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

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

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

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 ...

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.

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...

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.

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)

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

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.

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)

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.

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…

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.

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

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...

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…

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

Photometrical research geostationary satellite "SBIRS GEO-2"

Science.gov (United States)

Sukhov, P. P.; Epishev, V. P; Sukhov, K. P; Kudak, V. I.

The multicolor photometrical observations GSS "Sbirs Geo-2" were carried in B,V,R filters out during the autumn equinox 2014 and spring 2015 y. Periodic appearance of many light curves and dips of mirror reflections suggests that the GSS was not in orbit in a static position, predetermined three-axis orientation and in dynamic motion. On the basis of computer modeling suggests the following dynamics GSS "Sbirs Geo-2" in orbit. Helically scanning the visible Earth's surface infrared satellite sensors come with period P1 = 15.66 sec. and the rocking of the GSS about the direction of the motion vector of the satellite in orbit with P2 = 62.64 sec., most likely with the purpose to survey the greatest possible portion of the earth's surface.

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,...

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.

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.

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

Prostate Cancer Patients' Understanding of the Gleason Scoring System: Implications for Shared Decision-Making.

Science.gov (United States)

Tagai, Erin K; Miller, Suzanne M; Kutikov, Alexander; Diefenbach, Michael A; Gor, Ronak A; Al-Saleem, Tahseen; Chen, David Y T; Fleszar, Sara; Roy, Gem

2018-01-15

The Gleason scoring system is a key component of a prostate cancer diagnosis, since it indicates disease aggressiveness. It also serves as a risk communication tool that facilitates shared treatment decision-making. However, the system is highly complex and therefore difficult to communicate: factors which have been shown to undermine well-informed and high-quality shared treatment decision-making. To systematically explore prostate cancer patients' understanding of the Gleason scoring system (GSS), we assessed knowledge and perceived importance among men who had completed treatment (N = 50). Patients were administered a survey that assessed patient knowledge and patients' perceived importance of the GSS, as well as demographics, medical factors (e.g., Gleason score at diagnosis), and health literacy. Bivariate analyses were conducted to identify associations with patient knowledge and perceived importance of the GSS. The sample was generally well-educated (48% with a bachelor's degree or higher) and health literate (M = 12.9, SD = 2.2, range = 3-15). Despite this, patient knowledge of the GSS was low (M = 1.8, SD = 1.4, range = 1-4). Patients' understanding of the importance of the GSS was moderate (M = 2.8, SD = 1.0, range = 0-4) and was positively associated with GSS knowledge (p decision-making. Future studies are needed to explore the potential utility of a simplified Gleason grading system and improved patient-provider communication.

The roles of human values and generalized trust on stated preferences when food is labeled with environmental footprints

DEFF Research Database (Denmark)

Grebitus, Carola; Steiner, Bodo; Veeman, Michele

2015-01-01

(Rokeach 1973), and generalized trust attitudes using a version of the World Values Survey (WVS) / General Social Survey (GSS) standard question on trust. Consumer preferences for footprint-labeled potatoes were elicited by means of an attribute-based stated choice experiment. The results suggest...

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.

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.

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

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...

Modulation of Pacemaker Potentials in Murine Small Intestinal Interstitial Cells of Cajal by Gamisoyo-San, a Traditional Chinese Herbal Medicine.

Science.gov (United States)

Kim, Doeun; Kim, Jung Nam; Nam, Joo Hyun; Lee, Jong Rok; Kim, Sang Chan; Kim, Byung Joo

2018-04-19

The Gamisoyo-san (GSS) has been used for -improving the gastrointestinal (GI) symptoms. The purpose of this study was to investigate the effects of GSS, a traditional Chinese herbal medicine, on the pacemaker potentials of mouse small intestinal interstitial cells of Cajal (ICCs). ICCs from the small intestines were dissociated and cultured. Whole-cell patch-clamp configuration was used to record pacemaker potentials and membrane currents. GSS depolarized ICC pacemaker potentials in a dose-dependent manner. Pretreatment with 4-diphenylacetoxypiperidinium iodide completely inhibited GSS-induced pacemaker potential depolarizations. Intracellular GDP-β-S inhibited GSS-induced effects, and in the presence of U-73122, GSS-induced effects were inhibited. Also, GSS in the presence of a Ca2+-free solution or thapsigargin did not depolarize pacemaker potentials. However, in the presence of calphostin C, GSS slightly depolarized pacemaker potentials. Furthermore, GSS inhibited both transient receptor potential melastatin7 and Ca2+-activated Cl- channel (anoctamin1) currents. GSS depolarized pacemaker potentials of ICCs via G protein and muscarinic M3 receptor signaling pathways and through internal or external Ca2+-, phospholipase C-, and protein kinase C-dependent and transient receptor potential melastatin 7-, and anoctamin 1-independent pathways. The study shows that GSS may regulate GI tract motility, suggesting that GSS could be a basis for developing novel prokinetic agents for treating GI motility dysfunctions. © 2018 S. Karger AG, Basel.

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

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...

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...

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...

Effects of three different formulae of Gamisoyosan on lipid accumulation induced by oleic acid in HepG2 cells

Directory of Open Access Journals (Sweden)

Hiroe Go

2017-12-01

Full Text Available Background: Gamisoyosan (GSS is an herbal formula which has been used to treat women’s diseases for several hundred years in Korea. GSS is one of the three most common prescriptions among women and is used to treat menopausal symptoms. Fatty liver disease is also common in postmenopausal women and can precede more severe diseases, such as steatohepatitis. The present study compared the effects of GSS on fatty liver using three different formulae, Dongui-Bogam (KIOM A, Korean Pharmacopeia (KIOM B and Korean National Health Insurance (KIOM C. Methods: In oleic acid-induced HepG2 fatty liver cells, cellular lipid accumulation, triglycerides and total cholesterol were measured after treatment with three GSS formulae and simvastatin as a positive control. To investigate the phytoestrogen activity of GSS, MCF-7 cells were treated with GSS, and hormone levels were quantified. Also, qualitative analysis was performed with UPLC. Results: All types of GSS decreased cellular lipid accumulation. KIOM A was slightly less effective than the other two GSS formulae. KIOM B and KIOM C decreased cellular triglycerides more effective than simvastatin, but KIOM A did not affect cellular triglycerides. Cellular total cholesterol was decreased by all GSS and simvastatin. GSS showed phytoestrogen activity in MCF-7 cells. From the UPLC analysis data, geniposide, paeoniflorin and glycyrrhizin were detected form three GSS formulae. Conclusion: These results suggest that all GSS formulae have a beneficial effect on fatty liver disease during menopause and that differences of formula have no effect on the efficacy of the prescription. Keywords: fatty liver, Gamisoyosan, menopause, phytoestrogen

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...

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

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

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

Sociopolitical Viewpoints as Narrated by Family and Educational Background.

Science.gov (United States)

Sares, Timothy A.

1998-01-01

Investigates the role social and educational history have on people's views of helpfulness, trustfulness, liberalism, and confidence in the government and organized labor; results were obtained through General Social Survey (GSS) responses. Finds support for the premise that sociopolitical and prosocial views can be traced to educational and…

A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae

Directory of Open Access Journals (Sweden)

Sheina B. Sim

2017-06-01

Full Text Available Genetic sexing strains (GSS used in sterile insect technique (SIT programs are textbook examples of how classical Mendelian genetics can be directly implemented in the management of agricultural insect pests. Although the foundation of traditionally developed GSS are single locus, autosomal recessive traits, their genetic basis are largely unknown. With the advent of modern genomic techniques, the genetic basis of sexing traits in GSS can now be further investigated. This study is the first of its kind to integrate traditional genetic techniques with emerging genomics to characterize a GSS using the tephritid fruit fly pest Bactrocera cucurbitae as a model. These techniques include whole-genome sequencing, the development of a mapping population and linkage map, and quantitative trait analysis. The experiment designed to map the genetic sexing trait in B. cucurbitae, white pupae (wp, also enabled the generation of a chromosome-scale genome assembly by integrating the linkage map with the assembly. Quantitative trait loci analysis revealed SNP loci near position 42 MB on chromosome 3 to be tightly linked to wp. Gene annotation and synteny analysis show a near perfect relationship between chromosomes in B. cucurbitae and Muller elements A–E in Drosophila melanogaster. This chromosome-scale genome assembly is complete, has high contiguity, was generated using a minimal input DNA, and will be used to further characterize the genetic mechanisms underlying wp. Knowledge of the genetic basis of genetic sexing traits can be used to improve SIT in this species and expand it to other economically important Diptera.

ICT Requirements and Challenges for Provision of Grid Services from Renewable Generation Plants

DEFF Research Database (Denmark)

Shahid, Kamal; Olsen, Rasmus Løvenstein; Petersen, Lennart

2018-01-01

The penetration of renewable energy into the electricity supply mix necessitates the traditional power grid to become more resilient, reliable and efficient. One way of ensuring this is to require renewable power plants to have similar regulating properties as conventional power plants...... applications – in terms of data payloads, sampling rates, latency and reliability. Therefore, this paper presents a brief survey on the control and communication architectures for controlling renewable power plants in the future power grid, including the communication network technologies, requirements...... and to coordinate their grid support services (GSS) as well. Among other requirements, the coordination of GSS will highly depend on the communication between renewable plants and system operators’ control rooms, thereby imposing high responsibility on the under lying communication infrastructure. Despite...

[Granulomatous slack skin associated with metastatic testicular seminoma].

Science.gov (United States)

Carton de Tournai, D; Deschamps, L; Laly, P; Zeboulon, C; Bouaziz, J-D; Ram-Wolff, C; Doumecq-Lacoste, J-M; Ortonne, N; Rivet, J; Battistella, M; Bagot, M

Granulomatous slack skin (GSS) is an extremely rare subtype of T-cell lymphoma, a variant of mycosis fungoides (MF). Herein, we describe the first reported case of GSS associated with metastatic testicular seminoma. A 28-year-old male patient presented with circumscribed erythematous loose skin masses, especially in the body folds and which had been relapsing for 4years. Skin biopsy showed a loss of elastic fibers and an atypical granulomatous T-cell infiltrate with epidermotropism, enabling a diagnosis of GSS to be made. A biopsy of a retroperitoneal lymphadenopathy showed testicular seminoma metastasis. Patients suffering from GSS have a statistically higher risk of developing a second primary cancer, especially Hodgkin's lymphoma. The association found between GSS and a lymphoproliferative malignancy requires long-term follow-up and determines the patient's prognosis. It is not possible to prove a formal link between GSS and testicular seminoma. However, this case illustrates the value of screening for a second cancer, particularly where extra-cutaneous lesions appear during GSS treatment. Lymph node biopsy should be performed routinely in the event of GSS with possible lymph node involvement. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.

Science.gov (United States)

Thabet, Rahma; Rouault, J-D; Ayadi, Habib; Leignel, Vincent

2016-01-01

The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates. Copyright © 2016 Elsevier Inc. All rights reserved.

Predicting Social Trust with Binary Logistic Regression

Science.gov (United States)

Adwere-Boamah, Joseph; Hufstedler, Shirley

2015-01-01

This study used binary logistic regression to predict social trust with five demographic variables from a national sample of adult individuals who participated in The General Social Survey (GSS) in 2012. The five predictor variables were respondents' highest degree earned, race, sex, general happiness and the importance of personally assisting…

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

A New Conservative Cold Front? Democrat and Republican Responsiveness to the Passage of the Affordable Care Act

Directory of Open Access Journals (Sweden)

Stephen L. Morgan

2015-09-01

Full Text Available Through an analysis of the 2004 through 2014 General Social Survey (GSS, this article demonstrates that the 2010 passage of the Affordable Care Act (ACA decreased support for spending on health among Democrats, Independents, and Republicans, contrary to the conjecture that a rigid partisanship equilibrium has taken hold among voters in the United States. Instead, only a partisan deflection is present, with spending preferences declining more for Republicans than for Democrats, and with Independents in between. Through supplemental analysis of the GSS panel data, as well as comparative analysis of other GSS items on national spending preferences, government responsibility, and confidence in leaders, this article also undermines support for an alternative explanation that cannot be entirely eliminated from plausibility, which is that the identified period effect that emerged in 2010 and persisted through 2014 is a response to the Great Recession and resulting deficit spending by the federal government. Implications for public opinion research are discussed, lending support to current models of thermostat effects and policy-specific political mood from the political science literature, which are informed by an older literature on weather fronts in public opinion that originated in the sociology literature.

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 ...

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 […

Reliability-based design optimization using a generalized subset simulation method and posterior approximation

Science.gov (United States)

Ma, Yuan-Zhuo; Li, Hong-Shuang; Yao, Wei-Xing

2018-05-01

The evaluation of the probabilistic constraints in reliability-based design optimization (RBDO) problems has always been significant and challenging work, which strongly affects the performance of RBDO methods. This article deals with RBDO problems using a recently developed generalized subset simulation (GSS) method and a posterior approximation approach. The posterior approximation approach is used to transform all the probabilistic constraints into ordinary constraints as in deterministic optimization. The assessment of multiple failure probabilities required by the posterior approximation approach is achieved by GSS in a single run at all supporting points, which are selected by a proper experimental design scheme combining Sobol' sequences and Bucher's design. Sequentially, the transformed deterministic design optimization problem can be solved by optimization algorithms, for example, the sequential quadratic programming method. Three optimization problems are used to demonstrate the efficiency and accuracy of the proposed method.

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

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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.

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.

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...

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.

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

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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.

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

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

Survey of transposable elements in sugarcane expressed sequence tags (ESTs

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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.

The Continuum of Aging and Age-Related Diseases: Common Mechanisms but Different Rates

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Claudio Franceschi

2018-03-01

Full Text Available Geroscience, the new interdisciplinary field that aims to understand the relationship between aging and chronic age-related diseases (ARDs and geriatric syndromes (GSs, is based on epidemiological evidence and experimental data that aging is the major risk factor for such pathologies and assumes that aging and ARDs/GSs share a common set of basic biological mechanisms. A consequence is that the primary target of medicine is to combat aging instead of any single ARD/GSs one by one, as favored by the fragmentation into hundreds of specialties and sub-specialties. If the same molecular and cellular mechanisms underpin both aging and ARDs/GSs, a major question emerges: which is the difference, if any, between aging and ARDs/GSs? The hypothesis that ARDs and GSs such as frailty can be conceptualized as accelerated aging will be discussed by analyzing in particular frailty, sarcopenia, chronic obstructive pulmonary disease, cancer, neurodegenerative diseases such as Alzheimer and Parkinson as well as Down syndrome as an example of progeroid syndrome. According to this integrated view, aging and ARDs/GSs become part of a continuum where precise boundaries do not exist and the two extremes are represented by centenarians, who largely avoided or postponed most ARDs/GSs and are characterized by decelerated aging, and patients who suffered one or more severe ARDs in their 60s, 70s, and 80s and show signs of accelerated aging, respectively. In between these two extremes, there is a continuum of intermediate trajectories representing a sort of gray area. Thus, clinically different, classical ARDs/GSs are, indeed, the result of peculiar combinations of alterations regarding the same, limited set of basic mechanisms shared with the aging process. Whether an individual will follow a trajectory of accelerated or decelerated aging will depend on his/her genetic background interacting lifelong with environmental and lifestyle factors. If ARDs and GSs are

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.

Canadian residents' perceived manager training needs.

Science.gov (United States)

Stergiopoulos, Vicky; Lieff, Susan; Razack, Saleem; Lee, A Curtis; Maniate, Jerry M; Hyde, Stacey; Taber, Sarah; Frank, Jason R

2010-01-01

Despite widespread endorsement for administrative training during residency, teaching and learning in this area remains intermittent and limited in most programmes. To inform the development of a Manager Train-the-Trainer program for faculty, the Royal College of Physicians and Surgeons of Canada undertook a survey of perceived Manager training needs among postgraduate trainees. A representative sample of Canadian specialty residents received a web-based questionnaire in 2009 assessing their perceived deficiencies in 13 Manager knowledge and 11 Manager skill domains, as determined by gap scores (GSs). GSs were defined as the difference between residents' perceived current and desired level of knowledge or skill in selected Manager domains. Residents' educational preferences for furthering their Manager knowledge and skills were also elicited. Among the 549 residents who were emailed the survey, 199 (36.2%) responded. Residents reported significant gaps in most knowledge and skills domains examined. Residents' preferred educational methods for learning Manager knowledge and skills included workshops, web-based formats and interactive small groups. The results of this national survey, highlighting significant perceived gaps in multiple Manager knowledge and skills domains, may inform the development of Manager curricula and faculty development activities to address deficiencies in training in this important area.

Evaluation of CROES Nephrolithometry Nomogram as a Preoperative Predictive System for Percutaneous Nephrolithotomy Outcomes.

Science.gov (United States)

Kumar, Sumit; Sreenivas, Jayaram; Karthikeyan, Vilvapathy Senguttuvan; Mallya, Ashwin; Keshavamurthy, Ramaiah

2016-10-01

Scoring systems have been devised to predict outcomes of percutaneous nephrolithotomy (PCNL). CROES nephrolithometry nomogram (CNN) is the latest tool devised to predict stone-free rate (SFR). We aim to compare predictive accuracy of CNN against Guy stone score (GSS) for SFR and postoperative outcomes. Between January 2013 and December 2015, 313 patients undergoing PCNL were analyzed for predictive accuracy of GSS, CNN, and stone burden (SB) for SFR, complications, operation time (OT), and length of hospitalization (LOH). We further stratified patients into risk groups based on CNN and GSS. Mean ± standard deviation (SD) SB was 298.8 ± 235.75 mm 2 . SB, GSS, and CNN (area under curve [AUC]: 0.662, 0.660, 0.673) were found to be predictors of SFR. However, predictability for complications was not as good (AUC: SB 0.583, GSS 0.554, CNN 0.580). Single implicated calix (Adj. OR 3.644; p = 0.027), absence of staghorn calculus (Adj. OR 3.091; p = 0.044), single stone (Adj. OR 3.855; p = 0.002), and single puncture (Adj. OR 2.309; p = 0.048) significantly predicted SFR on multivariate analysis. Charlson comorbidity index (CCI; p = 0.020) and staghorn calculus (p = 0.002) were independent predictors for complications on linear regression. SB and GSS independently predicted OT on multivariate analysis. SB and complications significantly predicted LOH, while GSS and CNN did not predict LOH. CNN offered better risk stratification for residual stones than GSS. CNN and GSS have good preoperative predictive accuracy for SFR. Number of implicated calices may affect SFR, and CCI affects complications. Studies should incorporate these factors in scoring systems and assess if predictability of PCNL outcomes improves.

The Binary System Laboratory Activities Based on Students Mental Model

Science.gov (United States)

Albaiti, A.; Liliasari, S.; Sumarna, O.; Martoprawiro, M. A.

2017-09-01

Generic science skills (GSS) are required to develop student conception in learning binary system. The aim of this research was to know the improvement of students GSS through the binary system labotoratory activities based on their mental model using hypothetical-deductive learning cycle. It was a mixed methods embedded experimental model research design. This research involved 15 students of a university in Papua, Indonesia. Essay test of 7 items was used to analyze the improvement of students GSS. Each items was designed to interconnect macroscopic, sub-microscopic and symbolic levels. Students worksheet was used to explore students mental model during investigation in laboratory. The increase of students GSS could be seen in their N-Gain of each GSS indicators. The results were then analyzed descriptively. Students mental model and GSS have been improved from this study. They were interconnect macroscopic and symbolic levels to explain binary systems phenomena. Furthermore, they reconstructed their mental model with interconnecting the three levels of representation in Physical Chemistry. It necessary to integrate the Physical Chemistry Laboratory into a Physical Chemistry course for effectiveness and efficiency.

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.

A NEW FRAMEWORK FOR GEOSPATIAL SITE SELECTION USING ARTIFICIAL NEURAL NETWORKS AS DECISION RULES: A CASE STUDY ON LANDFILL SITES

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S. K. M. Abujayyab

2015-10-01

Full Text Available This paper briefly introduced the theory and framework of geospatial site selection (GSS and discussed the application and framework of artificial neural networks (ANNs. The related literature on the use of ANNs as decision rules in GSS is scarce from 2000 till 2015. As this study found, ANNs are not only adaptable to dynamic changes but also capable of improving the objectivity of acquisition in GSS, reducing time consumption, and providing high validation. ANNs make for a powerful tool for solving geospatial decision-making problems by enabling geospatial decision makers to implement their constraints and imprecise concepts. This tool offers a way to represent and handle uncertainty. Specifically, ANNs are decision rules implemented to enhance conventional GSS frameworks. The main assumption in implementing ANNs in GSS is that the current characteristics of existing sites are indicative of the degree of suitability of new locations with similar characteristics. GSS requires several input criteria that embody specific requirements and the desired site characteristics, which could contribute to geospatial sites. In this study, the proposed framework consists of four stages for implementing ANNs in GSS. A multilayer feed-forward network with a backpropagation algorithm was used to train the networks from prior sites to assess, generalize, and evaluate the outputs on the basis of the inputs for the new sites. Two metrics, namely, confusion matrix and receiver operating characteristic tests, were utilized to achieve high accuracy and validation. Results proved that ANNs provide reasonable and efficient results as an accurate and inexpensive quantitative technique for GSS.

Comparative proteome analysis of glutenin synthesis and accumulation in developing grains between superior and poor quality bread wheat cultivars.

Science.gov (United States)

Liu, Wan; Zhang, Yanzhen; Gao, Xuan; Wang, Ke; Wang, Shunli; Zhang, Yong; He, Zhonghu; Ma, Wujun; Yan, Yueming

2012-01-15

Wheat glutenins are the major determinants of wheat quality. In this study, grains at the development stage from three wheat cultivars (Jimai 20, Jin 411 and Zhoumai 16) with different bread-making quality were harvested based on thermal times from 150 °C(d) to 750 °C(d) , and were used to investigate glutenin accumulation patterns and their relationships with wheat quality. High and low molecular weight glutenin subunits (HMW-GSs and LMW-GSs) were synthesised concurrently. No obvious correlations between HMW/LMW glutenin ratios and dough property were observed. Accumulation levels of HMW-GSs and LMW-GSs as well as 1Bx13 + 1By16 and 1Dx4 + 1Dy12 subunits were higher in superior gluten quality cultivar Jimain 20 than in poor quality cultivar Jing 411 and Zhoumai 16. According to the results of two-dimensional gel electrophoresis, six types of accumulation patterns in LMW-GSs were identified and classified. The possible relationships between individual LMW-GSs and gluten quality were established. The high accumulation level of HMW-GSs and LMW-GSs as well as 1Bx13 + 1By16 and 1Dx4 + 1Dy12 subunits contributed to the superior gluten quality of Jimai 20. Two highly expressed and 16 specifically expressed LMW glutenin subunits in Jimain 20 had positive effects on dough quality, while 17 specifically expressed subunits in Zhoumai 16 and Jing 411 appeared to have negative effects on gluten quality. Copyright © 2011 Society of Chemical Industry.

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

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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

Development of a new marker system for identifying the complex members of the low-molecular-weight glutenin subunit gene family in bread wheat (Triticum aestivum L.).

Science.gov (United States)

Zhang, Xiaofei; Liu, Dongcheng; Yang, Wenlong; Liu, Kunfan; Sun, Jiazhu; Guo, Xiaoli; Li, Yiwen; Wang, Daowen; Ling, Hongqing; Zhang, Aimin

2011-05-01

Low-molecular-weight glutenin subunits (LMW-GSs) play an important role in determining the bread-making quality of bread wheat. However, LMW-GSs display high polymorphic protein complexes encoded by multiple genes, and elucidating the complex LMW-GS gene family in bread wheat remains challenging. In the present study, using conventional polymerase chain reaction (PCR) with conserved primers and high-resolution capillary electrophoresis, we developed a new molecular marker system for identifying LMW-GS gene family members. Based on sequence alignment of 13 LMW-GS genes previously identified in the Chinese bread wheat variety Xiaoyan 54 and other genes available in GenBank, PCR primers were developed and assigned to conserved sequences spanning the length polymorphism regions of LMW-GS genes. After PCR amplification, 17 DNA fragments in Xiaoyan 54 were detected using capillary electrophoresis. In total, 13 fragments were identical to previously identified LMW-GS genes, and the other 4 were derived from unique LMW-GS genes by sequencing. This marker system was also used to identify LMW-GS genes in Chinese Spring and its group 1 nulli-tetrasomic lines. Among the 17 detected DNA fragments, 4 were located on chromosome 1A, 5 on 1B, and 8 on 1D. The results suggest that this marker system is useful for large-scale identification of LMW-GS genes in bread wheat varieties, and for the selection of desirable LMW-GS genes to improve the bread-making quality in wheat molecular breeding programmes.

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

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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.

Ground System Survivability Overview

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2012-03-27

Avoidance Blast Mitigation Optimization Customer ILIR RDT&E Funding 5.0 % 0.5% GSS has a proven, technically proficient workforce that meets...Evaluation of Defensive-Aid Suites (ARMED) Common Automatic Fire Extinguishing System ( CAFES ) Transparent Armor Development Ground Combat Vehicle...Survey TRADOC (WFO, CNA, etc) Voice of the Customer Sy st em s En gi ne er in g Publish overarching MIL-STD, design guidelines, technical

Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu.

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Wang, Xin; Luo, Guangbin; Yang, Wenlong; Li, Yiwen; Sun, Jiazhu; Zhan, Kehui; Liu, Dongcheng; Zhang, Aimin

2017-07-01

Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei's gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.

Effect of CO2 enrichment on the glucosinolate contents under different nitrogen levels in bolting stem of Chinese kale (Brassica alboglabra L.).

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La, Gui-xiao; Fang, Ping; Teng, Yi-bo; Li, Ya-juan; Lin, Xian-yong

2009-06-01

The effects of CO(2) enrichment on the growth and glucosinolate (GS) concentrations in the bolting stem of Chinese kale (Brassica alboglabra L.) treated with three nitrogen (N) concentrations (5, 10, and 20 mmol/L) were investigated. Height, stem thickness, and dry weights of the total aerial parts, bolting stems, and roots, as well as the root to shoot ratio, significantly increased as CO(2) concentration was elevated from 350 to 800 microl/L at each N concentration. In the edible part of the bolting stem, 11 individual GSs were identified, including 7 aliphatic and 4 indolyl GSs. GS concentration was affected by the elevated CO(2) concentration, N concentration, and CO(2)xN interaction. At 5 and 10 mmol N/L, the concentrations of aliphatic GSs and total GSs significantly increased, whereas those of indolyl GSs were not affected, by elevated atmospheric CO(2). However, at 20 mmol N/L, elevated CO(2) had no significant effects on the concentrations of total GSs and total indolyl GSs, but the concentrations of total aliphatic GSs significantly increased. Moreover, the bolting stem carbon (C) content increased, whereas the N and sulfur (S) contents decreased under elevated CO(2) concentration in the three N treatments, resulting in changes in the C/N and N/S ratios. Also the C/N ratio is not a reliable predictor of change of GS concentration, while the changes in N and S contents and the N/S ratio at the elevated CO(2) concentration may influence the GS concentration in Chinese kale bolting stems. The results demonstrate that high nitrogen supply is beneficial for the growth of Chinese kale, but not for the GS concentration in bolting stems, under elevated CO(2) condition.

Effect of CO2 enrichment on the glucosinolate contents under different nitrogen levels in bolting stem of Chinese kale (Brassica alboglabra L.)*

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La, Gui-xiao; Fang, Ping; Teng, Yi-bo; Li, Ya-juan; Lin, Xian-yong

2009-01-01

The effects of CO2 enrichment on the growth and glucosinolate (GS) concentrations in the bolting stem of Chinese kale (Brassica alboglabra L.) treated with three nitrogen (N) concentrations (5, 10, and 20 mmol/L) were investigated. Height, stem thickness, and dry weights of the total aerial parts, bolting stems, and roots, as well as the root to shoot ratio, significantly increased as CO2 concentration was elevated from 350 to 800 μl/L at each N concentration. In the edible part of the bolting stem, 11 individual GSs were identified, including 7 aliphatic and 4 indolyl GSs. GS concentration was affected by the elevated CO2 concentration, N concentration, and CO2×N interaction. At 5 and 10 mmol N/L, the concentrations of aliphatic GSs and total GSs significantly increased, whereas those of indolyl GSs were not affected, by elevated atmospheric CO2. However, at 20 mmol N/L, elevated CO2 had no significant effects on the concentrations of total GSs and total indolyl GSs, but the concentrations of total aliphatic GSs significantly increased. Moreover, the bolting stem carbon (C) content increased, whereas the N and sulfur (S) contents decreased under elevated CO2 concentration in the three N treatments, resulting in changes in the C/N and N/S ratios. Also the C/N ratio is not a reliable predictor of change of GS concentration, while the changes in N and S contents and the N/S ratio at the elevated CO2 concentration may influence the GS concentration in Chinese kale bolting stems. The results demonstrate that high nitrogen supply is beneficial for the growth of Chinese kale, but not for the GS concentration in bolting stems, under elevated CO2 condition. PMID:19489111

Small Submucosal Tumors of the Stomach: Differentiation of Gastric Schwannoma from Gastrointestinal Stromal Tumor with CT

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Choi, Jin Wook; Choi, Dong Gil; Kim, Kyoung Mee; Sohn, Tae Sung; Lee, Jun Haeng; Kim, Hee Jung; Lee, Soon Jin [Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

2012-07-15

To identify the CT features that help differentiate gastric schwannomas (GS) from small (5 cm or smaller) gastrointestinal stromal tumors (GIST) and to assess the growth rates of both tumors. We included 16 small GSs and 56 GISTs located in the stomach. We evaluated the CT features including size, contour, surface pattern, margins, growth pattern, pattern and degree of contrast enhancement, and the presence of intralesional low attenuation area, hemorrhage, calcification, surface dimpling, fistula, perilesional lymph nodes (LNs), invasion to other organs, metastasis, ascites, and peritoneal seeding. We also estimated the tumor volume doubling time. Compared with GISTs, GSs more frequently demonstrated a homogeneous enhancement pattern, exophytic or mixed growth pattern, and the presence of perilesional LNs (each p < 0.05). The intralesional low attenuation area was more common in GISTs than GSs (p < 0.05). Multivariate analyses indicated that a homogeneous enhancement pattern, exophytic or mixed growth pattern, and the presence of perilesional LNs were statistically significant (p < 0.05). Tumor volume doubling times for GSs (mean, 1685.4 days) were significantly longer than that of GISTs (mean, 377.6 days) (p = 0.004). Although small GSs and GISTs show similar imaging findings, GSs more frequently show an exophytic or mixed growth pattern, homogeneous enhancement pattern, perilesional LNs and grow slower than GISTs.

Small Submucosal Tumors of the Stomach: Differentiation of Gastric Schwannoma from Gastrointestinal Stromal Tumor with CT

International Nuclear Information System (INIS)

Choi, Jin Wook; Choi, Dong Gil; Kim, Kyoung Mee; Sohn, Tae Sung; Lee, Jun Haeng; Kim, Hee Jung; Lee, Soon Jin

2012-01-01

To identify the CT features that help differentiate gastric schwannomas (GS) from small (5 cm or smaller) gastrointestinal stromal tumors (GIST) and to assess the growth rates of both tumors. We included 16 small GSs and 56 GISTs located in the stomach. We evaluated the CT features including size, contour, surface pattern, margins, growth pattern, pattern and degree of contrast enhancement, and the presence of intralesional low attenuation area, hemorrhage, calcification, surface dimpling, fistula, perilesional lymph nodes (LNs), invasion to other organs, metastasis, ascites, and peritoneal seeding. We also estimated the tumor volume doubling time. Compared with GISTs, GSs more frequently demonstrated a homogeneous enhancement pattern, exophytic or mixed growth pattern, and the presence of perilesional LNs (each p < 0.05). The intralesional low attenuation area was more common in GISTs than GSs (p < 0.05). Multivariate analyses indicated that a homogeneous enhancement pattern, exophytic or mixed growth pattern, and the presence of perilesional LNs were statistically significant (p < 0.05). Tumor volume doubling times for GSs (mean, 1685.4 days) were significantly longer than that of GISTs (mean, 377.6 days) (p = 0.004). Although small GSs and GISTs show similar imaging findings, GSs more frequently show an exophytic or mixed growth pattern, homogeneous enhancement pattern, perilesional LNs and grow slower than GISTs.

Esophageal Sensorimotor Function and Psychological Factors Each Contribute to Symptom Severity in Globus Patients.

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Rommel, Nathalie; Van Oudenhove, Lukas; Arts, Joris; Caenepeel, Philip; Tack, Jan; Pauwels, Ans

2016-10-01

Altered upper esophageal sphincter (UES) and esophageal body (EB) sensorimotor function and psychosocial factors may both be involved in symptom generation in globus, but their common impact is not yet assessed. The aim of the study is (1) to compare UES and EB sensitivity and compliance of globus patients with healthy controls (HC); (2) to study the association of globus symptom severity (GSS) with UES and EB sensitivity and compliance, UES motor function and psychosocial factors. In 58 globus patients, GSS, somatization, and anxiety disorders were determined using validated questionnaires. In 26 HC and 42/58 patients, UES and EB sensitivity and compliance were assessed twice using barostat measurements. UES function of 27 globus patients was evaluated using high-resolution manometry. Bivariate correlations and a general linear model tested the association of these factors with GSS. UES and EB compliance did not differ between globus patients and HC. Upon repeated distension, UES habituation was seen in both groups, whereas EB sensitization (23.3±1.3 vs. 19.5±1.5 mm Hg, Pdisorder (t=3.04, P=0.004), and post-traumatic stress severity (ρ=0.40, P=0.005) were associated with GSS. UES compliance and somatization were independently associated with GSS. A trend (P=0.061) was found for the association of GSS with change in EB compliance. UES compliance, change in EB compliance, and somatization explain 40% of the variance in GSS. This indicates that globus is a complex disorder of the brain-gut axis rather than a "psychosomatic" disorder or a peripheral esophageal disorder.

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

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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.

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

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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

A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources.

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Jun-Zhi Wen

Full Text Available MicroRNAs (miRNAs are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST+GSS. Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively. Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.

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

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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...

Gerstmann-Straüssler-Scheinker disease: novel PRNP mutation and VGKC-complex antibodies.

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Jones, Matthew; Odunsi, Sola; du Plessis, Daniel; Vincent, Angela; Bishop, Matthew; Head, Mark W; Ironside, James W; Gow, David

2014-06-10

To describe a unique case of Gerstmann-Straüssler-Scheinker (GSS) disease caused by a novel prion protein (PRNP) gene mutation and associated with strongly positive voltage-gated potassium channel (VGKC)-complex antibodies (Abs). Clinical data were gathered from retrospective review of the case notes. Postmortem neuropathologic examination was performed, and DNA was extracted from frozen brain tissue for full sequence analysis of the PRNP gene. The patient was diagnosed in life with VGKC-complex Ab-associated encephalitis based on strongly positive VGKC-complex Ab titers but no detectable LGI1 or CASPR2 Abs. He died despite 1 year of aggressive immunosuppressive treatment. The neuropathologic diagnosis was GSS disease, and a novel mutation, P84S, in the PRNP gene was found. VGKC-complex Abs are described in an increasingly broad range of clinical syndromes, including progressive encephalopathies, and may be amenable to treatment with immunosuppression. However, the failure to respond to aggressive immunotherapy warns against VGKC-complex Abs being pathogenic, and their presence does not preclude the possibility of prion disease. © 2014 American Academy of Neurology.

Gerstmann-Straüssler-Scheinker disease

Science.gov (United States)

Jones, Matthew; Odunsi, Sola; du Plessis, Daniel; Vincent, Angela; Bishop, Matthew; Head, Mark W.; Ironside, James W.

2014-01-01

Objective: To describe a unique case of Gerstmann-Straüssler-Scheinker (GSS) disease caused by a novel prion protein (PRNP) gene mutation and associated with strongly positive voltage-gated potassium channel (VGKC)-complex antibodies (Abs). Methods: Clinical data were gathered from retrospective review of the case notes. Postmortem neuropathologic examination was performed, and DNA was extracted from frozen brain tissue for full sequence analysis of the PRNP gene. Results: The patient was diagnosed in life with VGKC-complex Ab–associated encephalitis based on strongly positive VGKC-complex Ab titers but no detectable LGI1 or CASPR2 Abs. He died despite 1 year of aggressive immunosuppressive treatment. The neuropathologic diagnosis was GSS disease, and a novel mutation, P84S, in the PRNP gene was found. Conclusion: VGKC-complex Abs are described in an increasingly broad range of clinical syndromes, including progressive encephalopathies, and may be amenable to treatment with immunosuppression. However, the failure to respond to aggressive immunotherapy warns against VGKC-complex Abs being pathogenic, and their presence does not preclude the possibility of prion disease. PMID:24814844

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

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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.

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...

The last frontier? High-resolution, near-bottom measurements of the Hawaiian Jurassic magnetic anomaly sequence

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Tivey, M.; Tominaga, M.; Sager, W. W.

2012-12-01

The Jurassic sequence of marine magnetic anomalies i.e. older than M29 remain the last part of the marine magnetic anomaly sequence of the geomagnetic polarity timescale (GPTS) that can be gleaned from the ocean crustal record. While Jurassic crust is present in several areas of the world's ocean basins, the oldest and arguably best preserved sequence is in the western Pacific where three lineations sets (Japanese, Hawaiian and Phoenix) converge on the oldest remaining ocean crust on the planet (i.e. crust that has not been subducted). The magnetic anomalies in these 3 lineation sets are marked by low amplitude, relatively indistinct anomalies (tiny wiggles) that collectively have been called the Jurassic quiet Zone (JQZ). Over the past 20 years we have been working on resolving the character and origin of these anomalies with various technologies to improve our resolution of this period. Following an aeromagnetic survey that revealed the possible presence of lineated anomalies older than M29 in the Japanese lineations, we conducted a deeptow magnetometer survey of the Japanese sequence in 1992. In 2002/03 we extended and confirmed this deeptow record with a deeptowed sidescan and magnetometer survey of the Japanese lineation sequence by tying in ODP Hole 801C and extending the anomaly sequence between M29 and M44. These surveys reveal remarkably fast reversals that are lineated and decrease in intensity back in time until M38, prior to which the sequence becomes somewhat confused (the LAZ or low amplitude zone) before recovering in both amplitude and lineated character around Hole 801C (M42). These results are partially supported by recently reported terrestrial magnetostratigraphy records that show the existence of reversals back to M38. A Jurassic GPTS was constructed from this Japanese anomaly sequence, but the overall global significance of the reversal sequence and systematic field intensity changes require confirmation from crustal records created at

Nursing Student Perceptions Regarding Simulation Experience Sequencing.

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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.

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

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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.

Leaf and root glucosinolate profiles of Chinese cabbage (Brassica rapa ssp. pekinensis) as a systemic response to methyl jasmonate and salicylic acid elicitation.

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Zang, Yun-xiang; Ge, Jia-li; Huang, Ling-hui; Gao, Fei; Lv, Xi-shan; Zheng, Wei-wei; Hong, Seung-beom; Zhu, Zhu-jun

2015-08-01

Glucosinolates (GSs) are an important group of defensive phytochemicals mainly found in Brassicaceae. Plant hormones jasmonic acid (JA) and salicylic acid (SA) are major regulators of plant response to pathogen attack. However, there is little information about the interactive effect of both elicitors on inducing GS biosynthesis in Chinese cabbage (Brassica rapa ssp. pekinensis). In this study, we applied different concentrations of methyl jasmonate (MeJA) and/or SA onto the leaf and root of Chinese cabbage to investigate the time-course interactive profiles of GSs. Regardless of the site of the elicitation and the concentrations of the elicitors, the roots accumulated much more GSs and were more sensitive and more rapidly responsive to the elicitors than leaves. Irrespective of the elicitation site, MeJA had a greater inducing and longer lasting effect on GS accumulation than SA. All three components of indole GS (IGS) were detected along with aliphatic and aromatic GSs. However, IGS was a major component of total GSs that accumulated rapidly in both root and leaf tissues in response to MeJA and SA elicitation. Neoglucobrassicin (neoGBC) did not respond to SA but to MeJA in leaf tissue, while it responded to both SA and MeJA in root tissue. Conversion of glucobrassicin (GBC) to neoGBC occurred at a steady rate over 3 d of elicitation. Increased accumulation of 4-methoxy glucobrassicin (4-MGBC) occurred only in the root irrespective of the type of elicitors and the site of elicitation. Thus, accumulation of IGS is a major metabolic hallmark of SA- and MeJA-mediated systemic response systems. SA exerted an antagonistic effect on the MeJA-induced root GSs irrespective of the site of elicitation. However, SA showed synergistic and antagonistic effects on the MeJA-induced leaf GSs when roots and leaves are elicitated for 3 d, respectively.

A comparative study of electrochemical performance of graphene sheets, expanded graphite and natural graphite as anode materials for lithium-ion batteries

International Nuclear Information System (INIS)

Bai, Li-Zhong; Zhao, Dong-Lin; Zhang, Tai-Ming; Xie, Wei-Gang; Zhang, Ji-Ming; Shen, Zeng-Min

2013-01-01

Highlights: • Graphene sheets (GSs), expanded graphite (EG) and natural graphite (NG) were comparatively investigated as anode materials for lithium-ion batteries. • The reversible capacity of GS electrode was almost twice that of EG electrode and three times that of NG electrode. • The first-cycle coulombic efficiency and capacity retention of NG were much bigger than those of GSs and EG. • GS and EG electrodes exhibited higher electrochemical activity and more favorable kinetic properties. -- Abstract: Three kinds of carbon materials, i.e., graphene sheets (GSs), expanded graphite (EG) and natural graphite (NG) were comparatively investigated as anode materials for lithium-ion batteries via scanning electron microscope, high-resolution transmission electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, Raman spectroscopy and a variety of electrochemical testing techniques. The test results showed that the reversible capacities of GS electrode were 1130 and 636 mA h g −1 at the current densities of 0.2 and 1 mA cm −2 , respectively, which were almost twice those of EG electrode and three times those of NG electrode. The first-cycle coulombic efficiency and capacity retention of NG were much bigger than those of GSs and EG. The notable capacity fading observed in GSs and EG may be ascribed to the disorder-induced structure instability. The larger voltage hysteresis in GS and EG electrodes was not only related to the surface functional groups, but also to the active defects in GSs and EG, which results in greater hindrance and higher overvoltage during lithium extraction from electrode. The kinetics properties of GSs, EG and NG electrodes were compared by AC impedance measurements. GS and EG electrodes exhibited higher electrochemical activity and more favorable kinetic properties during charge and discharge process

Photometrical Observations "SBIRS GEO-2"

Science.gov (United States)

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

2015-08-01

Photometrical observations GSS "SBIRS GEO 2" in B,V,R filters were carried near the equinoxes 2014-2015. Used velocity electrophotometer based on the FEU-79 in the pulse-counting mode. Received more than 25 light curves. From the known dimensions are defined; effective reflecting area - Sγλ, the spectral reflectance index - γλ, periods of light variation. Color-indices showed that in the reflected light flux from the GSS prevails "red" component. In the light curves are periodically dips and specular flash. This shows that GSS orbit is not in a static position specified triaxial orientation as in dynamic motion. Assumed following dynamics of the satellite "SBIRS GEO 2" in orbit. Helical scanning the Earth's surface visible infrared sensors satellite occurs with a period P1 = 15.66 sec. and swinging of the GSS about the direction of the motion vector of the satellite in an orbit with P2 = 62.64 sec., from the northern to the southern pole. Thus, during the period of swinging GSS going on 2 scan the visible part of the northern and southern hemispheres. In some dates observations dynamics work satellite in orbit changed.

Alignment between chain quality management and chain governance in EU pork supply chains: a Transaction-Cost-Economics perspective.

Science.gov (United States)

Wever, Mark; Wognum, Nel; Trienekens, Jacques; Omta, Onno

2010-02-01

Although inter-firm coordination of quality management is increasingly important for meeting end-customer demand in agri-food chains, few researchers focus on the relation between inter-firm quality management systems (QMS) and inter-firm governance structures (GS). However, failure to align QMSs and GSs may lead to inefficiencies in quality management because of high transaction-costs. In addition, misalignment is likely to reduce the quality of end-customer products. This paper addresses this gap in research by empirically examining the relation between QMSs and GSs in pork meat supply chains. Transaction-Cost-Economic theory is used to develop propositions about the relation between three aspects of QMSs--ownership, vertical scope and scale of adoption--and the use of different types of GSs in pork meat supply chains. To validate the propositions, seven cases are examined from four different countries. The results show that the different aspects of QMSs largely relate to specific GSs used in chains in the manner predicted by the propositions. This supports the view that alignment between QMSs and GSs is important for the efficient coordination of quality management in (pork meat) supply chains.

Supercapacitors based on high-quality graphene scrolls

Science.gov (United States)

Zeng, Fanyan; Kuang, Yafei; Liu, Gaoqin; Liu, Rui; Huang, Zhongyuan; Fu, Chaopeng; Zhou, Haihui

2012-06-01

High-quality graphene scrolls (GSS) with a unique scrolled topography are designed using a microexplosion method. Their capacitance properties are investigated by cyclic voltammetry, galvanostatic charge-discharge and electrical impedance spectroscopy. Compared with the specific capacity of 110 F g-1 for graphene sheets, a remarkable capacity of 162.2 F g-1 is obtained at the current density of 1.0 A g-1 in 6 M KOH aqueous solution owing to the unique scrolled structure of GSS. The capacity value is increased by about 50% only because of the topological change of graphene sheets. Meanwhile, GSS exhibit excellent long-term cycling stability along with 96.8% retained after 1000 cycles at 1.0 A g-1. These encouraging results indicate that GSS based on the topological structure of graphene sheets are a kind of promising material for supercapacitors.

Group support system and explanatory feedback: An experimental study of mitigating halo effect

Directory of Open Access Journals (Sweden)

Intiyas Utami

2015-12-01

Full Text Available Comprehensive assessment potentially leads to halo effect that will affect accuracy of auditors decision-making process. Biased initial audit decision will potentially influence final audit decision. It is there-fore necessary to mitigate halo effect that is the consequence of auditors good impression on clients initial condition. This re-search aims to empirically show that halo effect can be mitigated by explanatory feedback and Group Support System (GSS. The researchers experimentally mani-pulate explanatory feedback and GSS using online web-site. The subjects are stu-dents who have already taken auditing courses. The results show that: 1 explanato-ry feedback can mitigate halo effect so that audit decision will be more accurate 2 GSS can also mitigate halo effect 3 explanatory feedback and GSS are the best me-thods to mitigate halo effect.

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

77 FR 21723 - Submission for OMB Review; Comment Request

Science.gov (United States)

2012-04-11

... on actual operational planning, development of procedures, and implementation of programs to update... clearance. Geographic Support System Initiative (GSS-I)--The GSS-I is an integrated program designed to... of children's demographic characteristics currently available. Information is distributed through the...

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.

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

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

World-wide sexual compatibility in Medfly, Ceratitis capitata (Wied.), and its implications for SIT

International Nuclear Information System (INIS)

Cayol, J.P.

2000-01-01

The concept of the sterile insect technique, described by Knipling (1953), to control and/or eradicate insect pest populations has been applied to many Lepidoptera and Diptera species. Among Diptera species, the Mediterranean fruit fly, Ceratitis capitata (Wied.) (Diptera: Tephritidae), is often referred to as the most important agricultural pest in the world (Liquido et al. 1990) and it is also a major target of SIT action programmes world-wide. The use of SIT requires that mass rearing facilities be developed to produce sterile insects for use in national programmes, with mass reared strains being established by colonising wild insects collected from the SIT target area. More recently, with the increasing demand for sterile Medflies and the limited number of production facilities, some rearing facilities began to export Medflies to other national/regional programmes. Eight facilities have now reached production levels which allow them to export sterile insects (Fisher and Caceres 199) on a regional or inter-regional basis. When this procedure is used, the flies released have to compete with wild flies of a different geographic origin. The increasing use of Medfly genetic sexing strains (GSS) has also resulted in the same strain being used in different countries. To date, five rearing facilities in the world produce GSS (Fisher and Caceres 1999). Since GSS are assembled from specific components, it is impossible to 'colonise' them from each country where sterile GSS flies are needed. The GSS are often backcrossed with insects from the target population to increase the genetic variability (Franz et al. 1996), although in some cases this presents problems (Franz, personal communication). In practice, a single wild population is used as a basis for the synthesis of the GSS. Consequently, the same GSS based on the same wild genetic material may be used in various countries/continents and the question was raised concerning the sexual compatibility of these strains with

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.

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.

Gap solitons in elongated geometries: The one-dimensional Gross-Pitaevskii equation and beyond

International Nuclear Information System (INIS)

Mateo, A. Munoz; Delgado, V.; Malomed, Boris A.

2011-01-01

We report results of a systematic analysis of matter-wave gap solitons (GSs) in three-dimensional self-repulsive Bose-Einstein condensates (BECs) loaded into a combination of a cigar-shaped trap and axial optical-lattice (OL) potential. Basic cases of the strong, intermediate, and weak radial (transverse) confinement are considered, as well as settings with shallow and deep OL potentials. Only in the case of the shallow lattice combined with tight radial confinement, which actually has little relevance to realistic experimental conditions, does the usual one-dimensional (1D) cubic Gross-Pitaevskii equation (GPE) furnish a sufficiently accurate description of GSs. However, the effective 1D equation with the nonpolynomial nonlinearity, derived in Ref. [Phys. Rev. A 77, 013617 (2008)], provides for quite an accurate approximation for the GSs in all cases, including the situation with weak transverse confinement, when the soliton's shape includes a considerable contribution from higher-order transverse modes, in addition to the usual ground-state wave function of the respective harmonic oscillator. Both fundamental GSs and their multipeak bound states are considered. The stability is analyzed by means of systematic simulations. It is concluded that almost all the fundamental GSs are stable, while their bound states may be stable if the underlying OL potential is deep enough.

Genetic stratigraphy and palaeoenvironmental controls on coal distribution in the Witbank Basin Coalfield

Energy Technology Data Exchange (ETDEWEB)

LeBlanc, G

1981-01-01

Subsurface data from over 1200 boreholes in the Witbank basin coalfield provided information for determining the coalfield stratigraphy and the palaeoenvironmental controls on coal distribution. The inadequacies of existing coalfield lithostratigraphy are obviated by the erection of a genetic coalfield stratigraphy. A total of ten areally extensive defined marker surfaces resolve the sedimentary succession into nine defined fundamental genetically realted stratal increments, termed Genetic increments of strata(GIS's); these are grouped into four defined Genetic Sequences of Strata (GSS's), termed from the base upwards, the Witbank, Coalville, Middleburg and Van Dyks Drift GSS's which are respectively grouped to comprise a single genetic Generation of strata, termed the Ogies Generation. Coalfield genetic stratigraphy is summarized in graphic mode in a composite stratigraphic column. It is concluded from this study that with the northward retreat of the late-Palaeozoic Gondwana ice sheet a series of glacial valleys, partially filled with diamicite, dominated the landscape along the northern edge of the Karoo basin. Consequent outwash sediments constitute the Witbank GSS and accumulated as paraglacial, glaciofluvial and glaciolacustrine deltaic deposits, in the primeval Dwyka-Ecca Sea. Upon abandonment, shallow-rooted Tundra vegetation proliferated, and multi-channel outwash streams were stabilised, confined and enveloped by areally extensive accumulation of peat, that reached up to 24 m in thickness, and which constituted precursors to the 1 and 2 Seam coals which attain a combined thickness of up to 12,5 m. Variations i coal petrographic character and ash content are attributed to: overbank splaying within the proximity of recognisable syndepositional (in-seam) vegetation-stabilised channels; and to the progressively increased introduction of suspended sediment as a consequence of transgressive inundation prior to burial.

Clobetasol propionate shampoo 0.05% is efficacious and safe for long-term control of moderate scalp psoriasis.

Science.gov (United States)

Poulin, Yves; Papp, Kim; Bissonnette, Robert; Barber, Kirk; Kerrouche, Nabil; Villemagne, Hervé

2010-05-01

We evaluated in this study the efficacy and safety of an alternate regimen using clobetasol propionate 0.05% shampoo (CP shampoo) for long-term control of scalp psoriasis. Patients with moderate scalp psoriasis (Global Severity Score [GSS] of 3 on a 0-5 scale) first received CP shampoo once daily for 4 weeks. Patients with a GSS shampoo or vehicle twice weekly. When relapse (GSS > 2) occurred, patients received the 4-week daily CP shampoo treatment. Patients who had a GSS shampoo, almost 4 months later than with vehicle (30.5 days;p shampoo (40.3%) than with vehicle (11.6%;p shampoo was also safe during the 7-month study period, without leading to more cases of skin atrophy, telangiectasia, hypothalamic-pituitary-adrenal (HPA) axis suppression or adverse events compared to vehicle. The alternate treatment regimen with CP shampoo is efficacious and safe for long-term management of moderate scalp psoriasis.

Epilepsy and its Impact on psychosocial outcomes in Canadian children: Data from the National Longitudinal Study of Children and Youth (NLSCY).

Science.gov (United States)

Prasad, A N; Corbett, B

2016-12-01

The purpose of this study was to use data from a population-based survey to evaluate the association between childhood epilepsy and social outcomes through tests of mathematics skills, and sense of general self-esteem (GSS). Using data from Cycles 1 to 8 of the National Longitudinal Survey of Children and Youth (NLSCY), Hierarchical linear modeling (HLM) was used to compare baseline math scores and changes in math scores and sense of general self esteem (GSS) over time in children with and without epilepsy. Scores of Health Utility Index (HUI) were factored into the analysis. Children with epilepsy do not significantly differ in their scaled math scores in comparison to their peers without epilepsy, at age 12; however, in the two level HLM model the children with epilepsy lagged behind the healthy comparison group in terms of their growth in acquiring knowledge in mathematics. Additionally, when children with epilepsy carry an added health impairment as measured by an imperfect health utility (HUI) score the group shows a slower rate of growth in their math scores over time. Self-esteem measures show variable effects in children with epilepsy alone, and those with added health impairments. The interaction with HUI scores shows a significant negative effect on self-esteem, when epilepsy is associated with added health impairment. The findings suggest that the population of Canadian children surveyed with epilepsy are vulnerable to poorer academic outcomes in mathematics in later years, and this problem is compounded further with the presence of other additional health impairments. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

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

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.

Influence of low-molecular-weight glutenin subunit haplotypes on dough rheology and baking quality in elite common wheat varieties

Science.gov (United States)

The low molecular weight glutenin subunits (LMW-GSs) are a class of wheat seed storage proteins directly involved in the formation of gluten. Depending on the first amino acid residue of the mature proteins, the LMW-GSs are divided into methionine, serine or isoleucine type. These proteins are encod...

Spatial prediction of ground subsidence susceptibility using an artificial neural network.

Science.gov (United States)

Lee, Saro; Park, Inhye; Choi, Jong-Kuk

2012-02-01

Ground subsidence in abandoned underground coal mine areas can result in loss of life and property. We analyzed ground subsidence susceptibility (GSS) around abandoned coal mines in Jeong-am, Gangwon-do, South Korea, using artificial neural network (ANN) and geographic information system approaches. Spatial data of subsidence area, topography, and geology, as well as various ground-engineering data, were collected and used to create a raster database of relevant factors for a GSS map. Eight major factors causing ground subsidence were extracted from the existing ground subsidence area: slope, depth of coal mine, distance from pit, groundwater depth, rock-mass rating, distance from fault, geology, and land use. Areas of ground subsidence were randomly divided into a training set to analyze GSS using the ANN and a test set to validate the predicted GSS map. Weights of each factor's relative importance were determined by the back-propagation training algorithms and applied to the input factor. The GSS was then calculated using the weights, and GSS maps were created. The process was repeated ten times to check the stability of analysis model using a different training data set. The map was validated using area-under-the-curve analysis with the ground subsidence areas that had not been used to train the model. The validation showed prediction accuracies between 94.84 and 95.98%, representing overall satisfactory agreement. Among the input factors, "distance from fault" had the highest average weight (i.e., 1.5477), indicating that this factor was most important. The generated maps can be used to estimate hazards to people, property, and existing infrastructure, such as the transportation network, and as part of land-use and infrastructure planning.

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.

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.)

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.

Choroba Gerstmanna-Sträusslera-Scheinkera

Directory of Open Access Journals (Sweden)

Paweł P. Liberski

2011-04-01

Full Text Available Choroba Gerstmanna-Sträusslera-Scheinkera (GSS jest genetycznie uwarunkowaną chorobą wywoływaną przez priony. Jest ona unikalna, ponieważ udało się przepasażować GSS na naczelne i gryzonie przynajmniej z mózgu obarczonego mutacją kodonu 102. Tym samym jest to jedyne schorzenie jednocześnie genetycznie uwarunkowane i zakaźne, aczkolwiek natura czynnika infekcyjnego (prionu nadal stanowi przedmiot dyskusji. W obrazie klinicznym GSS dominuje postępująca ataksja móżdżkowa z towarzyszącym otępieniem i objawami piramidowo-pozapiramidowymi. Jest to jednak choroba heterogenna, o różnym obrazie klinicznym u nosicieli różnych mutacji, a nawet u nosicieli tej samej mutacji. Obraz neuropatologiczny obejmuje obecność PrPd – immunododatnich złogów amyloidu pod postacią blaszek, zwłaszcza tzw. blaszek wielordzeniowych. Istnieje kilka modeli GSS. U myszy transgenicznych z nadekspresją zmutowanego genu kodującego PrP obserwuje się spontaniczną chorobę zwyrodnieniową, pasażowalną na myszy transgeniczne o niskiej liczbie transgenu. U myszy transgenicznych uzyskanych drogą wzajemnej rekombinacji, a więc bez nadeskpresji, nie występuje choroba spontaniczna, niemniej stają się one wrażliwe na zakażenie GSS.

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.

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.

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.

Clarification of the Memory Artefact in the Assessment of Suggestibility

Science.gov (United States)

Willner, P.

2008-01-01

Aim: The Gudjonsson Suggestibility Scale (GSS) assesses suggestibility by asking respondents to recall a short story, followed by exposure to leading questions and pressure to change their responses. Suggestibility, as assessed by the GSS, appears to be elevated in people with intellectual disabilities (ID). This has been shown to reflect to some…

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Indian Academy of Sciences (India)

the DNA that encodes them. There is a genetically inherited form of human prion disease, known as Gerstmann-Straussler-. Scheinker syndrome (GSS). GSS is accompanied by a single amino acid change in the normal PrP. When the corresponding change is introduced into the mouse PrP gene, it leads to spontanous ...

Sustainability of the Dissemination of an Occupational Sun Protection Program in a Randomized Trial

Science.gov (United States)

Buller, David B.; Walkosz, Barbara J.; Andersen, Peter A.; Scott, Michael D.; Dignan, Mark B.; Cutter, Gary R.; Zhang, Xiao; Kane, Ilima L.

2012-01-01

Sustainability of an occupational sun safety program, Go Sun Smart (GSS), was explored in a randomized trial, testing dissemination strategies at 68 U.S. and Canadian ski areas in 2004-2007. All ski areas received GSS from the National Ski Areas Association through a Basic Dissemination Strategy (BDS) using conference presentations and free…

Survey of bat populations from Mexico and Paraguay for rabies.

Science.gov (United States)

Sheeler-Gordon, L L; Smith, J S

2001-07-01

A mammalian survey was conducted in Mexico (October 1994-January 1996) and in Paraguay (August 1996-March 1997); a complete specimen was collected for each bat in the survey, including primary voucher specimen, ectoparasites, karyotype, and various frozen tissues. The surveys combined provided 937 brain samples (65 bat species) for rabies diagnosis. One male Lasiurus ega, collected in Paraguay, tested positive for the rabies virus (overall prevalence rate of 0.1%). Nucleotide sequence from a 300 bp region of the rabies nucleoprotein gene was compared with sequence obtained from representative rabies virus samples in the repository at the Centers for Disease Control and Prevention (Atlanta, Georgia, USA). Rabies virus extracted from the brain material of L. ega differed by only one nucleotide from a 300 bp consensus sequence (>99% homology) derived from samples for the variant of rabies virus transmitted by Lasiurus cinereus. Lasiurus ego differed by approximately 15% for the variant transmitted by Desmodus rotundus. Phylogenetic analysis found no evidence to suggest L. ego is a reservoir for rabies antigenic variant 6. The most likely explanation for rabies in L. ega was infection following contact with a rabid L. cinereus.

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

Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera

Directory of Open Access Journals (Sweden)

Elsik Chris

2010-10-01

Full Text Available Abstract Background The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera. Here we present an initial survey of the V. destructor genome carried out to advance our understanding of Varroa biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of Varroa-Apis interactions and defines the challenges ahead for a comprehensive Varroa genome project. Results The genome size was estimated by flow cytometry to be 565 Mbp, larger than most sequenced insects but modest relative to some other Acari. Genomic DNA pooled from ~1,000 mites was sequenced to 4.3× coverage with 454 pyrosequencing. The 2.4 Gbp of sequencing reads were assembled into 184,094 contigs with an N50 of 2,262 bp, totaling 294 Mbp of sequence after filtering. Genic sequences with homology to other eukaryotic genomes were identified on 13,031 of these contigs, totaling 31.3 Mbp. Alignment of protein sequence blocks conserved among V. destructor and four other arthropod genomes indicated a higher level of sequence divergence within this mite lineage relative to the tick Ixodes scapularis. A number of microbes potentially associated with V. destructor were identified in the sequence survey, including ~300 Kbp of sequence deriving from one or more bacterial species of the Actinomycetales. The presence of this bacterium was confirmed in individual mites by PCR assay, but varied significantly by age and sex of mites. Fragments of a novel virus related to the Baculoviridae were also identified in the survey. The rate of single nucleotide polymorphisms (SNPs in the pooled mites was estimated to be 6.2 × 10-5per bp, a low rate consistent with the historical demography and life history of the species. Conclusions This survey has provided general tools for the research community and novel directions for investigating the biology and control of

High-levels of acquired drug resistance in adult patients failing first-line antiretroviral therapy in a rural HIV treatment programme in KwaZulu-Natal, South Africa.

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Justen Manasa

Full Text Available To determine the frequency and patterns of acquired antiretroviral drug resistance in a rural primary health care programme in South Africa.Cross-sectional study nested within HIV treatment programme.Adult (≥ 18 years HIV-infected individuals initially treated with a first-line stavudine- or zidovudine-based antiretroviral therapy (ART regimen and with evidence of virological failure (one viral load >1000 copies/ml were enrolled from 17 rural primary health care clinics. Genotypic resistance testing was performed using the in-house SATuRN/Life Technologies system. Sequences were analysed and genotypic susceptibility scores (GSS for standard second-line regimens were calculated using the Stanford HIVDB 6.0.5 algorithms.A total of 222 adults were successfully genotyped for HIV drug resistance between December 2010 and March 2012. The most common regimens at time of genotype were stavudine, lamivudine and efavirenz (51%; and stavudine, lamivudine and nevirapine (24%. Median duration of ART was 42 months (interquartile range (IQR 32-53 and median duration of antiretroviral failure was 27 months (IQR 17-40. One hundred and ninety one (86% had at least one drug resistance mutation. For 34 individuals (15%, the GSS for the standard second-line regimen was <2, suggesting a significantly compromised regimen. In univariate analysis, individuals with a prior nucleoside reverse-transcriptase inhibitor (NRTI substitution were more likely to have a GSS <2 than those on the same NRTIs throughout (odds ratio (OR 5.70, 95% confidence interval (CI 2.60-12.49.There are high levels of drug resistance in adults with failure of first-line antiretroviral therapy in this rural primary health care programme. Standard second-line regimens could potentially have had reduced efficacy in about one in seven adults involved.

THE MID-INFRARED AND NEAR-ULTRAVIOLET EXCESS EMISSIONS OF QUIESCENT GALAXIES ON THE RED SEQUENCE

International Nuclear Information System (INIS)

Ko, Jongwan; Lee, Jong Chul; Hwang, Ho Seong; Sohn, Young-Jong

2013-01-01

We study the mid-infrared (IR) and near-ultraviolet (UV) excess emissions of spectroscopically selected quiescent galaxies on the optical red sequence. We use the Wide-field Infrared Survey Explorer mid-IR and Galaxy Evolution Explorer near-UV data for a spectroscopic sample of galaxies in the Sloan Digital Sky Survey Data Release 7 to study the possible connection between quiescent red-sequence galaxies with and without mid-IR/near-UV excess. Among 648 12 μm detected quiescent red-sequence galaxies without Hα emission, 26% and 55% show near-UV and mid-IR excess emissions, respectively. When we consider only bright (M r n 4000 than those without mid-IR and near-UV excess emissions. We also find that mid-IR weighted mean stellar ages of quiescent red-sequence galaxies with mid-IR excess are larger than those with near-UV excess, and smaller than those without mid-IR and near-UV excess. The environmental dependence of the fraction of quiescent red-sequence galaxies with mid-IR and near-UV excess seems strong even though the trends of quiescent red-sequence galaxies with near-UV excess differ from those with mid-IR excess. These results indicate that the recent star formation traced by near-UV (∼< 1 Gyr) and mid-IR (∼< 2 Gyr) excess is not negligible among nearby, quiescent, red, early-type galaxies. We suggest a possible evolutionary scenario of quiescent red-sequence galaxies from quiescent red-sequence galaxies with near-UV excess to those with mid-IR excess to those without near-UV and mid-IR excess.

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

Genetic counselors' views and experiences with the clinical integration of genome sequencing.

Science.gov (United States)

Machini, Kalotina; Douglas, Jessica; Braxton, Alicia; Tsipis, Judith; Kramer, Kate

2014-08-01

In recent years, new sequencing technologies known as next generation sequencing (NGS) have provided scientists the ability to rapidly sequence all known coding as well as non-coding sequences in the human genome. As the two emerging approaches, whole exome (WES) and whole genome (WGS) sequencing, have started to be integrated in the clinical arena, we sought to survey health care professionals who are likely to be involved in the implementation process now and/or in the future (e.g., genetic counselors, geneticists and nurse practitioners). Two hundred twenty-one genetic counselors- one third of whom currently offer WES/WGS-participated in an anonymous online survey. The aims of the survey were first, to identify barriers to the implementation of WES/WGS, as perceived by survey participants; second, to provide the first systematic report of current practices regarding the integration of WES/WGS in clinic and/or research across the US and Canada and to illuminate the roles and challenges of genetic counselors participating in this process; and third to evaluate the impact of WES/WGS on patient care. Our results showed that genetic counseling practices with respect to WES/WGS are consistent with the criteria set forth in the ACMG 2012 policy statement, which highlights indications for testing, reporting, and pre/post test considerations. Our respondents described challenges related to offering WES/WGS, which included billing issues, the duration and content of the consent process, result interpretation and disclosure of incidental findings and variants of unknown significance. In addition, respondents indicated that specialty area (i.e., prenatal and cancer), lack of clinical utility of WES/WGS and concerns about interpretation of test results were factors that prevented them from offering this technology to patients. Finally, study participants identified the aspects of their professional training which have been most beneficial in aiding with the integration of

Ordinary or peculiar men? Comparing the customers of prostitutes with a nationally representative sample of men.

Science.gov (United States)

Monto, Martin A; Milrod, Christine

2014-07-01

Recent media attention implies that prostitution seeking is widespread, an "ordinary" aspect of masculine sexual behavior. Other accounts suggest that customers are "peculiar," characterized by distinct qualities, perversions, or psychological impairments. Using the nationally representative General Social Survey (GSS), this study demonstrates that prostitution seeking is relatively uncommon. Only about 14% of men in the United States report having ever paid for sex, and only 1% report having done so during the previous year. Furthermore, this study dissects whether customers are ordinary or peculiar by comparing a new sample of active customers who solicit sex on the Internet with an older sample of arrested customers, a sample of customers from the GSS, and a nationally representative sample of noncustomers. The customers of Internet sexual service providers differed greatly from men in general and also from other customers. The remaining samples of customers differed slightly from noncustomers in general. We argue for a balanced perspective that recognizes the significant variety among customers. There is no evidence of a peculiar quality that differentiates customers in general from men who have not paid for sex. © The Author(s) 2013.

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.

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...

Green Supplier Selection Criteria

DEFF Research Database (Denmark)

Nielsen, Izabela Ewa; Banaeian, Narges; Golinska, Paulina

2014-01-01

Green supplier selection (GSS) criteria arise from an organization inclination to respond to any existing trends in environmental issues related to business management and processes, so GSS is integrating environmental thinking into conventional supplier selection. This research is designed...... to determine prevalent general and environmental supplier selection criteria and develop a framework which can help decision makers to determine and prioritize suitable green supplier selection criteria (general and environmental). In this research we considered several parameters (evaluation objectives......) to establish suitable criteria for GSS such as their production type, requirements, policy and objectives instead of applying common criteria. At first a comprehensive and deep review on prevalent and green supplier selection literatures performed. Then several evaluation objectives defined to assess the green...

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

Resistance to Spodoptera frugiperda (Lepidoptera: Noctuidae) and Euxesta stigmatias (Diptera: Ulidiidae) in sweet corn derived from exogenous and endogenous genetic systems.

Science.gov (United States)

Nuessly, G S; Scully, B T; Hentz, M G; Beiriger, R; Snook, M E; Widstrom, N W

2007-12-01

Field trials using Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) and Euxesta stigmatias Loew (Diptera: Ulidiidae) were conducted to evaluate resistance and potential damage interactions between these two primary corn, Zea mays L., pests against Lepidoptera-resistant corn varieties derived from both endogenous and exogenous sources. The endogenous source of resistance was maysin, a C-glycosyl flavone produced in high concentrations in varieties 'Zapalote Chico 2451' and 'Zapalote Chico sh2'. The exogenous resistance source was the Bacillus thuringiensis (Bt)11 gene that expresses Cry1A(b) insecticidal protein found in 'Attribute GSS-0966'. Damage by the two pests was compared among these resistant varieties and the susceptible 'Primetime'. Single-species tests determined that the Zapalote Chico varieties and GSS-0966 effectively reduced S. frugiperda larval damage compared with Primetime. E. stigmatias larval damage was less in the Zapalote Chico varieties than the other varieties in single-species tests. E. stigmatias damage was greater on S. frugiperda-infested versus S. frugiperda-excluded ears. Ears with S. frugiperda damage to husk, silk and kernels had greater E. stigmatias damage than ears with less S. frugiperda damage. Reversed phase high-performance liquid chromatography analysis of nonpollinated corn silk collected from field plots determined that isoorientin, maysin, and apimaysin plus 3'-methoxymaysin concentrations followed the order Zapalote Chico sh2 > Zapalote Chico 2451 > Attribute GSS-0966 = Primetime. Chlorogenic acid concentrations were greatest in Zapalote Chico 2451. The two high maysin Zapalote Chico varieties did as well against fall armyworm as the Bt-enhanced GSS-0966, and they outperformed GSS-0966 against E. stigmatias.

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.

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.

Mass rearing of the Medfly temperature sensitive lethal genetic sexing strain in Guatemala

International Nuclear Information System (INIS)

Caceres, C.; Fisher, K.; Rendon, P.

2000-01-01

Field tests have demonstrated the increased efficiency of the sterile insect technique (SIT) for the Mediterranean fruit fly (Ceratitis capitata Wied.), when only male Medflies are released (Robinson et al. 1986, Nitzan et al. 1993, McInnis et al. 1994, Rendon 1996). Genetic sexing strains (GSS) of Medflies, containing temperature sensitive lethal (tsl) and white pupae colour (wp) mutations (Franz et al. 1994) developed by FAO/IAEA, allow the separation of male flies from female flies. GSS technology has reached a stage where it is being used in large-scale operational programmes, such as the Moscamed Program in Guatemala. GSS based on the wp/tsl have the advantages of: 1) not requiring sophisticated equipment for sex separation, 2) a high accuracy of separation (> 99.5% males) is possible and, 3) separation is achieved during egg development, which excludes the unnecessary rearing of females (Franz et al. 1996). It was shown by Franz et al. (1994) that tsl GSS are genetically stable for many generations under small-scale rearing conditions. However, under the large-scale rearing of operational programmes such as Moscamed (Hentze and Mata 1987), a gradual loss of the sex separation mechanism through recombination remains a problem, as has been demonstrated in Guatemala during 1994-1996. This in no way precludes the use of GSS technology, but it does mean that a management system must be used to control this gradual loss of stability; a strategy for colony management which maintains a stable and high level of accuracy of male-only production. The El Pino facility, which mass produces sterile flies for the Guatemala Medflies SIT Program, has introduced a filter rearing system (FRS) (Fisher and Caceres 1999), and has demonstrated in a Medfly tsl GSS known as VIENNA 4/Tol-94, that genetic stability can be maintained. We report the operation of the FRS and its impact upon genetic stability and male-only production. The concept of the FRS has the potential to improve the

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.

Strain-induced phase transition and electron spin-polarization in graphene spirals.

Science.gov (United States)

Zhang, Xiaoming; Zhao, Mingwen

2014-07-16

Spin-polarized triangular graphene nanoflakes (t-GNFs) serve as ideal building blocks for the long-desired ferromagnetic graphene superlattices, but they are always assembled to planar structures which reduce its mechanical properties. Here, by joining t-GNFs in a spiral way, we propose one-dimensional graphene spirals (GSs) with superior mechanical properties and tunable electronic structures. We demonstrate theoretically the unique features of electron motion in the spiral lattice by means of first-principles calculations combined with a simple Hubbard model. Within a linear elastic deformation range, the GSs are nonmagnetic metals. When the axial tensile strain exceeds an ultimate strain, however, they convert to magnetic semiconductors with stable ferromagnetic ordering along the edges. Such strain-induced phase transition and tunable electron spin-polarization revealed in the GSs open a new avenue for spintronics devices.

Theoretical analysis of sound transmission loss through graphene sheets

International Nuclear Information System (INIS)

Natsuki, Toshiaki; Ni, Qing-Qing

2014-01-01

We examine the potential of using graphene sheets (GSs) as sound insulating materials that can be used for nano-devices because of their small size, super electronic, and mechanical properties. In this study, a theoretical analysis is proposed to predict the sound transmission loss through multi-layered GSs, which are formed by stacks of GS and bound together by van der Waals (vdW) forces between individual layers. The result shows that the resonant frequencies of the sound transmission loss occur in the multi-layered GSs and the values are very high. Based on the present analytical solution, we predict the acoustic insulation property for various layers of sheets under both normal incident wave and acoustic field of random incidence source. The scheme could be useful in vibration absorption application of nano devices and materials

Theoretical analysis of sound transmission loss through graphene sheets

Energy Technology Data Exchange (ETDEWEB)

Natsuki, Toshiaki, E-mail: natsuki@shinshu-u.ac.jp [Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda 386-8567 (Japan); Institute of Carbon Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano 380-8553 (Japan); Ni, Qing-Qing [Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda 386-8567 (Japan)

2014-11-17

We examine the potential of using graphene sheets (GSs) as sound insulating materials that can be used for nano-devices because of their small size, super electronic, and mechanical properties. In this study, a theoretical analysis is proposed to predict the sound transmission loss through multi-layered GSs, which are formed by stacks of GS and bound together by van der Waals (vdW) forces between individual layers. The result shows that the resonant frequencies of the sound transmission loss occur in the multi-layered GSs and the values are very high. Based on the present analytical solution, we predict the acoustic insulation property for various layers of sheets under both normal incident wave and acoustic field of random incidence source. The scheme could be useful in vibration absorption application of nano devices and materials.

Comparison of the ablation ability of nucleus pulposus after 1,064 nm Nd:YAG laser and 980 nm diode laser radiation.

Science.gov (United States)

Yin, Jian; Han, Zhengfeng; Guo, Baofeng; Guo, Han; Zhang, Tongtong; Zeng, Yanjun; Ren, Longxi

2015-07-01

To compare the ablation ability of nucleus pulposus after 1,064 nm Nd:YAG laser and 980 nm diode laser radiation. Goat spine specimen (GSS) was radiated using Nd:YAG laser and 980 nm diode laser and then divided into five groups based on the final energy--200, 400, 600, 800 and 1,000 J groups. The ablation quality of nucleus pulposus after radiation was recorded. The ablation quality of GSS was greater at higher radiation energies in both lasers. When compared at the same energy level, the ablation quality of GSS was greater in 980 nm diode laser than in 1,064 nm Nd:YAG laser. Statistical significance was observed in 200 and 400 J groups (P diode laser showed better ablation ability than 1,064 nm Nd:YAG laser.

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.

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...

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.

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.

County-level job automation risk and health: Evidence from the United States.

Science.gov (United States)

Patel, Pankaj C; Devaraj, Srikant; Hicks, Michael J; Wornell, Emily J

2018-04-01

Previous studies have observed a positive association between automation risk and employment loss. Based on the job insecurity-health risk hypothesis, greater exposure to automation risk could also be negatively associated with health outcomes. The main objective of this paper is to investigate the county-level association between prevalence of workers in jobs exposed to automation risk and general, physical, and mental health outcomes. As a preliminary assessment of the job insecurity-health risk hypothesis (automation risk → job insecurity → poorer health), a structural equation model was used based on individual-level data in the two cross-sectional waves (2012 and 2014) of General Social Survey (GSS). Next, using county-level data from County Health Rankings 2017, American Community Survey (ACS) 2015, and Statistics of US Businesses 2014, Two Stage Least Squares (2SLS) regression models were fitted to predict county-level health outcomes. Using the 2012 and 2014 waves of the GSS, employees in occupational classes at higher risk of automation reported more job insecurity, that, in turn, was associated with poorer health. The 2SLS estimates show that a 10% increase in automation risk at county-level is associated with 2.38, 0.8, and 0.6 percentage point lower general, physical, and mental health, respectively. Evidence suggests that exposure to automation risk may be negatively associated with health outcomes, plausibly through perceptions of poorer job security. More research is needed on interventions aimed at mitigating negative influence of automation risk on health. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impacts of care-giving and sources of support: a comparison of end-of-life and non-end-of-life caregivers in Canada.

Science.gov (United States)

Williams, Allison M; Wang, Li; Kitchen, Peter

2016-03-01

This is the second in a series of papers that deal with care-giving in Canada, as based on data available from the Canadian General Social Survey (2007). Building on the first paper, which reviewed the differences between short-term, long-term and end-of-life (EOL) caregivers, this paper uniquely examines the caregiver supports employed by EOL caregivers when compared to non-EOL caregivers (short-term and long-term caregivers combined). Both papers employ data from Statistics Canada's General Social Survey (GSS Cycle 21: 2007). The GSS includes three modules, where respondents were asked questions about the unpaid home care assistance that they had provided in the last 12 months to someone at EOL or with either a long-term health condition or a physical limitation. The objective of this research paper was to investigate the link between the impact of the care-giving experience and the caregiver supports received, while also examining the differences in these across EOL and non-EOL caregivers. By way of factor analysis and regression modelling, we examine differences between two types of caregivers: (i) EOL and (ii) non-EOL caregivers. The study revealed that with respect to socio-demographic characteristics, health outcomes and caregiver supports, EOL caregivers were consistently worse off. This suggests that although all non-EOL caregivers are experiencing negative impacts from their care-giving role, comparatively greater supports are needed for EOL caregivers. © 2015 The Authors. Health and Social Care in the Community Published by John Wiley & Sons Ltd.

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…

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...

Antiretroviral neuropenetration scores better correlate with cognitive performance of HIV-infected patients after accounting for drug susceptibility.

Science.gov (United States)

Fabbiani, Massimiliano; Grima, Pierfrancesco; Milanini, Benedetta; Mondi, Annalisa; Baldonero, Eleonora; Ciccarelli, Nicoletta; Cauda, Roberto; Silveri, Maria C; De Luca, Andrea; Di Giambenedetto, Simona

2015-01-01

The aim of the study was to explore how viral resistance and antiretroviral central nervous system (CNS) penetration could impact on cognitive performance of HIV-infected patients. We performed a multicentre cross-sectional study enrolling HIV-infected patients undergoing neuropsychological testing, with a previous genotypic resistance test on plasma samples. CNS penetration-effectiveness (CPE) scores and genotypic susceptibility scores (GSS) were calculated for each regimen. A composite score (CPE-GSS) was then constructed. Factors associated with cognitive impairment were investigated by logistic regression analysis. A total of 215 patients were included. Mean CPE was 7.1 (95% CI 6.9, 7.3) with 206 (95.8%) patients showing a CPE≥6. GSS correction decreased the CPE value in 21.4% (mean 6.5, 95% CI 6.3, 6.7), 26.5% (mean 6.4, 95% CI 6.1, 6.6) and 24.2% (mean 6.4, 95% CI 6.2, 6.6) of subjects using ANRS, HIVDB and REGA rules, respectively. Overall, 66 (30.7%) patients were considered cognitively impaired. No significant association could be demonstrated between CPE and cognitive impairment. However, higher GSS-CPE was associated with a lower risk of cognitive impairment (CPE-GSSANRS odds ratio 0.75, P=0.022; CPE-GSSHIVDB odds ratio 0.77, P=0.038; CPE-GSSREGA odds ratio 0.78, P=0.038). Overall, a cutoff of CPE-GSS≥5 seemed the most discriminatory according to each different interpretation system. GSS-corrected CPE score showed a better correlation with neurocognitive performance than the standard CPE score. These results suggest that antiretroviral drug susceptibility, besides drug CNS penetration, can play a role in the control of HIV-associated neurocognitive disorders.

Comparison of mating performance of medfly (Diptera: Tephritidae) genetic sexing and wild type strains: field cage and video recording experiments

International Nuclear Information System (INIS)

Calcagno, G.E.; Vilardi, J.C.; Manso, F.

2002-01-01

To improve the efficiency of the sterile insect technique (SIT) efforts are being devoted to obtain genetic sexing strains (GSS). The present work was carried out in order to compare the mating efficiency of flies from the GSS [(Ty34228 y + /X)sw x ] and from a wild type strain (Mendoza). Females of the GSS (T228) exhibit longer embryonic development, while males develop in a normal time period. In a field-cage experiment, mating competitiveness was compared between the T228 and the Mendoza, Argentina mass reared strain. The number and duration of matings and the location of copula in the tree were recorded. The analysis was repeated using irradiated males of T228. The results showed that mating efficiency of the GSS is good in comparison with that of the Mendoza strain. Although copulatory success in T228 is reduced by the radiation treatment, the high numbers of sterilized males released would compensate this effect in the control programs. In a second experiment, under laboratory conditions, video recording techniques were applied. In this case two virgin males, one of the GSS and one emerged from wild collected fruits, competed during 30 min for a virgin wild female. The proportion of successful males did not differ between strains, but some differences were observed between strains in the time spent in different stages of the courtship. Males of the T228 were more aggressive, and they attempted to copulate with the other male more frequently than did wild males. These differences may be due to selection for more aggressive individuals under the overcrowded laboratory breeding conditions for this strain. (author)

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.

Dicty_cDB: Contig-U04716-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available ( BV429027 ) S237P6215FG6.T0 PortugueseWaterDog Canis familiar... 38 6e-04 2 ( CE020668 ) tigr-gss-dog-1700...AFT ... 48 0.034 2 ( CE733596 ) tigr-gss-dog-17000315432205 Dog Library Canis lup... 38 0.034 2 ( BV431612 ) S237P656RA1.T0 Portugues...library Mus ... 38 0.13 2 ( BV431707 ) S237P6458FA8.T0 PortugueseWaterDog Canis familiar... 38 0.13 2 ( BV25... ( BV437326 ) S237P6229FG2.T0 PortugueseWaterDog Canis familiar... 38 0.13 2 ( CE358139 ) tigr-gss-dog-17000... Canis lup... 38 0.14 2 ( BV432826 ) S237P6430RB9.T0 PortugueseWaterDog Canis familiar... 36 0.14 2 ( CE4742

The Consequences of Parental Divorce on the Life Course Outcomes of Canadian Children

Directory of Open Access Journals (Sweden)

Valerie Martin

2005-12-01

Full Text Available Applying the theory of the intergenerational transmission of divorce, this paper examines the consequences of parental divorce on three aspects of the life course of children: union formation, nonmarital fertility, and marital dissolution. The 1995 Canadian General Social Survey (GSS is used to estimate various regression models (Cox proportional hazards. Results show that children of divorced parents have a significantly higher likelihood to have births outside of marriage, enter into cohabiting unions, and to experience higher levels of divorce. Throughout the paper, attention is placed on the markedly different behaviour observed in Quebec compared to elsewhere in Canada.

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.

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

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.

Providing for organizational memory in computer supported meetings

OpenAIRE

Schwabe, Gerhard

1994-01-01

Meeting memory features are poorly integrated into current group support systems (GSS). In this article, I discuss how to introduce meeting memory functionality into a GSS. The article first introduces the benefits of effective meetings and organizational memory to an organization. Then, the following challenges to design are discussed: How to store semantically rich output, how to build up the meeting memory with a minimum of additional effort, how to integrate meeting memory into organizati...

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

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

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.

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.

Clarification of the memory artefact in the assessment of suggestibility.

Science.gov (United States)

Willner, P

2008-04-01

The Gudjonsson Suggestibility Scale (GSS) assesses suggestibility by asking respondents to recall a short story, followed by exposure to leading questions and pressure to change their responses. Suggestibility, as assessed by the GSS, appears to be elevated in people with intellectual disabilities (ID). This has been shown to reflect to some extent the fact that people with ID have poor recall of the story; however, there are discrepancies in this relationship. The aim of the present study was to investigate whether a closer match between memory and suggestibility would be found using a measure of recognition memory rather than free recall. Three modifications to the procedure were presented to users of a learning disabilities day service. In all three experiments, a measure of forced-choice recognition memory was built into the suggestibility test. In experiments 1 and 2, the GSS was presented using either divided presentation (splitting the story into two halves, with memory and suggestibility tests after each half) or multiple presentation (the story was presented three times before presentation of the memory and suggestibility tests). Participants were tested twice, once with the standard version of the test and once with one of the modified versions. In experiment 3, an alternative suggestibility scale (ASS3) was created, based on real events in a learning disabilities day service. The ASS3 was presented to one group of participants who had been present at the events, and a second group who attended a different day service, to whom the events were unfamiliar. As observed previously, suggestibility was not closely related to free recall performance: recall was increased equally by all three manipulations, but they produced, respectively, no effect, a modest effect and a large effect on suggestibility. However, the effects on suggestibility were closely related to performance on the forced-choice recognition memory task: divided presentation of the GSS2 had no

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.

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

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.

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 ...

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

Inherited prion disease A117V is not simply a proteinopathy but produces prions transmissible to transgenic mice expressing homologous prion protein.

Science.gov (United States)

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

2013-01-01

Prions are infectious agents causing fatal neurodegenerative diseases of humans and animals. In humans, these have sporadic, acquired and inherited aetiologies. The inherited prion diseases are caused by one of over 30 coding mutations in the human prion protein (PrP) gene (PRNP) and many of these generate infectious prions as evidenced by their experimental transmissibility by inoculation to laboratory animals. However, some, and in particular an extensively studied type of Gerstmann-Sträussler-Scheinker syndrome (GSS) caused by a PRNP A117V mutation, are thought not to generate infectious prions and instead constitute prion proteinopathies with a quite distinct pathogenetic mechanism. Multiple attempts to transmit A117V GSS have been unsuccessful and typical protease-resistant PrP (PrP(Sc)), pathognomonic of prion disease, is not detected in brain. Pathogenesis is instead attributed to production of an aberrant topological form of PrP, C-terminal transmembrane PrP ((Ctm)PrP). Barriers to transmission of prion strains from one species to another appear to relate to structural compatibility of PrP in host and inoculum and we have therefore produced transgenic mice expressing human 117V PrP. We found that brain tissue from GSS A117V patients did transmit disease to these mice and both the neuropathological features of prion disease and presence of PrP(Sc) was demonstrated in the brains of recipient transgenic mice. This PrP(Sc) rapidly degraded during laboratory analysis, suggesting that the difficulty in its detection in patients with GSS A117V could relate to post-mortem proteolysis. We conclude that GSS A117V is indeed a prion disease although the relative contributions of (Ctm)PrP and prion propagation in neurodegeneration and their pathogenetic interaction remains to be established.

In vivo detection of prion amyloid plaques using [{sup 11}C]BF-227 PET

Energy Technology Data Exchange (ETDEWEB)

Okamura, Nobuyuki; Yanai, Kazuhiko [Tohoku University School of Medicine, Department of Pharmacology, Sendai (Japan); Shiga, Yusei; Itoyama, Yasuhito [Tohoku University School of Medicine, Department of Neurology, Sendai (Japan); Furumoto, Shozo [Tohoku University School of Medicine, Department of Pharmacology, Sendai (Japan); Tohoku University, Division of Radiopharmaceutical Chemistry, Cyclotron and Radioisotope Center, Sendai (Japan); Tashiro, Manabu [Tohoku University, Division of Cyclotron Nuclear Medicine, Cyclotron and Radioisotope Center, Sendai (Japan); Tsuboi, Yoshio [Fukuoka University School of Medicine, Department of Neurology, Fukuoka (Japan); Furukawa, Katsutoshi; Arai, Hiroyuki [Institute of Development, Aging, and Cancer, Tohoku University, Department of Geriatrics and Gerontology, Division of Brain Sciences, Sendai (Japan); Iwata, Ren [Tohoku University, Division of Radiopharmaceutical Chemistry, Cyclotron and Radioisotope Center, Sendai (Japan); Kudo, Yukitsuka [Tohoku University, Innovation of New Biomedical Engineering Center, Sendai (Japan); Doh-ura, Katsumi [Tohoku University School of Medicine, Department of Prion Research, 2-1 Seiryo-machi, Aoba-ku, Sendai (Japan)

2010-05-15

In vivo detection of pathological prion protein (PrP) in the brain is potentially useful for the diagnosis of transmissible spongiform encephalopathies (TSEs). However, there are no non-invasive ante-mortem means for detection of pathological PrP deposition in the brain. The purpose of this study is to evaluate the amyloid imaging tracer BF-227 with positron emission tomography (PET) for the non-invasive detection of PrP amyloid in the brain. The binding ability of BF-227 to PrP amyloid was investigated using autoradiography and fluorescence microscopy. Five patients with TSEs, including three patients with Gerstmann-Straeussler-Scheinker disease (GSS) and two patients with sporadic Creutzfeldt-Jakob disease (CJD), underwent [{sup 11}C]BF-227 PET scans. Results were compared with data from 10 normal controls and 17 patients with Alzheimer's disease (AD). The regional to pons standardized uptake value ratio was calculated as an index of BF-227 retention. Binding of BF-227 to PrP plaques was confirmed using brain samples from autopsy-confirmed GSS cases. In clinical PET study, significantly higher retention of BF-227 was detected in the cerebellum, thalamus and lateral temporal cortex of GSS patients compared to that in the corresponding tissues of normal controls. GSS patients also showed higher retention of BF-227 in the cerebellum, thalamus and medial temporal cortex compared to AD patients. In contrast, the two CJD patients showed no obvious retention of BF-227 in the brain. Although [{sup 11}C]BF-227 is a non-specific imaging marker of cerebral amyloidosis, it is useful for in vivo detection of PrP plaques in the human brain in GSS, based on the regional distribution of the tracer. PET amyloid imaging might provide a means for both early diagnosis and non-invasive disease monitoring of certain forms of TSEs. (orig.)

In vivo detection of prion amyloid plaques using [11C]BF-227 PET

International Nuclear Information System (INIS)

Okamura, Nobuyuki; Yanai, Kazuhiko; Shiga, Yusei; Itoyama, Yasuhito; Furumoto, Shozo; Tashiro, Manabu; Tsuboi, Yoshio; Furukawa, Katsutoshi; Arai, Hiroyuki; Iwata, Ren; Kudo, Yukitsuka; Doh-ura, Katsumi

2010-01-01

In vivo detection of pathological prion protein (PrP) in the brain is potentially useful for the diagnosis of transmissible spongiform encephalopathies (TSEs). However, there are no non-invasive ante-mortem means for detection of pathological PrP deposition in the brain. The purpose of this study is to evaluate the amyloid imaging tracer BF-227 with positron emission tomography (PET) for the non-invasive detection of PrP amyloid in the brain. The binding ability of BF-227 to PrP amyloid was investigated using autoradiography and fluorescence microscopy. Five patients with TSEs, including three patients with Gerstmann-Straeussler-Scheinker disease (GSS) and two patients with sporadic Creutzfeldt-Jakob disease (CJD), underwent [ 11 C]BF-227 PET scans. Results were compared with data from 10 normal controls and 17 patients with Alzheimer's disease (AD). The regional to pons standardized uptake value ratio was calculated as an index of BF-227 retention. Binding of BF-227 to PrP plaques was confirmed using brain samples from autopsy-confirmed GSS cases. In clinical PET study, significantly higher retention of BF-227 was detected in the cerebellum, thalamus and lateral temporal cortex of GSS patients compared to that in the corresponding tissues of normal controls. GSS patients also showed higher retention of BF-227 in the cerebellum, thalamus and medial temporal cortex compared to AD patients. In contrast, the two CJD patients showed no obvious retention of BF-227 in the brain. Although [ 11 C]BF-227 is a non-specific imaging marker of cerebral amyloidosis, it is useful for in vivo detection of PrP plaques in the human brain in GSS, based on the regional distribution of the tracer. PET amyloid imaging might provide a means for both early diagnosis and non-invasive disease monitoring of certain forms of TSEs. (orig.)

Achalasia symptom response after Heller myotomy segregated by high-resolution manometry subtypes.

Science.gov (United States)

Patel, Amit; Patel, Ami; Mirza, Faiz A; Soudagar, Samad; Sayuk, Gregory S; Gyawali, C Prakash

2016-02-01

Achalasia is classified into three HRM subtypes that predict outcomes from diverse management strategies. We assessed if symptomatic response varied when a single management strategy-Heller myotomy (HM)-is employed. Treatment-naive subjects with achalasia referred for HM were followed in this observational cohort study. Chicago criteria designated achalasia subtypes (subtype I: no esophageal pressurization; subtype II: panesophageal pressurization in ≥20 % swallows; subtype III: premature contractions in ≥20 % swallows). Symptom questionnaires assessed symptom burden before and after HM on five-point Likert scales (0 = no symptoms, 4 = severe symptoms) and on 10-cm visual analog scales (global symptom severity, GSS); satisfaction with HM was recorded similarly. Data were analyzed to determine predictors of GSS change across subtypes. Sixty achalasia subjects (56.1 ± 2.4 years, 55 % female) fulfilled inclusion criteria, 15 % with subtype I, 58 % with subtype II, and 27 % with subtype III achalasia. Baseline symptoms included dysphagia (solids: 85 %, liquids: 73 %), regurgitation (84 %), and chest pain (35 %); mean GSS was 7.1 ± 0.3. Upon follow-up 2.1 ± 0.2 years after HM, GSS declined to 1.9 ± 0.4 (p < 0.001), with surgical satisfaction score of 8.7 ± 0.3 out of 10; these were similar across achalasia subtypes. On univariate analysis, female gender, Eckardt score, severity of transit symptoms, and maximal IRP predicted linear GSS improvement; female gender (p = 0.003) and dysphagia for liquids (p = 0.043) remained predictive on multivariate analysis. When a uniform surgical approach is utilized, symptomatic outcome and satisfaction with therapy are similar across achalasia subtypes. Female gender and severity of dysphagia for solids may predict better HM outcome.

Inherited prion disease A117V is not simply a proteinopathy but produces prions transmissible to transgenic mice expressing homologous prion protein.

Directory of Open Access Journals (Sweden)

Emmanuel A Asante

Full Text Available Prions are infectious agents causing fatal neurodegenerative diseases of humans and animals. In humans, these have sporadic, acquired and inherited aetiologies. The inherited prion diseases are caused by one of over 30 coding mutations in the human prion protein (PrP gene (PRNP and many of these generate infectious prions as evidenced by their experimental transmissibility by inoculation to laboratory animals. However, some, and in particular an extensively studied type of Gerstmann-Sträussler-Scheinker syndrome (GSS caused by a PRNP A117V mutation, are thought not to generate infectious prions and instead constitute prion proteinopathies with a quite distinct pathogenetic mechanism. Multiple attempts to transmit A117V GSS have been unsuccessful and typical protease-resistant PrP (PrP(Sc, pathognomonic of prion disease, is not detected in brain. Pathogenesis is instead attributed to production of an aberrant topological form of PrP, C-terminal transmembrane PrP ((CtmPrP. Barriers to transmission of prion strains from one species to another appear to relate to structural compatibility of PrP in host and inoculum and we have therefore produced transgenic mice expressing human 117V PrP. We found that brain tissue from GSS A117V patients did transmit disease to these mice and both the neuropathological features of prion disease and presence of PrP(Sc was demonstrated in the brains of recipient transgenic mice. This PrP(Sc rapidly degraded during laboratory analysis, suggesting that the difficulty in its detection in patients with GSS A117V could relate to post-mortem proteolysis. We conclude that GSS A117V is indeed a prion disease although the relative contributions of (CtmPrP and prion propagation in neurodegeneration and their pathogenetic interaction remains to be established.

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.

Survey and alignment of high energy physics accelerators and transport lines

International Nuclear Information System (INIS)

Ruland, R.E.

1992-11-01

This talk 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 revisited and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step by 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

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.

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

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.

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

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...

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.

The APM galaxy survey: Pt. 2; Photometric corrections

Energy Technology Data Exchange (ETDEWEB)

Maddox, S.J.; Efstathiou, G.; Sutherland, W.J. (Oxford Univ. (UK). Dept. of Astrophysics)

1990-10-01

We describe the methods that we have used to establish accurate photometry in a survey of two million galaxies brighter then b{sub j} 20.5 covering over 4300 square degrees of the South Galactic cap. We apply a field correction for vignetting and differential desensitization which is accurate to ''< approx''0.04 mag across each of 185 Schmidt plates. Images in the overlapping regions of neighbouring plate pairs are used to establish a uniform magnitude system over the entire survey. We discuss the residual magnitude differences in the overlaps and the propagation of plate-to-plate magnitude errors across the network of plates. We argue that the rms plate zero-point error in the final matched survey is 0.04 mag. CCD photometry of 40 faint galaxy sequences is used to calibrate the matched magnitudes and to set stringent limits on large-scale gradients in the matched survey photometry. (author).

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

Dicty_cDB: Contig-U02528-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 6 0.32 2 ( EJ157760 ) 1092344036067 Global-Ocean-Sampling_GS-27-01-01-1... 44 0.32 2 ( CU695332 ) Brassica r...624568 ) 1092963131690 Global-Ocean-Sampling_GS-29-01-01-1... 46 1.7 1 ( EJ609086 ) 1092962030117 Global-Ocean-Sampli...187 ) 1095403375706 Global-Ocean-Sampling_GS-28-01-01-1... 42 3.6 2 ( BX322637 ) Zebrafish DNA sequence from clone DKEY-22A1 in li...ns IP1 GSS, clone inv066f05.p1k. 44 6.8 1 ( EJ091828 ) 1095460198059 Global-Ocean-Sampli... Leishmania major strain Friedlin,... 42 0.013 AY562978_1( AY562978 |pid:none) Drosophila simulans isolate m

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

DEFF Research Database (Denmark)

Sung, Wing-Kin; Zheng, Hancheng; Li, Shuyu

2012-01-01

To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than...

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....

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.

Angle-dependent bandgap engineering in gated graphene superlattices

Energy Technology Data Exchange (ETDEWEB)

García-Cervantes, H.; Sotolongo-Costa, O. [Centro de Investigación en Ciencias, IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62209 Cuernavaca, Morelos, México (Mexico); Gaggero-Sager, L. M. [CIICAp, IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62209 Cuernavaca, Morelos, México (Mexico); Naumis, G. G. [Instituto Física, Depto. de Física-Química, Universidad Nacional Autónoma de México (UNAM). Apdo. Postal 20-364, 01000, México D.F., México (Mexico); Rodríguez-Vargas, I., E-mail: isaac@fisica.uaz.edu.mx [Centro de Investigación en Ciencias, IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62209 Cuernavaca, Morelos, México (Mexico); Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, Zac., México (Mexico)

2016-03-15

Graphene Superlattices (GSs) have attracted a lot of attention due to its peculiar properties as well as its possible technological implications. Among these characteristics we can mention: the extra Dirac points in the dispersion relation and the highly anisotropic propagation of the charge carriers. However, despite the intense research that is carried out in GSs, so far there is no report about the angular dependence of the Transmission Gap (TG) in GSs. Here, we report the dependence of TG as a function of the angle of the incident Dirac electrons in a rather simple Electrostatic GS (EGS). Our results show that the angular dependence of the TG is intricate, since for moderated angles the dependence is parabolic, while for large angles an exponential dependence is registered. We also find that the TG can be modulated from meV to eV, by changing the structural parameters of the GS. These characteristics open the possibility for an angle-dependent bandgap engineering in graphene.

Angle-dependent bandgap engineering in gated graphene superlattices

International Nuclear Information System (INIS)

García-Cervantes, H.; Sotolongo-Costa, O.; Gaggero-Sager, L. M.; Naumis, G. G.; Rodríguez-Vargas, I.

2016-01-01

Graphene Superlattices (GSs) have attracted a lot of attention due to its peculiar properties as well as its possible technological implications. Among these characteristics we can mention: the extra Dirac points in the dispersion relation and the highly anisotropic propagation of the charge carriers. However, despite the intense research that is carried out in GSs, so far there is no report about the angular dependence of the Transmission Gap (TG) in GSs. Here, we report the dependence of TG as a function of the angle of the incident Dirac electrons in a rather simple Electrostatic GS (EGS). Our results show that the angular dependence of the TG is intricate, since for moderated angles the dependence is parabolic, while for large angles an exponential dependence is registered. We also find that the TG can be modulated from meV to eV, by changing the structural parameters of the GS. These characteristics open the possibility for an angle-dependent bandgap engineering in graphene.

Study of the compatibility and competitiveness of sterile males in the framework of the struggle by the sterile insect technique against the Ceratitis

International Nuclear Information System (INIS)

Azzabi, Jihene

2007-01-01

We evaluated under semi-natural field-cage conditions sexual compatibility and competitivity of laboratory strain (Genetic Sexing Strain GSS) ''Vienna 8''. The GSS strain is produced under mass (rearing conditions at the facility of production of sterile males at Sidi Thabat. Wild flies were obtained from infested Sommer oranges. Twenty-five wild males, 25 wild females and 25 GSS were released into cage and mating pairs collected. The determination of indices such as the Isolation Index (ISI), the Male Relative Index (MRPI), the Stalker Index (I) and the Relative Sterile Index (RSI) shows that there is no compatibility and competitiveness between the two strains with a tendency to behaviour of sexual isolation. Sterile male tests dissection irradiated at the dose of (0 Gy, 110 Gy, 120 Gy, 130 Gy and 145 Gy) and correspondent female spermatic show the important damage of the irradiation on the cells but decrease the quality of the sterile male (mating duration, sperm transfer.). (Author)

Gorham-Stout syndrome of the pelvic girdle treated by radiation therapy. A case report

International Nuclear Information System (INIS)

Heyd, Reinhard; Tselis, Nikolaos; Zamboglou, Nikolaos; Rabeneck, Daniela; Universitaetsklinikum Frankfurt, Frankfurt am Main; Doernenburg, Oliver

2011-01-01

The Gorham-Stout syndrome (GSS) is a rare, benign idiopathic and progressive disorder causing massive osteolysis due to a vascular hyperproliferation replacing the bony structure. Clinical experience concerning the efficacy of radiation therapy (RT) is limited to about 50 of an overall 200 cases reported worldwide. Case Report: A 24-year-old bedridden woman had histologically proven GSS with destruction of the anterior pelvic girdle and received RT for a total dose of 45.0 Gy applied in 5 weekly fractions of 1.8 Gy. In addition, the patient received intravenously 4 mg zoledronic acid once a month. One year after the combined treatment, complete pain relief occurred, and the patient was able to walk without the use of appliances. Imaging studies revealed no progression of the osteolysis but only minimal signs of remineralization. Conclusion: Combined treatment with RT and bisphosphonate administration can prevent the progression of osteolysis in GSS. Total doses of 40-45 Gy are recommended. (orig.)

Gorham-Stout syndrome of the pelvic girdle treated by radiation therapy. A case report

Energy Technology Data Exchange (ETDEWEB)

Heyd, Reinhard; Tselis, Nikolaos; Zamboglou, Nikolaos [Klinikum Offenbach, Offenbach am Main (Germany). Strahlenklinik; Rabeneck, Daniela [Klinikum Offenbach, Offenbach am Main (Germany). Strahlenklinik; Universitaetsklinikum Frankfurt, Frankfurt am Main (Germany). Klinik fuer Strahlentherapie und Onkologie; Doernenburg, Oliver [Klinikum Offenbach, Offenbach am Main (Germany). Inst. fuer Diagnostische und Interventionelle Radiologie

2011-02-15

The Gorham-Stout syndrome (GSS) is a rare, benign idiopathic and progressive disorder causing massive osteolysis due to a vascular hyperproliferation replacing the bony structure. Clinical experience concerning the efficacy of radiation therapy (RT) is limited to about 50 of an overall 200 cases reported worldwide. Case Report: A 24-year-old bedridden woman had histologically proven GSS with destruction of the anterior pelvic girdle and received RT for a total dose of 45.0 Gy applied in 5 weekly fractions of 1.8 Gy. In addition, the patient received intravenously 4 mg zoledronic acid once a month. One year after the combined treatment, complete pain relief occurred, and the patient was able to walk without the use of appliances. Imaging studies revealed no progression of the osteolysis but only minimal signs of remineralization. Conclusion: Combined treatment with RT and bisphosphonate administration can prevent the progression of osteolysis in GSS. Total doses of 40-45 Gy are recommended. (orig.)

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.

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...

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

Detection of M-Sequences from Spike Sequence in Neuronal Networks

Directory of Open Access Journals (Sweden)

Yoshi Nishitani

2012-01-01

Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

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...

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%

A Survey of the Hazards to Electrical Power Systems

International Nuclear Information System (INIS)

Johnson, Gary

2015-01-01

This paper presents the preliminary results of a survey of severe accidents and the lessons learned that are important to the design of electrical power systems. This survey of historical accidents since 1952 identified 19 known incidents in which significant fuel melt occurred within a reactor core. In each of these incidents unexpected events or event sequences played an important role. In all cases the event sequences resulted in bypass of two or more levels of defense in depth. This study offers clear lessons for electrical power robustness: 1) Robust design must be based upon a clear understanding of what can go wrong, and 2) Robust design will reduce, but cannot eliminate, the potential for failure of electrical power systems. In order to better understand 'what is the worst that can happen' known hazards are reviewed to identify the challenges that they can present to electrical power systems. Recognizing that unexpected events cannot always be prevented the paper discusses the need for methods to restore plant power sources or provide for alternate power supplies when the plant power sources fail. (authors)

The relationship between criminal conviction and interrogative suggestibility among delinquent boys.

Science.gov (United States)

Gudjonsson, G H; Singh, K K

1984-03-01

This study investigates the relationship between interrogative suggestibility, as measured by the Gudjonsson Suggestibility Scale (GSS), and number of previous convictions among 35 delinquent boys. The GSS measures two independent aspects of suggestibility. First, the extent to which subjects give in to suggestive questions. Second, the extent to which subjects give in to interpersonal pressure given in the form of critical feedback about test performance. The number of convictions were found to correlate negatively with the latter aspect of interrogative suggestibility, but not significantly with the former.

[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.

The SOAR Gravitational Arc Survey – I. Survey overview and photometric catalogues

Energy Technology Data Exchange (ETDEWEB)

Furlanetto, Cristina; Santiago, Basílio X.; Makler, Martín; Cypriano, Eduardo S.; Caminha, Gabriel B.; Pereira, Maria E. S.; Neto, Angelo Fausti; Estrada, Juan; Lin, Huan; Hao, Jiangang; McKay, Timothy A.; da Costa, Luiz N.; Maia, Marcio A. G.

2013-04-11

We present the first results of the SOAR (Southern Astrophysical Research) Gravitational Arc Survey (SOGRAS). The survey imaged 47 clusters in two redshift intervals centered at $z=0.27$ and $z=0.55$, targeting the richest clusters in each interval. Images were obtained in the $g'$, $r'$ and $i'$ bands using the SOAR Optical Imager (SOI), with a median seeing of 0.83, 0.76 and 0.71 arcsec, respectively, in these filters. Most of the survey clusters are located within the Sloan Digital Sky Survey (SDSS) Stripe 82 region and all of them are in the SDSS footprint. Photometric calibration was therefore performed using SDSS stars located in our SOI fields. We reached for galaxies in all fields the detection limits of $g \\sim 23.5$, $r \\sim 23$ and $i \\sim 22.5$ for a signal-to-noise ratio (S/N) = 3. As a by-product of the image processing, we generated a source catalogue with 19760 entries, the vast majority of which are galaxies, where we list their positions, magnitudes and shape parameters. We compared our galaxy shape measurements to those of local galaxies and concluded that they were not strongly affected by seeing. From the catalogue data, we are able to identify a red sequence of galaxies in most clusters in the lower $z$ range. We found 16 gravitational arc candidates around 8 clusters in our sample. They tend to be bluer than the central galaxies in the lensing cluster. A preliminary analysis indicates that $\\sim 10%$ of the clusters have arcs around them, with a possible indication of a larger efficiency associated to the high-$z$ systems when compared to the low-$z$ ones. Deeper follow-up images with Gemini strengthen the case for the strong lensing nature of the candidates found in this survey.

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.

Contraceptive sterilization among Canadians, 1984-1995

Directory of Open Access Journals (Sweden)

Vijaya Krishnan

2004-12-01

Full Text Available Prior to early 1970s, traditional methods were the principal means of controlling the number and spacing of births. Today, an estimated 57 per cent of the world’s married women use contraceptives and half use modern methods such as medical sterilizations. Recent statistics suggest that Canada has the highest sterilization rate in the Western world. This paper presents findings of research examining sterilization trends in Canada with respect to changing patterns in the use of modern contraceptives, using data from the 1984 Canadian Fertility Survey (CFS and the 1995 General Social Survey (GSS. The main finding is that there is a decrease in the use of tubal ligation and an increase in the use of hysterectomy over the period 1984-1995. Less educated women are more likely to be in the forefront of modern methods of contraception.

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Directory of Open Access Journals (Sweden)

Francisco Alexandre P

2012-05-01

Full Text Available Abstract Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

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

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Science.gov (United States)

Haas, Brian J.; Gevers, Dirk; Earl, Ashlee M.; Feldgarden, Mike; Ward, Doyle V.; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K.; Sodergren, Erica; Methé, Barbara; DeSantis, Todd Z.; Petrosino, Joseph F.; Knight, Rob; Birren, Bruce W.

2011-01-01

Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification products. Chimeras are hybrid products between multiple parent sequences that can be falsely interpreted as novel organisms, thus inflating apparent diversity. We developed a new chimera detection tool called Chimera Slayer (CS). CS detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. By benchmarking CS performance against sequences derived from a controlled DNA mixture of known organisms and a simulated chimera set, we provide insights into the factors that affect chimera formation such as sequence abundance, the extent of similarity between 16S genes, and PCR conditions. Chimeras were found to reproducibly form among independent amplifications and contributed to false perceptions of sample diversity and the false identification of novel taxa, with less-abundant species exhibiting chimera rates exceeding 70%. Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys. PMID:21212162

A novel PRNP Y218N mutation in Gerstmann-Sträussler-Scheinker disease with neurofibrillary degeneration.

Science.gov (United States)

Alzualde, Ainhoa; Indakoetxea, Begoña; Ferrer, Isidre; Moreno, Fermin; Barandiaran, Myriam; Gorostidi, Ana; Estanga, Ainara; Ruiz, Irune; Calero, Miguel; van Leeuwen, Fred W; Atares, Begoña; Juste, Ramón; Rodriguez-Martínez, Ana Belén; López de Munain, Adolfo

2010-08-01

Gerstmann-Sträussler-Scheinker (GSS) disease is a prion disease associated with prion protein gene (PRNP) mutations. We report a novel PRNP mutation (Y218N) associated with GSS disease in a pathologically confirmed case and in two other affected family members. The clinical features of these cases met criteria for possible Alzheimer disease and possible frontotemporal dementia. Neuropathologic analysis revealed deposition of proteinase K-resistant prion protein (PrP(res)), widespread hyperphosphorylated tau pathology, abnormal accumulation of mitochondria in the vicinity of PrP deposits, and expression of mutant ubiquitin (UBB(+1)) in neurofibrillary tangles and dystrophic neurites. Prion protein immunoblotting using 3F4 and 1E4 antibodies disclosed multiple bands ranging from approximately 20 kd to 80 kd and lower bands of 15 kd and approximately 10 kd, the latter only seen after a long incubation. These bands were partially resistant to proteinase K pretreatment. This pattern differs from those seen in Creutzfeldt-Jakob disease andresembles those reported in other GSS cases. The approximately 10kd band was recognized with anti-PrP C-terminus antibodies but not with anti-N terminus antibodies, suggesting PrP truncation at the N terminal. This new mutation extends the list of known mutations responsible for GSS disease and reinforces its clinical heterogeneity. Genetic examination of the PRNP gene should be included in the workup of patients with poorly classifiable dementia.

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…

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.

Barberry rust survey – developing tools for diagnosis, analysis and data management

DEFF Research Database (Denmark)

Justesen, Annemarie Fejer; Hansen, Jens Grønbech; Hovmøller, Mogens Støvring

Barberry (Berberis spp.) may serve as alternate host of several Puccinia species including Puccinia graminis and P. striiformis causing stem and yellow rust on cereals and grasses, respectively. In order to study the importance of barberry in the epidemiology of Puccinia species in the CWANA regi...... a rust survey was initiated. The aim was to 1) develop a surveillance protocol 2) develop molecular diagnostic tools for identifying Puccinia spp. from aecial samples, and 3) develop a data management and display system of results as part of the Wheat Rust ToolBox (http....... Due to variable quality of aecial samples DNA extraction was not successful for 40% of the samples. Sequences of EF1α, β-tubulin or ITS were analysed and compared to reference sequences of rust fungi infecting cereals and grasses. The analysis supported the presence of P. graminis s.l., P....... arrhenatheri and P. striiformoides on barberry species. Survey and DNA sample maps with species designation were displayed in the Wheat Rust ToolBox. The future aim is to integrate barberry rust survey data based on molecular diagnostics and infection assays from research groups world-wide in order to gain...

Microbiologic and Clinical Features of Salmonella Species Isolated From Bacteremic Children in Eastern Democratic Republic of Congo

DEFF Research Database (Denmark)

Vandenberg, Olivier; Nyarukweba, Deo Z.; Ndeba, Prudence M.

2010-01-01

Background: The morbidity of Salmonella bloodstream infections is unacceptably high in Africa. In 2000, the WHO Global Salmonella-Surveillance (GSS) program was founded to reduce the health burden of foodborne diseases. The incorporation, in 2002, of the Democratic Republic of Congo (DRC......) in this program allowed the improvement of laboratory capacities. In this retrospective study, we describe the first signs of impact the GSS program has had in DRC in the management of bacteremia. Methods: Between 2002 and 2006, we evaluated, in one pediatric hospital, the microbiologic and clinical features...

Spectrophotometric study of bio-sorption of uranium on glass grade spodumene shell powder

International Nuclear Information System (INIS)

Parakudyil, A.S.; Pillai, A.K.; Reddy, A.V.R.; Singal, R.K.; Sharma, P.K.; Michael, K.M.

2012-01-01

Separation of uranium found in iron ore leachates was done by extraction chromatography using glass grade spodumene shellpowder (GSS) in nitric acid medium and analyzed spectrophotometrically. The influences of metal ion concentration, pH and adsorption capacity of biomass were investigated. Biosorption is a potential method of separation of heavy and trace metals from waste water and effluents from various sources. The adsorption capacities of biomass were investigated by batch experiments and column experiments. In the present study, glass grade spodumene shell powder (GSS) in acidic medium is being used as a biosorbent

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.

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.

De-standardization of family-life trajectories of young adults: A cross-national comparison using sequence analyses

NARCIS (Netherlands)

Elzinga, C.H.; Liefbroer, A.C.

2007-01-01

We introduce a number of new methods based on sequence analysis to test hypotheses on the de-standardization of family-life trajectories in early adulthood, using Fertility and Family Survey data on 19 countries. Across cohorts, family-life trajectories of young adults have not become more

De-standardization of family-life trajectories of young adults: a cross-national comparison using sequence analysis

NARCIS (Netherlands)

Elzinga, C.; Liefbroer, A.C.

2007-01-01

We introduce a number of new methods based on sequence analysis to test hypotheses on the de-standardization of family-life trajectories in early adulthood, using Fertility and Family Survey data on 19 countries. Across cohorts, family-life trajectories of young adults have not become more

Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

Directory of Open Access Journals (Sweden)

Shan Wei

2018-05-01

Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

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.

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…

A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

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Robert J Elshire

Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

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Joern Toedling

Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

The new galaxy evolution paradigm revealed by the Herschel surveys

Science.gov (United States)

Eales, Stephen; Smith, Dan; Bourne, Nathan; Loveday, Jon; Rowlands, Kate; van der Werf, Paul; Driver, Simon; Dunne, Loretta; Dye, Simon; Furlanetto, Cristina; Ivison, R. J.; Maddox, Steve; Robotham, Aaron; Smith, Matthew W. L.; Taylor, Edward N.; Valiante, Elisabetta; Wright, Angus; Cigan, Philip; De Zotti, Gianfranco; Jarvis, Matt J.; Marchetti, Lucia; Michałowski, Michał J.; Phillipps, Steven; Viaene, Sebastien; Vlahakis, Catherine

2018-01-01

The Herschel Space Observatory has revealed a very different galaxyscape from that shown by optical surveys which presents a challenge for galaxy-evolution models. The Herschel surveys reveal (1) that there was rapid galaxy evolution in the very recent past and (2) that galaxies lie on a single Galaxy Sequence (GS) rather than a star-forming 'main sequence' and a separate region of 'passive' or 'red-and-dead' galaxies. The form of the GS is now clearer because far-infrared surveys such as the Herschel ATLAS pick up a population of optically red star-forming galaxies that would have been classified as passive using most optical criteria. The space-density of this population is at least as high as the traditional star-forming population. By stacking spectra of H-ATLAS galaxies over the redshift range 0.001 high stellar masses, high star-formation rates but, even several billion years in the past, old stellar populations - they are thus likely to be relatively recent ancestors of early-type galaxies in the Universe today. The form of the GS is inconsistent with rapid quenching models and neither the analytic bathtub model nor the hydrodynamical EAGLE simulation can reproduce the rapid cosmic evolution. We propose a new gentler model of galaxy evolution that can explain the new Herschel results and other key properties of the galaxy population.

Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

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Albert Geskin

Full Text Available Next Generation Sequencing (NGS methods are driving profound changes in biomedical research, with a growing impact on patient care. Many academic medical centers are evaluating potential models to prepare for the rapid increase in NGS information needs. This study sought to investigate (1 how and where sequencing data is generated and analyzed, (2 research objectives and goals for NGS, (3 workforce capacity and unmet needs, (4 storage capacity and unmet needs, (5 available and anticipated funding resources, and (6 future challenges. As a precursor to informed decision making at our institution, we undertook a systematic needs assessment of investigators using survey methods. We recruited 331 investigators from over 60 departments and divisions at the University of Pittsburgh Schools of Health Sciences and had 140 respondents, or a 42% response rate. Results suggest that both sequencing and analysis bottlenecks currently exist. Significant educational needs were identified, including both investigator-focused needs, such as selection of NGS methods suitable for specific research objectives, and program-focused needs, such as support for training an analytic workforce. The absence of centralized infrastructure was identified as an important institutional gap. Key principles for organizations managing this change were formulated based on the survey responses. This needs assessment provides an in-depth case study which may be useful to other academic medical centers as they identify and plan for future needs.

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...

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.

Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

Science.gov (United States)

Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

2016-01-01

It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

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.

Experimental investigation of attrition resistance of zeolite catalysts in two particle gas-solid-solid fluidization system

International Nuclear Information System (INIS)

Nawaz, Z.; Ziaoping, T.; Shu, Q.; Wei, F.; Naveed, S.

2010-01-01

In the study of mechanical degradation of 34 ZSM-5 and SAPO catalysts, using the gas jet attrition - ASTM standard fluidized bed test (D-5757), the effect of particle size and its quantitative analysis in co-fluidization environment was investigated on the air jet index (AJI) basis. In gas-solid-solid fluidized bed reactors (GSS-FBR), two different sized particles were fluidized under isothermal conditions. In case of ZSM-5 and SAPO-34, significant attrition resistance was observed, which was attributed to small pore size and specific structural strength of the mobile framework image (MFI) and chabasite (CHA) structures, respectively. The optimum AJI for SAPO-34 and ZSM-5 (of particle size 0.2 mm) in GSS-fluidization system was observed to be 0.0118 and 0.0062, respectively. In co-fluidization, deviations from Gwyn relationship were observed due to change in impact of collision. Therefore, zeolites are recommended as suitable catalysts or catalytic supports (for doping of expensive metals) and for commercial use in GSS-FBR. (author)

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.

Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.

Science.gov (United States)

Conlan, Sean; Kong, Heidi H; Segre, Julia A

2012-01-01

Outbreaks of antibiotic-resistant bacterial infections emphasize the importance of surveillance of potentially pathogenic bacteria. Genomic sequencing of clinical microbiological specimens expands our capacity to study cultivable, fastidious and uncultivable members of the bacterial community. Herein, we compared the primary data collected by the NIH's Human Microbiome Project (HMP) with published epidemiological surveillance data of Staphylococcus aureus. The HMP's initial dataset contained microbial survey data from five body regions (skin, nares, oral cavity, gut and vagina) of 242 healthy volunteers. A significant component of the HMP dataset was deep sequencing of the 16S ribosomal RNA gene, which contains variable regions enabling taxonomic classification. Since species-level identification is essential in clinical microbiology, we built a reference database and used phylogenetic placement followed by most recent common ancestor classification to look at the species distribution for Staphylococcus, Klebsiella and Enterococcus. We show that selecting the accurate region of the 16S rRNA gene to sequence is analogous to carefully selecting culture conditions to distinguish closely related bacterial species. Analysis of the HMP data showed that Staphylococcus aureus was present in the nares of 36% of healthy volunteers, consistent with culture-based epidemiological data. Klebsiella pneumoniae and Enterococcus faecalis were found less frequently, but across many habitats. This work demonstrates that large 16S rRNA survey studies can be used to support epidemiological goals in the context of an increasing awareness that microbes flourish and compete within a larger bacterial community. This study demonstrates how genomic techniques and information could be critically important to trace microbial evolution and implement hospital infection control.

Sequence diversity and copy number variation of Mutator-like transposases in wheat

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Nobuaki Asakura

2008-01-01

Full Text Available Partial transposase-coding sequences of Mutator-like elements (MULEs were isolated from a wild einkorn wheat, Triticum urartu, by degenerate PCR. The isolated sequences were classified into a MuDR or Class I clade and divided into two distinct subclasses (subclass I and subclass II. The average pair-wise identity between members of both subclasses was 58.8% at the nucleotide sequence level. Sequence diversity of subclass I was larger than that of subclass II. DNA gel blot analysis showed that subclass I was present as low copy number elements in the genomes of all Triticum and Aegilops accessions surveyed, while subclass II was present as high copy number elements. These two subclasses seemed uncapable of recognizing each other for transposition. The number of copies of subclass II elements was much higher in Aegilops with the S, Sl and D genomes and polyploid Triticum species than in diploid Triticum with the A genome, indicating that active transposition occurred in S, Sl and D genomes before polyploidization. DNA gel blot analysis of six species selected from three subfamilies of Poaceae demonstrated that only the tribe Triticeae possessed both subclasses. These results suggest that the differentiation of these two subclasses occurred before or immediately after the establishment of the tribe Triticeae.

A Statistical Study of Brown Dwarf Companions from the SDSS-III MARVELS Survey

Science.gov (United States)

Grieves, Nolan; Ge, Jian; Thomas, Neil; Ma, Bo; De Lee, Nathan M.; Lee, Brian L.; Fleming, Scott W.; Sithajan, Sirinrat; Varosi, Frank; Liu, Jian; Zhao, Bo; Li, Rui; Agol, Eric; MARVELS Team

2016-01-01

We present 23 new Brown Dwarf (BD) candidates from the Multi-object APO Radial-Velocity Exoplanet Large-Area Survey (MARVELS) of the Sloan Digital Sky Survey III (SDSS-III). The BD candidates were selected from the processed MARVELS data using the latest University of Florida 2D pipeline, which shows significant improvement and reduction of systematic errors over the 1D pipeline results included in the SDSS Data Release 12. This sample is the largest BD yield from a single radial velocity survey. Of the 23 candidates, 18 are around main sequence stars and 5 are around giant stars. Given a giant contamination rate of ~24% for the MARVELS survey, we find a BD occurrence rate around main sequence stars of ~0.7%, which agrees with previous studies and confirms the BD desert, while the BD occurrence rate around the MARVELS giant stars is ~0.6%. Preliminary results show that our new candidates around solar type stars support a two population hypothesis, where BDs are divided at a mass of ~42.5 MJup. BDs less massive than 42.5 MJup have eccentricity distributions consistent with planet-planet scattering models, where BDs more massive than 42.5 MJup have both period and eccentricity distributions similar to that of stellar binaries. Special Brown Dwarf systems such as multiple BD systems and highly eccentric BDs will also be presented.

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

A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal

Science.gov (United States)

Gregory M. Bonito; Andrii P. Gryganskyi; James M. Trappe; Rytas. Vilgalys

2010-01-01

Truffles (Tuber) are ectomycorrhizal fungi characterized by hypogeous fruitbodies. Their biodiversity, host associations and geographical distributions are not well documented. ITS rDNA sequences of Tuber are commonly recovered from molecular surveys of fungal communities, but most remain insufficiently identified making it...

On preconditioner updates for sequences of saddle-point linear systems

Directory of Open Access Journals (Sweden)

Simone Valentina De

2018-02-01

Full Text Available Updating preconditioners for the solution of sequences of large and sparse saddle- point linear systems via Krylov methods has received increasing attention in the last few years, because it allows to reduce the cost of preconditioning while keeping the efficiency of the overall solution process. This paper provides a short survey of the two approaches proposed in the literature for this problem: updating the factors of a preconditioner available in a block LDLT form, and updating a preconditioner via a limited-memory technique inspired by quasi-Newton methods.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

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Baldwin Stephen A

2011-03-01

Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

Science.gov (United States)

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Loss of anti-Bax function in Gerstmann-Sträussler-Scheinker syndrome-associated prion protein mutants.

Directory of Open Access Journals (Sweden)

Julie Jodoin

2009-08-01

Full Text Available Previously, we have shown the loss of anti-Bax function in Creutzfeldt Jakob disease (CJD-associated prion protein (PrP mutants that are unable to generate cytosolic PrP (CyPrP. To determine if the anti-Bax function of PrP modulates the manifestation of prion diseases, we further investigated the anti-Bax function of eight familial Gerstmann-Sträussler-Scheinker Syndrome (GSS-associated PrP mutants. These PrP mutants contained their respective methionine ((M or valine ((V at codon 129. All of the mutants lost their ability to prevent Bax-mediated chromatin condensation or DNA fragmentation in primary human neurons. In the breast carcinoma MCF-7 cells, the F198S(V, D202N(V, P102L(V and Q217R(V retained, whereas the P102L(M, P105L(V, Y145stop(M and Q212P(M PrP mutants lost their ability to inhibit Bax-mediated condensed chromatin. The inhibition of Bax-mediated condensed chromatin depended on the ability of the mutants to generate cytosolic PrP. However, except for the P102L(V, none of the mutants significantly inhibited Bax-mediated caspase activation. These results show that the cytosolic PrP generated from the GSS mutants is not as efficient as wild type PrP in inhibiting Bax-mediated cell death. Furthermore, these results indicate that the anti-Bax function is also disrupted in GSS-associated PrP mutants and is not associated with the difference between CJD and GSS.

Sequence embedding for fast construction of guide trees for multiple sequence alignment

LENUS (Irish Health Repository)

Blackshields, Gordon

2010-05-14

Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.

Sequencing of BAC pools by different next generation sequencing platforms and strategies

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Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

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.

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.

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

The SUMO project I. A survey of multiple populations in globular clusters

Science.gov (United States)

Monelli, M.; Milone, A. P.; Stetson, P. B.; Marino, A. F.; Cassisi, S.; del Pino Molina, A.; Salaris, M.; Aparicio, A.; Asplund, M.; Grundahl, F.; Piotto, G.; Weiss, A.; Carrera, R.; Cebrián, M.; Murabito, S.; Pietrinferni, A.; Sbordone, L.

2013-05-01

We present a general overview and the first results of the SUMO project (a SUrvey of Multiple pOpulations in Globular Clusters). The objective of this survey is the study of multiple stellar populations in the largest sample of globular clusters homogeneously analysed to date. To this aim we obtained high signal-to-noise (S/N > 50) photometry for main sequence stars with mass down to ˜0.5 M⊙ in a large sample of clusters using both archival and proprietary U, B, V and I data from ground-based telescopes. In this paper, we focus on the occurrence of multiple stellar populations in 23 clusters. We define a new photometric index, cU, B, I = (U - B) - (B - I), which turns out to be very effective for identifying multiple sequences along the red giant branch (RGB). We found that in the V-cU, B, I diagram all clusters presented in this paper show broadened or multimodal RGBs, with the presence of two or more components. We found a direct connection with the chemical properties of different sequences, which display different abundances of light elements (O, Na, C, N and Al). The cU, B, I index is also a powerful tool for identifying distinct sequences of stars along the horizontal branch and, for the first time in the case of NGC 104 (47 Tuc), along the asymptotic giant branch. Our results demonstrate that (i) the presence of more than two stellar populations is a common feature amongst globular clusters, as already highlighted in previous work; (ii) multiple sequences with different chemical contents can be easily identified by using standard Johnson photometry obtained with ground-based facilities; (iii) in the study of globular cluster multiple stellar populations the cU, B, I index is an alternative to spectroscopy, and has the advantage of larger statistics.

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.

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.

High prevalence of seasonal affective disorder among persons with severe visual impairment

DEFF Research Database (Denmark)

Madsen, Helle Østergaard; Dam, Henrik; Hageman, Ida

2016-01-01

BACKGROUND: Light severely affects the occurrence of seasonal affective disorder (SAD). AIMS: To compare the prevalence of SAD in persons with severe visual impairment and persons with full sight, and in persons with severe visual impairment with or without light perception. METHOD: This cross......-sectional study assessed the Global Seasonality Score (GSS) and the prevalence of SAD among 2781 persons with visual impairment and 4099 persons with full sight using the Seasonal Pattern Assessment Questionnaire (SPAQ). RESULTS: Respondents with visual impairment had significantly higher GSS and prevalence...... of SAD compared with full sight controls, Pvisual impairment and SPAQ-defined SAD parameters...

A picorna-like virus from the red imported fire ant, Solenopsis invicta: initial discovery, genome sequence, and characterization

International Nuclear Information System (INIS)

Valles, Steven M.; Strong, Charles A.; Dang, Phat M.; Hunter, Wayne B.; Pereira, Roberto M.; Oi, David H.; Shapiro, Alexandra M.; Williams, David F.

2004-01-01

We report the first discovery and genome sequence of a virus infecting the red imported fire ant, Solenopsis invicta. The 8026 nucleotide, polyadenylated, RNA genome encoded two large open reading frames (ORF1 and ORF2), flanked and separated by 27, 223, and 171 nucleotide untranslated regions, respectively. The predicted amino acid sequence of the 5' proximal ORF1 (nucleotides 28 to 4218) exhibited significant identity and possessed consensus sequences characteristic of the helicase, cysteine protease, and RNA-dependent RNA polymerase sequence motifs from picornaviruses, picorna-like viruses, comoviruses, caliciviruses, and sequiviruses. The predicted amino acid sequence of the 3' proximal ORF2 (nucleotides 4390-7803) showed similarity to structural proteins in picorna-like viruses, especially the acute bee paralysis virus. Electron microscopic examination of negatively stained samples from virus-infected fire ants revealed isometric particles with a diameter of 31 nm, consistent with Picornaviridae. A survey for the fire ant virus from areas around Florida revealed a pattern of fairly widespread distribution. Among 168 nests surveyed, 22.9% were infected. The virus was found to infect all fire ant caste members and developmental stages, including eggs, early (1st-2nd) and late (3rd-4th) instars, worker pupae, workers, sexual pupae, alates ( male and female ), and queens. The virus, tentatively named S. invicta virus (SINV-1), appears to belong to the picorna-like viruses. We did not observe any perceptible symptoms among infected nests in the field. However, in every case where an SINV-1-infected colony was excavated from the field with an inseminated queen and held in the laboratory, all of the brood in these colonies died within 3 months

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

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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.

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.

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....

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.

A PCR-based epidemiological survey of Hepatozoon canis in dogs in Nigeria.

Science.gov (United States)

Sasaki, Mizuki; Omobowale, Olutayo; Ohta, Kaisaku; Tozuka, Morito; Matsuu, Aya; Hirata, Haruyuki; Nottidge, Helen Oyebukola; Ikadai, Hiromi; Oyamada, Takashi

2008-07-01

The prevalence of Hepatozoon canis infections in dogs in Nigeria was surveyed using molecular methods. DNA was extracted from blood samples obtained from 400 dogs. A primer set that amplified the Babesia canis 18S rRNA gene, which has high similarity to the H. canis 18S rRNA gene, was used for the PCR. As a result, samples from 81 dogs (20.3%) produced 757 bp bands, which differed from the 698 bp band that corresponded to B. canis infection. The sequence of the PCR products of 10 samples were determined, all of which corresponded with the H. canis sequence.

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.

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

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Wadim L. Matochko

2013-01-01

Full Text Available Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N×1 frequency vector n=ni, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N×N matrix and a stochastic sampling operator (Sa. The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq. Sequencing without any bias and errors is Seq=Sa IN, where IN is a N×N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN, which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.

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.

Globules, dark clouds, and low mass pre-main sequence stars

International Nuclear Information System (INIS)

Hyland, A.R.

1981-01-01

The current observational and theoretical literature on Bok globules and their relationship to star formation is reviewed. Recent observations of globules at optical, infrared, and far infrared wavelengths are shown to provide important constraints on their structure and evolutionary status, and the suggestion that many globules are gravitationally unstable is seriously questioned. Dark clouds associated with T associations are well-known sites of recent and continuing star formation. In recent years molecular observations and far infrared surveys have provided maps of such regions from which possible sites of star formation may be identified. Optical (Hα) and near infrared surveys have enabled a clear identification of pre-main sequence (PMS) objects within the clouds. Methods of distinguishing these from background objects and the nature of their infrared excesses are examined in the light of recent observations in the near and far infrared. The perennial question as to the existence of anomalous reddening within dark clouds is also investigated. (Auth.)

Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.

Directory of Open Access Journals (Sweden)

Sean Conlan

Full Text Available BACKGROUND: Outbreaks of antibiotic-resistant bacterial infections emphasize the importance of surveillance of potentially pathogenic bacteria. Genomic sequencing of clinical microbiological specimens expands our capacity to study cultivable, fastidious and uncultivable members of the bacterial community. Herein, we compared the primary data collected by the NIH's Human Microbiome Project (HMP with published epidemiological surveillance data of Staphylococcus aureus. METHODS: The HMP's initial dataset contained microbial survey data from five body regions (skin, nares, oral cavity, gut and vagina of 242 healthy volunteers. A significant component of the HMP dataset was deep sequencing of the 16S ribosomal RNA gene, which contains variable regions enabling taxonomic classification. Since species-level identification is essential in clinical microbiology, we built a reference database and used phylogenetic placement followed by most recent common ancestor classification to look at the species distribution for Staphylococcus, Klebsiella and Enterococcus. MAIN RESULTS: We show that selecting the accurate region of the 16S rRNA gene to sequence is analogous to carefully selecting culture conditions to distinguish closely related bacterial species. Analysis of the HMP data showed that Staphylococcus aureus was present in the nares of 36% of healthy volunteers, consistent with culture-based epidemiological data. Klebsiella pneumoniae and Enterococcus faecalis were found less frequently, but across many habitats. CONCLUSIONS: This work demonstrates that large 16S rRNA survey studies can be used to support epidemiological goals in the context of an increasing awareness that microbes flourish and compete within a larger bacterial community. This study demonstrates how genomic techniques and information could be critically important to trace microbial evolution and implement hospital infection control.

Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

International Nuclear Information System (INIS)

Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

2002-01-01

The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

Directory of Open Access Journals (Sweden)

Martin Beránek

2012-01-01

Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

Science.gov (United States)

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

Gerstmann-Straussler-Scheinker Disease

Science.gov (United States)

... SEARCH Definition Treatment Prognosis Clinical Trials Organizations Publications Definition Gerstmann-Straussler-Scheinker disease (GSS) is an extremely rare, neurodegenerative brain disorder. ...

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...

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.

Directory of Open Access Journals (Sweden)

Sebastian Jünemann

Full Text Available De novo genome assembly is the process of reconstructing a complete genomic sequence from countless small sequencing reads. Due to the complexity of this task, numerous genome assemblers have been developed to cope with different requirements and the different kinds of data provided by sequencers within the fast evolving field of next-generation sequencing technologies. In particular, the recently introduced generation of benchtop sequencers, like Illumina's MiSeq and Ion Torrent's Personal Genome Machine (PGM, popularized the easy, fast, and cheap sequencing of bacterial organisms to a broad range of academic and clinical institutions. With a strong pragmatic focus, here, we give a novel insight into the line of assembly evaluation surveys as we benchmark popular de novo genome assemblers based on bacterial data generated by benchtop sequencers. Therefore, single-library assemblies were generated, assembled, and compared to each other by metrics describing assembly contiguity and accuracy, and also by practice-oriented criteria as for instance computing time. In addition, we extensively analyzed the effect of the depth of coverage on the genome assemblies within reasonable ranges and the k-mer optimization problem of de Bruijn Graph assemblers. Our results show that, although both MiSeq and PGM allow for good genome assemblies, they require different approaches. They not only pair with different assembler types, but also affect assemblies differently regarding the depth of coverage where oversampling can become problematic. Assemblies vary greatly with respect to contiguity and accuracy but also by the requirement on the computing power. Consequently, no assembler can be rated best for all preconditions. Instead, the given kind of data, the demands on assembly quality, and the available computing infrastructure determines which assembler suits best. The data sets, scripts and all additional information needed to replicate our results are freely

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

Science.gov (United States)

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2004-09-22

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

Early detection of abnormal prion protein in genetic human prion diseases now possible using real-time QUIC assay.

Directory of Open Access Journals (Sweden)

Kazunori Sano

Full Text Available INTRODUCTION: The definitive diagnosis of genetic prion diseases (gPrD requires pathological confirmation. To date, diagnosis has relied upon the finding of the biomarkers 14-3-3 protein and total tau (t-tau protein in the cerebrospinal fluid (CSF, but many researchers have reported that these markers are not sufficiently elevated in gPrD, especially in Gerstmann-Sträussler-Scheinker syndrome (GSS. We recently developed a new in vitro amplification technology, designated "real-time quaking-induced conversion (RT-QUIC", to detect the abnormal form of prion protein in CSF from sporadic Creutzfeldt-Jakob disease (sCJD patients. In the present study, we aimed to investigate the presence of biomarkers and evaluate RT-QUIC assay in patients with gPrD, as the utility of RT-QUIC as a diagnostic tool in gPrD has yet to be determined. METHOD/PRINCIPAL FINDINGS: 56 CSF samples were obtained from gPrD patients, including 20 cases of GSS with P102L mutation, 12 cases of fatal familial insomnia (FFI; D178N, and 24 cases of genetic CJD (gCJD, comprising 22 cases with E200K mutation and 2 with V203I mutation. We subjected all CSF samples to RT-QUIC assay, analyzed 14-3-3 protein by Western blotting, and measured t-tau protein using an ELISA kit. The detection sensitivities of RT-QUIC were as follows: GSS (78%, FFI (100%, gCJD E200K (87%, and gCJD V203I (100%. On the other hand the detection sensitivities of biomarkers were considerably lower: GSS (11%, FFI (0%, gCJD E200K (73%, and gCJD V203I (67%. Thus, RT-QUIC had a much higher detection sensitivity compared with testing for biomarkers, especially in patients with GSS and FFI. CONCLUSION/SIGNIFICANCE: RT-QUIC assay is more sensitive than testing for biomarkers in gPrD patients. RT-QUIC method would thus be useful as a diagnostic tool when the patient or the patient's family does not agree to genetic testing, or to confirm the diagnosis in the presence of a positive result for genetic testing.

THE REST-FRAME OPTICAL LUMINOSITY FUNCTION OF CLUSTER GALAXIES AT z < 0.8 AND THE ASSEMBLY OF THE CLUSTER RED SEQUENCE

International Nuclear Information System (INIS)

Rudnick, Gregory; Von der Linden, Anja; De Lucia, Gabriella; White, Simon; Pello, Roser; Aragon-Salamanca, Alfonso; Marchesini, Danilo; Clowe, Douglas; Halliday, Claire; Jablonka, Pascale; Milvang-Jensen, Bo; Poggianti, Bianca; Saglia, Roberto; Simard, Luc; Zaritsky, Dennis

2009-01-01

We present the rest-frame optical luminosity function (LF) of red-sequence galaxies in 16 clusters at 0.4 < z < 0.8 drawn from the ESO Distant Cluster Survey (EDisCS). We compare our clusters to an analogous sample from the Sloan Digital Sky Survey (SDSS) and match the EDisCS clusters to their most likely descendants. We measure all LFs down to M ∼ M * + (2.5-3.5). At z < 0.8, the bright end of the LF is consistent with passive evolution but there is a significant buildup of the faint end of the red sequence toward lower redshift. There is a weak dependence of the LF on cluster velocity dispersion for EDisCS but no such dependence for the SDSS clusters. We find tentative evidence that red-sequence galaxies brighter than a threshold magnitude are already in place, and that this threshold evolves to fainter magnitudes toward lower redshifts. We compare the EDisCS LFs with the LF of coeval red-sequence galaxies in the field and find that the bright end of the LFs agree. However, relative to the number of bright red galaxies, the field has more faint red galaxies than clusters at 0.6 < z < 0.8 but fewer at 0.4 < z < 0.6, implying differential evolution. We compare the total light in the EDisCS cluster red sequences to the total red-sequence light in our SDSS cluster sample. Clusters at 0.4 < z < 0.8 must increase their luminosity on the red sequence (and therefore stellar mass in red galaxies) by a factor of 1-3 by z = 0. The necessary processes that add mass to the red sequence in clusters predict local clusters that are overluminous as compared to those observed in the SDSS. The predicted cluster luminosities can be reconciled with observed local cluster luminosities by combining multiple previously known effects.

Seasonality of mood and behavior in the Old Order Amish.

Science.gov (United States)

Raheja, Uttam K; Stephens, Sarah H; Mitchell, Braxton D; Rohan, Kelly J; Vaswani, Dipika; Balis, Theodora G; Nijjar, Gagan V; Sleemi, Aamar; Pollin, Toni I; Ryan, Kathleen; Reeves, Gloria M; Weitzel, Nancy; Morrissey, Mary; Yousufi, Hassaan; Langenberg, Patricia; Shuldiner, Alan R; Postolache, Teodor T

2013-05-01

We examined seasonality and winter seasonal affective disorder (SAD) in the Old Order Amish of Lancaster County, Pennsylvania, a unique population that prohibits use of network electric light in their homes. We estimated SAD using the seasonal pattern assessment questionnaire (SPAQ) in 1306 Amish adults and compared the frequencies of SAD and total SAD (i.e., presence of either SAD or subsyndromal-SAD) between men and women, young and old, and awareness of (ever vs. never heard about) SAD. Heritability of global seasonality score (GSS) was estimated using the maximum likelihood method, including a household effect to capture shared environmental effects. The mean (±SD) GSS was 4.36 (±3.38). Prevalence was 0.84% (95% CI: 0.36-1.58) for SAD and 2.59% (95% CI: 1.69-3.73) for total SAD. Heritability of GSS was 0.14±0.06 (SE) (p=0.002) after adjusting for age, gender, and household effects. Limitations include likely overestimation of the rates of SAD by SPAQ, possible selection bias and recall bias, and limited generalizability of the study. In the Amish, GSS and SAD prevalence were lower than observed in earlier SPAQ-based studies in other predominantly Caucasian populations. Low heritability of SAD suggests dominant environmental effects. The effects of awareness, age and gender on SAD risk were similar as in previous studies. Identifying factors of resilience to SAD in the face of seasonal changes in the Amish could suggest novel preventative and therapeutic approaches to reduce the impact of SAD in the general population. Copyright © 2012 Elsevier B.V. All rights reserved.

A prospective study of three diagnostic sonographic methods in differentiation between benign and malignant salivary gland tumours

Science.gov (United States)

El-Khateeb, SM; Abou-Khalaf, AE; Farid, MM; Nassef, MA

2011-01-01

Objective The aim of this study was to evaluate the role of three diagnostic sonographic methods, greyscale sonography (GSS), colour Doppler sonography (CDS) and spectral Doppler (SPD), in differentiating between benign and malignant salivary gland (SG) tumours. Methods 44 patients with SG masses were examined using GSS, CDS and SPD. The morphological features of each tumour were evaluated using GSS, the distribution and number of detected blood vessels were assessed using CDS, and peak systolic velocity (PSV), resistive index (RI) and pulsatility index (PI) were measured on SPD. All cases underwent excisional biopsy and a definite tissue diagnosis was obtained. Results Histopathological examination revealed that 28 of the 44 tumours were benign and 16 were malignant. GSS showed that malignant SG tumours had a significantly higher incidence of ill-defined borders and lymph node involvement than benign tumours, but there was no significant difference between benign and malignant SG tumours regarding echogenicity, homogeneity or sonographic shape. CDS demonstrated malignant tumours with significantly higher vascularity and a scattered distribution. Using SPD, malignant tumours had significantly higher PSV, RI and PI compared with benign tumours. Conclusion RI values above 0.7, PI values above 1.2, PSV values above 44.3 cm s–1, ill-defined borders, lymph node involvement, Grade 2 or 3 vascularity and hilar distribution of blood vessels should alert the clinician to suspect a malignant SG tumour. After consensus on the threshold values of PSV, RI and PI in differentiating benign from malignant SG tumours, these numbers should be incorporated into the software of ultrasound machines to guide the sonographer in his or her analysis. PMID:22065796

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 ...

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

Science.gov (United States)

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

The Occurrence of Sequences Identical with Epitopes from the Allergen Pen a 1.0102 Among Food and Non-Food Proteins

Directory of Open Access Journals (Sweden)

Minkiewicz Piotr

2015-03-01

Full Text Available The presence of common epitopes among tropomyosins of invertebrates, including arthropods, e.g. edible ones, may help to explain the molecular basis of cross-reactivity between allergens. The work presented is the first survey concerning global distribution of epitopes from Pen a 1.0102 in universal proteome. In the group of known tropomyosin epitopes, the fragment with the sequence ESKIVELEEEL was found in the sequence of channel catfish (Ictalurus punctatus tropomyosin. To date, this is the first result suggesting the presence of a complete sequential epitope interacting with gE in vertebrate tropomyosin. Another fragment with the sequence VAALNRRIQL, a major part of the epitope, was found in 11 fish, 8 amphibians, 3 birds, 19 mammalians and 4 human tropomyosin sequences. Identical epitopes are common in sequences of invertebrate tropomyosins, including food and non-food allergens annotated in the Allergome database. The rare pentapeptide with the DEERM sequence occurs in proteins not sharing homology with tropomyosins. Pathogenic microorganisms are the most abundant category of organisms synthesizing such proteins.

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

Directory of Open Access Journals (Sweden)

Miri eMichaeli

2012-12-01

Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

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.

First Tests of a New Fast Waveform Digitizer for PMT Signal Read-out from Liquid Argon Dark Matter Detectors

Science.gov (United States)

Szelc, A. M.; Canci, N.; Cavanna, F.; Cortopassi, A.; D'Incecco, M.; Mini, G.; Pietropaolo, F.; Romboli, A.; Segreto, E.; Acciarri, R.

A new generation Waveform Digitizer board as been recently made available on the market by CAEN. The new board CAEN V1751 with 8 Channels per board, 10 bit, 1 GS/s Flash ADC Waveform Digitizer (or 4 channel, 10 bit, 2 GS/s Flash ADC Waveform Digitizer -Dual Edge Sampling mode) with threshold and Auto-Trigger capabilities provides an ideal (relatively low-cost) solution for reading signals from liquid Argon detectors for Dark Matter search equipped with an array of PMTs for the detection of scintillation light. The board was extensively used in real experimental conditions to test its usefulness for possible future uses and to compare it with a state of the art digital oscilloscope. As results, PMT Signal sampling at 1 or 2 GS/s is appropriate for the reconstruction of the fast component of the signal scintillation in Argon (characteristic time of about 4 ns) and the extended dynamic range, after a small customization, allows for the detection of signals in the range of energy needed. The bandwidth is found to be adequate and the intrinsic noise is very low.

Carbon nanofibers with radially grown graphene sheets derived from electrospinning for aqueous supercapacitors with high working voltage and energy density

Science.gov (United States)

Zhao, Lei; Qiu, Yejun; Yu, Jie; Deng, Xianyu; Dai, Chenglong; Bai, Xuedong

2013-05-01

Improvement of energy density is an urgent task for developing advanced supercapacitors. In this paper, aqueous supercapacitors with high voltage of 1.8 V and energy density of 29.1 W h kg-1 were fabricated based on carbon nanofibers (CNFs) and Na2SO4 electrolyte. The CNFs with radially grown graphene sheets (GSs) and small average diameter down to 11 nm were prepared by electrospinning and carbonization in NH3. The radially grown GSs contain between 1 and a few atomic layers with their edges exposed on the surface. The CNFs are doped with nitrogen and oxygen with different concentrations depending on the carbonizing temperature. The supercapacitors exhibit excellent cycling performance with the capacity retention over 93.7% after 5000 charging-discharging cycles. The unique structure, possessing radially grown GSs, small diameter, and heteroatom doping of the CNFs, and application of neutral electrolyte account for the high voltage and energy density of the present supercapacitors. The present supercapacitors are of high promise for practical application due to the high energy density and the advantages of neutral electrolyte including low cost, safety, low corrosivity, and convenient assembly in air.

Quantitative, functional MRI and neurophysiological markers in a case of Gerstmann-Sträussler-Scheinker syndrome.

Science.gov (United States)

Marino, Silvia; Morabito, Rosa; De Salvo, S; Bonanno, L; Bramanti, A; Pollicino, P; Giorgianni, R; Bramanti, Placido

Gerstmann-Sträussler-Scheinker syndrome (GSS) is an inherited autosomal dominant prion disease, caused by a codon 102 proline to leucine substitution (P102L) in the prion protein gene (PRNP). We describe the case of a 40-year-old male, affected by a slowly progressive gait disturbance, leg weakness and cognitive impairment. Genomic DNA revealed a point mutation of PRNP at codon 102, resulting in P102L, and the diagnosis of GSS was confirmed. Somatosensory evoked potentials showed alterations of principal parameters, particularly in the right upper and lower limbs. Laser-evoked potentials were indicative of nociceptive system impairment, especially in the right upper and lower limbs. Conventional magnetic resonance imaging (MRI) revealed marked atrophy of the vermis and cerebellar hemispheres and mild atrophy of the middle cerebellar peduncles and brainstem, as confirmed by a brain volume automatic analysis. Resting-state functional MRI showed increased functional connectivity in the bilateral visual cortex, and decreased functional connectivity in the bilateral frontal pole and supramarginal and precentral gyrus. Albeit limited to a single case, this is the first study to assess structural and functional connectivity in GSS using a multimodal approach.

Population survey of phytoseiid mites and spider mites on peach leaves and wild plants in Japanese peach orchard.

Science.gov (United States)

Wari, David; Yamashita, Jun; Kataoka, Yoko; Kohara, Yoko; Hinomoto, Norihide; Kishimoto, Hidenari; Toyoshima, Shingo; Sonoda, Shoji

2014-07-01

A population survey of phytoseiid mites and spider mites was conducted on peach leaves and wild plants in Japanese peach orchards having different pesticide practices. The phytoseiid mite species composition on peach leaves and wild plants, as estimated using quantitative sequencing, changed during the survey period. Moreover, it varied among study sites. The phytoseiid mite species compositions were similar between peach leaves and some wild plants, such as Veronica persica, Paederia foetida, Persicaria longiseta, and Oxalis corniculata with larger quantities of phytoseiid mites, especially after mid-summer. A PCR-based method to detect the ribosomal ITS sequences of Tetranychus kanzawai and Panonychus mori from phytoseiid mites was developed. Results showed that Euseius sojaensis (specialized pollen feeder/generalist predator) uses both spider mites as prey in the field.

Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

Science.gov (United States)

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-01-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering

Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

Science.gov (United States)

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-02-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the

One gigasample per second transient recorder: a performance demonstration

International Nuclear Information System (INIS)

Linnenbrink, T.E.; Gradl, D.A.; Ritt, D.M.; DeWitte, G.J.; Hutton, J.D.

1982-01-01

The performance demonstrated by a one gigasample per second (1 Gs/s) transient recorder currently in advanced development portends an important new instrument for recording single transient data. A Charge-Coupled Device (CCD) is used to sample a continuous analog signal. Samples acquired at the full sampling rate (1 Gs/s) are temporarily stored in the CCD, then read out at a slow rate (e.g., 250 Ks/s) into a conventional analog-to-digital converter prior to storage in nonvolatile, digital memory. Enhanced circuitry and techniques developed over the past three years have yielded higher performance than originally anticipated. Accordingly, the target specification has been revised to reflect higher expectations

Long term safety and tolerability of Tafluprost 0.0015% vs Timolol 0.1% preservative-free in ocular hypertensive and in primary open-angle glaucoma patients: a cross sectional study.

Science.gov (United States)

Rolle, Teresa; Spinetta, Roberta; Nuzzi, Raffaele

2017-08-03

The effects of preservatives of antiglaucoma medications on corneal surface and tear function have been widely shown in literature; it's not the same as regards the active compounds themselves. The purpose of our study was to compare Ocular Surface Disease (OSD) signs and symptoms of Tafluprost 0.0015% versus preservative free (PF) Timolol 0.1% eyedrops in ocular hypertensive (OH) and in primary open-angle glaucoma (POAG) patients. A cross-sectional study included patients in monotherapy for at least 36 months with Tafluprost 0.0015% (27) or PF Timolol 0.1% (24) and 20 healthy age and sex-matched volunteers. All subjects underwent clinical tests (Schirmer I and break-up time), in vivo confocal microscopy (IVCM) and were surveyed using Ocular Surface Disease Index (OSDI) and Glaucoma Symptoms Scale (GSS) questionnaires. The groups were compared with ANOVA, Kruskal-Wallis test, t-test, Mann-Whitney test and Bonferroni's adjustment of p-values. No significant differences were found in questionnaires scores, clinical tests, IVCM variables between therapy groups. Tafluprost 0.0015% group showed significantly higher OSDI score, basal epithelial cells density, stromal reflectivity, sub-basal nerves tortuosity (p = 0.0000, 0.037, 0.006, 0.0000) and less GSS score, number of sub-basal nerves (p = 0.0000, 0.037) than controls but similar clinical tests results (p > 0.05). PF Timolol group had significantly higher OSDI score, basal epithelial cells density, stromal reflectivity and sub-basal nerve tortuosity (p = 0.000, 0.014, 0.008, 0.002), less GSS score, BUT and number of sub-basal nerves (p = 0.0000, 0.026, 0.003) than controls. Compared to PF Timolol 0.1%, Tafluprost 0.0015% showed similar safety with regards to tear function and corneal status and a similar tolerability profile. Both therapy groups show some alterations in corneal microstructure but no side effects on tear function except for an increased tear instability in PF Timolol 0.1% group

Principles of primary survey and resuscitation in cases of pediatric trauma.

Directory of Open Access Journals (Sweden)

Saba Jafarpour

2015-04-01

Full Text Available Trauma is a common cause of death and disability in children. Proper approach to pediatric trauma involves adherence to ABCDE sequence in the primary survey and resuscitation in order to promptly recognize and manage life-threatening conditions immediately. This readily reviewed sequence includes A: establishment and maintenance of a patent airway while maintaining cervical spine immobilization; B: evaluation of breathing, ventilation and oxygenation, immediate treatment of tension pneumothorax, open pneumothorax and massive hemothorax; C: evaluation and treatment of circulatory compromise and shock; D: Disability and Neurologic Status, assessment of signs of increased intracranial pressure and impending cerebral herniation; and E: Exposure while preventing hypothermia. Implementing these assessment and management priorities can result in more favorable outcomes.

Principles of primary survey and resuscitation in cases of pediatric trauma.

Directory of Open Access Journals (Sweden)

Saba Jafarpour

2014-12-01

Full Text Available Trauma is a common cause of death and disability in children. Proper approach to pediatric trauma involves adherence to ABCDE sequence in the primary survey and resuscitation in order to promptly recognize and manage immediately life threatening conditions. This readily reviewed sequence includes A: establishment and maintenance of a patent airway while maintaining cervical spine immobilization; B: evaluation of breathing, ventilation and oxygenation, immediate treatment of tension pneumothorax, open pneumothorax and massive hemothorax; C: evaluation and treatment of circulatory compromise and shock; D: Disability and Neurologic Status, assessment of signs of increased intracranial pressure and impending cerebral herniation; and E: Exposure while preventing hypothermia. Implementing these assessment and management priorities can result in more favorable outcomes.

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....

DISSECTING THE QUASAR MAIN SEQUENCE: INSIGHT FROM HOST GALAXY PROPERTIES

International Nuclear Information System (INIS)

Sun, Jiayi; Shen, Yue

2015-01-01

The diverse properties of broad-line quasars appear to follow a well-defined main sequence along which the optical Fe ii strength increases. It has been suggested that this sequence is mainly driven by the Eddington ratio (L/L Edd ) of the black hole (BH) accretion. Shen and Ho demonstrated with quasar clustering analysis that the average BH mass decreases with increasing Fe ii strength when quasar luminosity is fixed, consistent with this suggestion. Here we perform an independent test by measuring the stellar velocity dispersion σ * (hence, the BH mass via the M–σ * relation) from decomposed host spectra in low-redshift Sloan Digital Sky Survey quasars. We found that at fixed quasar luminosity, σ * systematically decreases with increasing Fe ii strength, confirming that the Eddington ratio increases with Fe ii strength. We also found that at fixed luminosity and Fe ii strength, there is little dependence of σ * on the broad Hβ FWHM. These new results reinforce the framework that the Eddington ratio and orientation govern most of the diversity seen in broad-line quasar properties

Site Specific Advisory Board initiative, evaluation survey results supplementary appendix: Summary of individual site results

International Nuclear Information System (INIS)

1996-08-01

This Appendix presents results of the Site-Specific Advisory Board (SSAB) Initiative for each of the 11 sites that participated in the survey. These individual results are a supplement to the June 1996 Summary Report which presented overall survey results. Results are presented in 11 sections, arranged alphabetically by site. Each section includes a series of figures and tables that parallel those presented in the Summary Report. To facilitate comparison, figures are presented both for the individual site and for the overall long survey. The sequence of sections is: Fernald, Hanford, Idaho, Los Alamos, Monticello, Nevada, Pantex, Rocky Flats, St. Louis, Sandia, and Savannah River

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.

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.

ORF Alignment: NC_002689 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ylmutase [Thermoplasma volcanium GSS1] ... Length = 195 ... Query: 59 ... ARERYLFSKIVHAAGDFRLIDLIRMSPGFVDTV...AEKLRDGCRIVVDAKMVKAGIYNKNLL 118 ... ARERYLFSKIVHAAGDFRLIDLIRMSPGFVDTVAEKLRDGCRIVVDAKMVKAGIYNKNLL Sbjc...t: 23 ... ARERYLFSKIVHAAGDFRLIDLIRMSPGFVDTVAEKLRDGCRIVVDAKMVKAGIYNKNLL 82 ... Query: 17

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...

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

Science.gov (United States)

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

2013-05-01

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 multiple subjects, leading to a posterior probability of ASM. We flag SNPs with high posterior probabilities of ASM by accounting for multiple comparisons based on posterior false discovery rates. Applying the Bayesian approach to the in-house prostate cell line data, we identify 269 SNPs as candidates of ASM. A simulation study is carried out to demonstrate the quantitative performance of the proposed approach.

Close relationship of Plasmodium sequences detected from South American pampas deer (Ozotoceros bezoarticus to Plasmodium spp. in North American white-tailed deer

Directory of Open Access Journals (Sweden)

Masahito Asada

2018-04-01

Full Text Available We report, for the first time, the presence of ungulate malaria parasites in South America. We conducted PCR-based surveys of blood samples of multiple deer species and water buffalo from Brazil and detected Plasmodium sequences from pampas deer (Ozotoceros bezoarticus samples. Phylogenic analysis revealed that the obtained sequences are closely related to the Plasmodium odocoilei clade 2 sequence from North American white-tailed deer (Odocoileus virginianus. Nucleotide differences suggest that malaria parasites in South American pampas deer and North American P. odocoilei clade 2 branched more recently than the Great American Interchange. Keywords: Malaria, Pampas deer, South America, Plasmodium odocoilei, Brazil

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Science.gov (United States)

Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

2016-09-01

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China

Science.gov (United States)

Zhou, Hong; Zhang, Zhinan; Chen, Haiyan; Sun, Renhua; Wang, Hui; Guo, Lei; Pan, Haijian

2010-07-01

In this study, we integrated a DNA barcoding project with an ecological survey on intertidal polychaete communities and investigated the utility of CO1 gene sequence as a DNA barcode for the classification of the intertidal polychaetes. Using 16S rDNA as a complementary marker and combining morphological and ecological characterization, some of dominant and common polychaete species from Chinese coasts were assessed for their taxonomic status. We obtained 22 haplotype gene sequences of 13 taxa, including 10 CO1 sequences and 12 16S rDNA sequences. Based on intra- and inter-specific distances, we built phylogenetic trees using the neighbor-joining method. Our study suggested that the mitochondrial CO1 gene was a valid DNA barcoding marker for species identification in polychaetes, but other genes, such as 16S rDNA, could be used as a complementary genetic marker. For more accurate species identification and effective testing of species hypothesis, DNA barcoding should be incorporated with morphological, ecological, biogeographical, and phylogenetic information. The application of DNA barcoding and molecular identification in the ecological survey on the intertidal polychaete communities demonstrated the feasibility of integrating DNA taxonomy and ecology.

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.

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

Science.gov (United States)

2012-01-01

Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence

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...

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…

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.

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

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.

Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

Science.gov (United States)

Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

2016-01-01

On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

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.

A REVISED PARALLEL-SEQUENCE MORPHOLOGICAL CLASSIFICATION OF GALAXIES: STRUCTURE AND FORMATION OF S0 AND SPHEROIDAL GALAXIES

International Nuclear Information System (INIS)

Kormendy, John; Bender, Ralf

2012-01-01

We update van den Bergh's parallel-sequence galaxy classification in which S0 galaxies form a sequence S0a-S0b-S0c that parallels the sequence Sa-Sb-Sc of spiral galaxies. The ratio B/T of bulge-to-total light defines the position of a galaxy in this tuning-fork diagram. Our classification makes one major improvement. We extend the S0a-S0b-S0c sequence to spheroidal ('Sph') galaxies that are positioned in parallel to irregular galaxies in a similarly extended Sa-Sb-Sc-Im sequence. This provides a natural 'home' for spheroidals, which previously were omitted from galaxy classification schemes or inappropriately combined with ellipticals. To motivate our juxtaposition of Sph and Im galaxies, we present photometry and bulge-disk decompositions of four rare, late-type S0s that bridge the gap between the more common S0b and Sph galaxies. NGC 4762 is an edge-on SB0bc galaxy with a very small classical-bulge-to-total ratio of B/T = 0.13 ± 0.02. NGC 4452 is an edge-on SB0 galaxy with an even tinier pseudobulge-to-total ratio of PB/T = 0.017 ± 0.004. It is therefore an SB0c. VCC 2048, whose published classification is S0, contains an edge-on disk, but its 'bulge' plots in the structural parameter sequence of spheroidals. It is therefore a disky Sph. And NGC 4638 is similarly a 'missing link' between S0s and Sphs—it has a tiny bulge and an edge-on disk embedded in an Sph halo. In the Appendix, we present photometry and bulge-disk decompositions of all Hubble Space Telescope Advanced Camera for Surveys Virgo Cluster Survey S0s that do not have published decompositions. We use these data to update the structural parameter correlations of Sph, S+Im, and E galaxies. We show that Sph galaxies of increasing luminosity form a continuous sequence with the disks (but not bulges) of S0c-S0b-S0a galaxies. Remarkably, the Sph-S0-disk sequence is almost identical to that of Im galaxies and spiral galaxy disks. We review published observations for galaxy transformation processes

A Revised Parallel-sequence Morphological Classification of Galaxies: Structure and Formation of S0 and Spheroidal Galaxies

Science.gov (United States)

Kormendy, John; Bender, Ralf

2012-01-01

We update van den Bergh's parallel-sequence galaxy classification in which S0 galaxies form a sequence S0a-S0b-S0c that parallels the sequence Sa-Sb-Sc of spiral galaxies. The ratio B/T of bulge-to-total light defines the position of a galaxy in this tuning-fork diagram. Our classification makes one major improvement. We extend the S0a-S0b-S0c sequence to spheroidal ("Sph") galaxies that are positioned in parallel to irregular galaxies in a similarly extended Sa-Sb-Sc-Im sequence. This provides a natural "home" for spheroidals, which previously were omitted from galaxy classification schemes or inappropriately combined with ellipticals. To motivate our juxtaposition of Sph and Im galaxies, we present photometry and bulge-disk decompositions of four rare, late-type S0s that bridge the gap between the more common S0b and Sph galaxies. NGC 4762 is an edge-on SB0bc galaxy with a very small classical-bulge-to-total ratio of B/T = 0.13 ± 0.02. NGC 4452 is an edge-on SB0 galaxy with an even tinier pseudobulge-to-total ratio of PB/T = 0.017 ± 0.004. It is therefore an SB0c. VCC 2048, whose published classification is S0, contains an edge-on disk, but its "bulge" plots in the structural parameter sequence of spheroidals. It is therefore a disky Sph. And NGC 4638 is similarly a "missing link" between S0s and Sphs—it has a tiny bulge and an edge-on disk embedded in an Sph halo. In the Appendix, we present photometry and bulge-disk decompositions of all Hubble Space Telescope Advanced Camera for Surveys Virgo Cluster Survey S0s that do not have published decompositions. We use these data to update the structural parameter correlations of Sph, S+Im, and E galaxies. We show that Sph galaxies of increasing luminosity form a continuous sequence with the disks (but not bulges) of S0c-S0b-S0a galaxies. Remarkably, the Sph-S0-disk sequence is almost identical to that of Im galaxies and spiral galaxy disks. We review published observations for galaxy transformation processes

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

Directory of Open Access Journals (Sweden)

Stephan Pabinger

Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

Nonresponse Error in Mail Surveys: Top Ten Problems

Directory of Open Access Journals (Sweden)

Jeanette M. Daly

2011-01-01

Full Text Available Conducting mail surveys can result in nonresponse error, which occurs when the potential participant is unwilling to participate or impossible to contact. Nonresponse can result in a reduction in precision of the study and may bias results. The purpose of this paper is to describe and make readers aware of a top ten list of mailed survey problems affecting the response rate encountered over time with different research projects, while utilizing the Dillman Total Design Method. Ten nonresponse error problems were identified, such as inserter machine gets sequence out of order, capitalization in databases, and mailing discarded by postal service. These ten mishaps can potentiate nonresponse errors, but there are ways to minimize their frequency. Suggestions offered stem from our own experiences during research projects. Our goal is to increase researchers' knowledge of nonresponse error problems and to offer solutions which can decrease nonresponse error in future projects.

Opportunities to improve competitiveness in male sexual strain has genetic sex determination Ceratitis capitata Wiedemann (Diptera: Tephritidae)

International Nuclear Information System (INIS)

Tlemcani, Meriem

2010-01-01

The success of TIS program depends essentially on the capacity of the sterile males to compete with fertile males to couple with wild females. This program becomes more and more efficient if one good mastery its various factors, mainly the performances of males of the origin of ceratite in genetic sexing within the production unit of sterile flies of the National Center of the Sciences and Nuclear Technologies. Researches turned to the improvement of the competitiveness of the sterile males by the addition of bacteria in the nourishing circles of breeding. By basing itself on the symbiotic relations between the present bacteria in the bowel of the ceratite, we adopted, in this present work, a method of breeding which could improve the quality of the males of genetic sexing GSS. This method consists in introducing certain beneficial bacteria in the ceratite (Enterobacteriaceae and Pseudomonas aerogenes) into the middle of breeding according to various combinations. The effect of these bacteria was analyzed by making various tests of quality control (weight, emergence, capacity in the flight, the longevity) and of reproduction (competitiveness, lasted mating, latent period). It turns out that the addition of Enterobacteriaceae in the middle of breeding outstandingly improved the percentage of emergence of the males of the GSS. Besides, these bacteria contributed to the improvement of the competitiveness of these males with regard to those of the other circles. Besides, the addition of Pseudomonas aerogenes in the middle of breeding gave the best latent period to the males GSS. We also noticed that the association of Enterobacteriaceae with Pseudomonas aerogenes has a positive effect on the capacity in the flight of the males of the GSS and their duration of mating.

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

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

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.

Geochemical variations during the 2012 Emilia seismic sequence

Science.gov (United States)

Sciarra, Alessandra; Cantucci, Barbara; Galli, Gianfranco; Cinti, Daniele; Pizzino, Luca

2015-04-01

Several geochemical surveys (soil gas and shallow water) were performed in the Modena province (Massa Finalese, Finale Emilia, Medolla and S. Felice sul Panaro), during 2006-2014 period. In May-June 2012, a seismic sequence (main shocks of ML 5.9 and 5.8) was occurred closely to the investigated area. In this area 300 CO2 and CH4 fluxes measurements, 150 soil gas concentrations (He, H2, CO2, CH4 and C2H6), 30 shallow waters and their isotopic analyses (δ13C- CH4, δD- CH4 and δ13C- CO2) were performed in April-May 2006, October and December 2008, repeated in May and September 2012, June 2013 and July 2014 afterwards the 2012 Emilia seismic sequences. Chemical composition of soil gas are dominated by CH4 in the southern part by CO2 in the northern part. Very anomalous fluxes and concentrations are recorded in spot areas; elsewhere CO2 and CH4 values are very low, within the typical range of vegetative and of organic exhalation of the cultivated soil. After the seismic sequence the CH4 and CO2 fluxes are increased of one order of magnitude in the spotty areas, whereas in the surrounding area the values are within the background. On the contrary, CH4 concentration decrease (40%v/v in the 2012 surveys) and CO2 concentration increase until to 12.7%v/v (2013 survey). Isotopic gas analysis were carried out only on samples with anomalous values. Pre-seismic data hint a thermogenic origin of CH4 probably linked to leakage from a deep source in the Medolla area. Conversely, 2012/2013 isotopic data indicate a typical biogenic origin (i.e. microbial hydrocarbon production) of the CH4, as recognized elsewhere in the Po Plain and surroundings. The δ13C-CO2 value suggests a prevalent shallow origin of CO2 (i.e. organic and/or soil-derived) probably related to anaerobic oxidation of heavy hydrocarbons. Water samples, collected from domestic, industrial and hydrocarbons exploration wells, allowed us to recognize different families of waters. Waters are meteoric in origin and

PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

Directory of Open Access Journals (Sweden)

Sang Kyu Park

2005-03-01

Full Text Available An m-sequence (PN sequence preestimator scheme for direct-sequence spread spectrum (DS-SS signal acquisition by using block sequence estimation (BSE is proposed and analyzed. The proposed scheme consists of an estimator and a verifier which work according to the PN sequence chip clock, and provides not only the enhanced chip estimates with a threshold decision logic and one-chip error correction among the first m received chips, but also the reliability check of the estimates with additional decision logic. The probabilities of the estimator and verifier operations are calculated. With these results, the detection, the false alarm, and the missing probabilities of the proposed scheme are derived. In addition, using a signal flow graph, the average acquisition time is calculated. The proposed scheme can be used as a preestimator and easily implemented by changing the internal signal path of a generally used digital matched filter (DMF correlator or any other correlator that has a lot of sampling data memories for sampled PN sequence. The numerical results show rapid acquisition performance in a relatively good CNR.

GuiTope: an application for mapping random-sequence peptides to protein sequences.

Science.gov (United States)

Halperin, Rebecca F; Stafford, Phillip; Emery, Jack S; Navalkar, Krupa Arun; Johnston, Stephen Albert

2012-01-03

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

GuiTope: an application for mapping random-sequence peptides to protein sequences

Directory of Open Access Journals (Sweden)

Halperin Rebecca F

2012-01-01

Full Text Available Abstract Background Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. Results GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. Conclusions GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

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...

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-...

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 ...

Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L. Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic–Physical Map Integration

Directory of Open Access Journals (Sweden)

Juana M. Córdoba

2010-11-01

Full Text Available Microsatellite markers or simple sequence repeat (SSR loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs from the G19833 common bean ( L. library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]. Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

Dataset of the HOX1 gene sequences of the wheat polyploids and their diploid relatives

Directory of Open Access Journals (Sweden)

Andrey B. Shcherban

2018-02-01

Full Text Available The TaHOX-1 gene of common wheat Triticum aestivum L. (BAD-genome encodes transcription factor (HD-Zip I which is characterized by the presence of a DNA-binding homeodomain (HD with an adjacent Leucine zipper (LZ motif. This gene can play a role in adapting plant to a variety of abiotic stresses, such as drought, cold, salinity etc., which strongly affect wheat production. However, it's both functional role in stress resistance and divergence during wheat evolution has not yet been elucidated. This data in brief article is associated with the research paper “Structural and functional divergence of homoeologous copies of the TaHOX-1 gene in polyploid wheats and their diploid ancestors”. The data set represents a recent survey of the primary HOX-1 gene sequences isolated from the first wheat allotetraploids (BA-genome and their corresponding Triticum and Aegilops diploid relatives. Specifically, we provide detailed information about the HOX-1 nucleotide sequences of the promoter region and both nucleotide and amino acid sequences of the gene. The sequencing data used here is available at DDBJ/EMBL/GenBank under the accession numbers MG000630-MG000698. Keywords: Wheat, Polyploid, HOX-1 gene, Homeodomain, Transcription factor, Promoter, Triticum, Aegilops

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

Science.gov (United States)

Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

2014-02-01

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

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.

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.

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.

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

Directory of Open Access Journals (Sweden)

Jonathan A Shortt

2017-01-01

Full Text Available In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies.We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample.This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

Science.gov (United States)

Shortt, Jonathan A; Card, Daren C; Schield, Drew R; Liu, Yang; Zhong, Bo; Castoe, Todd A; Carlton, Elizabeth J; Pollock, David D

2017-01-01

In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies. We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample. This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other

Comparing an accelerated 3D fast spin-echo sequence (CS-SPACE) for knee 3-T magnetic resonance imaging with traditional 3D fast spin-echo (SPACE) and routine 2D sequences

Energy Technology Data Exchange (ETDEWEB)

Altahawi, Faysal F.; Blount, Kevin J.; Omar, Imran M. [Northwestern University Feinberg School of Medicine, Department of Radiology, Chicago, IL (United States); Morley, Nicholas P. [Marshfield Clinic, Department of Radiology, Marshfield, WI (United States); Raithel, Esther [Siemens Healthcare GmbH, Erlangen (Germany)

2017-01-15

To compare a faster, new, high-resolution accelerated 3D-fast-spin-echo (3D-FSE) acquisition sequence (CS-SPACE) to traditional 2D and high-resolution 3D sequences for knee 3-T magnetic resonance imaging (MRI). Twenty patients received knee MRIs that included routine 2D (T1, PD ± FS, T2-FS; 0.5 x 0.5 x 3 mm{sup 3}; ∝10 min), traditional 3D FSE (SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝7.5 min), and accelerated 3D-FSE prototype (CS-SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝5 min) acquisitions on a 3-T MRI system (Siemens MAGNETOM Skyra). Three musculoskeletal radiologists (MSKRs) prospectively and independently reviewed the studies with graded surveys comparing image and diagnostic quality. Tissue-specific signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were also compared. MSKR-perceived diagnostic quality of cartilage was significantly higher for CS-SPACE than for SPACE and 2D sequences (p < 0.001). Assessment of diagnostic quality of menisci and synovial fluid was higher for CS-SPACE than for SPACE (p < 0.001). CS-SPACE was not significantly different from SPACE but had lower assessments than 2D sequences for evaluation of bones, ligaments, muscles, and fat (p ≤ 0.004). 3D sequences had higher spatial resolution, but lower overall assessed contrast (p < 0.001). Overall image quality from CS-SPACE was assessed as higher than SPACE (p = 0.007), but lower than 2D sequences (p < 0.001). Compared to SPACE, CS-SPACE had higher fluid SNR and CNR against all other tissues (all p < 0.001). The CS-SPACE prototype allows for faster isotropic acquisitions of knee MRIs over currently used protocols. High fluid-to-cartilage CNR and higher spatial resolution over routine 2D sequences may present a valuable role for CS-SPACE in the evaluation of cartilage and menisci. (orig.)

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...

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

Science.gov (United States)

Khoe, Clairine V; Chung, Long H; Murray, Vincent

2018-06-01

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

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

"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.

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.

Clobetasol propionate shampoo 0.05% is efficacious and safe for long-term control of scalp psoriasis.

Science.gov (United States)

Poulin, Yves; Papp, Kim; Bissonnette, Robert; Guenther, Lyn; Tan, Jerry; Lynde, Charles; Kerrouche, Nabil; Villemagne, Hervé

2010-01-01

Clobetasol propionate (CP) shampoo 0.05% is an efficacious and safe treatment for scalp psoriasis. The aim of this double-blind, randomized, placebo-controlled study was to determine if CP shampoo is suitable for long-term disease control. Participants with moderate to severe scalp psoriasis (global severity score [GSS] of 3 or 4 on a scale of 0 [clear] to 5 [very severe]) first received once daily CP shampoo treatment for up to 4 weeks. Responders were subsequently randomized to receive the CP shampoo or vehicle twice weekly maintenance regimen for up to 6 months. When relapse occurred (defined as GSS > 2), participants resumed once daily CP shampoo treatment; when symptoms diminished (GSS shampoo did not relapse compared with participants treated with vehicle (P shampoo group. After 6 months 31.1% (33/106) of participants in the CP shampoo group were still relapse free versus 8.1% (9/111) of participants in the vehicle group. There was no greater incidence of skin atrophy, telangiectasia, or hypothalamic-pituitary-adrenal (HPA) axis suppression in the CP shampoo group compared with the vehicle group. Clobetasol propionate shampoo is efficacious and safe for acute management and long-term maintenance of moderate to severe scalp psoriasis.

Agricultural runoff pollution control by a grassed swales coupled with wetland detention ponds system: a case study in Taihu Basin, China.

Science.gov (United States)

Zhao, Jinhui; Zhao, Yaqian; Zhao, Xiaoli; Jiang, Cheng

2016-05-01

The performance of a field grassed swales (GSs) coupled with wetland detention ponds (WDPs) system was monitored under four typical rainfall events to assess its effectiveness on agricultural runoff pollution control in Taihu Basin, China. The results indicated that suspended solids (SS) derived from the flush process has significant influence on pollution loads in agricultural runoff. Determination of first flush effect (FFE) indicated that total suspended solids (TSS) and total phosphorus (TP) exhibited moderate FFE, while chemical oxygen demand (COD) and total nitrogen (TN) showed weak FFE. Average removal efficiencies of 83.5 ± 4.5, 65.3 ± 6.8, 91.6 ± 3.8, and 81.3 ± 5.8 % for TSS, COD, TN, and TP were achieved, respectively. The GSs played an important role in removing TSS and TP and acted as a pre-treatment process to prevent clogging of the subsequent WDPs. Particle size distributions (PSDs) analysis indicated that coarse particles larger than 75 μm accounted for 80 % by weight of the total particles in the runoff. GSs can effectively reduce coarse particles (≥75 μm) in runoff, while its removal efficiency for fine particles (runoff pollution control.

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations.

Science.gov (United States)

Fuentes-Pardo, Angela P; Ruzzante, Daniel E

2017-10-01

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology. © 2017 John Wiley & Sons Ltd.

Biological characterization and complete nucleotide sequence of a Tunisian isolate of Moroccan watermelon mosaic virus.

Science.gov (United States)

Yakoubi, S; Desbiez, C; Fakhfakh, H; Wipf-Scheibel, C; Marrakchi, M; Lecoq, H

2008-01-01

During a survey conducted in October 2005, cucurbit leaf samples showing virus-like symptoms were collected from the major cucurbit-growing areas in Tunisia. DAS-ELISA showed the presence of Moroccan watermelon mosaic virus (MWMV, Potyvirus), detected for the first time in Tunisia, in samples from the region of Cap Bon (Northern Tunisia). MWMV isolate TN05-76 (MWMV-Tn) was characterized biologically and its full-length genome sequence was established. MWMV-Tn was found to have biological properties similar to those reported for the MWMV type strain from Morocco. Phylogenetic analysis including the comparison of complete amino-acid sequences of 42 potyviruses confirmed that MWMV-Tn is related (65% amino-acid sequence identity) to Papaya ringspot virus (PRSV) isolates but is a member of a distinct virus species. Sequence analysis on parts of the CP gene of MWMV isolates from different geographical origins revealed some geographic structure of MWMV variability, with three different clusters: one cluster including isolates from the Mediterranean region, a second including isolates from western and central Africa, and a third one including isolates from the southern part of Africa. A significant correlation was observed between geographic and genetic distances between isolates. Isolates from countries in the Mediterranean region where MWMV has recently emerged (France, Spain, Portugal) have highly conserved sequences, suggesting that they may have a common and recent origin. MWMV from Sudan, a highly divergent variant, may be considered an evolutionary intermediate between MWMV and PRSV.

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...

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, ...

SpS1-Preparing for the harvest from large infrared surveys

Science.gov (United States)

Padgett, Deborah L.

2010-11-01

During the past decade, there has been a revolution in the availability of multi-wavelength astronomical surveys. From the Sloan Digital Sky Survey (SDSS) to the NRAO VLA Sky Survey (NVSS), astronomical research based on publicly accessible datasets is becoming standard practice in the community. Beginning with the Infrared Astronomical Satellite (IRAS) mission, infrared surveys have played a critical role in stellar astronomy by identifying cool and dusty stars worthy of spectroscopic characterization. IRAS' four photometric bands at 12, 25, 60, and 100 μm were ideal for detecting dusty circumstellar material. All-sky surveys like IRAS reveal the brightest members of each class of rare objects, optimizing their follow-up strategy. The case of debris disks around main sequence stars demonstrates this utility. IRAS detected dust disks around four nearby stars, Beta Pictoris, Fomalhaut, Epsilon Eridani, and Vega. The “Fabulous Four” remain the best studied debris disks, despite hundreds of additional examples discovered by the Spitzer Space Telescope. In the nearly 30 years since IRAS was launched, its highly reliable catalog of just 250000 sources, modest by modern standards, with arcminute scale resolution and 0.3 - 1 Jy sensitivity, has generated over 10,000 references in ADS. This is a success story by any measure.

Human Y chromosome copy number variation in the next generation sequencing era and beyond.

Science.gov (United States)

Massaia, Andrea; Xue, Yali

2017-05-01

The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.

EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

Energy Technology Data Exchange (ETDEWEB)

Zuiderweg, Erik R. P., E-mail: zuiderwe@umich.edu; Bagai, Ireena [The University of Michigan Medical School, Department of Biological Chemistry (United States); Rossi, Paolo [Rutgers University, Center for Integrative Proteomics Research (United States); Bertelsen, Eric B. [Arbor Communications, Inc. (United States)

2013-10-15

For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 Multiplication-Sign 10{sup 260} possible assignments. In 'EZ-ASSIGN', the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281-298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592-610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335-344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested.

EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

International Nuclear Information System (INIS)

Zuiderweg, Erik R. P.; Bagai, Ireena; Rossi, Paolo; Bertelsen, Eric B.

2013-01-01

For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 × 10 260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281–298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592–610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335–344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested

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.

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.

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.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

Science.gov (United States)

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

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

Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars?

Science.gov (United States)

Poole, Anthony M; Willerslev, Eske

2007-10-01

A central question in astrobiology is whether life exists elsewhere in the universe. If so, is it related to Earth life? Technologies exist that enable identification of DNA- or RNA-based microbial life directly from environmental samples here on Earth. Such technologies could, in principle, be applied to the search for life elsewhere; indeed, efforts are underway to initiate such a search. However, surveying for nucleic acid-based life on other planets, if attempted, must be carried out with caution, owing to the risk of contamination by Earth-based life. Here we argue that the null hypothesis must be that any DNA discovered and sequenced from samples taken elsewhere in the universe are Earth-based contaminants. Experience from studies of low-biomass ancient DNA demonstrates that some results, by their very nature, will not enable complete rejection of the null hypothesis. In terms of eliminating contamination as an explanation of the data, there may be value in identification of sequences that lie outside the known diversity of the three domains of life. We therefore have examined whether a fourth domain could be readily identified from environmental DNA sequence data alone. We concluded that, even on Earth, this would be far from trivial, and we illustrate this point by way of examples drawn from the literature. Overall, our conclusions do not bode well for planned PCR-based surveys for life on Mars, and we argue that other independent biosignatures will be essential in corroborating any claims for the presence of life based on nucleic acid sequences.

THE ELM SURVEY. II. TWELVE BINARY WHITE DWARF MERGER SYSTEMS

International Nuclear Information System (INIS)

Kilic, Mukremin; Brown, Warren R.; Kenyon, S. J.; Prieto, Carlos Allende; Agueeros, M. A.; Heinke, Craig

2011-01-01

We describe new radial velocity and X-ray observations of extremely low-mass white dwarfs (ELM WDs, ∼0.2 M sun ) in the Sloan Digital Sky Survey Data Release 4 and the MMT Hypervelocity Star survey. We identify four new short period binaries, including two merger systems. These observations bring the total number of short period binary systems identified in our survey to 20. No main-sequence or neutron star companions are visible in the available optical photometry, radio, and X-ray data. Thus, the companions are most likely WDs. Twelve of these systems will merge within a Hubble time due to gravitational wave radiation. We have now tripled the number of known merging WD systems. We discuss the characteristics of this merger sample and potential links to underluminous supernovae, extreme helium stars, AM CVn systems, and other merger products. We provide new observational tests of the WD mass-period distribution and cooling models for ELM WDs. We also find evidence for a new formation channel for single low-mass WDs through binary mergers of two lower mass objects.

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...

[Survey on the transmission of HIV drug resistance in Kunming, Yunnan province in 2010].

Science.gov (United States)

Chen, Min; Ma, Yan-ling; Chu, Cheng-xia; Xing, Hui; Xu, Yan-sheng; Su, Ying-zhen; Yang, Ying; Chen, Hui-chao; Luo, Hong-bing; Jia, Man-hong; Lu, Lin

2012-01-01

To study the HIV drug resistance (HIVDR) transmission in Kunming city of Yunnan province in 2010. Referring to the guidelines for HIV drug resistance threshold survey (HIVDR-TS) set by WHO, 62 plasma samples of recently reported HIV-infected individuals who were older than 25 years of age, were collected from January to August 2010. Genotyping of pol genetic mutations associated with HIVDR with reverse transcriptional PCR was performed and the prevalence of HIV-1 drug resistance transmission was evaluated. Of the 62 plasma samples, 54 were successfully sequenced and genotyped on pol sequence. Based on the pol sequences, HIV subtypes including CRF08_BC (53.2%), CRF07_BC (25.5%), CRF01_AE (19.1%) and C (2.1%) were identified. According to the time of sampling, the first 47 sequenced samples were used for drug resistance prevalence analysis. A protease inhibitor (PI) relative mutation was found in one sample. Based on the WHO standard, the prevalence of transmitted HIV-1 drug resistance was scientific management to AIDS patients seemed to be quite important.

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...

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

An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

Directory of Open Access Journals (Sweden)

Herring Christopher D

2007-08-01

Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

Short read sequence typing (SRST: multi-locus sequence types from short reads

Directory of Open Access Journals (Sweden)

Inouye Michael

2012-07-01

Full Text Available Abstract Background Multi-locus sequence typing (MLST has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. Results We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele at each MLST locus. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. Conclusions SRST is a novel

Source characteristics of the Fairview, OK, earthquake sequence and its relationship to industrial activities

Science.gov (United States)

Yeck, W. L.; Weingarten, M.; Benz, H.; McNamara, D. E.; Herrmann, R. B.; Rubinstein, J. L.; Earle, P. S.; Bergman, E.

2016-12-01

We characterize the spatio-temporal patterns of seismicity surrounding the February 13, 2016, Mw 5.1 Fairview, Oklahoma earthquake. This earthquake sequence accounts for the largest moment release in the central and eastern US since the November 06, 2011 Mw 5.6 Prague, OK earthquake sequence. To improve the location accuracy of the sequence and measure near-source ground motions, the United States Geological Survey (USGS) deployed eight seismometers and accelerometers in the epicentral region. With the added depth control from these stations, we show that earthquakes primarily occur in the Precambrian basement, at depths of 6-10 km below sea level. The Mw 5.1 mainshock, the largest event in the cluster, locates near the base of the seismicity. Relocated aftershocks delineate a partially unmapped, 14-km-long fault segment that strikes approximately N40°E, partially bridging the gap between previously mapped basement faults to the southwest and northeast. Gas production and hydraulic fracking data from the region show no evidence that either of these activities correlates spatio-temporally with the Fairview sequence. Instead, we suggest that a series of high-rate, Arbuckle injection wells (> 300,000 bbls/month) 8-25 km northeast of this sequence pressurized the reservoir in the far field. Regional injection into the Arbuckle formation increased 7-fold in the 24 months before the initiation of the sequence with some wells operating at rates greater than 1 million barrels per month. Seismicity in the proximity of the high-rate wells is diffuse whilst the energetic Fairview sequence occurs more than 15 km from this region. Our observations point to the critical role pre-existing geologic structures play in the occurrence of large induced earthquakes. This study demonstrates the need for a better understanding of the role of far-field pressurization. High-quality data sets such as this facilitate the USGS mission to improve earthquake hazard identification, especially

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.

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.

Belief in Life After Death and Attitudes Toward Voluntary Euthanasia.

Science.gov (United States)

Sharp, Shane

2017-01-01

Research has documented associations among religious affiliation, religious practice, and attitudes toward voluntary euthanasia, yet very few studies have investigated how particular religious beliefs influence these attitudes. I use data from the General Social Survey (GSS; N = 19,967) to evaluate the association between the belief in life after death and attitudes toward voluntary euthanasia. I find that those who believe in life after death are significantly less likely than those who do not believe in life after death or those who doubt the existence of life after death to have positive attitudes toward voluntary euthanasia. These associations hold even after controlling for religious affiliation, religious attendance, views of the Bible, and sociodemographic factors. The findings indicate that to understand individuals' views about voluntary euthanasia, one must pay attention to individuals' particular religious beliefs.

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

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)

Employment arrangement, job stress, and health-related quality of life.

Science.gov (United States)

Ray, Tapas K; Kenigsberg, Tat'Yana A; Pana-Cryan, Regina

2017-12-01

We aimed to understand the characteristics of U.S. workers in non-standard employment arrangements, and to assess associations between job stress and Health-related Quality of Life (HRQL) by employment arrangement. As employers struggle to stay in business under increasing economic pressures, they may rely more on non-standard employment arrangements, thereby increasing the pool of contingent workers. Worker exposure to job stress may vary by employment arrangement. Excessive exposure to stressors at work is considered to be a potential health hazard, and may adversely affect health and HRQL. We used the Quality of Worklife (QWL) module which supplemented the General Social Survey (GSS) in 2002, 2006, 2010, and 2014. GSS is a biannual, nationally representative cross-sectional survey of U.S. households that yields a representative sample of the civilian, non-institutionalized, English-speaking, U.S. adult population. The QWL module assesses an array of psychosocial working conditions and quality of work life topics among GSS respondents. We used pooled QWL responses from 2002 to 2014 by only those who reported being employed at the time of the survey. After adjusting for sampling probabilities, including subsampling for non-respondents and correcting for the number of adults in the household, 6005 respondents were included in our analyses. We grouped respondents according to their employment arrangement, including: (i) independent contractors (contractor), (ii) on call workers (on call), (iii) workers paid by a temporary agency (temporary), (iv) workers who work for a contractor (under contract), or (v) workers in standard employment arrangements (standard). Respondents were further grouped into those who were stressed and those who were not stressed at work. Descriptive population prevalence rates were calculated by employment arrangement for select demographic and organizational characteristics, psychosocial working conditions, work-family balance, and health and

Employment arrangement, job stress, and health-related quality of life ☆

Science.gov (United States)

Ray, Tapas K.; Kenigsberg, Tat’Yana A.; Pana-Cryan, Regina

2017-01-01

Objective We aimed to understand the characteristics of U.S. workers in non-standard employment arrangements, and to assess associations between job stress and Health-related Quality of Life (HRQL) by employment arrangement. Background As employers struggle to stay in business under increasing economic pressures, they may rely more on non-standard employment arrangements, thereby increasing the pool of contingent workers. Worker exposure to job stress may vary by employment arrangement. Excessive exposure to stressors at work is considered to be a potential health hazard, and may adversely affect health and HRQL. Methods We used the Quality of Worklife (QWL) module which supplemented the General Social Survey (GSS) in 2002, 2006, 2010, and 2014. GSS is a biannual, nationally representative cross-sectional survey of U.S. households that yields a representative sample of the civilian, non-institutionalized, English-speaking, U.S. adult population. The QWL module assesses an array of psychosocial working conditions and quality of work life topics among GSS respondents. We used pooled QWL responses from 2002 to 2014 by only those who reported being employed at the time of the survey. After adjusting for sampling probabilities, including subsampling for non-respondents and correcting for the number of adults in the household, 6005 respondents were included in our analyses. We grouped respondents according to their employment arrangement, including: (i) independent contractors (contractor), (ii) on call workers (on call), (iii) workers paid by a temporary agency (temporary), (iv) workers who work for a contractor (under contract), or (v) workers in standard employment arrangements (standard). Respondents were further grouped into those who were stressed and those who were not stressed at work. Descriptive population prevalence rates were calculated by employment arrangement for select demographic and organizational characteristics, psychosocial working conditions, work

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.

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.

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.

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.

Archaeological survey of the McGee Ranch vicinity, Hanford Site, Washington

Energy Technology Data Exchange (ETDEWEB)

Gard, H.A.; Poet, R.M.

1992-09-01

In response to a request for a cultural resources review from Westinghouse Hanford Company for the Action Plan for Characterization of McGee Ranch Soil, Pacific Northwest Laboratory's Hanford Cultural Resources Laboratory (HCRL) conducted an archaeological survey of the McGee Ranch vicinity, located in the northwest portion of the Hanford Site. Staff members covered 8.4 km{sup 2} and recorded 42 cultural resources; 22 sites, and 20 isolated artifacts. Only 2 sites and 3 isolates were attributed to a prehistoric Native American occupation. The historic sites date from the turn of the century to the 1940s and are representative of the settlement patterns that occurred throughout the Columbia Basin. In addition to an archaeological pedestrian survey of the project area, we conducted literature and records searches and examined available aerial photographs. Records kept at HCRL were reviewed to determine if any archaeological survey had been conducted previously within the project area. Although no survey had been conducted, portions of the area adjacent to project boundaries were surveyed in 1988 and 1990. During those surveys, historic and prehistoric cultural resources were observed, increasing the possibility that similar land usage had taken place within the current project boundaries. Literature searches established a general historical sequence for this area. Aerial photographs alerted researchers to homesteads and linear features, such as roads and irrigation ditches, that might not be apparent from ground level.

Archaeological survey of the McGee Ranch vicinity, Hanford Site, Washington

Energy Technology Data Exchange (ETDEWEB)

Gard, H.A.; Poet, R.M.

1992-09-01

In response to a request for a cultural resources review from Westinghouse Hanford Company for the Action Plan for Characterization of McGee Ranch Soil, Pacific Northwest Laboratory`s Hanford Cultural Resources Laboratory (HCRL) conducted an archaeological survey of the McGee Ranch vicinity, located in the northwest portion of the Hanford Site. Staff members covered 8.4 km{sup 2} and recorded 42 cultural resources; 22 sites, and 20 isolated artifacts. Only 2 sites and 3 isolates were attributed to a prehistoric Native American occupation. The historic sites date from the turn of the century to the 1940s and are representative of the settlement patterns that occurred throughout the Columbia Basin. In addition to an archaeological pedestrian survey of the project area, we conducted literature and records searches and examined available aerial photographs. Records kept at HCRL were reviewed to determine if any archaeological survey had been conducted previously within the project area. Although no survey had been conducted, portions of the area adjacent to project boundaries were surveyed in 1988 and 1990. During those surveys, historic and prehistoric cultural resources were observed, increasing the possibility that similar land usage had taken place within the current project boundaries. Literature searches established a general historical sequence for this area. Aerial photographs alerted researchers to homesteads and linear features, such as roads and irrigation ditches, that might not be apparent from ground level.

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.

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.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Science.gov (United States)

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Directory of Open Access Journals (Sweden)

Nathan D. Olson

2015-03-01

Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

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

Influence of Personality Type and Anonymity on Participation in a Group Support System

National Research Council Canada - National Science Library

Hartmann, Robert

2000-01-01

A group support system (GSS) uses a combination of networked personal computers, software that collects, manipulates, and aggregates member's individual input, and human facilitation to improve the group decision-making process...

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...

Design of Long Period Pseudo-Random Sequences from the Addition of m -Sequences over 𝔽 p

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 m -sequences with pairwise-prime linear spans (AMPLS. Using m -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 𝔽 2 , a signal set ( ( 2 n − 1 ( 2 m − 1 , ( 2 n + 1 ( 2 m + 1 , ( 2 ( n + 1 / 2 + 1 ( 2 ( m + 1 / 2 + 1 is constructed.

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

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)

Alignment efficiency and discomfort of three orthodontic archwire sequences: a randomized clinical trial.

Science.gov (United States)

Ong, Emily; Ho, Christopher; Miles, Peter

2011-03-01

To compare the efficiency of orthodontic archwire sequences produced by three manufacturers. Prospective, randomized clinical trial with three parallel groups. Private orthodontic practice in Caloundra, QLD, Australia. One hundred and thirty-two consecutive patients were randomized to one of three archwire sequence groups: (i) 3M Unitek, 0·014 inch Nitinol, 0·017 inch × 0·017 inch heat activated Ni-Ti; (ii) GAC international, 0·014 inch Sentalloy, 0·016 × 0·022 inch Bioforce; and (iii) Ormco corporation, 0·014 inch Damon Copper Ni-Ti, 0·014 × 0·025 inch Damon Copper Ni-Ti. All patients received 0·018 × 0·025 inch slot Victory Series™ brackets. Mandibular impressions were taken before the insertion of each archwire. Patients completed discomfort surveys according to a seven-point Likert Scale at 4 h, 24 h, 3 days and 7 days after the insertion of each archwire. Efficiency was measured by time required to reach the working archwire, mandibular anterior alignment and level of discomfort. No significant differences were found in the reduction of irregularity between the archwire sequences at any time-point (T1: P = 0·12; T2: P = 0·06; T3: P = 0·21) or in the time to reach the working archwire (P = 0·28). No significant differences were found in the overall discomfort scores between the archwire sequences (4 h: P = 0·30; 24 h: P = 0·18; 3 days: P = 0·53; 7 days: P = 0·47). When the time-points were analysed individually, the 3M Unitek archwire sequence induced significantly less discomfort than GAC and Ormco archwires 24 h after the insertion of the third archwire (P = 0·02). This could possibly be attributed to the progression in archwire material and archform. The archwire sequences were similar in alignment efficiency and overall discomfort. Progression in archwire dimension and archform may contribute to discomfort levels. This study provides clinical justification for three common archwire sequences in 0·018 × 0·025 inch slot brackets.

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.

High levels of diversity characterize mandrill (Mandrillus sphinx) Mhc-DRB sequences.

Science.gov (United States)

Abbott, Kristin M; Wickings, E Jean; Knapp, Leslie A

2006-08-01

The major histocompatibility complex (MHC) is highly polymorphic in most primate species studied thus far. The rhesus macaque (Macaca mulatta) has been studied extensively and the Mhc-DRB region demonstrates variability similar to humans. The extent of MHC diversity is relatively unknown for other Old World monkeys (OWM), especially among genera other than Macaca. A molecular survey of the Mhc-DRB region in mandrills (Mandrillus sphinx) revealed extensive variability, suggesting that other OWMs may also possess high levels of Mhc-DRB polymorphism. In the present study, 33 Mhc-DRB loci were identified from only 13 animals. Eleven were wild-born and presumed to be unrelated and two were captive-born twins. Two to seven different sequences were identified for each individual, suggesting that some mandrills may have as many as four Mhc-DRB loci on a single haplotype. From these sequences, representatives of at least six Mhc-DRB loci or lineages were identified. As observed in other primates, some new lineages may have arisen through the process of gene conversion. These findings indicate that mandrills have Mhc-DRB diversity not unlike rhesus macaques and humans.

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

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}.

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.

Molecular Survey of Hepatozoon canis in Red Foxes (Vulpes vulpes) from Romania.

Science.gov (United States)

Imre, Mirela; Dudu, Andreea; Ilie, Marius S; Morariu, Sorin; Imre, Kálmán; Dărăbuş, Gheorghe

2015-08-01

Blood samples of 119 red foxes, originating from 44 hunting grounds of 3 western counties (Arad, Hunedoara, and Timiş) of Romania, have been examined for the presence of Hepatozoon canis infection using the conventional polymerase chain reaction (PCR) of the fragment of 18S rRNA gene. Overall, 15 (12.6%) samples were found to be PCR-positive. Of the sampled hunting grounds, 29.5% (13/44) were found positive. Positive samples were recorded in all screened counties with the prevalence of 14.8% (9/61) in Arad, 9.8% (5/51) in Timiş, and 14.3% (1/7) in Hunedoara, respectively. No correlation was found (P > 0.05) between H. canis positivity and gender or territorial distribution of the infection. To confirm PCR results, 9 randomly selected amplicons were sequenced. The obtained sequences were identical to each other, confirmed the results of the conventional PCR, and showed 98-100% homology to other H. canis sequences. The results of the current survey support the role of red foxes as sylvatic reservoirs of H. canis in Romania.

Treatment of complex PTSD: results of the ISTSS expert clinician survey on best practices.

Science.gov (United States)

Cloitre, Marylene; Courtois, Christine A; Charuvastra, Anthony; Carapezza, Richard; Stolbach, Bradley C; Green, Bonnie L

2011-12-01

This study provides a summary of the results of an expert opinion survey initiated by the International Society for Traumatic Stress Studies Complex Trauma Task Force regarding best practices for the treatment of complex posttraumatic stress disorder (PTSD). Ratings from a mail-in survey from 25 complex PTSD experts and 25 classic PTSD experts regarding the most appropriate treatment approaches and interventions for complex PTSD were examined for areas of consensus and disagreement. Experts agreed on several aspects of treatment, with 84% endorsing a phase-based or sequenced therapy as the most appropriate treatment approach with interventions tailored to specific symptom sets. First-line interventions matched to specific symptoms included emotion regulation strategies, narration of trauma memory, cognitive restructuring, anxiety and stress management, and interpersonal skills. Meditation and mindfulness interventions were frequently identified as an effective second-line approach for emotional, attentional, and behavioral (e.g., aggression) disturbances. Agreement was not obtained on either the expected course of improvement or on duration of treatment. The survey results provide a strong rationale for conducting research focusing on the relative merits of traditional trauma-focused therapies and sequenced multicomponent approaches applied to different patient populations with a range of symptom profiles. Sustained symptom monitoring during the course of treatment and during extended follow-up would advance knowledge about both the speed and durability of treatment effects. Copyright © 2011 International Society for Traumatic Stress Studies.

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.

Virus surveys of Capsicum spp. in the Republic of Benin reveal the prevalence of pepper vein yellows virus and the identification of a previously uncharacterised polerovirus species.

Science.gov (United States)

Afouda, Leonard; Kone, Daouda; Zinsou, Valerien; Dossou, Laurence; Kenyon, Lawrence; Winter, Stephan; Knierim, Dennis

2017-06-01

Surveys were conducted in 2014 and 2015 in Southern and Northern Benin, respectively, to identify the viruses infecting peppers (Capsicum spp.). The samples were screened by ELISA for cucumber mosaic virus (CMV), pepper veinal mottle virus (PVMV), potato virus Y (PVY) and tomato yellow leaf curl virus (TYLCV). A generic reverse transcription PCR (RT-PCR) was used to test for the presence of poleroviruses. ELISA tests confirmed the prevalence of all viruses, while the RT-PCR detected pepper vein yellows virus (PeVYV) which is reported for the first time in Benin. A further, divergent polerovirus isolate was detected from a single pepper sample originating from southern Benin. Screening of samples collected from solanaceous plants during virus surveys in Mali (conducted in 2009) also detected this divergent polerovirus isolate in two samples from African eggplants. The complete genome sequence was obtained from the Mali isolate using transcriptome sequencing and by conventional Sanger sequencing of overlapping RT-PCR products. Based on the sequence characteristics of this isolate we propose a new polerovirus species, African eggplant yellowing virus (AeYV).

Germline Variants in Targeted Tumor Sequencing Using Matched Normal DNA.

Science.gov (United States)

Schrader, Kasmintan A; Cheng, Donavan T; Joseph, Vijai; Prasad, Meera; Walsh, Michael; Zehir, Ahmet; Ni, Ai; Thomas, Tinu; Benayed, Ryma; Ashraf, Asad; Lincoln, Annie; Arcila, Maria; Stadler, Zsofia; Solit, David; Hyman, David M; Hyman, David; Zhang, Liying; Klimstra, David; Ladanyi, Marc; Offit, Kenneth; Berger, Michael; Robson, Mark

2016-01-01

Tumor genetic sequencing identifies potentially targetable genetic alterations with therapeutic implications. Analysis has concentrated on detecting tumor-specific variants, but recognition of germline variants may prove valuable as well. To estimate the burden of germline variants identified through routine clinical tumor sequencing. Patients with advanced cancer diagnoses eligible for studies of targeted agents at Memorial Sloan Kettering Cancer Center are offered tumor-normal sequencing with MSK-IMPACT, a 341-gene panel. We surveyed the germline variants seen in 187 overlapping genes with Mendelian disease associations in 1566 patients who had undergone tumor profiling between March and October 2014. The number of presumed pathogenic germline variants (PPGVs) and variants of uncertain significance per person in 187 genes associated with single-gene disorders and the proportions of individuals with PPGVs in clinically relevant gene subsets, in genes consistent with known tumor phenotypes, and in genes with evidence of second somatic hits in their tumors. The mean age of the 1566 patients was 58 years, and 54% were women. Presumed pathogenic germline variants in known Mendelian disease-associated genes were identified in 246 of 1566 patients (15.7%; 95% CI, 14.0%-17.6%), including 198 individuals with mutations in genes associated with cancer susceptibility. Germline findings in cancer susceptibility genes were concordant with the individual's cancer type in only 81 of 198 cases (40.9%; 95% CI, 34.3%-47.9%). In individuals with PPGVs retained in the tumor, somatic alteration of the other allele was seen in 39 of 182 cases (21.4%; 95% CI, 16.1%-28.0%), of which 13 cases did not show a known correlation of the germline mutation and a known syndrome. Mutations in non-cancer-related Mendelian disease genes were seen in 55 of 1566 cases (3.5%; 95% CI, 27.1%-45.4%). Almost every individual had more than 1 variant of uncertain significance (1565 of 1566 patients; 99

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.

Percutaneous nephrolithotomy; alarming variables for postoperative bleeding

Directory of Open Access Journals (Sweden)

Shakhawan H.A. Said

2017-03-01

Conclusion: According to our present results stone complexity (GSS grade 3 and 4, history of ipsilateral renal stone surgery, and occurrence of intraoperative pelvicalyceal perforation are alarming variables for post-PCNL bleeding.

Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

Science.gov (United States)

Hu, Youna; Willer, Cristen; Zhan, Xiaowei; Kang, Hyun Min; Abecasis, Gonçalo R.

2013-01-01

Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate the accuracy of our method through simulations and analysis of samples sequenced by the 1000 Genomes Project and the NHLBI Grand Opportunity Exome Sequencing Project. In African Americans, we show that local-ancestry estimates derived by our method are very similar to those derived with Illumina’s Omni 2.5M genotyping array and much improved in relation to estimates that use only exome genotypes and ignore off-target sequencing reads. Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. PMID:24210252

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.

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

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.

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.

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

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.

Estimating health expectancies from two cross-sectional surveys: The intercensal method

Directory of Open Access Journals (Sweden)

Michel Guillot

2009-10-01

Full Text Available Health expectancies are key indicators for monitoring the health of populations, as well as for informing debates about compression or expansion of morbidity. However, current methodologies for estimating them are not entirely satisfactory. They are either of limited applicability because of high data requirements (the multistate method or based on questionable assumptions (the Sullivan method. This paper proposes a new method, called the "intercensal" method, which relies on the multistate framework but uses widely available data. The method uses age-specific proportions "healthy" at two successive, independent cross-sectional health surveys, and, together with information on general mortality, solves for the set of transition probabilities that produces the observed sequence of proportions healthy. The system is solved by making realistic parametric assumptions about the age patterns of transition probabilities. Using data from the Health and Retirement Survey (HRS and from the National Health Interview Survey (NHIS, the method is tested against both the multistate method and the Sullivan method. We conclude that the intercensal approach is a promising framework for the indirect estimation of health expectancies.

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

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.

The effect of governance mechanisms on food safety in the supply chain: Evidence from the Lebanese dairy sector.

Science.gov (United States)

Abebe, Gumataw K; Chalak, Ali; Abiad, Mohamad G

2017-07-01

Food safety is a key public health issue worldwide. This study aims to characterise existing governance mechanisms - governance structures (GSs) and food safety management systems (FSMSs) - and analyse the alignment thereof in detecting food safety hazards, based on empirical evidence from Lebanon. Firm-to-firm and public baseline are the dominant FSMSs applied in a large-scale, while chain-wide FSMSs are observed only in a small-scale. Most transactions involving farmers are relational and market-based in contrast to (large-scale) processors, which opt for hierarchical GSs. Large-scale processors use a combination of FSMSs and GSs to minimise food safety hazards albeit potential increase in coordination costs; this is an important feature of modern food supply chains. The econometric analysis reveals contract period, on-farm inspection and experience having significant effects in minimising food safety hazards. However, the potential to implement farm-level FSMS is influenced by formality of the contract, herd size, trading partner choice, and experience. Public baseline FSMSs appear effective in controlling food safety hazards; however, this may not be viable due to the scarcity of public resources. We suggest public policies to focus on long-lasting governance mechanisms by introducing incentive schemes and farm-level FSMSs by providing loans and education to farmers. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Long-term safety and efficacy of autologous platelet lysate drops for treatment of ocular GvHD.

Science.gov (United States)

Pezzotta, S; Del Fante, C; Scudeller, L; Rossi, G C; Perotti, C; Bianchi, P E; Antoniazzi, E

2017-01-01

Current ocular GvHD (oGvHD) treatments are suboptimal. We investigated the safety and efficacy of long-term continuous treatment with autologous platelet lysate (PL) drops in patients with oGvHD Dry Eye Syndrome (DES) score 2-3 refractory to topical conventional therapy. Ophthalmic evaluation was performed at 6 month intervals. Symptoms were assessed using the Glaucoma Symptom Scale (GSS). Patients were defined 'responders' when showing a reduction at least one grade on National Institutes of Health Eye Score from baseline at the 6 month visit. Thirty-one patients were included, and 16 (51%) completed 36 months of follow-up (range 6.5-72.7). At 6 months all patients were classified as responders: median GSS symptom score decreased from 70 to 41 (33 at 36 months), median GSS function score reduced from 68 to 46 (33 at 36 months) (all P<0.001). Median Tear Break Up Time improved from 3 to 6 s after 6 months and was maintained over time. All signs improved at 6 and 36 months (clinical and statistical significance). No severe adverse events occurred. Long-term treatment with PL drops is secure and effective for oGvHD and can be an efficient therapy option from initial stages of oGvHD to prevent permanent ocular impairment and improving quality of life.

Wet-Spun Superelastic Graphene Aerogel Millispheres with Group Effect.

Science.gov (United States)

Zhao, Xiaoli; Yao, Weiquan; Gao, Weiwei; Chen, Hao; Gao, Chao

2017-09-01

Graphene aerogel has attracted great attention due to its unique properties, such as ultralow density, superelasticity, and high specific surface area. It shows huge potential in energy devices, high-performance pressure sensors, contaminates adsorbents, and electromagnetic wave absorbing materials. However, there still remain some challenges to further promote the development and real application of graphene aerogel including cost-effective scalable fabrication and miniaturization with group effect. This study shows millimeter-scale superelastic graphene aerogel spheres (GSs) with group effect and multifunctionality. The GSs are continuously fabricated on a large scale by wet spinning of graphene oxide liquid crystals followed by facile drying and thermal annealing. Such GS has an unusual core-shell structure with excellent elasticity and specific strength. Significantly, both horizontally and vertically grouped spheres exhibit superelasticity comparable to individual spheres, enabling it to fully recover at 95% strain, and even after 1000 compressive cycles at 70% strain, paving the way to wide applications such as pressure-elastic and adsorbing materials. The GS shows a press-fly behavior with an extremely high jump velocity up to 1.2 m s -1 . For the first time, both free and oil-adsorbed GSs are remotely manipulated on water by electrostatic charge due to their ultralow density and hydrophobic properties. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of a hybrid anaerobic biofilm reactor treating winery effluents and using grape stalks as biofilm carrier.

Science.gov (United States)

Wahab, Mohamed Ali; Habouzit, Frédéric; Bernet, Nicolas; Jedidi, Naceur; Escudié, Renaud

2016-01-01

Wine production processes generate large amount of both winery wastewater and solid wastes. Furthermore, working periods, volumes and pollution loads greatly vary over the year. Therefore, it is recommended to develop a low-cost treatment technology for the treatment of winery effluents taking into account the variation of the organic loading rate (OLR). Accordingly, we have investigated the sequential operation of an anaerobic biofilm reactor treating winery effluents and using grape stalks (GSs) as biofilm carrier with an OLR ranging from 0.65 to 27 gCOD/L/d. The result showed that, during the start-up with wastewater influent, the chemical oxygen demand (COD) removal rate ranged from 83% to 93% and was about 91% at the end of the start-up period that lasted for 40 days. After 3 months of inactivity period of the reactor (no influent feeding), we have succeeded in restarting-up the reactor in only 15 days with a COD removal of 82% and a low concentration of volatile fatty acids (1 g/L), which confirms the robustness of the reactor. As a consequence, GSs can be used as an efficient carrier support, allowing a fast reactor start-up, while the biofilm conserves its activity during a non-feeding period. The proposed hybrid reactor thus permits to treat both winery effluents and GSs.

Double impact: what sibling data can tell us about the long-term negative effects of parental divorce.

Science.gov (United States)

Wolfinger, Nicholas H; Kowaleski-Jones, Lori; Smith, Ken R

2003-01-01

Most prior research on the adverse consequences of parental divorce has analyzed only one child per family. As a result, it is not known whether the same divorce affects siblings differently. We address this issue by analyzing paired sibling data from the 1994 General Social Survey (GSS) and 1994 Survey of American Families (SAF). Both seemingly unrelated regressions and random effects models are used to study the effect of family background on offspring's educational attainment and marital stability. Parental divorce adversely affects the educational attainment and the probability of divorce of both children within a sibship; in other words, siblings tend to experience the same divorce the same way. However, family structure of origin only accounts for a trivial portion of the shared variance in offspring's educational attainment and marital stability, so parental divorce is only one of many factors determining how offspring fare. These findings were unchanged when controlling for a number of differences both between and within sibships. Also, the negative effects of parental divorce largely do not vary according to respondent characteristics.

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

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

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.

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.

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.

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.

CUSTOMIZATION IN THE MANUFACTURING INDUSTRY: SURVEY RESULTS IN SOUTHEASTERN BRAZIL

Directory of Open Access Journals (Sweden)

Alexandre Reis Graeml

2009-12-01

Full Text Available This paper discusses the advantage of using kanban, postponement, modularization, just-in-time, production sequencing, milk-run and cross-docking by companies that intend to increase their flexibility, agility and reliability in order to support web-based businesses. It presents the results of a survey carried out with more than 600 manufacturing companies in the state of Sao Paulo, Brazil, and evaluates the changes that are taking place in operations, in order to make companies better suited to provide customized products, which are made to meet the individual requirements of each customer.

CUSTOMIZATION IN THE MANUFACTURING INDUSTRY: SURVEY RESULTS IN SOUTHEASTERN BRAZIL

Directory of Open Access Journals (Sweden)

Alexandre Reis Graeml

2010-01-01

Full Text Available This paper discusses the advantage of using kanban, postponement, modularization, just-in-time, production sequencing, milk-run and cross-docking by companies that intend to increase their flexibility, agility and reliability in order to support web-based businesses. It presents the results of a survey carried out with more than 600 manufacturing companies in the state of Sao Paulo, Brazil, and evaluates the changes that are taking place in operations, in order to make companies better suited to provide customized products, which are made to meet the individual requirements of each customer.

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.

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.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Directory of Open Access Journals (Sweden)

Jonas Binladen

2007-02-01

Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

Monitoring of Fasciola Species Contamination in Water Dropwort by cox1 Mitochondrial and ITS-2 rDNA Sequencing Analysis.

Science.gov (United States)

Choi, In-Wook; Kim, Hwang-Yong; Quan, Juan-Hua; Ryu, Jae-Gee; Sun, Rubing; Lee, Young-Ha

2015-10-01

Fascioliasis, a food-borne trematode zoonosis, is a disease primarily in cattle and sheep and occasionally in humans. Water dropwort (Oenanthe javanica), an aquatic perennial herb, is a common second intermediate host of Fasciola, and the fresh stems and leaves are widely used as a seasoning in the Korean diet. However, no information regarding Fasciola species contamination in water dropwort is available. Here, we collected 500 samples of water dropwort in 3 areas in Korea during February and March 2015, and the water dropwort contamination of Fasciola species was monitored by DNA sequencing analysis of the Fasciola hepatica and Fasciola gigantica specific mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 500 samples assessed, the presence of F. hepatica cox1 and 1TS-2 markers were detected in 2 samples, and F. hepatica contamination was confirmed by sequencing analysis. The nucleotide sequences of cox1 PCR products from the 2 F. hepatica-contaminated samples were 96.5% identical to the F. hepatica cox1 sequences in GenBank, whereas F. gigantica cox1 sequences were 46.8% similar with the sequence detected from the cox1 positive samples. However, F. gigantica cox1 and ITS-2 markers were not detected by PCR in the 500 samples of water dropwort. Collectively, in this survey of the water dropwort contamination with Fasciola species, very low prevalence of F. hepatica contamination was detected in the samples.

Low temperature (-15°C operational test of the battery package in the Antarctic penetrator

Directory of Open Access Journals (Sweden)

Kazuo Shibuya

2004-11-01

Full Text Available In order to perform seismic explosion experiments in the crevassed area of the Antarctic ice sheet, a seismometer deployable from the air is desired. We have developed such a helicopter-deployable system (called the Antarctic penetrator, which consists of a Ground System Segment (GSS and an Automatic Data Collection Segment (ADCS. Its test operation by the 43rd Japanese Antarctic Research Expedition (JARE-43 was, however, not successful. The reason was found to be leakage of 3.6mA current from the battery package during transportation. In order to re-examine the life time of the battery package under an operational environment at -15°C , we tested the lithium thionyl chloride batteries in a laboratory cryostat. The operational scenario is as follows. After initialization of the GSS, it enters into a sleep mode of 20days duration. At the 21st day, the GSS becomes awake and enters into the switching stage of 12 hours-awake and 12 hours-sleep modes for the following 20-30days. During the awake-period, the radio-telemeter module becomes active and transmits commands and/or recovers stored data to the ADCS once or twice a day. The current consumption in the sleep-mode was 60mA, while it was 135mA during the awake-mode. The current consumption attained about 230mA during the active mode, with an associated voltage fall of 0.5V. With 8 TL5930 cells in parallel and 2 in serial (cell capacity 19 Ah; Tadiran Co., Ltd., operation was successful with a life time of more than 50days. The life limit can be predicted from the time when the voltage becomes lower than 4.8V in the active mode. It was possible to recover the GSS-stored 4 event data (48Kbytes to the ADCS in about 40 s fifty times during the above 50days.

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.

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

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.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Directory of Open Access Journals (Sweden)

Jason D Thompson

Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Science.gov (United States)

Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

2012-01-01

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

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...