01

The aim of this study was to determine the systemic distribution of magnetic nanoparticles of 100 nm diameter (MNPs) coupled to a specific monoclonal antibody anti-Her2 in an experimental breast cancer (BC) model. The study was performed in two groups of Sprague-Dawley rats: control ( n = 6) and BC chemically induced ( n = 3). Bioconjugated "anti-Her2-MNPs" were intravenously administered, and magnetic resonance imaging (MRI) monitored its systemic distribution at seven times after administration. Non-heme iron presence associated with the location of the bioconjugated anti-Her2-MNPs in splenic, hepatic, cardiac and tumor tissues was detected by Perl's Prussian blue (PPB) stain. Optical density measurements were used to semiquantitatively determine the iron presence in tissues on the basis of a grayscale values integration of T1 and T2 MRI sequence images. The results indicated a delayed systemic distribution of MNPs in cancer compared to healthy conditions with a maximum concentration of MNPs in cancer tissue at 24 h post-infusion.

Ultrafast laser direct hard-mask writing for high efficiency c-Si texture designs

NASA Astrophysics Data System (ADS)

Kumar, Kitty; Lee, Kenneth K. C.; Nogami, Jun; Herman, Peter R.; Kherani, Nazir P.

2013-03-01

This study reports a high-resolution hard-mask laser writing technique to facilitate the selective etching of crystalline silicon (c-Si) into an inverted-pyramidal texture with feature size and periodicity on the order of the wavelength which, thus, provides for both anti-reflection and effective light-trapping of infrared and visible light. The process also enables engineered positional placement of the inverted-pyramid thereby providing another parameter for optimal design of an optically efficient pattern. The proposed technique, a non-cleanroom process, is scalable for large area micro-fabrication of high-efficiency thin c-Si photovoltaics. Optical wave simulations suggest the fabricated textured surface with 1.3 μm inverted-pyramids and a single anti-reflective coating increases the relative energy conversion efficiency by 11% compared to the PERL-cell texture with 9 μm inverted pyramids on a 400 μm thick wafer. This efficiency gain is anticipated to improve further for thinner wafers due to enhanced diffractive light trapping effects.

A Reliability Comparison of Classical and Stochastic Thickness Margin Approaches to Address Material Property Uncertainties for the Orion Heat Shield

NASA Technical Reports Server (NTRS)

Sepka, Steve; Vander Kam, Jeremy; McGuire, Kathy

2018-01-01

The Orion Thermal Protection System (TPS) margin process uses a root-sum-square approach with branches addressing trajectory, aerothermodynamics, and material response uncertainties in ablator thickness design. The material response branch applies a bond line temperature reduction between the Avcoat ablator and EA9394 adhesive by 60 C (108 F) from its peak allowed value of 260 C (500 F). This process is known as the Bond Line Temperature Material Margin (BTMM) and is intended to cover material property and performance uncertainties. The value of 60 C (108 F) is a constant, applied at any spacecraft body location and for any trajectory. By varying only material properties in a random (monte carlo) manner, the perl-based script mcCHAR is used to investigate the confidence interval provided by the BTMM. In particular, this study will look at various locations on the Orion heat shield forebody for a guided and an abort (ballistic) trajectory.

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.

PubMed

Kim, Jihoon; Levy, Eric; Ferbrache, Alex; Stepanowsky, Petra; Farcas, Claudiu; Wang, Shuang; Brunner, Stefan; Bath, Tyler; Wu, Yuan; Ohno-Machado, Lucila

2014-10-01

MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours->600% end-to-end performance improvement over state of the art. MAGI's salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication. MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu. © The Author 2014. Published by Oxford University Press.

A TALE-inspired computational screen for proteins that contain approximate tandem repeats

PubMed Central

Krwawicz, Joanna

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen. PMID:28617832

Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum

PubMed Central

Honts, Jerry E.

2003-01-01

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. PMID:14673489

DIEGO: detection of differential alternative splicing using Aitchison's geometry.

PubMed

Doose, Gero; Bernhart, Stephan H; Wagener, Rabea; Hoffmann, Steve

2018-03-15

Alternative splicing is a biological process of fundamental importance in most eukaryotes. It plays a pivotal role in cell differentiation and gene regulation and has been associated with a number of different diseases. The widespread availability of RNA-Sequencing capacities allows an ever closer investigation of differentially expressed isoforms. However, most tools for differential alternative splicing (DAS) analysis do not take split reads, i.e. the most direct evidence for a splice event, into account. Here, we present DIEGO, a compositional data analysis method able to detect DAS between two sets of RNA-Seq samples based on split reads. The python tool DIEGO works without isoform annotations and is fast enough to analyze large experiments while being robust and accurate. We provide python and perl parsers for common formats. The software is available at: www.bioinf.uni-leipzig.de/Software/DIEGO. steve@bioinf.uni-leipzig.de. Supplementary data are available at Bioinformatics online.