Science.gov

Sample records for 5th order sequence

  1. Instantaneous frequency measurement by in-fiber 0.5th order fractional differentiation

    NASA Astrophysics Data System (ADS)

    Poveda-Wong, L.; Carrascosa, A.; Cuadrado-Laborde, C.; Cruz, J. L.; Díez, A.; Andrés, M. V.

    2016-07-01

    We experimentally demonstrate the possibility to retrieve the instantaneous frequency profile of a given temporal light pulse by in-fiber fractional order differentiation of 0.5th-order. The signal's temporal instantaneous frequency profile is obtained by simple dividing two temporal intensity profiles, namely the intensities of the input and output pulses of a spectrally-shifted fractional order differentiation. The results are supported by the experimental measurement of the instantaneous frequency profile of a mode-locked laser.

  2. A Comparison of In-Channel Dead Zone and Hyporheic Zone Transient Storage Parameter Estimates Between a 1st and 5th Order Stream

    NASA Astrophysics Data System (ADS)

    Briggs, M.; Gooseff, M.; Morkeski, K.; Wollheim, W.; Hopkinson, C.; Peterson, B.; Vorosmarty, C.

    2007-12-01

    A major enhancement to our understanding of how watersheds function would be the ability to discriminate between in-channel dead zone ( DZ) and hyporheic zone ( HZ) transient storage, and an evaluation of how these properties scale across stream orders. The nature of DZ storage is to display faster exchange rates with the main channel and less overall sediment contact time than HZ storage. These differences have great significance to many in-stream processes such as nutrient cycling. The combination of high slope, coarse bed material and fluvial structure endemic to many 1st order streams can provide greater forcing of hyporheic flow paths than occurs within the lower gradient 5th order streams. Conversely many 5th order reaches exhibit large side pool and back eddy DZ areas not common along 1st order streams. This study builds on existing methods to delineate the DZ and HZ from the integrated signal of a conservative solute's breakthrough curve ( BTC). Data for this comparison were collected over the summer of 2007 within the Ipswich River watershed, a basin which drains into Plum Island Sound on the north shore of Massachusetts, USA. The conservative solute NaCl was injected into both a 1st order medium gradient stream and a 5th order low gradient stream. The BTCs collected in thalwegs from the NaCl injections were simulated using a version of the solute transport model OTIS containing two zones of transient storage. Hydrometric measurements of stream velocity were used to estimate average main channel cross sectional area ( A) and DZ cross sectional area ( ASDZ) for each reach to constrain parameter estimates and avoid model equifinality between the storage zones. Initial values for the exchange rate between main channel flow and DZ storage ( αDZ) were estimated from DZ BTCs. Our results indicate that although the overall storage zone is much larger in proportion to the main channel for the 1st order reach than for the 5th order reach, the percentage of median

  3. Isotropic sequence order learning.

    PubMed

    Porr, Bernd; Wörgötter, Florentin

    2003-04-01

    In this article, we present an isotropic unsupervised algorithm for temporal sequence learning. No special reward signal is used such that all inputs are completely isotropic. All input signals are bandpass filtered before converging onto a linear output neuron. All synaptic weights change according to the correlation of bandpass-filtered inputs with the derivative of the output. We investigate the algorithm in an open- and a closed-loop condition, the latter being defined by embedding the learning system into a behavioral feedback loop. In the open-loop condition, we find that the linear structure of the algorithm allows analytically calculating the shape of the weight change, which is strictly heterosynaptic and follows the shape of the weight change curves found in spike-time-dependent plasticity. Furthermore, we show that synaptic weights stabilize automatically when no more temporal differences exist between the inputs without additional normalizing measures. In the second part of this study, the algorithm is is placed in an environment that leads to closed sensor-motor loop. To this end, a robot is programmed with a prewired retraction reflex reaction in response to collisions. Through isotropic sequence order (ISO) learning, the robot achieves collision avoidance by learning the correlation between his early range-finder signals and the later occurring collision signal. Synaptic weights stabilize at the end of learning as theoretically predicted. Finally, we discuss the relation of ISO learning with other drive reinforcement models and with the commonly used temporal difference learning algorithm. This study is followed up by a mathematical analysis of the closed-loop situation in the companion article in this issue, "ISO Learning Approximates a Solution to the Inverse-Controller Problem in an Unsupervised Behavioral Paradigm" (pp. 865-884). PMID:12689389

  4. 168. GENERAL VIEW FROM 5TH AVE. VIEW SOUTH, ACROSS 5TH ...

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

    168. GENERAL VIEW FROM 5TH AVE. VIEW SOUTH, ACROSS 5TH AVE., TOWARD BUILDING 506 (ON LEFT) AND BUILDING 435. - Quonset Point Naval Air Station, Roger Williams Way, North Kingstown, Washington County, RI

  5. Recalling visual serial order for verbal sequences.

    PubMed

    Logie, Robert H; Saito, Satoru; Morita, Aiko; Varma, Samarth; Norris, Dennis

    2016-05-01

    We report three experiments in which participants performed written serial recall of visually presented verbal sequences with items varying in visual similarity. In Experiments 1 and 2 native speakers of Japanese recalled visually presented Japanese Kanji characters. In Experiment 3, native speakers of English recalled visually presented words. In all experiments, items varied in visual similarity and were controlled for phonological similarity. For Kanji and for English, performance on lists comprising visually similar items was overall poorer than for lists of visually distinct items across all serial positions. For mixed lists in which visually similar and visually distinct items alternated through the list, a clear "zig-zag" pattern appeared with better recall of the visually distinct items than for visually similar items. This is the first time that this zig-zag pattern has been shown for manipulations of visual similarity in serial-ordered recall. These data provide new evidence that retaining a sequence of visual codes relies on similar principles to those that govern the retention of a sequence of phonological codes. We further illustrate this by demonstrating that the data patterns can be readily simulated by at least one computational model of serial-ordered recall, the Primacy model (Page and Norris, Psychological Review, 105(4), 761-81, 1998). Together with previous evidence from neuropsychological studies and experimental studies with healthy adults, these results are interpreted as consistent with two domain-specific, limited-capacity, temporary memory systems for phonological material and for visual material, respectively, each of which uses similar processes that have evolved to be optimal for retention of serial order. PMID:26704711

  6. Kids & Family Reading Report™. 5th Edition

    ERIC Educational Resources Information Center

    Scholastic Inc., 2015

    2015-01-01

    This report presents the 5th Edition of Scholastic's biannual study of children's and parents' attitudes and behaviors about reading. The latest research touches on reading aloud to children of all ages, the impact of reading independently for fun at school and at home, the importance of frequent reading, and the books children want most to read.…

  7. BOOK REVIEW: ENVIRONMENTAL ENGINEERING, 5TH EDITION

    EPA Science Inventory

    Book Review of Environmental Engineering, 5th Edition (Joseph A. Salvato, Nelson L. Nemerow, Franklin J. Agardy (Editors), John Wiley and Sons, Inc. Hoboken, New Jersey. 2003.). Author wrote review per the request of the Editor-in-Chief of the Journal of Environmental Quality.

  8. Multifrequency Catalogue of Blazars - 5th Edition

    NASA Astrophysics Data System (ADS)

    Massaro, E.; Maselli, A.; Leto, C.; Marchegiani, P.; Perri, M.; Giommi, P.; Piranomonte, S.

    2014-12-01

    The 5th Edition of the Multifrequency Catalogue of Blazars is one of the most complete lists of Active Galactic Nuclei whose emission properties are recognised as typical of blazars. It includes the list of sources and an essential compilation of multifrequency data from radio to gamma rays. The source list for the entire sky is also available online at the ASDC web site (http://www.asdc.asi.it/bzcat/) where it is frequently updated to add new blazars and to improve the database.

  9. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Next-generation, whole genome shotgun (WGS) assemblies of complex genomes are highly enabling, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating popul...

  10. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

    PubMed Central

    Mascher, Martin; Muehlbauer, Gary J; Rokhsar, Daniel S; Chapman, Jarrod; Schmutz, Jeremy; Barry, Kerrie; Muñoz-Amatriaín, María; Close, Timothy J; Wise, Roger P; Schulman, Alan H; Himmelbach, Axel; Mayer, Klaus FX; Scholz, Uwe; Poland, Jesse A; Stein, Nils; Waugh, Robbie

    2013-01-01

    Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species. PMID:23998490

  11. Oral Persuasion: A Saleable Work Skill. Occupation Simulation Packet. Grades 5th-6th.

    ERIC Educational Resources Information Center

    Lee, Dennis W.

    This teacher's guide contains simulated work experiences for 5th and 6th grade students using the isolated skill concept - oral persuasion. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Two pre-skill activities are suggested, such as…

  12. Role sequencing: does order matter for mental health?

    PubMed

    Jackson, Pamela Braboy

    2004-06-01

    Role sequencing refers to the ordering of social roles. According to the normative order hypothesis, adults who follow a certain sequencing of their social roles will be better adjusted than their peers who follow other life course patterns. The normative order is defined as first entering the paid labor force, getting married, and later having children. This study tests this hypothesis by analyzing retrospective life history data from three subsamples of adults who completed the 1987--1988 National Survey of Families and Households: (1) married, working parents; (2) divorced, working parents; and (3) married, unemployed parents. The findings indicate significant race/ethnic (black/white), gender, and cohort differences in the type of role sequencing patterns that are conducive to positive mental health. For example, African Americans who work first, then have children, and later get married report better mental health than their peers who followed the normative order White men and women seem to benefit from following the normative course of role transitions. Among women, however, the psychological benefits of following typical life course patterns are especially evident among those born during the baby boom. PMID:15305756

  13. Overlay improvement by ASML HOWA 5th alignment strategy

    NASA Astrophysics Data System (ADS)

    Wang, Raf; Chiang, CY; Hsu, Wilson; Yang, Richer; Shih, Todd; Chen, Jackie; Chiu, Jonathan; Lin, Wythe

    2009-12-01

    Overlay control is more challenging when DRAM volume production continues to shrink its critical dimention (CD) to 70nm and beyond. Effected by process, the overlay behavior at wafer edge is quite different from wafer center. The big contribution to worse overlay at wafer edge which causes yield loss is misalignment. The analysis in wafer edge suggests that high order uncorrectable overlay residuals are often observed by certain process impact. Therefore, the basic linear model used for alignment correction is not sufficient and it is necessary to introduce an advanced alignment correction model for wafer edge overlay improvement. In this study, we demonstrated the achievement of moderating the poor overlay at wafer edge area by using a high order wafer alignment strategy. The mechanism is to use non-linear correction methods of high order models ( up to 5th order), with support by the function High Order Wafer Alignment (known as HOWA) in scanner. Instead of linear model for the 6 overlay parameters which come from average result, HOWA alignment strategy can do high order fitting through the wafer to get more accurate overlay parameters which represent the local wafer grid distortion better. As a result, the overlay improvement for wafer edge is achieved. Since alignment is a wafer dependent correction, with HOWA the wafer to wafer overlay variation can be improved dynamically as well. In addition, the effects of different mark quantity and sampling distribution from HOWA are also introduced in this paper. The results of this study indicate that HOWA can reduce uncorrectable overlay residual by 30~40% and improve wafer-to-wafer overlay variation significantly. We conclude that HOWA is a noteworthy strategy for overlay improvement. Moreover, optimized alignment mark numbers and distribution layout are also key factors to make HOWA successful.

  14. Working Together for Student Achievement. 5th Biennial Joint Report

    ERIC Educational Resources Information Center

    Washington State Board of Education, 2014

    2014-01-01

    The Washington state Board of Education (SBE) and the Professional Educator Standards Board (PESB) submitted this 5th biennial joint report to the Governor, Legislative Education Committees, and Superintendent of Public Instruction. The report outlines the collaborative work of the Boards, highlights accomplishments, and provides goals and…

  15. 5th Conference on Aerospace Materials, Processes, and Environmental Technology

    NASA Technical Reports Server (NTRS)

    Cook, M. B. (Editor); Stanley, D. Cross (Editor)

    2003-01-01

    Records are presented from the 5th Conference on Aerospace Materials, Processes, and Environmental Technology. Topics included pollution prevention, inspection methods, advanced materials, aerospace materials and technical standards,materials testing and evaluation, advanced manufacturing,development in metallic processes, synthesis of nanomaterials, composite cryotank processing, environmentally friendly cleaning, and poster sessions.

  16. 5th Latin American pesticide residue workshop (LAPRW 2015)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This invited editorial proceedings article introduces the 6 research papers published in the special topical collection for the 5th Latin American Pesticide Residue Workshop held in Santiago, Chile, May 10-13, 2015. The meeting was a great success with more than 50 talks, 140 posters, 21 vendors, a...

  17. Sequencing in SLA: Phonological Memory, Chunking, and Points of Order.

    ERIC Educational Resources Information Center

    Ellis, Nick C.

    1996-01-01

    Argues that much of language acquisition is sequence learning and that the resultant long-term knowledge base of language sequences serves as the database for grammar acquisition. The article also proposes mechanisms to analyze sequence information that result in knowledge of underlying grammar. (184 references) (Author/CK)

  18. From Cooks to Carpenters: Measuring - A Saleable Work Skill. Occupation Simulation Packet. Grades 5th-6th.

    ERIC Educational Resources Information Center

    Kennedy, Helena

    This teacher's guide contains simulated work experiences for 5th and 6th grade students using the isolated skill concept - measuring. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Three pre-skill activities are suggested, such as…

  19. Teacher and Parent Views on the Instruction of 5th Grade Students by Branch Teachers in the 4+4+4 Education System

    ERIC Educational Resources Information Center

    Yildizhan, Yusuf Hayri

    2015-01-01

    The objective of this study is to examine the teacher and parent views on the instruction of 5th grade students by branch teachers. This study is designed according to the phenomenology design and uses qualitative data. In order to collect data, open-ended questions were asked to 18 teachers and 16 parents of 5th grade students on the subject, and…

  20. Speed, Accuracy, and Serial Order in Sequence Production

    ERIC Educational Resources Information Center

    Pfordresher, Peter Q.; Palmer, Caroline; Jungers, Melissa K.

    2007-01-01

    The production of complex sequences like music or speech requires the rapid and temporally precise production of events (e.g., notes and chords), often at fast rates. Memory retrieval in these circumstances may rely on the simultaneous activation of both the current event and the surrounding context (Lashley, 1951). We describe an extension to a…

  1. Megabase sequencing of human genome by ordered-shotgun-sequencing (OSS) strategy

    NASA Astrophysics Data System (ADS)

    Chen, Ellson Y.

    1997-05-01

    So far we have used OSS strategy to sequence over 2 megabases DNA in large-insert clones from regions of human X chromosomes with different characteristic levels of GC content. The method starts by randomly fragmenting a BAC, YAC or PAC to 8-12 kb pieces and subcloning those into lambda phage. Insert-ends of these clones are sequenced and overlapped to create a partial map. Complete sequencing is then done on a minimal tiling path of selected subclones, recursively focusing on those at the edges of contigs to facilitate mergers of clones across the entire target. To reduce manual labor, PCR processes have been adapted to prepare sequencing templates throughout the entire operation. The streamlined process can thus lend itself to further automation. The OSS approach is suitable for large- scale genomic sequencing, providing considerable flexibility in the choice of subclones or regions for more or less intensive sequencing. For example, subclones containing contaminating host cell DNA or cloning vector can be recognized and ignored with minimal sequencing effort; regions overlapping a neighboring clone already sequenced need not be redone; and segments containing tandem repeats or long repetitive sequences can be spotted early on and targeted for additional attention.

  2. 5th Annual Global College of Neuroprotection and Neuroregeneration.

    PubMed

    Sharma, Hari Shanker

    2008-06-01

    The 5th Global College of Neuroprotection and Neuroregeneration (GCNN) was held in the historic charming capital city of Bucharest, Romania in JW Marriott Grand Hotel on 3-6 March, 2008. The meeting was a unique blend of basic researchers and clinicians across the Globe presenting their recent findings in neuroprotection and neuroregeneration in a beautiful exotic ambience. More than 300 students and researchers attended the congress and participated in deliberations. Over 60 representatives from various pharmaceutical industries from all over the world supported this event. This meeting was held for the first time as a joint venture with GCNN and the Society for study on Neuroproetction and Neuroplasticity (SSNN), and was a grand success both scientifically and socially. Thus, these joint meetings of the two societies (GCNN and SSNN) will continue in future in different European cities for the coming 5 years. PMID:18505353

  3. 167. GENERAL VIEW DOWN 5TH AVE. VIEW TO SOUTHWEST DOWN ...

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

    167. GENERAL VIEW DOWN 5TH AVE. VIEW TO SOUTHWEST DOWN 5TH AVE. SHOWING FROM LEFT TO RIGHT, BUILDING 504, 436, 11, AND 155. - Quonset Point Naval Air Station, Roger Williams Way, North Kingstown, Washington County, RI

  4. PREFACE: 5th Baltic Conference on Silicate Materials

    NASA Astrophysics Data System (ADS)

    Mezinskis, G.; Bragina, L.; Colombo, P.; Frischat, G. H.; Grabis, J.; Greil, P.; Deja, J.; Kaminskas, R.; Kliava, J.; Medvids, A.; Nowak, I.; Siauciunas, R.; Valancius, Z.; Zalite, I.

    2011-12-01

    Logo This Volume of IOP Conference Series: Materials Science and Engineering presents a selection of the contributions to the 5th Baltic Conference on Silicate Materials (BaltSilica2011) held at Riga Technical University, Riga, Latvia from 23-25 May 2011. The conference was organized by Riga Technical University (Latvia) and Kaunas University of Technology (Lithuania). The series of Baltic conferences on silicate materials was started since 2004: the first conference was held in Riga, Latvia, 2004; the second conference was held in Kaunas, Lithuania 2005; the third was held again in Riga, Latvia, 2007, and the fourth was held in Kaunas, Lithuania 2009. BaltSilica 2011 was attended by around 50 participants from Latvia, Lithuania, Estonia, Germany, Poland, Italy, France, Ukraine and Russia. In comparison with previous silicate materials conferences, the broadening of participating countries is an indication of the interest of scientists, engineers and students to exchange research ideas, latest results, and to find new research topics for cooperation in the fields of silicate, high temperature materials, and inorganic nanomaterials. The scientific programme included 8 invited plenary lectures 23 oral presentations and 25 posters [1]. Scientific themes covered in the conference and in this special issue: Natural and Artificial Stone Materials; Traditional and New Ceramic and Glass-Like Materials; Nanoparticles and Nanomaterials. This volume consists of 23 selected proceeding papers. The Editor of this special issue is grateful to all the contributors to BaltSilica 2011. I am also very grateful to the scientific committee, the local organizing committee, the session chairs, the referees who refereed the submitted articles to this issue, and to students from the Department of Silicate, High Temperature and Inorganic Nanomaterials Technology of the Riga Technical University who ensured the smooth running of the conference. Particular thanks goes to eight plenary

  5. Managing Haemophilia for Life: 5th Haemophilia Global Summit.

    PubMed

    Hermans, Cedric; Dolan, Gerry; Jennings, Ian; Windyga, Jerzy; Lobet, Sébastien; Rodríguez-Merchán, E Carlos; Di Minno, Matteo Nicola Dario; Jiménez-Yuste, Víctor; O'Mahony, Brian

    2015-10-01

    The 5th Haemophilia Global Summit was held in Barcelona, Spain, in September 2014. The programme was designed by an independent Scientific Steering Committee of haemophilia experts and explored issues relevant to the practical management of haemophilia, as well as key opportunities and challenges for care in the future. The topics outlined in this supplement were selected by the Scientific Steering Committee for their relevance to improving haemophilia care globally. In this supplement from the meeting, Gerry Dolan explores pharmacokinetics and dynamics in haemophilia, and Gerry Dolan and Ian Jennings jointly address the role of the laboratory in haemophilia care. The potential benefits of low-dose prophylaxis regimens for people with haemophilia in the developing world are reviewed by Jerzy Windyga, and the question of whether 'Future haemophilia research should be undertaken in the developing world' is debated by Jerzy Windyga and Cedric Hermans. Management strategies for ankle arthropathy are discussed by Sébastien Lobet and E. Carlos Rodríguez-Merchán, and the use of ultrasound for the early detection of haemophilic arthropathy is addressed by Matteo Nicola Dario Di Minno and Víctor Jiménez-Yuste. Finally, the role of patients in the future of haemophilia care is reviewed by Brian O'Mahony. PMID:26350039

  6. Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid Wheat

    PubMed Central

    Edae, Erena A.; Bowden, Robert L.; Poland, Jesse

    2015-01-01

    The advancement of next-generation sequencing technologies in conjunction with new bioinformatics tools enabled fine-tuning of sequence-based, high-resolution mapping strategies for complex genomes. Although genotyping-by-sequencing (GBS) provides a large number of markers, its application for association mapping and genomics-assisted breeding is limited by a large proportion of missing data per marker. For species with a reference genomic sequence, markers can be ordered on the physical map. However, in the absence of reference marker order, the use and imputation of GBS markers is challenging. Here, we demonstrate how the population sequencing (POPSEQ) approach can be used to provide marker context for GBS in wheat. The utility of a POPSEQ-based genetic map as a reference map to create genetically ordered markers on a chromosome for hexaploid wheat was validated by constructing an independent de novo linkage map of GBS markers from a Synthetic W7984 × Opata M85 recombinant inbred line (SynOpRIL) population. The results indicated that there is strong agreement between the independent de novo linkage map and the POPSEQ mapping approach in mapping and ordering GBS markers for hexaploid wheat. After ordering, a large number of GBS markers were imputed, thus providing a high-quality reference map that can be used for QTL mapping for different traits. The POPSEQ-based reference map and whole-genome sequence assemblies are valuable resources that can be used to order GBS markers and enable the application of highly accurate imputation methods to leverage the application GBS markers in wheat. PMID:26530417

  7. Teaching 5th grade science for aesthetic understanding

    NASA Astrophysics Data System (ADS)

    Girod, Mark A.

    Many scientists speak with great zeal about the role of aesthetics and beauty in their science and inquiry. Few systematic efforts have been made to teach science in ways that appeal directly to aesthetics and this research is designed to do just that. Drawing from the aesthetic theory of Dewey, I describe an analytic lens called learning for aesthetic understanding that finds power in the degree to which our perceptions of the world are transformed, our interests and enthusiasm piqued, and our actions changed as we seek further experiences in the world. This learning theory is contrasted against two other current and popular theories of science learning, that of learning for conceptual understanding via conceptual change theory and learning for a language-oriented or discourse-based understanding. After a lengthy articulation of the pedagogical strategies used to teach for aesthetic understanding the research is described in which comparisons are drawn between students in two 5th grade classrooms---one taught for the goal of conceptual understanding and the other taught for the goal of aesthetic understanding. Results of this comparison show that more students in the treatment classroom had aesthetic experiences with science ideas and came to an aesthetic understanding when studying weather, erosion, and structure of matter than students in the control group. Also statistically significant effects are shown on measures of interest, affect, and efficacy for students in the treatment class. On measures of conceptual understanding it appears that treatment class students learned more and forgot less over time than control class students. The effect of the treatment does not generally depend on gender, ethnicity, or prior achievement except in students' identity beliefs about themselves as science learners. In this case, a significant interaction for treatment class females on science identity beliefs did occur. A discussion of these results as well as elaboration and

  8. Genomics into Healthcare: The 5th Pan Arab Human Genetics Conference and 2013 Golden Helix Symposium

    PubMed Central

    Fortina, Paolo; AlKhaja, Najib; Al Ali, Mahmoud Taleb; Hamzeh, Abdul Rezzak; Nair, Pratibha; Innocenti, Federico; Patrinos, George P.; Kricka, Larry J.

    2014-01-01

    The joint 5th Pan Arab Human Genetics conference and 2013 Golden Helix Symposium, “Genomics into Healthcare” was coorganized by the Center for Arab Genomic Studies (http://www.cags.org.ae) in collaboration with the Golden Helix Foundation (http://www.goldenhelix.org) in Dubai, United Arab Emirates from 17 to 19 November, 2013. The meeting was attended by over 900 participants, doctors and biomedical students from over 50 countries and was organized into a series of nine themed sessions that covered cancer genomics and epigenetics, genomic and epigenetic studies, genomics of blood and metabolic disorders, cytogenetic diagnosis and molecular profiling, next-generation sequencing, consanguinity and hereditary diseases, clinical genomics, clinical applications of pharmacogenomics, and genomics in public health. PMID:24526565

  9. Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.

    PubMed

    Xu, Zheng; Lance, Britton; Vargas, Claudia; Arpinar, Budak; Bhandarkar, Suchendra; Kraemer, Eileen; Kochut, Krys J; Miller, John A; Wagner, Jeff R; Weise, Michael J; Wunderlich, John K; Stringer, James; Smulian, George; Cushion, Melanie T; Arnold, Jonathan

    2003-04-01

    A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is approximately 50% complete with approximately 200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock psi protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy. PMID:12702676

  10. PREFACE: 5th Workshop of Young Researchers in Astronomy & Astrophysics

    NASA Astrophysics Data System (ADS)

    Forgács-Dajka, Emese; Plachy, Emese; Molnár, László

    2010-04-01

    The 5th Workshop of Young Researchers in Astronomy and Astrophysics was held on 2-4 September 2009 at the Eötvös University in Budapest, Hungary. This meeting fits into a conference series which can already be considered a tradition where the younger generation has the opportunity to present their work. The event was also a great opportunity for senior astronomers and physicists to form new connections with the next generation of researchers. The selection of invited speakers concentrated on the researchers currently most active in the field, mostly on a post-doctoral/tenure/fresh faculty position level. A number of senior experts and PhD students were also invited. As the conference focused on people rather than a specific field, various topics from theoretical physics to planetology were covered in three days. The programme was divided into six sections: Physics of the Sun and the Solar System Gravity and high-energy physics Galactic and extragalactic astronomy, cosmology Celestial mechanics and exoplanets Infrared astronomy and young stars Variable stars We had the pleasure of welcoming 10 invited review talks from senior researchers and 42 contributed talks and a poster from the younger generation. Participants also enjoyed the hospitality of the pub Pál at the Pálvölgyi-cave after giving, hearing and disputing countless talks. Brave souls even descended to the unbuilt, adventurous Mátyásvölgyi-cave. Memories of the conference were shadowed though. Péter Csizmadia, one of our participants and three other climbers attempted a first ever ascent to the Ren Zhong Feng peak in Sichuan, China, but they never returned from the mountains. Péter departed to China shortly after the conference, with best wishes from participants and friends. We dedicate this volume to his memory. The organisers thankthe Physics Doctoral School of Eötvös University for its hospitality. The workshop was supported by the Mecenatúra and Polányi Mihály Programmes of the National

  11. On asymptotically lacunary statistical equivalent of order α of difference sequences

    NASA Astrophysics Data System (ADS)

    Et, Mikail; Şengül, Hacer; ćınar, Muhammed

    2015-09-01

    In this study, we introduce and examine the concepts of Δθm -asymptotically statistical equivalent of order α and strong Δθm -asymptotically equivalent of order α of sequences. Also, we give some relations connected to these concepts.

  12. The utility of a 5th nap in multiple sleep latency test

    PubMed Central

    Lykouras, Dimosthenis; Rees, Kate

    2016-01-01

    Background This is the first study that aimed to look specifically at the utility of the 5th nap in the multiple sleep latency test (MSLT), a test used to assist in the diagnosis of narcolepsy. Methods Data was retrospectively collected from the Sleep Disorders Centre of a Tertiary Hospital on patients that had a 5th nap during their MSLT from the 08th November 2011 to 12th November 2014. Results Fifty-three patients had a 5th nap performed out of 378 MSLT studies. In 16% of cases a diagnosis of narcolepsy was given directly due to the inclusion of the 5th nap on the MSLT. Here a 5th nap allowed diagnostic criteria of mean sleep latency <8 minutes and >2 SOREMPS to be met. In 53% of cases the mean sleep latency increased due to 5th nap inclusion; the mean sleep latency of the first four naps was 5.6 vs. 6.7 after inclusion of the 5th nap. Conclusions The 5th nap is not often performed within the MSLT studies. Our study shows that only a few patients may benefit from a 5th nap opportunity which also led to increase of the mean sleep latency at the expense of extra time, cost, labour and increased patient anxiety. PMID:26904269

  13. NASA-marks 5th anniversary of first lunar landing

    NASA Technical Reports Server (NTRS)

    1974-01-01

    The accomplishments of the Apollo 11 Flight are presented as a tribute to the fifth anniversary of the first landing on the moon. The document contains: (1) a general description of the Apollo 11 Flight, (2) Presidential statements, (3) Apollo historical summary, (4) Apollo mission facts, (5) information on astronauts who are no longer in the program, and (6) transcripts of the landing sequence and first extravehicular activities on the moon.

  14. Field Theory and Orientational Phase Ordering of Sequence Disordered LC Heteropolymers

    NASA Astrophysics Data System (ADS)

    Gutman, Lorin; Shakhnovich, Eugene

    2002-03-01

    A theory of fields for a solution of polymers with disordered sequences of flexible and mesogenic segments is solved using a novel creation-annihilation operator formalism. The 0 sequence disorder limit is the the A. M. Gupta and S. F. Edwards, J. Chem. Phys., 98, 1588, (1993) result for long homopolymer chains. Sequence disorder, alignment propensity, stiffness and lyotropic impact on orientation and coexistence of phases from numerical unconstrained iteration of orientational tensors are presented. We find that heterogeneity in sequence impacts strongly the density order/disorder threshold. The Maxwell construction shows a three fold increase in coexistence width compared with the homopolymer analogue. The non-equilibrium meta-stable domain scale, obtained by calculation of Doring free energy from field theory and nucleation theory is of the order of μ m, and agrees well with recent experiments on DLCPs.

  15. Disruption of Broca's Area Alters Higher-order Chunking Processing during Perceptual Sequence Learning.

    PubMed

    Alamia, Andrea; Solopchuk, Oleg; D'Ausilio, Alessandro; Van Bever, Violette; Fadiga, Luciano; Olivier, Etienne; Zénon, Alexandre

    2016-03-01

    Because Broca's area is known to be involved in many cognitive functions, including language, music, and action processing, several attempts have been made to propose a unifying theory of its role that emphasizes a possible contribution to syntactic processing. Recently, we have postulated that Broca's area might be involved in higher-order chunk processing during implicit learning of a motor sequence. Chunking is an information-processing mechanism that consists of grouping consecutive items in a sequence and is likely to be involved in all of the aforementioned cognitive processes. Demonstrating a contribution of Broca's area to chunking during the learning of a nonmotor sequence that does not involve language could shed new light on its function. To address this issue, we used offline MRI-guided TMS in healthy volunteers to disrupt the activity of either the posterior part of Broca's area (left Brodmann's area [BA] 44) or a control site just before participants learned a perceptual sequence structured in distinct hierarchical levels. We found that disruption of the left BA 44 increased the processing time of stimuli representing the boundaries of higher-order chunks and modified the chunking strategy. The current results highlight the possible role of the left BA 44 in building up effector-independent representations of higher-order events in structured sequences. This might clarify the contribution of Broca's area in processing hierarchical structures, a key mechanism in many cognitive functions, such as language and composite actions. PMID:26765778

  16. Two-Stage orders sequencing system for mixed-model assembly

    NASA Astrophysics Data System (ADS)

    Zemczak, M.; Skolud, B.; Krenczyk, D.

    2015-11-01

    In the paper, the authors focus on the NP-hard problem of orders sequencing, formulated similarly to Car Sequencing Problem (CSP). The object of the research is the assembly line in an automotive industry company, on which few different models of products, each in a certain number of versions, are assembled on the shared resources, set in a line. Such production type is usually determined as a mixed-model production, and arose from the necessity of manufacturing customized products on the basis of very specific orders from single clients. The producers are nowadays obliged to provide each client the possibility to determine a huge amount of the features of the product they are willing to buy, as the competition in the automotive market is large. Due to the previously mentioned nature of the problem (NP-hard), in the given time period only satisfactory solutions are sought, as the optimal solution method has not yet been found. Most of the researchers that implemented inaccurate methods (e.g. evolutionary algorithms) to solving sequencing problems dropped the research after testing phase, as they were not able to obtain reproducible results, and met problems while determining the quality of the received solutions. Therefore a new approach to solving the problem, presented in this paper as a sequencing system is being developed. The sequencing system consists of a set of determined rules, implemented into computer environment. The system itself works in two stages. First of them is connected with the determination of a place in the storage buffer to which certain production orders should be sent. In the second stage of functioning, precise sets of sequences are determined and evaluated for certain parts of the storage buffer under certain criteria.

  17. Some mice feature 5th pharyngeal arch arteries and double-lumen aortic arch malformations.

    PubMed

    Geyer, Stefan H; Weninger, Wolfgang J

    2012-01-01

    A 5th pair of pharyngeal arch arteries (PAAs) has never been identified with certainty in mice. Murines in general are considered to not develop a 5th pair. If true, the significance of the mouse as a model for researching the genesis of malformations of the great intrathoracic arteries is limited. We aimed to investigate whether mouse embryos develop a 5th pair of PAAs and to identify malformations known to be caused by defective remodelling of the 5th PAAs. We employed the high-resolution episcopic microscopy method for creating digital volume data and three-dimensional (3D) computer models of the great intrathoracic arteries of 30 mouse embryos from days 12-12.5 post conception and 180 mouse fetuses from days 14.5 and 15.5 post conception. The 3D models of the fetuses were screened for the presence of a double-lumen aortic arch malformation. We identified such a malformation in 1 fetus. The 3D models of the embryos were analysed for the presence of 5th PAAs. Six of the 30 embryos (20%) showed a 5th PAA bilaterally, and an additional 9 (30%) showed a 5th PAA unilaterally. Our results prove that some mice do develop a 5th pair of PAAs. They also show that malformations which occur rarely in humans and result from defective remodelling of the left 5th PAA can be identified in mice as well. Thus, the mouse does represent an excellent model for researching the mechanisms driving PAA remodelling and the genesis of malformations of the great intrathoracic arteries. PMID:22287557

  18. How is the serial order of a spatial sequence represented? Insights from transposition latencies.

    PubMed

    Hurlstone, Mark J; Hitch, Graham J

    2015-03-01

    How is the serial order of a spatial sequence represented in short-term memory (STM)? Previous research by Farrell and Lewandowsky (Farrell & Lewandowsky, 2004; Lewandowsky & Farrell, 2008) has shown that 5 alternative mechanisms for the representation of serial order can be distinguished on the basis of their predictions concerning the response times accompanying transposition errors. We report 3 experiments involving the output-timed serial recall of sequences of seen spatial locations that tested these predictions. The results of all 3 experiments revealed that transposition latencies are a negative function of transposition displacement, but with a reduction in the slope of the function for postponement, compared with anticipation errors. This empirical pattern is consistent with that observed in serial recall of verbal sequences reported by Farrell and Lewandowsky (2004), and with the predictions of a competitive queuing mechanism, within which serial order is represented via a primacy gradient of activations over items combined with associations between items and positional markers, and with suppression of items following recall. The results provide the first clear evidence that spatial and verbal STM rely on some common mechanisms and principles for the representation of serial order. PMID:25436478

  19. Work Values of 5th, 8th, and 11th Grade Students

    ERIC Educational Resources Information Center

    Hales, Loyde W.; Fenner, Bradford

    1972-01-01

    Self Realization, Job Security, Money, and Altruism were found to be the most important work values, with 5th and 8th grade students differing from 11th grade students on Altruism and Self Realization. (Author)

  20. 25. April 5th one month's work. View looking north. Storehouse ...

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

    25. April 5th one month's work. View looking north. Storehouse #1 under construction, storehouse #2 site work in progress toward foreground. - U.S. Navy Fleet Supply Base, Storehouse No. 1, 830 Third Avenue, Brooklyn, Kings County, NY

  1. 17. 4th floor roof, view south, 4th and 5th floor ...

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

    17. 4th floor roof, view south, 4th and 5th floor setback to left and atrium structure to right - Sheffield Farms Milk Plant, 1075 Webster Avenue (southwest corner of 166th Street), Bronx, Bronx County, NY

  2. 6. 5TH FLOOR, VIEW NORTH OF KETTLE SOAP STORAGE TANKS ...

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

    6. 5TH FLOOR, VIEW NORTH OF KETTLE SOAP STORAGE TANKS (RIGHT) AND WEIGH HOPPERS OVER SITES OF REMOVED AMALGAMATORS (LEFT) - Colgate & Company Jersey City Plant, Building No. B-14, 54-58 Grand Street, Jersey City, Hudson County, NJ

  3. Numerical Fluid Dynamics Symposium, 5th, Tokyo, Japan, Dec. 19-21, 1991, Proceedings

    NASA Astrophysics Data System (ADS)

    1991-07-01

    Various papers on numerical fluid dynamics are presented. Individual topics discussed include: numerical analysis (NA) of shock structure problems, CFD development and a future high-speed computer, simulating vortex motion by 3D method, application of CFD to turbomachine design, numerical simulation (NS) of converging shock waves, NS of unsteady 3D shock wave phenomenon, 5th-order accurate compact upwind scheme, development of a multidimensional upwind scheme, fortified solution algorithm, large-eddy simulation of a bound jet, construction of collision model of diatomic molecules, VSL analysis of nonequilibrium flows around a hypersonic body, NA of chemically nonequilibrium flow, topological transition of flow past some axisymmetric bodies, modeling of scalar transport in free turbulence, a contribution to general application of the vortex method. Also addressed are: vortex simulation of artificial control of mixing layers, 3D motion of vortex filaments, Navier-Stokes simulation of 2D mixing layer, active control of vortex shedding frequency by a jet, direct NS of homogeneous turbulent sheer flow, NA of fuel spray jet by Eulerian method, NS of ignition using a premixed pulsed jet, NS of a scram jet combustor flow, numerical simulation of supersonic flow CO chemical laser, adaptive grid generation using optimal control theory, NS of characteristics of the Stalker tube, imcompressible flow solver using velocity vector and a new variable, unsteady analysis of helicopter rotor.

  4. Complete Chloroplast Genome Sequence of Aquilaria sinensis (Lour.) Gilg and Evolution Analysis within the Malvales Order

    PubMed Central

    Wang, Ying; Zhan, Di-Feng; Jia, Xian; Mei, Wen-Li; Dai, Hao-Fu; Chen, Xiong-Ting; Peng, Shi-Qing

    2016-01-01

    Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal

  5. Application of population sequencing (POPSEQ) for ordering and inputting genotyping-by-sequencing markers in hexaploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advancement of next-generation sequencing technologies in conjunction with new bioinformatics tools enabled fine-tuning of sequence-based high resolution mapping strategies for complex genomes. Although genotyping-by-sequencing (GBS) provides a large number of markers, its application for assoc...

  6. Implicit Sequence Learning in Dyslexia: A Within-Sequence Comparison of First- and Higher-Order Information

    ERIC Educational Resources Information Center

    Du, Wenchong; Kelly, Steve W.

    2013-01-01

    The present study examines implicit sequence learning in adult dyslexics with a focus on comparing sequence transitions with different statistical complexities. Learning of a 12-item deterministic sequence was assessed in 12 dyslexic and 12 non-dyslexic university students. Both groups showed equivalent standard reaction time increments when the…

  7. Dynamic evolution of telomeric sequences in the green algal order Chlamydomonadales.

    PubMed

    Fulnečková, Jana; Hasíková, Tereza; Fajkus, Jiří; Lukešová, Alena; Eliáš, Marek; Sýkorová, Eva

    2012-01-01

    Telomeres, which form the protective ends of eukaryotic chromosomes, are a ubiquitous and conserved structure of eukaryotic genomes but the basic structural unit of most telomeres, a repeated minisatellite motif with the general consensus sequence T(n)A(m)G(o), may vary between eukaryotic groups. Previous studies on several species of green algae revealed that this group exhibits at least two types of telomeric sequences, a presumably ancestral type shared with land plants (Arabidopsis type, TTTAGGG) and conserved in, for example, Ostreococcus and Chlorella species, and a novel type (Chlamydomonas type, TTTTAGGG) identified in Chlamydomonas reinhardtii. We have employed several methodical approaches to survey the diversity of telomeric sequences in a phylogenetically wide array of green algal species, focusing on the order Chlamydomonadales. Our results support the view that the Arabidopsis-type telomeric sequence is ancestral for green algae and has been conserved in most lineages, including Mamiellophyceae, Chlorodendrophyceae, Trebouxiophyceae, Sphaeropleales, and most Chlamydomonadales. However, within the Chlamydomonadales, at least two independent evolutionary changes to the Chlamydomonas type occurred, specifically in a subgroup of the Reinhardtinia clade (including C. reinhardtii and Volvox carteri) and in the Chloromonadinia clade. Furthermore, a complex structure of telomeric repeats, including a mix of the ancestral Arabidopsis-type motifs and derived motifs identical to the human-type telomeric repeats (TTAGGG), was found in the chlamydomonadalean clades Dunaliellinia and Stephanosphaeria. Our results indicate that telomere evolution in green algae, particularly in the order Chlamydomonadales, is far more dynamic and complex than thought before. General implications of our findings for the mode of telomere evolution are discussed. PMID:22247428

  8. EDITORIAL: 'Best article' prize for the 5th anniversary of Environmental Research Letters 'Best article' prize for the 5th anniversary of Environmental Research Letters

    NASA Astrophysics Data System (ADS)

    Kammen, Dan; Wright, Guillaume

    2011-12-01

    To celebrate the 5th anniversary of Environmental Research Letters (ERL) the publishers of the journal, IOP Publishing, have awarded a prize for the five best articles published in ERL since the journal began in 2006. The procedure for deciding the winning articles was as thorough as possible to ensure that the most outstanding articles would win the prize. A shortlist of 25 nominated research articles, five for each year since ERL was launched, which were chosen based on a range of criteria including novelty, scientific impact, readership, broad appeal and wider media coverage, was selected. The ERL Editorial Board then assessed and rated these 25 articles in order to choose a winning article for each year. We would like to announce that the following articles have been awarded ERL's 5th anniversary best article prize: 2006/7 The Bodélé depression: a single spot in the Sahara that provides most of the mineral dust to the Amazon forest Ilan Koren, Yoram J Kaufman, Richard Washington, Martin C Todd, Yinon Rudich, J Vanderlei Martins and Daniel Rosenfeld 2006 Environ. Res. Lett. 1 014005 2008 Causes and impacts of the 2005 Amazon drought Ning Zeng, Jin-Ho Yoon, Jose A Marengo, Ajit Subramaniam, Carlos A Nobre, Annarita Mariotti and J David Neelin 2008 Environ. Res. Lett. 3 014002 2009 How difficult is it to recover from dangerous levels of global warming? J A Lowe, C Huntingford, S C B Raper, C D Jones, S K Liddicoat and L K Gohar 2009 Environ. Res. Lett. 4 014012 2010 Is physical water scarcity a new phenomenon? Global assessment of water shortage over the last two millennia Matti Kummu, Philip J Ward, Hans de Moel and Olli Varis 2010 Environ. Res. Lett. 5 034006 2011 Implications of urban structure on carbon consumption in metropolitan areas Jukka Heinonen and Seppo Junnila 2011 Environ. Res. Lett. 6 014018 Our congratulations go to these authors. In recognition of their outstanding work, we are delighted to offer all of the authors of the winning articles free

  9. EDITORIAL: 'Best article' prize for the 5th anniversary of Environmental Research Letters 'Best article' prize for the 5th anniversary of Environmental Research Letters

    NASA Astrophysics Data System (ADS)

    Kammen, Dan; Wright, Guillaume

    2011-12-01

    To celebrate the 5th anniversary of Environmental Research Letters (ERL) the publishers of the journal, IOP Publishing, have awarded a prize for the five best articles published in ERL since the journal began in 2006. The procedure for deciding the winning articles was as thorough as possible to ensure that the most outstanding articles would win the prize. A shortlist of 25 nominated research articles, five for each year since ERL was launched, which were chosen based on a range of criteria including novelty, scientific impact, readership, broad appeal and wider media coverage, was selected. The ERL Editorial Board then assessed and rated these 25 articles in order to choose a winning article for each year. We would like to announce that the following articles have been awarded ERL's 5th anniversary best article prize: 2006/7 The Bodélé depression: a single spot in the Sahara that provides most of the mineral dust to the Amazon forest Ilan Koren, Yoram J Kaufman, Richard Washington, Martin C Todd, Yinon Rudich, J Vanderlei Martins and Daniel Rosenfeld 2006 Environ. Res. Lett. 1 014005 2008 Causes and impacts of the 2005 Amazon drought Ning Zeng, Jin-Ho Yoon, Jose A Marengo, Ajit Subramaniam, Carlos A Nobre, Annarita Mariotti and J David Neelin 2008 Environ. Res. Lett. 3 014002 2009 How difficult is it to recover from dangerous levels of global warming? J A Lowe, C Huntingford, S C B Raper, C D Jones, S K Liddicoat and L K Gohar 2009 Environ. Res. Lett. 4 014012 2010 Is physical water scarcity a new phenomenon? Global assessment of water shortage over the last two millennia Matti Kummu, Philip J Ward, Hans de Moel and Olli Varis 2010 Environ. Res. Lett. 5 034006 2011 Implications of urban structure on carbon consumption in metropolitan areas Jukka Heinonen and Seppo Junnila 2011 Environ. Res. Lett. 6 014018 Our congratulations go to these authors. In recognition of their outstanding work, we are delighted to offer all of the authors of the winning articles free

  10. The Effect of Interference on Temporal Order Memory for Random and Fixed Sequences in Nondemented Older Adults

    ERIC Educational Resources Information Center

    Tolentino, Jerlyn C.; Pirogovsky, Eva; Luu, Trinh; Toner, Chelsea K.; Gilbert, Paul E.

    2012-01-01

    Two experiments tested the effect of temporal interference on order memory for fixed and random sequences in young adults and nondemented older adults. The results demonstrate that temporal order memory for fixed and random sequences is impaired in nondemented older adults, particularly when temporal interference is high. However, temporal order…

  11. Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences.

    PubMed

    Ishiwata, Keisuke; Sasaki, Go; Ogawa, Jiro; Miyata, Takashi; Su, Zhi-Hui

    2011-02-01

    Many attempts to resolve the phylogenetic relationships of higher groups of insects have been made based on both morphological and molecular evidence; nonetheless, most of the interordinal relationships of insects remain unclear or are controversial. As a new approach, in this study we sequenced three nuclear genes encoding the catalytic subunit of DNA polymerase delta and the two largest subunits of RNA polymerase II from all insect orders. The predicted amino acid sequences (In total, approx. 3500 amino acid sites) of these proteins were subjected to phylogenetic analyses based on the maximum likelihood and Bayesian analysis methods with various models. The resulting trees strongly support the monophyly of Palaeoptera, Neoptera, Polyneoptera, and Holometabola, while within Polyneoptera, the groupings of Isoptera/"Blattaria"/Mantodea (Superorder Dictyoptera), Dictyoptera/Zoraptera, Dermaptera/Plecoptera, Mantophasmatodea/Grylloblattodea, and Embioptera/Phasmatodea are supported. Although Paraneoptera is not supported as a monophyletic group, the grouping of Phthiraptera/Psocoptera is robustly supported. The interordinal relationships within Holometabola are well resolved and strongly supported that the order Hymenoptera is the sister lineage to all other holometabolous insects. The other orders of Holometabola are separated into two large groups, and the interordinal relationships of each group are (((Siphonaptera, Mecoptera), Diptera), (Trichoptera, Lepidoptera)) and ((Coleoptera, Strepsiptera), (Neuroptera, Raphidioptera, Megaloptera)). The sister relationship between Strepsiptera and Diptera are significantly rejected by all the statistical tests (AU, KH and wSH), while the affinity between Hymenoptera and Mecopterida are significantly rejected only by AU and KH tests. Our results show that the use of amino acid sequences of these three nuclear genes is an effective approach for resolving the relationships of higher groups of insects. PMID:21075208

  12. A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly.

    PubMed

    Stafuzza, N B; Naressi, B C M; Yang, E; Cai, J J; Amaral-Trusty, M E J

    2015-01-01

    River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. The new framework RH map of BBU1 contained 141 markers (55 genes, 2 ESTs, 10 microsatellites, and 74 SNPs) distributed within one linkage group spanning 2832.62 centirays. Comparison of the RH map to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation. PMID:26535622

  13. Development of a Three-Dimensional Finite Element Chest Model for the 5(th) Percentile Female.

    PubMed

    Kimpara, Hideyuki; Lee, Jong B; Yang, King H; King, Albert I; Iwamoto, Masami; Watanabe, Isao; Miki, Kazuo

    2005-11-01

    Several three-dimensional (3D) finite element (FE) models of the human body have been developed to elucidate injury mechanisms due to automotive crashes. However, these models are mainly focused on 50(th) percentile male. As a first step towards a better understanding of injury biomechanics in the small female, a 3D FE model of a 5(th) percentile female human chest (FEM-5F) has been developed and validated against experimental data obtained from two sets of frontal impact, one set of lateral impact, two sets of oblique impact and a series of ballistic impacts. Two previous FE models, a small female Total HUman Model for Safety (THUMS-AF05) occupant version 1.0Beta (Kimpara et al. 2002) and the Wayne State University Human Thoracic Model (WSUHTM, Wang 1995 and Shah et al. 2001) were integrated and modified for this model development. The model incorporated not only geometrical gender differences, such as location of the internal organs and structure of the bony skeleton, but also the biomechanical differences of the ribs due to gender. It includes a detailed description of the sternum, ribs, costal cartilage, thoracic spine, skin, superficial muscles, intercostal muscles, heart, lung, diaphragm, major blood vessels and simplified abdominal internal organs and has been validated against a series of six cadaveric experiments on the small female reported by Nahum et al. (1970), Kroell et al. (1974), Viano (1989), Talantikite et al. (1998) and Wilhelm (2003). Results predicted by the model were well-matched to these experimental data for a range of impact speeds and impactor masses. More research is needed in order to increase the accuracy of predicting rib fractures so that the mechanisms responsible for small female injury can be more clearly defined. PMID:17096277

  14. Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing

    PubMed Central

    Vandewalle, Kristof; Festjens, Nele; Plets, Evelyn; Vuylsteke, Marnik; Saeys, Yvan; Callewaert, Nico

    2015-01-01

    Reverse genetics research approaches require the availability of methods to rapidly generate specific mutants. Alternatively, where these methods are lacking, the construction of pre-characterized libraries of mutants can be extremely valuable. However, this can be complex, expensive and time consuming. Here, we describe a robust, easy to implement parallel sequencing-based method (Cartesian Pooling-Coordinate Sequencing or CP-CSeq) that reports both on the identity as well as on the location of sequence-tagged biological entities in well-plate archived clone collections. We demonstrate this approach using a transposon insertion mutant library of the Mycobacterium bovis BCG vaccine strain, providing the largest resource of mutants in any strain of the M. tuberculosis complex. The method is applicable to any entity for which sequence-tagged identification is possible. PMID:25960123

  15. Reflecting on the 5th World Environmental Education Congress, Montreal, 2009

    ERIC Educational Resources Information Center

    Jickling, Bob

    2010-01-01

    This article traces the development of the World Environmental Congress movement and its establishment as an important international forum. Reflecting on the 5th Congress, it notes the particular contribution of the Congress theme, "Our Common Home". Finally, it considers environmental education's place alongside other parallel transformative…

  16. 75 FR 63478 - 5th Annual PHEMCE Stakeholders Workshop and BARDA Industry Day

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-15

    ...The Department of Health and Human Services (HHS) is pleased to announce the upcoming 5th Annual Public Health Emergency Medical Countermeasures Enterprise (PHEMCE) Stakeholders Workshop and BARDA Industry Day to be held January 10-12, 2011 at the Walter E. Washington Convention Center in Washington, DC. This annual PHEMCE event will bring together private- and public-sector stakeholders......

  17. A Network Sets Things in Motion: TEDD Celebrates its 5(th) Anniversary.

    PubMed

    2015-01-01

    At the Annual Meeting at ZHAW Waedenswil on 22 October 2015, the TEDD-Network (Tissue Engineering for Drug Development and Substance Testing) celebrated its 5(th) anniversary. Since its foundation, TEDD has become an internationally renowned competence centre and includes currently 91 members from academia and industry. They cover the entire development and value chain. PMID:26671055

  18. Urban 5th Graders Conceptions during a Place-Based Inquiry Unit on Watersheds

    ERIC Educational Resources Information Center

    Endreny, Anna Henderson

    2010-01-01

    This study aimed to determine how 33 urban 5th grade students' science conceptions changed during a place-based inquiry unit on watersheds. Research on watershed and place-based education was used as a framework to guide the teaching of the unit as well as the research study. A teacher-researcher designed the curriculum, taught the unit and…

  19. The 5th World Environmental Education Congress, 2009: A Research Project

    ERIC Educational Resources Information Center

    Jickling, Bob; Sauve, Lucie; Briere, Laurence; Niblett, Blair; Root, Emily

    2010-01-01

    This paper contextualizes the 5th World Environmental Education Congress, discusses the theoretical underpinnings of the Congress theme "Earth Our Common Home," and relates this theorizing to the research project that was woven through the Congress. We provide a rationale for engaging in this research project, as an invitation for Congress…

  20. 10. Interior view, working house, scale floor (5th level). View ...

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

    10. Interior view, working house, scale floor (5th level). View facing across floor toward no. 2 scale and garner. Tile structure at left center is weighmaster's shack; view facing east. - Saint Anthony Elevator No. 3, 620 Malcom Avenue, Southeast, Minneapolis, Hennepin County, MN

  1. An Investigation of Science and Technology Teachers' Views on the 5th Grade Science Course

    ERIC Educational Resources Information Center

    Dasdemir, Ikramettin

    2014-01-01

    This study was conducted to explore the science and technology teachers' views on the implementation of 5th grade science course. Open-ended questions were used as a data collection tool. The study sample consisted of 28 science and technology teachers working in Erzurum in 2012-2013 education year. The data gathered were analysed via content…

  2. Vocabulary and Syntactic Knowledge Factors in 5th Grade Students' Reading Comprehension

    ERIC Educational Resources Information Center

    Mokhtari, Kouider; Niederhauser, Dale S.

    2013-01-01

    In this study, we examined 5th grade students' levels of vocabulary knowledge and syntactic awareness relative to their reading comprehension performance. The aim was to explore the contributions of vocabulary and syntactic awareness as potential sources of reading comprehension difficulty for these readers. Overall, we found that both vocabulary…

  3. 78 FR 53454 - Filing Dates for the Louisiana Special Elections in the 5th Congressional District

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-29

    ... From the Federal Register Online via the Government Publishing Office FEDERAL ELECTION COMMISSION Filing Dates for the Louisiana Special Elections in the 5th Congressional District AGENCY: Federal Election Commission. ACTION: Notice of filing dates for special election. SUMMARY: Louisiana has...

  4. The 5th edition of the Roma-BZCAT. A short presentation

    NASA Astrophysics Data System (ADS)

    Massaro, E.; Maselli, A.; Leto, C.; Marchegiani, P.; Perri, M.; Giommi, P.; Piranomonte, S.

    2015-05-01

    The 5th edition of the Roma-BZCAT Multifrequency Catalogue of Blazars is available in a printed version and online at the ASDC website (http://www.asdc.asi.it/bzcat); it is also in the NED database. It presents several relevant changes with respect to the past editions which are briefly described in this paper.

  5. A Longitudinal Study of a 5th Grade Science Curriculum Based on the 5E Model

    ERIC Educational Resources Information Center

    Scott, Timothy P.; Schroeder, Carolyn; Tolson, Homer; Huang, Tse-Yang; Williams, Omah M.

    2014-01-01

    The Center for Mathematics and Science Education at Texas A&M University contracted with Region 4 Education Service Center (ESC) and a large, diverse school district to conduct a longitudinal study from 2005-2009. The state achievement test scores of 5th graders who were taught using a Grade 5 science textbook designed by Region 4 ESC were…

  6. Socially, Developmentally, and Academically Appropriate Prevention Curriculum for 5th Graders

    ERIC Educational Resources Information Center

    Harthun, Mary L.; Dustman, Patricia A.; Reeves, Leslie J.; Marsiglia, Flavio F.; Hecht, Michael L.

    2009-01-01

    This paper reports on a process in which program designers, classroom teachers, and students worked together to adapt the 7th grade "keepin' it REAL" prevention curriculum to a developmentally, socially, and academically appropriate curriculum for 5th graders. A Community-Based Participatory Research methodology (CBPR), combined with a 9-step…

  7. 9. 5TH FLOOR, INTERIOR DETAIL TO EAST OF SOAP BIN ...

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

    9. 5TH FLOOR, INTERIOR DETAIL TO EAST OF SOAP BIN No. 4: UPPER SCREWS MOVED SOAP CHIPS HORIZONTALLY FROM BIN TO BIN; LOWER LEFT-AND RIGHT-HAND SCREWS MOVED CHIPS TO CHUTE LEADING TO 3RD FLOOR SOAP MILLS - Colgate & Company Jersey City Plant, Building No. B-14, 54-58 Grand Street, Jersey City, Hudson County, NJ

  8. How Arizona Compares: Real Numbers and Hot Topics. Policy Choices. 5th Edition

    ERIC Educational Resources Information Center

    Morrison Institute for Public Policy, 2005

    2005-01-01

    Morrison Institute for Public Policy is pleased to present "How Arizona Compares: Real Numbers and Hot Topics," the 5th edition of Arizona "Policy Choices." The Arizona "Policy Choices" volumes seek to do more than report. They are designed to assist decision making, stimulate debate, and serve as references. Arizona "Policy Choices" volumes have…

  9. The Effect of Progressive Sentence Development Activities on 5th Graders' Description Skills

    ERIC Educational Resources Information Center

    Hamzadayi, Ergun

    2015-01-01

    The aim of this study was to examine the effect of progressive sentence development activities on 5th graders' description skills. The study was conducted based on the pretest-posttest quasi-experimental model with a control group. A total of 58 students participated in the study; 29 in the control group, and 29 in the experimental group. The…

  10. Successfully Promoting 21st Century Online Research Skills: Interventions in 5th-Grade Classrooms

    ERIC Educational Resources Information Center

    Kingsley, Tara L.; Cassady, Jerrell C.; Tancock, Susan M.

    2015-01-01

    This quantitative study was developed to explore the ability to impact elementary student 21st Century online research skills with a planned classroom intervention curriculum. The repeated measures quasi-experimental study randomly assigned all 5th grade classes in a Midwestern, suburban school (n = 418) to a 12-week intervention or control…

  11. Effects of temperature and modified atmospheres on diapausing 5th instar codling moth metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diapausing 5th instars of codling moth, Cydia pomonella, are serious quarantine pests of in-shell walnuts. Previous research indicates that heat treatments in combination with high concentrations of carbon dioxide and low concentrations of oxygen may be effective for controlling this pest in walnuts...

  12. Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data.

    PubMed

    Di, Yanming; Emerson, Sarah C; Schafer, Daniel W; Kimbrel, Jeffrey A; Chang, Jeff H

    2013-03-01

    RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and quantifying gene expression changes. This next generation sequencing-based method provides unprecedented depth and resolution. The negative binomial (NB) probability distribution has been shown to be a useful model for frequencies of mapped RNA-Seq reads and consequently provides a basis for statistical analysis of gene expression. Negative binomial exact tests are available for two-group comparisons but do not extend to negative binomial regression analysis, which is important for examining gene expression as a function of explanatory variables and for adjusted group comparisons accounting for other factors. We address the adequacy of available large-sample tests for the small sample sizes typically available from RNA-Seq studies and consider a higher-order asymptotic (HOA) adjustment to likelihood ratio tests. We demonstrate that 1) the HOA-adjusted likelihood ratio test is practically indistinguishable from the exact test in situations where the exact test is available, 2) the type I error of the HOA test matches the nominal specification in regression settings we examined via simulation, and 3) the power of the likelihood ratio test does not appear to be affected by the HOA adjustment. This work helps clarify the accuracy of the unadjusted likelihood ratio test and the degree of improvement available with the HOA adjustment. Furthermore, the HOA test may be preferable even when the exact test is available because it does not require ad hoc library size adjustments. PMID:23502340

  13. Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

    PubMed

    Meganathan, P R; Dubey, Bhawna; Batzer, Mark A; Ray, David A; Haque, Ikramul

    2011-06-01

    Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution. PMID:21310220

  14. Th unnatural order of things: A history of the high school science sequence

    NASA Astrophysics Data System (ADS)

    Robbins, Dennis M.

    Historical studies of US high school science education are rare. This study examines the historical origins of a unique characteristic of the secondary science curriculum, the Biology-Chemistry-Physics (B-C-P) order of courses. Statements from scientists, educators and the media claim that B-C-P has been the traditional curriculum sequence for over a century and can be traced back to the influential educational commission known as the Committee of Ten (CoT) of 1893. This study examines the history of the ordering of high school science subjects over the last 150 years. The reports and primary documents of important national educational commissions, such as the CoT, were searched for their recommendations on secondary science, particularly on course ordering. These recommendations were then compared to national, state and local statistical data on subject offerings and student enrollments to measure the effect of these national commissions on school policy. This study concludes that the Committee of Ten did not create B-P-C. The CoT made six recommendations, five placed Chemistry before Physics (P-C). One recommendation for C-P met with strong disagreement because it was thought an illogical order. Biology as a "uniform" course did not exist at this time and so the CoT made no recommendations for its grade placement. Statistical data shows that B-C-P evolved over many decades. From 1860 up to 1920 most schools used a P-C curriculum believing Physics was a foundational prerequisite of Chemistry. Biology was introduced in the early 1900s and it assumed a position before the physical sciences. Through the 1920s Chemistry and Physics were placed equally likely in 11th or 12 th grades and Biology was in the 10th grade. After World War II, B-C-P became the dominant pattern, exhibited in over 90% of schools. But up to this point in time no educational body or national commission had recommended B-C-P. The Biology-Chemistry-Physics order of courses is a product of many

  15. A Computer Program for Generating Sequences of Primary Arithmetic Facts in Random Order.

    ERIC Educational Resources Information Center

    Burns, Edward

    A computer program which generates randomly sequenced problems for testing the abilities of students to add, subtract, and multiply one-digit numbers is described. Appendices provide tables of random sequences with directions for using the tables. The 54-statement FORTRAN program which can be used in generating additional sequences is also…

  16. News from the "5th International Meeting on Inflammatory Bowel Diseases" CAPRI 2010.

    PubMed

    Latella, Giovanni; Fiocchi, Claudio; Caprili, Renzo

    2010-12-01

    At the "5th International Meeting on Inflammatory Bowel Diseases selected topics of inflammatory bowel disease (IBD), including the environment, genetics, the gut flora, the cell response and immunomodulation were discussed in order to better understand specific clinical and therapeutic aspects. The incidence of IBD continues to rise, both in low and in high-incidence areas. It is believed that factors associated with 'Westernization' may be conditioning the expression of these disorders. The increased incidence of IBD among migrants from low-incidence to high-incidence areas within the same generation suggests a strong environmental influence. The development of genome-wide association scanning (GWAS) technologies has lead to the discovery of more than 100 IBD loci. Some, as the Th 17 pathway genes, are shared between Crohn's disease (CD) and ulcerative colitis (UC), while other are IBD subtype-specific (autophagy genes, epithelial barrier genes). Disease-specific therapies targeting these pathways should be developed. Epigenetic regulation of the inflammatory response also appears to play an important role in the pathogenesis of IBD. The importance of gut flora in intestinal homeostasis and inflammation was reinforced, the concepts of eubiosis and dysbiosis were introduced, and some strategies for reverting dysbiosis to a homeostatic state of eubiosis were proposed. The current status of studies on the human gut microbiota metagenome, metaprotome, and metabolome was also presented. The cell response in inflammation, including endoplasmic reticulum (ER) stress responses, autophagy and inflammasome-dependent events were related to IBD pathogenesis. It was suggested that inflammation-associated ER stress responses may be a common trait in the pathogenesis of various chronic immune and metabolic diseases. How innate and adaptive immunity signaling events can perpetuate chronic inflammation was discussed extensively. Signal transduction pathways provide intracellular

  17. VizieR Online Data Catalog: The Roma BZCAT - 5th edition (Massaro+, 2015)

    NASA Astrophysics Data System (ADS)

    Massaro, E.; Giommi, P.; Leto, C.; Marchegiani, P.; Maselli, A.; Perri, M.; Piranomonte, S.; Sclavi, S.

    2016-02-01

    In the 5th Edition we use similar denomination of blazars adopted in the previous editions. Each blazar is identified by a code, with 5BZ for all blazars, a fourth letter that specifies the type (B, G, Q or U), followed by the truncated equatorial coordinates (J2000). We introduced the edition number before the letters BZ to avoid possible confusion due to the fact that several sources changed their old names because of the new adopted classification. The codes are defined in the "Note (G1)" below. The 5th edition contains 1151 BZB sources, 92 of which are reported as candidates because we could not find their optical spectra in the literature, 1909 BZQ sources, 274 BZG sources and 227 BZU objects (1 data file).

  18. An 8 x 10 to the 5th bit bubble memory cell for spacecraft applications

    NASA Technical Reports Server (NTRS)

    Becker, F. J.; Murray, G. W.; Bohning, O. D.; Stermer, R. L.

    1980-01-01

    A multiple chip magnetic bubble memory cell design developed for NASA embodies the low power, low weight, environmental tolerance and reliability necessary for successful operation in spacecraft launch and mission environments. Packaging of multiple chips in a common magnetic bias, drive coil assembly reduces weight and volume overhead per chip and also reduces the number of coil drive components required. This 8 x 10 to the 5th bit cell is conduction cooled and provides a metal and ceramic sealed hermetic chip environment.

  19. Proceedings of the 5th International Symposium on Blue Laser and Light Emitting Diodes (ISBLLED-2004)

    NASA Astrophysics Data System (ADS)

    Suh, Eun-Kyung; Yoon, Euijoon; Lee, Hyung Jae

    2004-09-01

    The 5th International Symposium on Blue Laser and Light Emitting Diodes (ISBLLED-2004) was held in Gyeongju, Korea, 15-19 March 2004. The purpose of the symposium was to provide a forum for scientists and engineers to discuss recent progress and future trends in the rapidly advancing wide band gap semiconductor science and technologies and their applications in blue laser and light emitting diodes.

  20. Effects of the 5th and 7th Grade Enhanced Versions of the "keepin' it REAL" Substance Use Prevention Curriculum

    ERIC Educational Resources Information Center

    Elek, Elvira; Wagstaff, David A.; Hecht, Michael L.

    2010-01-01

    This study assessed the outcomes of adapting the culturally-grounded, middle school, substance-use prevention intervention, "keepin' it REAL" ("kiR"), to target elementary school students and to address acculturation. At the beginning of 5th grade, 29 schools were randomly assigned to conditions obtained by crossing grade of implementation (5th,…

  1. Measuring Listening Comprehension Skills of 5th Grade School Students with the Help of Web Based System

    ERIC Educational Resources Information Center

    Acat, M. Bahaddin; Demiral, Hilmi; Kaya, Mehmet Fatih

    2016-01-01

    The main purpose of this study is to measure listening comprehension skills of 5th grade school students with the help of web based system. This study was conducted on 5th grade students studying at the primary schools of Eskisehir. The scale used in the process of the study is "Web Based Listening Scale". In the process of the study,…

  2. The Effects of Reading from the Screen on the Reading Motivation Levels of Elementary 5th Graders

    ERIC Educational Resources Information Center

    Aydemir, Zeynep; Ozturk, Ergun

    2012-01-01

    This study aims to explore the effects of reading from the screen on elementary 5th grade students' reading motivation levels. It used the randomized control-group pretest-posttest model, which is a true experimental design. The study group consisted of 60 students, 30 experimental and 30 control, who were attending the 5th grade of a public…

  3. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC)...

  4. Preface to Special Topic: Selected Papers from the 5th International Conference on Optofluidics.

    PubMed

    Fan, Shih-Kang; Yang, Zhenchuan

    2016-01-01

    The 5th International Conference on Optofluidics (Optofluidics 2015) was held in Taipei, Taiwan, July 26-29, 2015. The aim of this conference was to provide a forum to promote scientific exchange and to foster closer networks and collaborative ties between leading international researchers in optics and micro/nanofluidics across various disciplines. The scope of Optofluidics 2015 was deliberately broad and interdisciplinary, encompassing the latest advances and the most innovative developments in micro/nanoscale science and technology. Topics ranged from fundamental research to its applications in chemistry, physics, biology, materials, and medicine. PMID:27076863

  5. Preface to Special Topic: Selected Papers from the 5th International Conference on Optofluidics

    PubMed Central

    Fan, Shih-Kang; Yang, Zhenchuan

    2016-01-01

    The 5th International Conference on Optofluidics (Optofluidics 2015) was held in Taipei, Taiwan, July 26–29, 2015. The aim of this conference was to provide a forum to promote scientific exchange and to foster closer networks and collaborative ties between leading international researchers in optics and micro/nanofluidics across various disciplines. The scope of Optofluidics 2015 was deliberately broad and interdisciplinary, encompassing the latest advances and the most innovative developments in micro/nanoscale science and technology. Topics ranged from fundamental research to its applications in chemistry, physics, biology, materials, and medicine. PMID:27076863

  6. A Social Medium: ASM's 5th Cell-Cell Communication in Bacteria Meeting in Review

    PubMed Central

    Federle, Michael J.

    2015-01-01

    The 5th American Society for Microbiology Conference on Cell-Cell Communication in Bacteria (CCCB-5), which convened from 18 to 21 October 2014 in San Antonio, TX, highlighted recent advances in our understanding of microbial intercellular signaling. While the CCCB meetings arose from interests in pheromone signaling and quorum sensing, it was evident at CCCB-5 that the cell-cell communication field is continuing to mature, expanding into new areas and integrating cutting-edge technologies. In this minireview, we recap some of the research discussed at CCCB-5 and the questions that have arisen from it. PMID:25917904

  7. PREFACE: The 5th International Conference on Radiotherapy Gel Dosimetry (DOSGEL 2008)

    NASA Astrophysics Data System (ADS)

    Maris, Thomas G.; Pappas, Evangelos

    2009-07-01

    The International Conference on Radiotherapy Gel Dosimetry (DOSGEL) is held every two years. Its purpose is to bring together basic science and clinical researchers, medical physicists and clinicians from around the world to discuss the state-of-the-art of the gel dosimetry technique and to set the directions and trends for its future improvements. Gel dosimetry can be broadly defined as using a gel that can react to the absorption of ionizing radiation, and that can retain this information which can subsequently be retrieved by an external imaging modality. Examples of radiation-sensitive gels include, but are not limited to, polymer gel dosimeters, Fricke gel dosimeters and others. Imaging modalities that are of general use in this field are (in alphabetical order) magnetic resonance imaging (MRI), optical light computed tomography and x-ray computed tomography. This volume comprises the proceedings of the 5th International Conference on Radiotherapy Gel Dosimetry (DOSGEL 2008). The conference, organised by the University of Crete, Medical Physics Department, took place in Hersonissos, Crete, Greece from 29 September to 3 October 2008. The meeting aimed to continue the series of biannual DOSGEL conferences and focused on the promotion of gel dosimetry techniques by setting the trends for their future improvements. The main scientific session topics of DOSGEL 2008 were the following: Chemistry and fundamental properties of polymer gel dosimeters Gel dosimetry with Optical Computed Tomography Gel dosimetry with Magnetic Resonance Imaging Gel dosimetry with other than Optical CT and MR scan Techniques Other 3D dosimeters Gel dosimetry applications Local Organizing Committee Thomas G Maris (University of Crete, Greece, Chairman DOSGEL 2008) John Damilakis (University of Crete, Greece) Evangelos Pappas (University of Crete, Greece) Antonios Papadakis (University of Crete, Greece) Fotini Zacharopoulou (University of Crete, Greece) John Stratakis (University of Crete

  8. Using Apatitic Conodont Oxygen Isotopic Values to Determine the Cause of Late Ordovician Third-Order Stratigraphic Sequences

    NASA Astrophysics Data System (ADS)

    Tyra, T. A.; Maya, E.; Atudorei, V.; Stephen, L. A.

    2007-12-01

    Recent work suggests a link between third-order (~1-5 Myr) sea-level fluctuations and climate change, even in greenhouse periods. Upper Ordovician third-order transgressive-regressive sequences are pervasive in the stratigraphic record, can be correlated worldwide (i.e. North America, Baltica, China), and ambiguous in cause. We are evaluating climate's role in third-order sea-level change by analyzing the δ18O of conodont apatite, which is a proxy for both glacio-eustasy and paleotemperature. Conodont phosphatic oxygen is a more robust repository of primary oxygen isotope values than more extensively-studied calcareous fossils, which have been extensively studied. If sea-level change is climatically-driven (glacio-eustasy and thermo-eustasy), δ18O values will decrease with sea-level rise and increase with sea-level fall. We report preliminary results from Upper Ordovician sequences in the Monitor Range of central Nevada. The six stratigraphic sequences (30m-95m thick) preserve basinal-to-outer-shelf carbonates with the youngest sequence representing the Hirnantian glaciation. We collected conodont samples at a 2-10m resolution and also determined bulk carbonate δ13C for additional chemostratigraphy. With this information, we hope to determine if glacio-eustasy has a role within the five pre-Hirnantian sequences.

  9. Systematically frameshifting by deletion of every 4th or 4th and 5th nucleotides during mitochondrial transcription: RNA self-hybridization regulates delRNA expression.

    PubMed

    Seligmann, Hervé

    2016-01-01

    In mitochondria, secondary structures punctuate post-transcriptional RNA processing. Recently described transcripts match the human mitogenome after systematic deletions of every 4th, respectively every 4th and 5th nucleotides, called delRNAs. Here I explore predicted stem-loop hairpin formation by delRNAs, and their associations with delRNA transcription and detected peptides matching their translation. Despite missing 25, respectively 40% of the nucleotides in the original sequence, del-transformed sequences form significantly more secondary structures than corresponding randomly shuffled sequences, indicating biological function, independently of, and in combination with, previously detected delRNA and thereof translated peptides. Self-hybridization decreases delRNA abundances, indicating downregulation. Systematic deletions of the human mitogenome reveal new, unsuspected coding and structural informations. PMID:27018206

  10. 5th Bionanotox and Applications International Research Conference, Peabody, Little Rock, Arkansas, USA

    NASA Astrophysics Data System (ADS)

    Sabb, Taneicie; Chowdhury, Parimal

    2011-06-01

    "BioNanoTox and Toxicity: using Technology to Advance Discovery" was this year's theme at the 5th BioNanoTox and Applications International Research Conference held at the Peabody Hotel, Little Rock, Arkansas on November 4-5th, 2010. This year, the international participation in this conference increased to 25 countries spanning the globe. The conference began with opening remarks by Paul Howard, Associate Director of the National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States. Two keynote speakers, Dr. Ananth V. Annapragada and Dr. Merle G. Paule presented lectures on "Toxicity of Novel Nanoparticles for CT imaging" and "The Biology of Neurotoxicity: using Technology to Advance Discovery", respectively. Teachers, students, faculty, and scientists presented oral and poster presentations on fundamental and translational research related to BioNanoTox and related fields of science. Six presentation sessions were held over the two-day conference. There were 31 presentations and 39 posters from disciplines ranging from biology to chemistry, toxicology, nanotechnology, computational sciences, mathematics, engineering, plant science, and biotechnology. Poster presentation awards were presented to three high school students, three high school teachers, and three college students. In addition to poster awards a memorial, travel, and BioNanoTox award were presented. This year's meeting paved the way for a more outstanding meeting for the future.

  11. Exploratory Factor Analysis of Diagnostic and Statistical Manual, 5th Edition, Criteria for Posttraumatic Stress Disorder.

    PubMed

    McSweeney, Lauren B; Koch, Ellen I; Saules, Karen K; Jefferson, Stephen

    2016-01-01

    One change to the posttraumatic stress disorder (PTSD) nomenclature highlighted in the Diagnostic and Statistical Manual, 5th Edition (DSM-5; American Psychiatric Association, 2013) is the conceptualization of PTSD as a diagnostic category with four distinct symptom clusters. This article presents exploratory factor analysis to test the structural validity of the DSM-5 conceptualization of PTSD via an online survey that included the PTSD Checklist-5. The study utilized a sample of 113 college students from a large Midwestern university and 177 Amazon Mechanical Turk users. Participants were primarily female, Caucasian, single, and heterosexual with an average age of 32 years. Approximately 30% to 35% of participants met diagnostic criteria for PTSD based on two different scoring criteria. Results of the exploratory factor analysis revealed five distinct symptom clusters. The implications for the classification of PTSD are discussed. PMID:26669983

  12. Dental health in antique population of Vinkovci - Cibalae in Croatia (3rd-5th century).

    PubMed

    Peko, Dunja; Vodanović, Marin

    2016-08-01

    Roman city Cibalae (Vinkovci) - the birthplace of Roman emperors Valentinian I and Valens was a very well developed urban ares in the late antique what was evidenced by numerous archaeological findings. The aim of this paper is to get insight in dental health of antique population of Cibalae. One hundred individuals with 2041 teeth dated to 3rd - 5th century AD have been analyzed for caries, antemortem tooth loss, periapical diseases and tooth wear. Prevalence of antemortem tooth loss was 4.3% in males, 5.2% in females. Prevalence of caries per tooth was 8.4% in males, 7.0% in females. Compared to other Croatian antique sites, ancient inhabitants of Roman Cibalae had rather good dental health with low caries prevalence and no gender differences. Statistically significant difference was found between males in females in the prevalence of periapical lesions and degree of tooth wear. Periapical lesions were found only in males. PMID:27598951

  13. Theoretical studies of Ir5Th and Ir5Ce nanoscale precipitates in Ir

    SciTech Connect

    Morris, James R; Averill, Frank; Cooper, Valentino R

    2014-01-01

    Experimentally, it is known that very small amounts of thorium and/or cerium added to iridium metal form a precipitate, Ir5Th / Ir5Ce, which improves the high temperature mechanical properties of the resulting alloys. We demonstrate that there are low-energy configurations for nano-scale precipitates of these phases in Ir, and that these coherent arrangements may assist in producing improved mechanical properties. One precipitate/matrix orientation gives a particularly low interfacial energy, and a low lattice misfit. Nanolayer precipitates with this orientation are found to be likely to form, with little driving force to coarsen. The predicted morphology of the precipitates and their orientation with the matrix phase provide a potential experiment that could be used to test these predictions.

  14. APTWG: The 5th Asia-Pacific Transport Working Group Meeting

    NASA Astrophysics Data System (ADS)

    Gao, X.; Ghim, Y.-C.; Sun, Y. W.; Gao, Z.; Inagaki, S.; Chen, W.; Zhang, T.; Wang, Z. X.

    2016-03-01

    This conference report gives a summary on the contributed papers and discussions presented at the 5th Asia-Pacific Transport Working Group Meeting held at Dalian, China from 9-12 June 2015. The main goal of the working group is to develop a predictive understanding of the basic mechanisms responsible for particle, momentum and energy transport in magnetically confined plasmas. The topics of the meeting in 2015 were organized under five main headings: (1) turbulence suppression and transport barrier formation, (2) effect of magnetic topology on MHD activity and transport, (3) non-diffusive contribution of momentum and particle transport, (4) non-local transport and turbulence spreading and coupling and (5) energetic particles and instability. The Young Researchers’ Forum which was held at this meeting is also described in this report.

  15. Recurrent Idiopathic Catatonia: Implications beyond the Diagnostic and Statistical Manual of Mental Disorders 5th Edition

    PubMed Central

    Caroff, Stanley N.; Hurford, Irene; Bleier, Henry R.; Gorton, Gregg E.; Campbell, E. Cabrina

    2015-01-01

    We describe a case of recurrent, life-threatening, catatonic stupor, without evidence of any associated medical, toxic or mental disorder. This case provides support for the inclusion of a separate category of “unspecified catatonia” in the Diagnostic and Statistical Manual of Mental Disorders 5th edition (DSM-5) to be used to classify idiopathic cases, which appears to be consistent with Kahlbaum’s concept of catatonia as a distinct disease state. But beyond the limited, cross-sectional, syndromal approach adopted in DSM-5, this case more importantly illustrates the prognostic and therapeutic significance of the longitudinal course of illness in differentiating cases of catatonia, which is better defined in the Wernicke-Kleist-Leonhard classification system. The importance of differentiating cases of catatonia is further supported by the efficacy of antipsychotics in treatment of this case, contrary to conventional guidelines. PMID:26243853

  16. Anomalous Diffusion Measured by a Twice-Refocused Spin Echo Pulse Sequence: Analysis Using Fractional Order Calculus

    PubMed Central

    2011-01-01

    Purpose To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. Materials and Methods The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2,600 s/mm2. For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β and μ values and the goodness-of-fit in three specific regions of interest (ROI) in white matter, gray matter, and cerebrospinal fluid were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. Results The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. Conclusion The diffusion-induced signal

  17. First- or second-order transition in the melting of repeat sequence DNA.

    PubMed Central

    Chen, Y Z; Prohofsky, E W

    1994-01-01

    Both theoretical analysis and observation of the continuity of the melted fraction of base pairs indicate that the melting transition in DNA is second order. Analysis of the salt dependence of the transition by polyelectrolyte limiting laws, however, has first-order dynamics imbedded in the analysis. This paper proposes that the observation taken to be a latent heat of melting in the limiting law analysis could instead be a specific heat anomaly associated with a second-order transition. The limiting laws can be reconstructed based on a second-order transition with a specific heat anomaly. The T2M dependence of this excess heat is also consistent with its being a specific heat anomaly of a system displaying classical critical behavior. Classical critical behavior indicates that theoretical mean field approaches such as MSPA should be particularly appropriate to helix melting studies. PMID:8130338

  18. LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

    PubMed

    Fontanesi, Luca; Di Palma, Federica; Flicek, Paul; Smith, Andrew T; Thulin, Carl-Gustaf; Alves, Paulo C

    2016-07-01

    The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration. PMID:26921276

  19. The complete genome sequence of a novel Fusarium graminearum RNA virus in a new proposed family within the order Tymovirales.

    PubMed

    Chen, Xiaoguang; He, Hao; Yang, Xiufen; Zeng, Hongmei; Qiu, Dewen; Guo, Lihua

    2016-10-01

    The complete nucleotide sequence of Fusarium graminearum deltaflexivirus 1 (FgDFV1), a novel positive single-stranded (+ss) RNA mycovirus, was sequenced and analyzed. The complete genome of FgDFV1/BJ59 was shown to be 8246 nucleotides (nt) long excluding the poly(A) tail. FgDFV1/BJ59 was predicted to contain a large open reading frame (ORF 1) and four smaller ORFs (2-5). ORF1 encodes a putative replication-associated polyprotein (RP) of 2042 amino acids (aa) and contains three conserved domains, viral RNA methyltransferase (Mtr), viral RNA helicase (Hel) and RNA-dependent RNA polymerase (RdRp). ORFs 2-5 encode four putative small hypothetical proteins (12-18 kDa) with unknown biological functions. Phylogenetic analysis based on RP sequences indicated that FgDFV1 is phylogenetically related to soybean leaf-associated mycoflexivirus 1 (SlaMyfV1) and Sclerotinia sclerotiorum deltaflexivirus 1 (SsDFV1), which form a well-supported and independent group belonging to a newly proposed family Deltaflexiviridae within the order Tymovirales. However, FgDFV1 is markedly different from SsDFV1 and SlaMyfV1 in genome organization and nucleotide sequence. FgDFV1 may represent an additional species in the new genus Deltaflexivirus or possibly a new genus in the proposed family Deltaflexiviridae. PMID:27376377

  20. The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE)

    SciTech Connect

    Karen S. Browning; Marie Petrocek; Bonnie Bartel

    2006-06-01

    The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE) will be held June 8-12, 2005 at the University of Texas at Austin. Exciting new and ongoing discoveries show significant regulation of gene expression occurs after transcription. These post-transcriptional control events in plants range from subtle regulation of transcribed genes and phosphorylation, to the processes of gene regulation through small RNAs. This meeting will focus on the regulatory role of RNA, from transcription, through translation and finally degradation. The cross-disciplinary design of this meeting is necessary to encourage interactions between researchers that have a common interest in post-transcriptional gene expression in plants. By bringing together a diverse group of plant molecular biologist and biochemists at all careers stages from across the world, this meeting will bring about more rapid progress in understanding how plant genomes work and how genes are finely regulated by post-transcriptional processes to ultimately regulate cells.

  1. Need for Specific Sugar-Sweetened Beverage Lessons for 4th and 5th Graders

    PubMed Central

    Bea, Jennifer W.; Jacobs, Laurel; Waits, Juanita; Hartz, Vern; Martinez, Stephanie H.; Standfast, Rebecca D.; Farrell, Vanessa A.; Bawden, Margine; Whitmer, Evelyn; Misner, Scottie

    2015-01-01

    Objective Consumption of sugar-sweetened beverages (SSB) is linked to obesity. We hypothesized that school-based nutrition education would decrease SSB consumption. Design Self-selected interventional cohort with random selection for pre and post measurements Setting Arizona SNAP-Ed eligible schools Participants Randomly selected (9%) 4th and 5th grade classroom students Intervention The University of Arizona Nutrition Network (UANN) provided general nutrition education training and materials to teachers, to be delivered to their students. The UANN administered behavioral questionnaires to students in both Fall and Spring. Main Outcome Measure(s) Change in SSB consumption Analyses Descriptive statistics were computed for student demographics and beverage consumption on the day prior to testing. Paired t-tests evaluated change in classroom averages. Linear regression assessed potential correlates of SSB consumption. Results Fall mean SSB consumption was 1.1 (±0.2) times; mean milk and water intake were 1.6 (±0.2) and 5.2 (±0.7) times, respectively. Beverage consumption increased (3.2%) in springtime, with increased SSBs (14.4%) accounting for the majority (p=0.006). Change in SSB consumption was negatively associated with baseline SSB and water consumption, but positively associated with baseline milk fat (p≤0.05). Conclusions and Implications The results suggest the need for beverage specific education to encourage children to consume more healthful beverages in warmer weather. PMID:25239840

  2. Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.

    PubMed

    Sakai, Sanae; Takaki, Yoshihiro; Shimamura, Shigeru; Sekine, Mitsuo; Tajima, Takahisa; Kosugi, Hiroki; Ichikawa, Natsuko; Tasumi, Eiji; Hiraki, Aiko T; Shimizu, Ai; Kato, Yumiko; Nishiko, Rika; Mori, Koji; Fujita, Nobuyuki; Imachi, Hiroyuki; Takai, Ken

    2011-01-01

    We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50), which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50) CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50), further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens. PMID:21829548

  3. Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales

    PubMed Central

    Sakai, Sanae; Takaki, Yoshihiro; Shimamura, Shigeru; Sekine, Mitsuo; Tajima, Takahisa; Kosugi, Hiroki; Ichikawa, Natsuko; Tasumi, Eiji; Hiraki, Aiko T.; Shimizu, Ai; Kato, Yumiko; Nishiko, Rika; Mori, Koji; Fujita, Nobuyuki; Imachi, Hiroyuki; Takai, Ken

    2011-01-01

    We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-IMRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-IMRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-IMRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens. PMID:21829548

  4. The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order.

    PubMed

    Fahrein, Kathrin; Masta, Susan E; Podsiadlowski, Lars

    2009-05-01

    Amblypygi (whip spiders) are terrestrial chelicerates inhabiting the subtropics and tropics. In morphological and rRNA-based phylogenetic analyses, Amblypygi cluster with Uropygi (whip scorpions) and Araneae (spiders) to form the taxon Tetrapulmonata, but there is controversy regarding the interrelationship of these three taxa. Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders. In the course of an ongoing project concerning arachnid mitochondrial genomics, we present the first two complete mitochondrial genomes from Amblypygi. Both genomes were found to be typical circular duplex DNA molecules with all 37 genes usually present in bilaterian mitochondrial genomes. In both species, gene order is identical to that of Limulus polyphemus (Xiphosura), which is assumed to reflect the putative arthropod ground pattern. All tRNA gene sequences have the potential to fold into structures that are typical of metazoan mitochondrial tRNAs, except for tRNA-Ala, which lacks the D arm in both amblypygids, suggesting the loss of this feature early in amblypygid evolution. Phylogenetic analysis resulted in weak support for Uropygi being the sister group of Amblypygi. PMID:19448726

  5. Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid development of next generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach fo...

  6. When should orthostatic blood pressure changes be evaluated in elderly: 1st, 3rd or 5th minute?

    PubMed

    Soysal, Pinar; Aydin, Ali Ekrem; Koc Okudur, Saadet; Isik, Ahmet Turan

    2016-01-01

    Detection of orthostatic hypotension (OH) is very important in geriatric practice, since OH is associated with mortality, ischemic stroke, falls, cognitive failure and depression. It was aimed to determine the most appropriate time for measuring blood pressure in transition from supine to upright position in order to diagnose OH in elderly. Comprehensive geriatric assessment (CGA) including Head up Tilt Table (HUT) test was performed in 407 geriatric patients. Orthostatic changes were assessed separately for the 1st, 3rd and 5th minutes (HUT1, HUT3 and HUT5, respectively) taking the data in supine position as the basis. The mean age, recurrent falls, presence of dementia and Parkinson's disease, number of drugs, alpha-blocker and anti-dementia drug use, and fasting blood glucose levels were significantly higher in the patients with versus without OH; whereas, albumin and 25-hydroxy vitamin D levels were significantly lower (p<0.05). However, different from HUT3 and HUT5, Charlson Comorbidity Index and the prevalence of diabetes mellitus were higher, the use of antidiabetics, antipsychotics, benzodiazepine, opioid and levodopa were more common (p<0.05). Statistical significance of the number of drugs and fasting blood glucose level was prominent in HUT1 as compared to HUT3 (p<0.01, p<0.05). Comparison of the patients that had OH only in HUT1, HUT3or HUT5 revealed no difference in terms of CGA parameters. These results suggests that orthostatic blood pressure changes determined at the 1st minute might be more important for geriatric practice. Moreover, 1st minute measurement might be more convenient in the elderly as it requires shorter time in practice. PMID:27077324

  7. 5th International conference on Physics and Astrophysics of Quark Gluon Plasma

    NASA Astrophysics Data System (ADS)

    Sinha, Bikash; Alam, Jan-E.; Nayak, Tapan K.

    2006-11-01

    The 5th International Conference on Physics and Astrophysics of Quark Gluon Plasma (ICPAQGP 2005) was held on 8 - 12 February 2005 at the Variable Energy Cyclotron Centre and Saha Institute of Nuclear Physics campus, Kolkata, India. The conference was enriched by the august presence of about 300 participants representing 18 countries across the globe. It had plenary talks and oral presentations, which form a part of these proceedings. Besides invited and contributed talks there were also a large number of poster presentations. The conference was energized by discussions of fresh experimental data from RHIC on strong elliptic flow, jet quenching, single photon spectra etc. Moreover, new theoretical results were brought to the discussion forum during this conference. Colour glass condensates, hydrodynamical flow, jet quenching and sQGP were intensely debated by the participants. The highlight of ICPAQGP 2005 was the presentation of fresh experimental results from the RHIC-IV run. The ICPAQGP series, since its inception in 1988, has placed emphasis on the role of quark matter in the fields of astrophysics and cosmology. The subsequent conferences held in 1993, 1997, 2001 and 2005 had also retained this focus. The conference was preceded by a Fest Colloquium in honour of Professor Bikash Sinha. Professor Sinha, regarded as the pioneer in establishing quark gluon plasma research in India, has successfully encouraged a group of young Indian researchers to devote themselves wholeheartedly to QGP research - both theoretical and experimental. Members of the International Advisory Committee played a pivotal role mainly in the selection of speakers. The contributions of the Organizing Committee in all aspects, from selecting the contributory talks posters down to arranging local hospitality, were much appreciated. We thank the members of both committees for making ICPAQGP 2005 an interesting platform for scientific deliberation. The ICPAQGP 2005 was supported financially by

  8. Freezing Rain Diagnostic Study Over Eastern Canada Using the 5th Generation Canadian Regional Climate Model

    NASA Astrophysics Data System (ADS)

    Bresson, É.; Paquin, D.; Laprise, R.; Theriault, J. M.; de Elía, R.

    2015-12-01

    Northeastern North America is often affected by freezing rain events during the cold season. They can have significant consequences (from road accidents, to severe power outages) despite their intensity and duration. The 1998 Ice Storm over Eastern Canada and Northeastern United States is an example of an extreme event with catastrophic consequences. A total of up to 150 mm of ice accumulated during 10 days were observed in some areas. This natural disaster has highlighted the need to better understand how such phenomena will evolve with future climate scenario. The goal is to investigate the feasibility of using regional climate modeling to diagnose the occurrence of freezing rain events over Quebec (Canada). To address this issue, we used the 5th generation of the Canadian Regional Climate Model (CRCM5), from 1979 to 2014. An empirical method (Bourgouin, 2000) developed to determine the type of winter precipitations was chosen to diagnose freezing rain events. The study focused in the Montreal area and the St. Lawrence River Valley (Quebec, Canada). The sensitivity of the model to horizontal resolution was explored by using three resolutions: 0.44°, 0.22° and 0.11°. In general, freezing rain was diagnosed consistently at all resolutions but the higher one (0.11°) produced more realistic results due to a better representation of the orography. Using the higher resolution, the results showed that the climatology of the freezing rain occurrence in the Montreal area is comparable to available observations. It also suggested that the role of the specific orography of the region with the St. Lawrence River Valley can impact the characteristics of freezing rain events in this area. Overall, this study will contribute to a better preparedness for such events in the future. High resolution regional climate simulations are essential to improve the reproduction of local scale orographically-forced phenomena.

  9. Black sea surface temperature anomaly on 5th August 1998 and the ozone layer thickness

    NASA Astrophysics Data System (ADS)

    Manev, A.; Palazov, K.; Raykov, St.; Ivanov, V.

    2003-04-01

    BLACK SEA SURFACE TEMPERATURE ANOMALY ON 5th AUGUST 1998 AND THE OZONE LAYER THICKNESS A. Manev , K. Palazov , St. Raykov, V. Ivanov Solar Terrestrial Influences Laboratory, Bulgarian Academy of Sciences amanev@abv.bg This paper focuses on the peculiarities of the Black Sea surface temperature anomaly on 05.08.1998. Researching the daily temperature changes in a number of control fields in the course of 8-10 years, we have found hidden correlations and anomalous deviations in the sea surface temperatures on a global scale. Research proves the statistical reliability of the temperature anomaly on the entire Black Sea surface registered on 04.-05.08.1998. In the course of six days around these dates the temperatures are up to 2°C higher than the maximum temperatures in this period in the other seven years. A more detailed analysis of the dynamics of the anomaly required the investigation of five Black Sea surface characteristic zones of 75x75 km. The analysis covers the period 20 days - 10 days before and 10 days after the anomaly. Investigations aimed at interpreting the reasons for the anomalous heating of the surface waters. We have tried to analyze the correlation between sea surface temperature and the global ozone above the Black Sea by using simultaneously data from the two satellite systems NOAA and TOMS. Methods of processing and comparing the data from the two satellite systems are described. The correlation coefficients values for the five characteristic zones are very high and close, which proves that the character of the correlation ozone - sea surface temperature is the same for the entire Black Sea surface. Despite the high correlation coefficient, we have proved that causality between the two phenomena at the time of the anomaly does not exit.

  10. Patterns of Irregular Burials in Western Europe (1st-5th Century A.D.)

    PubMed Central

    Milella, Marco; Mariotti, Valentina; Belcastro, Maria Giovanna; Knüsel, Christopher J.

    2015-01-01

    Background Irregular burials (IB—burials showing features that contrast with the majority of others in their geographic and chronological context) have been the focus of archaeological study because of their relative rarity and enigmatic appearance. Interpretations of IB often refer to supposed fear of the dead or to social processes taking place in time-specific contexts. However, a comprehensive and quantitative analysis of IB for various geographical contexts is still lacking, a fact that hampers any discussion of these burials on a larger scale. Methods Here, we collected a bibliographic dataset of 375 IB from both Britain and Continental Europe, altogether spanning a time period from the 1st to the 5th century AD. Each burial has been coded according to ten dichotomous variables, further analyzed by means of chi-squared tests on absolute frequencies, non-metric multidimensional scaling, and cluster analysis. Results Even acknowledging the limits of this study, and in particular the bias represented by the available literature, our results point to interesting patterns. Geographically, IB show a contrast between Britain and Continental Europe, possibly related to historical processes specific to these regions. Different types of IB (especially prone depositions and depositions with the cephalic extremity displaced) present a series of characteristics and associations between features that permit a more detailed conceptualization of these occurrences from a socio-cultural perspective that aids to elucidate their funerary meaning. Conclusions and Significance Altogether, the present work stresses the variability of IB, and the need to contextualize them in a proper archaeological and historical context. It contributes to the discussion of IB by providing a specific geographic and chronological frame of reference that supports a series of hypotheses about the cultural processes possibly underlying their occurrence. PMID:26115408

  11. Bit-rate-variable and order-switchable optical multiplexing of high-speed pseudorandom bit sequence using optical delays.

    PubMed

    Wu, Xiaoxia; Wang, Jian; Yilmaz, Omer F; Nuccio, Scott R; Bogoni, Antonella; Willner, Alan E

    2010-09-15

    We experimentally demonstrate high-speed optical pseudorandom bit sequence (PRBS) multiplexing with coarse and fine bit-rate tuning capability and a switchable order using optical delays. Data multiplexing of 80 Gbit/s and 160 Gbit/s is shown, each with a tunable rate using a conversion/dispersion-based continuously tunable optical delay and tunable PRBS order with large switchable fiber delays. A 7% bit-rate tunability, i.e., 80-85.6 Gbit/s and 160-171.2 Gbit/s, is shown for both 2(7)-1 and 2(15)-1 PRBS. The rf spectra before and after multiplexing are measured in each case and show a suppression ratio of >30 dB, exhibiting the expected PRBS spectral characteristics. PMID:20847772

  12. A helping hand putting in order: Visuomotor routines organize numerical and non-numerical sequences in space.

    PubMed

    Rinaldi, Luca; Di Luca, Samuel; Henik, Avishai; Girelli, Luisa

    2016-07-01

    Theories of embodied cognition emphasize the importance of sensorimotor schemas linked to external world experience for representing conceptual knowledge. Accordingly, some researchers have proposed that the spatial representation of numerical and non-numerical sequences relies on visuomotor routines, like reading habit and finger counting. There is a growing interest in how these two routines contribute to the spatial representation of ordinal sequences, although no investigation has so far directly compared them. The present study aims to investigate how these routines contribute to represent ordinal information in space. To address this issue, bilingual participants reading either from left-to-right or right-to-left were required to map ordinal information to all fingers of their right dominant hand. Critically, we manipulated both the direction of the mapping and the language of the verbal information. More specifically, a finger-mapping compatibility task was adopted in three experiments to explore the spatial representation of numerical (digit numbers and number words) and non-numerical (days of the week, presented in Hebrew and in English) sequences. Results showed that numerical information was preferentially mapped according to participants' finger counting habits, regardless of hand posture (prone and supine), number notation and reading habit. However, for non-numerical ordinal sequences, reading and finger counting directions both contributed to determine a preferential spatial mapping. These findings indicate that abstract knowledge representation relies on multiple over-trained visuomotor routines. More generally, these results highlight the capacity of our cognitive system to flexibly represent abstract ordered information, by relying on different directional experiences (finger counting, reading direction) depending on the stimuli and on the task at hand. PMID:27015351

  13. WWW.com: A Brief Intervention to Bolster a 5th Grader's Regrouping Skills in Math

    ERIC Educational Resources Information Center

    Waugh, Matthew; Harrison, Gina L.

    2014-01-01

    This study examined the efficacy of a brief math intervention using cognitive behaviour instruction (CBI) supplemented by a mnemonic cue system for a 5th grade student with math computation and fluency difficulties. Regrouping operations in addition and subtraction were the targeted skills. Curriculum-based measurements were conducted at the end…

  14. Proceedings of the International Conference on Educational Data Mining (EDM) (5th, Chania, Greece, June 19-21, 2012)

    ERIC Educational Resources Information Center

    International Educational Data Mining Society, 2012

    2012-01-01

    The 5th International Conference on Educational Data Mining (EDM 2012) is held in picturesque Chania on the beautiful Crete island in Greece, under the auspices of the International Educational Data Mining Society (IEDMS). The EDM 2012 conference is a leading international forum for high quality research that mines large data sets of educational…

  15. Comparing Science Learning among 4th-, 5th-, and 6th-Grade Students: STS versus Textbook-Based Instruction

    ERIC Educational Resources Information Center

    Yager, Robert E.; Choi, AeRan; Yager, Stuart O.; Akcay, Hakan

    2009-01-01

    Fifteen 4th-, 5th-, and 6th-grade teachers from five school districts each taught two sections of science--one with a Science-Technology-Society (STS) approach and the other with a more traditional textbook approach in which basic science concepts were the major organizers. Local, current, and personally relevant issues provided the context and…

  16. Process Evaluation of "Learn Young, Learn Fair": A Stress Management Programme for 5th and 6th Graders

    ERIC Educational Resources Information Center

    Kraag, Gerda; Van Breukelen, Gerard; Lamberts, Petra; Vugts, Odette; Kok, Gerjo; Fekkes, Minne; Abu-Saad, Huda Huijer

    2007-01-01

    This article describes the process evaluation of a stress management program called "Learn Young, Learn Fair" for 5th and 6th graders. Studies, reviews and meta-analyses of prevention programs report that a common limitation in studies is the restricted documentation of process factors that contribute to the success of interventions. Program…

  17. Communicating Science to Impact Learning? A Phenomenological Inquiry into 4th and 5th Graders' Perceptions of Science Information Sources

    ERIC Educational Resources Information Center

    Gelmez Burakgazi, Sevinc; Yildirim, Ali; Weeth Feinstein, Noah

    2016-01-01

    Rooted in science education and science communication studies, this study examines 4th and 5th grade students' perceptions of science information sources (SIS) and their use in communicating science to students. It combines situated learning theory with uses and gratifications theory in a qualitative phenomenological analysis. Data were gathered…

  18. Brief Report: Data on the Stanford-Binet Intelligence Scales (5th Ed.) in Children with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Coolican, Jamesie; Bryson, Susan E.; Zwaigenbaum, Lonnie

    2008-01-01

    The Fifth Edition of the Stanford-Binet Intelligence Scales (SB5; Roid, G. H. (2003). "Stanford Binet intelligence scales" (5th ed.). Itasca, IL: Riverside Publishing) is relatively new, with minimal published research on general populations and none with special populations. The present study provides information on the cognitive profiles of…

  19. 5th National Audit Project (NAP5) on accidental awareness during general anaesthesia: summary of main findings and risk factors.

    PubMed

    Pandit, J J; Andrade, J; Bogod, D G; Hitchman, J M; Jonker, W R; Lucas, N; Mackay, J H; Nimmo, A F; O'Connor, K; O'Sullivan, E P; Paul, R G; Palmer, J H M G; Plaat, F; Radcliffe, J J; Sury, M R J; Torevell, H E; Wang, M; Hainsworth, J; Cook, T M

    2014-10-01

    We present the main findings of the 5th National Audit Project (NAP5) on accidental awareness during general anaesthesia (AAGA). Incidences were estimated using reports of accidental awareness as the numerator, and a parallel national anaesthetic activity survey to provide denominator data. The incidence of certain/probable and possible accidental awareness cases was ~1:19,600 anaesthetics (95% confidence interval 1:16,700-23,450). However, there was considerable variation across subtypes of techniques or subspecialities. The incidence with neuromuscular block (NMB) was ~1:8200 (1:7030-9700), and without, it was ~1:135,900 (1:78,600-299,000). The cases of AAGA reported to NAP5 were overwhelmingly cases of unintended awareness during NMB. The incidence of accidental awareness during Caesarean section was ~1:670 (1:380-1300). Two-thirds (82, 66%) of cases of accidental awareness experiences arose in the dynamic phases of anaesthesia, namely induction of and emergence from anaesthesia. During induction of anaesthesia, contributory factors included: use of thiopental, rapid sequence induction, obesity, difficult airway management, NMB, and interruptions of anaesthetic delivery during movement from anaesthetic room to theatre. During emergence from anaesthesia, residual paralysis was perceived by patients as accidental awareness, and commonly related to a failure to ensure full return of motor capacity. One-third (43, 33%) of accidental awareness events arose during the maintenance phase of anaesthesia, mostly due to problems at induction or towards the end of anaesthesia. Factors increasing the risk of accidental awareness included: female sex, age (younger adults, but not children), obesity, anaesthetist seniority (junior trainees), previous awareness, out-of-hours operating, emergencies, type of surgery (obstetric, cardiac, thoracic), and use of NMB. The following factors were not risk factors for accidental awareness: ASA physical status, race, and use or omission

  20. Health in the 5th 5-years Development Plan of Iran: Main Challenges, General Policies and Strategies.

    PubMed

    Vosoogh Moghaddam, A; Damari, B; Alikhani, S; Salarianzedeh, Mh; Rostamigooran, N; Delavari, A; Larijani, B

    2013-01-01

    Access to the right to the highest attainable level of health is a constitutional right that obliges governments and other players to take step to increase all individuals' chances of obtaining good health. At the least, health and education are two crucial requirements for this as well. Iran's vision 2025 is going to lead the country to a developed state with the highest rank of economic, scientific and technological status in the region. Enjoying health, welfare, food security, social security, equal opportunities, etc, are also considered as part of characteristics of Iranian society in 2025. Although health system of Iran has many achievements in providing health services specially for the poor following the Islamic Revolution of 1979, but the evidences gathered to develop the 5(th) 5-years economical, social and cultural plan (5(th)5YDP:2011-2015), listed a variety of main challenges in stewardship, financing, resources generation and service provision functions of the existing health system. Thus, to overcome the main challenges, about 11% of general policies of 5(th)5YDP are directly address health related issues with emphasizing on healthy human and comprehensive health approach with considering: Integration of policy making, planning, evaluation, supervision and public financing; Developing both quantity and quality of health insurance system and reducing out-of-pocket expenditures for health services to 30% by the end of the 5th plan. The strategies of 5(th)5YDP adopted by the parliament as an Act will change the health system fundamentally through tuning the main drivers; so, its implementation needs brave leaders, capable managers, motivated technical staff and social mobilization. PMID:23865015

  1. FOREWORD: 5th International Workshop on New Computational Methods for Inverse Problems

    NASA Astrophysics Data System (ADS)

    Vourc'h, Eric; Rodet, Thomas

    2015-11-01

    This volume of Journal of Physics: Conference Series is dedicated to the scientific research presented during the 5th International Workshop on New Computational Methods for Inverse Problems, NCMIP 2015 (http://complement.farman.ens-cachan.fr/NCMIP_2015.html). This workshop took place at Ecole Normale Supérieure de Cachan, on May 29, 2015. The prior editions of NCMIP also took place in Cachan, France, firstly within the scope of ValueTools Conference, in May 2011, and secondly at the initiative of Institut Farman, in May 2012, May 2013 and May 2014. The New Computational Methods for Inverse Problems (NCMIP) workshop focused on recent advances in the resolution of inverse problems. Indeed, inverse problems appear in numerous scientific areas such as geophysics, biological and medical imaging, material and structure characterization, electrical, mechanical and civil engineering, and finances. The resolution of inverse problems consists of estimating the parameters of the observed system or structure from data collected by an instrumental sensing or imaging device. Its success firstly requires the collection of relevant observation data. It also requires accurate models describing the physical interactions between the instrumental device and the observed system, as well as the intrinsic properties of the solution itself. Finally, it requires the design of robust, accurate and efficient inversion algorithms. Advanced sensor arrays and imaging devices provide high rate and high volume data; in this context, the efficient resolution of the inverse problem requires the joint development of new models and inversion methods, taking computational and implementation aspects into account. During this one-day workshop, researchers had the opportunity to bring to light and share new techniques and results in the field of inverse problems. The topics of the workshop were: algorithms and computational aspects of inversion, Bayesian estimation, Kernel methods, learning methods

  2. PREFACE: 5th International EEIGM/AMASE/FORGEMAT Conference on Advanced Materials Research

    NASA Astrophysics Data System (ADS)

    Ayadi, Zoubir; Czerwiec, Thierry; Horwat, David; Jamart, Brigitte

    2009-07-01

    This issue of IOP Conference Series: Materials Science and Engineering, contains manuscripts of talks that will be presented at the 5th International EEIGM/AMASE/FORGEMAT Conference on Advanced Materials Research that will be held at the Ecole Européenne d'Ingénieurs en Génie des Matériaux - European School of Materials Science and Engineering (EEIGM) in Nancy on November 4-5 2009. The conference will be organized by the EEIGM. The aim of the conference is to bring together scientists from the six European universities involved in the EEIGM and in the ''Erasmus Mundus'' AMASE Master (Advanced Materials Science and Engineering) programmes and in the Tempus FORGEMAT European project: Nancy-Université - EEIGM/INPL (Nancy, France), Universität des Saarlandes (Saarbrücken, Germany), Universitat Politècnica de Catalunya - ETSEIB (Barcelona, Spain), Luleå Tekniska Universitet (Luleå, Sweden), Universidad Politecnica de Valencia - ETSII (Valencia, Spain) and AGH University of Science and Technology, (Kralow, Poland). This conference is also open to other universities who have strong links with the EEIGM and it will provide a forum for exchange of ideas, cooperation and future directions by means of regular presentations, posters and a round-table discussion. After careful refereeing of all manuscripts, equally shared between the four editors, 26 papers have been selected for publication in this issue. The papers are grouped together into different subject categories: polymers, metallurgy, ceramics, composites and nanocomposites, simulation and characterization. The editors would like to take this opportunity to thank all the participants who submitted their manuscripts during the conference and responded in time to the editors' request at every stage from reviewing to final acceptance. The editors are indebted to all the reviewers for painstakingly reviewing the papers at very short notice. Special thanks are called for the sponsors of the conference including

  3. Storm Peak Laboratory 5th-6th Grade Climate and Weather Program

    NASA Astrophysics Data System (ADS)

    McCubbin, I. B.; Hallar, A. G.

    2008-12-01

    science. At the end of the day each student has a data sheet with measurements recorded from 5 locations of different elevations to take back to the classroom. Following the field trip, SPL scientists and educators visit the school for a follow-up to help children grasp concepts, represent their data set collected in graphical formats, answer questions, and evaluate students" learning. Currently, approximately 250 students annually participate in the SPL 5th and 6th grade climate education program.

  4. Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order "Parvularculales" in the class Alphaproteobacteria.

    PubMed

    Oh, Hyun-Myung; Kang, Ilnam; Vergin, Kevin L; Kang, Dongmin; Rhee, Kwang-Hyun; Giovannoni, Stephen J; Cho, Jang-Cheon

    2011-01-01

    The order "Parvularculales" represents the seventh order in the class Alphaproteobacteria. Parvularcula bermudensis, the type species of the order, was isolated from the Sargasso Sea using dilution-to-extinction culturing. We present here the complete genome sequence of Parvularcula bermudensis HTCC2503(T), which contains genes for carotenoid biosynthesis, dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents. PMID:21037002

  5. The application of the reduced order model Kalman filter to motion estimation of degraded image sequences. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Simpson, Elizabeth C.

    1989-01-01

    Motion estimation is a field of great interest because of its many applications in areas such as robotics and image coding. The optic flow method is one such scheme which, although fairly accurate, is prone to error in the presence of noise. This thesis describes the use of the reduced order model Kalman filter (ROMKF) in reducing errors in displacement estimation due to degradation of the sequence. The implementation of filtering and motion estimation algorithms on the SUN workstation is also discussed. Results from preliminary testing were used to determine the degrees of freedom available for the ROMKF in the SUN software. The tests indicated that increasing the state to the left leads to slight improvement over the minimum state case. Therefore, the software uses the minimum model, with the option of adding states to the left only. The ROMKF was then used in conjunction with a hierarchical pel recursive motion estimation algorithm. Applying the ROMKF to the degraded displacements themselves generally yielded slight improvements in cases with noise degradation and noise plus blur. Filtering the images of the degraded sequence prior to motion estimation was less effective in these cases. Both methods performed badly in the case of blur alone, resulting in increased displacement errors. This is thought to be due in part to filter artifacts. Some improvements were obtained by varying the filter parameters when filtering the displacements directly. This result suggests that further study in varying filter parameters may lead to better results. The results of this thesis indicate that the ROMKF can play a part in reducing motion estimation errors from degraded sequences. However, more work needs to be done before the use of the ROMKF can be a practical solution.

  6. eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models

    PubMed Central

    Brylinski, Michal

    2014-01-01

    Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4–9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite. PMID

  7. The 5th National Audit Project (NAP5) on accidental awareness during general anaesthesia: summary of main findings and risk factors.

    PubMed

    Pandit, J J; Andrade, J; Bogod, D G; Hitchman, J M; Jonker, W R; Lucas, N; Mackay, J H; Nimmo, A F; O'Connor, K; O'Sullivan, E P; Paul, R G; Palmer, J H MacG; Plaat, F; Radcliffe, J J; Sury, M R J; Torevell, H E; Wang, M; Hainsworth, J; Cook, T M

    2014-10-01

    We present the main findings of the 5th National Audit Project on accidental awareness during general anaesthesia. Incidences were estimated using reports of accidental awareness as the numerator, and a parallel national anaesthetic activity survey to provide denominator data. The incidence of certain/probable and possible accidental awareness cases was ~1:19 600 anaesthetics (95% CI 1:16 700-23 450). However, there was considerable variation across subtypes of techniques or subspecialties. The incidence with neuromuscular blockade was ~1:8200 (1:7030-9700), and without it was ~1:135 900 (1:78 600-299 000). The cases of accidental awareness during general anaesthesia reported to 5th National Audit Project were overwhelmingly cases of unintended awareness during neuromuscular blockade. The incidence of accidental awareness during caesarean section was ~1:670 (1:380-1300). Two thirds (82, 66%) of cases of accidental awareness experiences arose in the dynamic phases of anaesthesia, namely induction of and emergence from anaesthesia. During induction of anaesthesia, contributory factors included: use of thiopental; rapid sequence induction; obesity; difficult airway management; neuromuscular blockade; and interruptions of anaesthetic delivery during movement from anaesthetic room to theatre. During emergence from anaesthesia, residual paralysis was perceived by patients as accidental awareness, and commonly related to a failure to ensure full return of motor capacity. One third (43, 33%) of accidental awareness events arose during the maintenance phase of anaesthesia, most due to problems at induction or towards the end of anaesthesia. Factors increasing the risk of accidental awareness included: female sex; age (younger adults, but not children); obesity; anaesthetist seniority (junior trainees); previous awareness; out-of-hours operating; emergencies; type of surgery (obstetric, cardiac, thoracic); and use of neuromuscular blockade. The following factors were

  8. PREFACE: 5th DAE-BRNS Workshop on Hadron Physics (Hadron 2011)

    NASA Astrophysics Data System (ADS)

    Jyoti Roy, Bidyut; Chatterjee, A.; Kailas, S.

    2012-07-01

    The 5th DAE-BRNS Workshop on Hadron Physics was held at the Bhabha Atomic Research Centre (BARC), Mumbai from 31 October to 4 November 2011. This workshop series, supported by the Board of Research in Nuclear Sciences, Department of Atomic Energy (BRNS, DAE), Govt. of India, began ten years ago with the first one being held at BARC, Mumbai in October 2002. The second one was held at Puri in 2005, organized jointly by Institute of Physics, Bhubneswar and Saha Institute of Nuclear Physics, Kolkata. The 3rd and 4th ones took place, respectively, at Shantineketan in 2006, organized by Visva Bharati University, and at Aligarh in 2008, organized by Aligarh Muslim University, Aligarh. The aim of the present workshop was to bring together the experts and young researchers in the field of hadron physics (both experiment and theory) and to have in-depth discussions on the current research activities in this field. The format of the workshop was: a series of review lectures by various experts from India and abroad, the presentation of advanced research results by researchers in the field, and a review of major experimental programs being planned and pursued in major laboratories in the field of hadron physics, with the aim of providing a platform for the young participants for interaction with their peers. The upcoming international FAIR facility at GSI is a unique future facility for studies of hadron physics in the charm sector and hyper nuclear physics. The Indian hadron physics community is involved in this mega science project and is working with the PANDA collaboration on the development of detectors, simulation and software tools for the hadron physics programme with antiprotons at FAIR. A one-day discussion session was held at this workshop to discuss India-PANDA activities, the current collaboration status and the work plan. This volume presents the workshop proceedings consisting of lectures and seminars which were delivered during the workshop. We are thankful to

  9. EDITORIAL: 5th International Symposium on Particle Image Velocimetry, PIV'03

    NASA Astrophysics Data System (ADS)

    Sung, Hyung Jin; Kim, Kyung Chun; Lee, Sang Joon

    2004-06-01

    The advent of particle image velocimetry (PIV) in the late 20th century brought about a paradigm change in the technique of flow field measurement, from point measurement to field measurement. This revolution is a result of the recent advances in computers, video cameras, optics and lasers and a deeper understanding of the theory of image processing, and such advances continue by keeping pace with leading-edge technologies such as biotechnology, nanotechnology and so forth. Recently, the PIV technique has been extended in new directions such as stereoscopic PIV, holographic PIV, dynamic PIV, micro PIV and simultaneous PLIF/PIV techniques. This special issue contains research dealing with many of the most recent developments in PIV. The papers were selected from more than 120 papers presented at the 5th International Symposium on Particle Image Velocimetry (PIV'03) held in Busan, Korea, during 22-24 September 2003. Special thanks are due to the invited speakers who have contributed their original work to this special issue, which will enhance the academic reputation of Measurement Science and Technology (MST). Fourteen papers were selected by the Scientific Committee of PIV'03. After the standard refereeing process of MST, nine papers were finally accepted for publication. The selected papers can be categorized into three groups: new PIV algorithms and evaluation methods, three-dimensional velocity field measurement techniques and micro/bio PIV applications. As a new PIV technique, Lecuona et al introduced PIV evaluation algorithms for industrial applications having high shear flow structures. Billy et al used a single-pixel-based cross-correlation method for measuring flow inside a microchannel. Foucaut et al carried out PIV optimization using spectral analysis for the study of turbulent flows. Doh et al applied a 3D PTV method to the wake behind a sphere using three CCD cameras. Hori and Sakakibara developed a high-speed scanning stereoscopic PIV system and

  10. The 5th Conference on Asian Trends in Prostate Cancer Hormone Therapy.

    PubMed

    Akaza, Hideyuki; Moore, Malcolm A; Chang, Shu-Jen; Cheng, Christopher; Choi, Han Yong; Esuvaranathan, Kesavan; Hinotsu, Shiro; Hong, Sung-Joon; Kim, Choung-Soo; Kim, Wun-Jae; Murai, Masaru; Naito, Seiji; Soebadi, Doddy; Song, Jae-Mann; Umbas, Rainy; Usami, Michiyuki; Xia, Shujie; Yang, Chi-Rei

    2007-01-01

    The Conference on Asian Trends in Prostate Cancer Hormone Therapy is an annual forum for Asian urologists now in its 5th year. The 2006 conference, held in Bali, Indonesia, was attended by 27 leading urologic oncologists from China, Indonesia, Japan, Korea, Singapore, and Taiwan and featured a packed program of presentations and discussions on a wide range of topics such as relationships among clinicians and the newly opened Asia Regional Office for Cancer Control of the International Union Against Cancer (UICC), detection rates of prostate cancer by biopsy in each of the 6 Asian countries, and favored treatment modalities for hormone-refractory prostate cancer (HRPC) in each country. The first session of the conference kicked off with a keynote lecture entitled "Activities of the UICC ARO". UICC's new office will be the nerve center for its activities in the Asia region. Along with the Asian Pacific Organization for Cancer Prevention (APOCP), UICC aims to shift the focus of attention to cancer control. As such APOCP's long-running publication the APJCP is to be re-launched as the Asian Pacific Journal of Cancer Control. Although UICC is primarily concerned with cancer, several risk factors for cancer are common also to other non-communicable diseases such as diabetes and heart disease, and an important strategy is to implement measures to control these various pathologic conditions as a whole. Apart from contributing to an Asian prostate cancer registry the UICC-ARO will provide training courses, working groups, and assistance in collecting and processing data. The keynote lecture was followed by a roundtable discussion on possible ways in which clinicians from each Asian country can work with UICC. A number of suggestions were put forth including better registration, epidemiology research, possible implementation of UICC prostate cancer guidelines, early detection and screening, and roles of diet and phytotherapy. The underlying reasons for the large but

  11. PREFACE: 5th International Workshop on Top Quark Physics (TOP2012)

    NASA Astrophysics Data System (ADS)

    Salamanna, G.; Boisvert, V.; Cerrito, L.; Khan, A.; Moretti, S.; Owen, M.; Schwanenberger, C.

    2013-07-01

    The 5th International Workshop on Top Quark Physics (TOP 2012) took place in Winchester, UK, from the 16-21 September. It gathered students as well as people active in the top quark sector and provided a framework to highlight the newest results and matters related to top quark physics. Discovered in 1995, the top quark is the sixth and heaviest of all quarks, and it is the only one with a lifetime short enough to be observed 'naked'. This makes it an important testing ground in the search for new physics. In fact, the fact of its mass being so much larger than the other quarks, hints at its special role in the Higgs mechanism. For the same reason, in many models of New Physics, new heavy resonances are expected to couple mostly with top quarks. Even if no new particles are observed, the direct correlation between its angular momentum and that of its detectable decay products allows us to probe indirectly New Physics in action when top quarks are created. In this edition of the TOP conference series, for the first time, the agenda was equally balanced between 'traditional' measurements and the now vast number of searches for physics BSM in the top quark sector, thanks mostly to the amount of data collected at the LHC in its Run I. New results were presented by both the Tevatron and the LHC collaborations: improved ttbar and single top cross-section measurements, refined techniques to measure the top quark mass and a large number of results on properties such as spin correlation and W boson polarization in top quark decays were shown. More technical discussions on the experimental issues, both from the detector and the simulation side also took place, drawing together experimentalists and theorists. Reviews of the latest results on ttbar asymmetry both from CDF and D0 and from ATLAS and CMS were shown, and theorists active in the field made some interesting points on this hot topic. Additionally, results on the search for fourth generation fermions and new

  12. Third-order sequences and parasequence stacking patterns of Lower Ordovician platform carbonates of the El Paso Group, Franklin Mountains, west Texas

    SciTech Connect

    Goldhammer, R.K.; Lehmann, P.J.; Dunn, P.A. )

    1991-03-01

    The Lower Ordovician passive margin succession of the Franklin Mountains is represented by the second-order Sauk C supersequence set consisting of the Bliss Sandstone and the overlying El Paso Group. The Bliss marks the second order basal lowstand-transgressive phase and the El Paso Group records the second-order highstand. The El Paso Group contains several third-order depositional sequences, which in this updip, shelfal position lack internal stratal geometries along dip. Thus, sequences and systems tracts are identified solely on the basis of the vertical stacking patterns of depositional subfacies and high frequency, fifth-order parasequences. 'Fischer plots' of high-frequency parasequences gauge systematic shifts in third-order accommodation of two complete third-order sequences within the Arenigian portion of the El Paso Group. This is expressed in the vertical succession of parasequence types, systematic changes in parasequence thicknesses, plus variations in subfacies as revealed by histograms of subfacies types tied to 'Fischer plots.' A complete El Paso shelfal sequence contains a thin lowstand (LST) of quartzarenite, a thick transgressive systems tract (TST) dominated by upward-thickening, thrombolitic subtidal parasequences, and a highstand systems tract (HST) marked by dolomitic, thinning-upward peritidal parasequences containing admixed quartz sand. The authors have investigated the mechanics of third-order sequence formation and contrasted allocyclic models with autocyclic models for high-frequency parasequence formation through 1-D and 2-D forward modeling.

  13. First-order kinetics of landfill leachate treatment in a pilot-scale anaerobic sequence batch biofilm reactor.

    PubMed

    Contrera, Ronan Cleber; da Cruz Silva, Katia Cristina; Morita, Dione Mari; Domingues Rodrigues, José Alberto; Zaiat, Marcelo; Schalch, Valdir

    2014-12-01

    This paper reports the kinetics evaluation of landfill leachate anaerobic treatment in a pilot-scale Anaerobic Sequence Batch Biofilm Reactor (AnSBBR). The experiment was carried out at room temperature (23.8 ± 2.1 °C) in the landfill area in São Carlos-SP, Brazil. Biomass from the bottom of a local landfill leachate stabilization pond was used as inoculum. After acclimated and utilizing leachate directly from the landfill, the AnSBBR presented efficiency over 70%, in terms of COD removal, with influent COD ranging from 4825 mg L(-1) to 12,330 mg L(-1). To evaluate the kinetics of landfill leachate treatment, temporal profiles of CODFilt. concentration were performed and a first-order kinetics model was adjusted for substrate consumption, obtaining an average k1 = 4.40 × 10(-5) L mgTVS(-1) d(-1), corrected to 25 °C. Considering the temperature variations, a temperature-activity coefficient θ = 1.07 was obtained. Statistical "Randomness" and "F" tests were used to successfully validate the model considered. Thus, the results demonstrate that the first-order kinetic model is adequate to model the anaerobic treatment of the landfill leachate in the AnSBBR. PMID:25127066

  14. Socioeconomic assessment of the proposed inactivation of the 5th Fighter Interceptor Squadron Minot Air Force Base, North Dakota

    SciTech Connect

    Kerley, C.R.; Sage, P.L.; Fichera, J.P.; Lufkin, P.; Stadelman, D.

    1988-12-01

    This assessment examines the potential socioeconomic impacts of inactivating the 5th Fighter Interceptor Squadron (FIS) at Minot Air Force Base (AFB), North Dakota. The study focuses on employment, population, and income impacts and estimates their effects on housing, community services, utilities, transportation, recreation and tourism, and public finance. This assessment is intended primarily for the use of Air Force and community planners concerned with the local consequences of the inactivation. 10 refs., 46 tabs.

  15. Summative assessment of 5th year medical students’ clinical reasoning by script concordance test: requirements and challenges

    PubMed Central

    2012-01-01

    Background The Script Concordance Test (SCT) has not been reported in summative assessment of students across the multiple domains of a medical curriculum. We report the steps used to build a test for summative assessment in a medical curriculum. Methods A 51 case, 158-question, multidisciplinary paper was constructed to assess clinical reasoning in 5th-year. 10–16 experts in each of 7 discipline-based reference panels answered questions on-line. A multidisciplinary group considered reference panel data and data from a volunteer group of 6th Years, who sat the same test, to determine the passing score for the 5th Years. Results The mean (SD) scores were 63.6 (7.6) and 68.6 (4.8) for the 6th Year (n = 23, alpha = 0.78) and and 5th Year (n = 132, alpha =0.62) groups (p < 0.05), respectively. The passing score was set at 4 SD from the expert mean. Four students failed. Conclusions The SCT may be a useful method to assess clinical reasoning in medical students in multidisciplinary summative assessments. Substantial investment in training of faculty and students and in the development of questions is required. PMID:22571351

  16. Emotional and Behavioral Disorders in 1.5th Generation, 2nd Generation Immigrant Children, and Foreign Adoptees.

    PubMed

    Tan, Tony Xing

    2016-10-01

    Existing theories (e.g., acculturative stress theory) cannot adequately explain why mental disorders in immigrants are less prevalent than in non-immigrants. In this paper, the culture-gene co-evolutionary theory of mental disorders was utilized to generate a novel hypothesis that connection to heritage culture reduces the risk for mental disorders in immigrant children. Four groups of children aged 2-17 years were identified from the 2007 United States National Survey of Children's Health: 1.5th generation immigrant children (n = 1378), 2nd generation immigrant children (n = 4194), foreign adoptees (n = 270), and non-immigrant children (n = 54,877). The 1.5th generation immigrant children's connection to their heritage culture is stronger than or similar to the 2nd generation immigrants, while the foreign adoptees have little connection to their birth culture. Controlling for age, sex, family type and SES, the odds for having ADD/ADHD, Conduct Disorder, Anxiety Disorder, and Depression diagnosis were the lowest for the 1.5th generation immigrant children, followed by the 2nd generation immigrant children and the foreign adoptees. The foreign adoptees and non-adopted children were similar in the odds of having these disorders. Connection to heritage culture might be the underlying mechanism that explained recent immigrants' lower rates of mental disorders. PMID:26972324

  17. Ordered shotgun sequencing of a 135 kb Xq25 YAC containing ANT2 and four possible genes, including three confirmed by EST matches.

    PubMed Central

    Chen, C N; Su, Y; Baybayan, P; Siruno, A; Nagaraja, R; Mazzarella, R; Schlessinger, D; Chen, E

    1996-01-01

    Ordered shotgun sequencing (OSS) has been successfully carried out with an Xq25 YAC substrate. yWXD703 DNA was subcloned into lambda phage and sequences of insert ends of the lambda subclones were used to generate a map to select a minimum tiling path of clones to be completely sequenced. The sequence of 135 038 nt contains the entire ANT2 cDNA as well as four other candidates suggested by computer-assisted analyses. One of the putative genes is homologous to a gene implicated in Graves' disease and it, ANT2 and two others are confirmed by EST matches. The results suggest that OSS can be applied to YACs in accord with earlier simulations and further indicate that the sequence of the YAC accurately reflects the sequence of uncloned human DNA. PMID:8918809

  18. PREFACE: The 5th International Symposium in Quantum Theory and Symmetries (QTS5)

    NASA Astrophysics Data System (ADS)

    Arratia, O.; Calzada, J. A.; Gómez-Cubillo, F.; Negro, J.; del Olmo, M. A.

    2008-02-01

    This volume of Journal of Physics: Conference Series contains the Proceedings of the 5th International Symposium in Quantum Theory and Symmetries (QTS5), held in Valladolid, Spain, 22-28 July 2007. This is the fifth of a series of conferences previously held in Goslar (Germany) 1999, QTS1; Cracow (Poland) 2001, QTS2; Cincinnati (USA) 2003, QTS3, and Varna (Bulgaria) 2005, QTS4. The QTS5 symposium gathered 181 participants from 39 countries working in different fields on Theoretical Physics. The spirit of the QTS conference series is to join researchers in a wide variety of topics in Theoretical Physics, as a way to make accessible recent results and the new lines of different fields. The QTS5 conference offered the following list of topics: Symmetries in String Theory, Quantum Gravity and related Symmetries in Quantum Field Theories, Conformal and Related Field Theories, Lattice and Noncommutative Theories, Gauge Theories Quantum Computing, Information and Control Foundations of Quantum Theory Quantum Optics, Coherent States, Wigner Functions Dynamical and Integrable Systems Symmetries in Condensed Matter and Statistical Physics Symmetries in Particle Physics, Nuclear, Atomic and Molecular Nonlinear Quantum Mechanics Time Asymmetric Quantum Mechanics SUSY Quantum Mechanics, PT symmetries and pseudo-Hamiltonians Mathematical Methods for Symmetries and Quantum Theories Symmetries in Chemistry Biology and other Sciences Papers accepted for publication in the present issue are based on the contributions from the participants in the QTS5 conference after a peer review process. In addition, a special issue of Journal Physics A: Mathematical and Theoretical contains contributions from plenary speakers, some participants as well as contributions from other authors whose works fit into the topics of the conference. The organization of the conference had the following pattern. In the morning there were five plenary or general sessions for all the participants, which aimed to

  19. PREFACE: The 5th International Symposium on Quantum Theory and Symmetries (QTS5)

    NASA Astrophysics Data System (ADS)

    Gadella, M.; Izquierdo, J. M.; Kuru, S.; Negro, J.; del Olmo, M. A.

    2008-08-01

    This special issue of Journal of Physics A: Mathematical and Theoretical appears on the occasion of the 5th International Symposium on Quantum Theory and Symmetries (QTS5), held in Valladolid, Spain, from 22-28 July 2007. This is the fith in a series of conferences previously held in Goslar (Germany) 1999, QTS1; Cracow (Poland) 2001, QTS2; Cincinnati (USA) 2003, QTS3; and Varna (Bulgaria) 2005, QTS4. The QTS5 symposium gathered 181 participants from 39 countries working in different fields of theoretical physics. The spirit of the QTS conference series is to join researchers in a wide variety of topics in theoretical physics, as a way of making accessible recent results and the new lines of different fields. This is based on the feeling that it is good for a physicist to have a general overview as well as expertise in his/her own field. There are many other conferences devoted to specific topics, which are of interest to gain deeper insight in many technical aspects and that are quite suitable for discussions due to their small size. However, we believe that general conferences like this are interesting and worth keeping. We like the talks, in both plenary and parallel sessions, which are devoted to specific topics, to be prepared so as to be accessible to any researcher in any branch of theoretical physics. We think that this objective is compatible with rigour and high standards. As is well known, similar methods and techniques can be useful for many problems in different fields. We hope that this has been appreciated during the sessions of the QTS5 conference. The QTS5 conference offered the following list of topics: 1. Symmetries in string theory, quantum gravity and related topics 2. Symmetries in quantum field theories, conformal and related field theories, lattice and noncommutative theories, gauge theories 3.Quantum computing, information and control 4. Foundations of quantum theory 5. Quantum optics, coherent states, Wigner functions 6. Dynamical and

  20. PREFACE: The 5th International Symposium in Quantum Theory and Symmetries (QTS5)

    NASA Astrophysics Data System (ADS)

    Arratia, O.; Calzada, J. A.; Gómez-Cubillo, F.; Negro, J.; del Olmo, M. A.

    2008-02-01

    This volume of Journal of Physics: Conference Series contains the Proceedings of the 5th International Symposium in Quantum Theory and Symmetries (QTS5), held in Valladolid, Spain, 22-28 July 2007. This is the fifth of a series of conferences previously held in Goslar (Germany) 1999, QTS1; Cracow (Poland) 2001, QTS2; Cincinnati (USA) 2003, QTS3, and Varna (Bulgaria) 2005, QTS4. The QTS5 symposium gathered 181 participants from 39 countries working in different fields on Theoretical Physics. The spirit of the QTS conference series is to join researchers in a wide variety of topics in Theoretical Physics, as a way to make accessible recent results and the new lines of different fields. The QTS5 conference offered the following list of topics: Symmetries in String Theory, Quantum Gravity and related Symmetries in Quantum Field Theories, Conformal and Related Field Theories, Lattice and Noncommutative Theories, Gauge Theories Quantum Computing, Information and Control Foundations of Quantum Theory Quantum Optics, Coherent States, Wigner Functions Dynamical and Integrable Systems Symmetries in Condensed Matter and Statistical Physics Symmetries in Particle Physics, Nuclear, Atomic and Molecular Nonlinear Quantum Mechanics Time Asymmetric Quantum Mechanics SUSY Quantum Mechanics, PT symmetries and pseudo-Hamiltonians Mathematical Methods for Symmetries and Quantum Theories Symmetries in Chemistry Biology and other Sciences Papers accepted for publication in the present issue are based on the contributions from the participants in the QTS5 conference after a peer review process. In addition, a special issue of Journal Physics A: Mathematical and Theoretical contains contributions from plenary speakers, some participants as well as contributions from other authors whose works fit into the topics of the conference. The organization of the conference had the following pattern. In the morning there were five plenary or general sessions for all the participants, which aimed to

  1. 5-Step Methodology for Evaluation and Adaptation of Print Patient Health Information to Meet the <5th Grade Readability Criterion

    PubMed Central

    Hill-Briggs, Felicia; Schumann, Kristina P.; Dike, Ogechi

    2012-01-01

    Background In the setting of declining U.S. literacy, new policies include use of clear communication and low literacy accessibility practices with all patients. Reliable methods for adapting health information to meet such criteria remain a pressing need. Objectives To report method validation (Study 1) and method replication (Study 2) procedures and outcomes for a 5-step method for evaluating and adapting print health information to meet the current low literacy criterion of <5th grade readability. Materials Sets of 18 and 11 publicly-disseminated patient education documents developed by a university-affiliated medical center. Measures Three low-literacy criteria were strategically targeted for efficient, systematic evaluation and text modification to meet a <5th grade reading level: sentence length <15 words, writing in active voice, and use of common words with multisyllabic words (>2–3 syllables) minimized or avoided. Inter-rater reliability for the document evaluations was determined. Results Training in the methodology resulted in inter-rater reliability of 0.99–1.00 in Study 1 and 0.98–1.00 in Study 2. Original documents met none of the targeted low literacy criteria. In Study 1, following low-literacy adaptation, mean reading grade level decreased from 10.4±1.8 to 3.8±0.6 (p<0.0001), with consistent achievement of criteria for words per sentence, passive voice, and syllables per word. Study 2 demonstrated similar achievement of all target criteria, with a resulting decrease in mean reading grade level from 11.0±1.8 to 4.6±0.3 (p < 0.0001). Conclusions The 5-step methodology proved teachable and efficient. Targeting a limited set of modifiable criteria was effective and reliable in achieving <5th grade readability. PMID:22354210

  2. Validation of the 5th and 95th Percentile Hybrid III Anthropomorphic Test Device Finite Element Model

    NASA Technical Reports Server (NTRS)

    Lawrence, C.; Somers, J. T.; Baldwin, M. A.; Wells, J. A.; Newby, N.; Currie, N. J.

    2014-01-01

    NASA spacecraft design requirements for occupant protection are a combination of the Brinkley criteria and injury metrics extracted from anthropomorphic test devices (ATD's). For the ATD injury metrics, the requirements specify the use of the 5th percentile female Hybrid III and the 95th percentile male Hybrid III. Furthermore, each of these ATD's is required to be fitted with an articulating pelvis and a straight spine. The articulating pelvis is necessary for the ATD to fit into spacecraft seats, while the straight spine is required as injury metrics for vertical accelerations are better defined for this configuration. The requirements require that physical testing be performed with both ATD's to demonstrate compliance. Before compliance testing can be conducted, extensive modeling and simulation are required to determine appropriate test conditions, simulate conditions not feasible for testing, and assess design features to better ensure compliance testing is successful. While finite element (FE) models are currently available for many of the physical ATD's, currently there are no complete models for either the 5th percentile female or the 95th percentile male Hybrid III with a straight spine and articulating pelvis. The purpose of this work is to assess the accuracy of the existing Livermore Software Technology Corporation's FE models of the 5th and 95th percentile ATD's. To perform this assessment, a series of tests will be performed at Wright Patterson Air Force Research Lab using their horizontal impact accelerator sled test facility. The ATD's will be placed in the Orion seat with a modified-advanced-crew-escape-system (MACES) pressure suit and helmet, and driven with loadings similar to what is expected for the actual Orion vehicle during landing, launch abort, and chute deployment. Test data will be compared to analytical predictions and modelling uncertainty factors will be determined for each injury metric. Additionally, the test data will be used to

  3. Order of Orifices: Sequence of Condom Use and Ejaculation by Orifice during Anal Intercourse among Women, Implications for HIV Transmission

    PubMed Central

    Gorbach, Pamina M.; Pines, Heather; Javanbakht, Marjan; Weiss, Robert E.; Jeffries, Robin; Cranston, Ross D.; Fuchs, Edward J; Hezerah, Marjan; Brown, Stephen; Voskanian, Alen; Anton, Peter

    2014-01-01

    Background For women the order of penile insertion, condom use, and ejaculation by orifice during sexual events affects the probability of HIV transmission and design of HIV prevention methods. Methods From October 2006-June 2009, 431 women in Los Angeles and Baltimore in a rectal health study reported the sequence of penile insertion, condom use, and ejaculation by orifice location by computer assisted self-interview. Multinomial logistic regression identified predictors of condom use by orifice among women who reported vaginal intercourse (VI) during their last anal intercourse (AI) event. Results Of the 192 reporting on a last AI event, 96.3% (180/187) reported VI. Of these, 83.1% had VI before AI; 66.1% reported ejaculation during VI and 45.2% during AI. Only one third used a condom for both VI and AI, less than 10% for VI only or AI only; and half used no condoms. After adjusting for race, partner type, and substance use, compared to women who used condoms for both VI and AI at last AI, being older (units=5 years) (adjusted odds ratio [AOR]=0.76, 95% confidence interval [CI]: 0.60, 0.96), with serodiscordant partners (AOR=0.22, 95% CI: 0.08, 0.61) and HIV-positive with seroconcordant partners (AOR = 0.15; 95% CI: 0.04, 0.54) were inversely associated with non-condom use. Conclusions For most of the women in our study VI accompanied AI, with AI usually occurring after VI. This evidence for use of multiple orifices during the same sexual encounter and low use of condoms across orifices supports the need for a multi-compartment HIV prevention strategy. PMID:25356778

  4. Obscured Star-Formation in Merging Galaxies: High Resolution Radio Imaging of a Time-Ordered Sequence

    NASA Technical Reports Server (NTRS)

    Neff, S. G.; Campion, S. D.; Ulvestad, J. S.

    2003-01-01

    We present new, deep, high resolution 6cm and 4cm radio continuum images of the central regions of a time-ordered sequence of seven large galaxy mergers. The radio observations are able to detect star-forming re- gions that are completely obscured at optical wavelengths. In all systems, we detect numerous compact radio sources embedded in more diffuse ra- dio emission, with limiting luminosities of approx. 1-5 x 10(exp l8) W Hz or approx. 1-5 times the luminosity of Cas A. Many of the compact radio sources are loosely associated with active starforming regions but not with specific optical or W emission sources. Several of the compact radio sources are coincident with Ultra-luminous X-ray objects (ULX's). In most systems, we are able to measure reliable spectral indices for the stronger sources. We find that the fraction of compact radio cources with nominally flat radio spectral indices (indicating they ae dominated by thermal radio emission from HII regions) decreases with merger age, while the fraction of sources with nonimally steep spectral indices (indicating they are dominated by nonthermal emission from supernova remnants) increases. For the flat-spectrum sources, we estimate the numbers of young massive stars, associated ionized gas masses, we estimate supernova rates and required star-formation rates, We compare these results with those from other well-studied merging galaxy systems and from other determinations of star-formation rates. We gratefully acknowledge use of the NRAO Very Large Array (VLA) and the VLA Archive. NRAO is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

  5. A report on 5th congress of Asia Pacific Pediatric Cardiac Society, New Delhi, India, 6-9 March 2014

    PubMed Central

    Gupta, Saurabh K; Saxena, Anita

    2015-01-01

    The 5th Congress of Asia Pacific Pediatric Cardiac Society was held in New Delhi from 6-9 March 2014. This article describes the journey of preparing and hosting one of the largest international events in the specialty of Pediatric Cardiac Care ever held in India. A total of 938 delegates, including 400 from outside India, participated. The scientific program was inclusive keeping in mind the diverse background of delegates from the member nations. Large numbers of research papers were presented, mostly by fellows in training. PMID:25684899

  6. IBA investigations of loose garnets from Pietroasa, Apahida and Cluj-Someşeni treasures (5th century AD)

    NASA Astrophysics Data System (ADS)

    Bugoi, R.; Oanţă-Marghitu, R.; Calligaro, T.

    2016-03-01

    This paper reports the archaeometric investigations of 418 loose garnets from Pietroasa and Cluj-Someşeni treasures and Apahida II and III princely grave inventories (5th century AD). The chemical composition of the gems was determined by external beam micro-PIXE technique at the AGLAE accelerator of C2RMF, Paris, France. Complementary observations made by Optical Microscopy revealed details on the gemstones cutting and polishing and permitted to identify certain mineral inclusions. The compositional results evidenced several types of garnets from the pyralspite series, suggesting distinct provenances for these Early Medieval gems.

  7. Effect of Gradient Sequencing on Copolymer Order-Disorder Transitions: Phase Behavior of Styrene/n-Butyl Acrylate Block and Gradient Copolymers

    SciTech Connect

    Mok, Michelle M; Ellison, Christopher J; Torkelson, John M

    2012-11-14

    We investigate the effect of gradient sequence distribution in copolymers on order-disorder transitions, using rheometry and small-angle X-ray scattering to compare the phase behavior of styrene/n-butyl acrylate (S/nBA) block and gradient copolymers. Relative to block sequencing, gradient sequencing increases the molecular weight necessary to induce phase segregation by over 3-fold, directly consistent with previous predictions from theory. Results also suggest the existence of both upper and lower order-disorder transitions in a higher molecular weight S/nBA gradient copolymer, made accessible by the shift in order-disorder temperatures from gradient sequencing. The combination of transitions is speculated to be inaccessible in S/nBA block copolymer systems due to their overlap at even modest molecular weights and also their location on the phase diagram relative to the polystyrene glass transition temperature. Finally, we discuss the potential impacts of polydispersity and chain-to-chain monomer sequence variation on gradient copolymer phase segregation.

  8. Data in support of crystal structures of highly-ordered long-period stacking-ordered phases with 18R, 14H and 10H-type stacking sequences in the Mg–Zn–Y system

    PubMed Central

    Kishida, Kyosuke; Nagai, Kaito; Matsumoto, Akihide; Inui, Haruyuki

    2015-01-01

    The crystal structures of highly-ordered Mg–Zn–Y long-period stacking-ordered (LPSO) phases with the 18R, 14H and 10H-type stacking sequences have been investigated by atomic-resolution scanning transmission electron microscopy (STEM) and transmission electron microscopy (Kishida et al., 2015) [1]. This data article provides supporting materials for the crystal structure analysis based on the crystallographic theory of the order–disorder (OD) structure and the crystallographic information obtained through the structural optimization for various simple polytypes of the highly-ordered Mg–Zn–Y LPSO phases with the 18R, 14H and 10H-type stacking sequences by first-principles density functional theory (DFT) calculations. PMID:26566542

  9. Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales.

    PubMed

    Nouioui, Imen; Gtari, Maher; Göker, Markus; Ghodhbane-Gtari, Faten; Tisa, Louis S; Fernandez, Maria P; Normand, Philippe; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Varghese, Neha; Reddy, T B K; Ivanova, Natalia; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter

    2016-01-01

    Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is characterized by its ability to nodulate actinorhizal plants of the Rhamnales order, but not its original host. It represents one of the largest Frankia genomes so far sequenced (9.5 Mbp). PMID:27231368

  10. Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales

    PubMed Central

    Nouioui, Imen; Gtari, Maher; Göker, Markus; Ghodhbane-Gtari, Faten; Tisa, Louis S.; Fernandez, Maria P.; Normand, Philippe; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Varghese, Neha; Reddy, T. B. K.; Ivanova, Natalia; Woyke, Tanja; Kyrpides, Nikos C.

    2016-01-01

    Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is characterized by its ability to nodulate actinorhizal plants of the Rhamnales order, but not its original host. It represents one of the largest Frankia genomes so far sequenced (9.5 Mbp). PMID:27231368

  11. Double Layers: Potential Formation and Related Nonlinear Phenomena in Plasmas: Proceedings of the 5th Symposium

    NASA Astrophysics Data System (ADS)

    Iizuka, S.

    1998-02-01

    Parallel Velocity Shear Instability (Invited) * Low-Frequency Instabilities under a Cross-Field Electric Field in a K+-C60- Plasma * 3.3 Vortex Formation * Vortex Dynamics in Low Frequency Electrostatic Turbulence * Development of Spiral-Vortex Structures of the Plasma During Rotation in a Neutral Gas * Vortex Formation of Particles in Magnetized Dusty Plasmas (Invited) * CHAPTER 4: SOLITONS, SHOCKS, WAVES AND INSTABILITIES, AND RELATED NONLINEAR PHENOMENA * 4.1 Solitons and Shocks * Refraction and Reflection of Ion Acoustic Solitons by Space Charge Sheath * 2D and 3D Solitons in Plasma: Structure, Stability, Dynamics * Solitary Waves in an Ion-Beam Multi-Component Plasma System * Shock Formation in a Q-Machine Plasma with Negative Ions * 4.2 Waves and Instabilities * Single-Ended Q-Machine as a Source of Oscillations (Invited) * Numerical and Experimental Investigations of Period Doubling of the Potential Relaxation Instability in an Electron-Rich Q-Machine Plasma * Large Amplitude Electrostatic Ion Waves in an e- - e+ - p Plasma * Measurements of Alfvén Waves around the CRIT Releases-Implications for Current Limitation in Alfvén Wings * 4.3 Nonlinear Phenomena * Self-Organization Phenomena in a Q-Machine Plasma * Nonlinearity Related to Self-Organization in a Thermionic Vacuum Arc Discharge * Spontaneous Formation of Ordered Spatio-Temporal Structures in Laboratory and Nature * Nonlinear Evolution and Stabilization of Linearly Unstable Waves in an Electron-Beam Plasma * Disruption of an Electron Hole Due to its Interaction with Ion Acoustic Waves in a Plasma * Expanding Plasma Clouds with Dust Particles (Invited) * LIST OF PARTICIPANTS * AUTHOR INDEX

  12. PREFACE: 5th International Conference on Materials and Applications for Sensors and Transducers (IC-MAST2015)

    NASA Astrophysics Data System (ADS)

    Hristoforou, E.; Vlachos, D. S.; Giouroudi, I.; Kar-Narayan, S.; Potirakis, S.

    2016-03-01

    The 5th International Conference on Materials and Applications for Sensors and Transducers, Mykonos island, Greece, hosted about 110 oral and poster papers and more than 90 participants. IC-MAS, as an international annual conference which tries to meet the needs for various types of sensors, particularly those which may be manufactured by low cost methods (i.e. hybrid sensors, smart specialization devices, particular applications not necessarily requiring integrated micro-nano technologies), covering all types of materials and physical effects, appears to be a necessity. IC-MAST has been established as a high quality international conference by: I. Gathering together multinational researchers from all over the world, working in different materials for sensors and transducers and technical applications of sensors, but also in some cases in the management of the data coming from sensors and transducers. The careful selection of the conference place (like Aegean Sea, Budapest, Prague, Bilbao, Mykonos etc) allows for enjoying the local hospitality and sightseeing. II. Emphasizing in hybrid sensors and smart specialization devices produced by inexpensive methods, without excluding of course micro-nano technology, from all kinds of solid state, liquid and gaseous materials, as well as in particular transducer applications (design and development, as well as use of sensing data) III. Innovatively implementing the Virtual Paper Concept, allowing for large impact of research works presented in the conference by authors who either have no time or no funding support for visiting a conference; this year more than 12 virtual papers are presented in the 5th IC MAST, following a standardized procedure via the our robust and reliable Conference Site (www.icmast.net!) > IV. Allowing for lengthy technical and managerial discussions in terms of sensor, material and instrumentation development; furthermore, the different research groups gathered together are offered the particular

  13. Primary School 5th and 8th Graders' Understanding and Mental Models about the Shape of the World and Gravity

    ERIC Educational Resources Information Center

    Öztürk, Ayse; Doganay, Ahmet

    2013-01-01

    This study investigated primary school 5th and 8th graders' understanding and mental models related to the shape of the world and gravity, and how these models reflected the fact and what kind of a change there is from 5th to 8th graders. This research is based on a cross-sectional design. The study was conducted in a low socioeconomic level…

  14. Macracanthorhynchus hirudinaceus Eggs in Canine Coprolite from the Sasanian Era in Iran (4(th)/5(th) Century CE).

    PubMed

    Mowlavi, Gholamreza; Makki, Mahsasadat; Heidari, Zahra; Rezaeian, Mostafa; Mohebali, Mehdi; Araujo, Adauto; Boenke, Nicole; Aali, Abolfazl; Stollner, Thomas; Mobedi, Iraj

    2015-01-01

    Present paper is the second publication introducing the paleoparasitological findings from animal coprolites obtained from archeological site of Chehrabad salt mine in northwestern Iran. The current archeological site is located in northwest of Iran, dated to the Sassanian Era (4(th)/5(th) century CE). In the summer 2012 the carnivore coprolite was obtained within the layers in the mine and were thoroughly analyzed for parasites using TSP rehydration technique. Eggs of 0 were successfully retrieved from the examined coprolite and were confidently identified based on reliable references. Identifying of M. hirudinaceus eggs in paleofeces with clear appearance as demonstrated herein, is much due to appropriate preservation condition has been existed in the salt mine .The present finding could be regarded as the oldest acanthocephalan infection in Iran. PMID:26246822

  15. Macracanthorhynchus hirudinaceus Eggs in Canine Coprolite from the Sasanian Era in Iran (4th/5th Century CE)

    PubMed Central

    MOWLAVI, Gholamreza; MAKKI, Mahsasadat; HEIDARI, Zahra; REZAEIAN, Mostafa; MOHEBALI, Mehdi; ARAUJO, Adauto; BOENKE, Nicole; AALI, Abolfazl; STOLLNER, Thomas; MOBEDI, Iraj

    2015-01-01

    Present paper is the second publication introducing the paleoparasitological findings from animal coprolites obtained from archeological site of Chehrabad salt mine in northwestern Iran. The current archeological site is located in northwest of Iran, dated to the Sassanian Era (4th/5th century CE). In the summer 2012 the carnivore coprolite was obtained within the layers in the mine and were thoroughly analyzed for parasites using TSP rehydration technique. Eggs of 0 were successfully retrieved from the examined coprolite and were confidently identified based on reliable references. Identifying of M. hirudinaceus eggs in paleofeces with clear appearance as demonstrated herein, is much due to appropriate preservation condition has been existed in the salt mine .The present finding could be regarded as the oldest acanthocephalan infection in Iran. PMID:26246822

  16. Method and software for using m-sequences to characterize parallel components of higher-order visual tracking behavior in Drosophila.

    PubMed

    Aptekar, Jacob W; Keles, Mehmet F; Mongeau, Jean-Michel; Lu, Patrick M; Frye, Mark A; Shoemaker, Patrick A

    2014-01-01

    A moving visual figure may contain first-order signals defined by variation in mean luminance, as well as second-order signals defined by constant mean luminance and variation in luminance envelope, or higher-order signals that cannot be estimated by taking higher moments of the luminance distribution. Separating these properties of a moving figure to experimentally probe the visual subsystems that encode them is technically challenging and has resulted in debated mechanisms of visual object detection by flies. Our prior work took a white noise systems identification approach using a commercially available electronic display system to characterize the spatial variation in the temporal dynamics of two distinct subsystems for first- and higher-order components of visual figure tracking. The method relied on the use of single pixel displacements of two visual stimuli according to two binary maximum length shift register sequences (m-sequences) and cross-correlation of each m-sequence with time-varying flight steering measurements. The resultant spatio-temporal action fields represent temporal impulse responses parameterized by the azimuthal location of the visual figure, one STAF for first-order and another for higher-order components of compound stimuli. Here we review m-sequence and reverse correlation procedures, then describe our application in detail, provide Matlab code, validate the STAFs, and demonstrate the utility and robustness of STAFs by predicting the results of other published experimental procedures. This method has demonstrated how two relatively modest innovations on classical white noise analysis--the inclusion of space as a way to organize response kernels and the use of linear decoupling to measure the response to two channels of visual information simultaneously--could substantially improve our basic understanding of visual processing in the fly. PMID:25400550

  17. Method and software for using m-sequences to characterize parallel components of higher-order visual tracking behavior in Drosophila

    PubMed Central

    Aptekar, Jacob W.; Keles, Mehmet F.; Mongeau, Jean-Michel; Lu, Patrick M.; Frye, Mark A.; Shoemaker, Patrick A.

    2014-01-01

    A moving visual figure may contain first-order signals defined by variation in mean luminance, as well as second-order signals defined by constant mean luminance and variation in luminance envelope, or higher-order signals that cannot be estimated by taking higher moments of the luminance distribution. Separating these properties of a moving figure to experimentally probe the visual subsystems that encode them is technically challenging and has resulted in debated mechanisms of visual object detection by flies. Our prior work took a white noise systems identification approach using a commercially available electronic display system to characterize the spatial variation in the temporal dynamics of two distinct subsystems for first- and higher-order components of visual figure tracking. The method relied on the use of single pixel displacements of two visual stimuli according to two binary maximum length shift register sequences (m-sequences) and cross-correlation of each m-sequence with time-varying flight steering measurements. The resultant spatio-temporal action fields represent temporal impulse responses parameterized by the azimuthal location of the visual figure, one STAF for first-order and another for higher-order components of compound stimuli. Here we review m-sequence and reverse correlation procedures, then describe our application in detail, provide Matlab code, validate the STAFs, and demonstrate the utility and robustness of STAFs by predicting the results of other published experimental procedures. This method has demonstrated how two relatively modest innovations on classical white noise analysis—the inclusion of space as a way to organize response kernels and the use of linear decoupling to measure the response to two channels of visual information simultaneously—could substantially improve our basic understanding of visual processing in the fly. PMID:25400550

  18. Tailored selection of study individuals to be sequenced in order to improve the accuracy of genotype imputation.

    PubMed

    Peil, Barbara; Kabisch, Maria; Fischer, Christine; Hamann, Ute; Bermejo, Justo Lorenzo

    2015-02-01

    The addition of sequence data from own-study individuals to genotypes from external data repositories, for example, the HapMap, has been shown to improve the accuracy of imputed genotypes. Early approaches for reference panel selection favored individuals who best reflect recombination patterns in the study population. By contrast, a maximization of genetic diversity in the reference panel has been recently proposed. We investigate here a novel strategy to select individuals for sequencing that relies on the characterization of the ancestral kernel of the study population. The simulated study scenarios consisted of several combinations of subpopulations from HapMap. HapMap individuals who did not belong to the study population constituted an external reference panel which was complemented with the sequences of study individuals selected according to different strategies. In addition to a random choice, individuals with the largest statistical depth according to the first genetic principal components were selected. In all simulated scenarios the integration of sequences from own-study individuals increased imputation accuracy. The selection of individuals based on the statistical depth resulted in the highest imputation accuracy for European and Asian study scenarios, whereas random selection performed best for an African-study scenario. Present findings indicate that there is no universal 'best strategy' to select individuals for sequencing. We propose to use the methodology described in the manuscript to assess the advantage of focusing on the ancestral kernel under own study characteristics (study size, genetic diversity, availability and properties of external reference panels, frequency of imputed variants…). PMID:25537753

  19. The Hetu'u Global Network: Using the rare June 5th/6th Transit of Venus to Bring Astronomy to the Remote Easter Island

    NASA Astrophysics Data System (ADS)

    Faherty, Jacqueline; Rodriguez, D.

    2013-01-01

    There are rare times in astronomy when a celestial event, visible in broad daylight, can be used to measure a fundamental parameter and inspire a globe full of school age students. The June 5th/6th transit of Venus was one such event. In celebration, nine astronomy postdocs from the Chilean mainland traveled to Easter Island to lead a series of astronomy outreach activities over three days, culminating in a transit-viewing event. Our team dubbed "Equipo Hetu'u" or "Team Star" in the Rapa Nui (Easter Island native) language spent two days giving astronomy talks and doing hands-on demonstrations at the Museo Antropologico P. Sebastian Englert. In the final day-and-a-half leading up to the transit, we visited the science classes in the majority of the schools on the island, in order to spread the message about the once-in-a-lifetime transit event, highlighting how we planned on using it to measure the distance to the Sun. We estimate over 25% 1500 people) of this remote island participated in one or more of our organized activities. Our experience with this project is an excellent lesson on how to organize, lead, and fully execute a major outreach endeavor that inspires hundreds with minimal resources (save the spectacular event provided by the cosmos).

  20. [The current situation and issues of medical English education and suggestions toward improvement--reports from the 5th meeting of the Japan Society for Medical English Education].

    PubMed

    Ohashi, Hiroshi

    2002-12-01

    This is a report from the 5th academic meeting of the Japan Society for Medical English Education held at Kawasaki University of Medical Welfare on August 3rd and 4th of 2002. It also includes a course description of our English courses, their problems and some suggestions for improvement. First, I report several papers presented at the meeting that are useful and suggestive for the English education at our university in order to bring them to everyone's attention and to improve our English program. The topics of the papers include; what "Medical English" is; reports of English courses taught by medical doctors; reports of English courses for developing specific proficiencies such as listening, writing summaries and delivering oral presentations. Next, I give a course description of our present English program and point out some problems that should be dealt with. In this connection, I make several suggestions for future improvement. Lastly, I refer to the "strategies to educate the Japanese who can use English", which were proposed recently by the Ministry of Education, Culture, Sports, Science and Technology and suggest our improvement be in line with these strategies. PMID:12506860

  1. Preparation and characterization of ordered libraries of transcribable sequences from human chromosome 19 from hybrid human-hamster cells

    SciTech Connect

    Obradovick, D.; Borodin, A.M.; Kopantsev, E.P.

    1994-08-20

    Improvements in the preparation of chromosome-specific libraries of transcribable sequences from the human genome using somatic hybrid cells are described. One of the main advantages of the new method is the enrichment of the starting material with human-specific heterogeneous nuclear RNA (hnRNA) sequences at each of the three steps in library construction. The method was used to prepare a chromosome-specific library from a hybrid cell line. The resulting ranged library was characterized. The primary structures of 80 randomly selected clones were determined, and these were analyzed. Some 95% of the clones were found to be human-specific and to have arisen from hnRNA, and the chromosomal localizations of a number of clones were identified. The advantages and disadvantages of the method are discussed. 34 refs., 3 figs., 2 tabs.

  2. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

    PubMed Central

    Hovde, Blake T.; Deodato, Chloe R.; Hunsperger, Heather M.; Ryken, Scott A.; Yost, Will; Jha, Ramesh K.; Patterson, Johnathan; Monnat, Raymond J.; Barlow, Steven B.; Starkenburg, Shawn R.; Cattolico, Rose Ann

    2015-01-01

    Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (∼40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes. PMID:26397803

  3. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae).

    PubMed

    Hovde, Blake T; Deodato, Chloe R; Hunsperger, Heather M; Ryken, Scott A; Yost, Will; Jha, Ramesh K; Patterson, Johnathan; Monnat, Raymond J; Barlow, Steven B; Starkenburg, Shawn R; Cattolico, Rose Ann

    2015-01-01

    Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (∼ 40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two "red" RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes. PMID:26397803

  4. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

    SciTech Connect

    Hovde, Blake T.; Deodato, Chloe R.; Hunsperger, Heather M.; Ryken, Scott A.; Yost, Will; Jha, Ramesh K.; Patterson, Johnathan; Monnat, Raymond J.; Barlow, Steven B.; Starkenburg, Shawn R.; Cattolico, Rose Ann; Richardson, Paul M.

    2015-09-23

    Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (∼40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. In conclusion, the Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

  5. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

    DOE PAGESBeta

    Hovde, Blake T.; Deodato, Chloe R.; Hunsperger, Heather M.; Ryken, Scott A.; Yost, Will; Jha, Ramesh K.; Patterson, Johnathan; Monnat, Raymond J.; Barlow, Steven B.; Starkenburg, Shawn R.; et al

    2015-09-23

    Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. Themore » nuclear genome of C. tobin is small (59 Mb), compact (∼40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. In conclusion, the Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.« less

  6. Co-conservation of rRNA tetraloop sequences and helix length suggests involvement of the tetraloops in higher-order interactions

    NASA Technical Reports Server (NTRS)

    Hedenstierna, K. O.; Siefert, J. L.; Fox, G. E.; Murgola, E. J.

    2000-01-01

    Terminal loops containing four nucleotides (tetraloops) are common in structural RNAs, and they frequently conform to one of three sequence motifs, GNRA, UNCG, or CUUG. Here we compare available sequences and secondary structures for rRNAs from bacteria, and we show that helices capped by phylogenetically conserved GNRA loops display a strong tendency to be of conserved length. The simplest interpretation of this correlation is that the conserved GNRA loops are involved in higher-order interactions, intramolecular or intermolecular, resulting in a selective pressure for maintaining the lengths of these helices. A small number of conserved UNCG loops were also found to be associated with conserved length helices, consistent with the possibility that this type of tetraloop also takes part in higher-order interactions.

  7. Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of Two Lilies (Lilium longiflorum and Alstroemeria aurea)

    PubMed Central

    Kim, Jung Sung; Kim, Joo-Hwan

    2013-01-01

    Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Liliumlongiflorum (Liliaceae) and 155,510bp in Alstroemeriaaurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium. PMID:23950788

  8. Comparative genome analysis and phylogenetic relationship of order Liliales insight from the complete plastid genome sequences of two Lilies (Lilium longiflorum and Alstroemeria aurea).

    PubMed

    Kim, Jung Sung; Kim, Joo-Hwan

    2013-01-01

    Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium. PMID:23950788

  9. 5th International ACC Symposium: Classification of Adrenocortical Cancers from Pathology to Integrated Genomics: Real Advances or Lost in Translation?

    PubMed

    de Krijger, Ronald E; Bertherat, Jérôme

    2016-02-01

    For the clinician, despite its rarity, adrenocortical cancer is a heterogeneous tumor both in term of steroid excess and tumor evolution. For patient management, it is crucial to have an accurate vision of this heterogeneity, in order to use a correct tumor classification. Pathology is the best way to classify operated adrenocortical tumors: to recognize their adrenocortical nature and to differentiate benign from malignant tumors. Among malignant tumors pathology also aims at prognosis assessment. Although progress has being made for prognosis assessment, there is still a need for improvement. Recent studies have established the value of Ki67 for adrenocortical cancer (ACC) prognostication, aiming also at standardization to reduce variability. The use of genomics to study adrenocortical tumors gives a very new insight in their pathogenesis and molecular classification. Genomics studies of ACC give now a clear description of the mRNA (transcriptome) and miRNA expression profile, as well as chromosomal and methylation alterations. Exome sequencing also established firmly the list of the main ACC driver genes. Interestingly, genomics study of ACC also revealed subtypes of malignant tumors with different pattern of molecular alterations, associated with different outcome. This leads to a new vision of adrenocortical tumors classification based on molecular analysis. Interestingly, these molecular classifications meet also the results of pathological analysis. This opens new perspectives on the development and use of various molecular tools to classify, along with pathological analysis, ACC, and guides patient management at the area of precision medicine. PMID:26676358

  10. Communicating Science to Impact Learning? A Phenomenological Inquiry into 4th and 5th Graders' Perceptions of Science Information Sources

    NASA Astrophysics Data System (ADS)

    Gelmez Burakgazi, Sevinc; Yildirim, Ali; Weeth Feinstein, Noah

    2016-04-01

    Rooted in science education and science communication studies, this study examines 4th and 5th grade students' perceptions of science information sources (SIS) and their use in communicating science to students. It combines situated learning theory with uses and gratifications theory in a qualitative phenomenological analysis. Data were gathered through classroom observations and interviews in four Turkish elementary schools. Focus group interviews with 47 students and individual interviews with 17 teachers and 10 parents were conducted. Participants identified a wide range of SIS, including TV, magazines, newspapers, internet, peers, teachers, families, science centers/museums, science exhibitions, textbooks, science books, and science camps. Students reported using various SIS in school-based and non-school contexts to satisfy their cognitive, affective, personal, and social integrative needs. SIS were used for science courses, homework/project assignments, examination/test preparations, and individual science-related research. Students assessed SIS in terms of the perceived accessibility of the sources, the quality of the content, and the content presentation. In particular, some sources such as teachers, families, TV, science magazines, textbooks, and science centers/museums ("directive sources") predictably led students to other sources such as teachers, families, internet, and science books ("directed sources"). A small number of sources crossed context boundaries, being useful in both school and out. Results shed light on the connection between science education and science communication in terms of promoting science learning.

  11. Clinical development of new prophylactic antimalarial drugs after the 5th Amendment to the Declaration of Helsinki

    PubMed Central

    Dow, Geoffrey S; Magill, Alan J; Ohrt, Colin

    2008-01-01

    Malaria is of continuing concern in nonimmune traveling populations. Traditionally, antimalarial drugs have been developed as agents for dual indications (treatment and prophylaxis). However, since 2000, when the 5th Amendment to the Declaration of Helsinki (DH2000) was adopted, development of new malaria prophylaxis drugs in this manner has ceased. As a consequence, there may not be any new drugs licensed for this indication in the foreseeable future. Major pharmaceutical companies have interpreted DH2000 to mean that the traditional development paradigm may be considered unethical because of doubt over the likelihood of benefit to endemic populations participating in clinical studies, the use of placebo, and the sustainability of post-trial access to study medications. In this article, we explore the basis of these concerns and suggest that the traditional development paradigm remains ethical under certain circumstances. We also consider alternative approaches that may be more attractive to sponsors as they either do not use placebo, or utilize populations in endemic countries who may unambiguously benefit. These approaches represent the way forward in the future, but are at present unproven in clinical practice, and face numerous regulatory, logistical and technical challenges. Consequently, in the short term, we argue that the traditional clinical development paradigm remains the most feasible approach and is ethical and consistent with the spirit of DH2000 under the appropriate circumstances. PMID:19209263

  12. Attitudes towards General Practice: a comparative cross-sectional survey of 1st and 5th year medical students

    PubMed Central

    Kruschinski, Carsten; Wiese, Birgitt; Hummers-Pradier, Eva

    2012-01-01

    Objective: Positive attitudes towards General Practice can be understood as a prerequisite for becoming a General Practitioner (GP) and for collaboration with GPs later on. This study aimed to assess attitudes of medical students at the beginning and the end of medical school. Methods: A total of 160 1st year students at Hannover Medical School were surveyed. Their attitudes were compared to those of 287 5th year students. Descriptive, bi- and multivariate analyses were performed to investigate influences of year of study and gender. Results: Year of study and gender both were associated with the attitudes towards General Practice. The interest in General Practice and patient-orientation (communication, care of older patients with chronic diseases) was higher in 1st year students compared to more advanced students. Female students valued such requirements more than male students, the differences in attitudes between the years of study being more pronounced in male students. Conclusion: Despite some limitations caused by the cross-sectional design, the attitudes towards General Practice competencies changed to their disadvantage during medical school. This suggests a formative influence of the strategies used in medical education. Educational strategies, however, could be used to bring about a change of attitudes in the other direction. PMID:23255966

  13. Fast food consumption and food prices: evidence from panel data on 5th and 8th grade children.

    PubMed

    Khan, Tamkeen; Powell, Lisa M; Wada, Roy

    2012-01-01

    Fast food consumption is a dietary factor associated with higher prevalence of childhood obesity in the United States. The association between food prices and consumption of fast food among 5th and 8th graders was examined using individual-level random effects models utilizing consumption data from the Early Childhood Longitudinal Study, Kindergarten Class of 1998-99 (ECLS-K), price data from American Chamber of Commerce Researchers Association (ACCRA), and contextual outlet density data from Dun and Bradstreet (D&B). The results found that contextual factors including the price of fast food, median household income, and fast food restaurant outlet densities were significantly associated with fast food consumption patterns among this age group. Overall, a 10% increase in the price of fast food was associated with 5.7% lower frequency of weekly fast food consumption. These results suggest that public health policy pricing instruments such as taxes may be effective in reducing consumption of energy-dense foods and possibly reducing the prevalence of overweight and obesity among US children and young adolescents. PMID:22292115

  14. Historical and future land carbon cycle, results from the 5th Coupled Model Intercomparison Project (CMIP5)

    NASA Astrophysics Data System (ADS)

    Friedlingstein, Pierre; Anav, Alessandro; Murray-Tortarolo, Guillermo; Wenzel, Sabrina; Cox, Peter; Eyring, Veronika

    2014-05-01

    The 5th Coupled Model Intercomparison Project (CMIP5) provided a unique source of Earth System Models simulations, generating an unprecedented range of analysis of many components of the climate system. In this presentation we will focus on the land carbon cycle, its response to the historical perturbation and its projected response in the future under the forcing of the different Representative Concentration Pathways (RCPs) scenarios. There is a broad agreement across models on the evolution of the carbon exchange between the atmosphere and the land since the beginning of the industrial revolution. Carbon sink driven by atmospheric CO2 increase more than compensates now the carbon sources due to land use changes, consistent with independent estimates. The future of the land carbon cycle is significantly more uncertain, even for a given RCP scenario. There is no overall agreement across models on the sign of the land carbon sink by the end of the 21st century, land carbon cycle sensitivity to atmospheric CO2 increase and climate change being strongly model dependent. Model evaluation and use of emerging constraint should help reduce uncertainties in future carbon cycle projections.

  15. Fast Food Consumption and Food Prices: Evidence from Panel Data on 5th and 8th Grade Children

    PubMed Central

    Khan, Tamkeen; Powell, Lisa M.; Wada, Roy

    2012-01-01

    Fast food consumption is a dietary factor associated with higher prevalence of childhood obesity in the United States. The association between food prices and consumption of fast food among 5th and 8th graders was examined using individual-level random effects models utilizing consumption data from the Early Childhood Longitudinal Study, Kindergarten Class of 1998-99 (ECLS-K), price data from American Chamber of Commerce Researchers Association (ACCRA), and contextual outlet density data from Dun and Bradstreet (D&B). The results found that contextual factors including the price of fast food, median household income, and fast food restaurant outlet densities were significantly associated with fast food consumption patterns among this age group. Overall, a 10% increase in the price of fast food was associated with 5.7% lower frequency of weekly fast food consumption. These results suggest that public health policy pricing instruments such as taxes may be effective in reducing consumption of energy-dense foods and possibly reducing the prevalence of overweight and obesity among US children and young adolescents. PMID:22292115

  16. Bond Strength of 5th, 6th and 7th Generation Bonding Agents to Intracanal Dentin of Primary Teeth

    PubMed Central

    Afshar, Hossein; Baradaran Nakhjavani, Yahya; Rahro Taban, Sedighe; Baniameri, Zahra; Nahvi, Azam

    2015-01-01

    Objectives: This in-vitro study sought to assess the push-out bond strength of a total etch and 2 self-etch bonding systems to intracanal dentin of primary anterior teeth (PAT). Materials and Methods: Thirty-six primary anterior teeth were randomly divided into 3 groups of 5th generation (Single Bond 2), 6th generation (Clearfil SE) and 7th generation (Single Bond Universal) bonding agents. The canal orifice was restored with composite resin and the push-out test was carried out to assess the bond strength. After applying the push-out load, specimens were evaluated under a light microscope at 40X magnification. One-way ANOVA and log-rank test on Kaplan-Meier curves were applied for the comparison of bond strength among the 3 groups. Results: The mean± standard deviation (SD) bond strength was 13.6±5.33 MPa for Single Bond 2, 13.85±5.86 MPa for Clearfil SE and 12.28±5.24 MPa for Single Bond Universal. The differences in bond strength among the 3 groups were not statistically significant (P>0.05). Conclusion: All three bonding agents are recommended for use with composite posts in PAT. However, due to high technical sensitivity of the Total Etch system, single or two-step self etch systems may be preferred for uncooperative children. PMID:26056518

  17. Final Report for DOE Support of 5th the International Workshop on Oxide Surfaces (IWOX-V)

    SciTech Connect

    Charles T. Campbell

    2007-02-02

    The 5th International Workshop on Oxide Surfaces (IWOX-V) was held at Granlibakken Conference center in Lake Tahoe, CA, January 7-12. The total attendance was ~90. The breakdown of attendees by country is as follows: USA 41 Germany 18 Japan 7 UK 5 Italy 5 France 4 Austria 3 Denmark 3 Cech. Repub. 1 Ireland 1 New Zealand 1 India 1 The technical program included oral sessions on the electronic and magnetic properties of oxide surfaces, surface and interface structure, advances in theory, surface defects, thin film oxides on metals and on oxides, thin film metals on oxides, surface photochemistry, surface reactivity, and interactions with water. Two evening poster sessions had similar themes. As in previous years, the program stimulated significant interest and discussion among the attendees. The local expenses (food and lodging, $918 per person) for eight foreign invited speakers were covered by BES funds. In addition, partial reimbursement for travel ($328 per person) was supported by BES funds for two more foreign invited speakers.

  18. Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura.

    PubMed

    Knudsen, Bjarne; Kohn, Andrea B; Nahir, Ben; McFadden, Catherine S; Moroz, Leonid L

    2006-02-01

    We have sequenced and characterized the complete mitochondrial genome of the sea slug, Aplysia californica, an important model organism in experimental biology and a representative of Anaspidea (Opisthobranchia, Gastropoda). The mitochondrial genome of Aplysia is in the small end of the observed sizes of animal mitochondrial genomes (14,117 bp, NCBI Accession No. NC_005827). The Aplysia genome, like most other mitochondrial genomes, encodes genes for 2 ribosomal subunit RNAs (small and large rRNAs), 22 tRNAs, and 13 protein subunits (cytochrome c oxidase subunits 1-3, cytochrome b apoenzyme, ATP synthase subunits 6 and 8, and NADH dehydrogenase subunits 1-6 and 4L). The gene order is virtually identical between opisthobranchs and pulmonates, with the majority of differences arising from tRNA translocations. In contrast, the gene order from representatives of basal gastropods and other molluscan classes is significantly different from opisthobranchs and pulmonates. The Aplysia genome was compared to all other published molluscan mitochondrial genomes and phylogenetic analyses were carried out using a concatenated protein alignment. Phylogenetic analyses using maximum likelihood based analyses of the well aligned regions of the protein sequences support both monophyly of Euthyneura (a group including both the pulmonates and opisthobranchs) and Opisthobranchia (as a more derived group). The Aplysia mitochondrial genome sequenced here will serve as an important platform in both comparative and neurobiological studies using this model organism. PMID:16230032

  19. Higher-order structure of bovine mitochondrial tRNA(Phe) lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing.

    PubMed Central

    Wakita, K; Watanabe, Y; Yokogawa, T; Kumazawa, Y; Nakamura, S; Ueda, T; Watanabe, K; Nishikawa, K

    1994-01-01

    Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order structure was investigated using RNaseT2 and chemical reagents as structural probes. The D and T loop regions as well as the anticodon loop region were accessible to RNaseT2, and the N-3 positions of cytidines present in the D and T loops were easily modified under the native conditions in the presence of 10mM Mg2+. On the other hand, the nucleotides present in the extra loop were protected from the chemical modification under the native conditions. From the results of these probing analyses and a comparison of the sequences of mitochondrial tRNA(Phe) genes from various organisms, it was inferred that bovine mt tRNA(Phe) lacks the D loop/T loop tertiary interactions, but does have the canonical extra loop/D stem interactions, which seem to be the main factor for bovine mt tRNA(Phe) to preserve its L-shaped higher-order structure. Images PMID:7510390

  20. Implementing SPRINTT [Student Polar Research with IPY National(and International)Teacher Training] in 5th Grade Science

    NASA Astrophysics Data System (ADS)

    Glass, D. S.

    2009-12-01

    I implemented the new NSF-funded SPRINTT (Student Polar Research with IPY National (and International) Teacher Training) curriculum with a 5th grade science class. SPRINTT, developed at U.S. Satellite Laboratory, Inc., is a 5-8 week science program teaching 5th through 10th graders to investigate climate change using polar data. The program includes perspectives of both Western scientists and the indigenous Northern population. The course contains three phases: Phase 1 includes content, data interpretation, and hands-on experiments to study Frozen Water, Frozen Land, and Food; Phase 2 (optional) includes further content on specific polar topics; and Phase 3 is a scaffolded research investigation. Before the course, teachers were trained via live webinars. This curriculum capitalizes on children’s innate fascination with our planet’s final frontier and combines it with the politically and scientifically relevant topic of climate change. In 2009, I used SPRINTT with 23 heterogeneous fifth grade students at National Presbyterian School in Washington DC for an environmental science unit. Overall, it was a success. The students met most of the learning objectives and showed enthusiasm for the material. I share my experiences to help other educators and curriculum developers. The Phase 1 course includes earth science (glaciers, sea ice, weather and climate, greenhouse gases, seasons, and human impacts on environments), life science (needs of living things, food and energy transfer, adaptations, and ecosystems and biomes) and physical science (phases of matter). Tailoring the program, I focused on Phase 1, the most accessible material and content, while deemphasizing the more cumbersome Phase 3 online research project. Pre-assessments documented the students’ misconceptions and informed instruction. The investigations were appropriately educational and interesting. For example, students enjoyed looking at environmental factors and their impact on the people in the

  1. Intraocular tissue ablation using an optical fibre to deliver the 5th harmonic of a Nd:YAG

    NASA Astrophysics Data System (ADS)

    Miller, Joseph; Yu, Xiaobo; Yu, Paula K.; Cringle, Stephen J.; Yu, Dao-Yi

    2009-02-01

    We report the evaluation of a system which delivers the 5th harmonic of an Nd:YAG (213nm) via optical fibre to ocular tissue sites. The 213nm beam is concentrated, using a hollow glass taper, prior to launch into 200 μm or 600 μm core diameter silica/silica optical fibre. The fibre tip was tapered to enhance the fluence delivered. An operating window of fluence values that could be delivered via 330 - 1100mm lengths of optical fibre was determined. The lower value of 0.2J/cm2 determined by the ablation threshold of the tissue and the upper value of 1.3J/cm2 by the launch, transmission and tip characteristics of the optical fibre. The fluence output decreased as a function of both transmitted pulse energy and number of pulses transmitted. Fresh retinal tissue was cleanly ablated with minimal damage to the surrounding tissue. Lesions were generated using 1, 3 and 10 pulses with fluences from 0.2 to 1.0J/cm2. The lesion depth demonstrated clear dose dependence. Lesions generated in ex vivo preparations of human trabecular meshwork in a fluid environment also demonstrated dose dependence, 50 pulses being sufficient to create a hole within the trabecular meshwork extending to Schlemm's canal. The dose dependence of the ablation depth combined with the ability of this technique to create a conduit through to Schlemm's canal demonstrates the potential of this technique for ophthalmological applications requiring precise and controlled intraocular tissue removal and has potential applications in the treatment and management of glaucoma.

  2. Indian Health Career Handbook and Report on Ned Hatathli Seminar for Southern Arizona Indian Students (5th, Tucson, Arizona, February 6-7, 1975).

    ERIC Educational Resources Information Center

    Taylor, Arnold, Ed.; And Others

    Utilizing comments from teachers, professionals, college and high school students, this report is derived from the 5th Ned Hatathli Seminar, sponsored by the Navajo Health Authority, and presents factual information relative to American Indian participation in Indian Health careers. The following major speeches are presented: (1) "The Practice of…

  3. Engaging Minds. Proceedings of the National Academy for Integration of Research, Teaching and Learning Annual Conference (5th, Galway, Ireland, June 9-10, 2011)

    ERIC Educational Resources Information Center

    National Academy for Integration of Research, Teaching and Learning (NJ1), 2011

    2011-01-01

    This publication contains the papers presented at the 5th Annual Conference of National Academy for Integration of Research, Teaching and Learning (NAIRTL) and the 9th Galway Symposium. Presenters from across Ireland and overseas share their perspectives. The theme of engagement touches on the very heart of what a "higher" education should be…

  4. Immediate and Short-Term Effects of the 5th Grade Version of the "keepin' it REAL" Substance Use Prevention Intervention

    ERIC Educational Resources Information Center

    Hecht, Michael L.; Elek, Elvira; Wagstaff, David A.; Kam, Jennifer A.; Marsiglia, Flavio; Dustman, Patricia; Reeves, Leslie; Harthun, Mary

    2009-01-01

    This study assessed the immediate and short-term outcomes of adapting a culturally-grounded middle school program, "keepin' it REAL", for elementary school students. After curriculum adaptation, 10 schools were randomly assigned to the intervention in 5th grade with follow-up boosters in 6th grade; 13 schools were randomly assigned to the control…

  5. International Roundtable on The Lifelong Learning and New Technologies Gap: Reaching the Disadvantaged (5th, Philadelphia, Pennsylvania, December 8-10, 1999). Preliminary Report.

    ERIC Educational Resources Information Center

    National Center on Adult Literacy, Philadelphia, PA.

    Three elements defined the focus of the 5th Roundtable: lifelong learning, the new technologies gap, and reaching the disadvantaged. Participants referred frequently to the digital divide, a term that captures differential access to and use of information and communication technology (ICT). The questions that guided discussion related to ICT and…

  6. Evaluation of the Effects of Argumentation Based Science Teaching on 5th Grade Students' Conceptual Understanding of the Subjects Related to "Matter and Change"

    ERIC Educational Resources Information Center

    Çinar, Derya; Bayraktar, Sule

    2014-01-01

    The aim of this study is to evaluate the effects of Argumentation Based Science Teaching on 5th grade students' conceptual understanding of the subjects related to "Matter and Change". This research is a qualitative research and its design is a multiple (compare) case study. In this study, semi-structured interviews related to the…

  7. Evaluation of the Effects of Argumentation Based Science Teaching on 5th Grade Students' Conceptual Understanding of the Subjects Related to "Matter and Change"

    ERIC Educational Resources Information Center

    Çinar, Derya; Bayraktar, Sule

    2014-01-01

    The aim of this study is to evaluate the effects of Argumentation Based Science Teaching on 5th grade students' conceptual understanding of the subjects related to "Matter and Change". This research is a qualitative research and its design is a multiple (compare) case study. In this study, semi-structured interviews related to the…

  8. Measures of self-efficacy and norms for low-fat milk consumption are reliable and related to beverage consumption among 5th graders at school lunch

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to determine the reliability and validity of scales measuring low-fat milk consumption self-efficacy and norms during school lunch among a cohort of 5th graders. Two hundred seventy-five students completed lunch food records and a psychosocial questionnaire measuring self-efficacy ...

  9. Determination of Motivation of 5th Grade Students Living in Rural and Urban Environments towards Science Learning and Their Attitudes towards Science-Technology Course

    ERIC Educational Resources Information Center

    Kenar, Ismail; Köse, Mücahit; Demir, Halil Ibrahim

    2016-01-01

    In this research, determination of motivation of 5th grade students living in rural and urban environments towards science learning and their attitudes towards science-technology course is aimed. This research is conducted based on descriptive survey model. Samples are selected through teleological model in accordance with the aim of this…

  10. The Effect of Direct Instruction Strategy on Math Achievement of Primary 4th and 5th Grade Students with Learning Difficulties

    ERIC Educational Resources Information Center

    Al-Makahleh, Ahmad Abdulhameed Aufan

    2011-01-01

    This study seeks to verify the effect of direct instruction strategy on Math achievment of students with learning difficulties in the fourth and fifth grade levels and measure the improvement in their attitudes to Mathematics. Sample consisted of sixty (60) students with Math learning difficulties attending 4th and 5th grade level resource rooms…

  11. Color Duplex Assessment of 4th and 5th Internal Mammary Artery Perforators: The Pedicles of the Medially Based Lower Pole Breast Flaps

    PubMed Central

    Abdel-Monem, Kareem; Elshahat, Ahmed; Abou-Gamrah, Sherif; Eldin Abol-Atta, Hossam; Abd Eltawab, Reda; Massoud, Karim

    2012-01-01

    Objective: Reconstruction of a breast after mastectomy using the contralateral lower pole breast flap is an appealing procedure because it uses the tissues that were going to be excised during reduction of the sound breast to achieve symmetry. Literature mentioned that these flaps are supplied by the lower internal mammary artery perforators (IMAPs) with no further details. The aim of this study was to determine the site, size, and number of the 4th and 5th IMAPs by using preoperative color Duplex ultrasound and intraoperative exploration. Method: Twenty breasts in 10 patients who presented for reduction mammoplasty were included in this study. Preoperative color duplex was used to determine IMAPs in the 4th and 5th intercostal spaces. These perforators were localized intraoperatively. Intravenous fluorescein injection was used to determine the perfusion of the lower pole breast flap on the basis of these perforators. Results: Statistically, the 4th IMAPs diameters were significantly larger than the 5th IMAPs diameters (P < .05). The lower pole breast flap was perfused through these perforators. Conclusion: Color Duplex ultrasound is an accurate tool to preoperatively determine the 4th and 5th IMAPs. PMID:22292100

  12. Final technical report: Partial support for US participants in the 5th International Marine Biotechnology Conference, Townsville, Australia, Sept 29 - Oct 5, 2000

    SciTech Connect

    Zohar, Yonathan; Hill, R.; Robb, F.

    2001-04-09

    Funding was provided for US participants in the 5th International Marine Biotechnology Conference held in Townsville, Australia from September 29 to October 5, 2000. DOE funds were used for travel awards for six US participants in this conference. DOE funds were successfully used to advance participation of US scientists in the important emerging field of marine biotechnology.

  13. An Analysis of the Learning Activities Covered in the 5th Grade Science Textbooks Based on 2005 and 2013 Turkish Science Curricula

    ERIC Educational Resources Information Center

    Aydogdu, Cemil; Idin, Sahin

    2015-01-01

    The aim of this study is to analyze the learning activities covered in 5th grade elementary science textbooks which depend on 2005 and 2013 elementary science curricula. Two elementary science textbooks [which] depend on 2005 science curriculum and two elementary science textbooks [which] depend on 2013 science curriculum were researched. The…

  14. An Analysis of the Learning Activities Covered in the 5th Grade Science Textbooks Based on 2005 and 2013 Turkish Science Curricula

    ERIC Educational Resources Information Center

    Aydogdu, Cemil; Idin, Sahin

    2015-01-01

    The aim of this study is to analyze the learning activities covered in 5th grade elementary science textbooks which depend on 2005 and 2013 elementary science curricula. Two elementary science textbooks depends on 2005 science curriculum and two elementary science textbooks depend on 2013 science curriculum were researched. The study is a…

  15. The Social Interactions of Students with Disabilities in a 5th Grade Level Inclusive Classroom and the Effect on Academic Achievement

    ERIC Educational Resources Information Center

    Marshall-Reed, Estella

    2010-01-01

    This dissertation is a qualitative, ethnographic case study of 3 students with disabilities. The purpose of this research study was to observe and collect descriptive accounts of the social interactions that exist between the cultures in a 5th grade level inclusive classroom, such as the interactions between the special education students, general…

  16. Comparison of the Leiter International Performance Scale-Revised and the Stanford-Binet Intelligence Scales, 5th Edition, in Children with Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Grondhuis, Sabrina Nicole; Mulick, James A.

    2013-01-01

    A review of hospital records was conducted for children evaluated for autism spectrum disorders who completed both the Leiter International Performance Scale-Revised (Leiter-R) and Stanford-Binet Intelligence Scales, 5th Edition (SB5). Participants were between 3 and 12 years of age. Diagnoses were autistic disorder (n = 26, 55%) and pervasive…

  17. U.S. Dietary and Physical Activity Guideline Knowledge and Corresponding Behaviors among 4th and 5th Grade Students: A Multi-Site Pilot Study

    ERIC Educational Resources Information Center

    Bea, Jennifer W.; Martinez, Stephanie; Armstrong-Florian, Traci; Farrell, Vanessa; Martinez, Cathy; Whitmer, Evelyn; Hartz, Vern; Blake, Samuel; Nicolini, Ariana; Misner, Scottie

    2014-01-01

    Knowledge of U.S. dietary and physical activity recommendations and corresponding behaviors were surveyed among 4th and 5th graders in five Arizona counties to determine the need for related education in SNAP-Ed eligible schools. A <70% target response rate was the criterion. Participants correctly identified recommendations for: fruit, 20%;…

  18. EUNIS '99: Information Technology Shaping European Universities. Proceedings of the International European University Information Systems (5th, Espoo, Finland, June 7-9, 1999).

    ERIC Educational Resources Information Center

    1999

    This document presents the proceedings from the 5th International European University Information Systems (EUNIS) Conference on Information Technology that took place in Helsinki, Finland on June 7-9, 1999. Topics of the conference proceedings were divided into five tracks (A through E): Use of Information Technology in Learning and Teaching;…

  19. Quantitative Estimates of Temporal Mixing across a 4th-order Depositional Sequence: Variation in Time-averaging along the Holocene Marine Succession of the Po Plain, Italy

    NASA Astrophysics Data System (ADS)

    Scarponi, D.; Kaufman, D.; Bright, J.; Kowalewski, M.

    2009-04-01

    Single fossiliferous beds contain biotic remnants that commonly vary in age over a time span of hundreds to thousands of years. Multiple recent studies suggest that such temporal mixing is a widespread phenomenon in marine depositional systems. This research focuses on quantitative estimates of temporal mixing obtained by direct dating of individual corbulid bivalve shells (Lentidium mediterraneum and Corbula gibba) from Po plain marine units of the Holocene 4th-order depositional sequence, including Transgressive Systems Tract [TST] and Highstand Systems Tract [HST]. These units displays a distinctive succession of facies consisting of brackish to marginal marine retrogradational deposits, (early TST), overlain by fully marine fine to coarse gray sands (late TST), and capped with progradational deltaic clays and sands (HST). More than 300 corbulid specimens, representing 19 shell-rich horizons evenly distributed along the depositional sequence and sampled from 9 cores, have been dated by means of aspartic acid racemization calibrated using 23 AMS-radiocarbon dates (14 dates for Lentidium mediterraneum and 9 dates for Corbula gibba, respectively). The results indicate that the scale of time-averaging is comparable when similar depositional environments from the same systems tract are compared across cores. However, time averaging is notably different when similar depositional environments from TST and HST segments of the sequence are compared. Specifically, late HST horizons (n=8) display relatively low levels of time-averaging: the mean within-horizon range of shell ages is 537 years and standard deviation averages 165 years. In contrast, late TST horizons (n=7) are dramatically more time-averaged: mean range of 5104 years and mean standard deviations of 1420 years. Thus, late TST horizons experience a 1 order of magnitude higher time-averaging than environmentally comparable late HST horizons. In conclusion the HST and TST systems tracts of the Po Plain display

  20. A pedagogical example of second-order arithmetic sequences applied to the construction of computer passwords by upper elementary grade students

    NASA Astrophysics Data System (ADS)

    Coggins, Porter E.

    2015-04-01

    The purpose of this paper is (1) to present how general education elementary school age students constructed computer passwords using digital root sums and second-order arithmetic sequences, (2) argue that computer password construction can be used as an engaging introduction to generate interest in elementary school students to study mathematics related to computer science, and (3) share additional mathematical ideas accessible to elementary school students that can be used to create computer passwords. This paper serves to fill a current gap in the literature regarding the integration of mathematical content accessible to upper elementary school students and aspects of computer science in general, and computer password construction in particular. In addition, the protocols presented here can serve as a hook to generate further interest in mathematics and computer science. Students learned to create a random-looking computer password by using biometric measurements of their shoe size, height, and age in months and to create a second-order arithmetic sequence, then converted the resulting numbers into characters that become their computer passwords. This password protocol can be used to introduce students to good computer password habits that can serve a foundation for a life-long awareness of data security. A refinement of the password protocol is also presented.

  1. Integration of physical activity and technology motion devices within a combined 5th and 6th grade science curriculum

    NASA Astrophysics Data System (ADS)

    Finn, Kevin Eugene

    Background: National recommendations to increase school-based physical activity and promote academic success advise incorporating movement into traditional classroom lessons. Classroom-based physical activities have favorable associations with indicators of cognitive functioning, academic behaviors, and academic achievement. Purpose: This study analyzed the Active Science framework, which incorporated school-based physical activity within interactive science classroom lessons. Specifically, the study measured the effects of the Active Science framework on student physical activity levels in the classroom, student learning of science inquiry skills and content knowledge, and student perceptions of physical activity and science. A secondary purpose was to evaluate the teachers' perceptions on the implementation of the framework. Subjects: Participants were 37 Hispanic girls (age=11.1 +/-0.8 yr) in mixed 5th/6th grade science classes in a private, urban middle school. Methods: Physical activity levels of the students during the Active Science framework were measured using pedometers and heart rate monitors. Pre- and post-tests were used to assess the levels of learning achieved by the students in science inquiry skills and content during the Active Science framework. Student perceptions and attitudes toward science and physical activity were measured during student focus groups and pre-post perception surveys. Lesson plan evaluations completed by the teachers and structured interviews provided data on implementation of the framework. Results: Physical activity results showed heart rate (146 +/-9 bpm); maximal heart rate (196 +/-10.6 bpm); time (35 +/-2.5 mins); steps (3050 +/-402.7); calories (99 +/-8.4 kcal); and distance (1.1 +/-0.2 miles) while performing the activity portion of the science lessons were consistent with national recommendations for accumulating school-based physical activity. Significant increases in science content and skills test scores with a 22

  2. Effect on Physical Activity of a Randomized Afterschool Intervention for Inner City Children in 3rd to 5th Grade

    PubMed Central

    Crouter, Scott E.; de Ferranti, Sarah D.; Whiteley, Jessica; Steltz, Sarah K.; Osganian, Stavroula K.; Feldman, Henry A.; Hayman, Laura L.

    2015-01-01

    Background Less than 45% of U.S. children meet the 60 min.d-1 physical activity (PA) guideline. Structured after-school PA programing is one approach to help increase activity levels. This study aimed to evaluate the feasibility and short-term impact of a supervised after-school PA and nutrition education program on activity levels. Methods Forty-two 3rd-5th graders from an inner-city school in Boston, MA were randomly assigned to a 10-wk after-school program of either: 1) weekly nutrition education, or 2) weekly nutrition education plus supervised PA 3 d.wk-1 at a community-based center. At baseline and follow-up, PA was measured using accelerometry and fitness (VO2max) was estimated using the PACER 15-m shuttle run. Additional measures obtained were non-fasting finger stick total cholesterol (TC) and glucose levels, waist circumference (WC), body mass index (BMI), percent body fat (%BF), and blood pressure (BP). Values are presented as mean±SE, unless noted otherwise. Results Thirty-six participants completed the study (mean±SD; age 9.7±0.9 years). Participants attended >80% of the sessions. After adjusting for accelerometer wear time and other design factors, light and moderate-to-vigorous PA (MVPA) increased in the nutrition+PA group (+21.5±14.5 and +8.6±8.0 min.d-1, respectively) and decreased in the nutrition only group (-35.2±16.3 and -16.0±9.0 min.d-1, respectively); mean difference between groups of 56.8±21.7 min.d-1 (light PA, p = 0.01) and 24.5±12.0 min.d-1 (MVPA, p = 0.04). Time spent in sedentary behaviors declined in the nutrition+PA group (-14.8±20.7 min.d-1) and increased in the nutrition only group (+55.4±23.2 min.d-1); mean difference between groups of -70.2±30.9 min.d-1 (p = 0.02). Neither group showed changes in TC, BP, WC, %BF, BMI percentile, or fitness (p>0.05). Conclusions The supervised afterschool community-based nutrition and PA program was well accepted and had high attendance. The changes in light PA and MVPA has potential

  3. PREFACE: PASREG 2005: The 5th International Workshop on Processing and Applications of Superconducting (RE)BCO Large Grain Materials

    NASA Astrophysics Data System (ADS)

    Murakami, Masato; Cardwell, David; Salama, Kamel; Izumi, Mitsuru

    2006-07-01

    Large grain, (RE)BCO bulk superconductors fabricated by top-seeded melt growth (TSMG) have outstanding potential for a variety of engineering applications such as magnetic separators, flywheel energy storage, magnetic bearings and permanent magnet-like devices due to their ability to generate large magnetic fields. Recent developments in materials and systems research has led to the manufacture of proto-type devices for use in magnetron sputtering, magnetic stirrers and a mobile magnetic separator based on bulk materials technology. This issue contains selected papers presented at the 5th International Workshop on the Processing and Applications of Superconducting (RE)BCO Large Grain Materials held on 21-23 October 2005 at Tokyo Marine University to report progress made in this field over the previous two years. The workshop followed those held previously in Cambridge, UK (1997), Morioka, Japan (1999), Seattle, USA (2001), and Jena, Germany (2003). A total of 76 papers were presented at this workshop, of which 27 were presented in oral form and 49 were presented as posters. This issue contains a total of 36 selected papers in the following categories of bulk (RE)BCO large grain material: processing, characterization, and applications. The editors are grateful for the support of many colleagues both within and outside the immediate bulk community who reviewed the manuscripts to guarantee their high technical quality. Finally, the attendees wish to acknowledge the efforts of Professor Mitsuru Izumi and his research staff from Tokyo Marine University for being generous hosts during the workshop, and the efforts of Professor Masato Murakami for the overall organization of the meeting. The International PASREG Board selected the following distinguished researchers as recipients of the 2005 PASREG Award of Excellence to acknowledge their contribution to the development of bulk high temperature superconductors: • Dr Michael Strasik (Boeing, Seattle, USA) • Dr Hiroshi

  4. Two Successful Outreach Programs at Storm Peak Laboratory: GRASP for Undergraduates and Partnership for 5th Grade Science Education

    NASA Astrophysics Data System (ADS)

    Hallar, A. G.; McCubbin, I. B.; Wright, J.

    2007-12-01

    The Desert Research Institute operates a high elevation facility, Storm Peak Laboratory (SPL), located on the Steamboat Springs Ski Resort at an elevation 10,500 ft. SPL provides an ideal location for long-term atmospheric research. The SPL mission statement is to ensure that the laboratory will continue to integrate climate research and education by advancing discovery and understanding within the field of pollution, aerosol and cloud interactions. During the last year, SPL has created two successful outreach programs reaching very different audiences. First, to engage students from local elementary schools, SPL established a 5th grade climate education program. This program is based on a partnership between SPL and Yampatika's&penvironmental educators. Yampatika is a non-profit outdoor environmental education organization. The program spans three days for each school and includes five elementary schools. During the first day, educators from Yampatika visit each classroom to introduce the concepts of climate and weather as well as teach students how to use scientific equipment. During the field program on the second day, students measure and record information about temperature, pressure, relative humidity, wind speed, and particle concentration while they travel to SPL via the gondola (in winter) or Suburban (in fall). Once at the laboratory, students tour the facility, discuss SPL research activities, and explore application of these activities to their curriculum. Following the field trip, Yampatika educators and SPL scientists will visit the school for a follow-up to help children explore concepts, answer questions, and evaluate students" learning. The second program, Geoscience Research at Storm Peak (GRASP), was designed to engage students from underrepresented groups and created a partnership between three Minority Serving Institutions and the University of Nevada, Reno (UNR). Undergraduate students from Tennessee State University, Howard University

  5. A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

    PubMed Central

    Xie, Lei; Xie, Li; Bourne, Philip E.

    2009-01-01

    Functional relationships between proteins that do not share global structure similarity can be established by detecting their ligand-binding-site similarity. For a large-scale comparison, it is critical to accurately and efficiently assess the statistical significance of this similarity. Here, we report an efficient statistical model that supports local sequence order independent ligand–binding-site similarity searching. Most existing statistical models only take into account the matching vertices between two sites that are defined by a fixed number of points. In reality, the boundary of the binding site is not known or is dependent on the bound ligand making these approaches limited. To address these shortcomings and to perform binding-site mapping on a genome-wide scale, we developed a sequence-order independent profile–profile alignment (SOIPPA) algorithm that is able to detect local similarity between unknown binding sites a priori. The SOIPPA scoring integrates geometric, evolutionary and physical information into a unified framework. However, this imposes a significant challenge in assessing the statistical significance of the similarity because the conventional probability model that is based on fixed-point matching cannot be applied. Here we find that scores for binding-site matching by SOIPPA follow an extreme value distribution (EVD). Benchmark studies show that the EVD model performs at least two-orders faster and is more accurate than the non-parametric statistical method in the previous SOIPPA version. Efficient statistical analysis makes it possible to apply SOIPPA to genome-based drug discovery. Consequently, we have applied the approach to the structural genome of Mycobacterium tuberculosis to construct a protein–ligand interaction network. The network reveals highly connected proteins, which represent suitable targets for promiscuous drugs. Contact: lxie@sdsc.edu PMID:19478004

  6. Proceedings for the 5th Asia-Pacific Conference on Disaster Medicine: creating an agenda for action.

    PubMed

    De Grace, M; Ericson, D; Folz, H; Greene, W; Ho, K; Pearce, L

    2001-01-01

    Disaster medicine has come to the forefront and has become the focus of interest not only in the medical community, but also in the eyes of the public. The 5th APCDM was convened in Vancouver, Canada, 27-30 September 2000. It brought together over 300 delegates from 32 countries to share their experiences and thoughts regarding disaster events and how to effectively manage them. The conference was devoted to the task of establishing priorities and creating an Agenda for Action. From the discussions, key actions required were defined: COMMUNICATIONS: (1) Identify existing regional telehealth groups and gather lessons to be learned from them; (2) Form a telehealth advisory group to work with regional groups to compile telehealth initiatives, identify international protocols in telehealth already in existence, and solicit feedback before setting international standards; and (3) Increase corporate partnerships in the fields of telehealth and telecommunications, and invite corporations to send delegates to future APCDM meetings. This should be an initiative of the APCDM, the World Association of Disaster and Emergency Medicine (WADEM), or the European Society of Emergency Medicine. EDUCATION AND RESEARCH: (1) Formalize education in disaster medicine and management. The World Health Organization and WADEM should take a leadership role; (2) WADEM is requested to hold a conference with a focus on qualitative research; (3) WHO is requested to continue the provision of international research teams, but to advocate for the development of national disaster research infrastructure; (4) Make research findings and reports available on web sites of such organizations as WHO and PAHO; (5) Develop the translation of research for community utilization. The WHO and PAHO are organizations that are requested to consider this action; and (6) WADEM/APCDM are requested to focus future conferences on applied research. INFORMATION AND DATA: (1) Create an "Information and Data Clearinghouse

  7. Altering Hydrophobic Sequence Lengths Shows That Hydrophobic Mismatch Controls Affinity for Ordered Lipid Domains (Rafts) in the Multitransmembrane Strand Protein Perfringolysin O*

    PubMed Central

    Lin, Qingqing; London, Erwin

    2013-01-01

    The hypothesis that mismatch between transmembrane (TM) length and bilayer width controls TM protein affinity for ordered lipid domains (rafts) was tested using perfringolysin O (PFO), a pore-forming cholesterol-dependent cytolysin. PFO forms a multimeric barrel with many TM segments. The properties of PFO mutants with lengthened or shortened TM segments were compared with that of PFO with wild type TM sequences. Both mutant and wild type length PFO exhibited cholesterol-dependent membrane insertion. Maximal PFO-induced pore formation occurred in vesicles with wider bilayers for lengthened TM segments and in thinner bilayers for shortened TM segments. In diC18:0 phosphatidylcholine (PC)/diC14:1 PC/cholesterol vesicles, which form ordered domains with a relatively thick bilayer and disordered domains with a relatively thin bilayer, affinity for ordered domains was greatest with lengthened TM segments and least with shortened TM segments as judged by FRET. Similar results were observed by microscopy in giant vesicles containing sphingomyelin in place of diC18:0 PC. In contrast, in diC16:0 PC/diC14:0 PC/diC20:1 PC/cholesterol vesicles, which should form ordered domains with a relatively thin bilayer and disordered domains with a relatively thick bilayer, relative affinity for ordered domains was greatest with shortened TM segments and least with lengthened TM segments. The inability of multi-TM segment proteins (unlike single TM segment proteins) to adapt to mismatch by tilting may explain the sensitivity of raft affinity to mismatch. The difference in width sensitivity for single and multi-TM helix proteins may link raft affinity to multimeric state and thus control the assembly of multimeric TM complexes in rafts. PMID:23150664

  8. It takes a community to define a discipline: the 5th anniversary of Environmental Research Letters It takes a community to define a discipline: the 5th anniversary of Environmental Research Letters

    NASA Astrophysics Data System (ADS)

    Kammen, Dan

    2012-03-01

    commentary environment, a unique service in itself, and also a specific forum for research published in ERL. Individual topics often come up that warrant not only single articles, but collections of assessments, and ERL has published focus issues in key areas of environmental science including: tropical deforestation, wind energy, the Deepwater Horizon oil spill and climate engineering. ERL is currently publishing seven high-quality focus issues in cutting-edge areas such as arctic vegetation dynamics and cryospheric changes. Research letters appearing in ERL have received regular and significant coverage in the wider media, with several major news outlets and agencies choosing to cover ERL research, such as Nature, BBC News, New Scientist, The Guardian, Scientific American, Le Monde and many others. 4.The future community of ERL The process of community support will take many forms at ERL. The journal is growing—we have published the highest number of articles ever in a single volume in 2011 and are looking to continue this growth through into 2012. ERL had an over 50% increase in submissions from 2010 to 2011. One initiative to mark the journal's 5th anniversary was the 'Best articles' collection [1] a nominated compilation of articles showcasing the quality of published work in ERL as well as the subject area breadth. Co-authors of the five winning articles have been awarded free publication in ERL until the end of 2012. We can also see the open access model working, in that our articles are highly downloaded outside of the traditionally strong geographical areas of academia (North America and Western Europe), showing that the journal's readership is geographically diverse with high interest from Asia, South America and Africa. The journal is committed to progress and innovation; coming soon will be a set of new communication tools and online innovations, including: Video abstracts from the start of 2012 (for example, the video commentary published alongside this

  9. The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology.

    PubMed

    Whiting, M F; Carpenter, J C; Wheeler, Q D; Wheeler, W C

    1997-03-01

    Phylogenetic relationships among the holometabolous insect orders were inferred from cladistic analysis of nucleotide sequences of 18S ribosomal DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological characters. Exemplar outgroup taxa were Collembola (1 sequence), Archaeognatha (1), Ephemerida (1), Odonata (2), Plecoptera (2), Blattodea (1), Mantodea (1), Dermaptera (1), Orthoptera (1), Phasmatodea (1), Embioptera (1), Psocoptera (1), Phthiraptera (1), Hemiptera (4), and Thysanoptera (1). Exemplar ingroup taxa were Coleoptera: Archostemata (1), Adephaga (2), and Polyphaga (7); Megaloptera (1); Raphidioptera (1); Neuroptera (sensu stricto = Planipennia): Mantispoidea (2), Hemerobioidea (2), and Myrmeleontoidea (2); Hymenoptera: Symphyta (4) and Apocrita (19); Trichoptera: Hydropsychoidea (1) and Limnephiloidea (2); Lepidoptera: Ditrysia (3); Siphonaptera: Pulicoidea (1) and Ceratophylloidea (2); Mecoptera: Meropeidae (1), Boreidae (1), Panorpidae (1), and Bittacidae (2); Diptera: Nematocera (1), Brachycera (2), and Cyclorrhapha (1); and Strepsiptera: Corioxenidae (1), Myrmecolacidae (1), Elenchidae (1), and Stylopidae (3). We analyzed approximately 1 kilobase of 18S rDNA, starting 398 nucleotides downstream of the 5' end, and approximately 400 bp of 28S rDNA in expansion segment D3. Multiple alignment of the 18S and 28S sequences resulted in 1,116 nucleotide positions with 24 insert regions and 398 positions with 14 insert regions, respectively. All Strepsiptera and Neuroptera have large insert regions in 18S and 28S. The secondary structure of 18S insert 23 is composed of long stems that are GC rich in the basal Strepsiptera and AT rich in the more derived Strepsiptera. A matrix of 176 morphological characters was analyzed for holometabolous orders. Incongruence length difference tests indicate that the 28S + morphological data sets are incongruent but that 28S + 18S, 18S + morphology, and 28S + 18S + morphology fail to reject the hypothesis of

  10. Effect of Anatomical Modeling on Space Radiation Dose Estimates: A Comparison of Doses for NASA Phantoms and 5th, 50th, and 95th Percentile UF Hybrid Phantoms

    NASA Technical Reports Server (NTRS)

    Bahadori, A.; VanBaalen, M.; Shavers, M.; Semones, E.; Dodge, C.; Bolch, W.

    2010-01-01

    The estimate of absorbed dose to individual organs of a space crewmember is affected by the geometry of the anatomical model of the astronaut used in the radiation transport calculation. For astronaut dosimetry, NASA currently uses the computerized anatomical male (CAM) and computerized anatomical female (CAF) stylized phantoms to represent astronauts in its operational radiation dose analyses. These phantoms are available in one size and in two body positions. In contrast, the UF Hybrid Adult Male and Female (UFHADM and UFHADF) phantoms have organ shapes based on actual CT data. The surfaces of these phantoms are defined by non-uniform rational B-spline surfaces, and are thus flexible in terms of body morphometry and extremity positioning. In this study, UFHADM and UFHADF are scaled to dimensions corresponding to 5th, 50th, and 95th percentile (PCTL) male and female astronauts. A ray-tracing program is written in Visual Basic 2008, which is then used to create areal density maps for dose points corresponding to various organs within the phantoms. The areal density maps, along with appropriate space radiation spectra, are input into the NASA program couplet HZETRN/BRYNTRN, and organ doses are calculated. The areal density maps selected tissues and organs of the 5th, 50th, and 95th PCTL male and female phantoms are presented and compared. In addition, the organ doses for the 5th, 50th, and 95th PCTL male and female phantoms are presented and compared to organ doses for CAM and CAF.

  11. Late quaternary sequence stratigraphy, South Florida margin

    SciTech Connect

    Locker, S.D.; Hine, A.C.

    1995-12-01

    Late Quaternary sea-level change and the Florida Current have combined to produce a progradational shelf-slope margin along the western portion of the south Florida Platform facing the Straits of Florida. Analysis of high resolution seismic reflection profiles suggest at least eight 5th order late Quaternary sequences downlap onto the Pourtales Terrace at 250 m water depth. Along most of the south Florida margin, this Late Quaternary section is very thin, and only where significant accumulations occur can the stratigraphic patterns produced by sea-level change be clearly observed. Recognition of systems tracts and their boundaries from high-resolution seismic data is important for prediction of sedimentary facies and stratigraphic development of margins. Many south Florida seismic boundaries can be fit to the Exxon sequence stratigraphy model. Others appear to reflect the added effect of bottom-current erosion that complicates the signal produced by sea-level change. Overall, the sea-level signal appears to dominate the stratigraphic record, especially from the 2-dimensional perspective of dip-oriented seismic profiles. However, the 3-dimensional geometry of deposits are strongly influenced by along slope accumulation patterns controlled by the Florida Current. This study provides new insight on the importance of both geostrophic boundary currents and sea-level change in controlling stratigraphic development of a carbonate platform margin. Similar anomalously thick slope deposits in ancient sequences may indicate similar controls on accumulation and could lend to predictions of related paleo-platform configurations.

  12. FOREWORD: The 5th International Colloquium on Atomic Spectra and Oscillator Strengths for Astrophysical and Laboratory Plasmas

    NASA Astrophysics Data System (ADS)

    Tchang-Brillet, Wad Lydia; Wyart, Jean-François; Zeippen, Claude

    1996-01-01

    The 5th International Colloquium on Atomic Spectra and Oscillator Strengths for Astrophysical and Laboratory Plasmas was held in Meudon, France, from August 28 to 31 1995. It was the fifth in a series started by the Atomic Spectroscopic Group at the University of Lund, Sweden, in 1983. Then followed the meetings in Toledo, USA, Amsterdam, The Nether- lands and Gaithersburg, USA, with a three year period. The original title of the series ended with "... for Astrophysics and Fusion Research" and became more general with the 4th colloquium in Gaithersburg. The purpose of the present meeting was, in line with tradition, to bring together "producers" and "users" of atomic data so as to ensure optimal coordination. Atomic physicists who study the structure of atoms and their radiative and collisional properties were invited to explain the development of their work, emphasizing the possibilities of producing precise transition wavelengths and relative line intensities. Astrophysicists and laboratory plasma physicists were invited to review their present research interests and the context in which atomic data are needed. The number of participants was about 70 for the first three meetings, then exploded to 170 at Gaithersburg. About 140 participants, coming from 13 countries, attended the colloquium in Meudon. This large gathering was partly due to a number of participants from Eastern Europe larger than in the past, and it certainly showed a steady interest for interdisciplinary exchanges between different communities of scientists. This volume includes all the invited papers given at the conference and, in the appendix, practical information on access to some databases. All invited speakers presented their talks aiming at good communication between scientists from different backgrounds. A separate bound volume containing extended abstracts of the poster papers has been published by the Publications de l'Observatoire de Paris, (Meudon 1996), under the responsibility of

  13. (S)Partners for Heart Health: a school-based program for enhancing physical activity and nutrition to promote cardiovascular health in 5th grade students

    PubMed Central

    Carlson, Joseph J; Eisenmann, Joey C; Pfeiffer, Karin A; Jager, Kathleen B; Sehnert, Scott T; Yee, Kimbo E; Klavinski, Rita A; Feltz, Deborah L

    2008-01-01

    Background The American Heart Association Position Statement on Cardiovascular Health Promotion in Public Schools encourages school-based interventions for the primary prevention of cardiovascular disease (CVD) through risk factor prevention or reduction in children with an emphasis on creating an environment that promotes healthy food choices and physical activity (PA). In an effort to address issues related to CVD risk factors including obesity in Michigan children, a multi-disciplinary team of Michigan State University (MSU) faculty, clinicians, and health profession students was formed to "(S)partner" with elementary school physical education (PE) teachers and MSU Extension staff to develop and implement a cost-effective, sustainable program aimed at CVD risk factor prevention and management for 5th grade students. This (S)partnership is intended to augment and improve the existing 5th grade PE, health and nutrition curriculum by achieving the following aims: 1) improve the students' knowledge, attitudes and confidence about nutrition, PA and heart health; 2) increase the number of students achieving national recommendations for PA and nutrition; and 3) increase the number of students with a desirable CVD risk factor status based on national pediatric guidelines. Secondary aims include promoting school staff and parental support for heart health to help children achieve their goals and to provide experiential learning and service for MSU health profession students for academic credit. Methods/Design This pilot effectiveness study was approved by the MSU IRB. At the beginning and the end of the school year students undergo a CVD risk factor assessment conducted by MSU medical students and graduate students. Key intervention components include eight lesson plans (conducted bi-monthly) designed to promote heart healthy nutrition and PA behaviors conducted by PE teachers with assistance from MSU undergraduate dietetic and kinesiology students (Spartners). The final

  14. Routing cancer immunology and immunotherapy from the lab to the clinic 4–5 th March 2014, Center for Applied Medical Research and University Clinic, Pamplona, Spain

    PubMed Central

    2014-01-01

    New approaches to generate effective anticancer responses by either inducing immune responses or inhibiting immunosuppression are under development to improve efficacy in patients. On March 4-5th, 2014, a symposium was held in Pamplona, Spain, to report the new strategies showing preclinical and clinical results regarding translational research efforts on the topic. Participants interacted through oral presentations of 15 speakers and further discussions on topics that included novel therapeutic agents for cancer immunotherapy, viral vectors and interferon-based approaches, experimental tumor imaging and immunostimulatory monoclonal antibodies. Promising agents to target cancer cells and therapeutic approaches that are under translation from bench to patients were presented. PMID:25060862

  15. Autism according to diagnostic and statistical manual of mental disorders 5(th) edition: The need for further improvements.

    PubMed

    Posar, Annio; Resca, Federica; Visconti, Paola

    2015-01-01

    The fifth edition of the diagnostic and statistical manual of mental disorders (DSM-5) introduced significant changes in the classification of autism spectrum disorders (ASD), including the abolition of the diagnostic subcategories proposed by DSM-IV-Text Revision. DSM-5 describes three levels of increasing severity of ASD. The authors report two explanatory cases with ASD (verbal boys, aged about 7 and a half years, without intellectual disability). According to DSM-5, both cases fall into the lowest severity level of ASD. However, their neuropsychological and neurobehavioral profile varies significantly. While the first boy showed a prevalent impairment of visuoconstructional and visuoperceptual abilities, the second one presented a predominant involvement of verbal functions, with qualitative impairments in communication. A further step forward in the definition and classification of ASD, taking into account both intensity and quality of symptoms, is recommended in order to formulate a reliable prognosis, plan an individualized treatment and monitor the clinical course over time. PMID:26167220

  16. Autism according to diagnostic and statistical manual of mental disorders 5th edition: The need for further improvements

    PubMed Central

    Posar, Annio; Resca, Federica; Visconti, Paola

    2015-01-01

    The fifth edition of the diagnostic and statistical manual of mental disorders (DSM-5) introduced significant changes in the classification of autism spectrum disorders (ASD), including the abolition of the diagnostic subcategories proposed by DSM-IV-Text Revision. DSM-5 describes three levels of increasing severity of ASD. The authors report two explanatory cases with ASD (verbal boys, aged about 7 and a half years, without intellectual disability). According to DSM-5, both cases fall into the lowest severity level of ASD. However, their neuropsychological and neurobehavioral profile varies significantly. While the first boy showed a prevalent impairment of visuoconstructional and visuoperceptual abilities, the second one presented a predominant involvement of verbal functions, with qualitative impairments in communication. A further step forward in the definition and classification of ASD, taking into account both intensity and quality of symptoms, is recommended in order to formulate a reliable prognosis, plan an individualized treatment and monitor the clinical course over time. PMID:26167220

  17. Using a Spreadsheet to Compute the Maximum Wind Sector 99.5th Percentile X/Q Value in Accordance with DOE-STD-3009-2014.

    PubMed

    Vickers, Linda

    2016-05-01

    The U.S. Department of Energy Standard 3009-2014 requires one of two methods to determine the simple Gaussian relative concentration (X/Q) of pollutant at plume centerline downwind to a receptor for a 2-h exposure duration from a ground-level release (i.e., less than 10 m height) which are (1) the 99.5th percentile X/Q for the directionally-dependent method and (2) the 95th percentile X/Q for the directionally-independent method. This paper describes how to determine the simple Gaussian 99.5th percentile X/Q for the directionally-dependent method using an electronic spreadsheet. Refer to a previous paper to determine the simple Gaussian 95th percentile X/Q for the directionally-independent method using an electronic spreadsheet (Vickers 2015). The method described herein is simple, quick, accurate, and transparent because all of the data, calculations, and results are visible for validation and verification. PMID:27023153

  18. The 5th IUPAP International Conference on Women in Physics: Making progress in the number of women in physics around the world

    NASA Astrophysics Data System (ADS)

    Cunningham, Beth

    2015-04-01

    A short report on the 5th IUPAP International Conference on Women in Physics (ICWIP) will be presented. In particular, a summary of the structure of the 5th ICWIP that occurred in Waterloo, Canada in August 2014 will be provided and placed into context of the previous four conferences. In addition, a synopsis of the recent efforts that are happening around the world to encourage girls and women to participate in physics will be given. Several US projects have been very successful in introducing girls to science and physics (e.g., ``Expanding Your Horizons'' intervention) and encouraging undergraduate women physics majors to continue into physics careers (e.g., Conferences for Undergraduate Women in Physics). Projects from other countries, such as the Juno Project in the UK that rates physics departments on their climate for women, might be implemented by US physics professional societies as well as colleges and universities. Several projects originating from the conference will be described: the new ``HERstories: Encouraging words from women in physics'' video based on interviews with delegates of the Conference, the My STEM Story project (http://mystemstory.wlu.ca), and the proceedings of the conference. Partial support provided by NSF #PHY-1419453.

  19. Factors Affecting the Duration of Nestling Period and Fledging Order in Tengmalm’s Owl (Aegolius funereus): Effect of Wing Length and Hatching Sequence

    PubMed Central

    Kouba, Marek; Bartoš, Luděk; Korpimäki, Erkki; Zárybnická, Markéta

    2015-01-01

    In altricial birds, the nestling period is an important part of the breeding phase because the juveniles may spend quite a long time in the nest, with associated high energy costs for the parents. The length of the nestling period can be variable and its duration may be influenced by both biotic and abiotic factors; however, studies of this have mostly been undertaken on passerine birds. We studied individual duration of nestling period of 98 Tengmalm’s owl chicks (Aegolius funereus) at 27 nests during five breeding seasons using a camera and chip system and radio-telemetry. We found the nestlings stayed in the nest box for 27 – 38 days from hatching (mean ± SD, 32.4 ± 2.2 days). The individual duration of nestling period was negatively related to wing length, but no formally significant effect was found for body weight, sex, prey availability and/or weather conditions. The fledging sequence of individual nestlings was primarily related to hatching order; no relationship with wing length and/or other factors was found in this case. We suggest the length of wing is the most important measure of body condition and individual quality in Tengmalm’s owl young determining the duration of the nestling period. Other differences from passerines (e.g., the lack of effect of weather or prey availability on nestling period) are considered likely to be due to different life-history traits, in particular different food habits and nesting sites and greater risk of nest predation among passerines. PMID:25793880

  20. Multiple sequence variations in SLC5A1 gene are associated with glucose-galactose malabsorption in a large cohort of Old Order Amish.

    PubMed

    Xin, B; Wang, H

    2011-01-01

    Glucose-galactose malabsorption (GGM) is an autosomal recessive disease with life-threatening newborn diarrhea caused by mutations in the Na(+) /glucose cotransporter gene SLC5A1. Because of its rarity, the clinical course of the disease has not been well studied. Here, we report 33 patients with GGM from a large Old Order Amish pedigree and the associated mutations in SLC5A1 gene. Clinically, all affected individuals presented with classic watery diarrhea and dehydration. The increased bowel sounds, distended abdomen, vigorous nursing regardless of their illness, and irritability and apathy were also noted as part of the initial presentation. Patients underwent a dramatic turnaround with an immediate cease of the diarrhea and a quick rehydration if they were correctly diagnosed and adequately managed, followed by a normal growth and development pattern afterwards; whereas a prolonged clinical course would follow if the disease was not recognized. Sequence analysis of the 15 protein-coding exons and the corresponding exon-intron boundaries of SLC5A1 gene revealed four homozygous missense mutations, c.152A>G (p.N51S), c.1231G>A (p.A411T), c.1673G>A (p.R558H), and c.1845C>G (p.H615Q), that co-segregate with the GGM phenotype in all of the affected individuals. These findings suggest that founder effect of the SLC5A1 mutations associated with the disease in Amish and a population specific genetic testing is in need to pursue an early diagnosis which is critical for a favorable outcome. PMID:20486940

  1. Teachers' Inclusive Strategies to Accommodate 5th Grade Pupils' Crossing of Cultural Borders in Two Greek Multicultural Science Classrooms

    NASA Astrophysics Data System (ADS)

    Piliouras, Panagiotis; Evangelou, Odysseas

    2012-04-01

    The demographic changes in Greek schools underline the need for reconsidering the way in which migrant pupils move from their everyday culture into the culture of school science (a process known as "cultural border crossing"). Migrant pupils might face difficulties when they attempt to transcend cultural borders and this may influence their progress in science as well as the construction of suitable academic identities as a means of promoting scientific literacy. In the research we present in this paper, adopting the socioculturally driven thesis that learning can be viewed and studied as a meaning-making, collaborative inquiry process, we implemented an action research program (school year 2008-2009) in cooperation with two teachers, in a primary school of Athens with 85% migrant pupils. We examined whether the two teachers, who became gradually acquainted with cross-cultural pedagogy during the project, act towards accommodating the crossing of cultural borders by implementing a variety of inclusive strategies in science teaching. Our findings reveal that both teachers utilized suitable cross-border strategies (strategies concerning the establishment of a collaborative inquiry learning environment, and strategies that were in accordance with a cross-border pedagogy) to help students cross smoothly from their "world" to the "world of science". A crucial key to the teachers' expertise was their previous participation in collaborative action research (school years 2004-2006), in which they analyzed their own discourse practices during science lessons in order to establish more collaborative inquiry environments.

  2. PREFACE: 5th International Workshop DICE2010: Space-Time-Matter - Current Issues in Quantum Mechanics and Beyond

    NASA Astrophysics Data System (ADS)

    Diósi, Lajos; Elze, Hans-Thomas; Fronzoni, Leone; Halliwell, Jonathan; Prati, Enrico; Vitiello, Giuseppe; Yearsley, James

    2011-07-01

    These proceedings present the Invited Lectures and Contributed Papers of the Fifth International Workshop on Decoherence, Information, Complexity and Entropy - DICE 2010, held at Castello Pasquini, Castiglioncello (Tuscany), 13-17 September 2010. These proceedings are intended to document the stimulating exchange of ideas at this conference for both the interested public and the wider scientific community, as well as for the participants. The number of participants attending this series of meetings has been growing steadily, which reflects its increasing attraction. Our intention to bring together leading researchers, advanced students, and renowned scholars from various areas in order to stimulate new ideas and their exchange across the borders of specialization seems to bear fruit. In this way, the series of meetings has continued successfully from the beginning with DICE 2002 [1], followed by DICE 2004 [2], DICE 2006 [3], and DICE 2008 [4], uniting more than 100 participants representing almost 30 countries worldwide. It has been a great honour and inspiration to have Professor Luc Montagnier (Nobel Prize for Medicine 2008) from the World Foundation for AIDS Research and Prevention with us, who presented the lecture DNA waves and water (included in this volume). The discussions took place under the wider theme Space-Time-Matter - current issues in quantum mechanics and beyond in the very pleasant and inspiring atmosphere of Castello Pasquini, which - with its beautiful surroundings, overlooking the Tuscany coast - hosted the conference very successfully for the second time. The five-day program was grouped according to the following topics: Gravity and Quantum Mechanics Quantum Coherent Processes in Biology / Many-Body Systems From Quantum Foundations to Particle Physics The Deep Structure of Spacetime Quantum - Relativity - Cosmology A Public Roundtable Discussion formed an integral part of the program under the theme Sull' Onda Della Coerenza" - le nuove

  3. PREFACE: 5th International Workshop DICE2010: Space-Time-Matter - Current Issues in Quantum Mechanics and Beyond

    NASA Astrophysics Data System (ADS)

    Diósi, Lajos; Elze, Hans-Thomas; Fronzoni, Leone; Halliwell, Jonathan; Prati, Enrico; Vitiello, Giuseppe; Yearsley, James

    2011-07-01

    These proceedings present the Invited Lectures and Contributed Papers of the Fifth International Workshop on Decoherence, Information, Complexity and Entropy - DICE 2010, held at Castello Pasquini, Castiglioncello (Tuscany), 13-17 September 2010. These proceedings are intended to document the stimulating exchange of ideas at this conference for both the interested public and the wider scientific community, as well as for the participants. The number of participants attending this series of meetings has been growing steadily, which reflects its increasing attraction. Our intention to bring together leading researchers, advanced students, and renowned scholars from various areas in order to stimulate new ideas and their exchange across the borders of specialization seems to bear fruit. In this way, the series of meetings has continued successfully from the beginning with DICE 2002 [1], followed by DICE 2004 [2], DICE 2006 [3], and DICE 2008 [4], uniting more than 100 participants representing almost 30 countries worldwide. It has been a great honour and inspiration to have Professor Luc Montagnier (Nobel Prize for Medicine 2008) from the World Foundation for AIDS Research and Prevention with us, who presented the lecture DNA waves and water (included in this volume). The discussions took place under the wider theme Space-Time-Matter - current issues in quantum mechanics and beyond in the very pleasant and inspiring atmosphere of Castello Pasquini, which - with its beautiful surroundings, overlooking the Tuscany coast - hosted the conference very successfully for the second time. The five-day program was grouped according to the following topics: Gravity and Quantum Mechanics Quantum Coherent Processes in Biology / Many-Body Systems From Quantum Foundations to Particle Physics The Deep Structure of Spacetime Quantum - Relativity - Cosmology A Public Roundtable Discussion formed an integral part of the program under the theme Sull' Onda Della Coerenza" - le nuove

  4. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.

    PubMed

    Patra, Ajit Kumar; Kwon, Yong Min; Kang, Sung Gyun; Fujiwara, Yoshihiro; Kim, Sang-Jin

    2016-04-01

    The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions. PMID:26776396

  5. Health effects of different dietary iron intakes: a systematic literature review for the 5th Nordic Nutrition Recommendations

    PubMed Central

    Domellöf, Magnus; Thorsdottir, Inga; Thorstensen, Ketil

    2013-01-01

    Background The present literature review is part of the NNR5 project with the aim of reviewing and updating the scientific basis of the 4th edition of the Nordic Nutrition Recommendations (NNR) issued in 2004. Objective The objective of this systematic literature review was to assess the health effects of different intakes of iron, at different life stages (infants, children, adolescents, adults, elderly, and during pregnancy and lactation), in order to estimate the requirement for adequate growth, development, and maintenance of health. Methods The initial literature search resulted in 1,076 abstracts. Out of those, 276 papers were identified as potentially relevant. Of those, 49 were considered relevant and were quality assessed (A, B, or C). An additional search on iron and diabetes yielded six articles that were quality assessed. Thus, a total of 55 articles were evaluated. The grade of evidence was classified as convincing (grade 1), probable (grade 2), suggestive (grade 3), and inconclusive (grade 4). Results There is suggestive evidence that prevention or treatment of iron deficiency (ID) and iron deficiency anemia (IDA) improves cognitive, motoric, and behavioral development in young children, and that treatment of IDA improves attention and concentration in school children and adult women. There is insufficient evidence to show negative health effects of iron intakes in doses suggested by the NNR 4. There is insufficient evidence to suggest that normal birth weight, healthy, exclusively breast-fed infants need additional dietary iron before 6 months of life in the Nordic countries. An iron concentration of 4–8 mg/L in infant formulas seems to be safe and effective for normal birth weight infants. There is probable evidence that iron supplements (1–2 mg/kg/day) given up to 6 months of age to infants with low birth weight (<2,500 g) prevents IDA and possibly reduce the risk of behavioral problems later on. There is probable evidence that ID and IDA in

  6. Comparison of Values in 5th, 6th, 7th and 8th Grade Primary Education Music Class Students'? Workbooks According to Rokeach?s and Akbas's Value Classifications

    ERIC Educational Resources Information Center

    Çakirer, H. Serdar

    2014-01-01

    The aim of the present study is to compare the values in the songs of 5th, 6th, 7th and 8th grade primary education music classes students? workbooks according to the value categorizations proposed by Rockeach and Akbas and which values among the categories mentioned are taught to the students in the 5th, 6th, 7th and 8th grade primary education…

  7. Using Community-based Participatory Research to Adapt keepin’ it REAL: Creating a Socially, Developmentally, and Academically Appropriate Prevention Curriculum for 5th Graders

    PubMed Central

    Harthun, Mary L.; Dustman, Patricia A.; Reeves, Leslie J.; Marsiglia, Flavio F.; Hecht, Michael L.

    2010-01-01

    This paper reports on a process in which program designers, classroom teachers, and students worked together to adapt the 7th grade “keepin’ it REAL” prevention curriculum to a developmentally, socially, and academically appropriate curriculum for 5th graders. A Community-Based Participatory Research methodology (CBPR), combined with a 9-step adaptation model, emphasized a collaborative approach, both transformative and empowering. Essential adaptation elements were the Risk-to-Resiliency Continuum; the teaching of a wide range of skills including risk assessment, decision making, and resistance strategies; and, maintaining the theoretical grounding of Narrative Theory, Communication Competence, and Focus Theory of Norms. This paper describes how CBPR methodology can be conducted successfully while focusing on sustained theoretical grounding and effective research practices in a school-based setting. PMID:21057596

  8. Investigation of the aerodynamic performance and noise characteristics of a 1/5th scale model of the Dowty Rotol R212 propeller

    NASA Astrophysics Data System (ADS)

    Trebble, W. J. G.

    1983-11-01

    The four-bladed Dowty Rotol R212 propeller (NACA 16 sections) was studied at 1/5th scale (0.7 m diameter) in 1.5 m acoustic tunnel. Propeller power absorption and thrust were measured over a range of rotational speeds up to 8000 rev/min at mainstream speeds from 15 to 60 m/sec for a range of blade settings. Slipstream wake surveys show outward movement of the position of the peak pressure as propeller loading is increased. Noise analysis demonstrates the predominance of multiple tones whose number and intensity increase with helical-tip Mach number. An empirical formula shows that the fundamental tone sound pressure level varies with tip speed and power loading in an identical manner to that observed on an ARA-D section propeller.

  9. [Synthesis of juvenile hormones in vitro by the corpora allata of 5th stage larva of Locusta migratoria migratorioides (R and F) (Insecta, Orthopteroida)].

    PubMed

    Caruelle, J P; Baehr, J C; Cassier, P

    1979-04-01

    Corpora allata of Locusta migratoria 5th stage larvae synthesize J.H.1, J.H.2 and J.H.3 in vitro. The C.A. of insects of different ages exbit different rates of J.H. synthesis. J.H.1 and J.H.2 synthesis is less than 1 ng/48 h/gland. During the same time the J.H.3 production may be as much as 25.6 ng/gland. J.H. synthetic activity is the same between right and left C.A. The release of J.H. from the C.A. occurs immediately following synthesis. These results are compared with in vivo haemolymphatic J.H. levels. PMID:113127

  10. Parasite-Antigen Driven Expansion of IL-5− and IL-5+ Th2 Human Subpopulations in Lymphatic Filariasis and Their Differential Dependence on IL-10 and TGFβ

    PubMed Central

    Anuradha, Rajamanickam; George, Parakkal Jovvian; Hanna, Luke E.; Chandrasekaran, Vedachalam; Kumaran, P. Paul; Nutman, Thomas B.; Babu, Subash

    2014-01-01

    Background Two different Th2 subsets have been defined recently on the basis of IL-5 expression – an IL-5+Th2 subset and an IL-5−Th2 subset in the setting of allergy. However, the role of these newly described CD4+ T cells subpopulations has not been explored in other contexts. Methods To study the role of the Th2 subpopulation in a chronic, tissue invasive parasitic infection (lymphatic filariasis), we examined the frequency of IL-5+IL-4+IL-13+ CD4+ T cells and IL-5−IL-4 IL-13+ CD4+ T cells in asymptomatic, infected individuals (INF) and compared them to frequencies (Fo) in filarial-uninfected (UN) individuals and to those with filarial lymphedema (CP). Results INF individuals exhibited a significant increase in the spontaneously expressed and antigen-induced Fo of both Th2 subpopulations compared to the UN and CP. Interestingly, there was a positive correlation between the Fo of IL-5+Th2 cells and the absolute eosinophil and neutrophil counts; in addition there was a positive correlation between the frequency of the CD4+IL-5−Th2 subpopulation and the levels of parasite antigen – specific IgE and IgG4 in INF individuals. Moreover, blockade of IL-10 and/or TGFβ demonstrated that each of these 2 regulatory cytokines exert opposite effects on the different Th2 subsets. Finally, in those INF individuals cured of infection by anti-filarial therapy, there was a significantly decreased Fo of both Th2 subsets. Conclusions Our findings suggest that both IL-5+ and IL-5−Th2 cells play an important role in the regulation of immune responses in filarial infection and that these two Th2 subpopulations may be regulated by different cytokine-receptor mediated processes. PMID:24498448

  11. Nuclear Electricity. 5th Edition.

    ERIC Educational Resources Information Center

    Hore-Lacy, Ian

    Educators must address the need for young people to be informed about both the scientific concepts and the reasons for controversy when dealing with controversial issues. Young people must be given the opportunity to form their own opinions when presented with evidence for conflicting arguments. Previous editions of "Nuclear Electricity" have…

  12. Environmental chemistry. 5th edition

    SciTech Connect

    Manahan, S.E. . Dept. of Chemistry)

    1991-01-01

    This book is organized around several major sections: aquatic Chemistry, atmospheric chemistry, the geosphere and hazardous wastes, toxicological chemistry, and resources and energy. Specific topics discussed in the book include a general introduction to environment chemistry, basic principles of aquatic chemistry, water pollution and water treatment, the essential role of microorganisms in aquatic chemical phenomena, atmospheric chemistry, a discussion of major threats to the global atmosphere (particularly greenhouse gases and ozone-depleting chemicals), the geosphere and hazardous substances, soil chemistry, and the nature and sources of hazardous wastes. The environmental chemistry of hazardous wastes, their treatment, minimization, and recycling, and the effects of these hazardous substances in also presented.

  13. Offshore observations of aftershocks following the January 5th 2013 Mw 7.5 Queen Charlotte-Fairweather fault earthquake, southeast Alaska

    NASA Astrophysics Data System (ADS)

    Roland, E. C.; Gulick, S. P.; Levoir, M. A.; Haeussler, P. J.

    2013-12-01

    We present initial results from a rapid-response ocean bottom seismometer (OBS) deployment that recorded aftershock activity on the Queen Charlotte-Fairweather (QC-F) fault following the Mw 7.5 earthquake on January 5th 2013 near Craig, Alaska. This earthquake was the second of two Mw > 7 events on this fault system in a 3 month time period; the Craig earthquake followed a Mw 7.8 thrust event that occurred in October 2012, west of Haida Gwaii, British Columbia. Although the QC-F is a major plate boundary fault, little is known about the regional fault structure, interseismic coupling, and rheological controls on the depth distribution of seismic slip along the continent-ocean transform. The majority of the QC-F fault system extends offshore western British Columbia and southeast Alaska, making it difficult to characterize earthquakes and fault deformation with land-based seismic and geodetic instruments. This experiment is the first ever offshore seismometer deployment to record earthquake activity along this northern segment of the QC-F system, and was set in motion with help from the US Coast Guard, who provided a vessel and crew to deploy and recover the OBS array on short notice. The seismic array utilized 6 GeoPro short period OBS from the University of Texas Institute for Geophysics, which recorded approximately 3 weeks of aftershock activity in April-May of 2013. Combining high-quality local OBS recordings with land-based seismic observations from Alaska Earthquake Information Center (AEIC) stations to the east, we present more precise aftershock locations and depths that help to better characterize fault zone architecture along the northern section of the QC-F. Although moment tensor solutions indicate that the January 5th mainshock sustained slip consistent with Pacific-North America plate motions, aftershock focal mechanisms indicate some interaction with neighboring faults, such as the Chatham Straight fault. This new OBS dataset will also help to

  14. The 5th National Audit Project (NAP5) on accidental awareness during general anaesthesia: patient experiences, human factors, sedation, consent and medicolegal issues.

    PubMed

    Cook, T M; Andrade, J; Bogod, D G; Hitchman, J M; Jonker, W R; Lucas, N; Mackay, J H; Nimmo, A F; O'Connor, K; O'Sullivan, E P; Paul, R G; Palmer, J H MacG; Plaat, F; Radcliffe, J J; Sury, M R J; Torevell, H E; Wang, M; Hainsworth, J; Pandit, J J

    2014-10-01

    The 5th National Audit Project of the Royal College of Anaesthetists and the Association of Anaesthetists of Great Britain and Ireland into accidental awareness during general anaesthesia yielded data related to psychological aspects from the patient, and the anaesthetist, perspectives; patients' experiences ranged from isolated auditory or tactile sensations to complete awareness. A striking finding was that 75% of experiences were for < 5 min, yet 51% of patients (95% CI 43-60%) experienced distress and 41% (95% CI 33-50%) suffered longer-term adverse effect. Distress and longer-term harm occurred across the full range of experiences but were particularly likely when the patient experienced paralysis (with or without pain). The patient's interpretation of what is happening at the time of the awareness seemed central to later impact; explanation and reassurance during suspected accidental awareness during general anaesthesia or at the time of report seemed beneficial. Quality of care before the event was judged good in 26%, poor in 39% and mixed in 31%. Three quarters of cases of accidental awareness during general anaesthesia (75%) were judged preventable. In 12% of cases of accidental awareness during general anaesthesia, care was judged good and the episode not preventable. The contributory and human factors in the genesis of the majority of cases of accidental awareness during general anaesthesia included medication, patient and education/training. The findings have implications for national guidance, institutional organisation and individual practice. The incidence of 'accidental awareness' during sedation (~1:15 000) was similar to that during general anaesthesia (~1:19 000). The project raises significant issues about information giving and consent for both sedation and anaesthesia. We propose a novel approach to describing sedation from the patient's perspective which could be used in communication and consent. Eight (6%) of the patients had resorted

  15. Reconsideration of systematic relationships within the order Euplotida (Protista, Ciliophora) using new sequences of the gene coding for small-subunit rRNA and testing the use of combined data sets to construct phylogenies of the Diophrys-complex.

    PubMed

    Yi, Zhenzhen; Song, Weibo; Clamp, John C; Chen, Zigui; Gao, Shan; Zhang, Qianqian

    2009-03-01

    Comprehensive molecular analyses of phylogenetic relationships within euplotid ciliates are relatively rare, and the relationships among some families remain questionable. We performed phylogenetic analyses of the order Euplotida based on new sequences of the gene coding for small-subunit RNA (SSrRNA) from a variety of taxa across the entire order as well as sequences from some of these taxa of other genes (ITS1-5.8S-ITS2 region and histone H4) that have not been included in previous analyses. Phylogenetic trees based on SSrRNA gene sequences constructed with four different methods had a consistent branching pattern that included the following features: (1) the "typical" euplotids comprised a paraphyletic assemblage composed of two divergent clades (family Uronychiidae and families Euplotidae-Certesiidae-Aspidiscidae-Gastrocirrhidae), (2) in the family Uronychiidae, the genera Uronychia and Paradiophrys formed a clearly outlined, well-supported clade that seemed to be rather divergent from Diophrys and Diophryopsis, suggesting that the Diophrys-complex may have had a longer and more separate evolutionary history than previously supposed, (3) inclusion of 12 new SSrRNA sequences in analyses of Euplotidae revealed two new clades of species within the family and cast additional doubt on the present classification of genera within the family, and (4) the intraspecific divergence among five species of Aspidisca was far greater than those of closely related genera. The ITS1-5.8S-ITS2 coding regions and partial histone H4 genes of six morphospecies in the Diophrys-complex were sequenced along with their SSrRNA genes and used to compare phylogenies constructed from single data sets to those constructed from combined sets. Results indicated that combined analyses could be used to construct more reliable, less ambiguous phylogenies of complex groups like the order Euplotida, because they provide a greater amount and diversity of information. PMID:19121402

  16. [Sequencing babies?].

    PubMed

    Jordan, Bertrand

    2015-10-01

    An extension of newborn screening to genome sequencing is now feasible but raises a number of scientific, organisational and ethical issues. This is being explored in discussions and in several funded trials, in order to maximize benefits and avoid some identified risks. As some companies are already offering such a service, this is quite an urgent matter. PMID:26481033

  17. Cornelia de Lange syndrome: further delineation of phenotype, cohesin biology and educational focus, 5th Biennial Scientific and Educational Symposium abstracts.

    PubMed

    Kline, Antonie D; Calof, Anne L; Schaaf, Cheri A; Krantz, Ian D; Jyonouchi, Soma; Yokomori, Kyoko; Gauze, Maria; Carrico, Cheri S; Woodman, Julie; Gerton, Jennifer L; Vega, Hugo; Levin, Alex V; Shirahige, Katsuhiko; Champion, Michele; Goodban, Marjorie T; O'Connor, Julia T; Pipan, Mary; Horsfield, Julia; Deardorff, Matthew A; Ishman, Stacey L; Dorsett, Dale

    2014-06-01

    Cornelia de Lange syndrome (CdLS) is the prototype for the cohesinopathy disorders that have mutations in genes associated with the cohesin subunit in all cells. Roberts syndrome is the next most common cohesinopathy. In addition to the developmental implications of cohesin biology, there is much translational and basic research, with progress towards potential treatment for these conditions. Clinically, there are many issues in CdLS faced by the individual, parents and caretakers, professionals, and schools. The following abstracts are presentations from the 5th Cornelia de Lange Syndrome Scientific and Educational Symposium on June 20-21, 2012, in conjunction with the Cornelia de Lange Syndrome Foundation National Meeting, Lincolnshire, IL. The research committee of the CdLS Foundation organizes the meeting, reviews and accepts abstracts and subsequently disseminates the information to the families. In addition to the basic science and clinical discussions, there were educationally-focused talks related to practical aspects of management at home and in school. AMA CME credits were provided by Greater Baltimore Medical Center, Baltimore, MD. PMID:24504889

  18. Consensus for Radiotherapy in Hepatocellular Carcinoma from The 5th Asia-Pacific Primary Liver Cancer Expert Meeting (APPLE 2014): Current Practice and Future Clinical Trials

    PubMed Central

    Park, Hee Chul; Yu, Jeong Il; Cheng, Jason Chia-Hsien; Zeng, Zhao Chong; Hong, Ji Hong; Wang, Michael Lian Chek; Kim, Mi Sook; Chi, Kwan Hwa; Liang, Po-Ching; Lee, Rheun-Chuan; Lau, Wan-Yee; Han, Kwang Hyub; Chow, Pierce Kah-Hoe; Seong, Jinsil

    2016-01-01

    A consensus meeting to develop practice guidelines and to recommend future clinical trials for radiation therapy (RT), including external beam RT (EBRT), and selective internal RT (SIRT) in hepatocellular carcinoma (HCC) was held at the 5th annual meeting of the Asia-Pacific Primary Liver Cancer Expert consortium. Although there is no randomized phase III trial evidence, the efficacy and safety of RT in HCC has been shown by prospective and retrospective studies using modern RT techniques. Based on these results, the committee came to a consensus on the utility and efficacy of RT in the management of HCC according to each disease stage as follows: in early and intermediate stage HCC, if standard treatment is not compatible, RT, including EBRT and SIRT can be considered. In locally advanced stage HCC, combined EBRT with transarterial chemoembolization or hepatic arterial infusion chemotherapy, and SIRT can be considered. In terminal stage HCC, EBRT can be considered for palliation of symptoms and reduction of morbidity caused by the primary tumor or its metastases. Despite the currently reported benefits of RT in HCC, the committee agreed that there is a compelling need for large prospective studies, including randomized phase III trial evidence evaluating the role of RT. Specifically studies evaluating the efficacy and safety of sequential combination of EBRT and SIRT are strongly recommended. PMID:27493892

  19. Vitamin D status and associated occupational factors in Korean wage workers: data from the 5th Korea national health and nutrition examination survey (KNHANES 2010–2012)

    PubMed Central

    2014-01-01

    Objectives Vitamin D deficiency is increasing worldwide. However, few studies have attempted to examine the vitamin D status of wage workers and the correlation between vitamin D deficiency and working conditions. Hence, we aimed to evaluate the prevalence of vitamin D deficiency and the association between occupational conditions and vitamin D deficiency among Korean wage workers. Methods Wage workers aged 20–65 years from the 5th Korea National Health and Nutrition Examination Survey (KNHANES 2010–2012; n = 5409) were included in our analysis. We measured the prevalence of vitamin D deficiency and identified the correlations with the working conditions of these subjects. Results The prevalence of vitamin D deficiency in male and female subjects was 69.5% and 83.1%, respectively. Among the male subjects, a significant correlation between vitamin D deficiency and working conditions was observed among shift workers, office workers, and permanent workers. No significant correlation with any type of working conditions was observed among female subjects. Conclusion The prevalence of vitamin D deficiency among Korean wage workers was very high and was found to correlate significantly with working conditions, likely because of insufficient exposure to sunlight associated with certain types of work. Wage workers require more frequent outdoor activity and nutrition management to maintain sufficient vitamin D level. PMID:25852939

  20. Consensus for Radiotherapy in Hepatocellular Carcinoma from The 5th Asia-Pacific Primary Liver Cancer Expert Meeting (APPLE 2014): Current Practice and Future Clinical Trials.

    PubMed

    Park, Hee Chul; Yu, Jeong Il; Cheng, Jason Chia-Hsien; Zeng, Zhao Chong; Hong, Ji Hong; Wang, Michael Lian Chek; Kim, Mi Sook; Chi, Kwan Hwa; Liang, Po-Ching; Lee, Rheun-Chuan; Lau, Wan-Yee; Han, Kwang Hyub; Chow, Pierce Kah-Hoe; Seong, Jinsil

    2016-07-01

    A consensus meeting to develop practice guidelines and to recommend future clinical trials for radiation therapy (RT), including external beam RT (EBRT), and selective internal RT (SIRT) in hepatocellular carcinoma (HCC) was held at the 5th annual meeting of the Asia-Pacific Primary Liver Cancer Expert consortium. Although there is no randomized phase III trial evidence, the efficacy and safety of RT in HCC has been shown by prospective and retrospective studies using modern RT techniques. Based on these results, the committee came to a consensus on the utility and efficacy of RT in the management of HCC according to each disease stage as follows: in early and intermediate stage HCC, if standard treatment is not compatible, RT, including EBRT and SIRT can be considered. In locally advanced stage HCC, combined EBRT with transarterial chemoembolization or hepatic arterial infusion chemotherapy, and SIRT can be considered. In terminal stage HCC, EBRT can be considered for palliation of symptoms and reduction of morbidity caused by the primary tumor or its metastases. Despite the currently reported benefits of RT in HCC, the committee agreed that there is a compelling need for large prospective studies, including randomized phase III trial evidence evaluating the role of RT. Specifically studies evaluating the efficacy and safety of sequential combination of EBRT and SIRT are strongly recommended. PMID:27493892

  1. SVSI: fast and powerful set-valued system identification approach to identifying rare variants in sequencing studies for ordered categorical traits.

    PubMed

    Bi, Wenjian; Kang, Guolian; Zhao, Yanlong; Cui, Yuehua; Yan, Song; Li, Yun; Cheng, Cheng; Pounds, Stanley B; Borowitz, Michael J; Relling, Mary V; Yang, Jun J; Liu, Zhifa; Pui, Ching-Hon; Hunger, Stephen P; Hartford, Christine M; Leung, Wing; Zhang, Ji-Feng

    2015-07-01

    In genetic association studies of an ordered categorical phenotype, it is usual to either regroup multiple categories of the phenotype into two categories and then apply the logistic regression (LG), or apply ordered logistic (oLG), or ordered probit (oPRB) regression, which accounts for the ordinal nature of the phenotype. However, they may lose statistical power or may not control type I error due to their model assumption and/or instable parameter estimation algorithm when the genetic variant is rare or sample size is limited. To solve this problem, we propose a set-valued (SV) system model to identify genetic variants associated with an ordinal categorical phenotype. We couple this model with a SV system identification algorithm to identify all the key system parameters. Simulations and two real data analyses show that SV and LG accurately controlled the Type I error rate even at a significance level of 10(-6) but not oLG and oPRB in some cases. LG had significantly less power than the other three methods due to disregarding of the ordinal nature of the phenotype, and SV had similar or greater power than oLG and oPRB. We argue that SV should be employed in genetic association studies for ordered categorical phenotype. PMID:25959545

  2. Draft Genome Sequence of “Candidatus Methanomethylophilus” sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the Methanomassiliicoccales Order

    PubMed Central

    Højberg, Ole; Urich, Tim

    2016-01-01

    Here, we present the draft genome of “Candidatus Methanomethylophilus” sp. 1R26, a member of the newly described Methanomassiliicoccales order of Euryarcheaota. The enrichment culture was established from bovine rumen contents and produced methane from trimethylamine and methanol. The draft genome contains genes for methanogenesis from methylated compounds. PMID:26893425

  3. Draft Genome Sequence of "Candidatus Methanomethylophilus" sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the Methanomassiliicoccales Order.

    PubMed

    Noel, Samantha Joan; Højberg, Ole; Urich, Tim; Poulsen, Morten

    2016-01-01

    Here, we present the draft genome of "Candidatus Methanomethylophilus" sp. 1R26, a member of the newly described Methanomassiliicoccales order of Euryarcheaota. The enrichment culture was established from bovine rumen contents and produced methane from trimethylamine and methanol. The draft genome contains genes for methanogenesis from methylated compounds. PMID:26893425

  4. Modulation of Corticospinal Excitability during Acquisition of Action Sequences by Observation

    PubMed Central

    Sakamoto, Masanori; Moriyama, Noriyoshi; Mizuguchi, Nobuaki; Muraoka, Tetsuro; Kanosue, Kazuyuki

    2012-01-01

    Excitability of the corticospinal pathway increases during observation of an action. However, how corticospinal excitability changes during observation of sequential actions in the course of acquiring novel skills (observational learning) remains unexplored. To investigate this, we used a previously unpracticed sequence of ten hand postures. Participants were asked to repeat observation and replication of the sequence. This block of observation and replication was repeated 5 times. During observation of a given hand posture (OK sign), motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation were recorded from hand muscles. In experiment 1, the OK sign appeared in the 9th position of the sequence. Almost all participants could replicate the OK sign only at the 5th block of the experiment. MEP amplitude was greater than that in the control, and decreased with the stages. This suggested that during observational learning of sequential hand postures MEP changed with the progress of the learning. To evaluate this idea, we performed two additional experiments. In experiment 2, the OK sign appeared in the 2nd position. Almost all participants replicated the OK sign even in the 1st block. The MEP amplitude did not change across stages. In experiment 3, the OK sign appeared in the 9th position, but the order of other signs was randomized in every stage. Many participants were not able to replicate the OK sign even during the 5th block of the experiment. The MEP amplitude did not change across stages. These results suggest that: (1) During observational learning modulation of corticospinal excitability is associated with the learning process. (2) Corticospinal excitability decreases as learning progresses. PMID:22615889

  5. The generalized quaternion sequence

    NASA Astrophysics Data System (ADS)

    Deveci, Ömür

    2016-04-01

    In this work, we define the recurrence sequence by using the relation matrix of the generalized quaternion group and then, we obtain miscellaneous properties of this sequence. Also, we obtain the cyclic groups and the semigroups which are produced by generating matrix of the sequence defined when read modulo m. Furthermore, we study this sequence modulo m, and then we derive the relationship among the order the cyclic groups obtained and the periods of the sequence defined.

  6. 5th National Audit Project (NAP5) on accidental awareness during general anaesthesia: patient experiences, human factors, sedation, consent, and medicolegal issues.

    PubMed

    Cook, T M; Andrade, J; Bogod, D G; Hitchman, J M; Jonker, W R; Lucas, N; Mackay, J H; Nimmo, A F; O'Connor, K; O'Sullivan, E P; Paul, R G; Palmer, J H M G; Plaat, F; Radcliffe, J J; Sury, M R J; Torevell, H E; Wang, M; Hainsworth, J; Pandit, J J

    2014-10-01

    The 5th National Audit Project (NAP5) of the Royal College of Anaesthetists and the Association of Anaesthetists of Great Britain and Ireland into accidental awareness during general anaesthesia (AAGA) yielded data related to psychological aspects from the patient, and the anaesthetist, perspectives; patients' experiences ranged from isolated auditory or tactile sensations to complete awareness. A striking finding was that 75% of experiences were for <5 min, yet 51% of patients [95% confidence interval (CI) 43-60%] experienced distress and 41% (95% CI 33-50%) suffered longer term adverse effect. Distress and longer term harm occurred across the full range of experiences but were particularly likely when the patient experienced paralysis (with or without pain). The patient's interpretation of what is happening at the time of the awareness seemed central to later impact; explanation and reassurance during suspected AAGA or at the time of report seemed beneficial. Quality of care before the event was judged good in 26%, poor in 39%, and mixed in 31%. Three-quarters of cases of AAGA (75%) were judged preventable. In 12%, AAGA care was judged good and the episode not preventable. The contributory and human factors in the genesis of the majority of cases of AAGA included medication, patient, and education/training. The findings have implications for national guidance, institutional organization, and individual practice. The incidence of 'accidental awareness' during sedation (~1:15,000) was similar to that during general anaesthesia (~1:19,000). The project raises significant issues about information giving and consent for both sedation and anaesthesia. We propose a novel approach to describing sedation from the patient's perspective which could be used in communication and consent. Eight (6%) of the patients had resorted to legal action (12, 11%, to formal complaint) at the time of reporting. NAP5 methodology provides a standardized template that might usefully inform

  7. 5th International AIDS Society Conference on HIV Pathogenesis, Treatment and Prevention: summary of key research and implications for policy and practice - operations research.

    PubMed

    Kort, Rodney

    2010-01-01

    Operations research was added as a fourth scientific track to the pathogenesis conference series at the 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention (IAS 2009) in recognition of the importance of this growing research field and the need for applied research to inform and evaluate the scale up of some key interventions in HIV treatment, care and prevention.Several studies demonstrated how task shifting and the decentralization of health services can leverage scarce health care resources to support scale-up efforts. For example, a Ugandan study comparing home-based and facility-based antiretroviral therapy (ART) delivery found that both delivered equivalent clinical outcomes, but home-based delivery resulted in substantial cost savings to patients; and a retrospective cohort analysis of an HIV care programme in Lesotho demonstrated that devolving routine patient management to nurses and trained counsellors resulted in impressive gains in annual enrolment, retention in care and other clinical indicators.Studies also demonstrated how the use of trained counsellors and public health advisors could effectively expand both clinical and public health capacity in low-income settings. Studies evaluating the impact of integrating HIV and TB care resulted in improved treatment outcomes in coinfected populations, the development of environmental interventions to reduce TB transmission, and uncovering of the extent of multi-drug-resistant and extremely drug-resistant tuberculosis (MDR-TB and XDR-TB) in KwaZulu-Natal, South Africa.Some mathematical modelling and cost-effectiveness studies presented at this meeting addressed interventions to increase retention in care, and strengthened the evidentiary basis for universal voluntary testing and immediate ART on reducing HIV transmission; debate continued about the relative merits of clinical versus laboratory monitoring. Finally, a provocative plenary presentation outlined the shortfalls of current prevention

  8. Relationship between Long Working Hours and Suicidal Thoughts: Nationwide Data from the 4th and 5th Korean National Health and Nutrition Examination Survey

    PubMed Central

    Yoon, Jin-Ha; Jung, Pil Kyun; Roh, Jaehoon; Seok, Hongdeok; Won, Jong-Uk

    2015-01-01

    Background Long working hours are a worldwide problem and may increase the risk of various health issues. However, the health effects of long working hours on suicidal thoughts have not been frequently studied. Our goal was to investigate the relationship between long working hours and suicidal thoughts in the rapidly developing country of Korea. Methods Data from 12,076 participants (7,164 men, 4,912 women) from the 4th and 5th Korean National Health and Nutrition Examination Surveys were used for the current analysis. Multivariate logistic regression models were used to estimate odds ratios and 95% confidence intervals for suicidal thoughts. Combined effects of long working hours and lower socioeconomic status or sleep disturbance were also estimated. Results Compared to groups who worked less than 52 hours per week, odds ratios (95% confidence intervals) for suicidal thoughts in groups who worked 60 hours or more per week were 1.36 (1.09–1.70) for males and 1.38 (1.11–1.72) for females, even after controlling for household income, marital status, history of hypertension or diabetes mellitus, health-related behaviors, and past two weeks’ experience of injury, intoxication, or acute or chronic diseases, as well as type of work. The combined effects of long working hours with lower socioeconomic status, or with sleep disturbance, were also significantly higher compared to participants who worked less than 52 hours per week with higher socioeconomic status, or with 6–8 hours of nighttime sleep. Conclusion In this study, long working hours were linked to suicidal thoughts for both genders. Additionally, the odds of those suicidal thoughts were higher for lower socioeconomic groups. To prevent adverse psychological health problems such as suicidal thoughts, a strategy regarding long working hours should be investigated. PMID:26080022

  9. Trial-by-trial updating of an internal reference in discrimination tasks: evidence from effects of stimulus order and trial sequence.

    PubMed

    Dyjas, Oliver; Bausenhart, Karin M; Ulrich, Rolf

    2012-11-01

    In psychophysics, participants are often asked to discriminate between a constant standard and a variable comparison. Previous studies have shown that discrimination performance is better when the comparison follows, rather than precedes, the standard. Prominent difference models of psychophysics and decision making cannot easily explain this order effect. However, a simple extension of this model class involving dynamical updating of an internal reference accounts for this order effect. In addition, this Internal Reference Model (IRM) predicts sequential response effects. We examined the predictions of IRM in two duration discrimination experiments. The obtained results are in agreement with the predictions of IRM, suggesting that participants update their internal reference on every trial. Additional simulations show that IRM also accounts for the negative sequential effects observed in single-stimulus paradigms. PMID:23055085

  10. Phylogenetic relationships of Russian far eastern flatfish (Pleuronectiformes, Pleuronectidae) based on two mitochondrial gene sequences, Co-1 and Cyt-b, with inferences in order phylogeny using complete mitogenome data.

    PubMed

    Kartavtsev, Yuri Phedorovich; Sharina, Svetlana N; Saitoh, Kenji; Imoto, Junichi M; Hanzawa, Naoto; Redin, Alexander D

    2016-01-01

    The systematics and phylogeny of flatfish is investigated on the complete sequence of nucleotides at subunit 1 cytochrome c oxidase (Co-1) and cytochrome b (Cyt-b) genes. In total 17 species from our collection and some species from GenBank were analyzed. Four types of trees were built: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor joining (NJ). These trees showed similar topology. Two separate clusters on the trees support subfamily Hippoglossoidinae and Hippoglossinae subdivision and monophyletic status of these taxa. The subfamily Pleuronectinae also can be considered monophyletic, if the tribe Microstomini is excluded from it and genus Lepidopsetta is moved into the tribe Pleuronectini. Mitogenomes represented by 25 complete sequences from NCBI GenBank were analyzed. After alignment two sets of nucleotide sequences were formed and investigated independently. One set included 13 structural genes (14,886 bp), the second set comprised by the mtDNA without ND6 gene (10,457 bp). Both data sets give congruent phylogenetic signal that agreed with conventional views on the taxonomy of the order Pleuronectiformes; however, the first set gives better topology. In BA gene tree there are two well supported nodes which include the representatives of suborders Pleuronectoidei and Psettoidei. Within Pleuronectoidei two superfamilies, Pleuronectoidea and Soleidea are highly supported in BA but in all four kinds of gene trees (BA, ML, MP and NJ) the only superfamily Pleuronectoidea is well supported. At the top of hierarchy, all flatfishes belonging to the order Pleuronectiformes forming also a monophyletic clade in our data, with support level of 100% but in BA tree only. The monophyly of the family Pleuronectidae is well supported both by single gene data and by complete mtDNA sequences. PMID:24841433

  11. How Do 4th, 5th, and 6th Grade Students' Categories of Cognitive Reflections in Interviews on Derivational Morphology Compare to Their Upper Level Spelling Inventory Orthographic Knowledge?

    ERIC Educational Resources Information Center

    Smith, Darcie D.

    2012-01-01

    Eighty-seven 4th, 5th and 6th grade students were administered the "Derivational Relatedness Interview" (DRI) (Templeton, Smith, Moloney, Van Pelt, & Ives, 2009). The purpose of this instrument is to explore students' understanding of derivational morphology. During the same week, the subjects were also administered an Upper…

  12. Mountain Dew[R] or Mountain Don't?: A Pilot Investigation of Caffeine Use Parameters and Relations to Depression and Anxiety Symptoms in 5th- and 10th-Grade Students

    ERIC Educational Resources Information Center

    Luebbe, Aaron M.; Bell, Debora J.

    2009-01-01

    Background: Caffeine, the only licit psychoactive drug available to minors, may have a harmful impact on students' health and adjustment, yet little is known about its use or effects on students, especially from a developmental perspective. Caffeine use in 5th- and 10th-grade students was examined in a cross-sectional design, and relations and…

  13. A Study on Reading Comprehension Skills of Primary School 5th Grade Students--Learning Basic Reading and Writing Skills through Phonics-Based Sentence Method or Decoding Method

    ERIC Educational Resources Information Center

    Kusdemir Kayiran, Bilge; Karabay, Aysegul

    2012-01-01

    This research aims at investigating the influence of two methods implemented in primary reading and writing teaching programs--phonics-based sentence method and decoding (analysis) method--on primary school 5th grade students' reading comprehension achievement. Also, the study considers the relationship between socio-economic status and reading…

  14. A Response to Lawrence Ferrara's Chapter Four in R. Phelps, R. Sadoff, E. Warburton, and L. Ferrara, "A Guide to Research in Music Education," 5th Edition (Lanham, Maryland, Scarecrow Press, Inc., 2005)

    ERIC Educational Resources Information Center

    Heller, Jack

    2006-01-01

    A reply to Lawrence Ferrara's Chapter 4 in R. Phelps, R. Sadoff, E. Warburton, and L. Ferrara, "A Guide to Research in Music Education," 5th Edition is presented. It it curious that Ferrara disagrees with Jack Heller and Edward J. P. O'Connor's view that "philosophy" is not "research," yet in the chapter headings in the book A Guide to Research in…

  15. Effect of Chronic Rhinosinusitis With or Without Nasal Polyp on Quality of Life in South Korea: 5th Korea National Health and Nutrition Examination Survey Korean

    PubMed Central

    Kim, Do Hyun; Han, Kyungdo; Kim, Soo Whan

    2016-01-01

    Objectives This is the first study of its kind to investigate the relationship between chronic rhinosinusitis (CRS) with or without nasal polyps (NP) and health-related quality of life (HRQoL) in the general adult Korean population. We sought to evaluate the association after adjustment for confounding factors. We also evaluated HRQoL according to presence of NP in CRS patients. Methods In this cross-sectional study we used nationally representative samples from the 5th Korea National Health and Nutrition Examination Survey (2010–2012). A total of 17,490 participants were included in the study, of which 613 were diagnosed with CRS. Univariate analysis was conducted on healthy versus CRS groups, segregated by gender with weighted prevalence of demographic characteristics, socioeconomic status, and comorbid diseases. Subanalysis was carried out to evaluate the relationship between CRS with or without NP and HRQoL using EuroQol 5-dimension (EQ-5D) and visual analog scale (EQ-VAS). The odds ratios for EQ-5D were estimated by multiple logistic regression analyses with confounder adjustment. Results Weighted prevalence of CRS of adult male was found to be 3.7% and CRS with nasal polyps (CRSwNP) 0.5%, while female CRS was 3.3% and CRSwNP 0.3%. There was no significant difference between the groups (P#x0003d;0.332). The scores for female, EQ-5D index (P for trend<0.001) and EQ-VAS (P for trend=0.002) showed decreasing trend from healthy participants to CRS without nasal polyps (CRSsNP) and from CRSsNp to CRSwNP. After adjusting for demographic characteristics, socioeconomic status, and comorbid diseases, EQ-5D scores; EQ-5D index (P<0.001) and EQ-VAS (P<0.001) exhibited poorer HRQoL compared to healthy participants, exclusively within the female group. Conclusion These data suggest that female patients with CRS are at higher risk of poor HRQoL. In addition, HRQoL of female CRSwNP was lower compared to those of CRSsNP and healthy participants. PMID:27090274

  16. EDITORIAL: PLASMA 2006: The 5th International Conference on the Intrinsic Josephson Effect and Plasma Oscillations in High-TC Superconductors

    NASA Astrophysics Data System (ADS)

    Warburton, Paul; Yurgens, August

    2007-02-01

    The 5th International Conference on the Intrinsic Josephson Effect and Plasma Oscillations in High-TC Superconductors (known as `PLASMA' for short) took place in London from July 17th to 19th 2006. The meeting was organised jointly by the Superconductivity Group of the Institute of Physics and the European Science Foundation network `Arrays of Quantum Dots and Josephson Junctions' (AQDJJ). It was sponsored by the UK Engineering and Physical Sciences Research Council, AQDJJ, the Japan Society for the Promotion of Physics and the National Institute of Materials Science (NIMS). The meeting was chaired by Paul Warburton of University College London who wishes to put on record his thanks to the conference sponsors for their generosity, without which the conference could not have taken place. Since the previous PLASMA conference in Tsukuba in 2004 the most significant advance in intrinsic Josephson junction (IJJ) research has arguably been the observation of macroscopic quantum tunnelling in IJJs. At the time of the conference this had been observed by both the RIEC/NIMS/AIST collaboration in Japan and by Paul M\\"uller's group in Erlangen. We therefore felt that the conference presented an ideal and timely opportunity for the IJJ community to learn from the more established community of researchers on macroscopic quantum phenomena in low-TC superconductors---and indeed vice versa. As a result a number of leading researchers from the field of low-TC Josephson qubit devices gave several illuminating presentations. Other sessions included those on Josephson vortex dynamics in layered systems and terahertz oscillations in IJJs, in addition to a lively poster session on the first evening. The conference was rounded off by an excellent summary of the highlights of the meeting given by Professor Hu-Jong Lee. The conference organisers would like to thank all those who made the meeting possible and contributed to its smooth running. In addition to the international organising

  17. The sequence of sequencers: The history of sequencing DNA

    PubMed Central

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  18. Overview of the 80(th) Annual Scientific Meeting of the Japanese Circulation Society - The Past, Present and Future of Cardiovascular Medicine in Japan - - The 5(th) Anniversary of the Great East Japan Earthquake.

    PubMed

    Takahashi, Jun; Satoh, Kimio; Fukuda, Koji; Sugimura, Koichiro; Matsumoto, Yasuharu; Nakano, Makoto; Tsuburaya, Ryuji; Aoki, Tatsuo; Hao, Kiyotaka; Nishimiya, Kensuke; Ito, Kenta; Sakata, Yasuhiko; Shimokawa, Hiroaki

    2016-07-25

    The 80(th)Annual Scientific Meeting of the Japanese Circulation Society was held in Sendai, Japan, on March 18-20, 2016, which coincided with the 5(th)anniversary of the Great East Japan Earthquake that hit the Tohoku area on March 11, 2011. Thus, the main themes for this meeting were "The Past, Present and Future of Cardiovascular Medicine in Japan" and "The 5(th)Anniversary of the Great East Japan Earthquake". Despite the provincial location, approximately 15,000 people attended during the 3-day meeting, and there were in-depth discussions in each of the various sessions on these themes. Especially, to our great pleasure, the Japanese Royals, Emperor Akihito and Empress Michiko, kindly visited the panel exhibition of the Great East Japan Earthquake and spoke words of appreciation to us. The meeting successfully completed and we sincerely appreciate the great cooperation and support from all affiliates. (Circ J 2016; 80: 1689-1694). PMID:27385500

  19. Lucky guess or knowledge: a cross-sectional study using the Bland and Altman analysis to compare confidence-based testing of pharmacological knowledge in 3rd and 5th year medical students.

    PubMed

    Kampmeyer, Daniela; Matthes, Jan; Herzig, Stefan

    2015-05-01

    Multiple-choice-questions are common in medical examinations, but guessing biases assessment results. Confidence-based-testing (CBT) integrates indicated confidence levels. It has been suggested that correctness of and confidence in an answer together indicate knowledge levels thus determining the quality of a resulting decision. We used a CBT approach to investigate whether decision quality improves during undergraduate medical education. 3rd- and 5th-year students attended formative multiple-choice exams on pharmacological issues. Students were asked to indicate their confidence in a given answer. Correctness of answers was scored binary (1-correct; 0-wrong) and confidence levels were transformed to an ordinal scale (guess: 0; rather unsure: 0.33; rather sure: 0.66; very sure: 1). 5th-year students gave more correct answers (73 ± 16 vs. 49 ± 13 %, p < 0.05) and were on average more confident regarding the correctness of their answers (0.61 ± 0.18 vs. 0.46 ± 0.13, p < 0.05). Correlation of these parameters was stronger for 5th-year students (r = 0.81 vs. r = 0.52), but agreement of confidence and correctness ('centration') was lower. By combining the Bland-and-Altman approach with categories of decision-quality we found that 5th-year students were more likely to be 'well-informed' (41 vs. 5 %), while more 3rd-students were 'uninformed' (24 vs. 76 %). Despite a good correlation of exam results and confidence in given answers increased knowledge might be accompanied by a more critical view at the own abilities. Combining the statistical Bland-and-Altman analysis with a theoretical approach to decision-quality, more advanced students are expected to apply correct beliefs, while their younger fellows are rather at risk to hesitate or to act amiss. PMID:25103688

  20. Classroom Order and Student Learning in Late Elementary School: A Multilevel Transactional Model of Achievement Trajectories

    ERIC Educational Resources Information Center

    Gaskins, Clare S.; Herres, Joanna; Kobak, Roger

    2012-01-01

    This study examines the association between classroom order in 4th and 5th grades and student achievement growth over a school year. A three level transactional model tested the effects of classroom order on students' rates of growth in math and reading during the school year controlling for starting achievement levels, student risk factors, and…

  1. The Fixed-Sequence Hypothesis: Ethnic Differences in the Development of Spatial Reasoning.

    ERIC Educational Resources Information Center

    Feldman, David H.

    This research tests the implicit assumption that cognitive development is independent of ethnic background. The testing instrument used was a newly designed spatial reasoning test intended to reflect the sequence of acquisition of skills requisite to map reading and drawing. A sample of 270 black, Chinese, and white subjects (90 each at the 5th,…

  2. PREFACE: MEM07: The 5th Annual Workshop on Mechanical and Electromagnetic Properties of Composite Superconductors (Princeton, NJ, USA, 21 24 August 2007)

    NASA Astrophysics Data System (ADS)

    Larbalestier, D. C.; Osamura, K.; Hampshire, D. P.

    2008-05-01

    MEM07 was the 5th international workshop concentrating on the mechanical and electrical properties of composite superconductors, which are the technological conductor forms from which practical superconducting devices are made. Such superconducting conductors respond to important challenges we currently face, especially those concerned with the proper management of the world's energy resources. Superconductivity provides a means to address the challenges in the generation, transmission and distribution, and use of energy. For energy generation, the ITER Fusion Tokomak (now underway in France) provides exciting new challenges for the whole superconductivity community, due to the enormous size and strong fields of the plasma confinement superconducting magnets that will form the largest and most powerful superconducting machine yet built. Significant attention was paid at MEM07 to the modeling, characterization, testing and validation of the high-amperage Nb3Sn cable-in-conduit conductors needed for ITER. As for electric energy industry uses, there was much discussion of both first generation (Bi,Pb)2Sr2Ca2Cu3Ox conductors and the rapidly emerging second generation coated conductors made from YBa2Cu37-x. High-performing, affordable conductors of these materials are vital for large capacity transmission cables, energy storage systems, fault current limiters, generators and motors—many prototypes of which are being pursued in technologically advanced countries. There is a broad consensus that the prototype stage for high-current-high-field superconducting applications is nearing its end and that large scale applications are technologically feasible. However full industrialization of large-scale superconducting technologies in electric utility applications will benefit from continuous improvement in critical current, lower ac loss, higher strength and other vital conductor properties. The establishment of optimal procedures for the system design accompanying scale

  3. On the inability of magnetically constricted transition regions to account for the 10 to the 5th to 10 to the 6th K plasma in the quiet solar atmosphere

    NASA Technical Reports Server (NTRS)

    Dowdy, James F., Jr.; Moore, Ronald L.; Emslie, A. Gordon

    1987-01-01

    Static models of the plasma in the quiet solar atmosphere incorporating not only conduction and radiation but also the effects of large magnetic constrictions are examined. It is found that the bulk of the solar plasma at temperatures below 7 x 10 to the 5th K cannot be produced by a conductive transition region when it is modeled by flux tubes with constriction compatible with observations. The present findings suggest that the major portion of the UEV plasma may be maintained in an ensemble of small, individual magnetic loops located within the supergranular network and having peak temperatures ranging from chromospheric to coronal values.

  4. Interplay between tectonics and eustasy on an uplifted Plio-Pleistocene marine sequence on Zakynthos island, Eastern Mediterranean.

    NASA Astrophysics Data System (ADS)

    Papanikolaou, M. D.; Triantaphyllou, M.; Head, M. J.; Platzman, E.; Gibbard, P.

    2009-04-01

    unconformity that equates to MIS 22, the hiatus of which is estimated at an average value of 30 kyr and varying between 5 and 65 kyr. Comparing the Zakynthos sedimentary succession of alternating sandstones and clayey silts to the global cycle chart (SEPM Sequences, 2004) it shows that it might respond to a fourth-order 200-kyr cyclicity if the most favoured age model of the sequence is adopted. Therefore, while the 4th -order cycles (0.5-0.1 myr) are probably represented the 5th- and 6th- order cycles (20 kyr and less) are not expressed in the lithostratigraphy,. The construction and comparison of different age model scenarios of the sequence to the global cycle chart displays the importance of a firm age constraint of a sedimentary succession in sequence stratigraphic interpretations.

  5. Nonlinear optical properties of organic materials V; Proceedings of the 5th Meeting, San Diego, CA, July 22-24, 1992

    NASA Astrophysics Data System (ADS)

    Williams, David J.

    The present volume on nonlinear optical properties of organic materials discusses organic nonlinear optics, polymers for nonlinear optics, characterization of nonlinear properties, photorefractive and second-order materials, harmonic generation in organic materials, and devices and applications. Particular attention is given to organic semiconductor-doped polymer glasses as novel nonlinear media, heterocyclic nonlinear optical materials, loss measurements in electrooptic polymer waveguides, the phase-matched second-harmonic generation in planar waveguides, electrooptic measurements in poled polymers, transient effects in spatial light modulation by nonlinearity-absorbing molecules, the electrooptic effects in organic single crystals, surface acoustic wave propagation in an organic nonlinear optical crystal, nonlinear optics of astaxanthin thin films; and advanced high-temperature polymers for integrated optical waveguides. (No individual items are abstracted in this volume)

  6. PIXE analyses over a long period: The case of Neolithic variscite jewels from Western Europe (5th-3th millennium BC)

    NASA Astrophysics Data System (ADS)

    Querré, G.; Calligaro, T.; Domínguez-Bella, S.; Cassen, S.

    2014-01-01

    PIXE analysis of archeological variscite beads and pendants from the Neolithic period that were excavated in Spain, Portugal and France and of variscite geological references samples from European occurrences were carried out from 1999 to 2013 in order to trace back the circulation of this precious gemstone over three millennia. Transformations of the AGLAE external beam system and progress in spectrum processing have induced some apparent compositional variation, affecting in particular the phosphorus/aluminum ratio. This long term evolution has been taken into account with the help of geostandards to build a large and coherent geochemical database of minor and trace elements in variscite. This database allowed us to determine the provenance of the raw material and thus of the circulation of the jewels.

  7. EDITORIAL: Artificial Muscles: Selected papers from the 5th World Congress on Biomimetics, Artificial Muscles and Nano-Bio (Osaka, Japan, 25-27 November 2009) Artificial Muscles: Selected papers from the 5th World Congress on Biomimetics, Artificial Muscles and Nano-Bio (Osaka, Japan, 25-27 November 2009)

    NASA Astrophysics Data System (ADS)

    Shahinpoor, Mohsen

    2011-12-01

    The 5th World Congress on Biomimetics, Artificial Muscles and Nano-Bio and the 4th International Conference on Artificial Muscles were held in Osaka, Japan, 23-27 November 2009. This special section of Smart Materials and Structures is devoted to a selected number of research papers presented at this international conference and congress. Of the 76 or so papers presented at the conference, only 10 papers were finally selected, reviewed and accepted for this special section, following the regular reviewing procedures of the journal. This special section is focused on polymeric artificial muscles, electroactive polymers, multifunctional nanocomposites and their applications. In particular, an electromechanical model for self-sensing ionic polymer-metal composite actuating devices with patterned surface electrodes is presented which discusses the concept of creating self-sensing ionic polymer-metal composite (IPMC) actuating devices with patterned surface electrodes where actuator and sensor elements are separated by a grounded shielding electrode. Eventually, an electromechanical model of the device is also proposed and validated. Following that, there is broad coverage of polytetrahydrofurane-polyethylene oxide-PEDOT conducting interpenetrating polymer networks (IPNs) for high speed actuators. The conducting polymer (poly(3,4-ethylenedioxythiophene)) is incorporated within the IPNs, which are synthesized from polyethylene oxide (PEO)/polytetrahydrofurane (PTHF) networks. PEO/PTHF IPNs are prepared using poly(ethylene glycol) methacrylate and dimethacrylate and hydroxythelechelic PTHF as starting materials. The conducting IPN actuators are prepared by oxidative polymerization of 3,4-ethylenedioxithiophene (EDOT) using FeCl3 as an oxidizing agent within the PEO/PTHF IPN host matrix. Subsequently, giant and reversible magnetorheology of carrageenan/iron oxide magnetic gels are discussed and the effect of magnetic fields on the viscoelastic properties

  8. Design of an optical system for a 5th generation multi-spectral air-to-air missile considering the imaging performance degradation due to the aerodynamic heating

    NASA Astrophysics Data System (ADS)

    Leite, Paulo R., Jr.; da Silva, Maurício; Paoli, Eduardo T.

    2009-05-01

    An air-to-air missile is always submitted to extremes conditions of temperature, such as a hot runway in the desert dropping down to very cold conditions at high altitudes. It is evident that the optical system must be able to provide satisfactory image quality under any circumstances without causing any major degradation to the image. Under this perspective, two different designs of optical systems will be considered for this missile: one catadioptric, using a modified Cassegrain telescope and another one purely dioptric. Both optical systems must be able to focus energy in two different arrays of detectors, one for the near infrared radiation and the other one for the medium infrared. Due to the special missile flight profile, the temperature operational range will be determined and considered in order to design and athermalize the optical systems. Due to the large temperatures range, the missile optical system will experience deformation effects that will cause defocus and image degradation. A correct choice of materials, including the telescope body and dome shroud must be determined to minimize the defocus effect. Also a thermal compensator ought to be strategically placed on both designs to provide focus correction for all the temperatures range. Following that, the optical designs will be analyzed for effects of stray light and ghost image to find out what are the most suitable absorbing paint and anti-reflective coatings to be used. In the last step, both systems will be classified accordingly to their characteristics of performance, weight, size, viability and price and the best will integrate the missile optical system.

  9. The effect of differentiated curriculum enhancements on the achievement of at-risk and normally achieving students in 5th grade science

    NASA Astrophysics Data System (ADS)

    Simpkins, Pamela Mccrea

    2007-12-01

    At-risk students show consistent patterns of under achievement and social maladjustment in school which leads to their demise in high school (McMillian & Reed, 1994). Similarly, special education students are at increased risk of not completing high school and do not perform as well on national achievement tests than their nondisabled peers (Land & Legters, 2002). It is possible that students at-risk for academic failure will not meet graduation requirements unless interventions are put in place to alleviate this problem. It has been documented that science textbooks contain difficult vocabulary and high reading levels that are challenging for struggling students. Using approaches such as activities oriented instruction, which supports the cooperative learning/peer tutoring model is one approach that has been successful with normally achieving and special education students. This research examined the effect of differentiated curriculum enhancements with peer tutoring on the achievement of at-risk and normally achieving students in science. A crossover design was implemented in three fifth grade inclusive classes, consisting of typically achieving students, students at-risk, and students with learning disabilities. The participants included 16 at-risk students, three special education students and 44 normally achieving students. The science review activities were implemented during two consecutive science units. One unit covered Earth and Space science. The other unit covered Light and Sound. Each curriculum enhancement had identification and production level activities. The identification level provided prompts; the production level did not provide prompts. Pretest and posttest were administered. Overall findings of the study revealed a significant interaction between experimental condition and treatment order, suggesting an advantage for students using differentiated curriculum enhancements. Main effects analysis suggested that students performed better on one

  10. Order Up

    ERIC Educational Resources Information Center

    Gibeault, Michael

    2005-01-01

    Change orders. The words can turn the stomachs of administrators. Horror stories about change orders create fear and distrust among school officials, designers and builders. Can change orders be avoided? If car manufacturers can produce millions of intricately designed vehicles, why can't the same quality control be achieved on a construction…

  11. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  12. The Fixed-Sequence Hypothesis: Individual Differences in the Development of School Related Spatial Reasoning.

    ERIC Educational Resources Information Center

    Feldman, David H.

    In order to gather data bearing on the effects of individual differences of the "invariant stages" assumption of cognitive-developmental theory, 270 black, Chinese, and white subjects from 5th, 7th, and ninth grades were administered a new, 25-item, spatial reasoning task. It was predicted that age, ethnic group, and sex would significantly…

  13. EDITORIAL: Artificial Muscles: Selected papers from the 5th World Congress on Biomimetics, Artificial Muscles and Nano-Bio (Osaka, Japan, 25-27 November 2009) Artificial Muscles: Selected papers from the 5th World Congress on Biomimetics, Artificial Muscles and Nano-Bio (Osaka, Japan, 25-27 November 2009)

    NASA Astrophysics Data System (ADS)

    Shahinpoor, Mohsen

    2011-12-01

    The 5th World Congress on Biomimetics, Artificial Muscles and Nano-Bio and the 4th International Conference on Artificial Muscles were held in Osaka, Japan, 23-27 November 2009. This special section of Smart Materials and Structures is devoted to a selected number of research papers presented at this international conference and congress. Of the 76 or so papers presented at the conference, only 10 papers were finally selected, reviewed and accepted for this special section, following the regular reviewing procedures of the journal. This special section is focused on polymeric artificial muscles, electroactive polymers, multifunctional nanocomposites and their applications. In particular, an electromechanical model for self-sensing ionic polymer-metal composite actuating devices with patterned surface electrodes is presented which discusses the concept of creating self-sensing ionic polymer-metal composite (IPMC) actuating devices with patterned surface electrodes where actuator and sensor elements are separated by a grounded shielding electrode. Eventually, an electromechanical model of the device is also proposed and validated. Following that, there is broad coverage of polytetrahydrofurane-polyethylene oxide-PEDOT conducting interpenetrating polymer networks (IPNs) for high speed actuators. The conducting polymer (poly(3,4-ethylenedioxythiophene)) is incorporated within the IPNs, which are synthesized from polyethylene oxide (PEO)/polytetrahydrofurane (PTHF) networks. PEO/PTHF IPNs are prepared using poly(ethylene glycol) methacrylate and dimethacrylate and hydroxythelechelic PTHF as starting materials. The conducting IPN actuators are prepared by oxidative polymerization of 3,4-ethylenedioxithiophene (EDOT) using FeCl3 as an oxidizing agent within the PEO/PTHF IPN host matrix. Subsequently, giant and reversible magnetorheology of carrageenan/iron oxide magnetic gels are discussed and the effect of magnetic fields on the viscoelastic properties

  14. A vision for ubiquitous sequencing

    PubMed Central

    Erlich, Yaniv

    2015-01-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. PMID:26430149

  15. Regression Analysis by Example. 5th Edition

    ERIC Educational Resources Information Center

    Chatterjee, Samprit; Hadi, Ali S.

    2012-01-01

    Regression analysis is a conceptually simple method for investigating relationships among variables. Carrying out a successful application of regression analysis, however, requires a balance of theoretical results, empirical rules, and subjective judgment. "Regression Analysis by Example, Fifth Edition" has been expanded and thoroughly…

  16. Designing Effective Instruction. 5th Edition

    ERIC Educational Resources Information Center

    Morrison, Gary R.; Ross, Steven M.; Kemp, Jerrold E.

    2006-01-01

    This valuable resource provides instructional designers with the guidance they need to meet the challenge of creating effective and efficient instruction. Maintaining a careful balance between theory and application, the Fifth Edition presents a practical, easy-to-follow approach to instructional design that can be applied to K-12 classrooms,…

  17. Radiology of bone diseases. 5th edition

    SciTech Connect

    Greenfield, G.

    1990-01-01

    This book reports on anatomy, physiology, and biochemistry of bone. This book presents alterations in overall characteristics such as density and bone texture. It describes Salterations in specific anatomic regions of bone, as well ad discuss solitary bone lesions. The style in which the diseases are grouped according to specific regions and morphologic alterations rather than by individual pathologic condition is the most powerful aspect of this format.

  18. 5TH BIOTECHNOLOGICAL INVESTIGATIONS OCEAN MARGINS PROGRAM

    SciTech Connect

    DR. ARTURO MASSOL, PROGRAM CHAIR; DR. ROSA BUXEDA, PROGRAM CO-CHAIR

    2004-01-08

    BI-OMP supports DOE's mission in Climate Change Research. The program provides the fundamental understanding of the linkages between carbon and nitrogen cycles in ocean margins. Researchers are providing a mechanistic understanding of these cycles, using the tools of modern molecular biology. The models that will allow policy makers to determine safe levels of greenhouse gases for the Earth System.

  19. 5th Annual Monoclonal Antibodies Conference

    PubMed Central

    2009-01-01

    The conference, which was organized by Visiongain and held at the BSG Conference Center in London, provided an excellent opportunity for participants to exchange views on the development, production and marketing of therapeutic antibodies, and discuss the current business environment. The conference included numerous interactive panel and group discussions on topics such as isotyping for therapeutic antibodies (panel chair: Nick Pullen, Pfizer), prospects for fully human monoclonal antibodies (chair: Christian Rohlff, Oxford BioTherapeutics), perspectives on antibody manufacturing and development (chair: Bo Kara, Avecia), market impact and post-marketing issues (chair: Keith Rodgers, Bodiam Consulting) and angiogenesis inhibitors (chair: David Blakey, AstraZeneca). PMID:20073132

  20. Measurement in Physical Education. 5th Edition.

    ERIC Educational Resources Information Center

    Mathews, Donald K.

    Concepts of measurement in physical education are presented in this college-level text to enable the preservice physical education major to develop skills in determining pupil status, designing effective physical activity programs, and measuring student progress. Emphasis is placed upon discussion of essential statistical methods, test…

  1. Peace Corps 5th Annual Report.

    ERIC Educational Resources Information Center

    Peace Corps, Washington, DC.

    Projects, operations, and future plans are covered in this annual report for the fifth year of the Peace Corps. An introduction overviews past and future activities of the Peace Corps and its volunteers. Section 2 reviews the year 1966 and covers these topics: the new director, Jack Vaughn; countries in which new programs were begun; the…

  2. Order Nidovirales

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter, entitled "Order Nidovirales", is for inclusion in the Ninth Report of the International Committee on Taxonomy of Viruses (ICTV), to be published as both a single volume text and online. The chapter details the taxonomy of members of the Nidovirus order, including family Arteriviridae o...

  3. A 4.5-megabase yeast artificial chromosome contig from human chromosome 13q14.3 ordering 9 polymorphic microsatellites (22 sequence-tagged sites) tightly linked to the Wilson disease locus.

    PubMed Central

    White, A; Tomfohrde, J; Stewart, E; Barnes, R; Le Paslier, D; Weissenbach, J; Cavalli-Sforza, L; Farrer, L; Bowcock, A

    1993-01-01

    We have previously performed a genetic analysis of multiply affected families to map a locus responsible for Wilson disease (WND) to a 0.3-centimorgan (cM) region within chromosome 13q14.3, between D13S31 and D13S59. Here we describe the construction of a contig of approximately 4.5 Mb, which spans this region and extends from D13S25 to D13S59. This contig consists of 28 genomic yeast artificial chromosome (YAC) clones. Five critical crossover events have been defined in this interval in two unaffected (Centre d'Etudes du Polymorphisme Humain) and three WND families. The combination of sequence tagged site content mapping of YACs with both polymorphic and nonpolymorphic markers and recombination breakpoint mapping resulted in the following order of polymorphic markers: centromere-RB1-D13S25-AFM205vh2-D13S31-D13S22 7-D13S228-AFM238vc3-D13S133- AFM084xc5-D13S137-D13S169, D13S155-D13S59-telomere. The recombination/physical distance ratio varies from approximately 3000 kb per cM in the region between D13S31 and D13S25 to 6000 kb per cM in the region between D13S31 and D13S59. Three WND families exhibiting recombination between the disease locus and D13S31 or D13S59 were genotyped for additional markers in this region and further refined the location of the WND gene to between D13S155 and D13S133. Nine of the markers in this region of < 1 cM are polymorphic microsatellites (seven have observed heterozygosities of 70% or above) that will be extremely useful in prenatal and preclinical diagnosis of this disease. This physical map is an essential step in the isolation of the WND gene and is a framework for the identification of candidate genes. PMID:8234264

  4. Nucleosome dynamics: Sequence matters.

    PubMed

    Eslami-Mossallam, Behrouz; Schiessel, Helmut; van Noort, John

    2016-06-01

    About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence. PMID:26896338

  5. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  6. Counterbalancing for Serial Order Carryover Effects in Experimental Condition Orders

    ERIC Educational Resources Information Center

    Brooks, Joseph L.

    2012-01-01

    Reactions of neural, psychological, and social systems are rarely, if ever, independent of previous inputs and states. The potential for serial order carryover effects from one condition to the next in a sequence of experimental trials makes counterbalancing of condition order an essential part of experimental design. Here, a method is proposed…

  7. Translational Research in Oncology Research & Development and Its Impact on Early Development in China: report of the 5th Annual Meeting of the US Chinese Anti-Cancer Association (USCACA) at 2013 AACR Annual Meeting

    PubMed Central

    Guan, Lingjie; Dai, Yun; Luo, Roger

    2013-01-01

    In April 2013, the US Chinese Anti-Cancer Association (USCACA) held its 5th annual meeting in conjunction with the American Association for Cancer Research (AACR) 2013 Annual Meeting in Washington DC. The USCACA executive committee reported activities and programs and highlighted the partnership and collaboration between USCACA and other major organizations. The key initiatives and programs of USCACA included 1) USCACA-TIGM Esophageal Cancer Program that funds translational research of esophageal cancer prevention and treatment at the Xinxiang Medical University in Henan province, China; 2) the USCACA-NFCR-AFCR Scholarship Program, which has supported 10 young outstanding Chinese cancer researchers and will award 4 fellowships at the Guangzhou International Symposium on Oncology in November this year; 3) USCACA-Hengrui Training Program for Early Phase Clinical Research, which has supported the training of a Chinese scholar at two major cancer centers in the US; and 4) USCACA has continued its partnership with the Chinese Journal of Cancer, which has reached significant international impact. PMID:23823625

  8. Analysis of archaeological triacylglycerols by high resolution nanoESI, FT-ICR MS and IRMPD MS/MS: Application to 5th century BC-4th century AD oil lamps from Olbia (Ukraine)

    NASA Astrophysics Data System (ADS)

    Garnier, Nicolas; Rolando, Christian; Høtje, Jakob Munk; Tokarski, Caroline

    2009-07-01

    This work presents the precise identification of triacylglycerols (TAGs) extracted from archaeological samples using a methodology based on nanoelectrospray and Fourier transform mass spectrometry. The archaeological TAG identification needs adapted sample preparation protocols to trace samples in advanced degradation state. More precisely, the proposed preparation procedure includes extraction of the lipid components from finely grinded ceramic using dichloromethane/methanol mixture with additional ultrasonication treatment, and TAG purification by solid phase extraction on a diol cartridge. Focusing on the analytical approach, the implementation of "in-house" species-dependent TAG database was investigated using MS and InfraRed Multiphoton Dissociation (IRMPD) MS/MS spectra; several vegetal oils, dairy products and animal fats were studied. The high mass accuracy of the Fourier transform analyzer ([Delta]m below 2.5 ppm) provides easier data interpretation, and allows distinction between products of different origins. In details, the IRMPD spectra of the lithiated TAGs reveal fragmentation reactions including loss of free neutral fatty acid and loss of fatty acid as [alpha],[beta]-unsaturated moieties. Based on the developed preparation procedure and on the constituted database, TAG extracts from 5th century BC to 4th century AD Olbia lamps were analyzed. The structural information obtained succeeds in identifying that bovine/ovine fats were used as fuel used in these archaeological Olbia lamps.

  9. Abdominal Organ Location, Morphology, and Rib Coverage for the 5th, 50th, and 95th Percentile Males and Females in the Supine and Seated Posture using Multi-Modality Imaging

    PubMed Central

    Hayes, Ashley R.; Gayzik, F. Scott; Moreno, Daniel P.; Martin, R. Shayn; Stitzel, Joel D.

    2013-01-01

    The purpose of this study was to use data from a multi-modality image set of males and females representing the 5th, 50th, and 95th percentile (n=6) to examine abdominal organ location, morphology, and rib coverage variations between supine and seated postures. Medical images were acquired from volunteers in three image modalities including Computed Tomography (CT), Magnetic Resonance Imaging (MRI), and upright MRI (uMRI). A manual and semi-automated segmentation method was used to acquire data and a registration technique was employed to conduct a comparative analysis between abdominal organs (liver, spleen, and kidneys) in both postures. Location of abdominal organs, defined by center of gravity movement, varied between postures and was found to be significant (p=0.002 to p=0.04) in multiple directions for each organ. In addition, morphology changes, including compression and expansion, were seen in each organ as a result of postural changes. Rib coverage, defined as the projected area of the ribs onto the abdominal organs, was measured in frontal, lateral, and posterior projections, and also varied between postures. A significant change in rib coverage between postures was measured for the spleen and right kidney (p=0.03 and p=0.02). The results indicate that posture affects the location, morphology and rib coverage area of abdominal organs and these implications should be noted in computational modeling efforts focused on a seated posture. PMID:24406951

  10. High-resolution sequence stratigraphic framework of carbonate deposition controlled by sea level and geostrophic bottom currents, south Florida platform margin

    SciTech Connect

    Locker, S.D.; Hine, A.C. ); Shinn, E.A. )

    1992-01-01

    High-resolution seismic reflection profiles seaward of the Marquesas Keys reveal at least eight late Quaternary sequences which downlap onto the Miocene ( ) age Pourtales Terrace at 250 m water depth. Inferred correlations are presented between these sequences and the last 7--8 sea-level cycles during the past 150 ky. The setting is unusual in that the present reef-rimmed, shallow inner shelf supplies minimal sediment to the adjacent margin where over 30 m of Holocene sediment has accumulated on portions of the outer shelf and slope. Seaward of the inner-shelf reef'' barrier, an outer-shelf terrace in 50--60 m water depth forms the upper boundary of the prograding late Quaternary sequences. These sequences exhibit both current-controlled internal geometries (e.g., sediment drifts) and sea-level controlled features such as lowstand slope erosion, transgressive unconformities, and paleoshorelines or reefs formed during lower stands of sea level. Bottom currents also severely eroded the slope at times, creating prominent unconformities. These 5th-6th order depositional sequences exhibit many features outlined by the Exxon sequence stratigraphy models. Systems tracts inferred from seismic records include lowstand wedge, shelf margin, and highstand deposits. Transgressive systems tracts are more difficult to identify and correspond to the flat outer-shelf terrace that experienced rapid lateral transgressions and regressions of sea level, and was exposed to subaerial processes during low stands. This study provides new insight on the importance of both geostrophic boundary currents and sea-level change in controlling stratigraphic development of a carbonate platform margin. Locally-thick accumulations off the Marquesas Keys may demonstrate sedimentation in response to a persistent cold cyclonic gyre in this area which causes weak counter-currents in an otherwise strong geostrophic current area.

  11. New high order schemes in BATS-R-US

    NASA Astrophysics Data System (ADS)

    Toth, G.; van der Holst, B.; Daldorff, L.; Chen, Y.; Gombosi, T. I.

    2013-12-01

    The University of Michigan global magnetohydrodynamics code BATS-R-US has long relied on the block-adaptive mesh refinement (AMR) to increase accuracy in regions of interest, and we used a second order accurate TVD scheme. While AMR can in principle produce arbitrarily accurate results, there are still practical limitations due to computational resources. To further improve the accuracy of the BATS-R-US code, recently, we have implemented a 4th order accurate finite volume scheme (McCorquodale and Colella, 2011}), the 5th order accurate Monotonicity Preserving scheme (MP5, Suresh and Huynh, 1997) and the 5th order accurate CWENO5 scheme (Capdeville, 2008). In the first implementation the high order accuracy is achieved in the uniform parts of the Cartesian grids, and we still use the second order TVD scheme at resolution changes. For spherical grids the new schemes are only second order accurate so far, but still much less diffusive than the TVD scheme. We show a few verification tests that demonstrate the order of accuracy as well as challenging space physics applications. The high order schemes are less robust than the TVD scheme, and it requires some tricks and effort to make the code work. When the high order scheme works, however, we find that in most cases it can obtain similar or better results than the TVD scheme on twice finer grids. For three dimensional time dependent simulations this means that the high order scheme is almost 10 times faster requires 8 times less storage than the second order method.

  12. Automated Identification of Nucleotide Sequences

    NASA Technical Reports Server (NTRS)

    Osman, Shariff; Venkateswaran, Kasthuri; Fox, George; Zhu, Dian-Hui

    2007-01-01

    STITCH is a computer program that processes raw nucleotide-sequence data to automatically remove unwanted vector information, perform reverse-complement comparison, stitch shorter sequences together to make longer ones to which the shorter ones presumably belong, and search against the user s choice of private and Internet-accessible public 16S rRNA databases. ["16S rRNA" denotes a ribosomal ribonucleic acid (rRNA) sequence that is common to all organisms.] In STITCH, a template 16S rRNA sequence is used to position forward and reverse reads. STITCH then automatically searches known 16S rRNA sequences in the user s chosen database(s) to find the sequence most similar to (the sequence that lies at the smallest edit distance from) each spliced sequence. The result of processing by STITCH is the identification of the most similar well-described bacterium. Whereas previously commercially available software for analyzing genetic sequences operates on one sequence at a time, STITCH can manipulate multiple sequences simultaneously to perform the aforementioned operations. A typical analysis of several dozen sequences (length of the order of 103 base pairs) by use of STITCH is completed in a few minutes, whereas such an analysis performed by use of prior software takes hours or days.

  13. An Assignment Sequence for Underprepared Writers.

    ERIC Educational Resources Information Center

    Nimmo, Kristi

    2000-01-01

    Presents a sequenced writing assignment on shopping to aid basic writers. Describes a writing assignment focused around online and mail-order shopping. Notes steps in preparing for the assignment, the sequence, and discusses responses to the assignments. (SC)

  14. Sequence in the Social Studies

    ERIC Educational Resources Information Center

    Ediger, Marlow

    2010-01-01

    Quality sequence in the social studies is of utmost importance. Sequence emphasizes "when" selected concepts should be stressed in ongoing lessons and units of study. The social studies teacher needs to observe pupils carefully in teaching and learning situations to ascertain suitable, ordered experiences for pupils. Pupils face frustration if the…

  15. The effect of anatomical modeling on space radiation dose estimates: a comparison of doses for NASA phantoms and the 5th, 50th, and 95th percentile male and female astronauts

    NASA Astrophysics Data System (ADS)

    Bahadori, Amir A.; Van Baalen, Mary; Shavers, Mark R.; Dodge, Charles; Semones, Edward J.; Bolch, Wesley E.

    2011-03-01

    The National Aeronautics and Space Administration (NASA) performs organ dosimetry and risk assessment for astronauts using model-normalized measurements of the radiation fields encountered in space. To determine the radiation fields in an organ or tissue of interest, particle transport calculations are performed using self-shielding distributions generated with the computer program CAMERA to represent the human body. CAMERA mathematically traces linear rays (or path lengths) through the computerized anatomical man (CAM) phantom, a computational stylized model developed in the early 1970s with organ and body profiles modeled using solid shapes and scaled to represent the body morphometry of the 1950 50th percentile (PCTL) Air Force male. With the increasing use of voxel phantoms in medical and health physics, a conversion from a mathematical-based to a voxel-based ray-tracing algorithm is warranted. In this study, the voxel-based ray tracer (VoBRaT) is introduced to ray trace voxel phantoms using a modified version of the algorithm first proposed by Siddon (1985 Med. Phys. 12 252-5). After validation, VoBRAT is used to evaluate variations in body self-shielding distributions for NASA phantoms and six University of Florida (UF) hybrid phantoms, scaled to represent the 5th, 50th, and 95th PCTL male and female astronaut body morphometries, which have changed considerably since the inception of CAM. These body self-shielding distributions are used to generate organ dose equivalents and effective doses for five commonly evaluated space radiation environments. It is found that dosimetric differences among the phantoms are greatest for soft radiation spectra and light vehicular shielding.

  16. Microchips for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Mastrangelo, Carlos H.; Palaniappan, S.; Man, Piu Francis; Burns, Mark A.; Burke, David T.

    1999-08-01

    Genetic information is vital for understanding features and response of an organism. In humans, genetic errors are linked to the development of major diseases such as cancer and diabetes. In order to maximally exploit this information it is necessary to develop miniature sequencing assays that are rapid and inexpensive. In this paper we show how this could be attained with microfluidic chips that contain integrated assays. To date simple silicon/glass chips aimed for sequencing purpose have been realized; but these chips are not yet practical. Some of the solutions that are used to bring these devices closer to commercial applications are discussed.

  17. The relationship between shellbed type and sequence architecture: examples from Japan and New Zealand

    NASA Astrophysics Data System (ADS)

    Kondo, Yasuo; Abbott, Stephen T.; Kitamura, Akihisa; Kamp, Peter J. J.; Naish, Tim R.; Kamataki, Takanobu; Saul, Gordon S.

    1998-12-01

    Examples of lithology, fossil content and taphonomic features of shellbeds and intervening less fossiliferous intervals are presented from four Plio-Pleistocene successions (Shimosa Group, Boso Peninsula, Omma Formation, Hokuriku area, Japan, and Okehu, Kai-iwi, and Shakespeare groups in Wanganui, and the Rangitikei Group along the Rangitikei River in New Zealand). As for pre-Pliocene 3rd- and 4th-order depositional sequences, Plio-Pleistocene 5th- to 7th-order depositional sequences contain a variety of shellbeds which are often associated with surfaces or intervals that are characterized by sedimentary condensation, omission or erosion (e.g. sequence boundaries, ravinement surfaces, downlap surfaces and condensed sections). Stratigraphic patterns of shellbed type tend to be similar and repetitive within a basin and a locality. This demonstrates that a specific palaeogeography played an important role in determining the nature of shellbeds. For example, shellbeds formed in the context of toplap are common only in the Shimosa Group, which was deposited in a moderately sheltered sea, the palaeo-Tokyo Bay. Toplap shellbeds are rare in other sequences formed in more open conditions. Despite the variability resulting from such basin characteristics, common styles of shellbeds can be recognized that formed under conditions of marine onlap, backlap, downlap and toplap. Each type of shellbed has a characteristic fossil composition and taphonomy. Onlap and toplap shellbeds contain low-diversity macrobenthic associations including Glycymeris, Mercenaria, Paphies or other bivalves having robust shells, which are often abraded or fragmented. Backlap shellbeds, which are equivalent to the condensed section formed at the maximum transgression, are characterized by dominance of epifaunal macrobenthos such as bryozoa, brachiopoda, pectinid and ostreid bivalves, preserved in a slightly cemented, glauconitic muddy matrix. In contrast to fossils in such condensed sections, the shell

  18. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  19. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  20. Controlled processing during sequencing

    PubMed Central

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations. PMID:26578941

  1. Scaling exponents for ordered maxima

    SciTech Connect

    Ben-Naim, E.; Krapivsky, P. L.; Lemons, N. W.

    2015-12-22

    We study extreme value statistics of multiple sequences of random variables. For each sequence with N variables, independently drawn from the same distribution, the running maximum is defined as the largest variable to date. We compare the running maxima of m independent sequences and investigate the probability SN that the maxima are perfectly ordered, that is, the running maximum of the first sequence is always larger than that of the second sequence, which is always larger than the running maximum of the third sequence, and so on. The probability SN is universal: it does not depend on the distribution from which the random variables are drawn. For two sequences, SN~N–1/2, and in general, the decay is algebraic, SN~N–σm, for large N. We analytically obtain the exponent σ3≅1.302931 as root of a transcendental equation. Moreover, the exponents σm grow with m, and we show that σm~m for large m.

  2. Scaling exponents for ordered maxima

    DOE PAGESBeta

    Ben-Naim, E.; Krapivsky, P. L.; Lemons, N. W.

    2015-12-22

    We study extreme value statistics of multiple sequences of random variables. For each sequence with N variables, independently drawn from the same distribution, the running maximum is defined as the largest variable to date. We compare the running maxima of m independent sequences and investigate the probability SN that the maxima are perfectly ordered, that is, the running maximum of the first sequence is always larger than that of the second sequence, which is always larger than the running maximum of the third sequence, and so on. The probability SN is universal: it does not depend on the distribution frommore » which the random variables are drawn. For two sequences, SN~N–1/2, and in general, the decay is algebraic, SN~N–σm, for large N. We analytically obtain the exponent σ3≅1.302931 as root of a transcendental equation. Moreover, the exponents σm grow with m, and we show that σm~m for large m.« less

  3. Source potential and sequence stratigraphic characterization of microbial evaporitic mudrocks: Upper Permian Zechstein Group, Northern Germany

    NASA Astrophysics Data System (ADS)

    Hammes, Ursula; Mutti, Maria

    2013-04-01

    Microbial evaporitic carbonate mudrocks are important source rocks throughout much of the earth history. Some of the largest hydrocarbon provinces are potentially sourced by evaporite source rocks such as the Cretaceous and Jurassic in the Middle East, the Tertiary in Spain, the Permian in northern Germany, the Devonian in Canada, and the Pennsylvanian in the USA. Carbonate mudrocks deposited under mesosaline conditions are often over-looked and dismissed as potential source rocks. However, preservation and accumulation of organic matter in salinity-layered intraplatform epeiric depressions and restricted basin centers are significant. These mudrocks may not only constitute the source but also exhibit reservoir qualities. Slope and basin laminated mudrocks were investigated for their source and reservoir potential using sequence stratigraphic and geochemical techniques to investigate the exploration potential of the northern German Upper Permian Zechstein Formation. The lower Zechstein cycles Z1 and Z2 are characterized by calcareous to argillaceous, laminated, organic-rich mudstones with TOC (total organic carbon) contents ranging mostly <1% in the Z2 and >6% in the Z1 cycle. Maturities range from 0.9 to >3% Ro depending on depth of burial for these two cycles. While the Z1 mudrocks deposited above the Rotliegend clastic section are more argillaceous and clay-rich grading upward from calcareous mudstones to intraclast, coated grain, thrombolitic wacke- and packstones into coated-grain grainstones, the Z2 mudrocks are dominated by calcareous to dolomitic laminated mudstones. Both cycles are characterized by microbially bound carbonates ranging from thrombolytic to crenulated laminated structures that are overlain by anhydrite and salt. Stacking patterns of the Z1 3rd-order cycle reveal three 5th-order parasequences stacking into two 4th-order sequences; Z2 3rd-order cycle is composed of three 4th-order parasequences that first deepen and then shallow upwards

  4. Program for Editing Spacecraft Command Sequences

    NASA Technical Reports Server (NTRS)

    Gladden, Roy; Waggoner, Bruce; Kordon, Mark; Hashemi, Mahnaz; Hanks, David; Salcedo, Jose

    2006-01-01

    Sequence Translator, Editor, and Expander Resource (STEER) is a computer program that facilitates construction of sequences and blocks of sequences (hereafter denoted generally as sequence products) for commanding a spacecraft. STEER also provides mechanisms for translating among various sequence product types and quickly expanding activities of a given sequence in chronological order for review and analysis of the sequence. To date, construction of sequence products has generally been done by use of such clumsy mechanisms as text-editor programs, translating among sequence product types has been challenging, and expanding sequences to time-ordered lists has involved arduous processes of converting sequence products to "real" sequences and running them through Class-A software (defined, loosely, as flight and ground software critical to a spacecraft mission). Also, heretofore, generating sequence products in standard formats has been troublesome because precise formatting and syntax are required. STEER alleviates these issues by providing a graphical user interface containing intuitive fields in which the user can enter the necessary information. The STEER expansion function provides a "quick and dirty" means of seeing how a sequence and sequence block would expand into a chronological list, without need to use of Class-A software.

  5. Reconstructing of a Sequence Using Similar Sequences

    1995-11-28

    SIMSEQ reconstructs sequences from oligos. Similar known sequences are used as a reference. At present, simulated data are being used to develop the algorithm. SIMSEQ generates an initial random sequence, then generates a second sequence that is 60 to 90 percent similar to the first. Next, the second sequence is chopped into its appropriate oligos. All possible sequences are reconstructed to determine the most similar. Those with the highest similarity are printed as output.

  6. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

    PubMed Central

    2014-01-01

    Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be

  7. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

    DOE PAGESBeta

    Scheuner, Carmen; Tindall, Brian J.; Lu, Megan; Nolan, Matt; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; et al

    2014-12-08

    Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448 T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published andmore » the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. We study phylogenomic analyses that indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. Lastly, in addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the

  8. Statistical analysis of nucleotide sequences.

    PubMed Central

    Stückle, E E; Emmrich, C; Grob, U; Nielsen, P J

    1990-01-01

    In order to scan nucleic acid databases for potentially relevant but as yet unknown signals, we have developed an improved statistical model for pattern analysis of nucleic acid sequences by modifying previous methods based on Markov chains. We demonstrate the importance of selecting the appropriate parameters in order for the method to function at all. The model allows the simultaneous analysis of several short sequences with unequal base frequencies and Markov order k not equal to 0 as is usually the case in databases. As a test of these modifications, we show that in E. coli sequences there is a bias against palindromic hexamers which correspond to known restriction enzyme recognition sites. PMID:2251125

  9. Aberrations of the cathode objective lens up to fifth order.

    PubMed

    Tromp, R M; Wan, W; Schramm, S M

    2012-08-01

    In this paper we discuss a topic that was close to Prof. Gertrude Rempfer s interests for many years. On this occasion of her 100th birthday, we remember and honor Gertrude for her many outstanding contributions, and for the inspiring example that she set. We derive theoretical expressions for the aberration coefficients of the uniform electrostatic field up to 5th order and compare these with raytracing calculations for the cathode lens used in Low Energy Electron Microscopy and Photo Electron Emission Microscopy experiments. These higher order aberration coefficients are of interest for aberration corrected experiments in which chromatic (C(c)) and spherical (C₃) aberrations of the microscope are set to zero. The theoretical predictions are in good agreement with the results of raytracing. Calculations of image resolution using the Contrast Transfer Function method show that sub-nanometer resolution is achievable in an aberration corrected LEEM system. PMID:22188906

  10. Elimination sequence optimization for SPAR

    NASA Technical Reports Server (NTRS)

    Hogan, Harry A.

    1986-01-01

    SPAR is a large-scale computer program for finite element structural analysis. The program allows user specification of the order in which the joints of a structure are to be eliminated since this order can have significant influence over solution performance, in terms of both storage requirements and computer time. An efficient elimination sequence can improve performance by over 50% for some problems. Obtaining such sequences, however, requires the expertise of an experienced user and can take hours of tedious effort to affect. Thus, an automatic elimination sequence optimizer would enhance productivity by reducing the analysts' problem definition time and by lowering computer costs. Two possible methods for automating the elimination sequence specifications were examined. Several algorithms based on the graph theory representations of sparse matrices were studied with mixed results. Significant improvement in the program performance was achieved, but sequencing by an experienced user still yields substantially better results. The initial results provide encouraging evidence that the potential benefits of such an automatic sequencer would be well worth the effort.

  11. Default processing of event sequences.

    PubMed

    Hymel, Alicia; Levin, Daniel T; Baker, Lewis J

    2016-02-01

    In a wide range of circumstances, it is important to perceive and represent the sequence of events. For example, sequence perception is necessary to learn statistical contingencies between events, and to generate predictions about events when segmenting actions. However, viewer's awareness of event sequence is rarely tested, and at least some means of encoding event sequence are likely to be resource-intensive. Therefore, previous research may have overestimated the degree to which viewers are aware of specific event sequences. In the experiments reported here, we tested viewers' ability to detect anomalies during visual event sequences. Participants viewed videos containing events that either did or did not contain an out-of-order action. Participants were unable to consistently detect the misordered events, and performance on the task decreased significantly to very low levels when performing a secondary task. In addition, participants almost never detected misorderings in an incidental version of the task, and performance increased when videos ended immediately after the misordering, We argue that these results demonstrate that viewers can effectively perceive the elements of events, but do not consistently test their expectations about the specific sequence of natural events unless bidden to do so by task-specific demands. (PsycINFO Database Record PMID:26348070

  12. Image analysis for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Palaniappan, Kannappan; Huang, Thomas S.

    1991-07-01

    There is a great deal of interest in automating the process of DNA (deoxyribonucleic acid) sequencing to support the analysis of genomic DNA such as the Human and Mouse Genome projects. In one class of gel-based sequencing protocols autoradiograph images are generated in the final step and usually require manual interpretation to reconstruct the DNA sequence represented by the image. The need to handle a large volume of sequence information necessitates automation of the manual autoradiograph reading step through image analysis in order to reduce the length of time required to obtain sequence data and reduce transcription errors. Various adaptive image enhancement, segmentation and alignment methods were applied to autoradiograph images. The methods are adaptive to the local characteristics of the image such as noise, background signal, or presence of edges. Once the two-dimensional data is converted to a set of aligned one-dimensional profiles waveform analysis is used to determine the location of each band which represents one nucleotide in the sequence. Different classification strategies including a rule-based approach are investigated to map the profile signals, augmented with the original two-dimensional image data as necessary, to textual DNA sequence information.

  13. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  14. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  15. Coordinate cytokine regulatory sequences

    DOEpatents

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  16. Science sequence design

    NASA Technical Reports Server (NTRS)

    Koskela, P. E.; Bollman, W. E.; Freeman, J. E.; Helton, M. R.; Reichert, R. J.; Travers, E. S.; Zawacki, S. J.

    1973-01-01

    The activities of the following members of the Navigation Team are recorded: the Science Sequence Design Group, responsible for preparing the final science sequence designs; the Advanced Sequence Planning Group, responsible for sequence planning; and the Science Recommendation Team (SRT) representatives, responsible for conducting the necessary sequence design interfaces with the teams during the mission. The interface task included science support in both advance planning and daily operations. Science sequences designed during the mission are also discussed.

  17. Variable Order and Distributed Order Fractional Operators

    NASA Technical Reports Server (NTRS)

    Lorenzo, Carl F.; Hartley, Tom T.

    2002-01-01

    Many physical processes appear to exhibit fractional order behavior that may vary with time or space. The continuum of order in the fractional calculus allows the order of the fractional operator to be considered as a variable. This paper develops the concept of variable and distributed order fractional operators. Definitions based on the Riemann-Liouville definitions are introduced and behavior of the operators is studied. Several time domain definitions that assign different arguments to the order q in the Riemann-Liouville definition are introduced. For each of these definitions various characteristics are determined. These include: time invariance of the operator, operator initialization, physical realization, linearity, operational transforms. and memory characteristics of the defining kernels. A measure (m2) for memory retentiveness of the order history is introduced. A generalized linear argument for the order q allows the concept of "tailored" variable order fractional operators whose a, memory may be chosen for a particular application. Memory retentiveness (m2) and order dynamic behavior are investigated and applications are shown. The concept of distributed order operators where the order of the time based operator depends on an additional independent (spatial) variable is also forwarded. Several definitions and their Laplace transforms are developed, analysis methods with these operators are demonstrated, and examples shown. Finally operators of multivariable and distributed order are defined in their various applications are outlined.

  18. Atypical regions in large genomic DNA sequences

    SciTech Connect

    Scherer, S. |; McPeek, M.S.; Speed, T.P.

    1994-07-19

    Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. The authors describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of >1000 nt and human sequences of >10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. The authors consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

  19. Genomic sequencing in clinical trials

    PubMed Central

    2011-01-01

    Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to find its way into clinical trials both nationally and worldwide. We highlight the currently available types of genomic sequencing platforms, outline the advantages and disadvantages of each, and compare first- and next-generation techniques with respect to capabilities, quality, and cost. We describe the current geographical distributions and types of disease conditions in which these technologies are used, and how next-generation sequencing is strategically being incorporated into new and existing studies. Lastly, recent major breakthroughs and the ongoing challenges of using genomic sequencing in clinical research are discussed. PMID:22206293

  20. High speed nucleic acid sequencing

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2011-05-17

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid. Each type of labeled nucleotide comprises an acceptor fluorophore attached to a phosphate portion of the nucleotide such that the fluorophore is removed upon incorporation into a growing strand. Fluorescent signal is emitted via fluorescent resonance energy transfer between the donor fluorophore and the acceptor fluorophore as each nucleotide is incorporated into the growing strand. The sequence is deduced by identifying which base is being incorporated into the growing strand.

  1. Detection of latent sequence periodicities.

    PubMed Central

    Pizzi, E; Liuni, S; Frontali, C

    1990-01-01

    A method is proposed for the automatic detection of serial periodicities in a linear sequence. Its application to DNA subtelomeric sequences from two lower eukaryotes, P.falciparum and S.cerevisiae, reveals ordered patterns organised in hierarchical periodicities, not easily recognizable by other methods. The possible implications concerning the evolution of tandemly repetitive arrays are discussed in light of a model which involves, as successive steps, random repeat modification, the fusion of differently modified repeat versions into longer units, and the amplification of (and/or homogenization to) the more recent repeat units. PMID:2197595

  2. Asteroid Ida Rotation Sequence

    NASA Technical Reports Server (NTRS)

    1994-01-01

    This montage of 14 images (the time order is right to left, bottom to top) shows Ida as it appeared in the field of view of Galileo's camera on August 28, 1993. Asteroid Ida rotates once every 4 hours, 39 minutes and clockwise when viewed from above the north pole; these images cover about one Ida 'day.' This sequence has been used to create a 3-D model that shows Ida to be almost croissant shaped. The earliest view (lower right) was taken from a range of 240,000 kilometers (150,000 miles), 5.4 hours before closest approach. The asteroid Ida draws its name from mythology, in which the Greek god Zeus was raised by the nymph Ida.

  3. An overview of task order 10

    SciTech Connect

    Rousculp, Christopher L

    2011-01-12

    Task Order 10 formalizes a collaboration in high explosive pulsed power (HEPP) experiments between LANL and VNIIEF. The focus is the VNIIEF disk explosive magnetic generator (DEMG) technology. The task order outlines a sequence of tasks and deliverables culminating in an experiment which takes place in the US utilizing US explosives and a Russian DEMG. This talk summarizes task order 10. It gives a brief history and present status in terms of the proposed high pressure EOS experiment (ALT-3).

  4. Distinguishing Proteins From Arbitrary Amino Acid Sequences

    PubMed Central

    Yau, Stephen S.-T.; Mao, Wei-Guang; Benson, Max; He, Rong Lucy

    2015-01-01

    What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

  5. Sequence Factorization with Multiple References

    PubMed Central

    Wandelt, Sebastian; Leser, Ulf

    2015-01-01

    The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1) the size of the factorization, 2) the time for factorization, and 3) the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%), factorization speed (0.01 MB/s to more than 600 MB/s), and main memory usage (few dozen MB to dozens of GB). Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization. PMID:26422374

  6. Detecting selection in immunoglobulin sequences.

    PubMed

    Uduman, Mohamed; Yaari, Gur; Hershberg, Uri; Stern, Jacob A; Shlomchik, Mark J; Kleinstein, Steven H

    2011-07-01

    The ability to detect selection by analyzing mutation patterns in experimentally derived immunoglobulin (Ig) sequences is a critical part of many studies. Such techniques are useful not only for understanding the response to pathogens, but also to determine the role of antigen-driven selection in autoimmunity, B cell cancers and the diversification of pre-immune repertoires in certain species. Despite its importance, quantifying selection in experimentally derived sequences is fraught with difficulties. The necessary parameters for statistical tests (such as the expected frequency of replacement mutations in the absence of selection) are non-trivial to calculate, and results are not easily interpretable when analyzing more than a handful of sequences. We have developed a web server that implements our previously proposed Focused binomial test for detecting selection. Several features are integrated into the web site in order to facilitate analysis, including V(D)J germline segment identification with IMGT alignment, batch submission of sequences and integration of additional test statistics proposed by other groups. We also implement a Z-score-based statistic that increases the power of detecting selection while maintaining specificity, and further allows for the combined analysis of sequences from different germlines. The tool is freely available at http://clip.med.yale.edu/selection. PMID:21665923

  7. The expanding scope of DNA sequencing

    PubMed Central

    Shendure, Jay; Aiden, Erez Lieberman

    2014-01-01

    In just seven years, next-generation technologies have reduced the cost and increased the speed of DNA sequencing by four orders of magnitude, and experiments requiring many millions of sequencing reads are now routine. In research, sequencing is being applied not only to assemble genomes and to investigate the genetic basis of human disease, but also to explore myriad phenomena in organismic and cellular biology. In the clinic, the utility of sequence data is being intensively evaluated in diverse contexts, including reproductive medicine, oncology and infectious disease. A recurrent theme in the development of new sequencing applications is the creative ‘recombination’ of existing experimental building blocks. However, there remain many potentially high-impact applications of next-generation DNA sequencing that are not yet fully realized. PMID:23138308

  8. Scaled Opposite Spin Second Order Moller-Plesset Correlation Energy: An Economical Electronic Structure Method

    SciTech Connect

    Jung, Yousung; Lochan, Rohini C.; Dutoi, Anthony D.; Head-Gordon, Martin

    2004-08-02

    A simplified approach to treating the electron correlation energy is suggested in which only the alpha-beta component of the second order Moller-Plesset energy is evaluated, and then scaled by an empirical factor which is suggested to be 1.3. This scaled opposite spin second order energy (SOS-MP2) yields results for relative energies and derivative properties that are statistically improved over the conventional MP2 method. Furthermore, the SOS-MP2 energy can be evaluated without the 5th order computational steps associated with MP2 theory, even without exploiting any spatial locality. A 4th order algorithm is given for evaluating the opposite spin MP2 energy using auxiliary basis expansions, and a Laplace approach, and timing comparisons are given.

  9. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  10. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  11. Secondary-task effects on sequence learning.

    PubMed

    Heuer, H; Schmidtke, V

    1996-01-01

    With a repeated sequence of stimuli, performance in a serial reaction-time task improves more than with a random sequence. The difference has been taken as a measure of implicit sequence learning. Implicit sequence learning is impaired when a secondary task is added to the serial RT task. In the first experiment, secondary-task effects on different types of sequences were studied to test the hypothesis that the learning of unique sequences (where each sequence element has a unique relation to the following one) is not impaired by the secondary task, while the learning of ambiguous sequences is. The sequences were random up to a certain order of sequential dependencies, where they became deterministic. Contrary to the hypothesis, secondary-task effects on the learning of unique sequences were as strong or stronger than such effects on the learning of ambiguous sequences. In the second experiment a hybrid sequence (with unique as well as ambiguous transitions) was used with different secondary tasks. A visuo-spatial and a verbal memory task did not interfere with the learning of the sequence, but interference was observed with an auditory go/no-go task in which high- and low-pitched tones were presented after each manual response and a foot pedal had to be pressed in response to high-pitched tones. Thus, interference seems to be specific to certain secondary tasks and may be related to memory processes (but most likely not to visuo-spatial and verbal memory) or to the organizations of sequences, consistent with previous suggestions. PMID:8810586

  12. FRESCO: Referential compression of highly similar sequences.

    PubMed

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware. PMID:24524158

  13. Order Theoretical Semantic Recommendation

    SciTech Connect

    Joslyn, Cliff A.; Hogan, Emilie A.; Paulson, Patrick R.; Peterson, Elena S.; Stephan, Eric G.; Thomas, Dennis G.

    2013-07-23

    Mathematical concepts of order and ordering relations play multiple roles in semantic technologies. Discrete totally ordered data characterize both input streams and top-k rank-ordered recommendations and query output, while temporal attributes establish numerical total orders, either over time points or in the more complex case of startend temporal intervals. But also of note are the fully partially ordered data, including both lattices and non-lattices, which actually dominate the semantic strcuture of ontological systems. Scalar semantic similarities over partially-ordered semantic data are traditionally used to return rank-ordered recommendations, but these require complementation with true metrics available over partially ordered sets. In this paper we report on our work in the foundations of partial order measurement in ontologies, with application to top-k semantic recommendation in workflows.

  14. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2001-01-01

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  15. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2001-02-20

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  16. Sequence information signal processor

    DOEpatents

    Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

    1999-01-01

    An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

  17. DNA sequencing conference, 2

    SciTech Connect

    Cook-Deegan, R.M.; Venter, J.C.; Gilbert, W.; Mulligan, J.; Mansfield, B.K.

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  18. Roles of repetitive sequences

    SciTech Connect

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  19. Sequence analysis on microcomputers.

    PubMed

    Cannon, G C

    1987-10-01

    Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further

  20. Function-Based Algorithms for Biological Sequences

    ERIC Educational Resources Information Center

    Mohanty, Pragyan Sheela P.

    2015-01-01

    Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

  1. Career Academy Course Sequences.

    ERIC Educational Resources Information Center

    Markham, Thom; Lenz, Robert

    This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

  2. T. cacao Transcriptome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To compliment the T. cacao genome sequencing initiative and to build a reference set of expressed genes for functional studies, a broad and state-of-the-art approach to transcriptome sequencing is underway. Using newly optimized methods, transcriptome sequencing libraries were prepared from RNA of o...

  3. Enhanced virome sequencing using targeted sequence capture

    PubMed Central

    Wylie, Todd N.; Wylie, Kristine M.; Herter, Brandi N.; Storch, Gregory A.

    2015-01-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications. PMID:26395152

  4. DNA Sequence Determination by Hybridization: A Strategy for Efficient Large-Scale Sequencing

    NASA Astrophysics Data System (ADS)

    Drmanac, R.; Drmanac, S.; Strezoska, Z.; Paunesku, T.; Labat, I.; Zeremski, M.; Snoddy, J.; Funkhouser, W. K.; Koop, B.; Hood, L.; Crkvenjakov, R.

    1993-06-01

    The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project.

  5. DNA sequence determination by hybridization: A strategy for efficient large-scale sequencing

    SciTech Connect

    Drmanac, R.; Drmanac, S.; Strezoska, Z.; Paunesku, T.; Labat, I.; Zeremski, M.; Snoody, J.; Crkvenjakov, R. ); Funkhouser, W.K.; Koop, B.; Hood, L. )

    1993-06-11

    The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project. 22 refs., 3 figs.

  6. Minimal Orderings Revisited

    SciTech Connect

    Peyton, B.W.

    1999-07-01

    When minimum orderings proved too difficult to deal with, Rose, Tarjan, and Leuker instead studied minimal orderings and how to compute them (Algorithmic aspects of vertex elimination on graphs, SIAM J. Comput., 5:266-283, 1976). This paper introduces an algorithm that is capable of computing much better minimal orderings much more efficiently than the algorithm in Rose et al. The new insight is a way to use certain structures and concepts from modern sparse Cholesky solvers to re-express one of the basic results in Rose et al. The new algorithm begins with any initial ordering and then refines it until a minimal ordering is obtained. it is simple to obtain high-quality low-cost minimal orderings by using fill-reducing heuristic orderings as initial orderings for the algorithm. We examine several such initial orderings in some detail.

  7. Behavioral Objectives, Sequence, and Aptitude Treatment Interactions in CAI.

    ERIC Educational Resources Information Center

    Tobias, Sigmund; Duchastel, Philippe C.

    The interaction of behavioral objectives, sequence order, and test and state anxiety were investigated. The study had four purposes: 1) to examine the effects of objectives on achievement; 2) to investigate the effects of sequencing; 3) to study the interaction of availability of objectives and sequence; 4) to study the effects of objectives and…

  8. Composition for nucleic acid sequencing

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-08-26

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  9. Low autocorrelation binary sequences

    NASA Astrophysics Data System (ADS)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  10. Uncorrectable sequences and telecommand

    NASA Technical Reports Server (NTRS)

    Ekroot, Laura; Mceliece, R.; Dolinar, S.; Swanson, L.

    1993-01-01

    The purpose of a tail sequence for command link transmission units is to fail to decode, so that the command decoder will begin searching for the start of the next unit. A tail sequence used by several missions and recommended for this purpose by the Consultative Committee on Space Data Standards is analyzed. A single channel error can cause the sequence to decode. An alternative sequence requiring at least two channel errors before it can possibly decode is presented. (No sequence requiring more than two channel errors before it can possibly decode exists for this code.)

  11. Complete genome sequence of Methanoculleus marisnigri type strain JR1

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Saunders, Elizabeth H; Han, Cliff; Brettin, Tom; Detter, J. Chris; Bruce, David; Mikhailova, Natalia; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.

  12. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  13. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    PubMed Central

    Anderson, Iain J.; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Pitluck, Sam; Hauser, Loren; Land, Miriam; Lucas, Susan; Richardson, Paul; Whitman, William B.; Kyrpides, Nikos C.

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal kingdom Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea. PMID:21304657

  14. Recreation Programming: Designing Leisure Experiences. 5th Edition

    ERIC Educational Resources Information Center

    Rossman, J. Robert; Schlatter, Barbara Elwood

    2008-01-01

    Originally published in 1989, "Recreation Programming: Designing Leisure Experiences" has become a standard in the park, recreation, and leisure service industry. This title has been used to teach beginning and experienced programmers in over 100 higher-education institutions, both nationally and internationally. Designed in a user-friendly…

  15. Immigration: Law, Customs, History. 5th Grade Curriculum.

    ERIC Educational Resources Information Center

    Mertz, Gayle; And Others

    A fifth grade unit presents the history of immigration to the United States from a legal perspective. The eight sections are suitable for a comprehensive unit but may also be used selectively. Section A contains teacher materials: a chronological chart tying immigration laws to historical and cultural events, an overview of immigration…

  16. Workshop report for the AIAA 5th Aeroacoustics Conference

    NASA Technical Reports Server (NTRS)

    Goldstein, M. E.

    1980-01-01

    Summaries of current understandings, technological tools and remaining controversies in the field of aeroacoustics are presented, with attention also given to developments in means of noise suppression to comply with proposed and projected regulations. Topics include jet noise mechanisms and their suppression; turbomachinery noise, including noise sources, noise prediction by the modal approach and experimental methods; duct acoustics, with discussion of sound attenuation and propagation, the application of finite element methods, and the radiation of sound from inlets; helicopter rotor, airplane propeller and V/STOL noise; aircraft interior noise; and general acoustics, atmospheric propagation and the sonic boom.

  17. Background Materials for Chairman's Workshop. 5th Edition.

    ERIC Educational Resources Information Center

    Kimble, Gregory A.

    Information for newly appointed heads of graduate departments of psychology is presented as background material for the 1974 Chairman's Workshop. Topics include the following: the budgetary situation, pressures for increased teaching loads, effects upon recruiting faculty, faculty morale, graduate and undergraduate student morale, the intellectual…

  18. The 5th Generation model of Particle Physics

    NASA Astrophysics Data System (ADS)

    Lach, Theodore

    2009-05-01

    The Standard model of Particle Physics is able to account for all known HEP phenomenon, yet it is not able to predict the masses of the quarks or leptons nor can it explain why they have their respective values. The Checker Board Model (CBM) predicts that there are 5 generation of quarks and leptons and shows a pattern to those masses, namely each three quarks or leptons (within adjacent generations or within a generation) are related to each other by a geometric mean relationship. A 2D structure of the nucleus can be imaged as 2D plate spinning on its axis, it would for all practical circumstances appear to be a 3D object. The masses of the hypothesized ``up'' and ``dn'' quarks determined by the CBM are 237.31 MeV and 42.392 MeV respectively. These new quarks in addition to a lepton of 7.4 MeV make up one of the missing generations. The details of this new particle physics model can be found at the web site: checkerboard.dnsalias.net. The only areas were this theory conflicts with existing dogma is in the value of the mass of the Top quark. The particle found at Fermi Lab must be some sort of composite particle containing Top quarks.

  19. The 5th Engineering Foundation Conference: Advanced Heterostructure Transistors

    NASA Astrophysics Data System (ADS)

    1992-12-01

    The session on Heterostructure FET's concentrated on power devices. L. Eastman of Cornell University reported 5 W at 4 GHz with 70% efficiency and 15 dB of gain from a GE device, and 1 W at 4 GHz with 80% efficiency from Raytheon. J. Wolter described avalanche breakdown via DX centers in AlGaAs, and theoretical optimization of deep submicron HFET's for power handling was reported by M. Das. Silicon-germanium HBT's have made several improvements. K. Ismail of Cairo University and IBM showed how the Si/SiGe band lineup can be changed by strain relief, producing barriers to electrons as well as holes. Very high mobilities were reported, and the claim was made that SiGe devices at 77 K may be operationally equivalent to III-V devices at room temperature. This would clearly be important given the fabrication advantages of silicon-based technologies. Silicon-germanium HBT technology seemed to be too complex to insert into digital processes, but SiGe FET's may not be. Resonant-tunneling diodes (RTD's) have been combined into potentially multigigahertz shift-register circuits by G. Sollner at MIT Lincoln Laboratory. R. Behringer of AT&T reported experiments in optically controlled patterned growth of Na gratings using a technique that may be applicable to imaging In or Ga atoms during MBE growth. The consequences of optical phonon propagation in AlGaAs structures were discussed experimentally by G. Maracas of Motorola and L. Eastman of Cornell, and theoretically by K. W. Kim of the University of North Carolina. Interesting effects occur because optical phonons in GaAs cannot propagate in AlAs and conversely. HBT papers from III-V materials dwelt on materials issues nad centered on carbon doping and its associated strain and activation.

  20. Multicultural Education: Issues and Perspectives. 5th Edition, Update

    ERIC Educational Resources Information Center

    Banks, James A.; Banks, Cherry A. McGee

    2004-01-01

    With this collection of chapters by leading scholars and researchers in the field, the reader can develop the knowledge and skills needed to maximize the opportunities that diversity offers while minimizing its challenges. The reader will explore current and emerging research, concepts, debates, and teaching strategies for educating students from…

  1. Screening and Brief Intervention Enter Their 5th Decade

    ERIC Educational Resources Information Center

    Saitz, Richard

    2007-01-01

    About 40 years since the first controlled study, screening and brief intervention (SBI) are being disseminated into practice. But many unanswered questions remain. Studies in this special issue address what we know and don't know about alcohol and drug SBI, cost-effectiveness, patient preferences, education for clinicians, quality performance…

  2. CAS CERN Accelerator School 5th General Accelerator Physics Course

    NASA Astrophysics Data System (ADS)

    Turner, S.

    1994-01-01

    The fifth CERN Accelerator School (CAS) basic course on General Accelerator Physics was given at the University of Jyvaeskylae, Finland, from 7 to 18 September 1992. Its syllabus was based on the previous similar courses held at Gif-sur-Yvette in 1984, Aarhus 1986, Salamanca 1988 and Juelich 1990, and whose proceedings were published as CERN Reports 85-19, 87-10, 89-05 and 91-04, respectively. However, certain topics were treated in a different way, improved or extended, while new subjects were introduced. As far as the proceedings of this school are concerned the opportunity was taken not only to include the lectures presented but also to select and revise the most appropriate chapters from the previous similar schools. In this way the present volumes constitute a rather complete introduction to all aspects of the design and construction of particle accelerators, including optics, emittance, luminosity, longitudinal and transverse beam dynamics, insertions, chromaticity, transfer lines, resonances, accelerating structures, tune shifts, coasting beams, lifetime, synchrotron radiation, radiation damping, beam-beam effects, diagnostics, cooling, ion and positron sources, RF and vacuum systems, injection and extraction, conventional, permanent and superconducting magnets, cyclotrons, RF linear accelerators, microtrons, as well as applications of particle accelerators (including therapy) and the history of accelerators. See hints under the relevant topics.

  3. 5th international photovoltaic science and engineering conference

    SciTech Connect

    Flood, D.J.

    1990-01-01

    The variety of potential future missions under consideration by NASA will impose a broad range of requirements on space solar arrays, and mandates the development of new solar cells which can offer a wide range of capabilities to mission planners. Major advances in performance have recently been achieved at several laboratories in a variety of solar cell types. Many of those recent advances are reviewed, the areas are examined where possible improvements are yet to be made, and the requirements are discussed that must be met by advanced solar cell if they are to be used in space. The solar cells of interest include single and multiple junction cells which are fabricated from single crystal, polycrystalline and amorphous materials. Single crystal cells on foreign substrates, thin film single crystal cells on superstrates, and multiple junction cells which are either mechanically stacked, monolithically grown, or hybrid structures incorporating both techniques are discussed. Advanced concentrator array technology for space applications is described, and the status of thin film, flexible solar array blanket technology is reported.

  4. Proceedings of the 5th Annual Users' Conference

    NASA Technical Reports Server (NTRS)

    Szczur, M. (Editor); Harris, E. (Editor)

    1985-01-01

    The Transportable Applications Executive (TAE) was conceived in 1979. It was proposed to be a general purpose software executive that could be applied in various systems. The success of this concept and of TAE was demonstrated. Topics included: TAE current status; TAE development; TAE applications; and UNIX emphasis.

  5. Highlights of the 5th Annual ATS Convention

    NASA Astrophysics Data System (ADS)

    Talbot, Stuart

    The convention was held in Bath, hosted by Ron Maddison. The Lord Mayor of Bath held a reception in the Roman Baths before the keynote address by Dr. Allan Chapman, The Brotherhood of Big Reflecting Telescopes: William Herschel to William Lassell. An ATS award was presented to Dr. Henry King for The History of the Telescope, as was one presented to Robert Hambleton, ATS editor. The lectures included one given by Patrick Moore, Peter Louwman, Rolf Willach, Eugene Rudd, and Ken Launie. Tours were conducted of the Science Museum London's Blythe House, the Royal Society, the Whipple Museum and the University Observatory, both at Cambridge, Wollsthorpe Manor, Issac Newton's home, the University of London Observatory at Mill Hill, and the Royal Observatory at Greenwich. Several pictures of the convention are included in the article.

  6. Purdue University Physics 152L [Manual] (5th Edition).

    ERIC Educational Resources Information Center

    Purdue Univ., Lafayette, IN.

    This document is a laboratory manual for an undergraduate physics course at Purdue University, the major goals of which are to develop students' laboratory skills, to illustrate principles and phenomena described in the physics lectures, and to promote conceptual change about the major topics in Newtonian mechanics. A hardware and software guide…

  7. Educational and Training Opportunities in Sustainable Agriculture. 5th Edition.

    ERIC Educational Resources Information Center

    Gates, Jane Potter

    This directory lists 151 programs in alternative farming systems (systems that aim at maintaining agricultural productivity and profitability, while protecting natural resources, especially sustainable, low-input, regenerative, biodynamic or organic farming and gardening). It includes programs conducted by colleges and universities, research…

  8. How Zucchini Won 5th-Grade Hearts.

    ERIC Educational Resources Information Center

    Cavaliere, Denise

    1987-01-01

    Describes an innovative gardening/nutrition education program in Tucson, Arizona, public elementary schools--Meals for Millions "Sow and Grow"--where children in kindergarten to sixth grade invest time and "tender loving cultivation" into their own school vegetable gardens and learn to like foods--zucchini--that are good for them. (Author/BB)

  9. Nutrition Super Stars [5th and 6th Grades].

    ERIC Educational Resources Information Center

    Houtkooper, Linda; And Others

    This nutrition and physical fitness curriculum kit provides a means for students, teachers, parents, and school health and food service staff to learn about the nutritional value of food and the relationship of food and physical fitness to growth, development, and health; develop food and activity habits which promote good health; and share this…

  10. PREFACE: 5th International Conference on Mechatronics (ICOM'13)

    NASA Astrophysics Data System (ADS)

    Akramin Shafie, Amir; Raisuddin Khan, Md

    2013-12-01

    The Fifth International Conference on Mechatronics (ICOM2013), took place in Kuala Lumpur Malaysia from 2-4 July 2013. The biannual conference which started in 2001 is regularly organized by Faculty of Engineering, International Islamic University Malaysia (IIUM) with the aims to serve as a platform for exchange of ideas on advances of in mechatronics and their applications as well as to foster research and worldwide collaboration. The theme for the 2013 conference was 'Mechatronics: Sustainable Development through Innovative Solutions'. The ICOM 2013 Conference consisted of Keynote Speeches (5) and oral contributions (150). The topics of the conference were: Mechatronic systems and Applications Intelligent Systems Control and Instrumentation Signal and Image Processing Machine Vision Robotics and Automation Manufacturing Mechatronics Green Mechatronics Mechatronic Education Smart Materials and Structures Active Vibration Control Computer and Information Technology MEMS and NEMS Biomechatronics and Rehabilitation Engineering Autonomous Systems Energy and Sustainability Transportation System It is our great pleasure to present this volume of IOP Conference Series: Materials Science and Engineering (MSE) to the scientific community to promote further research in these areas. We believe that this volume will be both an excellent source of scientific material in the fast evolving fields that were covered by ICOM 2013. We thank the authors for their enthusiastic and high-grade contributions. We would also like to express our gratitude to the Organizing Committee, the Institutions and Sponsors and everyone who contributed to this conference through their supports and invaluable efforts. Editors Amir A Shafie aashafie@iium.edu.my Raisuddin Khan raisuddin@iium.edu.my Mahbubur Rashid mahbub@iium.edu.my Department of Mechatronics, International Islamic University Malaysia (IIUM), Kuala Lumpur Malaysia Organizing Committee Md Raisuddin Khan Md Mozasser Rahman Shahrul Naim Sidek Muhammad Mahbubur Rashid Amir Akramin Shafie Nahrul Khair Alang Md Rasyid Rini Akmeliati Roslizar Mat Ali Hazlina Md Yusof Asan Gani Abdul Muthalif Wahju Sediono Salmiah Ahmad Iskandar Al-Thani Mahmood Yasir Mohd Mustafah Moinul Bhuiyan Zulkifli Zainal Abidin Nadzril Sulaiman Momoh J Salami Conference logos

  11. First-order inflation

    NASA Technical Reports Server (NTRS)

    Kolb, Edward W.

    1991-01-01

    In the original proposal, inflation occurred in the process of a strongly first-order phase transition. This model was soon demonstrated to be fatally flawed. Subsequent models for inflation involved phase transitions that were second-order, or perhaps weakly first-order; some even involved no phase transition at all. Recently the possibility of inflation during a strongly first-order phase transition has been revived. In this talk I will discuss some models for first-order inflation, and emphasize unique signatures that result if inflation is realized in a first-order transition. Before discussing first-order inflation, I will briefly review some of the history of inflation to demonstrate how first-order inflation differs from other models.

  12. First-order inflation

    SciTech Connect

    Kolb, E.W. Chicago Univ., IL . Enrico Fermi Inst.)

    1990-09-01

    In the original proposal, inflation occurred in the process of a strongly first-order phase transition. This model was soon demonstrated to be fatally flawed. Subsequent models for inflation involved phase transitions that were second-order, or perhaps weakly first-order; some even involved no phase transition at all. Recently the possibility of inflation during a strongly first-order phase transition has been revived. In this talk I will discuss some models for first-order inflation, and emphasize unique signatures that result in inflation is realized in a first-order transition. Before discussing first-order inflation, I will briefly review some of the history of inflation to demonstrate how first-order inflation differs from other models. 58 refs., 3 figs.

  13. Four-dimensional investigation of the 2nd order volume autocorrelation technique

    NASA Astrophysics Data System (ADS)

    Faucher, O.; Tzallas, P.; Benis, E. P.; Kruse, J.; Peralta Conde, A.; Kalpouzos, C.; Charalambidis, D.

    2009-10-01

    The 2nd order volume autocorrelation technique, widely utilized in directly measuring ultra-short light pulses durations, is examined in detail via model calculations that include three-dimensional integration over a large ionization volume, temporal delay and spatial displacement of the two beams of the autocorrelator at the focus. The effects of the inherent displacement to the 2nd order autocorrelation technique are demonstrated for short and long pulses, elucidating the appropriate implementation of the technique in tight focusing conditions. Based on the above investigations, a high accuracy 2nd order volume autocorrelation measurement of the duration of the 5th harmonic of a 50 fs long laser pulse, including the measurement of the carrier wavelength oscillation, is presented.

  14. High order conservative differencing for viscous terms and the application to vortex-induced vibration flows

    NASA Astrophysics Data System (ADS)

    Shen, Yiqing; Zha, Gecheng; Chen, Xiangying

    2009-12-01

    A new set of conservative 4th-order central finite differencing schemes for all the viscous terms of compressible Navier-Stokes equations are proposed and proved in this paper. These schemes are used with a 5th-order WENO scheme for inviscid flux and the stencil width of the central differencing scheme is designed to be within that of the WENO scheme. The central differencing schemes achieve the maximum order of accuracy in the stencil. This feature is important to keep the compactness of the overall discretization schemes and facilitate the boundary condition treatment. The algorithm is used to simulate the vortex-induced oscillations of an elastically mounted circular cylinder. The numerical results agree favorably with the experiment.

  15. Using SEQUEST with Theoretically Complete Sequence Databases

    NASA Astrophysics Data System (ADS)

    Sadygov, Rovshan G.

    2015-11-01

    SEQUEST has long been used to identify peptides/proteins from their tandem mass spectra and protein sequence databases. The algorithm has proven to be hugely successful for its sensitivity and specificity in identifying peptides/proteins, the sequences of which are present in the protein sequence databases. In this work, we report on work that attempts a new use for the algorithm by applying it to search a complete list of theoretically possible peptides, a de novo-like sequencing. We used freely available mass spectral data and determined a number of unique peptides as identified by SEQUEST. Using masses of these peptides and the mass accuracy of 0.001 Da, we have created a database of all theoretically possible peptide sequences corresponding to the precursor masses. We used our recently developed algorithm for determining all amino acid compositions corresponding to a mass interval, and used a lexicographic ordering to generate theoretical sequences from the compositions. The newly generated theoretical database was many-fold more complex than the original protein sequence database. We used SEQUEST to search and identify the best matches to the spectra from all theoretically possible peptide sequences. We found that SEQUEST cross-correlation score ranked the correct peptide match among the top sequence matches. The results testify to the high specificity of SEQUEST when combined with the high mass accuracy for intact peptides.

  16. Indexing Similar DNA Sequences

    NASA Astrophysics Data System (ADS)

    Huang, Songbo; Lam, T. W.; Sung, W. K.; Tam, S. L.; Yiu, S. M.

    To study the genetic variations of a species, one basic operation is to search for occurrences of patterns in a large number of very similar genomic sequences. To build an indexing data structure on the concatenation of all sequences may require a lot of memory. In this paper, we propose a new scheme to index highly similar sequences by taking advantage of the similarity among the sequences. To store r sequences with k common segments, our index requires only O(n + NlogN) bits of memory, where n is the total length of the common segments and N is the total length of the distinct regions in all texts. The total length of all sequences is rn + N, and any scheme to store these sequences requires Ω(n + N) bits. Searching for a pattern P of length m takes O(m + m logN + m log(rk)psc(P) + occlogn), where psc(P) is the number of prefixes of P that appear as a suffix of some common segments and occ is the number of occurrences of P in all sequences. In practice, rk ≤ N, and psc(P) is usually a small constant. We have implemented our solution and evaluated our solution using real DNA sequences. The experiments show that the memory requirement of our solution is much less than that required by BWT built on the concatenation of all sequences. When compared to the other existing solution (RLCSA), we use less memory with faster searching time.

  17. Symbols of a cosmic order

    NASA Astrophysics Data System (ADS)

    Madjid, F. Hadi; Myers, John M.

    2016-10-01

    The world runs on networks over which signals communicate sequences of symbols, e.g. numerals. Examining both engineered and natural communications networks reveals an unsuspected order that depends on contact with an unpredictable entity. This order has three roots. The first is a proof within quantum theory that no evidence can ever determine its explanation, so that an agent choosing an explanation must do so unpredictably. The second root is the showing that clocks that step computers do not "tell time" but serve as self-adjusting symbol-handling agents that regulate "logically synchronized" motion in response to unpredictable disturbances. Such a clock-agent has a certain independence as well as the capacity to communicate via unpredictable symbols with other clock-agents and to adjust its own tick rate in response to that communication. The third root is the noticing of unpredictable symbol exchange in natural systems, including the transmission of symbols found in molecular biology. We introduce a symbol-handling agent as a role played in some cases by a person, for example a physicist who chooses an explanation of given experimental outcomes, and in other cases by some other biological entity, and in still other cases by an inanimate device, such as a computer-based detector used in physical measurements. While we forbear to try to explain the propensity of agents at all levels from cells to civilizations to form and operate networks of logically synchronized symbol-handling agents, we point to this propensity as an overlooked cosmic order, an order structured by the unpredictability ensuing from the proof. Appreciating the cosmic order leads to a conception of agency that replaces volition by unpredictability and reconceives the notion of objectivity in a way that makes a place for agency in the world as described by physics. Some specific implications for physics are outlined.

  18. M-sequences in ophthalmic electrophysiology.

    PubMed

    Müller, Philipp L; Meigen, Thomas

    2016-01-01

    The aim of this review is to use the multimedia aspects of a purely digital online publication to explain and illustrate the highly capable technique of m-sequences in multifocal ophthalmic electrophysiology. M-sequences have been successfully applied in clinical routines during the past 20 years. However, the underlying mathematical rationale is often daunting. These mathematical properties of m-sequences allow one not only to separate the responses from different fields but also to analyze adaptational effects and impacts of former events. By explaining the history, the formation, and the different aspects of application, a better comprehension of the technique is intended. With this review we aim to clarify the opportunities of m-sequences in order to motivate scientists to use m-sequences in their future research. PMID:26818968

  19. Unlocking hidden genomic sequence

    PubMed Central

    Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.

    2004-01-01

    Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs. PMID:14973330

  20. Multiplexed Fragaria Chloroplast Genome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method to sequence multiple chloroplast genomes that uses the sequencing depth of ultra high throughput sequencing technologies was recently described. Sequencing complete chloroplast genomes can resolve phylogenetic relationships at low taxonomic levels and identify point mutations and indels tha...

  1. Multiple ordering in magnetite.

    NASA Technical Reports Server (NTRS)

    Cullen, J. R.; Callen, E. R.

    1973-01-01

    Results of a self-consistent band calculation of the ground-state energy and charge orderings based on a tight-binding scheme in magnetite are presented. They show that below a critical (about 2.2) value of the ratio of interatomic Coulomb energy to bandwidth the lowest energy state has no order. Between this critical value and 2.5, the preferred state is multiply ordered.

  2. After order 636

    SciTech Connect

    Katz, M.G.

    1995-02-01

    Through its Order 636, the Federal Energy Regulatory Commission (FERC) completed a restructuring of the natural gas industry. The order severed the last links in the chain linking gas producers to pipeline companies to local gas distribution companies (LDCs) to customers. Before Order 636 took effect, many predicted electric power generation, particularly by cogenerators and independent power producers (IPPs), would be a major growth area for natural gas. In fact, what Order 636 has shown is, that timing is everything, and that it`s difficult to sort out the effect of one agent of change when many others are at work.

  3. Order, Disorder and Confinement

    SciTech Connect

    D'Elia, M.; Di Giacomo, A.; Pica, C.

    2006-01-12

    Studying the order of the chiral transition for Nf = 2 is of fundamental importance to understand the mechanism of color confinement. We present results of a numerical investigation on the order of the transition by use of a novel strategy in finite size scaling analysis. The specific heat and a number of susceptibilities are compared with the possible critical behaviours. A second order transition in the O(4) and O(2) universality classes are excluded. Substantial evidence emerges for a first order transition. Results are in agreement with those found by studying the scaling properties of a disorder parameter related to the dual superconductivity mechanism of color confinement.

  4. An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm

    PubMed Central

    Kumar, Manish

    2015-01-01

    One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality. PMID:27065770

  5. An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm.

    PubMed

    Kumar, Manish

    2015-01-01

    One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality. PMID:27065770

  6. Bioregions and World Order.

    ERIC Educational Resources Information Center

    Breakthrough, 1985

    1985-01-01

    What bioregions can do to contribute to world order and security is discussed in this newsletter. A bioregion is defined as an identifiable geographical area of interacting life-systems that is relatively self-sustaining in the ever-renewing processes of nature. Articles included are: "Bioregionalism and World Order" (Gerald Mische); "Bioregions:…

  7. ASDC Order Tools

    Atmospheric Science Data Center

    2012-04-17

    ... users to search our data holdings without logging in to the system. The user, however, must log in before ordering the data. ... Reverb, developed by Earth Science Data and Information System (ESDIS), gives the user community an improved search and order ...

  8. The evolutionary sequence: origin and emergences.

    PubMed

    Fox, S W

    1986-03-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects. PMID:11542035

  9. The evolutionary sequence: origin and emergences

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1986-01-01

    The evolutionary sequence is being reexamined experimentally from a "Big Bang"origin to the protocell and from the emergence of protocell and variety of species to Darwin's mental power (mind) and society (The Descent of Man). A most fundamentally revisionary consequence of experiments is an emphasis on endogenous ordering. This principle, seen vividly in ordered copolymerization of amino acids, has had new impact on the theory of Darwinian evolution and has been found to apply to the entire sequence. Herein, I will discuss some problems of dealing with teaching controversial subjects.

  10. Lichenase and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2000-08-15

    The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding sequence, recombinant DNA molecules comprising the lichenase coding sequences, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.

  11. M&m Sequences

    ERIC Educational Resources Information Center

    Schultz, Harris S.; Shiflett, Ray C.

    2005-01-01

    Consider a sequence recursively formed as follows: Start with three real numbers, and then when k are known, let the (k +1)st be such that the mean of all k +1 equals the median of the first k. The authors conjecture that every such sequence eventually becomes stable. This article presents results related to their conjecture.

  12. Cosmetology: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  13. Twin Mitochondrial Sequence Analysis.

    PubMed

    Bouhlal, Yosr; Martinez, Selena; Gong, Henry; Dumas, Kevin; Shieh, Joseph T C

    2013-09-01

    When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high throughput-sequencing and evaluated variants with primer extension and mitochondrial pre-enrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mitochondrial DNA, and they were further evaluated. When we assessed calls in pre-enriched mitochondrial DNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mitochondrial DNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly since significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists. PMID:24040623

  14. Sequences for Student Investigation

    ERIC Educational Resources Information Center

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  15. Agriculture: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in agriculture. The guide consists of a course description; general course objectives;…

  16. Protein sequence databases.

    PubMed

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium. PMID:15036160

  17. Sequence History Update Tool

    NASA Technical Reports Server (NTRS)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  18. Representation of Numerical and Non-Numerical Order in Children

    ERIC Educational Resources Information Center

    Berteletti, Ilaria; Lucangeli, Daniela; Zorzi, Marco

    2012-01-01

    The representation of numerical and non-numerical ordered sequences was investigated in children from preschool to grade 3. The child's conception of how sequence items map onto a spatial scale was tested using the Number-to-Position task (Siegler & Opfer, 2003) and new variants of the task designed to probe the representation of the alphabet…

  19. Building Higher-Order Markov Chain Models with EXCEL

    ERIC Educational Resources Information Center

    Ching, Wai-Ki; Fung, Eric S.; Ng, Michael K.

    2004-01-01

    Categorical data sequences occur in many applications such as forecasting, data mining and bioinformatics. In this note, we present higher-order Markov chain models for modelling categorical data sequences with an efficient algorithm for solving the model parameters. The algorithm can be implemented easily in a Microsoft EXCEL worksheet. We give a…

  20. Regularization in Short-Term Memory for Serial Order

    ERIC Educational Resources Information Center

    Botvinick, Matthew; Bylsma, Lauren M.

    2005-01-01

    Previous research has shown that short-term memory for serial order can be influenced by background knowledge concerning regularities of sequential structure. Specifically, it has been shown that recall is superior for sequences that fit well with familiar sequencing constraints. The authors report a corresponding effect pertaining to serial…

  1. Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence

    PubMed Central

    Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E.

    2016-01-01

    It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

  2. A variation on lacunary quasi Cauchy sequences

    NASA Astrophysics Data System (ADS)

    Cakalli, Huseyin; Et, Mikail; Sengul, Hacer

    2016-08-01

    In the present paper, we introduce a concept of ideal lacunary statistical quasi-Cauchy sequence of order α of real numbers in the sense that a sequence (xk) of points in R is called I-lacunary statistically quasi-Cauchy of order α, if { r ∈N :1/hrα | { k ∈Ir:| Δ xk | ≥ɛ } | ≥δ } ∈I for each ɛ > 0 and for each δ > 0, where an ideal I is a family of subsets of positive integers N which is closed under taking finite unions and subsets of its elements. The main purpose of this paper is to investigate ideal lacunary statistical ward continuity of order α, where a function f is called I- lacunary statistically ward continuous of order α if it preserves I-lacunary statistically quasi-Cauchy sequences of order α, i.e. (f (xn)) is a Sθα(I ) -quasi-Cauchy sequence whenever (xn) is.

  3. Fluorescence-detected DNA sequencing

    SciTech Connect

    Haugland, R.P.

    1990-01-01

    Our research effort funded by this grant primarily focused on development of suitable fluorescent dyes for DNA sequencing studies. Prior to our efforts, the dyes being sued in commercial DNA sequencers were various versions of fluorescein dyes for the shorter wavelengths and of rhodamine dyes for the longer wavelengths. Our initial goal was to synthesize a set of four dyes that could all be excited by the 488 and 514 nm line of the argon laser lines and that have emission spectra that minimize spectral overlap. The specific result sought was higher fluorescent intensity, particularly of the longest wavelength dyes than was available using existing dyes. Another important property of the desired set of dyes was uniform ionic charge in order to have minimum interference on the electrophoretic mobility during the sequencing. During the period of this grant we prepared and characterized four types of dyes: fluorescent bifluorophores, derivatives of rhodamine dyes, derivatives of rhodol dyes and derivatives of boron dipyrromethene difluoride (BODIPY{trademark}) dyes.

  4. HIV Sequence Compendium 2015

    SciTech Connect

    Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette Tina Marie

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  5. Second order Standard Model

    NASA Astrophysics Data System (ADS)

    Espin, Johnny; Krasnov, Kirill

    2015-06-01

    It is known, though not commonly, that one can describe fermions using a second order in derivatives Lagrangian instead of the first order Dirac one. In this description the propagator is scalar, and the complexity is shifted to the vertex, which contains a derivative operator. In this paper we rewrite the Lagrangian of the fermionic sector of the Standard Model in such second order form. The new Lagrangian is extremely compact, and is obtained from the usual first order Lagrangian by integrating out all primed (or dotted) 2-component spinors. It thus contains just half of the 2-component spinors that appear in the usual Lagrangian, which suggests a new perspective on unification. We sketch a natural in this framework SU (2) × SU (4) ⊂ SO (9) unified theory.

  6. Court Ordered Desegregation

    ERIC Educational Resources Information Center

    Reber, Sarah J.

    2005-01-01

    The effect of the court ordered desegregation plans, on trends in segregation and white flight, are estimated. The effect of availability of school districts and other factors on the white flight across districts is also mentioned.

  7. 'Good palliative care' orders.

    PubMed

    Maddocks, I

    1993-01-01

    A Select Committee of the Parliament of South Australia, considering revisions to legislation governing care of the dying, did not support allowing doctors to assist suicide. They recommended that no liability attach to the provision of reasonable palliative care which happens to shorten life. The Committee affirmed the suggestion that positive open orders to provide 'good palliative care' should replace 'do not resuscitate' orders. PMID:7506978

  8. Automated DNA sequencing.

    PubMed

    Wallis, Yvonne; Morrell, Natalie

    2011-01-01

    Fluorescent cycle sequencing of PCR products is a multistage process and several methodologies are available to perform each stage. This chapter will describe the more commonly utilised dye-terminator cycle sequencing approach using BigDye® terminator chemistry (Applied Biosystems) ready for analysis on a 3730 DNA genetic analyzer. Even though DNA sequencing is one of the most common and robust techniques performed in molecular laboratories it may not always produce desirable results. The causes of the most common problems will also be discussed in this chapter. PMID:20938839

  9. Automatic Command Sequence Generation

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat

    2007-01-01

    Automatic Sequence Generator (Autogen) Version 3.0 software automatically generates command sequences for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL sequencing tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity sequence file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated Sequence Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing sequences through the use of configuration files. By automating the majority of the sequencing generation process, Autogen eliminates many sequence generation errors commonly introduced by manually constructing spacecraft command sequences. Through the layering of commands into the sequence by a series of scheduling algorithms, users are able to rapidly and reliably construct the

  10. A high-resolution radiation hybrid map of the human genome draft sequence.

    PubMed

    Olivier, M; Aggarwal, A; Allen, J; Almendras, A A; Bajorek, E S; Beasley, E M; Brady, S D; Bushard, J M; Bustos, V I; Chu, A; Chung, T R; De Witte, A; Denys, M E; Dominguez, R; Fang, N Y; Foster, B D; Freudenberg, R W; Hadley, D; Hamilton, L R; Jeffrey, T J; Kelly, L; Lazzeroni, L; Levy, M R; Lewis, S C; Liu, X; Lopez, F J; Louie, B; Marquis, J P; Martinez, R A; Matsuura, M K; Misherghi, N S; Norton, J A; Olshen, A; Perkins, S M; Perou, A J; Piercy, C; Piercy, M; Qin, F; Reif, T; Sheppard, K; Shokoohi, V; Smick, G A; Sun, W L; Stewart, E A; Fernando, J; Tejeda; Tran, N M; Trejo, T; Vo, N T; Yan, S C; Zierten, D L; Zhao, S; Sachidanandam, R; Trask, B J; Myers, R M; Cox, D R

    2001-02-16

    We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases. PMID:11181994

  11. SEQassembly: A Practical Tools Program for Coding Sequences Splicing

    NASA Astrophysics Data System (ADS)

    Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

    CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

  12. Quadruplex DNA: sequence, topology and structure

    PubMed Central

    Burge, Sarah; Parkinson, Gary N.; Hazel, Pascale; Todd, Alan K.; Neidle, Stephen

    2006-01-01

    G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes. PMID:17012276

  13. Ordered transport and identification of particles

    DOEpatents

    Shera, E. Brooks

    1993-01-01

    A method and apparatus are provided for application of electrical field gradients to induce particle velocities to enable particle sequence and identification information to be obtained. Particle sequence is maintained by providing electroosmotic flow for an electrolytic solution in a particle transport tube. The transport tube and electrolytic solution are selected to provide an electroosmotic radius of >100 so that a plug flow profile is obtained for the electrolytic solution in the transport tube. Thus, particles are maintained in the same order in which they are introduced in the transport tube. When the particles also have known electrophoretic velocities, the field gradients introduce an electrophoretic velocity component onto the electroosmotic velocity. The time that the particles pass selected locations along the transport tube may then be detected and the electrophoretic velocity component calculated for particle identification. One particular application is the ordered transport and identification of labeled nucleotides sequentially cleaved from a strand of DNA.

  14. Ordered transport and identification of particles

    DOEpatents

    Shera, E.B.

    1993-05-11

    A method and apparatus are provided for application of electrical field gradients to induce particle velocities to enable particle sequence and identification information to be obtained. Particle sequence is maintained by providing electroosmotic flow for an electrolytic solution in a particle transport tube. The transport tube and electrolytic solution are selected to provide an electroosmotic radius of >100 so that a plug flow profile is obtained for the electrolytic solution in the transport tube. Thus, particles are maintained in the same order in which they are introduced in the transport tube. When the particles also have known electrophoretic velocities, the field gradients introduce an electrophoretic velocity component onto the electroosmotic velocity. The time that the particles pass selected locations along the transport tube may then be detected and the electrophoretic velocity component calculated for particle identification. One particular application is the ordered transport and identification of labeled nucleotides sequentially cleaved from a strand of DNA.

  15. Nonspatial Sequence Coding in CA1 Neurons

    PubMed Central

    Allen, Timothy A.; Salz, Daniel M.; McKenzie, Sam

    2016-01-01

    The hippocampus is critical to the memory for sequences of events, a defining feature of episodic memory. However, the fundamental neuronal mechanisms underlying this capacity remain elusive. While considerable research indicates hippocampal neurons can represent sequences of locations, direct evidence of coding for the memory of sequential relationships among nonspatial events remains lacking. To address this important issue, we recorded neural activity in CA1 as rats performed a hippocampus-dependent sequence-memory task. Briefly, the task involves the presentation of repeated sequences of odors at a single port and requires rats to identify each item as “in sequence” or “out of sequence”. We report that, while the animals' location and behavior remained constant, hippocampal activity differed depending on the temporal context of items—in this case, whether they were presented in or out of sequence. Some neurons showed this effect across items or sequence positions (general sequence cells), while others exhibited selectivity for specific conjunctions of item and sequence position information (conjunctive sequence cells) or for specific probe types (probe-specific sequence cells). We also found that the temporal context of individual trials could be accurately decoded from the activity of neuronal ensembles, that sequence coding at the single-cell and ensemble level was linked to sequence memory performance, and that slow-gamma oscillations (20–40 Hz) were more strongly modulated by temporal context and performance than theta oscillations (4–12 Hz). These findings provide compelling evidence that sequence coding extends beyond the domain of spatial trajectories and is thus a fundamental function of the hippocampus. SIGNIFICANCE STATEMENT The ability to remember the order of life events depends on the hippocampus, but the underlying neural mechanisms remain poorly understood. Here we addressed this issue by recording neural activity in hippocampal

  16. Exploration of noncoding sequences in metagenomes.

    PubMed

    Tobar-Tosse, Fabián; Rodríguez, Adrián C; Vélez, Patricia E; Zambrano, María M; Moreno, Pedro A

    2013-01-01

    Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C) content, Codon Usage (Cd), Trinucleotide Usage (Tn), and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS) in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment. PMID:23536879

  17. Exploration of Noncoding Sequences in Metagenomes

    PubMed Central

    Tobar-Tosse, Fabián; Rodríguez, Adrián C.; Vélez, Patricia E.; Zambrano, María M.; Moreno, Pedro A.

    2013-01-01

    Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C) content, Codon Usage (Cd), Trinucleotide Usage (Tn), and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS) in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment. PMID:23536879

  18. Compact rotary sequencer

    NASA Technical Reports Server (NTRS)

    Appleberry, W. T.

    1980-01-01

    Rotary sequencer is assembled from conventional planetary differential gearset and latching mechanism utilizing inputs and outputs which are coaxial. Applications include automated production-line equipment in home appliances and in vehicles.

  19. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  20. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 2 of 2

  1. Authentication of byte sequences

    SciTech Connect

    Stearns, S.D.

    1991-06-01

    Algorithms for the authentication of byte sequences are described. The algorithms are designed to authenticate data in the Storage, Retrieval, Analysis, and Display (SRAD) Test Data Archive of the Radiation Effects and Testing Directorate (9100) at Sandia National Laboratories, and may be used in similar situations where authentication of stored data is required. The algorithms use a well-known error detection method called the Cyclic Redundancy Check (CRC). When a byte sequence is authenticated and stored, CRC bytes are generated and attached to the end of the sequence. When the authenticated data is retrieved, the authentication check consists of processing the entire sequence, including the CRC bytes, and checking for a remainder of zero. The error detection properties of the CRC are extensive and result in a reliable authentication of SRAD data.

  2. SINGLE CELL GENOME SEQUENCING

    PubMed Central

    Yilmaz, Suzan; Singh, Anup K.

    2011-01-01

    Whole genome amplification and next-generation sequencing of single cells has become a powerful approach for studying uncultivated microorganisms that represent 90–99 % of all environmental microbes. Single cell sequencing enables not only the identification of microbes but also linking of functions to species, a feat not achievable by metagenomic techniques. Moreover, it allows the analysis of low abundance species that may be missed in community-based analyses. It has also proved very useful in complementing metagenomics in the assembly and binning of single genomes. With the advent of drastically cheaper and higher throughput sequencing technologies, it is expected that single cell sequencing will become a standard tool in studying the genome and transcriptome of microbial communities. PMID:22154471

  3. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC 139T)

    SciTech Connect

    Land, Miriam L; Held, Brittany; Gronow, Sabine; Abt, Birte; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Arguments from Developmental Order.

    PubMed

    Stöckle-Schobel, Richard

    2016-01-01

    In this article, I investigate a special type of argument regarding the role of development in theorizing about psychological processes and cognitive capacities. Among the issues that developmental psychologists study, discovering the ontogenetic trajectory of mechanisms or capacities underpinning our cognitive functions ranks highly. The order in which functions are developed or capacities are acquired is a matter of debate between competing psychological theories, and also philosophical conceptions of the mind - getting the role and the significance of the different steps in this order right could be seen as an important virtue of such theories. Thus, a special kind of strategy in arguments between competing philosophical or psychological theories is using developmental order in arguing for or against a given psychological claim. In this article, I will introduce an analysis of arguments from developmental order, which come in two general types: arguments emphasizing the importance of the early cognitive processes and arguments emphasizing the late cognitive processes. I will discuss their role in one of the central tools for evaluating scientific theories, namely in making inferences to the best explanation. I will argue that appeal to developmental order is, by itself, an insufficient criterion for theory choice and has to be part of an argument based on other core explanatory or empirical virtues. I will end by proposing a more concerted study of philosophical issues concerning (cognitive) development, and I will present some topics that also pertain to a full-fledged 'philosophy of development.' PMID:27242648

  5. Birth Order and Psychopathology

    PubMed Central

    Risal, Ajay; Tharoor, Hema

    2012-01-01

    Context: Ordinal position the child holds within the sibling ranking of a family is related to intellectual functioning, personality, behavior, and development of psychopathology. Aim: To study the association between birth order and development of psychopathology in patients attending psychiatry services in a teaching hospital. Settings and Design: Hospital-based cross-sectional study. Materials and Methods: Retrospective file review of three groups of patients was carried out. Patient-related variables like age of onset, birth order, family type, and family history of mental illness were compared with psychiatry diagnosis (ICD-10) generated. Statistical Analysis: SPSS 13; descriptive statistics and one-way analysis of variance (ANOVA) were used. Results: Mean age of onset of mental illness among the adult general psychiatry patients (group I, n = 527) was found to be 33.01 ± 15.073, while it was 11.68 ± 4.764 among the child cases (group II, n = 47) and 26.74 ± 7.529 among substance abuse cases (group III, n = 110). Among group I patients, commonest diagnosis was depression followed by anxiety and somatoform disorders irrespective of birth order. Dissociative disorders were most prevalent in the first born child (36.7%) among group II patients. Among group III patients, alcohol dependence was maximum diagnosis in all birth orders. Conclusions: Depression and alcohol dependence was the commonest diagnosis in adult group irrespective of birth order. PMID:24479023

  6. Arguments from Developmental Order

    PubMed Central

    Stöckle-Schobel, Richard

    2016-01-01

    In this article1, I investigate a special type of argument regarding the role of development in theorizing about psychological processes and cognitive capacities. Among the issues that developmental psychologists study, discovering the ontogenetic trajectory of mechanisms or capacities underpinning our cognitive functions ranks highly. The order in which functions are developed or capacities are acquired is a matter of debate between competing psychological theories, and also philosophical conceptions of the mind – getting the role and the significance of the different steps in this order right could be seen as an important virtue of such theories. Thus, a special kind of strategy in arguments between competing philosophical or psychological theories is using developmental order in arguing for or against a given psychological claim. In this article, I will introduce an analysis of arguments from developmental order, which come in two general types: arguments emphasizing the importance of the early cognitive processes and arguments emphasizing the late cognitive processes. I will discuss their role in one of the central tools for evaluating scientific theories, namely in making inferences to the best explanation. I will argue that appeal to developmental order is, by itself, an insufficient criterion for theory choice and has to be part of an argument based on other core explanatory or empirical virtues. I will end by proposing a more concerted study of philosophical issues concerning (cognitive) development, and I will present some topics that also pertain to a full-fledged ‘philosophy of development.’ PMID:27242648

  7. HIV Sequence Compendium 2010

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Leitner, Thomas; Apetrei, Christian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. Burst diaphragm sequence valve

    NASA Astrophysics Data System (ADS)

    Wisneskie, Bradley D.; Hyman, Sheldon; Hallum, Charles E.

    1991-11-01

    A burst diaphragm sequence valve which effectively combines the structure of a burst diaphragm with that of an ordinary swing check valve, the pivot of the ordinary swing check valve being replaced by an integral flexural hinge. The sequence valve provides a way to sequentially burn solid propellant hot gas generators which exit into a common gas manifold, thereby enabling gas-powered devices to operate for a longer time than the duration of one gas generator burn.

  9. Pairwise Sequence Alignment Library

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  10. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  11. Nanapore Sequencing with MSPA

    NASA Astrophysics Data System (ADS)

    Gundlach, Jens H.

    2011-10-01

    Nanopore sequencing is the simplest concept of converting the sequence of a single DNA molecule directly into an electronic signal. We introduced the protein pore MspA. derived from Mycobacterium smegmatis, to nanpore sequencing [1]. MspA has a single, narrow (-1.2nm) and short (<1nm) constriction, ideal to identify single nucleotides. Compared to solid state devices, MspA is reproducible with sub-nanometer precision and is engineerable using genetic mutations. DNA moves through the pore at rates exceeding 1nt/microsec. too fast to observe the passage of each nucleotide. However, when DNA is held with double stranded DNA sections or an avidin anchor, single nucleotides resident in MspA's constriction can be identified with highly resolved current differences. We have provided proof of principle of a nanopore sequencing method [2] in which we use DNA modified by inserting double stranded DNA-sections between every nucleotide. The double stranded sections are designed to halt translocation for long enough to sequentially read the sequence of the original DNA molecule. Prospects and developments to sequence unmodified native DNA using MspA will be discussed.[4pt] [1] T.Z. Butler, et al, PNAS 105 20647 (2008)[0pt] [2] I.M. Derrington, et al, PNAS 107 16060 (2010).

  12. Concomitant Ordering and Symmetry Lowering

    ERIC Educational Resources Information Center

    Boo, William O. J.; Mattern, Daniell L.

    2008-01-01

    Examples of concomitant ordering include magnetic ordering, Jahn-Teller cooperative ordering, electronic ordering, ionic ordering, and ordering of partially-filled sites. Concomitant ordering sets in when a crystal is cooled and always lowers the degree of symmetry of the crystal. Concomitant ordering concepts can also be productively applied to…

  13. Complete mitochondrial genome sequence of Heteropneustes fossilis obtained by paired end next generation sequencing.

    PubMed

    Sahoo, Lakshman; Kumar, Santosh; Das, Sofia P; Patnaik, Siddhi; Bit, Amrita; Sundaray, Jitendra Kumar; Jayasankar, P; Das, Paramananda

    2016-07-01

    In the present study, the complete mitochondrial genome sequence of Heteropneustes fossilis is reported using massive parallel sequence technology. The complete mitogenome of H. fossilis is obtained by de novo assembly of paired end Illumina sequences using CLC Genomics Workbench version 7.0.4, which is 16,489 bp in length. It comprised of 13 protein- coding genes, 22 tRNAs, 2 rRNA genes and a putative control region along with the gene order and organization, being similar to most of vertebrates. The mitogenome in the present study has 99% similarity to the complete mitogneome sequence of H. Fossilis, as reported earlier. Phylogenetic analysis of Siluriformes depicted that Heteropneustids were closer to Clariids. The mitogenome sequence of H. fossilis contributes better understanding of population genetics, phylogenetics and evolution of Indian catfish species. PMID:26016883

  14. CpSAT-1, a transcribed satellite sequence from the codling moth, Cydia pomonella.

    PubMed

    Věchtová, Pavlína; Dalíková, Martina; Sýkorová, Miroslava; Žurovcová, Martina; Füssy, Zoltán; Zrzavá, Magda

    2016-08-01

    Satellite DNA (satDNA) is a non-coding component of eukaryotic genomes, located mainly in heterochromatic regions. Relevance of satDNA began to emerge with accumulating evidence of its potential yet hardly comprehensible role that it can play in the genome of many organisms. We isolated the first satDNA of the codling moth (Cydia pomonella, Tortricidae, Lepidoptera), a species with holokinetic chromosomes and a single large heterochromatic element, the W chromosome in females. The satDNA, called CpSAT-1, is located on all chromosomes of the complement, although in different amounts. Surprisingly, the satellite is almost missing in the heterochromatic W chromosome. Additionally, we isolated mRNA from all developmental stages (1st-5th instar larva, pupa, adult), both sexes (adult male and female) and several tissues (Malpighian tubules, gut, heart, testes, and ovaries) of the codling moth and showed the CpSAT-1 sequence was transcribed in all tested samples. Using CpSAT-1 specific primers we amplified, cloned and sequenced 40 monomers from cDNA and gDNA, respectively. The sequence analysis revealed a high mutation rate and the presence of potentially functional motifs, mainly in non-conserved regions of the monomers. Both the chromosomal distribution and the sequence analysis suggest that CPSAT-1 has no function in the C. pomonella genome. PMID:27236660

  15. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

    SciTech Connect

    Scheuner, Carmen; Tindall, Brian J.; Lu, Megan; Nolan, Matt; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Ivanova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Jeffries, Cynthia D.; Hauser, Loren John; Land, Miriam L.; Mwirichia, Romano; Rohde, Manfred; Abt, Birte; Detter, John Chris; Woyke, Tanja; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Goker, Markus; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2014-12-08

    Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448 T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. We study phylogenomic analyses that indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. Lastly, in addition to other features, the range of G + C values reported for

  16. Land and World Order.

    ERIC Educational Resources Information Center

    Mische, Patricia, Ed.; And Others

    1982-01-01

    The papers in this publication discuss the land and how what happens to the land affects us. The publication is one in a series of monographs that examine the linkages between local and global concerns and explore alternative world futures. Examples of topics discussed in the papers follow. The paper "Land and World Order" examines implications of…

  17. The Order Pseudonocardiales

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Order Pseudonocardiales is made of up a single family Pseudonocardiaceae which forms a distinct cluster between the Frankineae and Streptomycineae when members of the taxa are subjected to 16S rRNA gene phylogenetic analysis. The family contains 26 genera including Pseudonocardia, Actinoalloteic...

  18. Memory for Serial Order.

    ERIC Educational Resources Information Center

    Lewandowsky, Stephan; Murdock, Bennet B., Jr.

    1989-01-01

    An extension to Murdock's Theory of Distributed Associative Memory, based on associative chaining between items, is presented. The extended theory is applied to several serial order phenomena, including serial list learning, delayed recall effects, partial report effects, and buildup and release from proactive interference. (TJH)

  19. The Birth Order Puzzle.

    ERIC Educational Resources Information Center

    Zajonc, R. B.; And Others

    1979-01-01

    Discusses the controversy of the relationship between birth order and intellectual performance through a detailed evaluation of the confluence model which assumes that the rate of intellectual growth is a function of the intellectual environment within the family and associated with the special circumstances of last children. (CM)

  20. Birth Order Debate Resolved?

    ERIC Educational Resources Information Center

    Zajonc, R. B.

    2001-01-01

    Critiques Rodgers et al.'s June 2000 research on the relation between birth order and intelligence, which suggests that it is a methodological illusion. Explains how the intellectual environment and the teaching function (whereby older children tutor younger ones) contribute to the growth of intellectual maturity, the first negatively and the…

  1. Order Lepidoptera Linnaeus, 1758.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Based on two recent molecular analyses, augmented by the discovery of several published or unpublished novel morphological synapomorphies, a new classification is proposed for the order Lepidoptera. The new classification is more consistent with our growing knowledge of the phylogeny of the group an...

  2. Education and World Order

    ERIC Educational Resources Information Center

    Jones, Phillip W.

    2007-01-01

    The impact on educational analysis of mainstream international relations (IR) theories is yet to realize its full potential. The problem of education in relation to the construction of world order is considered in relation to core developments in IR theory since the Second World War. In particular, the global architecture of education is seen as a…

  3. Oligonucleotide Sequence Motifs as Nucleosome Positioning Signals

    PubMed Central

    Collings, Clayton K.; Fernandez, Alfonso G.; Pitschka, Chad G.; Hawkins, Troy B.; Anderson, John N.

    2010-01-01

    To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach entailed the identification and analysis of 24 unique tetranucleotides that were defined by 8 consensus sequences. These consensus sequences were shown to be responsible for most if not all of the tetranucleotide and dinucleotide periodicities displayed by the entire library, demonstrating that the periodicities of dinucleotides that characterize the yeast genome are, in actuality, due primarily to the 8 consensus sequences. A novel combination of experimental and bioinformatic approaches was then used to show that these tetranucleotides are important for preferred formation of nucleosomes at specific sites along DNA in vitro. These results were then compared to tetranucleotide patterns in genome-wide in vivo libraries from yeast and C. elegans in order to assess the contributions of DNA sequence in the control of nucleosome residency in the cell. These comparisons revealed striking similarities in the tetranucleotide occurrence profiles that are likely to be involved in nucleosome positioning in both in vitro and in vivo libraries, suggesting that DNA sequence is an important factor in the control of nucleosome placement in vivo. However, the strengths of the tetranucleotide periodicities were 3–4 fold higher in the in vitro as compared to the in vivo libraries, which implies that DNA sequence plays less of a role in dictating nucleosome positions in vivo. The results of this study have important implications for models of sequence-dependent positioning since they suggest that a defined subset of tetranucleotides is involved in preferred nucleosome occupancy and that these tetranucleotides are the major source of the dinucleotide periodicities that are characteristic of

  4. Quantitative texton sequences for legible bivariate maps.

    PubMed

    Ware, Colin

    2009-01-01

    Representing bivariate scalar maps is a common but difficult visualization problem. One solution has been to use two dimensional color schemes, but the results are often hard to interpret and inaccurately read. An alternative is to use a color sequence for one variable and a texture sequence for another. This has been used, for example, in geology, but much less studied than the two dimensional color scheme, although theory suggests that it should lead to easier perceptual separation of information relating to the two variables. To make a texture sequence more clearly readable the concept of the quantitative texton sequence (QTonS) is introduced. A QTonS is defined a sequence of small graphical elements, called textons, where each texton represents a different numerical value and sets of textons can be densely displayed to produce visually differentiable textures. An experiment was carried out to compare two bivariate color coding schemes with two schemes using QTonS for one bivariate map component and a color sequence for the other. Two different key designs were investigated (a key being a sequence of colors or textures used in obtaining quantitative values from a map). The first design used two separate keys, one for each dimension, in order to measure how accurately subjects could independently estimate the underlying scalar variables. The second key design was two dimensional and intended to measure the overall integral accuracy that could be obtained. The results show that the accuracy is substantially higher for the QTonS/color sequence schemes. A hypothesis that texture/color sequence combinations are better for independent judgments of mapped quantities was supported. A second experiment probed the limits of spatial resolution for QTonSs. PMID:19834229

  5. Program Synthesizes UML Sequence Diagrams

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

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

  6. Application of the order-of-magnitude analysis to a fourth-order RANS closure for simulating a 2D boundary layer

    NASA Astrophysics Data System (ADS)

    Poroseva, Svetlana V.

    2013-11-01

    Simulations of turbulent boundary-layer flows are usually conducted using a set of the simplified Reynolds-Averaged Navier-Stokes (RANS) equations obtained by order-of-magnitude analysis (OMA) of the original RANS equations. The resultant equations for the mean-velocity components are closed using the Boussinesq approximation for the Reynolds stresses. In this study OMA is applied to the fourth-order RANS (FORANS) set of equations. The FORANS equations are chosen as they can be closed on the level of the 5th-order correlations without using unknown model coefficients, i.e. no turbulent diffusion modeling is required. New models for the 2nd-, 3rd- and 4th-order velocity-pressure gradient correlations are derived for the current FORANS equations. This set of FORANS equations and models are analyzed for the case of two-dimensional mean flow. The equations include familiar transport terms for the mean-velocity components along with algebraic expressions for velocity correlations of different orders specific to the FORANS approach. Flat plate DNS data (Spalart, 1988) are used to verify these expressions and the areas of the OMA applicability within the boundary layer. The material is based upon work supported by NASA under award NNX12AJ61A.

  7. Sequence analysis by iterated maps, a review.

    PubMed

    Almeida, Jonas S

    2014-05-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results. PMID:24162172

  8. Spectral entropy criteria for structural segmentation in genomic DNA sequences

    NASA Astrophysics Data System (ADS)

    Chechetkin, V. R.; Lobzin, V. V.

    2004-07-01

    The spectral entropy is calculated with Fourier structure factors and characterizes the level of structural ordering in a sequence of symbols. It may efficiently be applied to the assessment and reconstruction of the modular structure in genomic DNA sequences. We present the relevant spectral entropy criteria for the local and non-local structural segmentation in DNA sequences. The results are illustrated with the model examples and analysis of intervening exon-intron segments in the protein-coding regions.

  9. Competing Orders and Anomalies.

    PubMed

    Moon, Eun-Gook

    2016-01-01

    A conservation law is one of the most fundamental properties in nature, but a certain class of conservation "laws" could be spoiled by intrinsic quantum mechanical effects, so-called quantum anomalies. Profound properties of the anomalies have deepened our understanding in quantum many body systems. Here, we investigate quantum anomaly effects in quantum phase transitions between competing orders and striking consequences of their presence. We explicitly calculate topological nature of anomalies of non-linear sigma models (NLSMs) with the Wess-Zumino-Witten (WZW) terms. The non-perturbative nature is directly related with the 't Hooft anomaly matching condition: anomalies are conserved in renormalization group flow. By applying the matching condition, we show massless excitations are enforced by the anomalies in a whole phase diagram in sharp contrast to the case of the Landau-Ginzburg-Wilson theory which only has massive excitations in symmetric phases. Furthermore, we find non-perturbative criteria to characterize quantum phase transitions between competing orders. For example, in 4D, we show the two competing order parameter theories, CP(1) and the NLSM with WZW, describe different universality class. Physical realizations and experimental implication of the anomalies are also discussed. PMID:27499184

  10. Audiotactile temporal order judgments.

    PubMed

    Zampini, Massimiliano; Brown, Timothy; Shore, David I; Maravita, Angelo; Röder, Brigitte; Spence, Charles

    2005-03-01

    We report a series of three experiments in which participants made unspeeded 'Which modality came first?' temporal order judgments (TOJs) to pairs of auditory and tactile stimuli presented at varying stimulus onset asynchronies (SOAs) using the method of constant stimuli. The stimuli were presented from either the same or different locations in order to explore the potential effect of redundant spatial information on audiotactile temporal perception. In Experiment 1, the auditory and tactile stimuli had to be separated by nearly 80 ms for inexperienced participants to be able to judge their temporal order accurately (i.e., for the just noticeable difference (JND) to be achieved), no matter whether the stimuli were presented from the same or different spatial positions. More experienced psychophysical observers (Experiment 2) also failed to show any effect of relative spatial position on audiotactile TOJ performance, despite having much lower JNDs (40 ms) overall. A similar pattern of results was found in Experiment 3 when silent electrocutaneous stimulation was used rather than vibrotactile stimulation. Thus, relative spatial position seems to be a less important factor in determining performance for audiotactile TOJ than for other modality pairings (e.g., audiovisual and visuotactile). PMID:15698825

  11. Competing Orders and Anomalies

    NASA Astrophysics Data System (ADS)

    Moon, Eun-Gook

    2016-08-01

    A conservation law is one of the most fundamental properties in nature, but a certain class of conservation “laws” could be spoiled by intrinsic quantum mechanical effects, so-called quantum anomalies. Profound properties of the anomalies have deepened our understanding in quantum many body systems. Here, we investigate quantum anomaly effects in quantum phase transitions between competing orders and striking consequences of their presence. We explicitly calculate topological nature of anomalies of non-linear sigma models (NLSMs) with the Wess-Zumino-Witten (WZW) terms. The non-perturbative nature is directly related with the ’t Hooft anomaly matching condition: anomalies are conserved in renormalization group flow. By applying the matching condition, we show massless excitations are enforced by the anomalies in a whole phase diagram in sharp contrast to the case of the Landau-Ginzburg-Wilson theory which only has massive excitations in symmetric phases. Furthermore, we find non-perturbative criteria to characterize quantum phase transitions between competing orders. For example, in 4D, we show the two competing order parameter theories, CP(1) and the NLSM with WZW, describe different universality class. Physical realizations and experimental implication of the anomalies are also discussed.

  12. Competing Orders and Anomalies

    PubMed Central

    Moon, Eun-Gook

    2016-01-01

    A conservation law is one of the most fundamental properties in nature, but a certain class of conservation “laws” could be spoiled by intrinsic quantum mechanical effects, so-called quantum anomalies. Profound properties of the anomalies have deepened our understanding in quantum many body systems. Here, we investigate quantum anomaly effects in quantum phase transitions between competing orders and striking consequences of their presence. We explicitly calculate topological nature of anomalies of non-linear sigma models (NLSMs) with the Wess-Zumino-Witten (WZW) terms. The non-perturbative nature is directly related with the ’t Hooft anomaly matching condition: anomalies are conserved in renormalization group flow. By applying the matching condition, we show massless excitations are enforced by the anomalies in a whole phase diagram in sharp contrast to the case of the Landau-Ginzburg-Wilson theory which only has massive excitations in symmetric phases. Furthermore, we find non-perturbative criteria to characterize quantum phase transitions between competing orders. For example, in 4D, we show the two competing order parameter theories, CP(1) and the NLSM with WZW, describe different universality class. Physical realizations and experimental implication of the anomalies are also discussed. PMID:27499184

  13. DNA sequencing: chemical methods

    SciTech Connect

    Ambrose, B.J.B.; Pless, R.C.

    1987-01-01

    Limited base-specific or base-selective cleavage of a defined DNA fragment yields polynucleotide products, the length of which correlates with the positions of the particular base (or bases) in the original fragment. Sverdlov and co-workers recognized the possibility of using this principle for the determination of DNA sequences. In 1977 a fully elaborated method was introduced based on this principle, which allowed routine analysis of DNA sequences over distances greater than 100 nucleotide unite from a defined, radiolabeled terminus. Six procedures for partial cleavage were described. Simultaneous parallel resolution of an appropriate set of partial cleavage mixtures by polyacrylamide gel electrophoresis, followed by visualization of the radioactive bands by autoradiography, allows the deduction of nucleotide sequence.

  14. Sequencing the Connectome

    PubMed Central

    Zador, Anthony M.; Dubnau, Joshua; Oyibo, Hassana K.; Zhan, Huiqing; Cao, Gang; Peikon, Ian D.

    2012-01-01

    Connectivity determines the function of neural circuits. Historically, circuit mapping has usually been viewed as a problem of microscopy, but no current method can achieve high-throughput mapping of entire circuits with single neuron precision. Here we describe a novel approach to determining connectivity. We propose BOINC (“barcoding of individual neuronal connections”), a method for converting the problem of connectivity into a form that can be read out by high-throughput DNA sequencing. The appeal of using sequencing is that its scale—sequencing billions of nucleotides per day is now routine—is a natural match to the complexity of neural circuits. An inexpensive high-throughput technique for establishing circuit connectivity at single neuron resolution could transform neuroscience research. PMID:23109909

  15. The problem of serial order in skilled typing.

    PubMed

    Snyder, Kristy M; Logan, Gordon D

    2014-08-01

    We address the problem of serial order in skilled typing, asking whether typists represent the identity and order of the keystrokes they type jointly by linking successive keystrokes into a chained sequence, or separately by associating keystrokes with position codes. In 4 experiments, typists prepared to type a prime word and were probed to type a target word. We varied the overlap between the identity and order of keystrokes in the prime and the target. Experiment 1 tested whether the identity of keystrokes can be primed separately from their order. Experiments 2 and 3 tested whether keystroke positions can be primed out of sequence. Experiment 4 tested whether keystrokes are primed equally across serial positions. The results were consistent with chaining theories: Keystroke identities were not primed separately from their order, keystroke positions were not primed out of sequence, and priming was graded across the keystroke sequence and depended on the number of keystrokes that were primed in sequence. We conclude by discussing the possibility that the problem of serial order may be solved differently for different sequential tasks. PMID:24979360

  16. A High Order Mixed Vector Finite Element Method for Solving the Time Dependent Maxwell Equations on Unstructured Grids

    SciTech Connect

    Rieben, R N; Rodrigue, G H; White, D A

    2004-03-09

    We present a mixed vector finite element method for solving the time dependent coupled Ampere and Faraday laws of Maxwell's equations on unstructured hexahedral grids that employs high order discretization in both space and time. The method is of arbitrary order accuracy in space and up to 5th order accurate in time, making it well suited for electrically large problems where grid anisotropy and numerical dispersion have plagued other methods. In addition, the method correctly models both the jump discontinuities and the divergence-free properties of the electric and magnetic fields, is charge and energy conserving, conditionally stable, and free of spurious modes. Several computational experiments are performed to demonstrate the accuracy, efficiency and benefits of the method.

  17. Method to amplify variable sequences without imposing primer sequences

    DOEpatents

    Bradbury, Andrew M.; Zeytun, Ahmet

    2006-11-14

    The present invention provides methods of amplifying target sequences without including regions flanking the target sequence in the amplified product or imposing amplification primer sequences on the amplified product. Also provided are methods of preparing a library from such amplified target sequences.

  18. Sequence stratigraphy of an apparently non-cyclic carbonate succession: Recognizing subaerial exposure in largely subtidal sequences, M. Ordovician, East Tennessee

    SciTech Connect

    Steinhauff, D.M. ); Walker, K.R. . Dept. of Geological Sciences)

    1992-01-01

    A 400 meter thick succession of Middle Ordovician non-cyclic carbonates occurs at four on-shelf localities exposed along a 6 km transect on the northwest limb of the Copper Creek allochthon of East Tennessee. By using paleobathymetric analysis the authors were able to unravel the sequencing of stratigraphic units in this succession. Inflection points in water-depth curves indicate stratigraphic intervals that, on further detailed analysis, also contain subtle indicators of subaerial exposure. Seven surfaces of subaerial exposure or drowning define six third order sequences in the entire Middle and Upper Ordovician. They have analyzed in detail the lower four and the lower part of the fifth third order sequences and their contained 22 fourth order sequences that appear to be correlative across the shelf. These third and fourth order sequences, contain many fifth order or meter-scale packages, here termed sub-sequences. Sub-sequences are not correlative from place to place and many of these are probably the result of fine scale, lateral environmental migration. Stratigraphic sequences and sub-sequences represent shallowing-upward packages similar to cycles. However, these sequences and sub-sequences differ from the usual cycles in that they mostly lack peritidal caps, and evidence for exposure and shoaling is subtle and generally revealed only through detailed microscopic examination. A Fischer plot, substituting sub-sequences for cycles, supports interpretations previously made for this succession based on other lines of evidence and helps clarify new observations revealed through water-depth analysis.

  19. Ranking and Sequencing Model

    2009-08-13

    This database application (commonly called the Supermodel) provides a repository for managing critical facility/project information, allows the user to subjectively an objectively assess key criteria , quantify project risks, develop ROM cost estimates, determine facility/project end states, ultimately performing risk-based modeling to rank facilities/project based on risk, sequencing project schedules and provides an optimized recommended sequencing/scheduling of these projects which maximize the S&M cost savings to perform closure projects which benefit all stakeholders.

  20. User guide for mapping-by-sequencing in Arabidopsis

    PubMed Central

    2013-01-01

    Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments. PMID:23773572

  1. Identification of a Flavivirus Sequence in a Marine Arthropod

    PubMed Central

    Conway, Michael J.

    2015-01-01

    Phylogenetic analysis has yet to uncover the early origins of flaviviruses. In this study, I mined a database of expressed sequence tags in order to discover novel flavivirus sequences. Flavivirus sequences were identified in a pool of mRNA extracted from the sea spider Endeis spinosa (Pycnogonida, Pantopoda). Reconstruction of the translated sequences and BLAST analysis matched the sequence to the flavivirus NS5 gene. Additional sequences corresponding to envelope and the NS5 MTase domain were also identified. Phylogenetic analysis of homologous NS5 sequences revealed that Endeis spinosa NS5 (ESNS5) is likely related to classical insect-specific flaviviruses. It is unclear if ESNS5 represents genetic material from an active viral infection or an integrated viral genome. These data raise the possibility that classical insect-specific flaviviruses and perhaps medically relevant flaviviruses, evolved from progenitors that infected marine arthropods. PMID:26717191

  2. Polynomials Generated by the Fibonacci Sequence

    NASA Astrophysics Data System (ADS)

    Garth, David; Mills, Donald; Mitchell, Patrick

    2007-06-01

    The Fibonacci sequence's initial terms are F_0=0 and F_1=1, with F_n=F_{n-1}+F_{n-2} for n>=2. We define the polynomial sequence p by setting p_0(x)=1 and p_{n}(x)=x*p_{n-1}(x)+F_{n+1} for n>=1, with p_{n}(x)= sum_{k=0}^{n} F_{k+1}x^{n-k}. We call p_n(x) the Fibonacci-coefficient polynomial (FCP) of order n. The FCP sequence is distinct from the well-known Fibonacci polynomial sequence. We answer several questions regarding these polynomials. Specifically, we show that each even-degree FCP has no real zeros, while each odd-degree FCP has a unique, and (for degree at least 3) irrational, real zero. Further, we show that this sequence of unique real zeros converges monotonically to the negative of the golden ratio. Using Rouche's theorem, we prove that the zeros of the FCP's approach the golden ratio in modulus. We also prove a general result that gives the Mahler measures of an infinite subsequence of the FCP sequence whose coefficients are reduced modulo an integer m>=2. We then apply this to the case that m=L_n, the nth Lucas number, showing that the Mahler measure of the subsequence is phi^{n-1}, where phi=(1+sqrt 5)/2.

  3. SEQOPTICS: a protein sequence clustering system

    PubMed Central

    Chen, Yonghui; Reilly, Kevin D; Sprague, Alan P; Guan, Zhijie

    2006-01-01

    Background Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering algorithms have been applied. OPTICS (Ordering Points To Identify the Clustering Structure) is an attractive approach due to its emphasis on visualization of results and support for interactive work, e.g., in choosing parameters. However, OPTICS has not been used, as far as we know, for protein sequence clustering. Results In this paper, a system of clustering proteins, SEQOPTICS (SEQuence clustering with OPTICS) is demonstrated. The system is implemented with Smith-Waterman as protein distance measurement and OPTICS at its core to perform protein sequence clustering. SEQOPTICS is tested with four data sets from different data sources. Visualization of the sequence clustering structure is demonstrated as well. Conclusion The system was evaluated by comparison with other existing methods. Analysis of the results demonstrates that SEQOPTICS performs better based on some evaluation criteria including Jaccard coefficient, Precision, and Recall. It is a promising protein sequence clustering method with future possible improvement on parallel computing and other protein distance measurements. PMID:17217502

  4. Sequencing proteins with transverse ionic transport

    NASA Astrophysics Data System (ADS)

    Boynton, Paul; di Ventra, Massimiliano

    2015-03-01

    De novo protein sequencing is essential for understanding cellular processes that govern the function of living organisms. By obtaining the order of the amino acids that composes a given protein one can determine both its secondary and tertiary structures through protein structure prediction, which is used to create models for protein aggregation diseases such as Alzheimer's Disease. Mass spectrometry is the current technique of choice for de novo sequencing, but because some amino acids have the same mass the sequence cannot be completely determined in many cases. In this paper we propose a new technique for de novo protein sequencing that involves translocating a polypeptide through a synthetic nanochannel and measuring the ionic current of each amino acid through an intersecting perpendicular nanochannel, similar to that proposed in for DNA sequencing. Indeed, we find that the distribution of ionic currents for each of the 20 proteinogenic amino acids encoded by eukaryotic genes is statistically distinct, showing this technique's potential for de novo protein sequencing.

  5. Benchmarking short sequence mapping tools

    PubMed Central

    2013-01-01

    Background The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison. Results We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others. Conclusion The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results. PMID:23758764

  6. Adaptive Learning Resources Sequencing in Educational Hypermedia Systems

    ERIC Educational Resources Information Center

    Karampiperis, Pythagoras; Sampson, Demetrios

    2005-01-01

    Adaptive learning resources selection and sequencing is recognized as among the most interesting research questions in adaptive educational hypermedia systems (AEHS). In order to adaptively select and sequence learning resources in AEHS, the definition of adaptation rules contained in the Adaptation Model, is required. Although, some efforts have…

  7. 47 CFR 32.21 - Sequence of accounts.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Sequence of accounts. 32.21 Section 32.21 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES General Instructions § 32.21 Sequence of accounts. The order in...

  8. 47 CFR 32.21 - Sequence of accounts.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 2 2014-10-01 2014-10-01 false Sequence of accounts. 32.21 Section 32.21 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES General Instructions § 32.21 Sequence of accounts. The order in...

  9. 47 CFR 32.21 - Sequence of accounts.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 2 2012-10-01 2012-10-01 false Sequence of accounts. 32.21 Section 32.21 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES General Instructions § 32.21 Sequence of accounts. The order in...

  10. 47 CFR 32.21 - Sequence of accounts.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 2 2013-10-01 2013-10-01 false Sequence of accounts. 32.21 Section 32.21 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES General Instructions § 32.21 Sequence of accounts. The order in...

  11. 47 CFR 32.21 - Sequence of accounts.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 2 2011-10-01 2011-10-01 false Sequence of accounts. 32.21 Section 32.21 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES General Instructions § 32.21 Sequence of accounts. The order in...

  12. Physella acuta: atypical mitochondrial gene order among panpulmonates (Gastropoda)

    PubMed Central

    Nolan, Journey R.; Bergthorsson, Ulfar; Adema, Coen M.

    2014-01-01

    Mitochondrial (mt) sequences are frequently used for phylogenetic reconstruction and for identification of species of molluscs. This study expands the phylogenetic range of Hygrophila (Panpulmonata) for which such sequence data are available by characterizing the full mt genome of the invasive freshwater snail Physella acuta (Physidae). The mt genome sequences of two P. acuta isolates from Stubblefield Lake, New Mexico, USA, differed in length (14,490 vs 14,314 bp) and showed 11.49% sequence divergence, whereas ITS1 and ITS2 sequences from the nuclear genome differed by 1.75%. The mt gene order of P. acuta (cox1, P, nad6, nad5, nad1, D, F, cox2, Y, W, nad4L, C, Q, atp6, R, E, rrnS, M, T, cox3, I, nad2, K, V, rrnL, L1, A, cytb, G, H, L2, atp8, N, nad2, S1, S2, nad4) differs considerably from the relatively conserved gene order within Panpulmonata. Phylogenetic trees show that the 13 protein-encoding mt gene sequences (equivalent codons) of P. acuta group according to gastropod phylogeny, yet branch lengths and dN/dS ratios for P. acuta indicate elevated amino acid substitutions relative to other gastropods. This study indicates that mt sequences of P. acuta are phylogenetically informative despite a considerable intraspecific divergence and the atypical gene order in its mt genome. PMID:25368439

  13. Multiple Sequence Alignment Based on Chaotic PSO

    NASA Astrophysics Data System (ADS)

    Lei, Xiu-Juan; Sun, Jing-Jing; Ma, Qian-Zhi

    This paper introduces a new improved algorithm called chaotic PSO (CPSO) based on the thought of chaos optimization to solve multiple sequence alignment. For one thing, the chaotic variables are generated between 0 and 1 when initializing the population so that the particles are distributed uniformly in the solution space. For another thing, the chaotic sequences are generated using the Logistic mapping function in order to make chaotic search and strengthen the diversity of the population. The simulation results of several benchmark data sets of BAliBase show that the improved algorithm is effective and has good performances for the data sets with different similarity.

  14. Artificial sequences and complexity measures

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Caglioti, Emanuele; Loreto, Vittorio

    2005-04-01

    In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools for extracting, in a automatic and agnostic way, information from a generic string of characters. We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters (e.g. texts) based on their relative information content. We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of artificial text and we show how these new tools can be used for information extraction purposes. We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them. We consider as a case study linguistic motivated problems and we present results for automatic language recognition, authorship attribution and self-consistent classification.

  15. Effects of fixed versus random condition sequencing during multielement functional analyses.

    PubMed

    Hammond, Jennifer L; Iwata, Brian A; Rooker, Griffin W; Fritz, Jennifer N; Bloom, Sarah E

    2013-01-01

    It has been suggested that a fixed condition sequence might facilitate differential responding during multielement functional analyses (FAs) by capitalizing on or limiting sequence effects (Iwata, Pace, et al., 1994); however, the effects of condition sequence have not been examined empirically. We conducted fixed- and random-sequence FAs for 7 individuals with developmental disabilities to determine the relative effects that sequence may have on assessment outcomes. Experimental conditions during the fixed sequence were conducted in the following order: ignore, attention, play, and demand; condition order during the random sequence was determined randomly. Results showed that sequence had no influence on the FA outcomes for 3 subjects, whereas differential responding emerged either faster (1 subject) or only (3 subjects) under the fixed sequence for the remaining subjects. These results suggest that the fixed sequence, a simple modification, should be used when conducting multielement FAs to accommodate the influence of establishing operations across assessment conditions. PMID:24114082

  16. Liquid Crystal Ordering of Random DNA Oligomers

    NASA Astrophysics Data System (ADS)

    Bellini, Tommaso; Zanchetta, Giuliano; Fraccia, Tommaso; Cerbino, Roberto; Tsai, Ethan; Moran, Mark; Smith, Gregory; Walba, David; Clark, Noel

    2012-02-01

    Concentrated solutions of DNA oligomers (6 to 20 base pairs) organize into chiral nematic (NEM) and columnar (COL) liquid crystal (LC) phases. When the oligomer duplexes are mixed with single strands, LC phase formation proceeds through macroscopic phase separation, as a consequence of the combination of various self-assembly processes including strand pairing, reversible linear aggregation, demixing and LC ordering. We extended our investigation to the case of LC ordering in oligonucleotides whose sequences are partially or entirely randomly chosen, and we observed LC phases even in entirely random 20mers, corresponding to a family of 4^20 10^12 different sequences. We have tracked the origin of this behaviour: random sequences pair into generally defected duplexes, a large fraction of them terminating with stretches of unpaired bases (overhangs); overhangs promote linear aggregation of duplexes, with a mean strength depending on the overhang length; LC formation is accompanied by a phase separation where the duplexes with longer overhangs aggregate to form COL LC domains that coexist with an isotropic fluid rich in duplexes whose structure cannot aggregate.

  17. The Compliment Sequence.

    ERIC Educational Resources Information Center

    Sims, Anntarie L.

    1989-01-01

    Describes and examines 150 tape-recorded compliment sequences. Reports that the course and outcome of compliments and compliment responses are affected by: (1) the way a compliment is worded; (2) the type of statement that precedes or follows the compliment; and (3) the status and sex of the compliment participants. (RAE)

  18. A Sequence of Cylinders

    ERIC Educational Resources Information Center

    Johnson, Erica

    2006-01-01

    Hoping to develop in her students an understanding of mathematics as a way of thinking more than a way of doing, the author of this article describes how her students worked on a spatial reasoning problem stemming from an iteratively constructed sequence of cylinders. She presents an activity of making cylinders out of paper models, and for every…

  19. Localization protected quantum order

    NASA Astrophysics Data System (ADS)

    Nandkishore, Rahul

    2015-03-01

    Many body localization occurs in isolated quantum systems, usually with strong disorder, and is marked by absence of dissipation, absence of thermal equilibration, and a memory of the initial conditions that survives in local observables for arbitrarily long times. The many body localized regime is a non-equilibrium, strongly disordered, non-self averaging regime that presents a new frontier for quantum statistical mechanics. In this talk, I point out that there exists a vast zoo of correlated many body localized states of matter, which may be classified using familiar notions of spontaneous symmetry breaking and topological order. I will point out that in the many body localized regime, spontaneous symmetry breaking can occur even at high energy densities in one dimensional systems, and topological order can occur even without a bulk gap. I will also discuss the phenomenology of imperfectly isolated many body localized systems, which are weakly coupled to a heat bath. I will conclude with a brief discussion of how these phenomena may best be detected in experiments. Collaborators: David Huse, S.L. Sondhi, Arijeet Pal, Vadim Oganesyan, A.C. Potter, Sarang Gopalakrishnan, S. Johri, R.N. Bhatt.

  20. Fractional order junctions

    NASA Astrophysics Data System (ADS)

    Machado, J. Tenreiro

    2015-01-01

    Gottfried Leibniz generalized the derivation and integration, extending the operators from integer up to real, or even complex, orders. It is presently recognized that the resulting models capture long term memory effects difficult to describe by classical tools. Leon Chua generalized the set of lumped electrical elements that provide the building blocks in mathematical models. His proposal of the memristor and of higher order elements broadened the scope of variables and relationships embedded in the development of models. This paper follows the two directions and proposes a new logical step, by generalizing the concept of junction. Classical junctions interconnect system elements using simple algebraic restrictions. Nevertheless, this simplistic approach may be misleading in the presence of unexpected dynamical phenomena and requires including additional "parasitic" elements. The novel γ -junction includes, as special cases, the standard series and parallel connections and allows a new degree of freedom when building models. The proposal motivates the search for experimental and real world manifestations of the abstract conjectures.

  1. Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms

    PubMed Central

    Shvartsburg, Alexandre A.; Mashkevich, Stefan V.; Smith, Richard D.

    2011-01-01

    Technologies for separating and characterizing ions based on their transport properties in gases have been around for three decades. The early method of ion mobility spectrometry (IMS) distinguished ions by absolute mobility that depends on the collision cross section with buffer gas atoms. The more recent technique of field asymmetric waveform IMS (FAIMS) measures the difference between mobilities at high and low electric fields. Coupling IMS and FAIMS to soft ionization sources and mass spectrometry (MS) has greatly expanded their utility, enabling new applications in biomedical and nanomaterials research. Here, we show that time-dependent electric fields comprising more than two intensity levels could, in principle, effect an infinite number of distinct differential separations based on the higher-order terms of expression for ion mobility. These analyses could employ the hardware and operational procedures similar to those utilized in FAIMS. Methods up to the 4th or 5th order (where conventional IMS is 1st order and FAIMS is 2nd order) should be practical at field intensities accessible in ambient air, with still higher orders potentially achievable in insulating gases. Available experimental data suggest that higher-order separations should be largely orthogonal to each other and to FAIMS, IMS, and MS. PMID:16494377

  2. Computerized Physician Order Entry

    PubMed Central

    Khanna, Raman; Yen, Tony

    2014-01-01

    Computerized physician order entry (CPOE) has been promoted as an important component of patient safety, quality improvement, and modernization of medical practice. In practice, however, CPOE affects health care delivery in complex ways, with benefits as well as risks. Every implementation of CPOE is associated with both generally recognized and unique local factors that can facilitate or confound its rollout, and neurohospitalists will often be at the forefront of such rollouts. In this article, we review the literature on CPOE, beginning with definitions and proceeding to comparisons to the standard of care. We then proceed to discuss clinical decision support systems, negative aspects of CPOE, and cultural context of CPOE implementation. Before concluding, we follow the experiences of a Chief Medical Information Officer and neurohospitalist who rolled out a CPOE system at his own health care organization and managed the resulting workflow changes and setbacks. PMID:24381708

  3. Birth order and myopia

    PubMed Central

    Guggenheim, Jeremy A.; McMahon, George; Northstone, Kate; Mandel, Yossi; Kaiserman, Igor; Stone, Richard A.; Lin, Xiaoyu; Saw, Seang Mei; Forward, Hannah; Mackey, David A.; Yazar, Seyhan; Young, Terri L.; Williams, Cathy

    2013-01-01

    Purpose An association between birth order and reduced unaided vision (a surrogate for myopia) has been observed previously. We examined the association between birth order and myopia directly in 4 subject groups. Methods Subject groups were participants in 1) the Avon Longitudinal Study of Parents and Children (ALSPAC; UK; age 15 years; N=4,401), 2) the Singapore Cohort Study of Risk Factors for Myopia (SCORM; Singapore; age 13 years; N=1,959), 3) the Raine Eye Health Study (REHS; Australia; age 20 years; N=1,344), and 4) Israeli Defense Force recruitment candidates (IDFC; Israel; age 16-22 years; N=888,277). Main outcome: Odds ratio (OR) for myopia in first born versus non-first born individuals after adjusting for potential risk factors. Results The prevalence of myopia was numerically higher in first-born versus non-first-born individuals in all study groups, but the strength of evidence varied widely. The adjusted ORs (95% CI) were: ALSPAC, 1.31 (1.05-1.64); SCORM, 1.25 (0.89-1.77); REHS, 1.18 (0.90-1.55); IDFC, 1.04 (1.03-1.06). In the large IDFC sample, the effect size was greater (a) for the first born versus fourth or higher born comparison than for the first born versus second/third born comparison (P<0.001) and (b) with increasing myopia severity (P<0.001). Conclusions Across all studies, the increased risk of myopia in first born individuals was low (OR <1.3). Indeed, only the studies with >4000 participants provided strong statistical support for the association. The available evidence suggested the relationship was independent of established risk factors such as time outdoors/reading, and thus may arise through a different causal mechanism. PMID:24168726

  4. Order without design.

    PubMed

    Kurakin, Alexei

    2010-01-01

    Experimental reality in molecular and cell biology, as revealed by advanced research technologies and methods, is manifestly inconsistent with the design perspective on the cell, thus creating an apparent paradox: where do order and reproducibility in living systems come from if not from design? I suggest that the very idea of biological design (whether evolutionary or intelligent) is a misconception rooted in the time-honored and thus understandably precious error of interpreting living systems/organizations in terms of classical mechanics and equilibrium thermodynamics. This error, introduced by the founders and perpetuated due to institutionalization of science, is responsible for the majority of inconsistencies, contradictions, and absurdities plaguing modern sciences, including one of the most startling paradoxes - although almost everyone agrees that any living organization is an open nonequilibrium system of continuous energy/matter flow, almost everyone interprets and models living systems/organizations in terms of classical mechanics, equilibrium thermodynamics, and engineering, i.e., in terms and concepts that are fundamentally incompatible with the physics of life. The reinterpretation of biomolecules, cells, organisms, ecosystems, and societies in terms of open nonequilibrium organizations of energy/matter flow suggests that, in the domain of life, order and reproducibility do not come from design. Instead, they are natural and inevitable outcomes of self-organizing activities of evolutionary successful, and thus persistent, organizations co-evolving on multiple spatiotemporal scales as biomolecules, cells, organisms, ecosystems, and societies. The process of self-organization on all scales is driven by economic competition, obeys empirical laws of nonequilibrium thermodynamics, and is facilitated and, thus, accelerated by memories of living experience persisting in the form of evolutionary successful living organizations and their constituents. PMID

  5. Order without design

    PubMed Central

    2010-01-01

    Experimental reality in molecular and cell biology, as revealed by advanced research technologies and methods, is manifestly inconsistent with the design perspective on the cell, thus creating an apparent paradox: where do order and reproducibility in living systems come from if not from design? I suggest that the very idea of biological design (whether evolutionary or intelligent) is a misconception rooted in the time-honored and thus understandably precious error of interpreting living systems/organizations in terms of classical mechanics and equilibrium thermodynamics. This error, introduced by the founders and perpetuated due to institutionalization of science, is responsible for the majority of inconsistencies, contradictions, and absurdities plaguing modern sciences, including one of the most startling paradoxes - although almost everyone agrees that any living organization is an open nonequilibrium system of continuous energy/matter flow, almost everyone interprets and models living systems/organizations in terms of classical mechanics, equilibrium thermodynamics, and engineering, i.e., in terms and concepts that are fundamentally incompatible with the physics of life. The reinterpretation of biomolecules, cells, organisms, ecosystems, and societies in terms of open nonequilibrium organizations of energy/matter flow suggests that, in the domain of life, order and reproducibility do not come from design. Instead, they are natural and inevitable outcomes of self-organizing activities of evolutionary successful, and thus persistent, organizations co-evolving on multiple spatiotemporal scales as biomolecules, cells, organisms, ecosystems, and societies. The process of self-organization on all scales is driven by economic competition, obeys empirical laws of nonequilibrium thermodynamics, and is facilitated and, thus, accelerated by memories of living experience persisting in the form of evolutionary successful living organizations and their constituents. PMID

  6. 40 CFR 305.27 - Accelerated order, order to dismiss.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 28 2014-07-01 2014-07-01 false Accelerated order, order to dismiss... Prehearing Procedures § 305.27 Accelerated order, order to dismiss. (a) General. The Presiding Officer, upon motion of any party or sua sponte, may at any time render an accelerated order in favor of the...

  7. Planning Complex Sequences Using Compressed Representations

    NASA Technical Reports Server (NTRS)

    Chien, Steve; Knight, Russell

    2009-01-01

    A method that notably includes the use of compressed representations interleaved with non-compressed (time-line) representations of a general scheduling problem has been conceived as a means of increasing, by orders of magnitude, the speeds of computations needed for scheduling complex sequences of activities that include cycles wherein subsets of the activities and/or sequences are repeated. The method was originally intended to be used in scheduling large campaigns of scientific observations by instruments aboard a spacecraft. A typical such campaign could include observations of millions of targets, many observations to be made during long repeated passes. The method would also be useful on Earth for scheduling complex sequences of activities that include cycles.

  8. Local alignment of two-base encoded DNA sequence

    PubMed Central

    Homer, Nils; Merriman, Barry; Nelson, Stanley F

    2009-01-01

    Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

  9. Sedimentary sequence evolution in a Foredeep basin: Eastern Venezuela

    SciTech Connect

    Bejarano, C.; Funes, D.; Sarzalho, S.; Audemard, F.; Flores, G.

    1996-08-01

    Well log-seismic sequence stratigraphy analysis in the Eastern Venezuela Foreland Basin leads to study of the evolution of sedimentary sequences onto the Cretaceous-Paleocene passive margin. This basin comprises two different foredeep sub-basins: The Guarico subbasin to the west, older, and the Maturin sub-basin to the east, younger. A foredeep switching between these two sub-basins is observed at 12.5 m.y. Seismic interpretation and well log sections across the study area show sedimentary sequences with transgressive sands and coastal onlaps to the east-southeast for the Guarico sub-basin, as well as truncations below the switching sequence (12.5 m.y.), and the Maturin sub-basin shows apparent coastal onlaps to the west-northwest, as well as a marine onlap (deeper water) in the west, where it starts to establish. Sequence stratigraphy analysis of these sequences with well logs allowed the study of the evolution of stratigraphic section from Paleocene to middle Miocene (68.0-12.0 m.y.). On the basis of well log patterns, the sequences were divided in regressive-transgressive-regressive sedimentary cycles caused by changes in relative sea level. Facies distributions were analyzed and the sequences were divided into simple sequences or sub- sequences of a greater frequencies than third order depositional sequences.

  10. 48 CFR 53.216-1 - Delivery orders and orders under basic ordering agreements (OF 347).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... under basic ordering agreements (OF 347). 53.216-1 Section 53.216-1 Federal Acquisition Regulations... Delivery orders and orders under basic ordering agreements (OF 347). OF 347, Order for Supplies or Services. OF 347, prescribed in 53.213(f), (or an approved agency form) may be used to place orders...

  11. A domain sequence approach to pangenomics: applications to Escherichia coli.

    PubMed

    Snipen, Lars-Gustav; Ussery, David W

    2012-01-01

    The study of microbial pangenomes relies on the computation of gene families, i.e. the clustering of coding sequences into groups of essentially similar genes. There is no standard approach to obtain such gene families. Ideally, the gene family computations should be robust against errors in the annotation of genes in various genomes. In an attempt to achieve this robustness, we propose to cluster sequences by their domain sequence, i.e. the ordered sequence of domains in their protein sequence. In a study of 347 genomes from Escherichia coli we find on average around 4500 proteins having hits in Pfam-A in every genome, clustering into around 2500 distinct domain sequence families in each genome. Across all genomes we find a total of 5724 such families. A binomial mixture model approach indicates this is around 95% of all domain sequences we would expect to see in E. coli in the future. A Heaps law analysis indicates the population of domain sequences is larger, but this analysis is also very sensitive to smaller changes in the computation procedure. The resolution between strains is good despite the coarse grouping obtained by domain sequence families. Clustering sequences by their ordered domain content give us domain sequence families, who are robust to errors in the gene prediction step. The computational load of the procedure scales linearly with the number of genomes, which is needed for the future explosion in the number of re-sequenced strains. The use of domain sequence families for a functional classification of strains clearly has some potential to be explored. PMID:24555018

  12. Evolution of gene order conservation in prokaryotes

    PubMed Central

    Tamames, Javier

    2001-01-01

    Background As more complete genomes are sequenced, conservation of gene order between different organisms is emerging as an informative property of the genomes. Conservation of gene order has been used for predicting function and functional interactions of proteins, as well as for studying the evolutionary relationships between genomes. The reasons for the maintenance of gene order are still not well understood, as the organization of the prokaryote genome into operons and lateral gene transfer cannot possibly account for all the instances of conservation found. Comprehensive studies of gene order are one way of elucidating the nature of these maintaining forces. Results Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order. Conclusions Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation. PMID:11423009

  13. Transposon facilitated DNA sequencing

    SciTech Connect

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  14. RNA Sequencing in Schizophrenia

    PubMed Central

    Li, Xin; Teng, Shaolei

    2015-01-01

    Schizophrenia (SCZ) is a serious psychiatric disorder that affects 1% of general population and places a heavy burden worldwide. The underlying genetic mechanism of SCZ remains unknown, but studies indicate that the disease is associated with a global gene expression disturbance across many genes. Next-generation sequencing, particularly of RNA sequencing (RNA-Seq), provides a powerful genome-scale technology to investigate the pathological processes of SCZ. RNA-Seq has been used to analyze the gene expressions and identify the novel splice isoforms and rare transcripts associated with SCZ. This paper provides an overview on the genetics of SCZ, the advantages of RNA-Seq for transcriptome analysis, the accomplishments of RNA-Seq in SCZ cohorts, and the applications of induced pluripotent stem cells and RNA-Seq in SCZ research. PMID:27053919

  15. Rapid Polymer Sequencer

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor (Inventor); Brock, Mathew W. (Inventor)

    2011-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  16. HIV sequence compendium 2002

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Freed, Eric; Hahn, Beatrice; Marx, Preston; McCutchan, Francine; Mellors, John; Wolinsky, Steven; Korber, Bette

    2002-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Traditionally, we present the sequence data themselves in the form of alignments: Section II, an alignment of a selection of HIV-1/SIVcpz full-length genomes (a lot of LAI-like sequences, for example, have been omitted because they are so similar that they bias the alignment); Section III, a combined HIV-1/HIV-2/SIV whole genome alignment; Sections IV–VI, amino acid alignments for HIV-1/SIV-cpz, HIV-2/SIV, and SIVagm. The HIV-2/SIV and SIVagm amino acid alignments are separate because the genetic distances between these groups are so great that presenting them in one alignment would make it very elongated because of the large number of gaps that have to be inserted. As always, tables with extensive background information gathered from the literature accompany the whole genome alignments. The collection of whole-gene sequences in the database is now large enough that we have abundant representation of most subtypes. For many subtypes, and especially for subtype B, a large number of sequences that span entire genes were not included in the printed alignments to conserve space. A more complete version of all alignments is available on our website, http://hiv-web.lanl.gov/content/hiv-db/ALIGN_CURRENT/ALIGN-INDEX.html. Importantly, all these alignments have been edited to include only one sequence per person, based on phylogenetic trees that were created for all of them, as well as on the literature. Because of the number of sequences available, we have decided to use a different selection principle this year, based on the epidemiological importance of the subtypes. Subtypes A–D and CRFs 01 and 02 are by far the most widespread variants, and for these (when available) we have included 8–10 representatives in the alignments. The other

  17. Sequencing BPS spectra

    NASA Astrophysics Data System (ADS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  18. Multiview image sequence enhancement

    NASA Astrophysics Data System (ADS)

    Jovanov, Ljubomir; Luong, Hiêp; Ružic, Tijana; Philips, Wilfried

    2015-03-01

    Realistic visualization is crucial for more intuitive representation of complex data, medical imaging, simulation and entertainment systems. Multiview autostereoscopic displays are great step towards achieving complete immersive user experience. However, providing high quality content for this type of displays is still a great challenge. Due to the different characteristics/settings of the cameras in the multivew setup and varying photometric characteristics of the objects in the scene, the same object may have different appearance in the sequences acquired by the different cameras. Images representing views recorded using different cameras in practice have different local noise, color and sharpness characteristics. View synthesis algorithms introduce artefacts due to errors in disparity estimation/bad occlusion handling or due to erroneous warping function estimation. If the input multivew images are not of sufficient quality and have mismatching color and sharpness characteristics, these artifacts may become even more disturbing. The main goal of our method is to simultaneously perform multiview image sequence denoising, color correction and the improvement of sharpness in slightly blurred regions. Results show that the proposed method significantly reduces the amount of the artefacts in multiview video sequences resulting in a better visual experience.

  19. Learning Interpretable SVMs for Biological Sequence Classification

    PubMed Central

    Rätsch, Gunnar; Sonnenburg, Sören; Schäfer, Christin

    2006-01-01

    Background Support Vector Machines (SVMs) – using a variety of string kernels – have been successfully applied to biological sequence classification problems. While SVMs achieve high classification accuracy they lack interpretability. In many applications, it does not suffice that an algorithm just detects a biological signal in the sequence, but it should also provide means to interpret its solution in order to gain biological insight. Results We propose novel and efficient algorithms for solving the so-called Support Vector Multiple Kernel Learning problem. The developed techniques can be used to understand the obtained support vector decision function in order to extract biologically relevant knowledge about the sequence analysis problem at hand. We apply the proposed methods to the task of acceptor splice site prediction and to the problem of recognizing alternatively spliced exons. Our algorithms compute sparse weightings of substring locations, highlighting which parts of the sequence are important for discrimination. Conclusion The proposed method is able to deal with thousands of examples while combining hundreds of kernels within reasonable time, and reliably identifies a few statistically significant positions. PMID:16723012

  20. Oligorotaxane Radicals under Orders.

    PubMed

    Wang, Yuping; Frasconi, Marco; Liu, Wei-Guang; Sun, Junling; Wu, Yilei; Nassar, Majed S; Botros, Youssry Y; Goddard, William A; Wasielewski, Michael R; Stoddart, J Fraser

    2016-02-24

    A strategy for creating foldameric oligorotaxanes composed of only positively charged components is reported. Threadlike components-namely oligoviologens-in which different numbers of 4,4'-bipyridinium (BIPY(2+)) subunits are linked by p-xylylene bridges, are shown to be capable of being threaded by cyclobis(paraquat-p-phenylene) (CBPQT(4+)) rings following the introduction of radical-pairing interactions under reducing conditions. UV/vis/NIR spectroscopic and electrochemical investigations suggest that the reduced oligopseudorotaxanes fold into highly ordered secondary structures as a result of the formation of BIPY(•+) radical cation pairs. Furthermore, by installing bulky stoppers at each end of the oligopseudorotaxanes by means of Cu-free alkyne-azide cycloadditions, their analogous oligorotaxanes, which retain the same stoichiometries as their progenitors, can be prepared. Solution-state studies of the oligorotaxanes indicate that their mechanically interlocked structures lead to the enforced interactions between the dumbbell and ring components, allowing them to fold (contract) in their reduced states and unfold (expand) in their fully oxidized states as a result of Coulombic repulsions. This electrochemically controlled reversible folding and unfolding process, during which the oligorotaxanes experience length contractions and expansions, is reminiscent of the mechanisms of actuation associated with muscle fibers. PMID:27163033