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Sample records for survey sequences gss

  1. ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

    Directory of Open Access Journals (Sweden)

    Alves-Ferreira Marcelo

    2008-09-01

    Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

  2. Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences.

    Science.gov (United States)

    Pironti, Alejandro; Pfeifer, Nico; Kaiser, Rolf; Walter, Hauke; Lengauer, Thomas

    2014-01-01

    Rules-based HIV-1 drug-resistance interpretation (DRI) systems disregard many amino-acid positions of the drug's target protein. The aims of this study are (1) the development of a drug-resistance interpretation system that is based on HIV-1 sequences from clinical practice rather than hard-to-get phenotypes, and (2) the assessment of the benefit of taking all available amino-acid positions into account for DRI. A dataset containing 34,934 therapy-naïve and 30,520 drug-exposed HIV-1 pol sequences with treatment history was extracted from the EuResist database and the Los Alamos National Laboratory database. 2,550 therapy-change-episode baseline sequences (TCEB) were assigned to test set A. Test set B contains 1,084 TCEB from the HIVdb TCE repository. Sequences from patients absent in the test sets were used to train three linear support vector machines to produce scores that predict drug exposure pertaining to each of 20 antiretrovirals: the first one uses the full amino-acid sequences (DEfull), the second one only considers IAS drug-resistance positions (DEonlyIAS), and the third one disregards IAS drug-resistance positions (DEnoIAS). For performance comparison, test sets A and B were evaluated with DEfull, DEnoIAS, DEonlyIAS, geno2pheno[resistance], HIVdb, ANRS, HIV-GRADE, and REGA. Clinically-validated cut-offs were used to convert the continuous output of the first four methods into susceptible-intermediate-resistant (SIR) predictions. With each method, a genetic susceptibility score (GSS) was calculated for each therapy episode in each test set by converting the SIR prediction for its compounds to integer: S=2, I=1, and R=0. The GSS were used to predict therapy success as defined by the EuResist standard datum definition. Statistical significance was assessed using a Wilcoxon signed-rank test. A comparison of the therapy-success prediction performances among the different interpretation systems for test set A can be found in Table 1, while those for test set

  3. Marker discovery in Trypanosoma vivax through GSS and comparative analysis. Preliminary data and perspectives

    International Nuclear Information System (INIS)

    Davila, A.M.R.; Guerreiro, L.T.A.; Souza, S.S.

    2005-01-01

    Trypanosoma vivax is a haemoparasite affecting the livestock industry in South America and Africa. Despite the high economic relevance of the disease caused by T. vivax, little work has been done on its molecular characterization, in contrast with human trypanosomes, such as T. brucei and T. cruzi. The present study reports the construction of a semi-normalized genomic library and the sequencing of 160 Genome Sequence Survey (GSS) ends of T. vivax. The analyses of this preliminary data show that this simple and rapid approach worked well to generate some potential new markers for this species. (author)

  4. Portuguese adaptation of the Gudjonsson Suggestibility Scales (GSS1 and GSS2): empirical findings

    OpenAIRE

    Pires, Rute; Silva, Danilo R.; Ferreira, Ana Sousa

    2012-01-01

    In study 1 (n = 51, M age = 21.4 years, SD = 5.7), the validity of the Portuguese adaptation of the Gudjonsson Suggestibility Scales (Pires, 2011) was shown through the comparison of means of the original (Gudjonsson, 1997) and the translated scales and the analysis of the correlations between the GSS1 and GSS2 scores. The relationships between interrogative suggestibility and the big five were also addressed and the results point to independence between suggestibility and personality, which ...

  5. The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

    Science.gov (United States)

    Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

    2014-01-01

    Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

  6. Question-answer sequences in survey interviews

    NARCIS (Netherlands)

    Dijkstra, W.; Ongena, Y.P.

    2006-01-01

    Interaction analysis was used to analyze a total of 14,265 question-answer sequences of (Q-A Sequences) 80 questions that originated from two face-to-face and three telephone surveys. The analysis was directed towards the causes and effects of particular interactional problems. Our results showed

  7. Determinant Representations of Sequences: A Survey

    Directory of Open Access Journals (Sweden)

    Moghaddamfar A. R.

    2014-01-01

    Full Text Available This is a survey of recent results concerning (integer matrices whose leading principal minors are well-known sequences such as Fibonacci, Lucas, Jacobsthal and Pell (subsequences. There are different ways for constructing such matrices. Some of these matrices are constructed by homogeneous or nonhomogeneous recurrence relations, and others are constructed by convolution of two sequences. In this article, we will illustrate the idea of these methods by constructing some integer matrices of this type.

  8. Evaluation of the AN/GSS-20 motion detection system

    International Nuclear Information System (INIS)

    1979-01-01

    A series of tests was performed on the AN/GSS-20 motion detection system. The primary objectives of these tests were to determine sensor detection patterns and to quantitate the effects of intruder velocity. System susceptibility to environmental factors was also examined

  9. A case of severe glutathione synthetase deficiency with novel GSS mutations

    Science.gov (United States)

    Xia, H.; Ye, J.; Wang, L.; Zhu, J.; He, Z.

    2018-01-01

    Glutathione synthetase deficiency (GSSD) is a rare inborn error of glutathione metabolism with autosomal recessive inheritance. The severe form of the disease is characterized by acute metabolic acidosis, usually present in the neonatal period with hemolytic anemia and progressive encephalopathy. A case of a male newborn infant who had severe metabolic acidosis with high anion gap, hemolytic anemia, and hyperbilirubinemia is reported. A high level of 5-oxoproline was detected in his urine and a diagnosis of generalized GSSD was made. DNA sequence analysis revealed the infant to be compound heterozygous with two mutations, c.738dupG in exon 8 of GSS gene resulting in p.S247fs and a repetitive sequence in exon 3 of GSS gene. Treatment after diagnosis of GSSD included supplementation with antioxidants and oral sodium hydrogen bicarbonate. However, he maintained a variable degree of metabolic acidosis and succumbed shortly after his parents requested discontinuation of therapy because of dismal prognosis and medical futility when he was 18 days old. PMID:29340523

  10. A case of severe glutathione synthetase deficiency with novel GSS mutations

    Directory of Open Access Journals (Sweden)

    H. Xia

    2018-01-01

    Full Text Available Glutathione synthetase deficiency (GSSD is a rare inborn error of glutathione metabolism with autosomal recessive inheritance. The severe form of the disease is characterized by acute metabolic acidosis, usually present in the neonatal period with hemolytic anemia and progressive encephalopathy. A case of a male newborn infant who had severe metabolic acidosis with high anion gap, hemolytic anemia, and hyperbilirubinemia is reported. A high level of 5-oxoproline was detected in his urine and a diagnosis of generalized GSSD was made. DNA sequence analysis revealed the infant to be compound heterozygous with two mutations, c.738dupG in exon 8 of GSS gene resulting in p.S247fs and a repetitive sequence in exon 3 of GSS gene. Treatment after diagnosis of GSSD included supplementation with antioxidants and oral sodium hydrogen bicarbonate. However, he maintained a variable degree of metabolic acidosis and succumbed shortly after his parents requested discontinuation of therapy because of dismal prognosis and medical futility when he was 18 days old.

  11. 75 FR 28298 - Avaya Inc., Worldwide Services Group, Global Support Services (GSS) Organization, Including On...

    Science.gov (United States)

    2010-05-20

    ...., Worldwide Services Group, Global Support Services (GSS) Organization, Including On-Site Leased Workers From..., Highlands Ranch, CO; Including Employees in Support of Avaya Inc., Worldwide Services Group, Global Support... workers of Avaya Inc., Worldwide Services Group, Global Support Services (GSS) Organization, including on...

  12. The Emilia 2012 sequence: a macroseismic survey

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    Andrea Tertulliani

    2012-10-01

    Full Text Available On May 20, 2012, at 4:03 local time (2:03 UTC, a large part of the Po Valley between the cities of Ferrara, Modena and Mantova was struck by a damaging earthquake (Ml 5.9. The epicenter was located by the Istituto Nazionale di Geo-fisica e Vulcanologia (INGV seismic network [ISIDe 2010] at 44.889 ˚N and 11.228 ˚E, approximately 30 km west of Ferrara (Figure 1. The event was preceded by a foreshock that occurred at 01:13 local time, with a magnitude of Ml 4. The mainshock started an intense seismic sequence that lasted for weeks, counting more than 2,000 events, six of which had Ml >5. The strongest earthquakes of this sequence occurred on May 29, 2012, with Ml 5.8 and Ml 5.3, recorded at 9:00 and 12:55 local time, respectively. The epicenters of the May 29, 2012, events were located at the westernmost part of the rupture zone of the May 20, 2012, earthquake (Figure 2. The May 20 and 29, 2012, earthquakes were felt through the whole of northern and central Italy, and as far as Switzerland, Slovenia, Croatia, Austria, south-eastern France and southern Germany. Historical information reveals that the seismic activity in the Po Valley is moderate […

  13. The Surveillance Dynamic State GSS "Intelsat 10-02" on Base Multicolored Photometrical Data

    Science.gov (United States)

    Sukhov, P. P.; Karpenko, G. F.; Epishev, V. P.; Motrunich, I. I.

    2011-09-01

    Complex coordinate and multicolored photometric observations of active geostationary satellite (GSS) "Intelsat 10-02" (28358/2004022A, sub point GSS 359.0 E, with inclination to the equator i=0.05, the eccentricity e=0.00) took place at the "Mayaki" station, located nearby Odessa, on October 6,7,12,13,14, 2010 and on March 4, 2011. On those dates the satellite was nearby the border of the Earth's shadow. On basis of multicolored photometric observations some of its optical and geometrical characteristics were calculated. The analysis of light variation of GSS in B,V,R spectral regions of Johnson's system and the color indexes variation show that during the dates of observation the systems of stabilization of the platform of the transceiver antenna and the solar panels worked in the normal operating mode. During the observations the tracking panels of GSS "Intelsat 10-02" are well preserved relatively to the direction of Sun. The rotation of SB panels happens about axis, which is perpendicular to the equatorial plane. The orientation of the main axis of the platform, within calculation errors, remained unchanged in to the direction of the Earth's mass center. The analyses of the coordinate and photometric information for this GSS show how we can effectively control the dynamic state of the satellite and evaluate the optical characteristics of visible surface of spacecraft components and their behavior on its orbit using the photometric observations

  14. A 2-GS/s 6-bit self-calibrated flash ADC

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Youtao; Chen Chen [National Key Laboratory of Monolithic Integrated Circuits and Modules, Nanjing Electronic Devices Institute, Nanjing 210016 (China); Li Xiaopeng; Zhang Min; Liu Ao, E-mail: zhangyt@nedc-ic.co [Nanjing Electronic Devices Institute, Nanjing 210016 (China)

    2010-09-15

    A single channel 2-GS/s 6-bit ADC with cascade resistive averaging and self foreground calibration is demonstrated in 0.18-{mu}m CMOS. The calibration method based on DAC trimming improves the linearity and dynamic performance further. The peak DNL and INL are measured as 0.34 and 0.22 LSB, respectively. The SNDR and SFDR have achieved 36.5 and 45.9 dB, respectively, with 1.22 MHz input signal and 2 GS/s. The proposed ADC, including on-chip track-and-hold amplifiers and clock buffers, consumes 570 mW from a single 1.8 V supply while operating at 2 GS/s. (semiconductor integrated circuits)

  15. Application of Logic to Integer Sequences: A Survey

    Science.gov (United States)

    Makowsky, Johann A.

    Chomsky and Schützenberger showed in 1963 that the sequence d L (n), which counts the number of words of a given length n in a regular language L, satisfies a linear recurrence relation with constant coefficients for n, or equivalently, the generating function g_L(x)=sumn d_L(n) x^n is a rational function. In this talk we survey results concerning sequences a(n) of natural numbers which satisfy linear recurrence relations over ℤ or ℤ m , and

  16. Facilitating genome navigation : survey sequencing and dense radiation-hybrid gene mapping

    NARCIS (Netherlands)

    Hitte, C; Madeoy, J; Kirkness, EF; Priat, C; Lorentzen, TD; Senger, F; Thomas, D; Derrien, T; Ramirez, C; Scott, C; Evanno, G; Pullar, B; Cadieu, E; Oza, [No Value; Lourgant, K; Jaffe, DB; Tacher, S; Dreano, S; Berkova, N; Andre, C; Deloukas, P; Fraser, C; Lindblad-Toh, K; Ostrander, EA; Galibert, F

    Accurate and comprehensive sequence coverage for large genomes has been restricted to only a few species of specific interest. Lower sequence coverage (survey sequencing) of related species can yield a wealth of information about gene content and putative regulatory elements. But survey sequences

  17. Transmission Properties of Human PrP 102L Prions Challenge the Relevance of Mouse Models of GSS.

    Science.gov (United States)

    Asante, Emmanuel A; Grimshaw, Andrew; Smidak, Michelle; Jakubcova, Tatiana; Tomlinson, Andrew; Jeelani, Asif; Hamdan, Shyma; Powell, Caroline; Joiner, Susan; Linehan, Jacqueline M; Brandner, Sebastian; Wadsworth, Jonathan D F; Collinge, John

    2015-07-01

    Inherited prion disease (IPD) is caused by autosomal-dominant pathogenic mutations in the human prion protein (PrP) gene (PRNP). A proline to leucine substitution at PrP residue 102 (P102L) is classically associated with Gerstmann-Sträussler-Scheinker (GSS) disease but shows marked clinical and neuropathological variability within kindreds that may be caused by variable propagation of distinct prion strains generated from either PrP 102L or wild type PrP. To-date the transmission properties of prions propagated in P102L patients remain ill-defined. Multiple mouse models of GSS have focused on mutating the corresponding residue of murine PrP (P101L), however murine PrP 101L, a novel PrP primary structure, may not have the repertoire of pathogenic prion conformations necessary to accurately model the human disease. Here we describe the transmission properties of prions generated in human PrP 102L expressing transgenic mice that were generated after primary challenge with ex vivo human GSS P102L or classical CJD prions. We show that distinct strains of prions were generated in these mice dependent upon source of the inoculum (either GSS P102L or CJD brain) and have designated these GSS-102L and CJD-102L prions, respectively. GSS-102L prions have transmission properties distinct from all prion strains seen in sporadic and acquired human prion disease. Significantly, GSS-102L prions appear incapable of transmitting disease to conventional mice expressing wild type mouse PrP, which contrasts strikingly with the reported transmission properties of prions generated in GSS P102L-challenged mice expressing mouse PrP 101L. We conclude that future transgenic modeling of IPDs should focus exclusively on expression of mutant human PrP, as other approaches may generate novel experimental prion strains that are unrelated to human disease.

  18. Mechanical and chemical cleaning of the tubes bundles of the moisture separator reheaters (GSS) of Nuclear power plants

    International Nuclear Information System (INIS)

    Guerra, Patrice; Ruiz, Jose T.; Ureta, Roman; Carreres, Cristina; Virginie, Le-Guerroue

    2012-09-01

    The cleaning operation concerns the 'GSS' system (GSS stands for moisture separator reheaters, MSR) which are classified as 'watch quality guarantee', not classified as safety facility and subjected to Pressure Equipment regulations. The follow-up of the operational GSS (steel carbon) of EDF nuclear power plants CP0 group reveals a clog rate due to a relevant magnetite deposits that could result in equipment damage, loss of availability and loss of plant productivity. The pressure drop between inlet and outlet of the heating steam is close to maximum design criterion. The service consisted in designing, developing, qualifying and carrying out a process which removes clog from the inside of GSS U-tubes bundle located in the vapor circuit and which respects the equipment integrity and ensures the process harmlessness. This cleaning has to enable the complete removal of deposits and oxides (magnetite) in order to recover a passage diameter and a surface finish equivalent to the origin, thus avoiding the replacement of the GSS and obtaining a considerable reduction of costs. To do so, LAINSA and SOLARCA designed, developed, qualified and operated on 14 GSS bundles, by carrying out the following operations: - Cartography of the GSS tubes bundles clogging state; - Pre-Mechanical cleaning to un-block the sealed tubes and release the inside tubes passing; - Isolation of the bundle and check of leaks of the system; - Chemical cleaning with the efficiency and harmlessness parameters follow-up: - Acid Phase by means of weak organic acids to eliminate all the deposits; - Passivation phase; - Final Rinsing respecting the customer criteria; - Drying; - Waste management and waste treatment. The implementation of this operation enables the elimination of the whole deposits (magnetite) and oxides located inside the GSS tube bundle and thus to recover a passage diameter inside the tubes, and a pressure drop close to a new system and therefore to enables the

  19. Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine

    Science.gov (United States)

    Craig S Echt; Surya Saha; Dennis L Deemer; C Dana Nelson

    2011-01-01

    Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine (Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant...

  20. The Portuguese adaptation of the Gudjonsson Suggestibility Scale (GSS1) in a sample of inmates.

    Science.gov (United States)

    Pires, Rute; Silva, Danilo R; Ferreira, Ana Sousa

    2014-01-01

    This paper comprises two studies which address the validity of the Portuguese adaptation of the Gudjonsson Suggestibility Scale, GSS1. In study 1, the means and standard deviations for the suggestibility results of a sample of Portuguese inmates (N=40, Mage=37.5 years, SD=8.1) were compared to those of a sample of Icelandic inmates (Gudjonsson, 1997; Gudjonsson & Sigurdsson, 1996). Portuguese inmates' results were in line with the original results. In study 2, the means and standard deviations for the suggestibility results of the sample of Portuguese inmates were compared to those of a general Portuguese population sample (N=57, Mage=36.1 years, SD=12.7). The forensic sample obtained significantly higher scores in suggestibility measures than the general population sample. ANOVA confirmed that the increased suggestibility in the inmates sample was due to the limited memory capacity of this latter group. Given that the results of both studies 1 and 2 are in keeping with the author's original results (Gudjonsson, 1997), this may be regarded as a confirmation of the validity of the Portuguese GSS1. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. RANCANG BANGUN PROTOTIPE GARDENING SMART SYSTEM (GSS UNTUK PERAWATAN TANAMAN ANGGREK BERBASIS WEB

    Directory of Open Access Journals (Sweden)

    Deni Kurnia

    2016-04-01

    Full Text Available Gardening Smart System (GSS adalah protitipe sistem perawatan tanaman yang pengontrolannya dirancang melalui web. Prototipe ini dimaksudkan untuk membantu pengontrolan sistem perawatan tanaman berjenis anggrek pada tingkat perorangan (personal user yang kedepannya dapat dikembangkan lebih luas lagi aplikasinya. Perancangan prototipe ini meliputi aspek hardware dan software. Dari sisi hardware prototipe dirancang menggunakan soil mosturise sensor, arduino, ethernet shield dan waterpump, sedangkan dari sisi software prototipe dirancang dengan membangun user interface berbasis HTML dan CSS. Komunikasi data antara software dengan hardware dilakukan melalui IP address yang dapat diakses melalui mobile phone (HP maupun desktop/PC. Pengujian prototipe diterapkan pada salah satu tanaman anggrek berjenis Phalaenopsis. Setelah dilakukan pengujian pada aspek hardware dan software, hasil yang diperoleh sesuai dengan desain dan spesifikasi yang telah direncanakan. Kedepan, pengembangan prototipe ini masih terbuka lebar untuk mengontrol sistem berbasis web dengan aplikasi lebih kompleks lagi. Kata kunci: aplikasi berbasis web, komunikasi data, IOT (internet of thing.

  2. A 2 GS/s 8-bit folding and interpolating ADC in 90 nm CMOS

    International Nuclear Information System (INIS)

    He Wenwei; Meng Qiao; Zhang Yi; Tang Kai

    2014-01-01

    A single-channel 2 GS/s 8-bit analog-to-digital converter in 90 nm CMOS process technology is presented. It utilizes cascade folding architecture, which incorporates an additional inter-stage sample-and-hold amplifier between the folding circuits to enhance the quantization time. It also uses the foreground on-chip digital-assisted calibration circuit to improve the linearity of the circuit. The post simulation results demonstrate that it has a differential nonlinearity < ±0.3 LSB and an integral nonlinearity < ±0.25 LSB at the Nyquist frequency. Moreover, 7.338 effective numbers of bits can be achieved at 2 GSPS. The whole chip area is 0.88 × 0.88 mm 2 with the pad. It consumes 210 mW from a 1.2 V single supply. (semiconductor integrated circuits)

  3. An 11b 3.6GS/s time-Iiterleaved SAR ADC in 65nm CMOS

    NARCIS (Netherlands)

    Janssen, E.J.G.; Doris, K.; Zanikopoulos, A.; Murroni, A.; Weide, van der G.; Lin, Y.; Alvado, L.; Darthenay, F.; Fregeais, Y.

    2013-01-01

    Over the last years several low-power time-interleaved (TI) ADC designs in the 2.5-to-3.0GS/s range have been published [1-3], intended for integration in applications like radar, software-defined radio, full-spectrum cable modems, and multi-channel satellite reception. It is to be expected that

  4. Survey of transposable elements in sugarcane expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Rossi Magdalena

    2001-01-01

    Full Text Available The sugarcane expressed sequence tag (SUCEST project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac, Mutator (MuDR, Suppressor-mutator (En/Spm and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

  5. Development of a 1 GS/s high-resolution transient recorder

    CERN Document Server

    Bartknecht, S; Herrmann, F; Königsmann, K; Lauser, L; Schill, C; Schopferer, S; Wollny, H

    2009-01-01

    With present-day detectors in high energy physics one is often faced with short analog pulses of a few nanoseconds length which may cover large dynamic ranges. In many experiments both amplitude and timing information have to be measured with high accuracy. Additionally, the data rate per readout channel can reach several MHz, which makes high demands on the separation of pile-up pulses. For such applications we have built the GANDALF transient recorder with a resolution of 12bit@1GS/s and an analog bandwidth of 500 MHz. Signals are digitized and processed by fast algorithms to extract pulse arrival times and amplitudes in real-time and to generate experiment trigger signals. With up to 16 analog channels, deep memories and a high data rate interface, this 6U-VME64x/VXS module is not only a dead-time free digitization unit but also has huge numerical capabilities provided by the implementation of a Virtex5-SXT FPGA. Fast algorithms implemented in the FPGA may be used to disentangle possible pile-up pulses and...

  6. Ground System Architectures Workshop GMSEC SERVICES SUITE (GSS): an Agile Development Story

    Science.gov (United States)

    Ly, Vuong

    2017-01-01

    The GMSEC (Goddard Mission Services Evolution Center) Services Suite (GSS) is a collection of tools and software services along with a robust customizable web-based portal that enables the user to capture, monitor, report, and analyze system-wide GMSEC data. Given our plug-and-play architecture and the needs for rapid system development, we opted to follow the Scrum Agile Methodology for software development. Being one of the first few projects to implement the Agile methodology at NASA GSFC, in this presentation we will present our approaches, tools, successes, and challenges in implementing this methodology. The GMSEC architecture provides a scalable, extensible ground and flight system for existing and future missions. GMSEC comes with a robust Application Programming Interface (GMSEC API) and a core set of Java-based GMSEC components that facilitate the development of a GMSEC-based ground system. Over the past few years, we have seen an upbeat in the number of customers who are moving from a native desktop application environment to a web based environment particularly for data monitoring and analysis. We also see a need to provide separation of the business logic from the GUI display for our Java-based components and also to consolidate all the GUI displays into one interface. This combination of separation and consolidation brings immediate value to a GMSEC-based ground system through increased ease of data access via a uniform interface, built-in security measures, centralized configuration management, and ease of feature extensibility.

  7. A 6-bit 4 GS/s pseudo-thermometer segmented CMOS DAC

    Science.gov (United States)

    Yijun, Song; Wenyuan, Li

    2014-06-01

    A 6-bit 4 GS/s, high-speed and power-efficient DAC for ultra-high-speed transceivers in 60 GHz band millimeter wave technology is presented. A novel pseudo-thermometer architecture is proposed to realize a good compromise between the fast conversion speed and the chip area. Symmetrical and compact floor planning and layout techniques including tree-like routing, cross-quading and common-centroid method are adopted to guarantee the chip is fully functional up to near-Nyquist frequency in a standard 0.18 μm CMOS process. Post simulation results corroborate the feasibility of the designed DAC, which canperform good static and dynamic linearity without calibration. DNL errors and INL errors can be controlled within ±0.28 LSB and ±0.26 LSB, respectively. SFDR at 4 GHz clock frequency for a 1.9 GHz near-Nyquist sinusoidal output signal is 40.83 dB and the power dissipation is less than 37 mW.

  8. A 6-bit 4 GS/s pseudo-thermometer segmented CMOS DAC

    International Nuclear Information System (INIS)

    Song Yijun; Li Wenyuan

    2014-01-01

    A 6-bit 4 GS/s, high-speed and power-efficient DAC for ultra-high-speed transceivers in 60 GHz band millimeter wave technology is presented. A novel pseudo-thermometer architecture is proposed to realize a good compromise between the fast conversion speed and the chip area. Symmetrical and compact floor planning and layout techniques including tree-like routing, cross-quading and common-centroid method are adopted to guarantee the chip is fully functional up to near-Nyquist frequency in a standard 0.18 μm CMOS process. Post simulation results corroborate the feasibility of the designed DAC, which canperform good static and dynamic linearity without calibration. DNL errors and INL errors can be controlled within ±0.28 LSB and ±0.26 LSB, respectively. SFDR at 4 GHz clock frequency for a 1.9 GHz near-Nyquist sinusoidal output signal is 40.83 dB and the power dissipation is less than 37 mW. (semiconductor integrated circuits)

  9. The Results of Complex Research of GSS "SBIRS-Geo 2" Behavior in the Orbit

    Science.gov (United States)

    Sukhov, P. P.; Epishev, V. P.; Sukhov, K. P.; Karpenko, G. F.; Motrunich, I. I.

    2017-04-01

    The new generation of geosynchronous satellites SBIRS of US Air Force early warning system series (Satellite Early Warning System) replaced the previous DSP-satellite series (Defense Support Program). Currently from the territory of Ukraine, several GSS of DSP series and one "SBIRS-Geo 2" are available to observation. During two years of observations, we have received and analyzed for two satellites more than 30 light curves in B, V, R photometric system. As a result of complex research, we propose a model of "SBIRS-Geo" 2 orbital behavior compared with the same one of the DSP-satellite. To control the entire surface of the Earth with 15-16 sec interval, including the polar regions, 4 SBIRS satellites located every 90 deg. along the equator are enough in GEO orbit. Since DSP-satellites provide the coverage of the Earth's surface to 83 deg. latitudes with a period of 50 sec, DSP-satellites should be 8. All the conclusions were made based on an analysis of photometric and coordinate observations using the simulation of the dynamics of their orbital behavior.

  10. Test of Detonation Locator System AN/GSS-4. Operation PLUMBBOB, Desert Rock VII and VIII, Project 50.3

    Science.gov (United States)

    1979-10-01

    GSS-k was assigned in May 1957 to the system of equipments as used in Operation Plumbbob. Quantitative measurements of the em pulse have been made... quantitative data from the recordings of the SWR vavefoims, It vas necessary to record other infoimation on the photographs. Figure 35, a typical...Capilla vuvefonnG. The Heef’s I’dne and other Gleeson triplet observations confirmed the In/if ground wave positiv « half cycle and indicated a sharply

  11. A 12b 2.9GS/s DAC with IM3>60dB beyond 1 GHz in 65nm CMOS

    NARCIS (Netherlands)

    Lin, C.H.; Goes, F.; Westra, J.; Mulder, J.; Lin, Y.; Arslan, E.; Ayranci, E.; Liu, X.; Bult, K.

    2009-01-01

    A 12b 2.9GS/s current-steering DAC implemented in 65nm CMOS is presented, with an IM3 «-60dBc beyond 1GHz while driving a 50¿ load with an output swing of 2.5Vpp-diff and dissipating a power of 188mW. The SFDR measured at 2.9GS/s is better than 60dB beyond 340MHz.

  12. A near-infrared survey for pre-main sequence stars in Taurus

    Science.gov (United States)

    Gomez, Mercedes; Kenyon, Scott J.; Hartmann, Lee

    1994-01-01

    We present a near-infrared survey of approximately 2 sq deg covering parts of L1537, L1538, and Heiles cloud 2 in the Taurus-Auriga molecular cloud. Although this study is more sensitive than previous attempts to identify pre-main sequence stars in Taurus-Auriga, our survey regions contain only one new optically visible, young star. We did find several candidate embedded protostars; additional 10 micrometer photometry is necessary to verify the pre-main sequence nature of these sources. Our results--combined with those of previous surveys--show that the L1537/L1538 clouds contain no pre-main sequence stars. These two clouds are less dense than the active star formation sites in Taurus-Auriga, which suggests a cloud must achieve a threshold density to form stars.

  13. Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii genome.

    Directory of Open Access Journals (Sweden)

    Byrappa Venkatesh

    2007-04-01

    Full Text Available Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4x coverage and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element-like and long interspersed element-like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.

  14. Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing.

    Science.gov (United States)

    Zhou, Wei; Hu, Yiyi; Sui, Zhenghong; Fu, Feng; Wang, Jinguo; Chang, Lianpeng; Guo, Weihua; Li, Binbin

    2013-01-01

    Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon.

  15. Genome Survey Sequencing and Genetic Background Characterization of Gracilariopsis lemaneiformis (Rhodophyta) Based on Next-Generation Sequencing

    Science.gov (United States)

    Sui, Zhenghong; Fu, Feng; Wang, Jinguo; Chang, Lianpeng; Guo, Weihua; Li, Binbin

    2013-01-01

    Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon. PMID:23875008

  16. THE SPLASH SURVEY: A SPECTROSCOPIC PORTRAIT OF ANDROMEDA'S GIANT SOUTHERN STREAM

    International Nuclear Information System (INIS)

    Gilbert, Karoline M.; Guhathakurta, Puragra; Kollipara, Priya; Kalirai, Jason S.; Kirby, Evan N.; Beaton, Rachael L.; Majewski, Steven R.; Patterson, Richard J.; Geha, Marla C.

    2009-01-01

    The giant southern stream (GSS) is the most prominent tidal debris feature in M31's stellar halo and covers a significant fraction of its southern quadrant. The GSS is a complex structure composed of a relatively metal-rich, high-surface-brightness 'core' and a lower metallicity, lower-surface-brightness 'envelope'. We present spectroscopy of red giant stars in six fields in the vicinity of M31's GSS (including four new fields and improved spectroscopic reductions for two previously published fields) and one field on stream C, an arc-like feature seen in star-count maps on M31's southeast minor axis at R ∼ 60 kpc. These data are part of our ongoing Spectroscopic and Photometric Landscape of Andromeda's Stellar Halo survey of M31 using the DEIMOS instrument on the Keck II 10 m telescope. Several GSS-related findings and measurements are presented here. We present the innermost kinematical detection of the GSS core to date (R = 17 kpc). This field also contains the inner continuation of a second kinematically cold component that was originally seen in a GSS core field at R ∼ 21 kpc. The velocity gradients of the GSS and the second component in the combined data set are parallel over a range of ΔR = 7 kpc, suggesting that this may represent a bifurcation in the line-of-sight velocities of GSS stars. We present the first kinematical detection of substructure in the GSS envelope (S quadrant, R ∼ 58 kpc). Using kinematically identified samples, we show that the envelope debris has a ∼0.7 dex lower mean photometric metallicity and possibly higher intrinsic velocity dispersion than the GSS core. The GSS is also identified in the field of the M31 dwarf spheroidal satellite And I; the GSS in this field has a metallicity distribution identical to that of the GSS core. We confirm the previous finding of two kinematically cold components in stream C, and measure intrinsic velocity dispersions of ∼10 and ∼4 km s -1 . This compilation of the kinematical (mean

  17. The Generalized Support Software (GSS) Domain Engineering Process: An Object-Oriented Implementation and Reuse Success at Goddard Space Flight Center

    Science.gov (United States)

    Condon, Steven; Hendrick, Robert; Stark, Michael E.; Steger, Warren

    1997-01-01

    The Flight Dynamics Division (FDD) of NASA's Goddard Space Flight Center (GSFC) recently embarked on a far-reaching revision of its process for developing and maintaining satellite support software. The new process relies on an object-oriented software development method supported by a domain specific library of generalized components. This Generalized Support Software (GSS) Domain Engineering Process is currently in use at the NASA GSFC Software Engineering Laboratory (SEL). The key facets of the GSS process are (1) an architecture for rapid deployment of FDD applications, (2) a reuse asset library for FDD classes, and (3) a paradigm shift from developing software to configuring software for mission support. This paper describes the GSS architecture and process, results of fielding the first applications, lessons learned, and future directions

  18. A sequence-based survey of the complex structural organization of tumor genomes

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela; Tao, Quanzhou; Aerni, Sarah J.; Brown, Raymond P.; Bashir, Ali; Gray, Joe W.; Cheng, Jan-Fang; de Jong, Pieter; Nefedov, Mikhail; Ried, Thomas; Padilla-Nash, Hesed M.; Collins, Colin C.

    2008-04-03

    The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

  19. The SAMI Galaxy Survey: spatially resolving the main sequence of star formation

    Science.gov (United States)

    Medling, Anne M.; Cortese, Luca; Croom, Scott M.; Green, Andrew W.; Groves, Brent; Hampton, Elise; Ho, I.-Ting; Davies, Luke J. M.; Kewley, Lisa J.; Moffett, Amanda J.; Schaefer, Adam L.; Taylor, Edward; Zafar, Tayyaba; Bekki, Kenji; Bland-Hawthorn, Joss; Bloom, Jessica V.; Brough, Sarah; Bryant, Julia J.; Catinella, Barbara; Cecil, Gerald; Colless, Matthew; Couch, Warrick J.; Drinkwater, Michael J.; Driver, Simon P.; Federrath, Christoph; Foster, Caroline; Goldstein, Gregory; Goodwin, Michael; Hopkins, Andrew; Lawrence, J. S.; Leslie, Sarah K.; Lewis, Geraint F.; Lorente, Nuria P. F.; Owers, Matt S.; McDermid, Richard; Richards, Samuel N.; Sharp, Robert; Scott, Nicholas; Sweet, Sarah M.; Taranu, Dan S.; Tescari, Edoardo; Tonini, Chiara; van de Sande, Jesse; Walcher, C. Jakob; Wright, Angus

    2018-04-01

    We present the ˜800 star formation rate maps for the Sydney-AAO Multi-object Integral field spectrograph (SAMI) Galaxy Survey based on H α emission maps, corrected for dust attenuation via the Balmer decrement, that are included in the SAMI Public Data Release 1. We mask out spaxels contaminated by non-stellar emission using the [O III]/H β, [N II]/H α, [S II]/H α, and [O I]/H α line ratios. Using these maps, we examine the global and resolved star-forming main sequences of SAMI galaxies as a function of morphology, environmental density, and stellar mass. Galaxies further below the star-forming main sequence are more likely to have flatter star formation profiles. Early-type galaxies split into two populations with similar stellar masses and central stellar mass surface densities. The main-sequence population has centrally concentrated star formation similar to late-type galaxies, while galaxies >3σ below the main sequence show significantly reduced star formation most strikingly in the nuclear regions. The split populations support a two-step quenching mechanism, wherein halo mass first cuts off the gas supply and remaining gas continues to form stars until the local stellar mass surface density can stabilize the reduced remaining fuel against further star formation. Across all morphologies, galaxies in denser environments show a decreased specific star formation rate from the outside in, supporting an environmental cause for quenching, such as ram-pressure stripping or galaxy interactions.

  20. CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L. methylation filtered genomic genespace sequences

    Directory of Open Access Journals (Sweden)

    Spraggins Thomas A

    2007-04-01

    Full Text Available Abstract Background Cowpea [Vigna unguiculata (L. Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical West and Central Africa. Cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. The goal of the Cowpea Genomics Initiative (CGI, funded by the Kirkhouse Trust, a UK-based charitable organization, is to leverage modern molecular genetic tools for gene discovery and cowpea improvement. One aspect of the initiative is the sequencing of the gene-rich region of the cowpea genome (termed the genespace recovered using methylation filtration technology and providing annotation and analysis of the sequence data. Description CGKB, Cowpea Genespace/Genomics Knowledge Base, is an annotation knowledge base developed under the CGI. The database is based on information derived from 298,848 cowpea genespace sequences (GSS isolated by methylation filtering of genomic DNA. The CGKB consists of three knowledge bases: GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs knowledge base for molecular marker discovery. A homology-based approach was applied for annotations of the GSS, mainly using BLASTX against four public FASTA formatted protein databases (NCBI GenBank Proteins, UniProtKB-Swiss-Prot, UniprotKB-PIR (Protein Information Resource, and UniProtKB-TrEMBL. Comparative genome analysis was done by BLASTX searches of the cowpea GSS against four plant proteomes from Arabidopsis thaliana, Oryza sativa, Medicago truncatula, and Populus trichocarpa. The possible exons and introns on each cowpea GSS were predicted using the HMM-based Genscan gene predication program and the

  1. WHITE-DWARF-MAIN-SEQUENCE BINARIES IDENTIFIED FROM THE LAMOST PILOT SURVEY

    International Nuclear Information System (INIS)

    Ren Juanjuan; Luo Ali; Li Yinbi; Wei Peng; Zhao Jingkun; Zhao Yongheng; Song Yihan; Zhao Gang

    2013-01-01

    We present a set of white-dwarf-main-sequence (WDMS) binaries identified spectroscopically from the Large sky Area Multi-Object fiber Spectroscopic Telescope (LAMOST, also called the Guo Shou Jing Telescope) pilot survey. We develop a color selection criteria based on what is so far the largest and most complete Sloan Digital Sky Survey (SDSS) DR7 WDMS binary catalog and identify 28 WDMS binaries within the LAMOST pilot survey. The primaries in our binary sample are mostly DA white dwarfs except for one DB white dwarf. We derive the stellar atmospheric parameters, masses, and radii for the two components of 10 of our binaries. We also provide cooling ages for the white dwarf primaries as well as the spectral types for the companion stars of these 10 WDMS binaries. These binaries tend to contain hot white dwarfs and early-type companions. Through cross-identification, we note that nine binaries in our sample have been published in the SDSS DR7 WDMS binary catalog. Nineteen spectroscopic WDMS binaries identified by the LAMOST pilot survey are new. Using the 3σ radial velocity variation as a criterion, we find two post-common-envelope binary candidates from our WDMS binary sample

  2. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Schierup, M.H.; Jorgensen, F.G.

    2005-01-01

    sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human...

  3. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Benjamin M

    2008-03-01

    Full Text Available Abstract Background Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications followed by pyrosequencing, shotgun Sanger sequencing, and denaturing gradient gel electrophoresis were utilized to survey the major populations of bacteria that occur in the pathogenic biofilms of three types of chronic wound types: diabetic foot ulcers (D, venous leg ulcers (V, and pressure ulcers (P. Results There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, including Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia spp. Each of the wound types reveals marked differences in bacterial populations, such as pressure ulcers in which 62% of the populations were identified as obligate anaerobes. There were also populations of bacteria that were identified but not recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also compared to those obtained using traditional culture-based diagnostics. Only in one wound type did culture methods correctly identify the primary bacterial population indicating the need for improved diagnostic methods. Conclusion If clinicians can gain a better understanding of the wound's microbiota, it will give them a greater understanding of the wound's ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in

  4. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Li Wei

    2005-05-01

    Full Text Available Abstract Background Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls. Results We have generated ~3.84 million shotgun sequences (0.66X coverage from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human. Conclusion The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.

  5. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  6. Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of a hospital

    OpenAIRE

    Manaka, Akihiro; Tokue, Yutaka; Murakami, Masami

    2017-01-01

    Background Nosocomial infection is one of the most common complications within health care facilities. Certain studies have reported outbreaks resulting from contaminated hospital environments. Although the identification of bacteria in the environment can readily be achieved using culturing methods, these methods detect live bacteria. Sequencing of the 16S ribosomal RNA (16S rRNA) gene is recognized to be effective for bacterial identification. In this study, we surveyed wards where drug-res...

  7. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

    OpenAIRE

    Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

    2010-01-01

    Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resoluti...

  8. Proficiency Testing for Bacterial Whole Genome Sequencing: An End-User Survey of Current Capabilities, Requirements and Priorities

    DEFF Research Database (Denmark)

    Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne

    2015-01-01

    The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of ‘wet’ laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories...... and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://​www.​globalmicrobiali​dentifier.​org/​) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted...... by Working Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range...

  9. Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

    DEFF Research Database (Denmark)

    Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne

    2015-01-01

    The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of 'wet' laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories...... and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://www.globalmicrobialidentifier.org/) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted by Working...... Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range of costs...

  10. Survey of methods for integrated sequence analysis with emphasis on man-machine interaction

    Energy Technology Data Exchange (ETDEWEB)

    Kahlbom, U; Holmgren, P [RELCON, Stockholm (Sweden)

    1995-05-01

    This report presents a literature study concerning recently developed monotonic methodologies in the human reliability area. The work was performed by RELCON AB on commission by NKS/RAK-1, subproject 3. The topic of subproject 3 is `Integrated Sequence Analysis with Emphasis on Man-Machine Interaction`. The purpose with the study was to compile recently developed methodologies and to propose some of these methodologies for use in the sequence analysis task. The report describes mainly non-dynamic (monotonic) methodologies. One exception is HITLINE, which is a semi-dynamic method. Reference provides a summary of approaches to dynamic analysis of man-machine-interaction, and explains the differences between monotonic and dynamic methodologies. (au) 21 refs.

  11. Survey of methods for integrated sequence analysis with emphasis on man-machine interaction

    International Nuclear Information System (INIS)

    Kahlbom, U.; Holmgren, P.

    1995-05-01

    This report presents a literature study concerning recently developed monotonic methodologies in the human reliability area. The work was performed by RELCON AB on commission by NKS/RAK-1, subproject 3. The topic of subproject 3 is 'Integrated Sequence Analysis with Emphasis on Man-Machine Interaction'. The purpose with the study was to compile recently developed methodologies and to propose some of these methodologies for use in the sequence analysis task. The report describes mainly non-dynamic (monotonic) methodologies. One exception is HITLINE, which is a semi-dynamic method. Reference provides a summary of approaches to dynamic analysis of man-machine-interaction, and explains the differences between monotonic and dynamic methodologies. (au) 21 refs

  12. Next-Generation Survey Sequencing and the Molecular Organization of Wheat Chromosome 6B

    Czech Academy of Sciences Publication Activity Database

    Tanaka, T.; Kobayashi, F.; Joshi, G.P.; Šimková, Hana; Nasuda, S.; Doležel, Jaroslav; Handa, H.

    2014-01-01

    Roč. 21, č. 2 (2014), s. 103-114 ISSN 1340-2838 R&D Projects: GA ČR GBP501/12/G090 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional support: RVO:61389030 Keywords : wheat * chromosome 6B * genome sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.477, year: 2014

  13. A 5bit 1GS/s 2.7mW 0.05mm^2 asynchronous digital slope ADC in 90nm CMOS for IR UWB radio

    NARCIS (Netherlands)

    Ding, M.; Harpe, P.J.A.; Hegt, J.A.; Philips, K.J.P.; Groot, de H.W.H.; Roermund, van A.H.M.

    2012-01-01

    A 5bit 1GS/s 0.05mm2 4× time-interleaved asynchronous digital slope ADC in 90nm CMOS for IR UWB radio is presented. New delay cells are introduced to double the speed over prior art, yielding the 250MS/s single-channel slope converter. A self-disabled comparator eliminates static leakage and

  14. Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates

    Science.gov (United States)

    We have previously published extensive genomic surveys [1-3], reporting NAT-homologous sequences in hundreds of sequenced bacterial, fungal and vertebrate genomes. We present here the results of our latest search of 2445 genomes, representing 1532 (70 archaeal, 1210 bacterial, 43 protist, 97 fungal,...

  15. Combined use of real-time PCR and nested sequence-based typing in survey of human Legionella infection.

    Science.gov (United States)

    Qin, T; Zhou, H; Ren, H; Shi, W; Jin, H; Jiang, X; Xu, Y; Zhou, M; Li, J; Wang, J; Shao, Z; Xu, X

    2016-07-01

    Legionnaires' disease (LD) is a globally distributed systemic infectious disease. The burden of LD in many regions is still unclear, especially in Asian countries including China. A survey of Legionella infection using real-time PCR and nested sequence-based typing (SBT) was performed in two hospitals in Shanghai, China. A total of 265 bronchoalveolar lavage fluid (BALF) specimens were collected from hospital A between January 2012 and December 2013, and 359 sputum specimens were collected from hospital B throughout 2012. A total of 71 specimens were positive for Legionella according to real-time PCR focusing on the 5S rRNA gene. Seventy of these specimens were identified as Legionella pneumophila as a result of real-time PCR amplification of the dotA gene. Results of nested SBT revealed high genetic polymorphism in these L. pneumophila and ST1 was the predominant sequence type. These data revealed that the burden of LD in China is much greater than that recognized previously, and real-time PCR may be a suitable monitoring technology for LD in large sample surveys in regions lacking the economic and technical resources to perform other methods, such as urinary antigen tests and culture methods.

  16. A novel Gerstmann-Sträussler-Scheinker disease mutation defines a precursor for amyloidogenic 8 kDa PrP fragments and reveals N-terminal structural changes shared by other GSS alleles

    Science.gov (United States)

    Mercer, Robert C. C.; Fu, Ze-Lin; Mays, Charles E.; Gapeshina, Hristina; Wohlgemuth, Serene L.; Acevedo-Morantes, Claudia Y.; Cashman, Neil R.; Coulthart, Michael B.; Jansen, Gerard H.; Stepanova, Maria

    2018-01-01

    To explore pathogenesis in a young Gerstmann-Sträussler-Scheinker Disease (GSS) patient, the corresponding mutation, an eight-residue duplication in the hydrophobic region (HR), was inserted into the wild type mouse PrP gene. Transgenic (Tg) mouse lines expressing this mutation (Tg.HRdup) developed spontaneous neurologic syndromes and brain extracts hastened disease in low-expressor Tg.HRdup mice, suggesting de novo formation of prions. While Tg.HRdup mice exhibited spongiform change, PrP aggregates and the anticipated GSS hallmark of a proteinase K (PK)-resistant 8 kDa fragment deriving from the center of PrP, the LGGLGGYV insertion also imparted alterations in PrP's unstructured N-terminus, resulting in a 16 kDa species following thermolysin exposure. This species comprises a plausible precursor to the 8 kDa PK-resistant fragment and its detection in adolescent Tg.HRdup mice suggests that an early start to accumulation could account for early disease of the index case. A 16 kDa thermolysin-resistant signature was also found in GSS patients with P102L, A117V, H187R and F198S alleles and has coordinates similar to GSS stop codon mutations. Our data suggest a novel shared pathway of GSS pathogenesis that is fundamentally distinct from that producing structural alterations in the C-terminus of PrP, as observed in other prion diseases such as Creutzfeldt-Jakob Disease and scrapie. PMID:29338055

  17. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing.

    Science.gov (United States)

    Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

    2010-08-01

    Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons and upstream open reading frames, which provide remarkable insight into the A. oryzae transcriptome. We were also able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes and pathways that might be involved in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae is much more complex than previously anticipated, and these results may provide a blueprint for further study of the A. oryzae transcriptome.

  18. Intelligence Makes People Think like Economists: Evidence from the General Social Survey

    Science.gov (United States)

    Caplan, Bryan; Miller, Stephen C.

    2010-01-01

    Education is by far the strongest predictor of whether a non-economist will share the economic beliefs of the average economist. (Caplan, 2001) Is the effect of education as large as it seems? Or is education largely a proxy for cognitive ability? Using data from the General Social Survey (GSS), we show that the estimated effect of education…

  19. Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils.

    Directory of Open Access Journals (Sweden)

    Zewei Song

    Full Text Available Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS. The following treatments were considered: 1 the amount of soil used in DNA extraction, 2 the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation in the extraction procedure, 3 the amount of DNA template used in PCR, and 4 the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.

  20. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  1. Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

    OpenAIRE

    Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; ?oban, Nergiz; G?zel, Hatice

    2016-01-01

    Background Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm cha...

  2. THE ALLEN TELESCOPE ARRAY Pi GHz SKY SURVEY. I. SURVEY DESCRIPTION AND STATIC CATALOG RESULTS FOR THE BOOeTES FIELD

    International Nuclear Information System (INIS)

    Bower, Geoffrey C.; Croft, Steve; Keating, Garrett; Whysong, David; Backer, Don; Bauermeister, Amber; Blitz, Leo; Bock, Douglas; Cheng, Calvin; Dexter, Matt; Engargiola, Greg; Ackermann, Rob; Atkinson, Shannon; Backus, Peter; Bradford, Tucker; Davis, Mike; Dreher, John; Barott, Billy; Cork, Chris; DeBoer, Dave

    2010-01-01

    The Pi GHz Sky Survey (PiGSS) is a key project of the Allen Telescope Array. PiGSS is a 3.1 GHz survey of radio continuum emission in the extragalactic sky with an emphasis on synoptic observations that measure the static and time-variable properties of the sky. During the 2.5 year campaign, PiGSS will twice observe ∼250,000 radio sources in the 10,000 deg 2 region of the sky with b>30 0 to an rms sensitivity of ∼1 mJy. Additionally, sub-regions of the sky will be observed multiple times to characterize variability on timescales of days to years. We present here observations of a 10 deg 2 region in the Booetes constellation overlapping the NOAO Deep Wide Field Survey field. The PiGSS image was constructed from 75 daily observations distributed over a 4 month period and has an rms flux density between 200 and 250 μJy. This represents a deeper image by a factor of 4-8 than we will achieve over the entire 10,000 deg 2 . We provide flux densities, source sizes, and spectral indices for the 425 sources detected in the image. We identify ∼100 new flat-spectrum radio sources; we project that when completed PiGSS will identify 10 4 flat-spectrum sources. We identify one source that is a possible transient radio source. This survey provides new limits on faint radio transients and variables with characteristic durations of months.

  3. A search for pre-main sequence stars in the high-latitude molecular clouds. II - A survey of the Einstein database

    Science.gov (United States)

    Caillault, Jean-Pierre; Magnani, Loris

    1990-01-01

    The preliminary results are reported of a survey of every EINSTEIN image which overlaps any high-latitude molecular cloud in a search for X-ray emitting pre-main sequence stars. This survey, together with complementary KPNO and IRAS data, will allow the determination of how prevalent low mass star formation is in these clouds in general and, particularly, in the translucent molecular clouds.

  4. A Re-Assessment of Factors Associated with Environmental Concern and Behavior Using the 2010 General Social Survey

    Science.gov (United States)

    Newman, Todd P.; Fernandes, Ronald

    2016-01-01

    The associations between social and psychological influences and environmental attitudes, intentions and behavior have generated considerable interest, both in the fields of environmental behavior and of environmental education. We use the 2010 General Social Survey (GSS) to study these associations and expand the scope of earlier studies by…

  5. Rocuronium Versus Suxamethonium: A Survey of First-line Muscle Relaxant Use in UK Prehospital Rapid Sequence Induction.

    Science.gov (United States)

    Hartley, Emma L; Alcock, Roger

    2015-04-01

    Prehospital anaesthesia in the United Kingdom (UK) is provided by Helicopter Emergency Medical Service (HEMS) and British Association for Immediate Care (BASICS), a road-based service. Muscle relaxation in rapid sequence induction (RSI) has been traditionally undertaken with the use of suxamethonium; however, rocuronium at higher doses has comparable intubating conditions with fewer side effects. The aim of this survey was to establish how many prehospital services in the UK are now using rocuronium as first line in RSI. An online survey was constructed identifying choice of first-line muscle relaxant for RSI and emailed to lead clinicians for BASICS and HEMS services across the UK. If rocuronium was used, further questions regarding optimal dose, sugammadex, contraindications, and difference in intubating conditions were asked. A total of 29 full responses (93.5%) were obtained from 31 services contacted. Suxamethonium was used first line by 17 prehospital services (58.6%) and rocuronium by 12 (41.4%). In 11 services (91.7%), a dose of 1 mg/kg of rocuronium was used, and in one service, 1.2 mg/kg (8.3%) was used. No services using rocuronium carried sugammadex. In five services, slower relaxation time was found using rocuronium (41.7%), and in seven services, no difference in intubation conditions were noted (58.3%). Contraindications to rocuronium use included high probability of difficult airway and anaphylaxis. Use of rocuronium as first-line muscle relaxant in prehospital RSI is increasing. Continued auditing of practice will ascertain which services have adopted change and identify if complications of failed intubation increase as a result.

  6. Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys.

    Science.gov (United States)

    Andersson, Emmi; Shao, Wei; Bontell, Irene; Cham, Fatim; Cuong, Do Duy; Wondwossen, Amogne; Morris, Lynn; Hunt, Gillian; Sönnerborg, Anders; Bertagnolio, Silvia; Maldarelli, Frank; Jordan, Michael R

    2013-08-01

    Identification of recent HIV infection within populations is a public health priority for accurate estimation of HIV incidence rates and transmitted drug resistance at population level. Determining HIV incidence rates by prospective follow-up of HIV-uninfected individuals is challenging and serological assays have important limitations. HIV diversity within an infected host increases with duration of infection. We explore a simple bioinformatics approach to assess viral diversity by determining the percentage of ambiguous base calls in sequences derived from standard genotyping of HIV-1 protease and reverse transcriptase. Sequences from 691 recently infected (≤1 year) and chronically infected (>1 year) individuals from Sweden, Vietnam and Ethiopia were analyzed for ambiguity. A significant difference (p<0.0001) in the proportion of ambiguous bases was observed between sequences from individuals with recent and chronic infection in both HIV-1 subtype B and non-B infection, consistent with previous studies. In our analysis, a cutoff of <0.47% ambiguous base calls identified recent infection with a sensitivity and specificity of 88.8% and 74.6% respectively. 1,728 protease and reverse transcriptase sequences from 36 surveys of transmitted HIV drug resistance performed following World Health Organization guidance were analyzed for ambiguity. The 0.47% ambiguity cutoff was applied and survey sequences were classified as likely derived from recently or chronically infected individuals. 71% of patients were classified as likely to have been infected within one year of genotyping but results varied considerably amongst surveys. This bioinformatics approach may provide supporting population-level information to identify recent infection but its application is limited by infection with more than one viral variant, decreasing viral diversity in advanced disease and technical aspects of population based sequencing. Standardization of sequencing techniques and base calling

  7. More evidence for trends in the intergenerational transmission of divorce: a completed cohort approach using data from the general social survey.

    Science.gov (United States)

    Wolfinger, Nicholas H

    2011-05-01

    Many studies have demonstrated that the children of divorce are disproportionately likely to end their own marriages. In previous work, I showed that the transmission of divorce between generations weakened substantially for General Social Survey (GSS) respondents interviewed between 1973 and 1996 (Wolfinger 1999); Li and Wu (2006, 2008) contended that my finding is a methodological artifact of the GSS's lack of marriage duration data. This article presents a completed-cohort approach to studying divorce using the GSS. The results confirm a decline in the probability of divorce transmission that cannot be explained by the right-censoring bias alleged by Li and Wu. This finding contributes to an ongoing debate about trends in the negative consequences of parental divorce, as well as demonstrating a useful approach to right-censored phenomena when event history data are not available.

  8. SPECTROSCOPIC CONFIRMATION OF A MASSIVE RED-SEQUENCE-SELECTED GALAXY CLUSTER AT z = 1.34 IN THE SpARCS-SOUTH CLUSTER SURVEY

    International Nuclear Information System (INIS)

    Wilson, Gillian; Demarco, Ricardo; Muzzin, Adam; Yee, H. K. C.; Lacy, Mark; Surace, Jason; Gilbank, David; Blindert, Kris; Hoekstra, Henk; Majumdar, Subhabrata; Gardner, Jonathan P.; Gladders, Michael D.; Lonsdale, Carol

    2009-01-01

    The Spitzer Adaptation of the Red-sequence Cluster Survey (SpARCS) is a z'-passband imaging survey, consisting of deep (z' ≅ 24 AB) observations made from both hemispheres using the CFHT 3.6 m and CTIO 4 m telescopes. The survey was designed with the primary aim of detecting galaxy clusters at z > 1. In tandem with pre-existing 3.6 μm observations from the Spitzer Space Telescope SWIRE Legacy Survey, SpARCS detects clusters using an infrared adaptation of the two-filter red-sequence cluster technique. The total effective area of the SpARCS cluster survey is 41.9 deg 2 . In this paper, we provide an overview of the 13.6 deg 2 Southern CTIO/MOSAIC II observations. The 28.3 deg 2 Northern CFHT/MegaCam observations are summarized in a companion paper by Muzzin et al. In this paper, we also report spectroscopic confirmation of SpARCS J003550-431224, a very rich galaxy cluster at z = 1.335, discovered in the ELAIS-S1 field. To date, this is the highest spectroscopically confirmed redshift for a galaxy cluster discovered using the red-sequence technique. Based on nine confirmed members, SpARCS J003550-431224 has a preliminary velocity dispersion of 1050 ± 230 km s -1 . With its proven capability for efficient cluster detection, SpARCS is a demonstration that we have entered an era of large, homogeneously selected z > 1 cluster surveys.

  9. A Comprehensive Survey of Sequence Variation in the ABCA4 (ABCR) Gene in Stargardt Disease and Age-Related Macular Degeneration

    OpenAIRE

    Rivera, Andrea; White, Karen; Stöhr, Heidi; Steiner, Klaus; Hemmrich, Nadine; Grimm, Timo; Jurklies, Bernhard; Lorenz, Birgit; Scholl, Hendrik P. N.; Apfelstedt-Sylla, Eckhart; Weber, Bernhard H. F.

    2000-01-01

    Stargardt disease (STGD) is a common autosomal recessive maculopathy of early and young-adult onset and is caused by alterations in the gene encoding the photoreceptor-specific ATP-binding cassette (ABC) transporter (ABCA4). We have studied 144 patients with STGD and 220 unaffected individuals ascertained from the German population, to complete a comprehensive, population-specific survey of the sequence variation in the ABCA4 gene. In addition, we have assessed the proposed role for ABCA4 in ...

  10. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

    Science.gov (United States)

    Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

  11. A survey of the sequence-specific interaction of damaging agents with DNA: emphasis on antitumor agents.

    Science.gov (United States)

    Murray, V

    1999-01-01

    This article reviews the literature concerning the sequence specificity of DNA-damaging agents. DNA-damaging agents are widely used in cancer chemotherapy. It is important to understand fully the determinants of DNA sequence specificity so that more effective DNA-damaging agents can be developed as antitumor drugs. There are five main methods of DNA sequence specificity analysis: cleavage of end-labeled fragments, linear amplification with Taq DNA polymerase, ligation-mediated polymerase chain reaction (PCR), single-strand ligation PCR, and footprinting. The DNA sequence specificity in purified DNA and in intact mammalian cells is reviewed for several classes of DNA-damaging agent. These include agents that form covalent adducts with DNA, free radical generators, topoisomerase inhibitors, intercalators and minor groove binders, enzymes, and electromagnetic radiation. The main sites of adduct formation are at the N-7 of guanine in the major groove of DNA and the N-3 of adenine in the minor groove, whereas free radical generators abstract hydrogen from the deoxyribose sugar and topoisomerase inhibitors cause enzyme-DNA cross-links to form. Several issues involved in the determination of the DNA sequence specificity are discussed. The future directions of the field, with respect to cancer chemotherapy, are also examined.

  12. Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats

    Czech Academy of Sciences Publication Activity Database

    Pagán, H.J.T.; Macas, Jiří; Novák, Petr; McCulloch, E.S.; Stevens, R.D.; Ray, D.A.

    2012-01-01

    Roč. 4, č. 4 (2012), s. 575-585 ISSN 1759-6653 Institutional research plan: CEZ:AV0Z50510513 Keywords : HORIZONTAL TRANSFER * AUTOMATED CLASSIFICATION * GENOME SEQUENCE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.759, year: 2012

  13. A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome.

    Science.gov (United States)

    Keel, B N; Nonneman, D J; Rohrer, G A

    2017-08-01

    Genetic variants detected from sequence have been used to successfully identify causal variants and map complex traits in several organisms. High and moderate impact variants, those expected to alter or disrupt the protein coded by a gene and those that regulate protein production, likely have a more significant effect on phenotypic variation than do other types of genetic variants. Hence, a comprehensive list of these functional variants would be of considerable interest in swine genomic studies, particularly those targeting fertility and production traits. Whole-genome sequence was obtained from 72 of the founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the founding boars (12 Duroc and 12 Landrace) and 48 Yorkshire-Landrace composite sows. Sequence reads were mapped to the Sscrofa10.2 genome build, resulting in a mean of 6.1 fold (×) coverage per genome. A total of 22 342 915 high confidence SNPs were identified from the sequenced genomes. These included 21 million previously reported SNPs and 79% of the 62 163 SNPs on the PorcineSNP60 BeadChip assay. Variation was detected in the coding sequence or untranslated regions (UTRs) of 87.8% of the genes in the porcine genome: loss-of-function variants were predicted in 504 genes, 10 202 genes contained nonsynonymous variants, 10 773 had variation in UTRs and 13 010 genes contained synonymous variants. Approximately 139 000 SNPs were classified as loss-of-function, nonsynonymous or regulatory, which suggests that over 99% of the variation detected in our pigs could potentially be ignored, allowing us to focus on a much smaller number of functional SNPs during future analyses. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  14. Rediscovering medicinal plants' potential with OMICS: microsatellite survey in expressed sequence tags of eleven traditional plants with potent antidiabetic properties.

    Science.gov (United States)

    Sahu, Jagajjit; Sen, Priyabrata; Choudhury, Manabendra Dutta; Dehury, Budheswar; Barooah, Madhumita; Modi, Mahendra Kumar; Talukdar, Anupam Das

    2014-05-01

    Herbal medicines and traditionally used medicinal plants present an untapped potential for novel molecular target discovery using systems science and OMICS biotechnology driven strategies. Since up to 40% of the world's poor people have no access to government health services, traditional and folk medicines are often the only therapeutics available to them. In this vein, North East (NE) India is recognized for its rich bioresources. As part of the Indo-Burma hotspot, it is regarded as an epicenter of biodiversity for several plants having myriad traditional uses, including medicinal use. However, the improvement of these valuable bioresources through molecular breeding strategies, for example, using genic microsatellites or Simple Sequence Repeats (SSRs) or Expressed Sequence Tags (ESTs)-derived SSRs has not been fully utilized in large scale to date. In this study, we identified a total of 47,700 microsatellites from 109,609 ESTs of 11 medicinal plants (pineapple, papaya, noyontara, bitter orange, bermuda brass, ratalu, barbados nut, mango, mulberry, lotus, and guduchi) having proven antidiabetic properties. A total of 58,159 primer pairs were designed for the non-redundant 8060 SSR-positive ESTs and putative functions were assigned to 4483 unique contigs. Among the identified microsatellites, excluding mononucleotide repeats, di-/trinucleotides are predominant, among which repeat motifs of AG/CT and AAG/CTT were most abundant. Similarity search of SSR containing ESTs and antidiabetic gene sequences revealed 11 microsatellites linked to antidiabetic genes in five plants. GO term enrichment analysis revealed a total of 80 enriched GO terms widely distributed in 53 biological processes, 17 molecular functions, and 10 cellular components associated with the 11 markers. The present study therefore provides concrete insights into the frequency and distribution of SSRs in important medicinal resources. The microsatellite markers reported here markedly add to the genetic

  15. A survey of endogenous retrovirus (ERV) sequences in the vicinity of multiple sclerosis (MS)-associated single nucleotide polymorphisms (SNPs).

    Science.gov (United States)

    Brütting, Christine; Emmer, Alexander; Kornhuber, Malte; Staege, Martin S

    2016-08-01

    Although multiple sclerosis (MS) is one of the most common central nervous system diseases in young adults, little is known about its etiology. Several human endogenous retroviruses (ERVs) are considered to play a role in MS. We are interested in which ERVs can be identified in the vicinity of MS associated genetic marker to find potential initiators of MS. We analysed the chromosomal regions surrounding 58 single nucleotide polymorphisms (SNPs) that are associated with MS identified in one of the last major genome wide association studies. We scanned these regions for putative endogenous retrovirus sequences with large open reading frames (ORFs). We observed that more retrovirus-related putative ORFs exist in the relatively close vicinity of SNP marker indices in multiple sclerosis compared to control SNPs. We found very high homologies to HERV-K, HCML-ARV, XMRV, Galidia ERV, HERV-H/env62 and XMRV-like mouse endogenous retrovirus mERV-XL. The associated genes (CYP27B1, CD6, CD58, MPV17L2, IL12RB1, CXCR5, PTGER4, TAGAP, TYK2, ICAM3, CD86, GALC, GPR65 as well as the HLA DRB1*1501) are mainly involved in the immune system, but also in vitamin D regulation. The most frequently detected ERV sequences are related to the multiple sclerosis-associated retrovirus, the human immunodeficiency virus 1, HERV-K, and the Simian foamy virus. Our data shows that there is a relation between MS associated SNPs and the number of retroviral elements compared to control. Our data identifies new ERV sequences that have not been associated with MS, so far.

  16. Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes.

    Science.gov (United States)

    An, Jianyu; Yin, Mengqi; Zhang, Qin; Gong, Dongting; Jia, Xiaowen; Guan, Yajing; Hu, Jin

    2017-09-11

    Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica , about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N 50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both "Zheda 23" and "Zheda 83". Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.

  17. A survey of a population of anaesthesiologists from South India regarding practices for rapid sequence intubation in patients with head injury

    Directory of Open Access Journals (Sweden)

    Satyen Parida

    2016-01-01

    Full Text Available Background and Aims: Evidence and utility of the individual steps of the rapid sequence induction and tracheal intubation protocols have been debated, especially in the setting of traumatic brain injury. The purpose of this survey was to determine preferences in the current approach to rapid sequence intubation ( RSI in head injury patients among a population of anaesthesiologists from South India. Methods: A questionnaire was E-mailed to all the members of the Indian Society of Anaesthesiologists′ South Zone Chapter to ascertain their preferences, experience and comfort level with regard to their use of rapid sequence intubation techniques in adult patients with head injury. Participants were requested to indicate their practices for RSI technique for a head-injured patient upon arrival at the Emergency Medical Services department of their hospital. Results: The total response rate was 56.9% (530/932. Of the total respondents, 35% of the clinicians used cricoid pressure routinely, most respondents (68% stated that they pre-oxygenate the patients for about 3 min prior to RSI, thiopentone (61% and propofol (34% were commonly used prior to intubation. Rocuronium was the muscle relaxant of choice for RSI among the majority (44%, compared to succinylcholine (39%. Statistical analyses were performed after the initial entry onto a spreadsheet. Data were summarised descriptively using frequency distribution. Conclusion: In a rapid sequence intubation situation, the practice differed significantly among anaesthesiologists. Owing to disagreements and paucity of evidence-based data regarding the standards of RSI, it is apparent that RSI practice still has considerable variability in clinical practice.

  18. Survey of Postdoctorates at FFRDCs: Final Report [Federally Funded Research and Development Centers

    Energy Technology Data Exchange (ETDEWEB)

    Mulrow, Jeri

    2010-06-30

    The 2009 FFRDC survey collected the total number of postdocs employed by FFRDCs in the United States—categorized by source of support, citizenship, sex, and field of research—as of October 1, 2009. The universe for the 2009 GSS-FFRDC survey was the Master Government List of Federally Funded Research and Development Centers. The 2009 survey also contacted the NIH’s Intramural Research Program because it employs the largest number of postdocs in the federal government. The FFRDC survey collected data via a web instrument. Topics included the type of support the postdocs received (federal and nonfederal), their sex, citizenship, race/ethnicity, and field of research.

  19. Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species.

    Science.gov (United States)

    Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; Çoban, Nergiz; Gözel, Hatice

    2016-12-07

    Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.

  20. Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites

    Directory of Open Access Journals (Sweden)

    Lelley Tamas

    2008-12-01

    Full Text Available Abstract Background Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner. Results Our in silico survey of microsatellite clustering in genomes of Homo sapiens, Maccaca mulatta, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus, Gallus gallus, Danio rerio and Drosophila melanogaster revealed an unexpected high abundance of compound microsatellites. About 4 – 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90% these motifs differ only by a single mutation (base substitution or indel. We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track. Conclusion Our findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the "death" of microsatellites they might also result in their "birth".

  1. Temporal sequencing of nicotine dependence and bipolar disorder in the national epidemiologic survey on alcohol and related conditions (NESARC)

    Science.gov (United States)

    Martínez-Ortega, José M.; Goldstein, Benjamin I.; Gutiérrez-Rojas, Luis; Sala, Regina; Wang, Shuai; Blanco, Carlos

    2013-01-01

    Bipolar disorder (BD) and nicotine dependence (ND) often co-occur. However, the mechanisms underlying this association remain unclear. We aimed to examine, for the first time in a national and representative sample, the magnitude and direction of the temporal relationship between BD and ND; and to compare, among individuals with lifetime ND and BD, the sociodemographic and clinical characteristics of individuals whose onset of ND preceded the onset of BD (ND-prior) with those whose onset of ND followed the onset of BD (BD-prior). The sample included individuals with lifetime BD type I or ND (n=7958) from the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC, n=43093). Survival analyses and logistic regression models were computed to study the temporal association between ND and BD, and to compare ND-prior (n=135) and BD-prior (n=386) individuals. We found that ND predicted the onset of BD and BD also predicted the onset of ND. Furthermore, the risk of developing one disorder following the other one was greatest early in the course of illness. Most individuals with lifetime ND and BD were BD-prior (72.6%). BD-prior individuals had an earlier onset of BD and a higher number of manic episodes. By contrast, ND-prior individuals had an earlier onset of both daily smoking and ND, and an increased prevalence of alcohol use disorder. In conclusion, ND and BD predict the development of each other. The phenomenology and course of ND and BD varied significantly depending on which disorder had earlier onset. PMID:23582710

  2. The Gaia-ESO Survey: the present-day radial metallicity distribution of the Galactic disc probed by pre-main-sequence clusters

    Science.gov (United States)

    Spina, L.; Randich, S.; Magrini, L.; Jeffries, R. D.; Friel, E. D.; Sacco, G. G.; Pancino, E.; Bonito, R.; Bravi, L.; Franciosini, E.; Klutsch, A.; Montes, D.; Gilmore, G.; Vallenari, A.; Bensby, T.; Bragaglia, A.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Donati, P.; Frasca, A.; Hourihane, A.; Jofré, P.; Lewis, J.; Lind, K.; Monaco, L.; Morbidelli, L.; Prisinzano, L.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

    2017-05-01

    Context. The radial metallicity distribution in the Galactic thin disc represents a crucial constraint for modelling disc formation and evolution. Open star clusters allow us to derive both the radial metallicity distribution and its evolution over time. Aims: In this paper we perform the first investigation of the present-day radial metallicity distribution based on [Fe/H] determinations in late type members of pre-main-sequence clusters. Because of their youth, these clusters are therefore essential for tracing the current interstellar medium metallicity. Methods: We used the products of the Gaia-ESO Survey analysis of 12 young regions (age ages is not easily explained by the models. Our results reveal a complex interplay of several processes (e.g. star formation activity, initial mass function, supernova yields, gas flows) that controlled the recent evolution of the Milky Way. Based on observations made with the ESO/VLT, at Paranal Observatory, under program 188.B-3002 (The Gaia-ESO Public Spectroscopic Survey).Full Table 1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/601/A70

  3. A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).

    Science.gov (United States)

    Gallus, S; Kumar, V; Bertelsen, M F; Janke, A; Nilsson, M A

    2015-10-25

    Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Wide Field Radio Transient Surveys

    Science.gov (United States)

    Bower, Geoffrey

    2011-04-01

    The time domain of the radio wavelength sky has been only sparsely explored. Nevertheless, serendipitous discovery and results from limited surveys indicate that there is much to be found on timescales from nanoseconds to years and at wavelengths from meters to millimeters. These observations have revealed unexpected phenomena such as rotating radio transients and coherent pulses from brown dwarfs. Additionally, archival studies have revealed an unknown class of radio transients without radio, optical, or high-energy hosts. The new generation of centimeter-wave radio telescopes such as the Allen Telescope Array (ATA) will exploit wide fields of view and flexible digital signal processing to systematically explore radio transient parameter space, as well as lay the scientific and technical foundation for the Square Kilometer Array. Known unknowns that will be the target of future transient surveys include orphan gamma-ray burst afterglows, radio supernovae, tidally-disrupted stars, flare stars, and magnetars. While probing the variable sky, these surveys will also provide unprecedented information on the static radio sky. I will present results from three large ATA surveys (the Fly's Eye survey, the ATA Twenty CM Survey (ATATS), and the Pi GHz Survey (PiGSS)) and several small ATA transient searches. Finally, I will discuss the landscape and opportunities for future instruments at centimeter wavelengths.

  5. Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015–2016

    Directory of Open Access Journals (Sweden)

    Joana Revez

    2017-12-01

    Full Text Available Whole-genome sequencing (WGS has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupled with epidemiological and environmental investigations, it delivers ultimate resolution for tracing sources of epidemic infections. To ascertain the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritized diseases in the European Union (EU/European Economic Area (EEA, two surveys were conducted in 2015 and 2016. The surveys were designed to determine the national public health reference laboratories’ access to WGS and operational WGS-based typing capacity for national surveillance of selected foodborne pathogens, antimicrobial-resistant pathogens, and vaccine-preventable diseases identified as priorities for European genomic surveillance. Twenty-eight and twenty-nine out of the 30 EU/EEA countries participated in the survey in 2015 and 2016, respectively. National public health reference laboratories in 22 and 25 countries had access to WGS-based typing for public health applications in 2015 and 2016, respectively. Reported reasons for limited or no access were lack of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was limited. By mid-2016, half of the EU/EEA countries were using WGS analysis either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame as well as bioinformatics analysis varied by pathogen/resistance issue and country. Core genome multilocus allelic profiling, also called cgMLST, was the most frequently used annotation

  6. Numerical Analysis of Residual Stress and Distortion Use Finite Element Method on Inner Bottom Construction of Geomarin IV Survey Ship with Welding Sequence Variations

    Science.gov (United States)

    Syahroni, N.; Hartono, A. B. W.; Murtedjo, M.

    2018-03-01

    In the ship fabrication industry, welding is the most critical stage. If the quality of welding on ship fabrication is not good, then it will affect the strength and overall appearance of the structure. One of the factors that affect the quality of welding is residual stress and distortion. In this research welding simulation is performed on the inner bottom construction of Geomarin IV Ship Survey using shell element and has variation to welding sequence. In this study, welding simulations produced peak temperatures at 2490 K at variation 4. While the lowest peak temperature was produced by variation 2 with a temperature of 2339 K. After welding simulation, it continued simulating residual stresses and distortion. The smallest maximum tensile residual stress found in the inner bottom construction is 375.23 MPa, and the maximum tensile pressure is -20.18 MPa. The residual stress is obtained from variation 3. The distortion occurring in the inner bottom construction for X=720 mm is 4.2 mm and for X=-720 mm, the distortion is 4.92 mm. The distortion is obtained from the variation 3. Near the welding area, distortion value reaches its minimum point. This is because the stiffeners in the form of frames serves as anchoring.

  7. The elusive ideal of inclusiveness: lessons from a worldwide survey of neurologists on the ethical issues raised by whole-genome sequencing.

    Science.gov (United States)

    Hurlimann, Thierry; Jaitovich Groisman, Iris; Godard, Béatrice

    2017-04-11

    The anticipation of ethical issues that may arise with the clinical use of genomic technologies is crucial to envision their future implementation in a manner sensitive to local contexts. Yet, populations in low- and middle-income countries are underrepresented in studies that aim to explore stakeholders' perspectives on the use of such technologies. Within the framework of a research project entitled "Personalized medicine in the treatment of epilepsy", we sought to increase inclusiveness by widening the reach of our survey, inviting neurologists from around the world to share their views and practices regarding the use of whole-genome sequencing in clinical neurology and its associated ethics. We discuss herein the compelling scientific and ethical reasons that led us to attempt to recruit neurologists worldwide, despite the lack, in many low- or middle-income countries, of access to genomic technologies. Recruitment procedures and their results are presented and discussed, as well as the barriers we faced. We conclude that inclusive recruitment remains a challenging, albeit necessary and legitimate, endeavour.

  8. The VIMOS Public Extragalactic Redshift Survey (VIPERS):. A quiescent formation of massive red-sequence galaxies over the past 9 Gyr

    Science.gov (United States)

    Fritz, A.; Scodeggio, M.; Ilbert, O.; Bolzonella, M.; Davidzon, I.; Coupon, J.; Garilli, B.; Guzzo, L.; Zamorani, G.; Abbas, U.; Adami, C.; Arnouts, S.; Bel, J.; Bottini, D.; Branchini, E.; Cappi, A.; Cucciati, O.; De Lucia, G.; de la Torre, S.; Franzetti, P.; Fumana, M.; Granett, B. R.; Iovino, A.; Krywult, J.; Le Brun, V.; Le Fèvre, O.; Maccagni, D.; Małek, K.; Marulli, F.; McCracken, H. J.; Paioro, L.; Polletta, M.; Pollo, A.; Schlagenhaufer, H.; Tasca, L. A. M.; Tojeiro, R.; Vergani, D.; Zanichelli, A.; Burden, A.; Di Porto, C.; Marchetti, A.; Marinoni, C.; Mellier, Y.; Moscardini, L.; Nichol, R. C.; Peacock, J. A.; Percival, W. J.; Phleps, S.; Wolk, M.

    2014-03-01

    We explore the evolution of the colour-magnitude relation (CMR) and luminosity function (LF) at 0.4 contamination varies for the different methods and with redshift, but regardless of the method we measure a consistent evolution of the red-sequence (RS). Between 0.4 1011 M⊙) and expeditious RS formation over a short period of ~1.5 Gyr starting before z = 1. This is supported by the detection of ongoing SF in early-type galaxies at 0.9 Chile, using the Very Large Telescope under programs 182.A-0886 and partly 070.A-9007. Also based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at TERAPIX and the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. The VIPERS website is http://www.vipers.inaf.it/.Appendices are available in electronic form at http://www.aanda.org

  9. Culture and Next-generation sequencing-based drug susceptibility testing unveil high levels of drug-resistant-TB in Djibouti: results from the first national survey.

    Science.gov (United States)

    Tagliani, Elisa; Hassan, Mohamed Osman; Waberi, Yacine; De Filippo, Maria Rosaria; Falzon, Dennis; Dean, Anna; Zignol, Matteo; Supply, Philip; Abdoulkader, Mohamed Ali; Hassangue, Hawa; Cirillo, Daniela Maria

    2017-12-15

    Djibouti is a small country in the Horn of Africa with a high TB incidence (378/100,000 in 2015). Multidrug-resistant TB (MDR-TB) and resistance to second-line agents have been previously identified in the country but the extent of the problem has yet to be quantified. A national survey was conducted to estimate the proportion of MDR-TB among a representative sample of TB patients. Sputum was tested using XpertMTB/RIF and samples positive for MTB and resistant to rifampicin underwent first line phenotypic susceptibility testing. The TB supranational reference laboratory in Milan, Italy, undertook external quality assurance, genotypic testing based on whole genome and targeted-deep sequencing and phylogenetic studies. 301 new and 66 previously treated TB cases were enrolled. MDR-TB was detected in 34 patients: 4.7% of new and 31% of previously treated cases. Resistance to pyrazinamide, aminoglycosides and capreomycin was detected in 68%, 18% and 29% of MDR-TB strains respectively, while resistance to fluoroquinolones was not detected. Cluster analysis identified transmission of MDR-TB as a critical factor fostering drug resistance in the country. Levels of MDR-TB in Djibouti are among the highest on the African continent. High prevalence of resistance to pyrazinamide and second-line injectable agents have important implications for treatment regimens.

  10. Lithofacies and sequence stratigraphic description of the upper part of the Avon Park Formation and the Arcadia Formation in U.S. Geological Survey G–2984 test corehole, Broward County, Florida

    Science.gov (United States)

    Cunningham, Kevin J.; Robinson, Edward

    2017-07-18

    Rock core and sediment from U.S. Geological Survey test corehole G–2984 completed in 2011 in Broward County, Florida, provide an opportunity to improve the understanding of the lithostratigraphic, sequence stratigraphic, and hydrogeologic framework of the intermediate confining unit and Floridan aquifer system in southeastern Florida. A multidisciplinary approach including characterization of sequence stratigraphy, lithofacies, ichnology, foraminiferal paleontology, depositional environments, porosity, and permeability was used to describe the geologic samples from this test corehole. This information has produced a detailed characterization of the lithofacies and sequence stratigraphy of the upper part of the middle Eocene Avon Park Formation and Oligocene to middle Miocene Arcadia Formation. This enhancement of the knowledge of the sequence stratigraphic framework is especially important, because subaerial karst unconformities at the upper boundary of depositional cycles at various hierarchical scales are commonly associated with secondary porosity and enhanced permeability in the Floridan aquifer system.

  11. A comprehensive survey of sequence variation in the ABCA4 (ABCR) gene in Stargardt disease and age-related macular degeneration.

    Science.gov (United States)

    Rivera, A; White, K; Stöhr, H; Steiner, K; Hemmrich, N; Grimm, T; Jurklies, B; Lorenz, B; Scholl, H P; Apfelstedt-Sylla, E; Weber, B H

    2000-10-01

    Stargardt disease (STGD) is a common autosomal recessive maculopathy of early and young-adult onset and is caused by alterations in the gene encoding the photoreceptor-specific ATP-binding cassette (ABC) transporter (ABCA4). We have studied 144 patients with STGD and 220 unaffected individuals ascertained from the German population, to complete a comprehensive, population-specific survey of the sequence variation in the ABCA4 gene. In addition, we have assessed the proposed role for ABCA4 in age-related macular degeneration (AMD), a common cause of late-onset blindness, by studying 200 affected individuals with late-stage disease. Using a screening strategy based primarily on denaturing gradient gel electrophoresis, we have identified in the three study groups a total of 127 unique alterations, of which 90 have not been previously reported, and have classified 72 as probable pathogenic mutations. Of the 288 STGD chromosomes studied, mutations were identified in 166, resulting in a detection rate of approximately 58%. Eight different alleles account for 61% of the identified disease alleles, and at least one of these, the L541P-A1038V complex allele, appears to be a founder mutation in the German population. When the group with AMD and the control group were analyzed with the same methodology, 18 patients with AMD and 12 controls were found to harbor possible disease-associated alterations. This represents no significant difference between the two groups; however, for detection of modest effects of rare alleles in complex diseases, the analysis of larger cohorts of patients may be required.

  12. A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes

    Directory of Open Access Journals (Sweden)

    Baldiri Salvado

    2015-08-01

    Full Text Available Two Component Systems and Phosphorelays (TCS/PR are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK, Response Regulator (RR and Histidine Phosphotranfer (HPt domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.

  13. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

    Directory of Open Access Journals (Sweden)

    Scholz Uwe

    2009-11-01

    Full Text Available Abstract Background De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L. is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable. Results To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes. By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies. Conclusion The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.

  14. Improving ability measurement in surveys by following the principles of IRT: The Wordsum vocabulary test in the General Social Survey.

    Science.gov (United States)

    Cor, M Ken; Haertel, Edward; Krosnick, Jon A; Malhotra, Neil

    2012-09-01

    Survey researchers often administer batteries of questions to measure respondents' abilities, but these batteries are not always designed in keeping with the principles of optimal test construction. This paper illustrates one instance in which following these principles can improve a measurement tool used widely in the social and behavioral sciences: the GSS's vocabulary test called "Wordsum". This ten-item test is composed of very difficult items and very easy items, and item response theory (IRT) suggests that the omission of moderately difficult items is likely to have handicapped Wordsum's effectiveness. Analyses of data from national samples of thousands of American adults show that after adding four moderately difficult items to create a 14-item battery, "Wordsumplus" (1) outperformed the original battery in terms of quality indicators suggested by classical test theory; (2) reduced the standard error of IRT ability estimates in the middle of the latent ability dimension; and (3) exhibited higher concurrent validity. These findings show how to improve Wordsum and suggest that analysts should use a score based on all 14 items instead of using the summary score provided by the GSS, which is based on only the original 10 items. These results also show more generally how surveys measuring abilities (and other constructs) can benefit from careful application of insights from the contemporary educational testing literature. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. THE EVOLUTION OF DUSTY STAR FORMATION IN GALAXY CLUSTERS TO z = 1: SPITZER INFRARED OBSERVATIONS OF THE FIRST RED-SEQUENCE CLUSTER SURVEY

    International Nuclear Information System (INIS)

    Webb, T. M. A.; O'Donnell, D.; Coppin, Kristen; Faloon, Ashley; Geach, James E.; Noble, Allison; Yee, H. K. C.; Gilbank, David; Ellingson, Erica; Gladders, Mike; Muzzin, Adam; Wilson, Gillian; Yan, Renbin

    2013-01-01

    We present the results of an infrared (IR) study of high-redshift galaxy clusters with the MIPS camera on board the Spitzer Space Telescope. We have assembled a sample of 42 clusters from the Red-Sequence Cluster Survey-1 over the redshift range 0.3 14-15 M ☉ . We statistically measure the number of IR-luminous galaxies in clusters above a fixed inferred IR luminosity of 2 × 10 11 M ☉ , assuming a star forming galaxy template, per unit cluster mass and find it increases to higher redshift. Fitting a simple power-law we measure evolution of (1 + z) 5.1±1.9 over the range 0.3 cluster ). The evolution is similar, with ΣSFR/M cluster ∼ (1 + z) 5.4±1.9 . We show that this can be accounted for by the evolution of the IR-bright field population over the same redshift range; that is, the evolution can be attributed entirely to the change in the in-falling field galaxy population. We show that the ΣSFR/M cluster (binned over all redshift) decreases with increasing cluster mass with a slope (ΣSFR/M cluster ∼M cluster -1.5±0.4 ) consistent with the dependence of the stellar-to-total mass per unit cluster mass seen locally. The inferred star formation seen here could produce ∼5%-10% of the total stellar mass in massive clusters at z = 0, but we cannot constrain the descendant population, nor how rapidly the star-formation must shut-down once the galaxies have entered the cluster environment. Finally, we show a clear decrease in the number of IR-bright galaxies per unit optical galaxy in the cluster cores, confirming star formation continues to avoid the highest density regions of the universe at z ∼ 0.75 (the average redshift of the high-redshift clusters). While several previous studies appear to show enhanced star formation in high-redshift clusters relative to the field we note that these papers have not accounted for the overall increase in galaxy or dark matter density at the location of clusters. Once this is done, clusters at z ∼ 0.75 have the same

  16. A Survey of Agreement Rate between Simple MTC and Post Contrast T1 Sequence MRI for Diagnosing Active Multiple Sclerosis Plaques

    Directory of Open Access Journals (Sweden)

    N. Farshchian

    2016-07-01

    Full Text Available Introduction & Objective: MS is the most common disabling neurological disorder. Identifying new active MS plaques at the onset and clinical status and faster onset of treatment as well as evaluating the response to treatment is important and MRI with contrast is the best indicator for these measures. Materials & Methods: This study was cross-sectional including 62 patients with diagnosed MS. Whose clinical symptoms suggested the recurrence of MS. They were referred to the radiol-ogy department to undergo brain MRI with injection for the diagnosis of active plaques by a neurologist,The Data were analyzed using statistical tests and SPSS 21 software. Results: Based on the sequences of post contrast T1, pre contrast MTC and post contrast MTC 74, 272 and 271 plaques were respectively discovered. Detection of active MS plaques on T1 sequences after injection were in poor accordance and had significant difference with MTC before and after injection. Moreover, detection of active MS plaques on MTC sequences be-fore injection were in good accordance and did not show significant difference with MTC se-quences after injection. Conclusion: Based on these results, it seems that the purpose of MRI in MS patients is deter-mining the amount of active plaques. Sequences of pre contrast and post contrast MTC are significantly more than sequences of post contrast T1. Therefore, using sequences of MTC can be helpful in MRI. (Sci J Hamadan Univ Med Sci 2016; 23 (2:97-102

  17. THE EVOLUTION OF DUSTY STAR FORMATION IN GALAXY CLUSTERS TO z = 1: SPITZER INFRARED OBSERVATIONS OF THE FIRST RED-SEQUENCE CLUSTER SURVEY

    Energy Technology Data Exchange (ETDEWEB)

    Webb, T. M. A.; O' Donnell, D.; Coppin, Kristen; Faloon, Ashley; Geach, James E.; Noble, Allison [McGill University, 3600 rue University, Montreal, QC, H3A 2T8 (Canada); Yee, H. K. C. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George St., Toronto, ON, M5S 3H4 (Canada); Gilbank, David [South African Astronomical Observatory, P.O. Box 9, Observatory, 7935 (South Africa); Ellingson, Erica [Department of Astrophysical and Planetary Sciences, University of Colorado at Boulder, Boulder, CO 80309 (United States); Gladders, Mike [Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Ave., Chicago, IL 60637 (United States); Muzzin, Adam [Leiden Observatory, University of Leiden, Niels Bohrweg 2, NL-2333 CA, Leiden (Netherlands); Wilson, Gillian [Department of Physics and Astronomy, University of California at Riverside, 900 University Avenue, Riverside, CA 92521 (United States); Yan, Renbin [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Place, New York, NY 10003 (United States)

    2013-10-01

    We present the results of an infrared (IR) study of high-redshift galaxy clusters with the MIPS camera on board the Spitzer Space Telescope. We have assembled a sample of 42 clusters from the Red-Sequence Cluster Survey-1 over the redshift range 0.3 < z < 1.0 and spanning an approximate range in mass of 10{sup 14-15} M {sub ☉}. We statistically measure the number of IR-luminous galaxies in clusters above a fixed inferred IR luminosity of 2 × 10{sup 11} M {sub ☉}, assuming a star forming galaxy template, per unit cluster mass and find it increases to higher redshift. Fitting a simple power-law we measure evolution of (1 + z){sup 5.1±1.9} over the range 0.3 < z < 1.0. These results are tied to the adoption of a single star forming galaxy template; the presence of active galactic nuclei, and an evolution in their relative contribution to the mid-IR galaxy emission, will alter the overall number counts per cluster and their rate of evolution. Under the star formation assumption we infer the approximate total star formation rate per unit cluster mass (ΣSFR/M {sub cluster}). The evolution is similar, with ΣSFR/M {sub cluster} ∼ (1 + z){sup 5.4±1.9}. We show that this can be accounted for by the evolution of the IR-bright field population over the same redshift range; that is, the evolution can be attributed entirely to the change in the in-falling field galaxy population. We show that the ΣSFR/M {sub cluster} (binned over all redshift) decreases with increasing cluster mass with a slope (ΣSFR/M{sub cluster}∼M{sub cluster}{sup -1.5±0.4}) consistent with the dependence of the stellar-to-total mass per unit cluster mass seen locally. The inferred star formation seen here could produce ∼5%-10% of the total stellar mass in massive clusters at z = 0, but we cannot constrain the descendant population, nor how rapidly the star-formation must shut-down once the galaxies have entered the cluster environment. Finally, we show a clear decrease in the number of IR

  18. Deep Sea Coral voucher sequence dataset - Identification of deep-sea corals collected during the 2009 - 2014 West Coast Groundfish Bottom Trawl Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data for this project resides in the West Coast Groundfish Bottom Trawl Survey Database. Deep-sea corals are often components of trawling bycatch, though their...

  19. Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

    Science.gov (United States)

    Ostria-Hernández, Martha Lorena; Sánchez-Vallejo, Carlos Javier; Ibarra, J Antonio; Castro-Escarpulli, Graciela

    2015-08-04

    In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes. The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in

  20. A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

    Science.gov (United States)

    Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

    1995-01-01

    In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

  1. Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins

    OpenAIRE

    Gutiérrez Acosta, Olga B; Schleheck, David; Schink, Bernhard

    2014-01-01

    Background The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. Results In this study, a draft genome sequence of D. biacutus ...

  2. Off-platform Silurian sequences in the Ambler River quadrangle: A section in Geologic studies in Alaska by the U.S. Geological Survey during 1987

    Science.gov (United States)

    Dumoulin, Julie A.; Harris, Anita G.

    1988-01-01

    Lithofacies changes in coeval upper Paleozoic rocks have been used to unravel the tectonic history of northern Alaska (for example, Mayfield and others, 1983). Conodont biostratigraphy and detailed petrologic studies are now revealing facies differences in lower Paleozoic rocks that can also be used to constrain their tectono-sedimentary framework (Dumoulin and Harris, 1987). A basic element of basin analysis is the discrimination of shallow-water shelf and platform sequences from deeper water slope and basinal deposits. This report documents several new localities of deeper water, off-platform Silurian deposits in the Ambler River quadrangle and briefly outlines some of their paleogeographic implications.

  3. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  4. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  5. Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins.

    Science.gov (United States)

    Gutiérrez Acosta, Olga B; Schleheck, David; Schink, Bernhard

    2014-07-11

    The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions. In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B12- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone. We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation.

  6. Field investigation with regard to the impermeability of clay formations. Helium-4 soil gas surveys in sedimentary basins as a tentative study of secondary permeability in clayey sequences

    International Nuclear Information System (INIS)

    Lombardi, S.; Benvegnu, F.; Brondi, A.; Polizzano, C.

    1993-01-01

    This report deals with a tentative study for the detection of the secondary permeability in clayey formations conducted in several sedimentary basins in Central Italy, by means of geochemical methods. The main purposes are: to try a geochemical method, based on the distribution of deep origin gases in soil gas ( 4 He and 222 Rn), to detect buried fault systems and to study the permeability of clay as a potential migration pathway for nuclides of radioactive waste deposits; to verify the effectiveness of this method for the selection of suitable sites for radwaste disposal. This research programme consists in a collaboration between ENEA and the University of Rome within the communitarian programme for the disposal of high level and long-live radwaste. Investigations concerned sedimentary basins filled by sand-clay formations 1000-2000 meters thick and characterized by different tectonic: Era and Chiani-Paglia Valleys (Tuscany and North Latium), structural trenches due to extensive tectonics along the tyrrhenian edge, and Vasto region, a basin in the 'Adriatic foretrench', characterized by compressive tectonics. The investigated areas are near or directly correspond to geothermal fields or to hydrocarbon reservoirs supplying gases which may migrate upward along fractures. Almost 4000 soil gas samples were collected in the three surveyed areas; the sampling density was of about 1.5 points / km 2 , normally used in the regional scale surveys. The obtained results show that the observed helium anomalies are distributed or elongated according to the main tectonic features of the substratum (fault systems, fractures, deep structures); the magnitude of anomalies seems to correlate with the nature of the deep gas reservoir (i.e. oil in Vasto), geothermal reservoir in the Paglia valley. These observations seem to confirm that the presence of deep origin gases in soils is controlled by tectonics. Clay thickness does not significantly control the uprising of deep gases: in

  7. A CENSUS OF ROTATION AND VARIABILITY IN L1495: A UNIFORM ANALYSIS OF TRANS-ATLANTIC EXOPLANET SURVEY LIGHT CURVES FOR PRE-MAIN-SEQUENCE STARS IN TAURUS

    International Nuclear Information System (INIS)

    Xiao Hongyu; Covey, Kevin R.; Lloyd, James P.; Rebull, Luisa; Charbonneau, David; Mandushev, Georgi; O'Donovan, Francis; Slesnick, Catherine

    2012-01-01

    We analyze light curves obtained by the Trans-atlantic Exoplanet Survey (TrES) for a field centered on the L1495 dark cloud in Taurus. The Spitzer Taurus Legacy Survey catalog identifies 179 bona fide Taurus members within the TrES field; 48 of the known Taurus members are detected by TrES, as well as 26 candidate members identified by the Spitzer Legacy team. We quantify the variability of each star in our sample using the ratio of the standard deviation of the original light curve (σ orig. ) to the standard deviation of a light curve that has been smoothed by 9 or 1001 epochs (σ 9 and σ 1001 , respectively). Known Taurus members typically demonstrate (σ orig. /σ 9 ) orig. /σ 1001 ) orig. /σ 9 ) ∼ 3.0 and (σ orig. /σ 1001 ) ∼ 10, as expected for light curves dominated by unstructured white noise. Of the 74 Taurus members/candidates with TrES light curves, we detect significant variability in 49 sources. Adapting a quantitative metric originally developed to assess the reliability of transit detections, we measure the amount of red and white noise in each light curve and identify 18 known or candidate Taurus members with highly significant period measurements. These appear to be the first periods measured for four of these sources (HD 282276, CX Tau, FP Tau, TrES J042423+265008), and in two other cases, the first non-aliased periods (LkCa 21 and DK Tau AB). For the remainder, the TrES measurements typically agree very well (δP < 1%) with previously reported values. Including periods measured at lower confidence for 15 additional sources, we report periods for 11 objects where no previous periods were found, including 8 confirmed Taurus members. We also identify 10 of the 26 candidate Taurus members that demonstrate variability levels consistent with being bona fide T Tauri stars. A Kolomgorov-Smirnov (K-S) test confirms that these new periods confirm the distinction between the rotation period distributions of stars with and without circumstellar

  8. A deep x-ray survey of the Pleiades cluster and the B6-A3 main sequence stars in Orion

    Science.gov (United States)

    Caillault, Jean-Pierre

    1993-01-01

    We have obtained deep ROSAT images of three regions within the Pleiades open cluster. We have detected 317 X-ray sources in these ROSAT PSPC images, 171 of which we associate with certain probable members of the Pleiades cluster. We detect nearly all Pleiades members with spectral types later than G0 and within 25 arcminutes of our three field centers where our sensitivity is highest. This has allowed us to derive for the first time the luminosity function for the G, K, and M dwarfs of an open cluster without the need to use statistical techniques to account for the presence of upper limits in the data sample. Because of our high X-ray detection frequency down to the faint limit of the optical catalog, we suspect that some of our unidentified X-ray sources are previously unknown, very low-mass members of the Pleiades. A large fraction of the Pleiades members detected with ROSAT have published rotational velocities. Plots of L(sub x)/L(sub bol) versus spectroscopic rotational velocity show tightly correlated 'saturation' type relations for stars with (B - V)(sub O) greater than 0.60. For each of several color ranges, X-ray luminosities rise rapidly with increasing rotation rate until v sin i approximately equals 15 km/s, and then remain essentially flat for rotation rates up to at least v sin i approximately equal to 100 km/s. The dispersion in rotation among low-mass stars in the Pleiades is by far the dominant contributor to the dispersion in L(subx) at a given mass. Only about 35 percent of the B.A. and early F stars in the Pleiades are detected as X-ray sources in our survey. There is no correlation between X-ray flux and rotation for these stars. The X-ray luminosity function for the early-type Pleiades stars appears to be bimodal, with only a few exceptions. We either detect these stars at fluxes in the range found for low-mass stars or we derive X-ray limits below the level found for most Pleiades dwarfs. The X-ray spectra for the early-type Pleiades stars

  9. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    The objective of this research was to identify novel miRNAs in the mammary gland ofdairy goats with a bioinformatics approach that was based on expressed sequence tag (EST) and genome survey sequence (GSS) analyses. We applied all known major mammals, miRNAs to search against the goat EST and GSS ...

  10. Surveying Future Surveys

    Science.gov (United States)

    Carlstrom, John E.

    2016-06-01

    The now standard model of cosmology has been tested and refined by the analysis of increasingly sensitive, large astronomical surveys, especially with statistically significant millimeter-wave surveys of the cosmic microwave background and optical surveys of the distribution of galaxies. This talk will offer a glimpse of the future, which promises an acceleration of this trend with cosmological information coming from new surveys across the electromagnetic spectrum as well as particles and even gravitational waves.

  11. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  12. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  13. False memories and some scales : GSS, CIS, and DES

    OpenAIRE

    仲, 真紀子

    1998-01-01

    記憶が変容し, 再構成されるものであることは古くから指摘されている(Bartlett, 1932; Loftus, 1982; Neisser, 1988; Spiro, 1980)。だがこのような指摘は実際にあった出来事が幾分なりとも記銘され, 保持されていることを前提としている。これに対し近年では, 実際に体験しなかったことまでもが「記憶」として植えつけられ, 「想起」され得ることが問題とされるようになった(Ceci, 1995; Ceci, Leichtman & Gordon, 1995; Loftus, 1997; Loftus, Coan & Pickrell, 1996; Loftus, Feldman & Dashiell, 1995; Loftus, 1994; 高橋, 1997)。例えばCeciらは幼児に, 幼稚園を訪問したサム・ストーンという人物について, 実際にはなかったことの「記憶」を植えつけている。彼らはサムの訪問に先がけ, 幼児にバイアスのかかった情報を与え, またサム訪問後, 繰り返しバイアスのかかった質問を行うことで, サムが本を破いたり, 熊の...

  14. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  17. STRUCTURE AND POPULATION OF THE ANDROMEDA STELLAR HALO FROM A SUBARU/SUPRIME-CAM SURVEY

    International Nuclear Information System (INIS)

    Tanaka, Mikito; Chiba, Masashi; Komiyama, Yutaka; Iye, Masanori; Guhathakurta, Puragra; Kalirai, Jason S.

    2010-01-01

    We present a photometric survey of the stellar halo of the nearest giant spiral galaxy, Andromeda (M31), using Suprime-Cam on the Subaru Telescope. A detailed analysis of VI color-magnitude diagrams of the resolved stellar population is used to measure properties such as line-of-sight distance, surface brightness, metallicity, and age. These are used to isolate and characterize different components of the M31 halo: (1) the giant southern stream (GSS); (2) several other substructures; and (3) the smooth halo. First, the GSS is characterized by a broad red giant branch (RGB) and a metal-rich/intermediate-age red clump (RC). The I magnitude of the well-defined tip of the RGB suggests that the distance to the observed GSS field is (m - M) 0 = 24.73 ± 0.11 (883 ± 45 kpc) at a projected radius of R ∼ 30 kpc from M31's center. The GSS shows a high metallicity peaked at [Fe/H]∼>-0.5 with a mean (median) of -0.7 (-0.6), estimated via comparison with theoretical isochrones. Combined with the luminosity of the RC, we estimate the mean age of its stellar population to be ∼8 Gyr. The mass of its progenitor galaxy is likely in the range of 10 7 -10 9 M sun . Second, we study M31's halo substructure along the northwest/southeast minor axis out to R ∼ 100 kpc and the southwest major-axis region at R ∼ 60 kpc. We confirm two substructures in the southeast halo reported by Ibata et al. and discover two overdense substructures in the northwest halo. We investigate the properties of these four substructures as well as other structures including the western shelf and find that differences in stellar populations among these systems, thereby suggesting each has a different origin. Our statistical analysis implies that the M31 halo as a whole may contain at least 16 substructures, each with a different origin, so its outer halo has experienced at least this many accretion events involving dwarf satellites with mass 10 7 -10 9 M sun since a redshift of z ∼ 1. Third, we

  18. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  19. Gene Discovery through Genomic Sequencing of Brucella abortus

    OpenAIRE

    Sánchez, Daniel O.; Zandomeni, Ruben O.; Cravero, Silvio; Verdún, Ramiro E.; Pierrou, Ester; Faccio, Paula; Diaz, Gabriela; Lanzavecchia, Silvia; Agüero, Fernán; Frasch, Alberto C. C.; Andersson, Siv G. E.; Rossetti, Osvaldo L.; Grau, Oscar; Ugalde, Rodolfo A.

    2001-01-01

    Brucella abortus is the etiological agent of brucellosis, a disease that affects bovines and human. We generated DNA random sequences from the genome of B. abortus strain 2308 in order to characterize molecular targets that might be useful for developing immunological or chemotherapeutic strategies against this pathogen. The partial sequencing of 1,899 clones allowed the identification of 1,199 genomic sequence surveys (GSSs) with high homology (BLAST expect value < 10−5) to sequences deposit...

  20. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  3. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  5. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    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.

  6. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  7. Comparative Study of Complex Survey Estimation Software in ONS

    Directory of Open Access Journals (Sweden)

    Andy Fallows

    2015-09-01

    Full Text Available Many official statistics across the UK Government Statistical Service (GSS are produced using data collected from sample surveys. These survey data are used to estimate population statistics through weighting and calibration techniques. For surveys with complex or unusual sample designs, the weighting can be fairly complicated. Even in more simple cases, appropriate software is required to implement survey weighting and estimation. As with other stages of the survey process, it is preferable to use a standard, generic calibration tool wherever possible. Standard tools allow for efficient use of resources and assist with the harmonisation of methods. In the case of calibration, the Office for National Statistics (ONS has experience of using the Statistics Canada Generalized Estimation System (GES across a range of business and social surveys. GES is a SAS-based system and so is only available in conjunction with an appropriate SAS licence. Given recent initiatives and encouragement to investigate open source solutions across government, it is appropriate to determine whether there are any open source calibration tools available that can provide the same service as GES. This study compares the use of GES with the calibration tool ‘R evolved Generalized software for sampling estimates and errors in surveys’ (ReGenesees available in R, an open source statistical programming language which is beginning to be used in many statistical offices. ReGenesees is a free R package which has been developed by the Italian statistics office (Istat and includes functionality to calibrate survey estimates using similar techniques to GES. This report describes analysis of the performance of ReGenesees in comparison to GES to calibrate a representative selection of ONS surveys. Section 1.1 provides a brief introduction to the current use of SAS and R in ONS. Section 2 describes GES and ReGenesees in more detail. Sections 3.1 and 3.2 consider methods for

  8. Microbial survey of ready-to-eat salad ingredients sold at retail reveals the occurrence and the persistence of Listeria monocytogenes Sequence Types 2 and 87 in pre-packed smoked salmon.

    Science.gov (United States)

    Chau, Man Ling; Aung, Kyaw Thu; Hapuarachchi, Hapuarachchige Chanditha; Lee, Pei Sze Valarie; Lim, Pei Ying; Kang, Joanne Su Lin; Ng, Youming; Yap, Hooi Ming; Yuk, Hyun-Gyun; Gutiérrez, Ramona Alikiiteaga; Ng, Lee Ching

    2017-02-28

    As the preparation of salads involves extensive handling and the use of uncooked ingredients, they are particularly vulnerable to microbial contamination. This study aimed to determine the microbial safety and quality of pre-packed salads and salad bar ingredients sold in Singapore, so as to identify public health risks that could arise from consuming salads and to determine areas for improvement in the management of food safety. The most frequently encountered organism in pre-packed salad samples was B. cereus, particularly in pasta salads (33.3%, 10/30). The most commonly detected organism in salad bar ingredients was L. monocytogenes, in particular seafood ingredients (44.1%, 15/34), largely due to contaminated smoked salmon. Further investigation showed that 21.6% (37/171) of the pre-packed smoked salmon sold in supermarkets contained L. monocytogenes. Significantly higher prevalence of L. monocytogenes and higher Standard Plate Count were detected in smoked salmon at salad bars compared to pre-packed smoked salmon in supermarkets, which suggested multiplication of the organism as the products move down the supply chain. Further molecular analysis revealed that L. monocytogenes Sequence Type (ST) 2 and ST87 were present in a particular brand of pre-packed salmon products over a 4-year period, implying a potential persistent contamination problem at the manufacturing level. Our findings highlighted a need to improve manufacturing and retail hygiene processes as well as to educate vulnerable populations to avoid consuming food prone to L. monocytogenes contamination.

  9. Nursing Student Perceptions Regarding Simulation Experience Sequencing.

    Science.gov (United States)

    Woda, Aimee A; Gruenke, Theresa; Alt-Gehrman, Penny; Hansen, Jamie

    2016-09-01

    The use of simulated learning experiences (SLEs) have increased within nursing curricula with positive learning outcomes for nursing students. The purpose of this study is to explore nursing students' perceptions of their clinical decision making (CDM) related to the block sequencing of different patient care experiences, SLEs versus hospital-based learning experiences (HLEs). A qualitative descriptive design used open-ended survey questions to generate information about the block sequencing of SLEs and its impact on nursing students' perceived CDM. Three themes emerged from the data: Preexperience Anxiety, Real-Time Decision Making, and Increased Patient Care Experiences. Nursing students identified that having SLEs prior to HLEs provided several benefits. Even when students preferred SLEs prior to HLEs, the sequence did not impact their CDM. This suggests that alternating block sequencing can be used without impacting the students' perceptions of their ability to make decisions. [J Nurs Educ. 2016;55(9):528-532.]. Copyright 2016, SLACK Incorporated.

  10. "Suntelligence" Survey

    Science.gov (United States)

    ... to the American Academy of Dermatology's "Suntelligence" sun-smart survey. Please answer the following questions to measure ... be able to view a ranking of major cities suntelligence based on residents' responses to this survey. ...

  11. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    Directory of Open Access Journals (Sweden)

    Jia Yi Har

    2015-09-01

    Full Text Available We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e. Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P, polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins. We hypothesize that such activities may mediate acclimation and persistence of bacteria in N. vectensis.

  12. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.

    Science.gov (United States)

    Har, Jia Y; Helbig, Tim; Lim, Ju H; Fernando, Samodha C; Reitzel, Adam M; Penn, Kevin; Thompson, Janelle R

    2015-01-01

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and

  13. Sequences for Student Investigation

    Science.gov (United States)

    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…

  14. Sequence History Update Tool

    Science.gov (United States)

    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.

  15. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    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.

  16. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  17. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  18. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  19. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  20. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  1. Survey research.

    Science.gov (United States)

    Alderman, Amy K; Salem, Barbara

    2010-10-01

    Survey research is a unique methodology that can provide insight into individuals' perspectives and experiences and can be collected on a large population-based sample. Specifically, in plastic surgery, survey research can provide patients and providers with accurate and reproducible information to assist with medical decision-making. When using survey methods in research, researchers should develop a conceptual model that explains the relationships of the independent and dependent variables. The items of the survey are of primary importance. Collected data are only useful if they accurately measure the concepts of interest. In addition, administration of the survey must follow basic principles to ensure an adequate response rate and representation of the intended target sample. In this article, the authors review some general concepts important for successful survey research and discuss the many advantages this methodology has for obtaining limitless amounts of valuable information.

  2. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  3. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    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.

  4. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  5. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. Surveys & Programs

    Science.gov (United States)

    Employment and Payroll Survey of Business Owners Work from Home Our statistics highlight trends in household statistics from multiple surveys. Data Tools & Apps Main American FactFinder Census Business Builder My residential construction. Business Dynamics Statistics (BDS) Provides measures of openings and closings, job

  7. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  8. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  9. Engineering surveying

    CERN Document Server

    Schofield, W

    2001-01-01

    The aim of Engineering Surveying has always been to impart and develop a clear understanding of the basic topics of the subject. The author has fully revised the book to make it the most up-to-date and relevant textbook available on the subject.The book also contains the latest information on trigonometric levelling, total stations and one-person measuring systems. A new chapter on satellites ensures a firm grasp of this vitally important topic.The text covers engineering surveying modules for civil engineering students on degree courses and forms a reference for the engineering surveying module in land surveying courses. It will also prove to be a valuable reference for practitioners.* Simple clear introduction to surveying for engineers* Explains key techniques and methods* Details reading systems and satellite position fixing

  10. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  11. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  12. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  13. Predictors of positive mental health among refugees: Results from Canada's General Social Survey.

    Science.gov (United States)

    Beiser, Morton; Hou, Feng

    2017-01-01

    Do refugees have lower levels of positive mental health than other migrants? If so, to what extent is this attributable to post-migration experiences, including discrimination? How does gender affect the relationships between post-migration experience and positive mental health? To address these questions, the current study uses data from Statistics Canada's 2013 General Social Survey (GSS), a nationally representative household study that included 27,695 Canadians 15 years of age and older. The study compares self-reported positive mental health among 651 refugees, 309 economic immigrants, and 448 family class immigrants from 50 source countries. Immigration-related predictors of mental health were examined including sociodemographic characteristics, discrimination, acculturation variables, and experiences of reception. Separate analyses were carried out for women and men. Refugees had lower levels of positive mental health than other migrants. Affiliative feelings towards the source country jeopardized refugee, but not immigrant mental health. A sense of belonging to Canada was a significant predictor of mental health. Perceived discrimination explained refugee mental health disadvantage among men, but not women. Bridging social networks were a mental health asset, particularly for women. The implications of anti-refugee discrimination net of the effects of anti-immigrant and anti-visible minority antipathies are discussed, as well as possible reasons for gender differences in the salience of mental health predictors.

  14. Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Nutrition and Agriculture.

    Science.gov (United States)

    Next-generation sequencing technologies are able to produce high-throughput short sequence reads in a cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also changed the landscape of life sciences. Here I survey their major applications ranging...

  15. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

    Full Text Available Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides 16S rRNA gene fragment data with natural immunity against the biases raised during priming and thus the potential of uncovering the true structure of microbial community by giving more accurate predictions of operational taxonomic units (OTUs. Nonetheless, the lack of statistically rigorous comparison between 16S rRNA gene fragments and other data types makes it difficult to interpret previously reported results using 16S rRNA gene fragments. Therefore, in the present work, we established a standard analysis pipeline that would help confirm if the differences in the data are true or are just due to potential technical bias. This pipeline is built by using simulated data to find optimal mapping and OTU prediction methods. The comparison between simulated datasets revealed a relationship between 16S rRNA gene fragments and full-length 16S rRNA sequences that a 16S rRNA gene fragment having a length >150 bp provides the same accuracy as a full-length 16S rRNA sequence using our proposed pipeline, which could serve as a good starting point for experimental design and making the comparison between 16S rRNA gene fragment-based and targeted 16S rRNA sequencing-based surveys possible.

  16. Survey Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Cleaned and QCd data for the Fishing Effort Survey. Questions on fishing and other out are asked on weather and outdoor activity, including fishing trips. Used for...

  17. Surveying Humaness

    DEFF Research Database (Denmark)

    Markussen, Randi; Gad, Christopher

    carried out in a Danish county in order to improve treatment of people who have suffered from long-term illnesses. The surveys concern not only feed back on how people experience their present and past interaction with the social services and health care system; they also ask people to indicate the state......Christopher Gad. Ph.d. Dept. of Information and Media Studies Randi Markussen. Associate Professor, Dept. of Information and Media Studies. rmark@imv.au.dk   Abstract:   Surveying humanness -politics of care improvement   For various reasons we both were subjected to a specific survey procedure...... and development of a large collection of biological and psychological symptoms and psycho-social problems. However, the surveys say nothing about how the information will be of use to the people who answer the procedure or how this scientific intervention will be put to use more specifically within the public...

  18. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  19. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  20. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  1. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  2. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  3. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  4. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  5. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  6. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  7. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  8. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    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.

  9. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    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.

  10. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  11. Engineering surveying

    CERN Document Server

    Schofield, W

    2007-01-01

    Engineering surveying involves determining the position of natural and man-made features on or beneath the Earth's surface and utilizing these features in the planning, design and construction of works. It is a critical part of any engineering project. Without an accurate understanding of the size, shape and nature of the site the project risks expensive and time-consuming errors or even catastrophic failure.Engineering Surveying 6th edition covers all the basic principles and practice of this complex subject and the authors bring expertise and clarity. Previous editions of this classic text have given readers a clear understanding of fundamentals such as vertical control, distance, angles and position right through to the most modern technologies, and this fully updated edition continues that tradition.This sixth edition includes:* An introduction to geodesy to facilitate greater understanding of satellite systems* A fully updated chapter on GPS, GLONASS and GALILEO for satellite positioning in surveying* Al...

  12. Surveying Education

    DEFF Research Database (Denmark)

    Enemark, Stig

    2009-01-01

    In relation to surveying education there is one big question to be asked: Is the role of the surveyors changing? In a global perspective the answer will be "Yes". There is a big swing that could be entitled "From Measurement to Management". This does not imply that measurement is no longer....... In surveying education there are a range of other challenges to be faced. These relate to the focus on learning to learn; the need for flexible curriculum to deal with constant change; the move towards introducing virtual academy; the demand for creating a quality culture; and the perspective of lifelong...... on an efficient interaction between education, research, and professional practice....

  13. Environmental surveys

    International Nuclear Information System (INIS)

    Costa-Ribeiro, C.

    1977-01-01

    An environmental survey conducted in high natural radioactivity areas and methods used to evaluated radiation doses received by the population are presented. It is shown doses absorved due to ingestion of radioactively contaminated food and water. Exposure to external gamma radiation fields or inhalation of abnormal quantities of natural airborne radioactivity are discussed [pt

  14. Survey < > Creation

    DEFF Research Database (Denmark)

    2017-01-01

    The project, Survey Creation suggests that point cloud models from 3D scans of an existing space can be the source for explorative drawings. By probing into the procedure of 3D laser scanning, it became possible to make use of the available point clouds to both access geometric representation......) and the creation drawing (of the anticipated)....

  15. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  16. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  17. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  18. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  19. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  20. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    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 direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore 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.

  1. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  2. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  3. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  4. Readership survey

    International Nuclear Information System (INIS)

    Anon.

    1984-01-01

    The article reviews the last readership survey, which helped to check readers' reactions and the level and style of the journal. The majority of readers (32 per cent), not surprisingly, work in high energy physics. In fact, if the estimate of the world high energy physics population as some 5000 people is correct, CERN Courier reaches every one of them. The next large category of readers is the teaching profession (21 percent), with industrialists (12 per cent) in third place

  5. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  6. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  7. Total Survey Error for Longitudinal Surveys

    NARCIS (Netherlands)

    Lynn, Peter; Lugtig, P.J.

    2016-01-01

    This article describes the application of the total survey error paradigm to longitudinal surveys. Several aspects of survey error, and of the interactions between different types of error, are distinct in the longitudinal survey context. Furthermore, error trade-off decisions in survey design and

  8. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  9. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  10. Multiple Surveys of Students and Survey Fatigue

    Science.gov (United States)

    Porter, Stephen R.; Whitcomb, Michael E.; Weitzer, William H.

    2004-01-01

    This chapter reviews the literature on survey fatigue and summarizes a research project that indicates that administering multiple surveys in one academic year can significantly suppress response rates in later surveys. (Contains 4 tables.)

  11. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  12. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  13. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract 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 fin...

  14. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  15. Reader survey

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1993-10-15

    Many, thanks to the hundreds of people who took the time to reply to the CERN Courier readership survey questionnaire published in our May issue. Bringing out a monthly journal is a lonely business. Issue after issue goes out, and the only response is when there's an occasional factual error. Send out a readership survey and a faint echo comes back. Most striking was the sheer enthusiasm of the replies. Despite the current erosion of support in the US (see page 2), subatomic physics has significant world-wide box-office appeal. Most important was to find out who our readers are. 61% of the replies came from Europe, 21% from the USA, 14% from elsewhere, (including the former Soviet Union), and 4% from inside CERN. Not surprisingly, the main audience (37%) is in the high energy physics sector. Then comes teaching (31%), followed closely by accelerators operations and design (12%) and industry (11%). Apart from detailed breakdowns of readership and feedback on the journal's content and style, the replies revealed several major features. Firstly, the CERN Courier is widely read and appreciated. There are a lot of people outside the immediate research field who want to keep broadly up to date with the latest developments in high energy physics and related fields, without getting too involved in details. It was gratifying to receive replies from far-flung places (Nepal, Indonesia,....), and learn how much distant readers appreciate getting such regular information. 'It helps us feel part of the world scene,' was a typical such reply, from Australia. Despite jet airplanes, fax and electronic mail, our planet is still big.

  16. Reader survey

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Many, thanks to the hundreds of people who took the time to reply to the CERN Courier readership survey questionnaire published in our May issue. Bringing out a monthly journal is a lonely business. Issue after issue goes out, and the only response is when there's an occasional factual error. Send out a readership survey and a faint echo comes back. Most striking was the sheer enthusiasm of the replies. Despite the current erosion of support in the US (see page 2), subatomic physics has significant world-wide box-office appeal. Most important was to find out who our readers are. 61% of the replies came from Europe, 21% from the USA, 14% from elsewhere, (including the former Soviet Union), and 4% from inside CERN. Not surprisingly, the main audience (37%) is in the high energy physics sector. Then comes teaching (31%), followed closely by accelerators operations and design (12%) and industry (11%). Apart from detailed breakdowns of readership and feedback on the journal's content and style, the replies revealed several major features. Firstly, the CERN Courier is widely read and appreciated. There are a lot of people outside the immediate research field who want to keep broadly up to date with the latest developments in high energy physics and related fields, without getting too involved in details. It was gratifying to receive replies from far-flung places (Nepal, Indonesia,....), and learn how much distant readers appreciate getting such regular information. 'It helps us feel part of the world scene,' was a typical such reply, from Australia. Despite jet airplanes, fax and electronic mail, our planet is still big

  17. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  18. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  19. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  20. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  1. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  2. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  3. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  4. The ISOGAL survey

    Science.gov (United States)

    Omont, A.; ISOGAL Collaboration

    1999-03-01

    ISOGAL is a 7-15 μm ISOCAM survey, with 6'' pixels and sensitivity below 10 mJy, of ~20 deg2, in the galactic plane mostly interior to |l| = 30o. In combination with KJI DENIS data, the ISO images allow detailed studies of cold stellar populations and galactic structures in regions highly obscured throughout the inner Galaxy, with a sensitivity and pixel surface two orders of magnitude better than IRAS. Data reduction is particularly difficult because of the high density of strong sources, of memory effects and of short integration times. However, an improved data reduction is almost complete for all the fields observed, with the use of CIA ISOCAM software and of a special source extraction. The data quality is acceptable, as concerns reliability, completeness and photometric accuracy of the sources, to allow a systematic scientific analysis. A few fields, in the bulge and in the galactic disk, exemplify the results expected from the ~200 fields observed. These results include: A complete census of mass-losing AGB stars in fields of the inner bulge. Even very weak mass-loss are very well characterised, down to the RGB tip. Such stars are by far the most numerous there. They form a very well defined sequence in ISOGAL-DENIS infrared colour-magnitude diagrams. The knowledge of Long Period Variables in two Baade's Window fields confirm that their luminosity is just above the tip of this sequence, and that the spectral type of the stars of the sequence is M6-9III. The same AGB sequence is also quite visible in 7-15 μm colour-magnitude diagrams in the galactic disk, even with a very large extinction. Such AGB stars are thus particularly numerous among the ~105 sources detected by ISOGAL. However, foreground red giants and dusty young stars are also quite numerous. The latter with a few solar masses are detectable through the galactic centre distance. A number of bright young stars are identified on lines of sight close to the Galactic Centre, The combination of ISOGAL

  5. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  6. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  7. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  9. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  10. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  11. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  12. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art 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. Accelerator and transport line survey and alignment

    International Nuclear Information System (INIS)

    Ruland, R.E.

    1991-10-01

    This paper summarizes the survey and alignment processes of accelerators and transport lines and discusses the propagation of errors associated with these processes. The major geodetic principles governing the survey and alignment measurement space are introduced and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step sequence from initial absolute alignment to final smoothing. Emphasis is given to the relative alignment of components, in particular to the importance of incorporating methods to remove residual systematic effects in surveying and alignment operations. Various approaches to smoothing used at major laboratories are discussed. 47 refs., 19 figs., 1 tab

  14. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  15. Literature survey

    International Nuclear Information System (INIS)

    Drury, J.S.; Michelson, D.; Ensminger, J.T.

    1982-01-01

    Literature was searched for methods of removing uranium from drinking water. No relevant papers were found, but approximately 1000 publications were identified in a less specific search for methods of removing uranium from water. Most of the latter publications dealt with the recovery of uranium from ores, industrial and analytical chemistry solutions, or seawater. The conditions under which these studies were performed were usually quite different from those normally occurring in municipal water treatment practice, but some potentially interesting systems of recovery were identified. A few papers addressed the problem of removing uranium from natural fresh waters and established the effectiveness of using adsorbents or coprecipitants, such as aluminum hydroxide, ferric hydroxide, activated carbon, and ion exchangers, under certain conditions. Also, many US manufacturers and users of water treatment equipment and products were contacted regarding recommended methods of removing uranium from potable water. Based on the results of these surveys, it is recommended that untreated, partially treated, and finished water samples from municipal water treatment facilities be analyzed to determine their extent of removal of uranium by presently used procedures. In addition, laboratory studies are suggested to determine what changes, if any, are needed to maximize the effectiveness of treatments that are already in use in existing water treatment plants

  16. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  17. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  18. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  19. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  20. MX Siting Investigation Gravity Survey - Wah Wah Valley, Utah.

    Science.gov (United States)

    1981-05-15

    Bouguer Anomaly (see Section A1.4, Appendix A1.0). The Defense Mapping Agency Aerospace Center (DMAAC), St. Louis, Missouri, calculates outer zone...Utah .... 12 LIST OF DRAWINGS Drawing Number 1 Complete Bouguer Anomaly Contours In Pocket at 2 Deptn to Rock - Interpreted from End of Report...DMAHTC/GSS obtained the basic observations for the new stations and reduced them to Simple Bouguer Anomalies (SBA) as described in Appendix A1.0. Up to

  1. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  2. IRAS IDENTIFICATION OF PRE-MAIN-SEQUENCE STARS IN THE CHAMELEON-II ASSOCIATION

    NARCIS (Netherlands)

    PRUSTI, T; WHITTET, DCB; ASSENDORP, R; WESSELIUS, PR

    We report the results of a search for new pre-main sequence candidates in the Chamaeleon II dark cloud based on three IRAS catalogues (the Point Source Catalog, the Serendipitous Survey Catalog and the Faint Source Survey). A total of 30 sources were selected. Twelve of these display IRAS colours

  3. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  4. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  5. Perceived ambiguity as a barrier to intentions to learn genome sequencing results.

    Science.gov (United States)

    Taber, Jennifer M; Klein, William M P; Ferrer, Rebecca A; Han, Paul K J; Lewis, Katie L; Biesecker, Leslie G; Biesecker, Barbara B

    2015-10-01

    Many variants that could be returned from genome sequencing may be perceived as ambiguous-lacking reliability, credibility, or adequacy. Little is known about how perceived ambiguity influences thoughts about sequencing results. Participants (n = 494) in an NIH genome sequencing study completed a baseline survey before sequencing results were available. We examined how perceived ambiguity regarding sequencing results and individual differences in medical ambiguity aversion and tolerance for uncertainty were associated with cognitions and intentions concerning sequencing results. Perceiving sequencing results as more ambiguous was associated with less favorable cognitions about results and lower intentions to learn and share results. Among participants low in tolerance for uncertainty or optimism, greater perceived ambiguity was associated with lower intentions to learn results for non-medically actionable diseases; medical ambiguity aversion did not moderate any associations. Results are consistent with the phenomenon of "ambiguity aversion" and may influence whether people learn and communicate genomic information.

  6. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  7. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  8. A Literature Survey on Inverse Scattering for Electron Density Profile Determination. Volume II.

    Science.gov (United States)

    1981-09-24

    THE INVERSE SCATTERING PROBLEM4 FOR THE EQUAT ION Of ACOUSTIC$ AVILA, G.S.S. DEPT. DE MATEMATICA . INST. DE CIENCIAS EXATAS. UNIV. Of BRASILIA...of Colict support Portinari. Joao C. Departamento do Matematica . Pontificia Universidade Catolica do Rio de Janeiro, Rio do Janeiro. Brasil J. Math

  9. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  10. Transiting Exoplanet Survey Satellite (TESS)

    Science.gov (United States)

    Ricker, G. R.; Clampin, M.; Latham, D. W.; Seager, S.; Vanderspek, R. K.; Villasenor, J. S.; Winn, J. N.

    2012-01-01

    The Transiting Exoplanet Survey Satellite (TESS) will discover thousands of exoplanets in orbit around the brightest stars in the sky. In a two-year survey, TESS will monitor more than 500,000 stars for temporary drops in brightness caused by planetary transits. This first-ever spaceborne all-sky transit survey will identify planets ranging from Earth-sized to gas giants, around a wide range of stellar types and orbital distances. No ground-based survey can achieve this feat. A large fraction of TESS target stars will be 30-100 times brighter than those observed by Kepler satellite, and therefore TESS . planets will be far easier to characterize with follow-up observations. TESS will make it possible to study the masses, sizes, densities, orbits, and atmospheres of a large cohort of small planets, including a sample of rocky worlds in the habitable zones of their host stars. TESS will provide prime targets for observation with the James Webb Space Telescope (JWST), as well as other large ground-based and space-based telescopes of the future. TESS data will be released with minimal delay (no proprietary period), inviting immediate community-wide efforts to study the new planets. The TESS legacy will be a catalog of the very nearest and brightest main-sequence stars hosting transiting exoplanets, thus providing future observers with the most favorable targets for detailed investigations.

  11. Alumni Perspectives Survey, 2010. Survey Report

    Science.gov (United States)

    Sheikh, Sabeen

    2010-01-01

    During the months of April and September of 2009, the Graduate Management Admission Council[R] (GMAC[R]) conducted the Alumni Perspectives Survey, a longitudinal study of prior respondents to the Global Management Education Graduate Survey of management students nearing graduation. A total of 3,708 alumni responded to the April 2009 survey,…

  12. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  13. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  14. Lesotho - Enterprise Survey

    Data.gov (United States)

    Millennium Challenge Corporation — The 2011 MCA-Lesotho baseline enterprise survey is a national survey of enterprises. The main objective of the survey was to assess the current status of businesses...

  15. 2015 Community Survey Data

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — These are the answers to the 2015 Community Survey.A comprehensive summary of the survey results can be found here.The survey asked town members to address their...

  16. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available 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.

  17. Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, N O; Tok, J B; Tarasow, T M

    2008-02-08

    Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  18. Massively parallel interrogation of aptamer sequence, structure and function.

    Directory of Open Access Journals (Sweden)

    Nicholas O Fischer

    Full Text Available BACKGROUND: Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. METHODOLOGY/PRINCIPAL FINDINGS: High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and inter-chip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. CONCLUSION AND SIGNIFICANCE: The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  19. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  20. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  1. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  2. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  3. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  4. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  5. Matrix transformations and sequence spaces

    International Nuclear Information System (INIS)

    Nanda, S.

    1983-06-01

    In most cases the most general linear operator from one sequence space into another is actually given by an infinite matrix and therefore the theory of matrix transformations has always been of great interest in the study of sequence spaces. The study of general theory of matrix transformations was motivated by the special results in summability theory. This paper is a review article which gives almost all known results on matrix transformations. This also suggests a number of open problems for further study and will be very useful for research workers. (author)

  6. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  7. MMT hypervelocity star survey. III. The complete survey

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Warren R.; Geller, Margaret J.; Kenyon, Scott J., E-mail: wbrown@cfa.harvard.edu, E-mail: mgeller@cfa.harvard.edu, E-mail: skenyon@cfa.harvard.edu [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States)

    2014-05-20

    We describe our completed spectroscopic survey for unbound hypervelocity stars (HVSs) ejected from the Milky Way. Three new discoveries bring the total number of unbound late B-type stars to 21. We place new constraints on the nature of the stars and on their distances using moderate resolution MMT spectroscopy. Half of the stars are fast rotators; they are certain 2.5-4 M {sub ☉} main sequence stars at 50-120 kpc distances. Correcting for stellar lifetime, our survey implies that unbound 2.5-4 M {sub ☉} stars are ejected from the Milky Way at a rate of 1.5 × 10{sup –6} yr{sup –1}. These unbound HVSs are likely ejected continuously over the past 200 Myr and do not share a common flight time. The anisotropic spatial distribution of HVSs on the sky remains puzzling. Southern hemisphere surveys like SkyMapper will soon allow us to map the all-sky distribution of HVSs. Future proper motion measurements with Hubble Space Telescope and Gaia will provide strong constraints on origin. Existing observations are all consistent with HVS ejections from encounters with the massive black hole in the Galactic center.

  8. MMT hypervelocity star survey. III. The complete survey

    International Nuclear Information System (INIS)

    Brown, Warren R.; Geller, Margaret J.; Kenyon, Scott J.

    2014-01-01

    We describe our completed spectroscopic survey for unbound hypervelocity stars (HVSs) ejected from the Milky Way. Three new discoveries bring the total number of unbound late B-type stars to 21. We place new constraints on the nature of the stars and on their distances using moderate resolution MMT spectroscopy. Half of the stars are fast rotators; they are certain 2.5-4 M ☉ main sequence stars at 50-120 kpc distances. Correcting for stellar lifetime, our survey implies that unbound 2.5-4 M ☉ stars are ejected from the Milky Way at a rate of 1.5 × 10 –6 yr –1 . These unbound HVSs are likely ejected continuously over the past 200 Myr and do not share a common flight time. The anisotropic spatial distribution of HVSs on the sky remains puzzling. Southern hemisphere surveys like SkyMapper will soon allow us to map the all-sky distribution of HVSs. Future proper motion measurements with Hubble Space Telescope and Gaia will provide strong constraints on origin. Existing observations are all consistent with HVS ejections from encounters with the massive black hole in the Galactic center.

  9. Using Electronic Surveys: Advice from Survey Professionals.

    Directory of Open Access Journals (Sweden)

    David M. Shannon

    2002-01-01

    Full Text Available The study reports the perceptions and recommendations of sixty-two experienced survey..researchers from the American Educational Research Association regarding the use of..electronic surveys. The most positive aspects cited for the use of electronic surveys were..reduction of costs (i.e., postage, phone charges, the use of electronic mail for pre-notification or..follow-up purposes, and the compatibility of data with existing software programs. These..professionals expressed limitations in using electronic surveys pertaining to the limited..sampling frame as well as issues of confidentiality, privacy, and the credibility of the sample...They advised that electronic surveys designed with the varied technological background and..capabilities of the respondent in mind, follow sound principles of survey construction, and be..administered to pre-notified, targeted populations with published email addresses.

  10. A Window Into Clinical Next-Generation Sequencing-Based Oncology Testing Practices.

    Science.gov (United States)

    Nagarajan, Rakesh; Bartley, Angela N; Bridge, Julia A; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J; Lindeman, Neal I; Moncur, Joel; Rai, Alex J; Routbort, Mark J; Vasalos, Patricia; Merker, Jason D

    2017-12-01

    - Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. - These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. - This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

  11. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  12. Probabilistic studies of accident sequences

    International Nuclear Information System (INIS)

    Villemeur, A.; Berger, J.P.

    1986-01-01

    For several years, Electricite de France has carried out probabilistic assessment of accident sequences for nuclear power plants. In the framework of this program many methods were developed. As the interest in these studies was increasing and as adapted methods were developed, Electricite de France has undertaken a probabilistic safety assessment of a nuclear power plant [fr

  13. MRI sequences and their parameters

    International Nuclear Information System (INIS)

    Teissier, J.M.

    1993-01-01

    Listing basic sequences and their present variants makes a synthetic classification of the various acquisition modes possible. The knowledge of the advantages of each of them, as well as of their disadvantages and restraints, seems to be an essential prerequisite to an optimal utilization of each magnetic resonance imaging system. (author)

  14. Degree sequence in message transfer

    Science.gov (United States)

    Yamuna, M.

    2017-11-01

    Message encryption is always an issue in current communication scenario. Methods are being devised using various domains. Graphs satisfy numerous unique properties which can be used for message transfer. In this paper, I propose a message encryption method based on degree sequence of graphs.

  15. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  16. On primes in Lucas sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2015-01-01

    Roč. 53, č. 1 (2015), s. 2-23 ISSN 0015-0517 R&D Projects: GA ČR GA14-02067S Institutional support: RVO:67985840 Keywords : Lucas sequence * primes Subject RIV: BA - General Mathematics http://www.fq.math.ca/Abstracts/53-1/somer.pdf

  17. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Teaching Task Sequencing via Verbal Mediation.

    Science.gov (United States)

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  19. Repdigits in k-Lucas sequences

    Indian Academy of Sciences (India)

    57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

  20. The environmental survey manual

    International Nuclear Information System (INIS)

    1987-08-01

    The purpose of this manual is to provide guidance to the Survey and Sampling and Analysis teams that conduct the one-time Environmental Survey of the major US Department of Energy (DOE) operating facilities. This manual includes a discussion of DOE's policy on environmental issues, a review of statutory guidance as it applies to the Survey, the procedures and protocols to be used by the Survey teams, criteria for the use of the Survey teams in evaluating existing environmental data for the Survey effort, generic technical checklists used in every Survey, health and safety guidelines for the personnel conducting the Survey, including the identification of potential hazards, prescribed protective equipment, and emergency procedures, the required formats for the Survey reports, guidance on identifying environmental problems that need immediate attention by the Operations Office responsible for the particular facility, and procedures and protocols for the conduct of sampling and analysis

  1. Genetic stability of the VHSV consensus sequence of G-gene in diagnostic samples from an acute outbreak

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Ahrens, Peter; Lorenzen, Niels

    2006-01-01

    The negative stranded RNA virus viral haemorrhagic septicaemia virus (VHSV) is an important disease-causing agent in aquacultured fish and internationally harmonized diagnostic procedures are continuously under development. The present study concerns the suitability of genotyping by sequencing...... collected tissue material as well as from inoculated cell culture. No nucleotide substitutions where identified when aligning the obtained sequence data for the two sample types. The presented data indicate that the overall consensus sequence of the virus outbreak was stable during the survey...

  2. Aerial radiation surveys

    International Nuclear Information System (INIS)

    Jobst, J.

    1980-01-01

    A recent aerial radiation survey of the surroundings of the Vitro mill in Salt Lake City shows that uranium mill tailings have been removed to many locations outside their original boundary. To date, 52 remote sites have been discovered within a 100 square kilometer aerial survey perimeter surrounding the mill; 9 of these were discovered with the recent aerial survey map. Five additional sites, also discovered by aerial survey, contained uranium ore, milling equipment, or radioactive slag. Because of the success of this survey, plans are being made to extend the aerial survey program to other parts of the Salt Lake valley where diversions of Vitro tailings are also known to exist

  3. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  4. Multi-qubit compensation sequences

    International Nuclear Information System (INIS)

    Tomita, Y; Merrill, J T; Brown, K R

    2010-01-01

    The Hamiltonian control of n qubits requires precision control of both the strength and timing of interactions. Compensation pulses relax the precision requirements by reducing unknown but systematic errors. Using composite pulse techniques designed for single qubits, we show that systematic errors for n-qubit systems can be corrected to arbitrary accuracy given either two non-commuting control Hamiltonians with identical systematic errors or one error-free control Hamiltonian. We also examine composite pulses in the context of quantum computers controlled by two-qubit interactions. For quantum computers based on the XY interaction, single-qubit composite pulse sequences naturally correct systematic errors. For quantum computers based on the Heisenberg or exchange interaction, the composite pulse sequences reduce the logical single-qubit gate errors but increase the errors for logical two-qubit gates.

  5. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  6. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  7. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  8. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data

    OpenAIRE

    Hu, Bo; Ji, Yuan; Xu, Yaomin; Ting, Angela H

    2013-01-01

    Allele-specific methylation (ASM) has long been studied but mainly documented in the context of genomic imprinting and X chromosome inactivation. Taking advantage of the next-generation sequencing technology, we conduct a high-throughput sequencing experiment with four prostate cell lines to survey the whole genome and identify single nucleotide polymorphisms (SNPs) with ASM. A Bayesian approach is proposed to model the counts of short reads for each SNP conditional on its genotypes of multip...

  9. SURVEY, BUFFALO COUNTY, NE

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  10. Patient survey (HCAHPS) - National

    Data.gov (United States)

    U.S. Department of Health & Human Services — The national average for the HCAHPS survey categories. HCAHPS is a national, standardized survey of hospital patients about their experiences during a recent...

  11. Survey, OCONEE COUNTY, SC

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  12. SURVEY, DOUGLAS COUNTY, MN

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  13. GDOT employee survey.

    Science.gov (United States)

    2017-07-04

    The research team worked in collaboration with GDOT to conduct the 2016 GDOT Employee Survey. This research study aimed to increase the response rate and the usefulness of the feedback from the GDOT employee survey to support organizational decisions...

  14. SURVEY, KENAI PENINSULSA, AK

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  15. SURVEY, BROADWATER COUNTY, MT

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  16. SURVEY, OSCEOLA COUNTY, FLORIDA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  17. SURVEY, POTTAWATTAMIE COUNTY, IA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  18. Large Pelagics Intercept Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Large Pelagics Intercept Survey (LPIS) is a dockside survey of private and charterboat captains who have just completed fishing trips directed at large pelagic...

  19. MAX and Survey Linkages

    Data.gov (United States)

    U.S. Department of Health & Human Services — CMS is interested in linking MAX files with survey data, including four surveys conducted by the National Center for Health Statistics (NCHS) - the National Health...

  20. SURVEY, LAKE COUNTY, MT

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  1. NGS Survey Control Map

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Survey Control Map provides a map of the US which allows you to find and display geodetic survey control points stored in the database of the National...

  2. SURVEY, Lowndes County, MS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  3. SURVEY, REFUGIO COUNTY, TEXAS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  4. SURVEY, FAIRFIELD COUNTY, CT

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  5. Designing an Effective Survey

    National Research Council Canada - National Science Library

    Kasunic, Mark

    2005-01-01

    ... of them. However, to protect the validity of conclusions drawn from a survey, certain procedures must be followed throughout the process of designing, developing, and distributing the survey questionnaire...

  6. Sea Scallop Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The standardized NEFSC Sea Scallop Survey began in 1980 and has covered an area from Cape Hatteras to Georges Bank. The survey aims to determine the distribution and...

  7. SURVEY, MISSOULA COUNTY, MT

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  8. SURVEY, Northumberland County, VA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The field survey data for this coastal study includes a field report that exhibits photos and transect information collected in the field survey phase of the study....

  9. SURVEY, BARNSTABLE COUNTY, MA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  10. SURVEY, CASCADE COUNTY, MT

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  11. SURVEY, NATCHITOCHES PARISH, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  12. SURVEY, HOLMES COUNTY, MS

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  13. Iowa Intensive Archaeological Survey

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — This shape file contains intensive level archaeological survey areas for the state of Iowa. All intensive Phase I surveys that are submitted to the State Historic...

  14. SURVEY, MONO COUNTY, CALIFORNIA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  15. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  16. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  17. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  18. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  19. Primer on Health Surveys

    OpenAIRE

    David L Nordstrom; David L Nordstrom

    2012-01-01

    The aim of this paper is to introduce novice researchers to surveys as a method of data collection. It starts with the definition of a survey, its major purposes and types as well as changes in the goals surveys have helped to achieve over time. Advantages and disadvantages of surveys over population censuses and medical examinations are discussed. Approaches to questionnaire construction are introduced along with properties that questionnaires are evaluated for. Modes of administration, sam...

  20. Protein 3D structure computed from evolutionary sequence variation.

    Directory of Open Access Journals (Sweden)

    Debora S Marks

    Full Text Available The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org. This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of

  1. Surveying ethnic minorities

    NARCIS (Netherlands)

    Joost Kappelhof

    2015-01-01

    Obtaining accurate survey data on ethnic minorities is not easy. Ethnic minorities are usually underrepresented in surveys, and it is moreover not certain that those who do take part in surveys are representative of the group the researcher is interested in. For example, is it only people with

  2. GIS Readiness Survey 2014

    DEFF Research Database (Denmark)

    Schrøder, Lise; Hvingel, Line Træholt; Hansen, Henning Sten

    2014-01-01

    The GIS Readiness Survey 2014 is a follow-up to the corresponding survey that was carried out among public institutions in Denmark in 2009. The present survey thus provides an updated image of status and challenges in relation to the use of spatial information, the construction of the com- mon...

  3. Conducting online surveys

    NARCIS (Netherlands)

    Selm, M. van; Jankowski, N.W.

    2006-01-01

    The World Wide Web (WWW) is increasingly being used as a tool and platform for survey research. Two types of electronic or online surveys available for data collection are the email and Web based survey, and they constitute the focus of this paper. We address a multitude of issues researchers should

  4. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  5. A Subaru galaxy redshift survey: WFMOS survey

    International Nuclear Information System (INIS)

    Takada, M

    2008-01-01

    A planned galaxy redshift survey with the Subaru 8.2m telescope, the WFMOS survey, offers a unique opportunity for probing detailed properties of large-scale structure formation in the expanding universe by measuring clustering strength of galaxy distribution as a function of distance scale and redshift. In particular, the precise measurement of the galaxy power spectrum, combined with the cosmic microwave background experiments, allows us to obtain stringent constraints on or even determine absolute mass scales of the Big-Bang relic neutrinos as the neutrinos imprint characteristic scale- and redshift-dependent modifications onto the galaxy power spectrum shape. Here we describe the basic concept of how the galaxy clustering measurement can be used to explore the neutrino masses, with particular emphasis on advantages of the WFMOS survey over the existing low-redshift surveys such as SDSS

  6. Gene Discovery through Genomic Sequencing of Brucella abortus

    Science.gov (United States)

    Sánchez, Daniel O.; Zandomeni, Ruben O.; Cravero, Silvio; Verdún, Ramiro E.; Pierrou, Ester; Faccio, Paula; Diaz, Gabriela; Lanzavecchia, Silvia; Agüero, Fernán; Frasch, Alberto C. C.; Andersson, Siv G. E.; Rossetti, Osvaldo L.; Grau, Oscar; Ugalde, Rodolfo A.

    2001-01-01

    Brucella abortus is the etiological agent of brucellosis, a disease that affects bovines and human. We generated DNA random sequences from the genome of B. abortus strain 2308 in order to characterize molecular targets that might be useful for developing immunological or chemotherapeutic strategies against this pathogen. The partial sequencing of 1,899 clones allowed the identification of 1,199 genomic sequence surveys (GSSs) with high homology (BLAST expect value < 10−5) to sequences deposited in the GenBank databases. Among them, 925 represent putative novel genes for the Brucella genus. Out of 925 nonredundant GSSs, 470 were classified in 15 categories based on cellular function. Seven hundred GSSs showed no significant database matches and remain available for further studies in order to identify their function. A high number of GSSs with homology to Agrobacterium tumefaciens and Rhizobium meliloti proteins were observed, thus confirming their close phylogenetic relationship. Among them, several GSSs showed high similarity with genes related to nodule nitrogen fixation, synthesis of nod factors, nodulation protein symbiotic plasmid, and nodule bacteroid differentiation. We have also identified several B. abortus homologs of virulence and pathogenesis genes from other pathogens, including a homolog to both the Shda gene from Salmonella enterica serovar Typhimurium and the AidA-1 gene from Escherichia coli. Other GSSs displayed significant homologies to genes encoding components of the type III and type IV secretion machineries, suggesting that Brucella might also have an active type III secretion machinery. PMID:11159979

  7. Taxonomic evaluation of selected Ganoderma species and database sequence validation

    Directory of Open Access Journals (Sweden)

    Suldbold Jargalmaa

    2017-07-01

    Full Text Available Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II. These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species.

  8. The Bergshamra earthquake sequence of December 23, 1979

    International Nuclear Information System (INIS)

    Kulhanek, O.; John, N.; Meyer, K.; Eck, T. van; Wahlstroem, R.

    1980-08-01

    On December 23, 1979 an earthquake sequence occurred near Bergshamra-Roslagen, Sweden, about 50 km northeast of Stockholm. The main shock, which has been assigned a magnitude Msub(L)=3.2, has been followed, with a 3 minute delay, by a shock of magnitude Msub(L)=2.6 and, with additional 21-minute delay, by a third shock of magnitude Msub(L)=2.0. Whereas the main shock was recorded by almost all Finnish, Norwegian and Swedish permanent stations, the whole sequence has been observed only at UPP (Δ=68 km). A six-week field survey in the epicentral area revealed a number of small aftershocks located close to the main shock. The Bergshamra sequence took place in a zone of very low seismicity in eastern central Sweden and for Swedish earthquakes at unusual shallow depth. Since the epicentre lies less than 100 km from a nuclear power plant in Forsmark, the sequence received publicity which was not in proportion to the size of the shock. At his occasion, some rather strange explanations of the shock emerged. (Auth.)

  9. Templated sequence insertion polymorphisms in the human genome

    Science.gov (United States)

    Onozawa, Masahiro; Aplan, Peter

    2016-11-01

    Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including 1) target-site duplication (TSD), 2) polyadenylation 10-30 nucleotides downstream of a “cryptic” polyadenylation signal, and 3) preference for insertion at a 5’-TTTT/A-3’ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25-30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.

  10. Taxonomic evaluation of selected Ganoderma species and database sequence validation

    Science.gov (United States)

    Jargalmaa, Suldbold; Eimes, John A.; Park, Myung Soo; Park, Jae Young; Oh, Seung-Yoon

    2017-01-01

    Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II). These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species. PMID:28761785

  11. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  12. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  13. Environmental Survey preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    1988-04-01

    This report presents the preliminary findings from the first phase of the Environmental Survey of the United States Department of Energy (DOE) Sandia National Laboratories conducted August 17 through September 4, 1987. The objective of the Survey is to identify environmental problems and areas of environmental risk associated with Sandia National Laboratories-Albuquerque (SNLA). The Survey covers all environmental media and all areas of environmental regulation. It is being performed in accordance with the DOE Environmental Survey Manual. This phase of the Survey involves the review of existing site environmental data, observations of the operations carried on at SNLA, and interviews with site personnel. 85 refs., 49 figs., 48 tabs.

  14. Primer on Health Surveys

    Directory of Open Access Journals (Sweden)

    David L Nordstrom

    2012-06-01

    Full Text Available The aim of this paper is to introduce novice researchers to surveys as a method of data collection. It starts with the definition of a survey, its major purposes and types as well as changes in the goals surveys have helped to achieve over time. Advantages and disadvantages of surveys over population censuses and medical examinations are discussed. Approaches to questionnaire construction are introduced along with properties that questionnaires are evaluated for. Modes of administration, sample size issues, and data analysis approaches are also introduced. The primer is illustrated with examples of surveys conducted in different countries with various public health purposes.

  15. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  16. MX Siting Investigation, Gravity Survey - Delamar Valley, Nevada.

    Science.gov (United States)

    1981-07-20

    reduces the data to Simple Bouguer Anomaly (see Section A1.4, Appendix A1.0). The Defense Mapping Agency Aerospace Center (DMAAC), St. Louis, Missouri...DRAWINGS Drawing Number 1 Complete Bouguer Anomaly Contours 2 Depth to Rock -Interpreted from In Pocket at Gravity Data End of Report iv E-TR-33-DM...ErtPX E-TR-3 3-DM 6 2.0 GRAVITY DATA REDUCTION DMAHTC/GSS obtained the basic observations for the new stations and reduced them to Simple Bouguer

  17. Developing the online survey.

    Science.gov (United States)

    Gordon, Jeffry S; McNew, Ryan

    2008-12-01

    Institutions of higher education are now using Internet-based technology tools to conduct surveys for data collection. Research shows that the type and quality of responses one receives with online surveys are comparable with what one receives in paper-based surveys. Data collection can take place on Web-based surveys, e-mail-based surveys, and personal digital assistants/Smartphone devices. Web surveys can be subscription templates, software packages installed on one's own server, or created from scratch using Web programming development tools. All of these approaches have their advantages and disadvantages. The survey owner must make informed decisions as to the right technology to implement. The correct choice can save hours of work in sorting, organizing, and analyzing data.

  18. Seqenv: linking sequences to environments through text mining.

    Science.gov (United States)

    Sinclair, Lucas; Ijaz, Umer Z; Jensen, Lars Juhl; Coolen, Marco J L; Gubry-Rangin, Cecile; Chroňáková, Alica; Oulas, Anastasis; Pavloudi, Christina; Schnetzer, Julia; Weimann, Aaron; Ijaz, Ali; Eiler, Alexander; Quince, Christopher; Pafilis, Evangelos

    2016-01-01

    Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.

  19. Seqenv: linking sequences to environments through text mining

    Directory of Open Access Journals (Sweden)

    Lucas Sinclair

    2016-12-01

    Full Text Available Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.

  20. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  1. Computational analysis of sequence selection mechanisms.

    Science.gov (United States)

    Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

    2004-04-01

    Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

  2. The recurrence sequences via Sylvester matrices

    Science.gov (United States)

    Karaduman, Erdal; Deveci, Ömür

    2017-07-01

    In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

  3. ON SOME RECURRENCE TYPE SMARANDACHE SEQUENCES

    OpenAIRE

    MAJUMDAR, A.A.K.; GUNARTO, H.

    2000-01-01

    In this paper, we study some properties of ten recurrence type Smarandache sequences, namely, the Smarandache odd, even, prime product, square product, higher-power product, permutation, consecutive, reverse, symmetric, and pierced chain sequences.

  4. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  5. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  6. Perfect sequences over the real quaternions

    OpenAIRE

    Kuznetsov, Oleg

    2017-01-01

    In this Thesis, perfect sequences over the real quaternions are first considered. Definitions for the right and left periodic autocorrelation functions are given, and right and left perfect sequences introduced. It is shown that the right (left) perfection of any sequence implies the left (right) perfection, so concepts of right and left perfect sequences over the real quaternions are equivalent. Unitary transformations of the quaternion space ℍ are then considered. Using the equivalence of t...

  7. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  8. Parallel sequencing lives, or what makes large sequencing projects successful.

    Science.gov (United States)

    Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

    2017-11-01

    T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

  9. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  10. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  11. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  12. Compact flow diagrams for state sequences

    NARCIS (Netherlands)

    Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.

    2016-01-01

    We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,

  13. Blazar Sequence in Fermi Era Liang Chen

    Indian Academy of Sciences (India)

    Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

  14. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  15. 76 FR 26255 - Takes of Marine Mammals Incidental to Specified Activities; Marine Geophysical Survey in the...

    Science.gov (United States)

    2011-05-06

    ..., whose earthquake recurrence interval is 50 to 75 years and which last ruptured in 1938. The survey will... sequence such that the source level of the array will increase in steps not exceeding six dB per five min...

  16. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  17. Web survey methodology

    CERN Document Server

    Callegaro, Mario; Vehovar, Asja

    2015-01-01

    Web Survey Methodology guides the reader through the past fifteen years of research in web survey methodology. It both provides practical guidance on the latest techniques for collecting valid and reliable data and offers a comprehensive overview of research issues. Core topics from preparation to questionnaire design, recruitment testing to analysis and survey software are all covered in a systematic and insightful way. The reader will be exposed to key concepts and key findings in the literature, covering measurement, non-response, adjustments, paradata, and cost issues. The book also discusses the hottest research topics in survey research today, such as internet panels, virtual interviewing, mobile surveys and the integration with passive measurements, e-social sciences, mixed modes and business intelligence. The book is intended for students, practitioners, and researchers in fields such as survey and market research, psychological research, official statistics and customer satisfaction research.

  18. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  19. Data selector group sequencer interface

    International Nuclear Information System (INIS)

    Zizka, G.; Turko, B.

    1984-01-01

    A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence

  20. A main sequence for quasars

    Science.gov (United States)

    Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

    2018-03-01

    The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  1. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  2. A Main Sequence for Quasars

    Directory of Open Access Journals (Sweden)

    Paola Marziani

    2018-03-01

    Full Text Available The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  3. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  4. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  5. Aerial radiation survey

    International Nuclear Information System (INIS)

    Pradeep Kumar, K.S.

    1998-01-01

    Aerial gamma spectrometry surveys are the most effective, comprehensive and preferred tool to delimit the large area surface contamination in a radiological emergency either due to a nuclear accident or following a nuclear strike. The airborne survey apart from providing rapid and economical evaluation of ground contamination over large areas due to larger ground clearance and higher speed, is the only technique to overcome difficulties posed by ground surveys of inaccessible region. The aerial survey technique can also be used for searching of lost radioactive sources, tracking of radioactive plume and generation of background data on the Emergency Planning Zone (EPZ) of nuclear installations

  6. Survey of photovoltaic systems

    Energy Technology Data Exchange (ETDEWEB)

    1979-08-01

    In developing this survey of photovoltaic systems, the University of Alabama in Huntsville assembled a task team to perform an extensive telephone survey of all known photovoltaic manufacturers. Three US companies accounted for 77% of the total domestic sales in 1978. They are Solarex Corporation, Solar Power Croporation, and ARCO Solar, Inc. This survey of solar photovoltaic (P/V) manufacturers and suppliers consists of three parts: a catalog of suppliers arranged alphabetically, data sheets on specific products, and typical operating, installation, or maintenance instructions and procedures. This report does not recommend or endorse any company product or information presented within as the results of this survey.

  7. Management Satisfaction Survey

    Data.gov (United States)

    Office of Personnel Management — The Chief Human Capital Officers' Managers' Satisfaction Survey asks managers to rate their perception of workforce planning, interaction with and levels of support...

  8. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  9. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  10. Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing

    Science.gov (United States)

    Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identif...

  11. Magnetism Teaching Sequences Based on an Inductive Approach for First-Year Thai University Science Students

    Science.gov (United States)

    Narjaikaew, Pattawan; Emarat, Narumon; Arayathanitkul, Kwan; Cowie, Bronwen

    2010-01-01

    The study investigated the impact on student motivation and understanding of magnetism of teaching sequences based on an inductive approach. The study was conducted in large lecture classes. A pre- and post-Conceptual Survey of Electricity and Magnetism was conducted with just fewer than 700 Thai undergraduate science students, before and after…

  12. A Survey of the Innovation Surveys

    NARCIS (Netherlands)

    Hong, Shangqin; Oxley, Les; McCann, Philip

    Both theoretical and conceptual understanding of innovation has developed significantly since the early 1980s. More noticeable, however, are the major changes that have been experienced in empirically-oriented innovation research as a result of the introduction of firm level innovation surveys.

  13. Surveying the global virome

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Simmonds, Peter; Kapoor, Amit

    2015-01-01

    Recent advances in sequencing technologies have greatly enhanced our abilities to identify novel microbial sequences. Thus, our understanding of the global virome and the virome of specific host species in particular is rapidly expanding. Identification of animal viruses is important for understa......Recent advances in sequencing technologies have greatly enhanced our abilities to identify novel microbial sequences. Thus, our understanding of the global virome and the virome of specific host species in particular is rapidly expanding. Identification of animal viruses is important....... Much remains to be learned on the novel hepaciviruses, including their association with disease, and thereby how relevant they will become as HCV model systems and for studies of animal disease. This review discusses how virome analysis led to identification of novel hepaci- and pegiviruses...

  14. Results of the 2010 Survey on Teaching Chemical Reaction Engineering

    Science.gov (United States)

    Silverstein, David L.; Vigeant, Margot A. S.

    2012-01-01

    A survey of faculty teaching the chemical reaction engineering course or sequence during the 2009-2010 academic year at chemical engineering programs in the United States and Canada reveals change in terms of content, timing, and approaches to teaching. The report consists of two parts: first, a statistical and demographic characterization of the…

  15. Short timescale variability in the faint sky variability survey

    NARCIS (Netherlands)

    Morales-Rueda, L.; Groot, P.J.; Augusteijn, T.; Nelemans, G.A.; Vreeswijk, P.M.; Besselaar, E.J.M. van den

    2006-01-01

    We present the V-band variability analysis of the Faint Sky Variability Survey (FSVS). The FSVS combines colour and time variability information, from timescales of 24 minutes to tens of days, down to V = 24. We find that �1% of all point sources are variable along the main sequence reaching �3.5%

  16. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  17. American Housing Survey (AHS)

    Science.gov (United States)

    Employment and Payroll Survey of Business Owners Work from Home Our statistics highlight trends in household statistics from multiple surveys. Data Tools & Apps Main American FactFinder Census Business Builder My Classification Codes (i.e., NAICS) Economic Census Economic Indicators Economic Studies Industry Statistics

  18. Our Surveys & Programs

    Science.gov (United States)

    Employment and Payroll Survey of Business Owners Work from Home Our statistics highlight trends in household statistics from multiple surveys. Data Tools & Apps Main American FactFinder Census Business Builder My Classification Codes (i.e., NAICS) Economic Census Economic Indicators Economic Studies Industry Statistics

  19. Marine gamma spectrometric survey

    International Nuclear Information System (INIS)

    Kostoglodov, V.V.

    1979-01-01

    Presented are theoretical problems physical and geochemical prerequisites and possibilities of practical application of the method of continuous submarine gamma-spectrometric survey and radiometric survey destined for rapid study of the surface layer of marine sediments. Shown is high efficiency and advantages of this method in comparison with traditional and widely spread in marine geology methods of bottom sediments investigation

  20. IT Barometer survey, Denmark

    DEFF Research Database (Denmark)

    Howard, Rob

    1998-01-01

    Survey results from Danish architects, engineers, contractors and property managers in the construction industry concerning their use of computers, communications, problems and needs.......Survey results from Danish architects, engineers, contractors and property managers in the construction industry concerning their use of computers, communications, problems and needs....

  1. Cosmology with cluster surveys

    Indian Academy of Sciences (India)

    Abstract. Surveys of clusters of galaxies provide us with a powerful probe of the den- sity and nature of the dark energy. The red-shift distribution of detected clusters is highly sensitive to the dark energy equation of state parameter w. Upcoming Sunyaev–. Zel'dovich (SZ) surveys would provide us large yields of clusters to ...

  2. The VLA Sky Survey

    Science.gov (United States)

    Lacy, Mark; VLASS Survey Team, VLASS Survey Science Group

    2018-01-01

    The VLA Sky Survey (VLASS), which began in September 2017, is a seven year project to image the entire sky north of Declination -40 degrees in three epochs. The survey is being carried out in I,Q and U polarization at a frequency of 2-4GHz, and a resolution of 2.5 arcseconds, with each epoch being separated by 32 months. Raw data from the survey, along with basic "quicklook" images are made freely available shortly after observation. Within a few months, NRAO will begin making available further basic data products, including refined images and source lists. In this talk I shall describe the science goals and methodology of the survey, the current survey status, and some early results, along with plans for collaborations with external groups to produce enhanced, high level data products.

  3. Physics Survey Overview

    International Nuclear Information System (INIS)

    2002-01-01

    An overview of a series of assignments of the branches of physics carried out by the Board on Physics and Astronomy of the National Research Council. It identifies further theories in physics and makes recommendations on preventive priorities. The Board on Physics and Astronomy (BPA) has conducted a new decadal survey of physics entitled ''Physics in a New Era''. The survey includes assessments of the main branches of physics as well as certain selected emerging areas. The various elements of the survey were prepared by separately-appointed National Research Council (NRC) committees. The BPA formed the Physics Survey Overview Committee (PSOVC) to complete the survey by preparing an overview of the field of physics to summarize and synthesize the results of the various assessments and to address cross-cutting issues that concern physics as a whole

  4. Genome sequence and genetic diversity of European ash trees.

    Science.gov (United States)

    Sollars, Elizabeth S A; Harper, Andrea L; Kelly, Laura J; Sambles, Christine M; Ramirez-Gonzalez, Ricardo H; Swarbreck, David; Kaithakottil, Gemy; Cooper, Endymion D; Uauy, Cristobal; Havlickova, Lenka; Worswick, Gemma; Studholme, David J; Zohren, Jasmin; Salmon, Deborah L; Clavijo, Bernardo J; Li, Yi; He, Zhesi; Fellgett, Alison; McKinney, Lea Vig; Nielsen, Lene Rostgaard; Douglas, Gerry C; Kjær, Erik Dahl; Downie, J Allan; Boshier, David; Lee, Steve; Clark, Jo; Grant, Murray; Bancroft, Ian; Caccamo, Mario; Buggs, Richard J A

    2017-01-12

    Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.

  5. Regulatory and licensee surveys

    International Nuclear Information System (INIS)

    2009-01-01

    Prior to the workshop two CSNI/WGHOF surveys were distributed. One survey was directed at regulatory bodies and the other was directed at plant licensees. The surveys were: 1 - Regulatory Expectations of Licensees' Arrangements to Ensure Suitable Organisational Structure, Resources and Competencies to Manage Safety (sent to WGHOF regulatory members). The survey requested that the respondents provide a brief overview of the situation related to plant organisations in their country, their regulatory expectations and their formal requirements. The survey addressed three subjects: the demonstration and documentation of organisational structures, resources and competencies, organisational changes, issues for improvement (for both current and new plants). Responses were received from eleven regulatory bodies. 2 - Approaches to Justify Organisational Suitability (sent to selected licensees). The purpose of the survey to was to gain an understanding of how licensees ensure organisational suitability, resources and competencies. This information was used to assist in the development of the issues and subjects that were addressed at the group discussion sessions. Responses were received from over fifteen licensees from nine countries. The survey requested that the licensees provide information on how they ensure effective organisational structures at their plants. The survey grouped the questions into the following four categories: organisational safety functions, resource and competence, decision-making and communication, good examples and improvement needs. The findings from these surveys were used in conjunction with other factors to identify the key issues for the workshop discussion sessions. The responses from these two surveys are discussed briefly in Sections 4 and 5 of this report. More extensive reviews of the regulatory and licensee responses are provided in Appendix 1

  6. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  7. Hierarchically nested river landform sequences

    Science.gov (United States)

    Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

    2017-12-01

    River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

  8. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  9. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  10. Web-based Surveys: Changing the Survey Process

    OpenAIRE

    Gunn, Holly

    2002-01-01

    Web-based surveys are having a profound influence on the survey process. Unlike other types of surveys, Web page design skills and computer programming expertise play a significant role in the design of Web-based surveys. Survey respondents face new and different challenges in completing a Web-based survey. This paper examines the different types of Web-based surveys, the advantages and challenges of using Web-based surveys, the design of Web-based surveys, and the issues of validity, error, ...

  11. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  12. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  13. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  14. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  15. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, nois...... patterns of mutual exclusivity. These techniques, coupled with advances in high-throughput DNA sequencing, are enabling precision medicine approaches to the diagnosis and treatment of cancer....

  16. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  17. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  18. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    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.

  19. Web-Based Surveys: Not Your Basic Survey Anymore

    Science.gov (United States)

    Bertot, John Carlo

    2009-01-01

    Web-based surveys are not new to the library environment. Although such surveys began as extensions of print surveys, the Web-based environment offers a number of approaches to conducting a survey that the print environment cannot duplicate easily. Since 1994, the author and others have conducted national surveys of public library Internet…

  20. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  1. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  2. Digital Recovery Sequencer - Advanced Concept Ejection Seats

    National Research Council Canada - National Science Library

    Ross, David A; Cotter, Lee; Culhane, David; Press, Matthew J

    2005-01-01

    .... Continued usage of the Analog Sequencer is undesirable due to limitations with respect to its installed life, electronic component obsolescence, flexibility to accommodate seat safety improvements...

  3. Quantitative phenotyping via deep barcode sequencing.

    Science.gov (United States)

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  4. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  5. Multipliers on Generalized Mixed Norm Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Oscar Blasco

    2014-01-01

    Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jsequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

  6. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  7. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  8. Polynomial sequences generated by infinite Hessenberg matrices

    Directory of Open Access Journals (Sweden)

    Verde-Star Luis

    2017-01-01

    Full Text Available We show that an infinite lower Hessenberg matrix generates polynomial sequences that correspond to the rows of infinite lower triangular invertible matrices. Orthogonal polynomial sequences are obtained when the Hessenberg matrix is tridiagonal. We study properties of the polynomial sequences and their corresponding matrices which are related to recurrence relations, companion matrices, matrix similarity, construction algorithms, and generating functions. When the Hessenberg matrix is also Toeplitz the polynomial sequences turn out to be of interpolatory type and we obtain additional results. For example, we show that every nonderogative finite square matrix is similar to a unique Toeplitz-Hessenberg matrix.

  9. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  10. SDSS-IV MaNGA: Spatially Resolved Star Formation Main Sequence and LI(N)ER Sequence

    Science.gov (United States)

    Hsieh, B. C.; Lin, Lihwai; Lin, J. H.; Pan, H. A.; Hsu, C. H.; Sánchez, S. F.; Cano-Díaz, M.; Zhang, K.; Yan, R.; Barrera-Ballesteros, J. K.; Boquien, M.; Riffel, R.; Brownstein, J.; Cruz-González, I.; Hagen, A.; Ibarra, H.; Pan, K.; Bizyaev, D.; Oravetz, D.; Simmons, A.

    2017-12-01

    We present our study on the spatially resolved Hα and M * relation for 536 star-forming and 424 quiescent galaxies taken from the MaNGA survey. We show that the star formation rate surface density ({{{Σ }}}{SFR}), derived based on the Hα emissions, is strongly correlated with the M * surface density ({{{Σ }}}* ) on kiloparsec scales for star-forming galaxies and can be directly connected to the global star-forming sequence. This suggests that the global main sequence may be a consequence of a more fundamental relation on small scales. On the other hand, our result suggests that ∼20% of quiescent galaxies in our sample still have star formation activities in the outer region with lower specific star formation rate (SSFR) than typical star-forming galaxies. Meanwhile, we also find a tight correlation between {{{Σ }}}{{H}α } and {{{Σ }}}* for LI(N)ER regions, named the resolved “LI(N)ER” sequence, in quiescent galaxies, which is consistent with the scenario that LI(N)ER emissions are primarily powered by the hot, evolved stars as suggested in the literature.

  11. Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

    Directory of Open Access Journals (Sweden)

    Wang Jintu

    2011-04-01

    Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

  12. Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

    Science.gov (United States)

    2011-01-01

    Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

  13. Using a Calendar and Explanatory Instructions to Aid Within-Household Selection in Mail Surveys

    Science.gov (United States)

    Stange, Mathew; Smyth, Jolene D.; Olson, Kristen

    2016-01-01

    Although researchers can easily select probability samples of addresses using the U.S. Postal Service's Delivery Sequence File, randomly selecting respondents within households for surveys remains challenging. Researchers often place within-household selection instructions, such as the next or last birthday methods, in survey cover letters to…

  14. An Unbiased Survey of 500 Nearby Stars for Debris Disks: A JCMT Legacy Program

    NARCIS (Netherlands)

    Matthews, B.C.; Greaves, J.S.; Holland, W.S.; Wyatt, M.C.; Barlow, M.J.; Bastien, P.; Beichman, C.A.; Biggs, A.; Butner, H.M.; Dent, W.R.F.; Francesco, J. Di; Dominik, C.; Fissel, L.; Friberg, P.; Gibb, A.G.; Halpern, M.; Ivison, R.J.; Jayawardhana, R.; Jenness, T.; Johnstone, D.; Kavelaars, J.J.; Marshall, J.L.; Phillips, N.; Schieven, G.; Snellen, I.A.G.; Walker, H.J.; Ward-Thompson, D.; Weferling, B.; White, G.J.; Yates, J.; Zhu, M.; Craigon, A.

    2007-01-01

    We present the scientific motivation and observing plan for an upcoming detection survey for debris disks using the James Clerk Maxwell Telescope. The SCUBA-2 Unbiased Nearby Stars (SUNS) survey will observe 500 nearby main-sequence and subgiant stars (100 of each of the A, F, G, K, and M spectral

  15. Indexing contamination surveys

    International Nuclear Information System (INIS)

    Brown, R.L.

    1998-01-01

    The responsibility for safely managing the Tank Farms at Hanford belongs to Lockheed Martin Hanford Corporation which is part of the six company Project Hanford Management Team led by Fluor Daniel Hanford, Inc.. These Tank Farm Facilities contain numerous outdoor contamination areas which are surveyed at a periodicity consistent with the potential radiological conditions, occupancy, and risk of changes in radiological conditions. This document describes the survey documentation and data tracking method devised to track the results of contamination surveys this process is referred to as indexing. The indexing process takes a representative data set as an indicator for the contamination status of the facility. The data are further manipulated into a single value that can be tracked and trended using standard statistical methodology. To report meaningful data, the routine contamination surveys must be performed in a manner that allows the survey method and the data collection process to be recreated. Three key criteria are necessary to accomplish this goal: Accurate maps, consistent documentation, and consistent consolidation of data meeting these criteria provides data of sufficient quality to be tracked. Tracking of survey data is accomplished by converting the individual survey results into a weighted value, corrected for the actual number of survey points. This information can be compared over time using standard statistical analysis to identify trends. At the Tank Farms, the need to track and trend the facility's radiological status presents unique challenges. Many of these Tank Farm facilities date back to the second world war. The Tank Farm Facilities are exposed to weather extremes, plant and animal intrusion, as well as all of the normal challenges associated with handling radiological waste streams. Routine radiological surveys did not provide a radiological status adequate for continuing comparisons

  16. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  17. Plane and geodetic surveying

    CERN Document Server

    Johnson, Aylmer

    2014-01-01

    IntroductionAim And ScopeClassification Of SurveysThe Structure Of This BookGeneral Principles Of SurveyingErrorsRedundancyStiffnessAdjustmentPlanning And Record KeepingPrincipal Surveying ActivitiesEstablishing Control NetworksMappingSetting OutResectioningDeformation MonitoringAngle MeasurementThe Surveyor's CompassThe ClinometerThe Total StationMaking ObservationsChecks On Permanent AdjustmentsDistance MeasurementGeneralTape MeasurementsOptical Methods (Tachymetry)Electromagnetic Distance Measurement (EDM)Ultrasonic MethodsGNSSLevellingTheoryThe InstrumentTechniqueBookingPermanent Adjustmen

  18. Minerals industry survey, 1984

    Energy Technology Data Exchange (ETDEWEB)

    1984-01-01

    This is the seventh edition of the statistical survey commissioned by the Australian Mining Industry Council. It represents the most comprehensive review of the financial position of the Australian minerals industry and provides timely financial data on the minerals industry. The tables of this survey have been prepared for AMIC by Coopers and Lybrand, Chartered Accountants, based on information supplied to them in confidence by the respondent companies. For the purpose of the survey, the minerals industry has been defined as including exploration for, and extraction and primary processing of, minerals in Australia. The oil and gas industry is not included.

  19. Minerals industry survey 1987

    Energy Technology Data Exchange (ETDEWEB)

    1987-01-01

    This is the eleventh Minerals Industry Survey produced by the Australian Mining Industry Council. It represents an invaluable time series on the minerals industry's financial performance, as well as an up to date description of the industry for the latest financial year. The survey has been conceived as a supplement to and expansion of the various Australian Bureau of Statistics and Bureau of Mineral Resources, Geology and Geophysics publications which describe the exploration, mining and smelting and refining industries in Australia. The tables in this survey have been prepared by Coopers and Lybrand, Chartered Accountants, based on information supplied to them in confidence by the respondent companies.

  20. GPS satellite surveying

    CERN Document Server

    Leick, Alfred; Tatarnikov, Dmitry

    2015-01-01

    THE MOST COMPREHENSIVE, UP-TO-DATE GUIDE ON GPS TECHNOLOGY FOR SURVEYING Three previous editions have established GPS Satellite Surveying as the definitive industry reference. Now fully updated and expanded to reflect the newest developments in the field, this Fourth Edition features cutting-edge information on GNSS antennas, precise point positioning, real-time relative positioning, lattice reduction, and much more. Expert authors examine additional tools and applications, offering complete coverage of geodetic surveying using satellite technologies. The past decade has seen a major evolut

  1. Geothermal survey handbook

    Energy Technology Data Exchange (ETDEWEB)

    1974-01-01

    The objective of this handbook is to publicize widely the nature of geothermal surveys. It covers geothermal survey planning and measurement as well as measurement of thermal conductivity. Methods for the detection of eruptive areas, the measurement of radiative heat using snowfall, the measurement of surface temperature using infrared radiation and the measurement of thermal flow are described. The book also contains information on physical detection of geothermal reservoirs, the measurement of spring wells, thermographic measurement of surface heat, irregular layer surveying, air thermographics and aerial photography. Isotope measurement techniques are included.

  2. Telephony user survey

    CERN Multimedia

    IT Department

    2016-01-01

    Let us know your needs to better plan the transition to a new CERN telephony system.   CERN is planning to upgrade its telephony network and replace the system with a new and modern VoIP infrastructure. We strive to make this transition as beneficial and smooth as possible for you. Please let us know more about your current working environment, expectations and suggestions by responding to this survey: https://cern.ch/tel-survey. The more answers we get, the better the new system will serve everyone in the future. The survey will take you about five minutes to complete; we are counting on your feedback!

  3. EPRINT ARCHIVE USER SURVEY

    CERN Multimedia

    2001-01-01

    University of Southampton invites the CERN community to participate in a survey Professor Stevan Harnad is conducting on current users and non-users of Eprint Archives. http://www.eprints.org/survey/ The findings will be used to suggest potential enhancements of the services as well as to get a deeper understanding of the very rapid developments in the on-line dissemination and use of scientific and scholarly research. (The survey is anonymous. Revealing your identity is optional and it will be kept confidential.)

  4. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  5. Pilot pulsar surveys with LOFAR

    NARCIS (Netherlands)

    Coenen, T.

    2013-01-01

    We are performing two complementary pilot pulsar surveys as part of LOFAR commissioning. The LOFAR Pilot Pulsar Survey (LPPS) is a shallow all-sky survey using an incoherent combination of LOFAR stations. The LOFAR Tied-Array Survey (LOTAS) is a deeper pilot survey using 19 simultaneous tied-array

  6. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  7. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

    Science.gov (United States)

    Straub, Shannon C K; Parks, Matthew; Weitemier, Kevin; Fishbein, Mark; Cronn, Richard C; Liston, Aaron

    2012-02-01

    Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 30×, respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.

  8. Lesotho - Health Facility Survey

    Data.gov (United States)

    Millennium Challenge Corporation — The main objective of the 2011 Health Facility Survey (HFS) was to establish a baseline for informing the Health Project performance indicators on health facilities,...

  9. Hake Survey ADCP (2003)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shipboard acoustic Doppler current profiler data collected during the Integrated Acoustic and Trawl Surveys of Pacific Hake. Processing by: Stephen Pierce, Oregon...

  10. Fall Bottom Trawl Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The standardized NEFSC Fall Bottom Trawl Survey was initiated in 1963 and covered an area from Hudson Canyon, NY to Nova Scotia, Canada. Throughout the years,...

  11. Food Labels Survey

    Science.gov (United States)

    ... 2016 Nationally-Representative Phone Survey April 6, 2016 Consumer Reports® National Research Center Introduction In February, 2016, the Consumer Reports® National Research Center conducted a nationally representative phone ...

  12. IT User Community Survey

    CERN Document Server

    Peter Jones (IT-CDA-WF)

    2016-01-01

    IT-CDA is gathering information to more accurately form a snapshot of the CERN IT user community and we would appreciate you taking time to complete the following survey.   We want to use this survey to better understand how the user community uses their devices and our services, and how the delivery of those services could be improved. You will need to authenticate to complete the survey. However please note that your responses are confidential and will be compiled together and analysed as a group. You can also volunteer to offer additional information if you so wish. This survey should take no longer than 5 minutes. Thanks in advance for your collaboration.

  13. Hake Survey ADCP (2005)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shipboard acoustic Doppler current profiler data collected during the Integrated Acoustic and Trawl Surveys of Pacific Hake. Processing by: Stephen Pierce, Oregon...

  14. Hake Survey ADCP (1998)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shipboard acoustic Doppler current profiler data collected during the Integrated Acoustic and Trawl Surveys of Pacific Hake. Processing by: Stephen Pierce, Oregon...

  15. Hake Survey ADCP (1995)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shipboard acoustic Doppler current profiler data collected during the Integrated Acoustic and Trawl Surveys of Pacific Hake. Processing by: Stephen Pierce, Oregon...

  16. Hake Survey ADCP (2001)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Shipboard acoustic Doppler current profiler data collected during the Integrated Acoustic and Trawl Surveys of Pacific Hake. Processing by: Stephen Pierce, Oregon...

  17. 2000 LEPC Survey

    Science.gov (United States)

    This is the summary report of the 1999 nationwide Local Emergency Planning Committee survey, released in May 2000. It measured their levels of compliance and proactivity, roles in prevention and counter-terrorism, communication, and response plans.

  18. Large Pelagics Telephone Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Large Pelagics Telephone Survey (LPTS) collects fishing effort information directly from captains holding Highly Migratory Species (HMS) permits (required by...

  19. Deep Water Survey Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The deep water biodiversity surveys explore and describe the biodiversity of the bathy- and bentho-pelagic nekton using Midwater and bottom trawls centered in the...

  20. Shrimp Survey Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Northern Shrimp Survey was initiated in 1983 by the Atlantic States Marine Fisheries Commission (ASMFC) and monitors the relative abundance (number of shrimp),...

  1. American Housing Survey (AHS)

    Data.gov (United States)

    Department of Housing and Urban Development — The AHS is the largest, regular national housing sample survey in the United States. The U.S. Census Bureau conducts the AHS to obtain up-to-date housing statistics...

  2. Patient survey (ICH CAHPS)

    Data.gov (United States)

    U.S. Department of Health & Human Services — In-Center Hemodialysis Facilites Patient evaluations from the In-Center Hemodialysis Consumer Assessment of Healthcare Providers and Systems (ICH-CAHPS) Survey. The...

  3. National Health Interview Survey

    Data.gov (United States)

    U.S. Department of Health & Human Services — The National Health Interview Survey (NHIS) is the principal source of information on the health of the civilian noninstitutionalized population of the United States...

  4. Public Land Survey filled

    Data.gov (United States)

    California Natural Resource Agency — The 'PLSFILL' layer is a polygon coverage depicting the township, range and sections contained in the Public Land Survey System grid for the State of California....

  5. ASD Customer Satisfaction Survey

    Data.gov (United States)

    Department of Veterans Affairs — ASD implemented a customer satisfaction survey for our products and services. This feedback will provide a better understanding of how ASD products and services can...

  6. 2005 Resident Survey

    Data.gov (United States)

    City and County of Durham, North Carolina — The purpose of the annual City/County survey: To objectively assess citizen satisfaction with the delivery of City/County servicesTo set a baseline for future...

  7. Applicant Satisfaction Survey

    Data.gov (United States)

    Office of Personnel Management — The Chief Human Capital Officers developed 3 surveys that asks applicants to assess their satisfaction with the application process on a 1-10 point scale, with 10...

  8. 2013 Resident Survey

    Data.gov (United States)

    City and County of Durham, North Carolina — The purpose of the annual City/County survey: To objectively assess citizen satisfaction with the delivery of City/County servicesTo set a baseline for future...

  9. Industry Based Monkfish Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Monkfish industry leaders expressed concerns that the NEFSC bottom trawl surveys did not sample in all monkfish habitats; particularly the deeper water outside the...

  10. NMFS Reef Survey Forms

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Reef Environmental Survey Project (REEF) mission to educate and enlist divers in the conservation of marine habitats is accomplished primarily through its Fish...

  11. Large Pelagics Biological Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Large Pelagics Biological Survey (LPBS) collects additional length and weight information and body parts such as otoliths, caudal vertebrae, dorsal spines, and...

  12. Atlantic Herring Acoustic Surveys

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NEFSC Advanced Sampling Technologies Research Group conducts annual fisheries acoustic surveys using state-of-the-art acoustic, midwater trawling, and underwater...

  13. Fisheries Disaster Survey, 2000

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Responses to selected questions from the Social and Economic Survey administered in spring and summer 2000 to recipients of the second round (Round II) of financial...

  14. Spring Bottom Trawl Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The standardized NEFSC Spring Bottom Trawl Survey was initiated in 1968 and covered an area from Cape Hatteras, NC, to Nova Scotia, Canada, at depths >27m....

  15. Winter Bottom Trawl Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The standardized NEFSC Winter Bottom Trawl Survey was initiated in 1992 and covered offshore areas from the Mid-Atlantic to Georges Bank. Inshore strata were covered...

  16. Billfish Angler Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Billfish Angler Survey provides estimates of billfish angling activities in the Pacific and Indian Oceans. This collection of recreational billfish catch and...

  17. Infrared Sky Surveys

    Science.gov (United States)

    Price, Stephan D.

    2009-02-01

    A retrospective is given on infrared sky surveys from Thomas Edison’s proposal in the late 1870s to IRAS, the first sensitive mid- to far-infrared all-sky survey, and the mid-1990s experiments that filled in the IRAS deficiencies. The emerging technology for space-based surveys is highlighted, as is the prominent role the US Defense Department, particularly the Air Force, played in developing and applying detector and cryogenic sensor advances to early mid-infrared probe-rocket and satellite-based surveys. This technology was transitioned to the infrared astronomical community in relatively short order and was essential to the success of IRAS, COBE and ISO. Mention is made of several of the little known early observational programs that were superseded by more successful efforts.

  18. 2011 Resident Survey

    Data.gov (United States)

    City and County of Durham, North Carolina — The purpose of the annual City/County survey: To objectively assess citizen satisfaction with the delivery of City/County servicesTo set a baseline for future...

  19. 2009 Resident Survey

    Data.gov (United States)

    City and County of Durham, North Carolina — The purpose of the annual City/County survey: To objectively assess citizen satisfaction with the delivery of City/County servicesTo set a baseline for future...

  20. 2007 Resident Survey

    Data.gov (United States)

    City and County of Durham, North Carolina — The purpose of the annual City/County survey: To objectively assess citizen satisfaction with the delivery of City/County servicesTo set a baseline for future...

  1. Radon survey techniques

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    The report reviews radon measurement surveys in soils and in water. Special applications, and advantages and limitations of the radon measurement techniques are considered. The working group also gives some directions for further research in this field

  2. Medicare Current Beneficiary Survey

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Characteristics and Perceptions of the Medicare Population Data from the 2010 Medicare Current Beneficiary Survey is a series of source books based on the...

  3. Annual Omnibus Survey: A survey of life in Qatar 2014

    OpenAIRE

    Diop, Abdoulaye; Gengler, Justin John; Khan, Mohammad N.; Traugott, Michael; Elawad, Elmogiera Fadlallh; Al Ansari, Majed; Le, Kien T.; El-Maghraby, Engi; Elkassem, Rima Charbaji; Qutteina, Yara; Al Khulaifi, Buthaina; Nasrallah, Catherine; Al Subaey, Mohammed; Mustafa, Semsia Al-Ali; Alqassass, Haneen

    2015-01-01

    This Executive Summary presents the highlights of the 2014 Omnibus survey, the fourth in a series of Omnibus surveys since 2010. The surveys were carried out by the Social and Economic Survey Research Institute (SESRI) of Qatar University. Each Omnibus survey interviews a large and representative sample of Qatari citizens, resident expatriates and laborers. In these surveys, we asked a number of questions covering several topics of importance to Qatari society, including their ...

  4. Site surveying and levelling

    CERN Document Server

    Clancy, John

    2013-01-01

    This popular and useful text has been completely revised and up-dated so that it forms and indipensible handbook for any student of surveying. An additional chapter on modern developments is included and the text has also been extended to cover ordnance survey; calculation of areas; computation of true horizontal length; measurement of vertical angles; Code of Measuring Practice; curve ranging and calculations of volumes for earthworks.

  5. Benchmarking survey for recycling.

    Energy Technology Data Exchange (ETDEWEB)

    Marley, Margie Charlotte; Mizner, Jack Harry

    2005-06-01

    This report describes the methodology, analysis and conclusions of a comparison survey of recycling programs at ten Department of Energy sites including Sandia National Laboratories/New Mexico (SNL/NM). The goal of the survey was to compare SNL/NM's recycling performance with that of other federal facilities, and to identify activities and programs that could be implemented at SNL/NM to improve recycling performance.

  6. Nearshore Survey System Evaluation

    Science.gov (United States)

    2017-12-01

    environmental challenges. ERDC develops innovative solutions in civil and military engineering , geospatial sciences, water resources, and environmental...CRAB: A Unique Nearshore Surveying Vehicle.” American Society of Civil Engineers , Journal of Surveying Engineering 110(1): 1–7. Clausner, J. E., W...unlimited. The U.S. Army Engineer Research and Development Center (ERDC) solves the nation’s toughest engineering and

  7. DSM-5 field survey

    DEFF Research Database (Denmark)

    Lochner, Christine; Grant, Jon E; Odlaug, Brian Lawrence

    2012-01-01

    The aim of this multisite field survey was to examine the DSM-IV-TR criteria, proposed DSM-5 diagnostic criteria, as well as a number of possible additional diagnostic criteria, in patients with hair-pulling disorder (HPD, or trichotillomania).......The aim of this multisite field survey was to examine the DSM-IV-TR criteria, proposed DSM-5 diagnostic criteria, as well as a number of possible additional diagnostic criteria, in patients with hair-pulling disorder (HPD, or trichotillomania)....

  8. Step out - Step in Sequencing Games

    NARCIS (Netherlands)

    Musegaas, M.; Borm, P.E.M.; Quant, M.

    2014-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out - Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order.

  9. Step out-step in sequencing games

    NARCIS (Netherlands)

    Musegaas, Marieke; Borm, Peter; Quant, Marieke

    2015-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out–Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order. First,

  10. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  11. Thread extraction for polyadic instruction sequences

    NARCIS (Netherlands)

    Bergstra, J.; Middelburg, C.

    2011-01-01

    In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

  12. Genome sequence of Lactobacillus rhamnosus ATCC 8530.

    Science.gov (United States)

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

    2012-02-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  13. Genome Sequence of Lactobacillus rhamnosus ATCC 8530

    OpenAIRE

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

    2012-01-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  14. Trace maps for arbitrary substitution sequences

    International Nuclear Information System (INIS)

    Avishai, Y.

    1993-01-01

    The discovery of quasi-crystals and their 1-dimensional modeling have led to a deep mathematical study of Schroedinger operators with an arbitrary deterministic potential sequence. In this work we address this problem and find trace maps for an arbitrary substitution sequence. our trace maps have lower dimensionality than those of Kolar and Nori, which make them quite attractive for actual applications. (authors)

  15. Learning of Sensory Sequences in Cerebellar Patients

    Science.gov (United States)

    Frings, Markus; Boenisch, Raoul; Gerwig, Marcus; Diener, Hans-Christoph; Timmann, Dagmar

    2004-01-01

    A possible role of the cerebellum in detecting and recognizing event sequences has been proposed. The present study sought to determine whether patients with cerebellar lesions are impaired in the acquisition and discrimination of sequences of sensory stimuli of different modalities. A group of 26 cerebellar patients and 26 controls matched for…

  16. On peculiar Šindel sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2010-01-01

    Roč. 17, č. 2 (2010), s. 129-140 ISSN 0972-5555 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional research plan: CEZ:AV0Z10190503 Keywords : quadratic residue * Chinese remainder theorem * primitive Šindel sequences * Prague clock sequence Subject RIV: BA - General Mathematics http://www.pphmj.com/abstract/5095.htm

  17. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  18. Occupational Sequences: Auto Engines 1. AT 121.

    Science.gov (United States)

    Korb, A. W.; And Others

    In an attempt to individualize an automotive course, the Vocational-Technical Division of Northern Montana College has developed Occupational Sequences for an engine rebuilding course. Occupational Sequences, a learning or teaching aid, is an analysis of numbered operations involved in engine rebuilding. Job sheets, included in the book, provide a…

  19. Sequencing Events: Exploring Art and Art Jobs.

    Science.gov (United States)

    Stephens, Pamela Geiger; Shaddix, Robin K.

    2000-01-01

    Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

  20. Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2013-01-01

    in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

  1. Nitrogen chronology of massive main sequence stars

    NARCIS (Netherlands)

    Köhler, K.; Borzyszkowski, M.; Brott, I.; Langer, N.; de Koter, A.

    2012-01-01

    Context. Rotational mixing in massive main sequence stars is predicted to monotonically increase their surface nitrogen abundance with time. Aims. We use this effect to design a method for constraining the age and the inclination angle of massive main sequence stars, given their observed luminosity,

  2. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

  3. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  4. Cyprinus carpio Genome sequencing and assembly

    NARCIS (Netherlands)

    Kolder, I.C.R.M.; Plas-Duivesteijn, van der Suzanne J.; Tan, G.; Wiegertjes, G.; Forlenza, M.; Guler, A.T.; Travin, D.Y.; Nakao, M.; Moritomo, T.; Irnazarow, I.; Jansen, H.J.

    2013-01-01

    Sequencing of the common carp (Cyprinus carpio carpio Linnaeus, 1758) genome, with the objective of establishing carp as a model organism to supplement the closely related zebrafish (Danio rerio). The sequenced individual is a homozygous female (by gynogenesis) of R3 x R8 carp, the heterozygous

  5. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

  6. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  7. Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

    Data.gov (United States)

    National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

  8. From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2004-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  9. Micropathogen Community Analysis in Hyalomma rufipes via High-Throughput Sequencing of Small RNAs

    Science.gov (United States)

    Luo, Jin; Liu, Min-Xuan; Ren, Qiao-Yun; Chen, Ze; Tian, Zhan-Cheng; Hao, Jia-Wei; Wu, Feng; Liu, Xiao-Cui; Luo, Jian-Xun; Yin, Hong; Wang, Hui; Liu, Guang-Yuan

    2017-01-01

    Ticks are important vectors in the transmission of a broad range of micropathogens to vertebrates, including humans. Because of the role of ticks in disease transmission, identifying and characterizing the micropathogen profiles of tick populations have become increasingly important. The objective of this study was to survey the micropathogens of Hyalomma rufipes ticks. Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. rufipes ticks in Gansu Province, China. The resultant sRNA library data revealed that the surveyed tick populations produced reads that were homologous to St. Croix River Virus (SCRV) sequences. We also observed many reads that were homologous to microbial and/or pathogenic isolates, including bacteria, protozoa, and fungi. As part of this analysis, a phylogenetic tree was constructed to display the relationships among the homologous sequences that were identified. The study offered a unique opportunity to gain insight into the micropathogens of H. rufipes ticks. The effective control of arthropod vectors in the future will require knowledge of the micropathogen composition of vectors harboring infectious agents. Understanding the ecological factors that regulate vector propagation in association with the prevalence and persistence of micropathogen lineages is also imperative. These interactions may affect the evolution of micropathogen lineages, especially if the micropathogens rely on the vector or host for dispersal. The sRNA deep-sequencing approach used in this analysis provides an intuitive method to survey micropathogen prevalence in ticks and other vector species. PMID:28861401

  10. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Monnat, R.J. Jr.; Loeb, L.A.

    1985-01-01

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  11. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  12. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  13. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  14. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  15. Divide and conquer: enriching environmental sequencing data.

    Directory of Open Access Journals (Sweden)

    Anne Bergeron

    2007-09-01

    Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

  16. Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

    Science.gov (United States)

    Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

    2016-01-01

    How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

  17. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

  18. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  19. Issues in environmental survey design

    International Nuclear Information System (INIS)

    Iachan, R.

    1989-01-01

    Several environmental survey design issues are discussed and illustrated with surveys designed by Research Triangle Institute statisticians. Issues related to sampling and nonsampling errors are illustrated for indoor air quality surveys, radon surveys, pesticide surveys, and occupational and personal exposure surveys. Sample design issues include the use of auxiliary information (e.g. for stratification), and sampling in time. We also discuss the reduction and estimation of nonsampling errors, including nonresponse and measurement bias

  20. Does the sequence of data collection influence participants' responses to closed and open-ended questions? A methodological study.

    Science.gov (United States)

    Covell, Christine L; Sidani, Souraya; Ritchie, Judith A

    2012-06-01

    The sequence used for collecting quantitative and qualitative data in concurrent mixed-methods research may influence participants' responses. Empirical evidence is needed to determine if the order of data collection in concurrent mixed methods research biases participants' responses to closed and open-ended questions. To examine the influence of the quantitative-qualitative sequence on responses to closed and open-ended questions when assessing the same variables or aspects of a phenomenon simultaneously within the same study phase. A descriptive cross-sectional, concurrent mixed-methods design was used to collect quantitative (survey) and qualitative (interview) data. The setting was a large multi-site health care centre in Canada. A convenience sample of 50 registered nurses was selected and participated in the study. Participants were randomly assigned to one of two sequences for data collection, quantitative-qualitative or qualitative-quantitative. Independent t-tests were performed to compare the two groups' responses to the survey items. Directed content analysis was used to compare the participants' responses to the interview questions. The sequence of data collection did not greatly affect the participants' responses to the closed-ended questions (survey items) or the open-ended questions (interview questions). The sequencing of data collection, when using both survey and semi-structured interviews, may not bias participants' responses to closed or open-ended questions. Additional research is required to confirm these findings. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Retirement Applicant Satisfaction Survey Results

    Data.gov (United States)

    Social Security Administration — This dataset contains information about the Retirement Applicant Survey (RAS). The survey measured satisfaction results with the retirement application process. The...

  2. Redshift Survey Strategies

    Science.gov (United States)

    Jones, A. W.; Bland-Hawthorn, J.; Kaiser, N.

    1994-12-01

    In the first half of 1995, the Anglo-Australian Observatory is due to commission a wide field (2.1(deg) ), 400-fiber, double spectrograph system (2dF) at the f/3.3 prime focus of the AAT 3.9m bi-national facility. The instrument should be able to measure ~ 4000 galaxy redshifts (assuming a magnitude limit of b_J ~\\ 20) in a single dark night and is therefore ideally suited to studies of large-scale structure. We have carried out simple 3D numerical simulations to judge the relative merits of sparse surveys and contiguous surveys. We generate a survey volume and fill it randomly with particles according to a selection function which mimics a magnitude-limited survey at b_J = 19.7. Each of the particles is perturbed by a gaussian random field according to the dimensionless power spectrum k(3) P(k) / 2pi (2) determined by Feldman, Kaiser & Peacock (1994) from the IRAS QDOT survey. We introduce some redshift-space distortion as described by Kaiser (1987), a `thermal' component measured from pairwise velocities (Davis & Peebles 1983), and `fingers of god' due to rich clusters at random density enhancements. Our particular concern is to understand how the window function W(2(k)) of the survey geometry compromises the accuracy of statistical measures [e.g., P(k), xi (r), xi (r_sigma ,r_pi )] commonly used in the study of large-scale structure. We also examine the reliability of various tools (e.g. genus) for describing the topological structure within a contiguous region of the survey.

  3. Key Issues in Modeling of Complex 3D Structures from Video Sequences

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available Construction of three-dimensional structures from video sequences has wide applications for intelligent video analysis. This paper summarizes the key issues of the theory and surveys the recent advances in the state of the art. Reconstruction of a scene object from video sequences often takes the basic principle of structure from motion with an uncalibrated camera. This paper lists the typical strategies and summarizes the typical solutions or algorithms for modeling of complex three-dimensional structures. Open difficult problems are also suggested for further study.

  4. THE BOTTOM OF THE WHITE DWARF COOLING SEQUENCE IN THE OLD OPEN CLUSTER NGC 2158

    International Nuclear Information System (INIS)

    Bedin, L. R.; Anderson, J.; Salaris, M.; King, I. R.; Piotto, G.; Cassisi, S.

    2010-01-01

    We use 10 orbits of Advanced Camera for Surveys observations to reach the end of the white dwarf (WD) cooling sequence in the solar-metallicity open cluster NGC 2158. Our photometry and completeness tests show that the end falls at magnitude m F606W = 27.5 ± 0.15, which implies an age between ∼1.8 and ∼2.0 Gyr, consistent with the age of 1.9 ± 0.2 Gyr obtained from fits to the main-sequence turn-off. The faintest WDs show a clear turn toward bluer colors, as predicted by theoretical isochrones.

  5. A comparative evaluation of sequence classification programs

    Directory of Open Access Journals (Sweden)

    Bazinet Adam L

    2012-05-01

    Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

  6. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  7. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available 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.

  8. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    International Nuclear Information System (INIS)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-01-01

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis

  9. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  10. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  11. ESR teleradiology survey: results.

    Science.gov (United States)

    2016-08-01

    With recent developments of teleradiology technology and services, it has become necessary to better evaluate its extent and use among different countries in Europe. With this goal in mind, the ESR launched two specific surveys intended to gather the current state of adoption and implementation of teleradiology in clinical practice. A special focus on differentiating between insourcing teleradiology services among partners of the same organisation and outsourcing to external services was an essential part of the design of these surveys. The first survey was addressed to 44 national societies of different countries in Europe, while the second survey was intended for all practicing radiologist ESR members. While the results of these surveys reported here may provide a wealth of information to better understand the trends in adoption of teleradiology in Europe, they only represent a snapshot at a certain point in time. The rapid development of telecommunication tools as well as a fundamental change in practice and healthcare economics will certainly influence these observations in the upcoming years. These data, however, will provide objective and relevant parameters for supporting the efforts of experts and policy makers in promoting appropriate criteria and guidelines for adequate use of teleradiology in clinical practice. Main Messages • Understand concepts and challenges of teleradiology • Provide insight into current trends and solutions for teleradiology • Compare differences in teleradiolgy strategies between countries in Europe • Establish a reference on statistical data of usage of teleradiology in Europe.

  12. 2012 Mask Industry Survey

    Science.gov (United States)

    Malloy, Matt; Litt, Lloyd C.

    2012-11-01

    A survey supported by SEMATECH and administered by David Powell Consulting was sent to semiconductor industry leaders to gather information about the mask industry as an objective assessment of its overall condition. The survey was designed with the input of semiconductor company mask technologists and merchant mask suppliers. 2012 marks the 11th consecutive year for the mask industry survey. This year's survey and reporting structure are similar to those of the previous years with minor modifications based on feedback from past years and the need to collect additional data on key topics. Categories include general mask information, mask processing, data and write time, yield and yield loss, delivery times, and maintenance and returns. Within each category are multiple questions that result in a detailed profile of both the business and technical status of the mask industry. Results, initial observations, and key comparisons between the 2011 and 2012 survey responses are shown here, including multiple indications of a shift towards the manufacturing of higher end photomasks.

  13. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  14. Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

    Science.gov (United States)

    Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

    2017-10-01

    Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  15. Computer simulation of replacement sequences in copper

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Schwartz, D.W.; Ariyasu, R.G.; Cascadden, S.E.

    1978-01-01

    Results of computer simulations of , , and replacement sequences in copper are presented, including displacement thresholds, focusing energies, energy losses per replacement, and replacement sequence lengths. These parameters are tabulated for six interatomic potentials and shown to vary in a systematic way with potential stiffness and range. Comparisons of results from calculations made with ADDES, a quasi-dynamical code, and COMENT, a dynamical code, show excellent agreement, demonstrating that the former can be calibrated and used satisfactorily in the analysis of low energy displacement cascades. Upper limits on , , and replacement sequences were found to be approximately 10, approximately 30, and approximately 14 replacements, respectively. (author)

  16. Whole-genome sequencing of veterinary pathogens

    DEFF Research Database (Denmark)

    Ronco, Troels

    -electrophoresis and single-locus sequencing has been widely used to characterize such types of veterinary pathogens. However, DNA sequencing techniques have become fast and cost effective in recent years and whole-genome sequencing data provide a much higher discriminative power and reproducibility than any...... genetic background. This indicates that dairy cows can be natural carriers of S. aureus subtypes that in certain cases lead to CM. A group of isolates that mostly belonged to ST151 carried three pathogenicity islands that were primarily found in this group. The prevalence of resistance genes was generally...

  17. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  18. Tensor products of higher almost split sequences

    OpenAIRE

    Pasquali, Andrea

    2015-01-01

    We investigate how the higher almost split sequences over a tensor product of algebras are related to those over each factor. Herschend and Iyama gave a precise criterion for when the tensor product of an $n$-representation finite algebra and an $m$-representation finite algebra is $(n+m)$-representation finite. In this case we give a complete description of the higher almost split sequences over the tensor product by expressing every higher almost split sequence as the mapping cone of a suit...

  19. Arbitrarily accurate twin composite π -pulse sequences

    Science.gov (United States)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  20. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    2017-01-01

    algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping...... sequence. The model is based on a transient finite element analysis with the material’s constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping...