WorldWideScience

Sample records for two-hour test sequence

  1. A two-hour antibiotic susceptibility test by ATP-bioluminescence.

    Science.gov (United States)

    March Rosselló, Gabriel Alberto; García-Loygorri Jordán de Urries, María Cristina; Gutiérrez Rodríguez, María Purificación; Simarro Grande, María; Orduña Domingo, Antonio; Bratos Pérez, Miguel Ángel

    2016-01-01

    The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours.

  2. The Effect of a Two-Hour, Room Temperature Incubation of Human Spermatozoa in TEST-Yolk Buffer on the Rate of Fertilization in Vitro

    OpenAIRE

    Jensen, Julie R.; Walker, John H.; Milki, Amin A.; Westphal, Lynn; Behr, Barry

    2004-01-01

    Patients: To reassess the use of TEST-yolk buffer (TYB) in an in vitro fertilization (IVF) program by comparing fertilization rates achieved in a glucose-free cleavage medium by the standard IVF preparation of sperm versus a 2-h, room temperature incubation of sperm in TYB.

  3. Reviewing 741 patients records in two hours with FASTVISU

    Science.gov (United States)

    Escudié, Jean-Baptiste; Jannot, Anne-Sophie; Zapletal, Eric; Cohen, Sarah; Malamut, Georgia; Burgun, Anita; Rance, Bastien

    2015-01-01

    The secondary use of electronic health records opens up new perspectives. They provide researchers with structured data and unstructured data, including free text reports. Many applications been developed to leverage knowledge from free-text reports, but manual review of documents is still a complex process. We developed FASTVISU a web-based application to assist clinicians in reviewing documents. We used FASTVISU to review a set of 6340 documents from 741 patients suffering from the celiac disease. A first automated selection pruned the original set to 847 documents from 276 patients’ records. The records were reviewed by two trained physicians to identify the presence of 15 auto-immune diseases. It took respectively two hours and two hours and a half to evaluate the entire corpus. Inter-annotator agreement was high (Cohen’s kappa at 0.89). FASTVISU is a user-friendly modular solution to validate entities extracted by NLP methods from free-text documents stored in clinical data warehouses. PMID:26958189

  4. Latent error detection: A golden two hours for detection.

    Science.gov (United States)

    Saward, Justin R E; Stanton, Neville A

    2017-03-01

    Undetected error in safety critical contexts generates a latent condition that can contribute to a future safety failure. The detection of latent errors post-task completion is observed in naval air engineers using a diary to record work-related latent error detection (LED) events. A systems view is combined with multi-process theories to explore sociotechnical factors associated with LED. Perception of cues in different environments facilitates successful LED, for which the deliberate review of past tasks within two hours of the error occurring and whilst remaining in the same or similar sociotechnical environment to that which the error occurred appears most effective. Identified ergonomic interventions offer potential mitigation for latent errors; particularly in simple everyday habitual tasks. It is thought safety critical organisations should look to engineer further resilience through the application of LED techniques that engage with system cues across the entire sociotechnical environment, rather than relying on consistent human performance. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  5. Timing-Sequence Testing of Parallel Programs

    Institute of Scientific and Technical Information of China (English)

    LIANG Yu; LI Shu; ZHANG Hui; HAN Chengde

    2000-01-01

    Testing of parallel programs involves two parts-testing of controlflow within the processes and testing of timing-sequence.This paper focuses on the latter, particularly on the timing-sequence of message-passing paradigms.Firstly the coarse-grained SYN-sequence model is built up to describe the execution of distributed programs. All of the topics discussed in this paper are based on it. The most direct way to test a program is to run it. A fault-free parallel program should be of both correct computing results and proper SYN-sequence. In order to analyze the validity of observed SYN-sequence, this paper presents the formal specification (Backus Normal Form) of the valid SYN-sequence. Till now there is little work about the testing coverage for distributed programs. Calculating the number of the valid SYN-sequences is the key to coverage problem, while the number of the valid SYN-sequences is terribly large and it is very hard to obtain the combination law among SYN-events. In order to resolve this problem, this paper proposes an efficient testing strategy-atomic SYN-event testing, which is to linearize the SYN-sequence (making it only consist of serial atomic SYN-events) first and then test each atomic SYN-event independently. This paper particularly provides the calculating formula about the number of the valid SYN-sequences for tree-topology atomic SYN-event (broadcast and combine). Furthermore,the number of valid SYN-sequences also,to some degree, mirrors the testability of parallel programs. Taking tree-topology atomic SYN-event as an example, this paper demonstrates the testability and communication speed of the tree-topology atomic SYN-event under different numbers of branches in order to achieve a more satisfactory tradeoff between testability and communication efficiency.

  6. Test sequence construction from SFC specification

    OpenAIRE

    Provost, Julien; Roussel, Jean-Marc; Faure, Jean-Marc

    2009-01-01

    International audience; This paper focuses on conformance test of electronic programmable devices whose specification is given in Sequential Function Chart (SFC). More precisely, a method is proposed to obtain automatically, from this specication, one minimum length test sequence which permits the exhaustive test of the behavior of the device. This method takes advantage of previous results on construction of the state machine representation of a SFC and on test of Mealy machines; conversely,...

  7. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

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

  8. Education on Adult Urinary Incontinence in Nursing School Curricula: Can It Be Done in Two Hours?

    Science.gov (United States)

    Morishita, Lynne; And Others

    1994-01-01

    Responses from 339 undergraduate nursing programs (74%) showed that 98% included urinary incontinence content in their curricula. Although most agreed the subject was important and felt their teaching was effective, the didactic component averaged two hours, and clinical experience was not systematic; few faculty are prepared to teach this…

  9. Diagnostic Testing and the Development of CAL Remedial Sequences.

    Science.gov (United States)

    Ferraris, M.; And Others

    1984-01-01

    Presents methodology for designing and delivering computer-assisted diagnostic tests and discusses two natural applications of this methodology: for testing purposes, and for implementing adaptive computer-assisted learning sequences based on test results. (MBR)

  10. 16 CFR 1610.7 - Test sequence and classification criteria.

    Science.gov (United States)

    2010-01-01

    ... REGULATIONS STANDARD FOR THE FLAMMABILITY OF CLOTHING TEXTILES The Standard § 1610.7 Test sequence and... classification. (b) Test sequence and classification criteria. (1) Step 1, Plain Surface Textile Fabrics in the... Textile Fabrics after refurbishing in accordance with § 1610.6(b)(1). (i) Conduct preliminary tests...

  11. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    of the individual event handlers of the application. The second phase builds event sequences backward from the target, using the summaries together with a UI model of the application. Our experiments on a collection of open source Android applications show that this technique can successfully produce event...

  12. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    of the individual event handlers of the application. The second phase builds event sequences backward from the target, using the summaries together with a UI model of the application. Our experiments on a collection of open source Android applications show that this technique can successfully produce event...

  13. Minimal-Length Interoperability Test Sequences Generation via Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHONG Ning; KUANG Jing-ming; HE Zun-wen

    2008-01-01

    A novel interoperability test sequences optimization scheme is proposed in which the genetic algo-rithm(GA)is used to obtain the minimal-length interoperability test sequences.During our work,the basicin teroperability test sequences are generated based on the minimal-complete-coverage criterion,which removes the redundancy from conformance test sequences.Then interoperability sequences minimization problem can be considered as an instance of the set covering problem,and the GA is applied to remove redundancy in interoperability transitions.The results show that compared to conventional algorithm,the proposed algorithm is more practical to avoid the state space explosion problem,for it can reduce the length of the test sequences and maintain the same transition coverage.

  14. An efficient test for comparing sequence diversity between two populations.

    Science.gov (United States)

    Gilbert, P B; Novitsky, V A; Montano, M A; Essex, M

    2001-01-01

    We address the problem of comparing interindividual genomic sequence diversity between two populations. Although the methods are general, for concreteness we focus on comparing two human immunodeficiency virus (HIV) infected populations. From a viral isolate(s) taken from each individual in a sample of persons from each population, suppose one or multiple measurements are made on the genetic sequence of a coding region of HIV. Given a definition of genetic distance between sequences, the goal is to test if the distribution of interindividual distances differs between populations. If distances between all pairs of sequences within each group are used, then data-dependencies arising from the use of multiple sequences from individuals invalidates the use of a standard two-sample test such as the t-test. Where this problem has been recognized, a typical solution has been to apply a standard test to a reduced dataset comprised of one sequence or a consensus sequence from each patient. Disadvantages of this procedure are that the conclusion of the test depends on the choice of utilized sequences, often an arbitrary decision, and exclusion of replicate sequences from the analysis may needlessly sacrifice statistical power. We present a new test free of these drawbacks, which is based on a statistic that linearly combines all possible standard test statistics calculated from independent sequence subsamples. We describe statistical power advantages of the test and illustrate its use by application to nucleotide sequence distances measured from HIV-1 infected populations in southern Africa (GenBank accession numbers AF110959--AF110981) and North America/Europe. The test makes minimal assumptions, is maximally efficient and objective, and is broadly applicable.

  15. Improvements of knowledge and perception towards HIV/AIDS among secondary school students after two hours talk.

    Science.gov (United States)

    Jahanfar, S; Lim, A W; Loh, M A; Yeoh, A G; Charles, A

    2008-10-01

    Malaysia is confronted with an increasing incidence of HIV and AIDS among adolescents and young adults. The effectiveness of various programs offered to school going teenagers is unknown. The objective of this study is to measure the effectiveness of two hours talk on sex education offered by a non governmental organization (NGO) in improving youngsters' knowledge and perception towards HIV and AIDS. A cross sectional study was conducted among the adolescent students from a secondary school in Ipoh, Perak, a province of Malaysia. A total of 182 students participated in the study. A standard questionnaire consisting of demographic data, knowledge and perception towards HIV/ADIS were distributed before (pre-test) and after the intervention (post-test). Performance of participants was compared to establish the effectiveness of the intervention. Our findings suggests that there was a significant increase in participants' knowledge and perception after the intervention (p = 0.000). Knowledge improvement was found in both genders however, improvement in perception was higher among female students. Interestingly, 80% of participants disagree that sexual education will encourage sex among youngsters. NGOs are playing a supplementary role in providing sex education programs in schools. This program although of short duration but it is effective in enhancing adolescence awareness about HIV/AIDS.

  16. 40 CFR 86.230-11 - Test sequence: general requirements.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Test sequence: general requirements. 86.230-11 Section 86.230-11 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... New Medium-Duty Passenger Vehicles; Cold Temperature Test Procedures § 86.230-11 Test...

  17. 40 CFR 86.230-94 - Test sequence: general requirements.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Test sequence: general requirements. 86.230-94 Section 86.230-94 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... New Medium-Duty Passenger Vehicles; Cold Temperature Test Procedures § 86.230-94 Test...

  18. 40 CFR 86.1773-99 - Test sequence; general requirements.

    Science.gov (United States)

    2010-07-01

    ... required for fuel-flexible and dual-fuel vehicles when operating on gasoline. Natural gas, hybrid electric and diesel-fueled vehicles shall also be exempt from 50 °F testing. (3) The following schedule... vehicle shall be approximately level during all phases of the test sequence to prevent abnormal fuel...

  19. Application of Next Generation Sequencing on Genetic Testing

    DEFF Research Database (Denmark)

    Li, Jian

    The discovery of genetic factors behind increasing number of human diseases and the growth of education of genetic knowledge to the public make demands for genetic testing increase rapidly. However, traditional genetic testing methods cannot meet all kinds of the requirements. Next generation...... sequencing (NGS) featured with high throughput and low cost of sequencing capacity develops fast, especially with the improvement of its read length, read accuracy and the immergence of small-sized machines, making it a powerful genetic testing tool. In this study, we applied NGS to develop novel genetic...... developed a targeted sequencing based preimplantation genetic diagnosis (PGD) method for monogenic diseases and tested it in a family suffering from β-thalassaemia major undergoing PGD. Moreover, we developed a method which can achieve detection of point mutation and copy number variation simultaneously...

  20. Application of Next Generation Sequencing on Genetic Testing

    DEFF Research Database (Denmark)

    Li, Jian

    The discovery of genetic factors behind increasing number of human diseases and the growth of education of genetic knowledge to the public make demands for genetic testing increase rapidly. However, traditional genetic testing methods cannot meet all kinds of the requirements. Next generation...... sequencing (NGS) featured with high throughput and low cost of sequencing capacity develops fast, especially with the improvement of its read length, read accuracy and the immergence of small-sized machines, making it a powerful genetic testing tool. In this study, we applied NGS to develop novel genetic...... developed a targeted sequencing based preimplantation genetic diagnosis (PGD) method for monogenic diseases and tested it in a family suffering from β-thalassaemia major undergoing PGD. Moreover, we developed a method which can achieve detection of point mutation and copy number variation simultaneously...

  1. Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing

    DEFF Research Database (Denmark)

    Jiang, Haojun; Xie, Yifan; Li, Xuchao

    2016-01-01

    Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we...... developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels...... paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future....

  2. Hypothesis testing in students: Sequences, stages, and instructional strategies

    Science.gov (United States)

    Moshman, David; Thompson, Pat A.

    Six sequences in the development of hypothesis-testing conceptions are proposed, involving (a) interpretation of the hypothesis; (b) the distinction between using theories and testing theories; (c) the consideration of multiple possibilities; (d) the relation of theory and data; (e) the nature of verification and falsification; and (f) the relation of truth and falsity. An alternative account is then provided involving three global stages: concrete operations, formal operations, and a postformal metaconstructivestage. Relative advantages and difficulties of the stage and sequence conceptualizations are discussed. Finally, three families of teaching strategy are distinguished, which emphasize, respectively: (a) social transmission of knowledge; (b) carefully sequenced empirical experience by the student; and (c) self-regulated cognitive activity of the student. It is argued on the basis of Piaget's theory that the last of these plays a crucial role in the construction of such logical reasoning strategies as those involved in testing hypotheses.

  3. PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbakova

    2014-01-01

    Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

  4. Regulating whole exome sequencing as a diagnostic test.

    Science.gov (United States)

    Lapin, Valentina; Mighion, Lindsey C; da Silva, Cristina P; Cuperus, Ymkje; Bean, Lora J H; Hegde, Madhuri R

    2016-06-01

    In the last decade, there has been a flood of new technology in the sequencing arena. The onset of next-generation sequencing (NGS) technology has resulted in the vast increase in genetic diagnostic testing available to the ordering physician. Whole exome sequencing (WES) has become available as a diagnostic test performed in certified clinical laboratories. This has led to increased presence in the diagnostic marketplace, increased consumer awareness, and the question has been raised by various stakeholders to whether there is sufficient stringent regulation of WES and other NGS-based tests. We discuss the various WES services currently available in the marketplace, current regulation of WES as a laboratory developed test, the proposed FDA involvement in its oversight as well as the response of various laboratory groups that provide these diagnostic services. Overall, a rigorous process oversight and assessment of inter-lab reproducibility is strongly warranted for WES as it is used as a diagnostic test, but regulation should be mindful of the excessive administrative burden on academic and smaller diagnostic laboratories.

  5. A blind testing design for authenticating ancient DNA sequences.

    Science.gov (United States)

    Yang, H; Golenberg, E M; Shoshani, J

    1997-04-01

    Reproducibility is a serious concern among researchers of ancient DNA. We designed a blind testing procedure to evaluate laboratory accuracy and authenticity of ancient DNA obtained from closely related extant and extinct species. Soft tissue and bones of fossil and contemporary museum proboscideans were collected and identified based on morphology by one researcher, and other researchers carried out DNA testing on the samples, which were assigned anonymous numbers. DNA extracted using three principal isolation methods served as template in PCR amplifications of a segment of the cytochrome b gene (mitochondrial genome), and the PCR product was directly sequenced and analyzed. The results show that such a blind testing design performed in one laboratory, when coupled with phylogenetic analysis, can nonarbitrarily test the consistency and reliability of ancient DNA results. Such reproducible results obtained from the blind testing can increase confidence in the authenticity of ancient sequences obtained from postmortem specimens and avoid bias in phylogenetic analysis. A blind testing design may be applicable as an alternative to confirm ancient DNA results in one laboratory when independent testing by two laboratories is not available.

  6. Modelling of pool fire environments using experimental results of a two-hour test of a railcar/cask system

    Energy Technology Data Exchange (ETDEWEB)

    Hamann, J.E.; Klein, D.E.; Pope, R.B.; Yoshimura, H.R.

    1980-01-01

    It was demonstrated that time and spatial variations in the local source temperatures, the radiant shielding of intervening structure and the effects of wind can significantly affect the amount of heat input to a large package in a simulated accidental fire. The pool fire provided a significantly non-uniform heat source to the package. Despite these effects, however, the amount of heat input to the package was generally equivalent to that which would be received from a regulatory 800/sup 0/C uniform thermal source. 7 firegures.

  7. Maternal Plasma DNA and RNA Sequencing for Prenatal Testing.

    Science.gov (United States)

    Tamminga, Saskia; van Maarle, Merel; Henneman, Lidewij; Oudejans, Cees B M; Cornel, Martina C; Sistermans, Erik A

    2016-01-01

    Cell-free DNA (cfDNA) testing has recently become indispensable in diagnostic testing and screening. In the prenatal setting, this type of testing is often called noninvasive prenatal testing (NIPT). With a number of techniques, using either next-generation sequencing or single nucleotide polymorphism-based approaches, fetal cfDNA in maternal plasma can be analyzed to screen for rhesus D genotype, common chromosomal aneuploidies, and increasingly for testing other conditions, including monogenic disorders. With regard to screening for common aneuploidies, challenges arise when implementing NIPT in current prenatal settings. Depending on the method used (targeted or nontargeted), chromosomal anomalies other than trisomy 21, 18, or 13 can be detected, either of fetal or maternal origin, also referred to as unsolicited or incidental findings. For various biological reasons, there is a small chance of having either a false-positive or false-negative NIPT result, or no result, also referred to as a "no-call." Both pre- and posttest counseling for NIPT should include discussing potential discrepancies. Since NIPT remains a screening test, a positive NIPT result should be confirmed by invasive diagnostic testing (either by chorionic villus biopsy or by amniocentesis). As the scope of NIPT is widening, professional guidelines need to discuss the ethics of what to offer and how to offer. In this review, we discuss the current biochemical, clinical, and ethical challenges of cfDNA testing in the prenatal setting and its future perspectives including novel applications that target RNA instead of DNA.

  8. Acidemia at birth, related to obstetric characteristics and to oxytocin use, during the last two hours of labor.

    Science.gov (United States)

    Jonsson, Maria; Nordén-Lindeberg, Solveig; Ostlund, Ingrid; Hanson, Ulf

    2008-01-01

    Evaluate obstetric characteristics during the last two hours of labor in neonates born with acidemia. Case-control study. Delivery units at two university hospitals in Sweden. Out of 28,486 deliveries during 1994-2004, 305 neonates had an umbilical artery pH value or = 7.05 and an Apgar score > or =7 at 5 minutes. Obstetric characteristics, cardiotocographic patterns and oxytocin treatment during the last two hours of labor were recorded. In the univariate analysis, > or =6 contractions/10 minutes (odds ratio (OR) 4.94, 95% confidence interval (CI) 3.25-7.49), oxytocin use (OR 2.20, 95% CI 1.66-2.92), bearing down > or =45 minutes (OR 1.77, 95% CI 1.31-2.38) and occipito-posterior position (OR 2.18, 95% CI 1.19-3.98) were associated with acidemia at birth. In the multivariate analysis, only > or =6 contractions/10 minutes (OR 5.36, 95% CI 3.32-8.65) and oxytocin use (OR 1.89, 95% CI 1.21-2.97) were associated with acidemia at birth. Among cases with > or =6 contractions/10 minutes, 75% had been treated with oxytocin. Pathological cardiotocographic patterns occurred in 68.8% of cases and in 26.1% of controls (poxytocin use are the most important risk factors for acidemia at birth. The increased uterine activity was related to overstimulation in the majority of cases. The duration of bearing down is less important when uterine contraction frequency has been considered.

  9. Investigation of Correlation of Test Sequences for Reliability Testing of Digital Physical System Components

    Science.gov (United States)

    Kushik, N. G.; López, J. E.; Yevtushenko, N. V.

    2016-12-01

    The topical problem of effective verification of digital circuits of different physical systems remains a hot topic. Devices ranging from embedded components to perform specific tasks or experiments to modern communication clusters used for data transmission are concerned. The method of synthesis of the test sequences is based on injection of faults into a reference circuit and deriving a corresponding distinguishing sequence which detects this fault. The method is known as mutation testing and is widely used for the synthesis of high-quality verification tests for digital circuits. Naturally, test suits that detect faults of various classes, and larger amount of faults, are of greater interest. The paper studies the correlation between different test suits derived for different mutant types. The considered fault types include 1) single stuck-at faults, 2) bridges, and 3) hardly detectable faults, i.e., slightly modifying the behavior of a single circuit gate. Tests for detecting faults of each type are derived for the B01-B10 benchmark package (ITC'99 benchmarks (Second Release)), which are components of physical systems intended for various applications including processing of data obtained, load balancing systems, etc. Experiments aim to access the fault coverage of the test derived for one mutant type against faults of other types. It is shown experimentally that the synthesis of tests of one type, including a single stuck-at fault test, is insufficient, because its fault coverage for faults of other types cannot exceed 60%.

  10. Enhanced muscle strength with carbohydrate supplement two hours before open cholecystectomy: a randomized, double-blind study.

    Science.gov (United States)

    Gava, Marcella Giovana; Castro-Barcellos, Heloísa Michelon; Caporossi, Cervantes; Aguilar-Nascimento, José Eduardo de

    2016-02-01

    to investigate the effects of preoperative fasting abbreviation with oral supplementation with carbohydrate in the evolution of grip strength in patients undergoing cholecystectomy by laparotomy. we conducted a clinical, randomizeddouble blind study with adult female patients, aged 18-60 years. Patients were divided into two groups: Control Group, with fasting prescription 6-8h until the time of operation; and Intervention Group, which received prescription of fasting for solids 6-8h before surgery, but ingested an oral supplement containing 12.5% carbohydrate, six (400ml) and two (200ml) hours before theprocedure. The handgrip strength was measured in both hands in both groups, at patient's admission (6h before surgery), the immediate pre-operative time (1h before surgery) and 12-18h postoperatively. we analyzed 27 patients, 14 in the intervention group and 13 in the control group. There was no mortality. The handgrip strength (mean [standard deviation]) was significantly higher in the intervention group in the three periods studied, in at least one hand: preoperatively in the dominant hand (27.8 [2.6] vs 24.1 [3.7] kg; p=0.04), in the immediate preoperative in both hands, and postoperatively in the non-dominant hand (28.5 [3.0] vs 21.3 [5.9] kg; p=0.01). the abbreviation of preoperative fasting to two hours with drink containing carbohydrate improves muscle function in the perioperative period.

  11. Enhanced muscle strength with carbohydrate supplement two hours before open cholecystectomy: a randomized, double-blind study

    Directory of Open Access Journals (Sweden)

    Marcella Giovana Gava

    Full Text Available Objective: to investigate the effects of preoperative fasting abbreviation with oral supplementation with carbohydrate in the evolution of grip strength in patients undergoing cholecystectomy by laparotomy. Methods : we conducted a clinical, randomizeddouble blind study with adult female patients, aged 18-60 years. Patients were divided into two groups: Control Group, with fasting prescription 6-8h until the time of operation; and Intervention Group, which received prescription of fasting for solids 6-8h before surgery, but ingested an oral supplement containing 12.5% carbohydrate, six (400ml and two (200ml hours before theprocedure. The handgrip strength was measured in both hands in both groups, at patient's admission (6h before surgery, the immediate pre-operative time (1h before surgery and 12-18h postoperatively. Results : we analyzed 27 patients, 14 in the intervention group and 13 in the control group. There was no mortality. The handgrip strength (mean [standard deviation] was significantly higher in the intervention group in the three periods studied, in at least one hand: preoperatively in the dominant hand (27.8 [2.6] vs 24.1 [3.7] kg; p=0.04, in the immediate preoperative in both hands, and postoperatively in the non-dominant hand (28.5 [3.0] vs 21.3 [5.9] kg; p=0.01. Conclusion : the abbreviation of preoperative fasting to two hours with drink containing carbohydrate improves muscle function in the perioperative period.

  12. Comparison of Effect of Two-Hour Exposure to Forest and Urban Environments on Cytokine, Anti-Oxidant, and Stress Levels in Young Adults

    National Research Council Canada - National Science Library

    Im, Su Geun; Choi, Han; Jeon, Yo-Han; Song, Min-Kyu; Kim, Won; Woo, Jong-Min

    2016-01-01

    The purpose of this study was to investigate the effect of two-hour exposure to a forest environment on cytokine, anti-oxidant and stress levels among university students and to compare the results...

  13. Quality Control Test for Sequence-Phenotype Assignments

    OpenAIRE

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-p...

  14. Determination of Test Sequence for Intrusive Measurement of VTQoS in Environment Offixed Telecommunication Network

    Directory of Open Access Journals (Sweden)

    Peter Pocta

    2006-01-01

    Full Text Available This paper describes simulations of test sequences transmission for intrusive measurement of VTQoS inenvironment of fixed telecommunication network. The aim of simulations was a detection on the influence of this environment on the quality of transmission sequences. Evaluation the generated sequences was based on the calculation of mean square measure and correlation coefficient. These measures were used as a criterion for suitable test sequences selection. Reconsideration of a convenience of the given test sequence, which is composed from simple signals, on intrusive measurement of VTQoS in the environment of fixed telecommunication networks is the aim of this paper.

  15. Quality control test for sequence-phenotype assignments.

    Directory of Open Access Journals (Sweden)

    Maria Teresa Lara Ortiz

    Full Text Available Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10-20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas.

  16. Quality Control Test for Sequence-Phenotype Assignments

    Science.gov (United States)

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

  17. Quality control test for sequence-phenotype assignments.

    Science.gov (United States)

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10-20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas.

  18. A new approach to determine the susceptibility of bacteria to antibiotics directly from positive blood culture bottles in two hours.

    Science.gov (United States)

    March, Gabriel A; García-Loygorri, María C; Simarro, María; Gutiérrez, María P; Orduña, Antonio; Bratos, Miguel A

    2015-02-01

    The rapid identification and antibiotic susceptibility test of bacteria causing bloodstream infections are given a very high priority by clinical laboratories. In an effort to reduce the time required for performing antibiotic susceptibility test (AST), we have developed a new method to be applied from positive blood culture bottles. The design of method was performed using blood culture bottles prepared artificially with five strains which have a known susceptibility. An aliquot of the blood culture was subcultured in the presence of specific antibiotics and bacterial counts were monitored using the Sysmex UF-1000i flow cytometer at different times up to 180min. Receiver operating curve (ROC) analysis allowed us to find out the cut-off point for differentiating between sensitive and resistant strains to the tested antibiotic. This procedure was then validated against standard commercial methods on a total of 100 positive blood culture bottles from patients. First, bacterial identification was performed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) directly from positive blood culture bottles as we have previously reported. Secondly, antibiotic susceptibility test was performed in the same way that was carried out in artificially prepared blood culture bottles. Our results indicate that antibiotic susceptibility test can be determined as early as 120min since a blood culture bottle is flagged as positive. The essential agreement between our susceptibility test and commercial methods (E-test, MicroScan and Vitek) was 99%. In summary, we conclude that reliable results on bacterial identification and antibiotic susceptibility test performed directly from positive blood culture bottles can be obtained within 3h.

  19. Researching of Coders Influence on Basic Measurement Signals Used in Optimal Test Sequence

    Directory of Open Access Journals (Sweden)

    Peter Pocta

    2006-01-01

    Full Text Available This document describes processing basic measurement signals, which were used in test sequence with different coders. The determination of degradation degree of these signals and the elimination of these coders influences on these signals was the aim of this paper. At the end of this paper the test sequence is defined. We can use this sequence for intrusive measurement VTQoS in the networks, using the coders with lower transfer rate.

  20. On HMI's Mod-L Sequence: Test and Evaluation

    Science.gov (United States)

    Liu, Yang; Baldner, Charles; Bogart, R. S.; Bush, R.; Couvidat, S.; Duvall, Thomas L.; Hoeksema, Jon Todd; Norton, Aimee Ann; Scherrer, Philip H.; Schou, Jesper

    2016-05-01

    HMI Mod-L sequence can produce full Stokes parameters at a cadence of 90 seconds by combining filtergrams from both cameras, the front camera and the side camera. Within the 90-second, the front camera takes two sets of Left and Right Circular Polarizations (LCP and RCP) at 6 wavelengths; the side camera takes one set of Linear Polarizations (I+/-Q and I+/-U) at 6 wavelengths. By combining two cameras, one can obtain full Stokes parameters of [I,Q,U,V] at 6 wavelengths in 90 seconds. In norminal Mod-C sequence that HMI currently uses, the front camera takes LCP and RCP at a cadence of 45 seconds, while the side camera takes observation of the full Stokes at a cadence of 135 seconds. Mod-L should be better than Mod-C for providing vector magnetic field data because (1) Mod-L increases cadence of full Stokes observation, which leads to higher temporal resolution of vector magnetic field measurement; (2) decreases noise in vector magnetic field data because it uses more filtergrams to produce [I,Q,U,V]. There are two potential issues in Mod-L that need to be addressed: (1) scaling intensity of the two cameras’ filtergrams; and (2) if current polarization calibration model, which is built for each camera separately, works for the combined data from both cameras. This presentation will address these questions, and further place a discussion here.

  1. The CLASS blazar survey: testing the blazar sequence

    CERN Document Server

    Caccianiga, A

    2004-01-01

    We discuss the properties of the sources in the CLASS Blazar survey which aims at the selection of low radio power (P(5GHz)<10^25 W Hz^-1) blazars. We use VLA data from available catalogues and from our own observations to constrain the radio core-dominance of the sample which, together with the flat radio spectral index, is a signature of the blazar activity. X-ray data from the ROSAT All Sky Survey were also collected in order to constrain the radio-to-X-ray luminosity ratio (alpha_RX) of the sources. The data analysis shows that more than 30% of sources at low radio power (P(5 GHz)<10^25 W Hz^-1) have an alpha_RX steeper than that expected in the framework of the ``blazar sequence'' recently put forward to unify the high and low power blazars. The possibility that this result is influenced by contaminating sources in the current sample is discussed. The conclusion is that, even if a number of non-blazars (typically CSO/GPS sources) are expected in the survey, it is unlikely that this constitutes the ...

  2. Tests of Sunspot Number Sequences: 1. Using Ionosonde Data

    CERN Document Server

    Lockwood, M; Owens, M J; Barnard, L; Willis, D M

    2016-01-01

    More than 70 years ago it was recognised that ionospheric F2-layer critical frequencies $foF2$ had a strong relationship to sunspot number. Using historic datasets from the Slough and Washington ionosondes, we evaluate the best statistical fits of $foF2$ to sunspot numbers (at each Universal Time [UT] separately) in order to search for drifts and abrupt changes in the fit residuals over Solar Cycles 17 - 21. Polynomial fits are made both with and without allowance for the white-light facular area, which has been reported as being associated with cycle-to-cycle changes in the sunspot number - $foF2$ relationship. Over the interval studied here, the ISN, $R$, the backbone group number $Rbb$, and the corrected number $Rc$ largely differ in their allowance for the 'Waldmeier discontinuity' around 1945 (the correction factor for which for $R$, $Rbb$ and $Rc$ is, respectively, zero, effectively over 20%, and explicitly 11.6%). It is shown that for Solar Cycles 18 - 21, all three sunspot data sequences perform well,...

  3. Relationship of glycaemic level of mother in last two hours before delivery and occurrence of acute neonatal complications

    Directory of Open Access Journals (Sweden)

    Georgy Joy Eralil

    2014-06-01

    Full Text Available Background: Diabetes is the most common pre-existing medical disorder seen in pregnancy. Between 2-5% of pregnancies are complicated by diabetes. 87.5% of these women have gestational diabetes, 7.5% have type 1 and 5% have type 2. The study was designed to know the relation of control of diabetes to neonatal outcome in terms of metabolic complications. Methods: Study was conducted in laboring women in government medical college hospital Kottayam. Selection criteria was based on oral GTT. Patients with multiple gestations, other medical disorders were excluded. All the patients were monitored with hourly RBS in active phase of labor. It was compared with cord levels of RBS, calcium, haematocrit and admission to SCNU. For data measured at normal level Chi square test was used to study the significance of difference between the groups. For statistically significant differences odds ratios were computed and 95% confidence limits are calculated. Whenever necessary for quantitative data t- test was used to study the difference in mean values. Results: All normal RBS had live births and all the intrauterine deaths were associated with maternal hyperglycaemia. Among the SCNU admission 87.5% had hyperglycaemia in mother. 33.3 % of abnormal RBS had admission to SCNU whereas only 3.4% of the normal RBS group had admission. The risk of SCNU admission is 14 times more among babies of mothers with abnormal maternal RBS. X2 = 16.188 P = 0.000. The correlation coefficient between maternal RBS and cord RBS is 0.35 indicating a negative relationship between maternal RBS and Cord RBS. The coefficient of determination (r2 is 12 indicates 12% of variation of RBS is explained by maternal RBS. The average RBs cord among mothers with abnormal maternal RBS is 58.4 and among mothers with normal RBS is 72.4 and the observed difference is statistically significant. Conclusions: Heart The study shows that tight regulation of maternal glucose levels during labor can reduce

  4. Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study.

    Science.gov (United States)

    Jiang, Haojun; Xie, Yifan; Li, Xuchao; Ge, Huijuan; Deng, Yongqiang; Mu, Haofang; Feng, Xiaoli; Yin, Lu; Du, Zhou; Chen, Fang; He, Nongyue

    2016-01-01

    Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels in order to verify the performance in clinical cases. Combining targeted deep sequencing of selective SNP and informative bioinformatics pipeline, we calculated the combined paternity index (CPI) of 17 cases to determine paternity. Sequencing-based NIPAT results fully agreed with invasive prenatal paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future.

  5. ISO 17025 validation of a next-generation sequencing assay for relationship testing

    DEFF Research Database (Denmark)

    Buchard, Anders; Kampmann, Marie-Louise; Poulsen, Lena

    2016-01-01

    The HID-Ion AmpliSeq™ Identity Panel is a next-generation sequencing assay with 90 autosomal and 34 Y-chromosome SNPs that are amplified in one PCR step and subsequently sequenced using the Ion Personal Genome Machine (Ion PGM™) System. This assay was validated for relationship testing in our ISO...

  6. Countering Gattaca: Efficient and Secure Testing of Fully-Sequenced Human Genomes

    CERN Document Server

    Baldi, Pierre; De Cristofaro, Emiliano; Gasti, Paolo; Tsudik, Gene

    2011-01-01

    Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA sequence. Widespread and affordable availability of fully sequenced genomes immediately opens up important opportunities in a number of health-related fields. In particular, common genomic applications and tests performed in vitro today will soon be conducted computationally, using digitized genomes. New applications will be developed as genome-enabled medicine becomes increasingly preventive and personalized. However, this progress also prompts significant privacy challenges associated with potential loss, theft, or misuse of genomic data. In this paper, we begin to address genomic privacy by focusing on three important applications: Paternity Tests, Personalized Medicine, and Genetic Compatibility Tests. After carefully analyzing these applications and their privacy requiremen...

  7. Divergence of conserved non-coding sequences: rate estimates and relative rate tests.

    Science.gov (United States)

    Wagner, Günter P; Fried, Claudia; Prohaska, Sonja J; Stadler, Peter F

    2004-11-01

    In many eukaryotic genomes only a small fraction of the DNA codes for proteins, but the non-protein coding DNA harbors important genetic elements directing the development and the physiology of the organisms, like promoters, enhancers, insulators, and micro-RNA genes. The molecular evolution of these genetic elements is difficult to study because their functional significance is hard to deduce from sequence information alone. Here we propose an approach to the study of the rate of evolution of functional non-coding sequences at a macro-evolutionary scale. We identify functionally important non-coding sequences as Conserved Non-Coding Nucleotide (CNCN) sequences from the comparison of two outgroup species. The CNCN sequences so identified are then compared to their homologous sequences in a pair of ingroup species, and we monitor the degree of modification these sequences suffered in the two ingroup lineages. We propose a method to test for rate differences in the modification of CNCN sequences among the two ingroup lineages, as well as a method to estimate their rate of modification. We apply this method to the full sequences of the HoxA clusters from six gnathostome species: a shark, Heterodontus francisci; a basal ray finned fish, Polypterus senegalus; the amphibian, Xenopus tropicalis; as well as three mammalian species, human, rat and mouse. The results show that the evolutionary rate of CNCN sequences is not distinguishable among the three mammalian lineages, while the Xenopus lineage has a significantly increased rate of evolution. Furthermore the estimates of the rate parameters suggest that in the stem lineage of mammals the rate of CNCN sequence evolution was more than twice the rate observed within the placental amniotes clade, suggesting a high rate of evolution of cis-regulatory elements during the origin of amniotes and mammals. We conclude that the proposed methods can be used for testing hypotheses about the rate and pattern of evolution of putative

  8. Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing.

    Science.gov (United States)

    Xue, Yuan; Ankala, Arunkanth; Wilcox, William R; Hegde, Madhuri R

    2015-06-01

    Next-generation sequencing is changing the paradigm of clinical genetic testing. Today there are numerous molecular tests available, including single-gene tests, gene panels, and exome sequencing or genome sequencing. As a result, ordering physicians face the conundrum of selecting the best diagnostic tool for their patients with genetic conditions. Single-gene testing is often most appropriate for conditions with distinctive clinical features and minimal locus heterogeneity. Next-generation sequencing-based gene panel testing, which can be complemented with array comparative genomic hybridization and other ancillary methods, provides a comprehensive and feasible approach for heterogeneous disorders. Exome sequencing and genome sequencing have the advantage of being unbiased regarding what set of genes is analyzed, enabling parallel interrogation of most of the genes in the human genome. However, current limitations of next-generation sequencing technology and our variant interpretation capabilities caution us against offering exome sequencing or genome sequencing as either stand-alone or first-choice diagnostic approaches. A growing interest in personalized medicine calls for the application of genome sequencing in clinical diagnostics, but major challenges must be addressed before its full potential can be realized. Here, we propose a testing algorithm to help clinicians opt for the most appropriate molecular diagnostic tool for each scenario.

  9. A likelihood ratio test for species membership based on DNA sequence data

    DEFF Research Database (Denmark)

    Matz, Mikhail V.; Nielsen, Rasmus

    2005-01-01

    DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled...... sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability....

  10. Implementation of whole genome massively parallel sequencing for noninvasive prenatal testing in laboratories

    NARCIS (Netherlands)

    Thung, G.W.D.T.; Beulen, L.; Hehir-Kwa, J.Y.; Faas, B.H.W.

    2015-01-01

    Noninvasive prenatal testing (NIPT) for fetal aneuploidies using cell-free fetal DNA in maternal plasma has revolutionized the field of prenatal care and methods using massively parallel sequencing are now being implemented almost worldwide. Substantial progress has been made from initially testing

  11. [Next generation sequencing and its applications in non-invasive prenatal testing of aneuploidies].

    Science.gov (United States)

    Babay, Lilla Éva; Horányi, Dániel; Rigó, János; Nagy, Gyula Richárd

    2015-06-28

    The development of the new generation sequencing techniques brought a new era in the field of DNA sequencing, that also revolutionized the prenatal screening for aneuploidy. In order to provide a more complete view, the authors describe some first generation methods as well as the theoretical and technical background of the next generation methods. In the second part of this review, the authors focuse on non-invasive prenatal testing, which is a fetal cell-free DNA based method requiring advanced sequencing procedures. After discussing the theoretical and technical background, the authors review current application and utility of non-invasive prenatal testing. They conclude that non-invasive prenatal testing is the most effective screening test in high risk pregnancies and its efficiency can be justified in studies involving low risk pregnancies as well.

  12. Dietary Patterns Predict Changes in Two-Hour Post-Oral Glucose Tolerance Test Plasma Glucose Concentrations in Middle-Aged Adults

    DEFF Research Database (Denmark)

    Lau, C.; Toft, U.; Tetens, Inge

    2009-01-01

    ) and a score for a modern dietary pattern (characterized by higher intakes of vegetables, fruit, vegetable oil/vinegar dressing, poultry, pasta, rice, and cereals) were estimated for each person at baseline. Random effect models adjusting for relevant confounders were used to estimate changes in repetitive...

  13. Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study

    Science.gov (United States)

    Ge, Huijuan; Deng, Yongqiang; Mu, Haofang; Feng, Xiaoli; Yin, Lu; Du, Zhou; Chen, Fang; He, Nongyue

    2016-01-01

    Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels in order to verify the performance in clinical cases. Combining targeted deep sequencing of selective SNP and informative bioinformatics pipeline, we calculated the combined paternity index (CPI) of 17 cases to determine paternity. Sequencing-based NIPAT results fully agreed with invasive prenatal paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future. PMID:27631491

  14. Genetic counselors' (GC) knowledge, awareness, understanding of clinical next-generation sequencing (NGS) genomic testing.

    Science.gov (United States)

    Boland, P M; Ruth, K; Matro, J M; Rainey, K L; Fang, C Y; Wong, Y N; Daly, M B; Hall, M J

    2015-12-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation.

  15. Sequence Diagram Test Case Specification and Virtual Integration Analysis using Timed-Arc Petri Nets

    Directory of Open Access Journals (Sweden)

    Sven Sieverding

    2013-02-01

    Full Text Available In this paper, we formally define Test Case Sequence Diagrams (TCSD as an easy-to-use means to specify test cases for components including timing constraints. These test cases are modeled using the UML2 syntax and can be specified by standard UML-modeling-tools. In a component-based design an early identification of errors can be achieved by a virtual integration of components before the actual system is build. We define such a procedure which integrates the individual test cases of the components according to the interconnections of a given architecture and checks if all specified communication sequences are consistent. Therefore, we formally define the transformation of TCSD into timed-arc Petri nets and a process for the combination of these nets. The applicability of our approach is demonstrated on an avionic use case from the ARP4761 standard.

  16. 40 CFR Table C-2 to Subpart C of... - Sequence of Test Measurements

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Sequence of Test Measurements C Table C-2 to Subpart C of Part 53 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Medium. 2 High High. 3 Medium Low. 4 High High. 5 Low Medium. 6 Medium Low. 7 Low Medium. 8 Medium Low....

  17. Test sequencing problem arising at the design stage for reducing life cycle cost

    Institute of Scientific and Technical Information of China (English)

    Zhang Shigang; Hu Zheng; Wen Xisen

    2013-01-01

    Previous test sequencing algorithms only consider the execution cost of a test at the application stage.Due to the fact that the placement cost of some tests at the design stage is considerably high compared with the execution cost,the sequential diagnosis strategy obtained by previous methods is actually not optimal from the view of life cycle.In this paper,the test sequencing problem based on life cycle cost is presented.It is formulated as an optimization problem,which is non-deterministic polynomial-time hard (NP-hard).An algorithm and a strategy to improve its computational efficiency are proposed.The formulation and algorithms are tested on various simulated systems and comparisons are made with the extant test sequencing methods.Application on a pump rotational speed control (PRSC) system of a spacecraft is studied in detail.Both the simulation results and the real-world case application results suggest that the solution proposed in this paper can significantly reduce the life cycle cost of a sequential fault diagnosis strategy.

  18. Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT).

    Science.gov (United States)

    Urrutia, Eugene; Lee, Seunggeun; Maity, Arnab; Zhao, Ni; Shen, Judong; Li, Yun; Wu, Michael C

    Analysis of rare genetic variants has focused on region-based analysis wherein a subset of the variants within a genomic region is tested for association with a complex trait. Two important practical challenges have emerged. First, it is difficult to choose which test to use. Second, it is unclear which group of variants within a region should be tested. Both depend on the unknown true state of nature. Therefore, we develop the Multi-Kernel SKAT (MK-SKAT) which tests across a range of rare variant tests and groupings. Specifically, we demonstrate that several popular rare variant tests are special cases of the sequence kernel association test which compares pair-wise similarity in trait value to similarity in the rare variant genotypes between subjects as measured through a kernel function. Choosing a particular test is equivalent to choosing a kernel. Similarly, choosing which group of variants to test also reduces to choosing a kernel. Thus, MK-SKAT uses perturbation to test across a range of kernels. Simulations and real data analyses show that our framework controls type I error while maintaining high power across settings: MK-SKAT loses power when compared to the kernel for a particular scenario but has much greater power than poor choices.

  19. The Application of Next Generation Sequencing Technology on Noninvasive Prenatal Test

    DEFF Research Database (Denmark)

    Jiang, Hui

    of effective treatment. The rapid development of next generation sequencing technology boosts the discovery of new causative gene for these rare diseases, as well as the genetic diagnosis in clinic practice. Carrier screening, prenatal diagnosis and newborn screening are wildly used in the world to prevent...... an invasive process, which might lead to maternal anxiety, or even miscarriage. Therefore, developing an effective approach to perform noninvasive prenatal test (NIPT) for rare diseases is the key challenge to prevent birth defect in the future. The discovery of cell-­free fetal DNA, coupling with next......, and maternal plasma. In order to obtain accurate result, we combined the haplotype information from the parents with maternal plasma deep sequencing data to recover the fetal genotype. Our study demonstrated that the sequencing-based new approach could be used to detect rare diseases, including chromosomal...

  20. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

    Directory of Open Access Journals (Sweden)

    Thiele Bernhard

    2011-05-01

    Full Text Available Abstract Background Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4 variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Methods Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Results Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%, and defining a minority cutoff of 5%, the results were concordant in all but one isolate. Conclusions The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

  1. Advanced spatio-temporal filtering techniques for photogrammetric image sequence analysis in civil engineering material testing

    Science.gov (United States)

    Liebold, F.; Maas, H.-G.

    2016-01-01

    The paper shows advanced spatial, temporal and spatio-temporal filtering techniques which may be used to reduce noise effects in photogrammetric image sequence analysis tasks and tools. As a practical example, the techniques are validated in a photogrammetric spatio-temporal crack detection and analysis tool applied in load tests in civil engineering material testing. The load test technique is based on monocular image sequences of a test object under varying load conditions. The first image of a sequence is defined as a reference image under zero load, wherein interest points are determined and connected in a triangular irregular network structure. For each epoch, these triangles are compared to the reference image triangles to search for deformations. The result of the feature point tracking and triangle comparison process is a spatio-temporally resolved strain value field, wherein cracks can be detected, located and measured via local discrepancies. The strains can be visualized as a color-coded map. In order to improve the measuring system and to reduce noise, the strain values of each triangle must be treated in a filtering process. The paper shows the results of various filter techniques in the spatial and in the temporal domain as well as spatio-temporal filtering techniques applied to these data. The best results were obtained by a bilateral filter in the spatial domain and by a spatio-temporal EOF (empirical orthogonal function) filtering technique.

  2. Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.

    Science.gov (United States)

    Ruiz, Anna; Llort, Gemma; Yagüe, Carmen; Baena, Neus; Viñas, Marina; Torra, Montse; Brunet, Anna; Seguí, Miquel A; Saigí, Eugeni; Guitart, Miriam

    2014-01-01

    High throughput methods such as next generation sequencing are increasingly used in molecular diagnosis. The aim of this study was to develop a workflow for the detection of BRCA1 and BRCA2 mutations using massive parallel sequencing in a 454 GS Junior bench top sequencer. Our approach was first validated in a panel of 23 patients containing 62 unique variants that had been previously Sanger sequenced. Subsequently, 101 patients with familial breast and ovarian cancer were studied. BRCA1 and BRCA2 exon enrichment has been performed by PCR amplification using the BRCA MASTR kit (Multiplicom). Bioinformatic analysis of reads is performed with the AVA software v2.7 (Roche). In total, all 62 variants were detected resulting in a sensitivity of 100%. 71 false positives were called resulting in a specificity of 97.35%. All of them correspond to deletions located in homopolymeric stretches. The analysis of the homopolymers stretches of 6 bp or longer using the BRCA HP kit (Multiplicom) increased the specificity of the detection of BRCA1 and BRCA2 mutations to 99.99%. We show here that massive parallel pyrosequencing can be used as a diagnostic strategy to test for BRCA1 and BRCA2 mutations meeting very stringent sensitivity and specificity parameters replacing traditional Sanger sequencing with a lower cost.

  3. Online Diagnosis System: a webserver for analysis of Sanger sequencing-based genetic testing data.

    Science.gov (United States)

    Sun, Kun; Yuen, Yuet-Ping; Wang, Huating; Sun, Hao

    2014-10-01

    Sanger sequencing is a well-established molecular technique for diagnosis of genetic diseases. In these tests, DNA sequencers produce vast amounts of data that need to be examined and annotated within a short period of time. To achieve this goal, an online bioinformatics platform that can automate the process is essential. However, to date, there is no such integrated bioinformatics platform available. To fulfill this gap, we developed the Online Diagnosis System (ODS), which is a freely available webserver and supports the commonly used file format of Sanger sequencing data. ODS seamlessly integrates base calling, single nucleotide variation (SNV) identification, and SNV annotation into one single platform. It also allows laboratorians to manually inspect the quality of the identified SNVs in the final report. ODS can significantly reduce the data analysis time therefore allows Sanger sequencing-based genetic testing to be finished in a timely manner. ODS is freely available at http://sunlab.lihs.cuhk.edu.hk/ODS/. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Validation of two-channel sequencing-by-synthesis for noninvasive prenatal testing of fetal whole and partial chromosome aberrations

    NARCIS (Netherlands)

    Neveling, K.; Thung, G.W.D.T.; Beulen, L.; Rens-Buijsman, W. van; Gomes, I.; Heuvel, S. van den; Mieloo, H.; Derks-Prinsen, I.; Kater-Baats, E.; Faas, B.H.W.

    2016-01-01

    OBJECTIVE: To validate Illumina's two-channel NextSeq 500 sequencing system for noninvasive prenatal testing (NIPT) of fetal whole chromosome and partial aberrations. METHODS: A total of 162 plasma samples, previously sequenced for NIPT on a SOLiD 5500xl platform, were sequenced on the NextSeq 500 u

  5. Current practices and guidelines for clinical next-generation sequencing oncology testing

    Institute of Scientific and Technical Information of China (English)

    Samuel P. Strom

    2016-01-01

    Next-generation sequencing (NGS) has been rapidly integrated into molecular pathology, dramatically increasing the breadth genomic of information available to oncologists and their patients. This review will explore the ways in which this new technology is currently applied to bolster care for patients with solid tumors and hematological malignancies, focusing on practices and guidelines for assessing the technical validity and clinical utility of DNA variants identified during clinical NGS oncology testing.

  6. Testing the Origins of Nonmarine Stratigraphic Sequences, Iglesia Basin, Northwest Argentina

    Science.gov (United States)

    Ruskin, B. G.; Jordan, T.

    2003-12-01

    notable sedimentary hiatuses, allow pedofacies definition, and provide material for temporally constrained 13C and 18O analysis as a proxy for climate fluctuation. Preliminary interpretation of paleosol micromorphology and isotopic time series suggests minimal diagenesis, as well as an evolution towards moisture-stressed conditions and depletion of heavy isotopes, possibly caused by the orographic effect of the rising Andes. Isotopic signal variability can be compared to sequence chronostratigraphy to test the hypothesis that sequence formation results from stream discharge variations.

  7. Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features

    Directory of Open Access Journals (Sweden)

    Gillet Laurent

    2011-08-01

    Full Text Available Abstract Background Bovine herpesvirus 4 (BoHV-4 is a useful model for the human pathogenic gammaherpesviruses Epstein-Barr virus and Kaposi's Sarcoma-associated Herpesvirus. Although genome manipulations of this virus have been greatly facilitated by the cloning of the BoHV-4 V.test strain as a Bacterial Artificial Chromosome (BAC, the lack of a complete genome sequence for this strain limits its experimental use. Methods In this study, we have determined the complete sequence of BoHV-4 V.test strain by a pyrosequencing approach. Results The long unique coding region (LUR consists of 108,241 bp encoding at least 79 open reading frames and is flanked by several polyrepetitive DNA units (prDNA. As previously suggested, we showed that the prDNA unit located at the left prDNA-LUR junction (prDNA-G differs from the other prDNA units (prDNA-inner. Namely, the prDNA-G unit lacks the conserved pac-2 cleavage and packaging signal in its right terminal region. Based on the mechanisms of cleavage and packaging of herpesvirus genomes, this feature implies that only genomes bearing left and right end prDNA units are encapsulated into virions. Conclusions In this study, we have determined the complete genome sequence of the BAC-cloned BoHV-4 V.test strain and identified genome organization features that could be important in other herpesviruses.

  8. Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests

    Directory of Open Access Journals (Sweden)

    Jihun Kim

    2017-05-01

    Full Text Available Next-generation sequencing (NGS has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS. This consensus standard proposal consists of two parts: laboratory guidelines and requirements for clinical NGS laboratories. The laboratory guidelines part addressed several important issues across multistep NGS cancer panel tests including choice of gene panel and platform, sample handling, nucleic acid management, sample identity tracking, library preparation, sequencing, analysis and reporting. Requirements for clinical NGS tests were summarized in terms of documentation, validation, quality management, and other required written policies. Together with appropriate pathologist training and international laboratory standards, these laboratory standards would help molecular pathology laboratories to successfully implement NGS cancer panel tests in clinic. In this way, the oncology community would be able to help patients to benefit more from personalized cancer medicine.

  9. Noninvasive Measurement of Carbon Dioxide during One-Lung Ventilation with Low Tidal Volume for Two Hours: End-Tidal versus Transcutaneous Techniques.

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    Full Text Available There may be significant difference between measurement of end-tidal carbon dioxide partial pressure (PetCO2 and arterial carbon dioxide partial pressure (PaCO2 during one-lung ventilation with low tidal volume for thoracic surgeries. Transcutaneous carbon dioxide partial pressure (PtcCO2 monitoring can be used continuously to evaluate PaCO2 in a noninvasive fashion. In this study, we compared the accuracy between PetCO2 and PtcCO2 in predicting PaCO2 during prolonged one-lung ventilation with low tidal volume for thoracic surgeries.Eighteen adult patients who underwent thoracic surgeries with one-lung ventilation longer than two hours were included in this study. Their PetCO2, PtcCO2, and PaCO2 values were collected at five time points before and during one-lung ventilation. Agreement among measures was evaluated by Bland-Altman analysis.Ninety sample sets were obtained. The bias and precision when PtcCO2 and PaCO2 were compared were 4.1 ± 6.5 mmHg during two-lung ventilation and 2.9 ± 6.1 mmHg during one-lung ventilation. Those when PetCO2 and PaCO2 were compared were -11.8 ± 6.4 mmHg during two-lung ventilation and -11.8 ± 4.9 mmHg during one-lung ventilation. The differences between PtcCO2 and PaCO2 were significantly lower than those between PetCO2 and PaCO2 at all five time-points (p < 0.05.PtcCO2 monitoring was more accurate for predicting PaCO2 levels during prolonged one-lung ventilation with low tidal volume for patients undergoing thoracic surgeries.

  10. Comparison of Effect of Two-Hour Exposure to Forest and Urban Environments on Cytokine, Anti-Oxidant, and Stress Levels in Young Adults

    Directory of Open Access Journals (Sweden)

    Su Geun Im

    2016-06-01

    Full Text Available The purpose of this study was to investigate the effect of two-hour exposure to a forest environment on cytokine, anti-oxidant and stress levels among university students and to compare the results to those measured in urban environments. Forty-one subjects were recruited. For our crossover design, subjects were divided into two groups based on similar demographic characteristics. Group A remained in the urban environment and was asked to perform regular breathing for 2 h. Blood samples were collected and the serum levels of cytokines including interleukin-6 (IL-6, IL-8, tumor necrosis factor-α (TNF-α, and glutathione peroxidase (GPx were examined. Subjects were moved to a small town in a rural area for an equal amount of time to exclude carryover effects, and then remained for another 2 h in a forest environment. The second set of blood samples was collected to assess the effect of exposure to the forest environment. Using the same method, Group B was first exposed to the forest environment, followed by exposure to the urban environment. Blood samples collected after the subjects were exposed to the forest environment showed significantly lower levels of IL-8 and TNF-α compared to those in samples collected after urban environment exposure (10.76 vs. 9.21, t = 4.559, p < 0.001, and 0.97 vs. 0.87, t = 4.130, p < 0.001. The GPx concentration increased significantly after exposure to the forest environment (LnGPx = 5.09 vs. LnGPx = 5.21, t = −2.039, p < 0.05.

  11. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee

    DEFF Research Database (Denmark)

    Ellington, M J; Ekelund, O; Aarestrup, Frank Møller

    2017-01-01

    Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility test...

  12. The Application of Next Generation Sequencing Technology on Noninvasive Prenatal Test

    DEFF Research Database (Denmark)

    Jiang, Hui

    and diagnosis of rare diseases. Among them, genetic test for pregnant women is the most powerful and cost-­effective tool to identify and prevent rare diseases related birth defect. However, most of the current routine prenatal genetic testing for rare diseases requires of collecting fetal samples through...... an invasive process, which might lead to maternal anxiety, or even miscarriage. Therefore, developing an effective approach to perform noninvasive prenatal test (NIPT) for rare diseases is the key challenge to prevent birth defect in the future. The discovery of cell-­free fetal DNA, coupling with next...... a sensitivity and specificity of over 99%, which can provide accurate and reliable results and thus avoid most of invasive process compared to standard prenatal test. Moreover,we also designed probes for genes related to Monogenetic disorders and conducted target region sequencing for parents, proband...

  13. Hypothesis testing on the fractal structure of behavioral sequences: the Bayesian assessment of scaling methodology.

    Science.gov (United States)

    Moscoso del Prado Martín, Fermín

    2013-12-01

    I introduce the Bayesian assessment of scaling (BAS), a simple but powerful Bayesian hypothesis contrast methodology that can be used to test hypotheses on the scaling regime exhibited by a sequence of behavioral data. Rather than comparing parametric models, as typically done in previous approaches, the BAS offers a direct, nonparametric way to test whether a time series exhibits fractal scaling. The BAS provides a simpler and faster test than do previous methods, and the code for making the required computations is provided. The method also enables testing of finely specified hypotheses on the scaling indices, something that was not possible with the previously available methods. I then present 4 simulation studies showing that the BAS methodology outperforms the other methods used in the psychological literature. I conclude with a discussion of methodological issues on fractal analyses in experimental psychology.

  14. Case-control association testing of common variants from sequencing of DNA pools.

    Directory of Open Access Journals (Sweden)

    Allan F McRae

    Full Text Available While genome-wide association studies (GWAS have been successful in identifying a large number of variants associated with disease, the challenge of locating the underlying causal loci remains. Sequencing of case and control DNA pools provides an inexpensive method for assessing all variation in a genomic region surrounding a significant GWAS result. However, individual variants need to be ranked in terms of the strength of their association to disease in order to prioritise follow-up by individual genotyping. A simple method for testing for case-control association in sequence data from DNA pools is presented that allows the partitioning of the variance in allele frequency estimates into components due to the sampling of chromosomes from the pool during sequencing, sampling individuals from the population and unequal contribution from individuals during pool construction. The utility of this method is demonstrated on a sequence from the alcohol dehydrogenase (ADH gene cluster on a case-control sample for heavy alcohol consumption.

  15. Single stars in the Hyades open cluster. Fiducial sequence for testing stellar and atmospheric models

    Science.gov (United States)

    Kopytova, Taisiya G.; Brandner, Wolfgang; Tognelli, Emanuele; Prada Moroni, Pier Giorgio; Da Rio, Nicola; Röser, Siegfried; Schilbach, Elena

    2016-01-01

    Context. Age and mass determinations for isolated stellar objects remain model-dependent. While stellar interior and atmospheric theoretical models are rapidly evolving, we need a powerful tool to test them. Open clusters are good candidates for this role. Aims: We aim to create a fiducial sequence of stellar objects for testing stellar and atmospheric models. Methods: We complement previous studies on the Hyades multiplicity by Lucky Imaging observations with the AstraLux Norte camera. This allows us to exclude possible binary and multiple systems with companions outside a 2-7 AU separation and to create a single-star sequence for the Hyades. The sequence encompasses 250 main-sequence stars ranging from A5V to M6V. Using the Tool for Astrophysical Data Analysis (TA-DA), we create various theoretical isochrones applying different combinations of interior and atmospheric models. We compare the isochrones with the observed Hyades single-star sequence on J vs. J-Ks, J vs. J-H, and Ks vs. H-Ks color-magnitude diagrams. As a reference we also compute absolute fluxes and magnitudes for all stars from X-ray to mid-infrared based on photometric measurements available in the literature(ROSAT X-ray, GALEX UV, APASS gri, 2MASS JHKs, and WISE W1 to W4). Results: We find that combinations of both PISA and DARTMOUTH stellar interior models with BT-Settl 2010 atmospheric models describe the observed sequence well. We use PISA in combination with BT-Settl 2010 models to derive theoretical predictions for physical parameters (Teff, mass, log g) of 250 single stars in the Hyades. The full sequence covers the mass range of 0.13-2.30 M⊙, and effective temperatures between 3060 K and 8200 K. Conclusions: Within the measurement uncertainties, the current generation of models agree well with the single-star sequence. The primary limitations are the uncertainties in the measurement of the distances to individual Hyades members, and uncertainties in the photometry. Gaia parallaxes

  16. From psychological need satisfaction to intentional behavior: testing a motivational sequence in two behavioral contexts.

    Science.gov (United States)

    Hagger, Martin S; Chatzisarantis, Nikos L D; Harris, Jemma

    2006-02-01

    The present study tested a motivational sequence in which global-level psychological need satisfaction from self-determination theory influenced intentions and behavior directly and indirectly through contextual-level motivation and situational-level decision-making constructs from the theory of planned behavior. Two samples of university students (N = 511) completed measures of global-level psychological need satisfaction, contextual-level autonomous motivation, and situational-level attitudes, subjective norms, perceived behavioral control, intentions, and behavior in two behavioral contexts: exercise and dieting. A structural equation model supported the proposed sequence in both samples. The indirect effect was present for exercise behavior, whereas both direct and indirect effects were found for dieting behavior. Findings independently supported the component theories and provided a comprehensive integrated explanation of volitional behavior.

  17. Testing orbital forcing in the Eocene deltaic sequences of the South-Pyrenean Foreland Basins.

    Science.gov (United States)

    Garcés, Miguel; López-Blanco, Miguel; Valero, Luis; Beamud, Elisabet; Pueyo-Morer, Emilio; Rodríguez-Pinto, Adriana

    2014-05-01

    Paleoclimate proxy records from marine pelagic sediments show that a link exists between long-period orbital cyclicity and the pattern of high latitude glaciations. Thus, a sound possibility exist that transgressive-regressive third-order sequences from shallow marine environments reflect long-period orbital (glacioeustatic) forcing, as suggested from a variety of shallow marine settings of different ages, from Mesozoic to Paleogene. In this study we aim at testing the role of the 400 kyr eccentricity cycle in the sequential organization of the Late Eocene deltaic sequences of the Belsue-Atares Formation, in the Jaca-Pamplona Basin. The overall record spans from latest Lutetian to early Priabonian and consists of nearly 1000 meters of siliciclastic deltaic to mixed platform sequences of various scales. Very notorious lateral changes in both stratigraphic thickness and sedimentary facies witness the synkinematic character of these sediments, deposited simultaneously to intrabasinal fold growth. A magnetostratigraphy based chronostratigraphic framework is used, first, to determine the age and duration of the sequences and, second, to establish a robust correlation with other deltaic sequences within the south-pyrenean foreland. The long-distance correlation exercise is used to discriminate between local (tectonic) and global (climatic) forcing factors, under the assumption that climate signature is synchronous, while tectonic forcing is prone to yield diachronic units at basin scale. Astronomical tuning with the 400-kyr cycle of the eccentricity solution of the Earth orbit is attempted on the basis of derived magnetostratigraphic age constrains. Our results suggest that transgressive (regressive) trends correlate with maxima (minima) of eccentricity cycle, a phase-relationship which is compatible with a base-level (accommodation) driven forcing.

  18. Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests.

    Science.gov (United States)

    Waddell, Peter J; Ota, Rissa; Penny, David

    2009-10-01

    Testing fit of data to model is fundamentally important to any science, but publications in the field of phylogenetics rarely do this. Such analyses discard fundamental aspects of science as prescribed by Karl Popper. Indeed, not without cause, Popper (Unended quest: an intellectual autobiography. Fontana, London, 1976) once argued that evolutionary biology was unscientific as its hypotheses were untestable. Here we trace developments in assessing fit from Penny et al. (Nature 297:197-200, 1982) to the present. We compare the general log-likelihood ratio (the G or G (2) statistic) statistic between the evolutionary tree model and the multinomial model with that of marginalized tests applied to an alignment (using placental mammal coding sequence data). It is seen that the most general test does not reject the fit of data to model (P approximately 0.5), but the marginalized tests do. Tests on pairwise frequency (F) matrices, strongly (P < 0.001) reject the most general phylogenetic (GTR) models commonly in use. It is also clear (P < 0.01) that the sequences are not stationary in their nucleotide composition. Deviations from stationarity and homogeneity seem to be unevenly distributed amongst taxa; not necessarily those expected from examining other regions of the genome. By marginalizing the 4( t ) patterns of the i.i.d. model to observed and expected parsimony counts, that is, from constant sites, to singletons, to parsimony informative characters of a minimum possible length, then the likelihood ratio test regains power, and it too rejects the evolutionary model with P < 0.001. Given such behavior over relatively recent evolutionary time, readers in general should maintain a healthy skepticism of results, as the scale of the systematic errors in published trees may really be far larger than the analytical methods (e.g., bootstrap) report.

  19. Impact of order of movement on nerve strain and longitudinal excursion: a biomechanical study with implications for neurodynamic test sequencing.

    Science.gov (United States)

    Nee, Robert J; Yang, Chich-Haung; Liang, Chung-Chao; Tseng, Guo-Fang; Coppieters, Michel W

    2010-08-01

    It is assumed that strain in a nerve segment at the end of a neurodynamic test will be greatest if the joint nearest that nerve segment is moved first in the neurodynamic test sequence. To test this assumption, the main movements of the median nerve biased neurodynamic test were applied in three different sequences to seven fresh-frozen human cadavers. Strain and longitudinal excursion were measured in the median nerve at the distal forearm. Strain and relative position of the nerve at the end of a test did not differ between sequences. The nerve was subjected to higher levels of strain for a longer duration during the sequence where wrist extension occurred first. The pattern of excursion was different for each sequence. The results highlight that order of movement does not affect strain or relative position of the nerve at the end of a test when joints are moved through comparable ranges of motion. When used clinically, different neurodynamic sequences may still change the mechanical load applied to a nerve segment. Changes in load may occur because certain sequences apply increased levels of strain to the nerve for a longer time period, or because sequences differ in ranges of joint motions.

  20. Fault Tree Based Diagnosis with Optimal Test Sequencing for Field Service Engineers

    Science.gov (United States)

    Iverson, David L.; George, Laurence L.; Patterson-Hine, F. A.; Lum, Henry, Jr. (Technical Monitor)

    1994-01-01

    When field service engineers go to customer sites to service equipment, they want to diagnose and repair failures quickly and cost effectively. Symptoms exhibited by failed equipment frequently suggest several possible causes which require different approaches to diagnosis. This can lead the engineer to follow several fruitless paths in the diagnostic process before they find the actual failure. To assist in this situation, we have developed the Fault Tree Diagnosis and Optimal Test Sequence (FTDOTS) software system that performs automated diagnosis and ranks diagnostic hypotheses based on failure probability and the time or cost required to isolate and repair each failure. FTDOTS first finds a set of possible failures that explain exhibited symptoms by using a fault tree reliability model as a diagnostic knowledge to rank the hypothesized failures based on how likely they are and how long it would take or how much it would cost to isolate and repair them. This ordering suggests an optimal sequence for the field service engineer to investigate the hypothesized failures in order to minimize the time or cost required to accomplish the repair task. Previously, field service personnel would arrive at the customer site and choose which components to investigate based on past experience and service manuals. Using FTDOTS running on a portable computer, they can now enter a set of symptoms and get a list of possible failures ordered in an optimal test sequence to help them in their decisions. If facilities are available, the field engineer can connect the portable computer to the malfunctioning device for automated data gathering. FTDOTS is currently being applied to field service of medical test equipment. The techniques are flexible enough to use for many different types of devices. If a fault tree model of the equipment and information about component failure probabilities and isolation times or costs are available, a diagnostic knowledge base for that device can be

  1. Adaptive combination of P-values for family-based association testing with sequence data.

    Science.gov (United States)

    Lin, Wan-Yu

    2014-01-01

    Family-based study design will play a key role in identifying rare causal variants, because rare causal variants can be enriched in families with multiple affected subjects. Furthermore, different from population-based studies, family studies are robust to bias induced by population substructure. It is well known that rare causal variants are difficult to detect from single-locus tests. Therefore, burden tests and non-burden tests have been developed, by combining signals of multiple variants in a chromosomal region or a functional unit. This inevitably incorporates some neutral variants into the test statistics, which can dilute the power of statistical methods. To guard against the noise caused by neutral variants, we here propose an 'adaptive combination of P-values method' (abbreviated as 'ADA'). This method combines per-site P-values of variants that are more likely to be causal. Variants with large P-values (which are more likely to be neutral variants) are discarded from the combined statistic. In addition to performing extensive simulation studies, we applied these tests to the Genetic Analysis Workshop 17 data sets, where real sequence data were generated according to the 1000 Genomes Project. Compared with some existing methods, ADA is more robust to the inclusion of neutral variants. This is a merit especially when dichotomous traits are analyzed. However, there are some limitations for ADA. First, it is more computationally intensive. Second, pedigree structures and founders' sequence data are required for the permutation procedure. Third, unrelated controls cannot be included. We here show that, for family-based studies, the application of ADA is limited to dichotomous trait analyses with full pedigree information.

  2. Adaptive combination of P-values for family-based association testing with sequence data.

    Directory of Open Access Journals (Sweden)

    Wan-Yu Lin

    Full Text Available Family-based study design will play a key role in identifying rare causal variants, because rare causal variants can be enriched in families with multiple affected subjects. Furthermore, different from population-based studies, family studies are robust to bias induced by population substructure. It is well known that rare causal variants are difficult to detect from single-locus tests. Therefore, burden tests and non-burden tests have been developed, by combining signals of multiple variants in a chromosomal region or a functional unit. This inevitably incorporates some neutral variants into the test statistics, which can dilute the power of statistical methods. To guard against the noise caused by neutral variants, we here propose an 'adaptive combination of P-values method' (abbreviated as 'ADA'. This method combines per-site P-values of variants that are more likely to be causal. Variants with large P-values (which are more likely to be neutral variants are discarded from the combined statistic. In addition to performing extensive simulation studies, we applied these tests to the Genetic Analysis Workshop 17 data sets, where real sequence data were generated according to the 1000 Genomes Project. Compared with some existing methods, ADA is more robust to the inclusion of neutral variants. This is a merit especially when dichotomous traits are analyzed. However, there are some limitations for ADA. First, it is more computationally intensive. Second, pedigree structures and founders' sequence data are required for the permutation procedure. Third, unrelated controls cannot be included. We here show that, for family-based studies, the application of ADA is limited to dichotomous trait analyses with full pedigree information.

  3. Discounting of Reward Sequences: a Test of Competing Formal Models of Hyperbolic Discounting

    Directory of Open Access Journals (Sweden)

    Noah eZarr

    2014-03-01

    Full Text Available Humans are known to discount future rewards hyperbolically in time. Nevertheless, a formal recursive model of hyperbolic discounting has been elusive until recently, with the introduction of the hyperbolically discounted temporal difference (HDTD model. Prior to that, models of learning (especially reinforcement learning have relied on exponential discounting, which generally provides poorer fits to behavioral data. Recently, it has been shown that hyperbolic discounting can also be approximated by a summed distribution of exponentially discounted values, instantiated in the µAgents model. The HDTD model and the µAgents model differ in one key respect, namely how they treat sequences of rewards. The µAgents model is a particular implementation of a parallel discounting model, which values sequences based on the summed value of the individual rewards whereas the HDTD model contains a nonlinear interaction. To discriminate among these models, we ascertained how subjects discounted a sequence of three rewards, and then we tested how well each candidate model fit the subject data. The results show that the parallel model generally provides a better fit to the human data.

  4. A functional test of Neandertal and modern human mitochondrial targeting sequences

    Energy Technology Data Exchange (ETDEWEB)

    Gralle, Matthias, E-mail: gralle@bioqmed.ufrj.br [Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, CCS, Ilha do Fundao, 21941-590 Rio de Janeiro (Brazil); Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany); Schaefer, Ingo; Seibel, Peter [Department of Molecular Cell Therapy, Leipzig University, Deutscher Platz 5, 04103 Leipzig (Germany); Paeaebo, Svante [Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany)

    2010-11-26

    Research highlights: {yields} Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. {yields} The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. {yields} In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  5. Retrospective Forecast Test for the 1989 Loma Prieta Sequence Based on Physical and Statistical Modeling

    Science.gov (United States)

    Segou, M.; Parsons, T.; Ellsworth, W. L.

    2012-12-01

    We implement a retrospective forecast test specific to the 1989 Loma Prieta sequence and we focus on the comparison between two realizations of the epidemic-type aftershock sequence (ETAS) model and twenty-one models based on Coulomb stress change calculations and rate-and-state theory (CRS). We find that: (1) ETAS models forecast the spatial evolution of seismicity better in the near-source region, (2) CRS models can compete with ETAS models at off-fault regions and short-periods after the mainshock, (3) adopting optimally oriented planes as receivers could lead to better performance for short-time period up to a few days, whereas geologically specified planes should be implemented at long-term forecasting, and (4) CRS models based on shear stress have comparable performance with other CRS models, with the benefit of fewer free parameters involved in the stress calculations. The above results show that physics-based and statistical forecast models are complimentary, and that future forecasts should be combinations of ETAS and CRS models in space and time. We note that the realization in time and space of the CRS models involves a number of critical parameters ('learning' phase seismicity rates, regional stress field, loading rates on faults), which should be retrospectively tested to improve the predictive power of physics-based models.During our experiment the forecast covers Northern California [123.0-121.3°W in longitude 36.4-38.2°N in latitude] in a 2.5 km spatial grid within a 10-day interval following a mainshock, but here we focus on the results related with the post-seismic period of Loma Prieta earthquake. We consider for CRS models a common learning phase (1974-1980) to ensure consistency in our comparison, and we take into consideration stress perturbations imparted by 9 M>5.0 earthquakes between 1980-1989 in Northern California, including the 1988-1989 Lake Ellsman events. ETAS parameters correspond to the maximum likelihood estimations derived after

  6. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

    Directory of Open Access Journals (Sweden)

    Cardle Linda

    2008-12-01

    Full Text Available Abstract Background Microsatellites or single sequence repeats (SSRs are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. Results A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAGn, (AGGn and (AGCn were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae. This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. Conclusion Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as

  7. The sensitivity and specificity of a diagnostic test of sequence-space synesthesia.

    Science.gov (United States)

    Rothen, Nicolas; Jünemann, Kristin; Mealor, Andy D; Burckhardt, Vera; Ward, Jamie

    2016-12-01

    People with sequence-space synesthesia (SSS) report stable visuo-spatial forms corresponding to numbers, days, and months (amongst others). This type of synesthesia has intrigued scientists for over 130 years but the lack of an agreed upon tool for assessing it has held back research on this phenomenon. The present study builds on previous tests by measuring the consistency of spatial locations that is known to discriminate controls from synesthetes. We document, for the first time, the sensitivity and specificity of such a test and suggest a diagnostic cut-off point for discriminating between the groups based on the area bounded by different placement attempts with the same item.

  8. Tests of Sunspot Number Sequences: 2. Using Geomagnetic and Auroral Data

    CERN Document Server

    Lockwood, Mike; Barnard, Luke A; Scott, Chris J; Usoskin, Ilya G; Nevanlinna, Heikki

    2016-01-01

    We compare four sunspot-number data sequences against geomagnetic and terrestrial auroral observations. The comparisons are made for the original SIDC composite of Wolf-Zurich-International sunspot number [$R_{ISNv1}$], the group sunspot number [$R_{G}$] by Hoyt and Schatten (Solar Phys., 1998), the new "backbone" group sunspot number [$R_{BB}$] by Svalgaard and Schatten (Solar Phys., 2016), and the "corrected" sunspot number [$R_{C}$] by Lockwood at al. (J.G.R., 2014). Each sunspot number is fitted with terrestrial observations, or parameters derived from terrestrial observations to be linearly proportional to sunspot number, over a 30-year calibration interval of 1982-2012. The fits are then used to compute test sequences, which extend further back in time and which are compared to $R_{ISNv1}$, $R_{G}$, $R_{BB}$, and $R_{C}$. To study the long-term trends, comparisons are made using averages over whole solar cycles (minimum-to-minimum). The test variations are generated in four ways: i) using the IDV(1d) an...

  9. 454 sequencing put to the test using the complex genome of barley

    Science.gov (United States)

    Wicker, Thomas; Schlagenhauf, Edith; Graner, Andreas; Close, Timothy J; Keller, Beat; Stein, Nils

    2006-01-01

    Background During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising a ~100-fold increase in throughput over Sanger technology – an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley. Results To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences. Conclusion Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence

  10. 454 sequencing put to the test using the complex genome of barley

    Directory of Open Access Journals (Sweden)

    Keller Beat

    2006-10-01

    Full Text Available Abstract Background During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing", promising a ~100-fold increase in throughput over Sanger technology – an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley. Results To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences. Conclusion Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing

  11. Polymorphic DNA sequences and their application in paternity testing; Polimorficzne sekwencje DNA i ich zastosowanie w dochodzeniu spornego ojcostwa

    Energy Technology Data Exchange (ETDEWEB)

    Slomski, R. [Polska Akademia Nauk, Poznan (Poland). Zaklad Genetyki Czlowieka]|[Akademia Rolnicza, Poznan (Poland)]|[Laboratorium Genetyki Molekularnej, Poznan (Poland); Kwiatkowska, J.; Chlebowska, H. [Polska Akademia Nauk, Poznan (Poland). Zaklad Genetyki Czlowieka; Siemieniallo, B. [Akademia Rolnicza, Poznan (Poland); Slomska, M. [Laboratorium Genetyki Molekularnej, Poznan (Poland)

    1994-12-31

    Characteristics of polymorphic sequences of DNA, especially satellite, mini satellite and micro satellite sequences are presented. Own experience from the use of multi and single locus analysis of DNA in paternity testing has been compared with the results of research in other laboratories. Critical points of both types of analysis are discussed. (author). 53 refs, 4 figs, 2 tabs.

  12. Targeted genetic testing for familial hypercholesterolaemia using next generation sequencing: a population-based study.

    Science.gov (United States)

    Norsworthy, Penny J; Vandrovcova, Jana; Thomas, Ellen R A; Campbell, Archie; Kerr, Shona M; Biggs, Jennifer; Game, Laurence; Soutar, Anne K; Smith, Blair H; Dominiczak, Anna F; Porteous, David J; Morris, Andrew D; Scotland, Generation; Aitman, Timothy J

    2014-06-23

    Familial hypercholesterolaemia (FH) is a common Mendelian condition which, untreated, results in premature coronary heart disease. An estimated 88% of FH cases are undiagnosed in the UK. We previously validated a method for FH mutation detection in a lipid clinic population using next generation sequencing (NGS), but this did not address the challenge of identifying index cases in primary care where most undiagnosed patients receive healthcare. Here, we evaluate the targeted use of NGS as a potential route to diagnosis of FH in a primary care population subset selected for hypercholesterolaemia. We used microfluidics-based PCR amplification coupled with NGS and multiplex ligation-dependent probe amplification (MLPA) to detect mutations in LDLR, APOB and PCSK9 in three phenotypic groups within the Generation Scotland: Scottish Family Health Study including 193 individuals with high total cholesterol, 232 with moderately high total cholesterol despite cholesterol-lowering therapy, and 192 normocholesterolaemic controls. Pathogenic mutations were found in 2.1% of hypercholesterolaemic individuals, in 2.2% of subjects on cholesterol-lowering therapy and in 42% of their available first-degree relatives. In addition, variants of uncertain clinical significance (VUCS) were detected in 1.4% of the hypercholesterolaemic and cholesterol-lowering therapy groups. No pathogenic variants or VUCS were detected in controls. We demonstrated that population-based genetic testing using these protocols is able to deliver definitive molecular diagnoses of FH in individuals with high cholesterol or on cholesterol-lowering therapy. The lower cost and labour associated with NGS-based testing may increase the attractiveness of a population-based approach to FH detection compared to genetic testing with conventional sequencing. This could provide one route to increasing the present low percentage of FH cases with a genetic diagnosis.

  13. Transcriptome using Illumina sequencing reveals the traits of spermatogenesis and developing testes in Eriocheir sinensis

    Science.gov (United States)

    Qian, Hui

    2017-01-01

    Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145.19 M clean reads representing with a total of 21.34 Gb bases and 45.48% GC content. 56.30% clean reads were mapped to the draft genome of E. sinensis. The assembly of the transcriptome yielded contigs of 5691802 sequences and unigenes of 406527 sequences. Total 24246 and 40793 transcripts were annotated using Swissprot and Nr database, respectively. There were 48213 (70.31%) and 7858 (46.25%) transcripts with identity of more than 99 matching to mature testis unigenes in the databases of Nr and EST, respectively. The analytic results of KOG, GO and KEGG showed wide potential molecular functions of transcripts in the developing testes. KEGG analysis of unigenes yielded total 9422 predicted genes. Those predicted genes were involved in total 216 KEGG pathways related to the physiological activities of developing testis. 1975 predicted genes were involved in cellular and subcellular structural alteration of male germ cells. There were important roles of some pathways in the processes of morphological and structural biogenesis pertaining to testis development and spermatogenesis. Other 583 unigenes encoding the genetic and epigenetic factors also be found, which might contribute to the decondensation and stability of decondensed nuclei in the spermatozoa. These predicted events provide a view of the potential molecular mechanisms of development of testis and spermatogenesis in E. sinensis. PMID

  14. Next-generation sequencing in post-mortem genetic testing of young sudden cardiac death cases

    Directory of Open Access Journals (Sweden)

    Najim eLahrouchi

    2016-05-01

    Full Text Available Sudden cardiac death (SCD in the young (<40 years occurs in the setting of a variety of rare inherited cardiac disorders and is a disastrous event for family members. Establishing the cause of SCD is important as it permits the pre-symptomatic identification of relatives at risk of SCD. Sudden arrhythmic death syndrome (SADS is defined as SCD in the setting of negative autopsy findings and toxicological analysis. In such cases reaching a diagnosis is even more challenging and post mortem genetic testing can crucially contribute to the identification of the underlying cause of death. In this review, we will discuss the current achievements of ‘the molecular autopsy’ in young SADS cases and provide an overview of key challenges in assessing pathogenicity (i.e. causality of genetic variants identified through next-generation sequencing.

  15. A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders

    Science.gov (United States)

    Simeoni, Ilenia; Stephens, Jonathan C.; Hu, Fengyuan; Deevi, Sri V. V.; Megy, Karyn; Bariana, Tadbir K.; Lentaigne, Claire; Schulman, Sol; Sivapalaratnam, Suthesh; Vries, Minka J. A.; Westbury, Sarah K.; Greene, Daniel; Papadia, Sofia; Alessi, Marie-Christine; Attwood, Antony P.; Ballmaier, Matthias; Baynam, Gareth; Bermejo, Emilse; Bertoli, Marta; Bray, Paul F.; Bury, Loredana; Cattaneo, Marco; Collins, Peter; Daugherty, Louise C.; Favier, Rémi; French, Deborah L.; Furie, Bruce; Gattens, Michael; Germeshausen, Manuela; Ghevaert, Cedric; Goodeve, Anne C.; Guerrero, Jose A.; Hampshire, Daniel J.; Hart, Daniel P.; Heemskerk, Johan W. M.; Henskens, Yvonne M. C.; Hill, Marian; Hogg, Nancy; Jolley, Jennifer D.; Kahr, Walter H.; Kelly, Anne M.; Kerr, Ron; Kostadima, Myrto; Kunishima, Shinji; Lambert, Michele P.; Liesner, Ri; López, José A.; Mapeta, Rutendo P.; Mathias, Mary; Millar, Carolyn M.; Nathwani, Amit; Neerman-Arbez, Marguerite; Nurden, Alan T.; Nurden, Paquita; Othman, Maha; Peerlinck, Kathelijne; Perry, David J.; Poudel, Pawan; Reitsma, Pieter; Rondina, Matthew T.; Smethurst, Peter A.; Stevenson, William; Szkotak, Artur; Tuna, Salih; van Geet, Christel; Whitehorn, Deborah; Wilcox, David A.; Zhang, Bin; Revel-Vilk, Shoshana; Gresele, Paolo; Bellissimo, Daniel B.; Penkett, Christopher J.; Laffan, Michael A.; Mumford, Andrew D.; Rendon, Augusto; Freson, Kathleen; Ouwehand, Willem H.; Turro, Ernest

    2016-01-01

    Inherited bleeding, thrombotic, and platelet disorders (BPDs) are diseases that affect ∼300 individuals per million births. With the exception of hemophilia and von Willebrand disease patients, a molecular analysis for patients with a BPD is often unavailable. Many specialized tests are usually required to reach a putative diagnosis and they are typically performed in a step-wise manner to control costs. This approach causes delays and a conclusive molecular diagnosis is often never reached, which can compromise treatment and impede rapid identification of affected relatives. To address this unmet diagnostic need, we designed a high-throughput sequencing platform targeting 63 genes relevant for BPDs. The platform can call single nucleotide variants, short insertions/deletions, and large copy number variants (though not inversions) which are subjected to automated filtering for diagnostic prioritization, resulting in an average of 5.34 candidate variants per individual. We sequenced 159 and 137 samples, respectively, from cases with and without previously known causal variants. Among the latter group, 61 cases had clinical and laboratory phenotypes indicative of a particular molecular etiology, whereas the remainder had an a priori highly uncertain etiology. All previously detected variants were recapitulated and, when the etiology was suspected but unknown or uncertain, a molecular diagnosis was reached in 56 of 61 and only 8 of 76 cases, respectively. The latter category highlights the need for further research into novel causes of BPDs. The ThromboGenomics platform thus provides an affordable DNA-based test to diagnose patients suspected of having a known inherited BPD. PMID:27084890

  16. A SNP panel for identity and kinship testing using massive parallel sequencing.

    Science.gov (United States)

    Grandell, Ida; Samara, Raed; Tillmar, Andreas O

    2016-07-01

    Within forensic genetics, there is still a need for supplementary DNA marker typing in order to increase the power to solve cases for both identity testing and complex kinship issues. One major disadvantage with current capillary electrophoresis (CE) methods is the limitation in DNA marker multiplex capability. By utilizing massive parallel sequencing (MPS) technology, this capability can, however, be increased. We have designed a customized GeneRead DNASeq SNP panel (Qiagen) of 140 previously published autosomal forensically relevant identity SNPs for analysis using MPS. One single amplification step was followed by library preparation using the GeneRead Library Prep workflow (Qiagen). The sequencing was performed on a MiSeq System (Illumina), and the bioinformatic analyses were done using the software Biomedical Genomics Workbench (CLC Bio, Qiagen). Forty-nine individuals from a Swedish population were genotyped in order to establish genotype frequencies and to evaluate the performance of the assay. The analyses showed to have a balanced coverage among the included loci, and the heterozygous balance showed to have less than 0.5 % outliers. Analyses of dilution series of the 2800M Control DNA gave reproducible results down to 0.2 ng DNA input. In addition, typing of FTA samples and bone samples was performed with promising results. Further studies and optimizations are, however, required for a more detailed evaluation of the performance of degraded and PCR-inhibited forensic samples. In summary, the assay offers a straightforward sample-to-genotype workflow and could be useful to gain information in forensic casework, for both identity testing and in order to solve complex kinship issues.

  17. Non-invasive prenatal testing using massively parallel sequencing of maternal plasma DNA: from molecular karyotyping to fetal whole-genome sequencing.

    Science.gov (United States)

    Lo, Y M Dennis

    2013-12-01

    The discovery of cell-free fetal DNA in maternal plasma in 1997 has stimulated a rapid development of non-invasive prenatal testing. The recent advent of massively parallel sequencing has allowed the analysis of circulating cell-free fetal DNA to be performed with unprecedented sensitivity and precision. Fetal trisomies 21, 18 and 13 are now robustly detectable in maternal plasma and such analyses have been available clinically since 2011. Fetal genome-wide molecular karyotyping and whole-genome sequencing have now been demonstrated in a number of proof-of-concept studies. Genome-wide and targeted sequencing of maternal plasma has been shown to allow the non-invasive prenatal testing of β-thalassaemia and can potentially be generalized to other monogenic diseases. It is thus expected that plasma DNA-based non-invasive prenatal testing will play an increasingly important role in future obstetric care. It is thus timely and important that the ethical, social and legal issues of non-invasive prenatal testing be discussed actively by all parties involved in prenatal care.

  18. Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing: Enhanced data acquisition for DNA samples encountered in forensic testing.

    Science.gov (United States)

    Davis, Carey; Peters, Dixie; Warshauer, David; King, Jonathan; Budowle, Bruce

    2015-03-01

    Mitochondrial DNA testing is a useful tool in the analysis of forensic biological evidence. In cases where nuclear DNA is damaged or limited in quantity, the higher copy number of mitochondrial genomes available in a sample can provide information about the source of a sample. Currently, Sanger-type sequencing (STS) is the primary method to develop mitochondrial DNA profiles. This method is laborious and time consuming. Massively parallel sequencing (MPS) can increase the amount of information obtained from mitochondrial DNA samples while improving turnaround time by decreasing the numbers of manipulations and more so by exploiting high throughput analyses to obtain interpretable results. In this study 18 buccal swabs, three different tissue samples from five individuals, and four bones samples from casework were sequenced at hypervariable regions I and II using STS and MPS. Sample enrichment for STS and MPS was PCR-based. Library preparation for MPS was performed using Nextera® XT DNA Sample Preparation Kit and sequencing was performed on the MiSeq™ (Illumina, Inc.). MPS yielded full concordance of base calls with STS results, and the newer methodology was able to resolve length heteroplasmy in homopolymeric regions. This study demonstrates short amplicon MPS of mitochondrial DNA is feasible, can provide information not possible with STS, and lays the groundwork for development of a whole genome sequencing strategy for degraded samples.

  19. [Lung cancer molecular testing, what role for Next Generation Sequencing and circulating tumor DNA].

    Science.gov (United States)

    Pécuchet, Nicolas; Legras, Antoine; Laurent-Puig, Pierre; Blons, Hélène

    2016-01-01

    Molecular screening has become a standard of care for patients with advanced cancers and impacts on how to treat a patient. Advances in genomic technologies with the development of high throughput sequencing methods will certainly improve the possibilities to access a more accurate molecular diagnosis and to go beyond the identification of validated targets as a large number of genes can be screened for actionable changes. Moreover, accurate high throughput testing may help tumor classification in terms of prognosis and drug sensitivity. Finally, it will be possible to assess tumor heterogeneity and changes in molecular profiles during follow-up using ultra-deep sequencing technologies and circulating tumor DNA characterization. The accumulation of somatic ADN alterations is considered as the main contributing factor in carcinogenesis. The alterations can occur at different levels: mutation, copy number variations or gene translocations resulting in altered expression of the corresponding genes or impaired protein functions. Genes involved are mainly tumor suppressors, oncogenes or ADN repair genes whose modifications in tumors will impinge cell fate and proliferation from tumor initiation to metastasis. The entire genome of various tumor types, have now been sequenced. In lung cancer, the average number of mutations is very high with more than 8.9 mutations/Mb (Network TCGAR, 2014) that is to say more than 10,000 mutations/genome. These alterations need to be classified, indeed, some are true drivers that directly impact proliferation and some are passenger mutations linked to genetic instability. The development of targeted therapies relies on the identification of oncogenic drivers. The identification of genotype-phenotype associations as in the case of EGFR-TKI (Epidermal growth factor receptor-tyrosine kinase inhibitor) and EGFR mutations in lung cancer led to the restriction of drugs to patients for which tumor genotype predicts efficacy. Tumor

  20. Performance assessment of the GenoType MTBDRplus test and DNA sequencing in detection of multidrug-resistant Mycobacterium tuberculosis.

    Science.gov (United States)

    Huang, Wei-Lun; Chen, Huang-Yau; Kuo, Yuh-Min; Jou, Ruwen

    2009-08-01

    To facilitate the management of multidrug-resistant (MDR) tuberculosis, two nucleic acid sequence-based methods, the GenoType MTBDRplus test and DNA sequencing, were assessed for the rapid detection of drug-resistant Mycobacterium tuberculosis for the first time in the Asia-Pacific region. The performances of these two assays in detecting the presence of rifampin (rifampicin) (RIF) and isoniazid (INH) resistance-associated mutations in the rpoB, katG, inhA regulatory region, inhA, and oxyR-ahpC genes were compared to that of a conventional agar proportion drug susceptibility test. A total of 242 MDR and 30 pansusceptible M. tuberculosis isolates were evaluated in this study. The sensitivities obtained for RIF-resistant detection by the GenoType MTBDRplus test and by resistance gene sequencing were 95.5% and 97.9%, respectively. The sensitivities for INH resistance detection by the GenoType MTBDRplus test and by resistance gene sequencing were 81.8% and 93.4%, respectively. Together, the sensitivity for MDR tuberculosis detection was 78.5% with the GenoType MTBDRplus test and 91.3% by resistance gene sequencing. The specificity for RIF resistance, INH resistance, and MDR detection was 100% by both methods. The GenoType MTBDRplus test has the advantage of a short turnaround time for drug-resistant M. tuberculosis detection. Overall, the two assays performed equally well in detecting RIF resistance (P = 0.13). However, DNA sequencing demonstrated superior performance in detecting INH resistance (P tuberculosis (P GenoType MTBDRplus test, especially for different geographic areas with genetically diverse M. tuberculosis strains.

  1. Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data.

    Directory of Open Access Journals (Sweden)

    Gu Mi

    Full Text Available This work is about assessing model adequacy for negative binomial (NB regression, particularly (1 assessing the adequacy of the NB assumption, and (2 assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for RNA sequencing (RNA-Seq data analysis. The typically small number of biological samples and large number of genes in RNA-Seq analysis motivate us to address the trade-offs between robustness and statistical power using NB regression models. One widely-used power-saving strategy, for example, is to assume some commonalities of NB dispersion parameters across genes via simple models relating them to mean expression rates, and many such models have been proposed. As RNA-Seq analysis is becoming ever more popular, it is appropriate to make more thorough investigations into power and robustness of the resulting methods, and into practical tools for model assessment. In this article, we propose simulation-based statistical tests and diagnostic graphics to address model adequacy. We provide simulated and real data examples to illustrate that our proposed methods are effective for detecting the misspecification of the NB mean-variance relationship as well as judging the adequacy of fit of several NB dispersion models.

  2. Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data.

    Science.gov (United States)

    Mi, Gu; Di, Yanming; Schafer, Daniel W

    2015-01-01

    This work is about assessing model adequacy for negative binomial (NB) regression, particularly (1) assessing the adequacy of the NB assumption, and (2) assessing the appropriateness of models for NB dispersion parameters. Tools for the first are appropriate for NB regression generally; those for the second are primarily intended for RNA sequencing (RNA-Seq) data analysis. The typically small number of biological samples and large number of genes in RNA-Seq analysis motivate us to address the trade-offs between robustness and statistical power using NB regression models. One widely-used power-saving strategy, for example, is to assume some commonalities of NB dispersion parameters across genes via simple models relating them to mean expression rates, and many such models have been proposed. As RNA-Seq analysis is becoming ever more popular, it is appropriate to make more thorough investigations into power and robustness of the resulting methods, and into practical tools for model assessment. In this article, we propose simulation-based statistical tests and diagnostic graphics to address model adequacy. We provide simulated and real data examples to illustrate that our proposed methods are effective for detecting the misspecification of the NB mean-variance relationship as well as judging the adequacy of fit of several NB dispersion models.

  3. Beyond BRAFV600: clinical mutation panel testing by next-generation sequencing in advanced melanoma

    Science.gov (United States)

    Siroy, Alan E.; Boland, Genevieve M.; Milton, Denái R.; Roszik, Jason; Frankian, Silva; Malke, Jared; Haydu, Lauren; Prieto, Victor G.; Tetzlaff, Michael; Ivan, Doina; Wang, Wei-Lien; Torres-Cabala, Carlos; Curry, Jonathan; Roy-Chowdhuri, Sinchita; Broaddus, Russell; Rashid, Asif; Stewart, John; Gershenwald, Jeffrey E.; Amaria, Rodabe N.; Patel, Sapna P.; Papadopoulos, Nicholas E.; Bedikian, Agop; Hwu, Wen-Jen; Hwu, Patrick; Diab, Adi; Woodman, Scott E.; Aldape, Kenneth D.; Luthra, Rajyalakshmi; Patel, Keyur P.; Shaw, Kenna R.; Mills, Gordon B.; Mendelsohn, John; Meric-Bernstam, Funda; Kim, Kevin B.; Routbort, Mark J.; Lazar, Alexander J.; Davies, Michael A.

    2014-01-01

    The management of melanoma has evolved due to improved understanding of its molecular drivers. To augment the current understanding of the prevalence, patterns, and associations of mutations in this disease, the results of clinical testing of 699 advanced melanoma patients using a pan-cancer next generation sequencing (NGS) panel of hotspot regions in 46 genes were reviewed. Mutations were identified in 43 of the 46 genes on the panel. The most common mutations were BRAFV600 (36%), NRAS (21%), TP53 (16%), BRAFNon-V600 (6%), and KIT (4%). Approximately one-third of melanomas had >1 mutation detected, and the number of mutations per tumor was associated with melanoma subtype. Concurrent TP53 mutations were the most frequent event in tumors with BRAFV600 and NRAS mutations. Melanomas with BRAFNon-V600 mutations frequently harbored concurrent NRAS mutations (18%), which were rare in tumors with BRAFV600 mutations (1.6%). The prevalence of BRAFV600 and KIT mutations were significantly associated with melanoma subtypes, and BRAFV600 and TP53 mutations were significantly associated with cutaneous primary tumor location. Multiple potential therapeutic targets were identified in metastatic unknown primary and cutaneous melanomas that lacked BRAFV600 and NRAS mutations. These results enrich our understanding of the patterns and clinical associations of oncogenic mutations in melanoma. PMID:25148578

  4. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

    DEFF Research Database (Denmark)

    Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer;

    2013-01-01

    genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types. Results: A total of 3051 different phenotypic tests were performed; 482 led......-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures. Methods: Antimicrobial susceptibility tests were performed...... on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to identify acquired antimicrobial resistance...

  5. Effect of load ratio, testing frequency, temperature, moisture, notch and stacking sequence on the fatigue resistance of woven CFRP laminates

    OpenAIRE

    Lani, Frédéric; 6th International Conference on Fatigue of Composite ICFC2015

    2015-01-01

    A woven CFRP composite laminate has been thoroughly characterized under fatigue. Over 150 tests were performed in order to address the effect of sample geometry (Open Hole Tension, Open Hole Compression, Plain Compression, …), testing frequency (5Hz, 30Hz) with and without cooling system, load ratio (R=10., R=-1., R=0.1), temperature (RT and 120°C), moisture intake (50% RH and 85+% RH at RT), notch (Open Hole Vs. Plain Specimen), stacking sequence (3 different stacking sequences) on the measu...

  6. Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

    Science.gov (United States)

    Jonker, Tanya R.; MacLeod, Colin M.

    2017-01-01

    Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

  7. Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

    Science.gov (United States)

    Jonker, Tanya R.; MacLeod, Colin M.

    2017-01-01

    Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

  8. A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients.

    Directory of Open Access Journals (Sweden)

    Ron M Kagan

    Full Text Available A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4 coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5 or X4 variants that utilizes triplicate population sequencing (TPS followed by ultradeep sequencing (UDS for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno([coreceptor] and PSSM(x4r5. Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327 in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log(10 viral load change at week 8 was -2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were -1.2 for TF-ES or the Reflex Test and -1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001. At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.

  9. Some new methods for testing randomness of a binomial sequence and its applications in two sample problems

    Directory of Open Access Journals (Sweden)

    P.V. Krishna Iyer

    1957-01-01

    Full Text Available The t-test commonly used for testing two samples is based on the assumption that the sample are random and belong to the same normal population. These assumptions may or may not be valid for different types of experimental data. In cases where these assumptions do not hold good, it would be preferable to use tests which are independent of the nature of the distribution of the parent population. A number of such tests, some developed in the Defence Science Laboratory, is given in this paper. The test depend on a sequence of A's and B's obtained by pooling together the two samples {Xm}and {Yn} and arranging them in ascending or descending order and treating the observations belonging to {xm} and {yn} as A's and B's respectively. For this sequence the number of AB's or AB's and BA's are noted for the following cases: (1 Between any two observations of the sequence separated by (k-1 observations or less; (2 Between any two observations in blocks of (k+1 consecutive observations moving from one end to the other end. It has been found that the standardized deviates of these statics serve as more reliable tests than any of other existing tests. Further work is in progress to confirm these findings.

  10. Testing scaling relations for solar-like oscillations from the main sequence to red giants using Kepler data

    NARCIS (Netherlands)

    Huber, D.; Bedding, T.R.; Stello, D.; Hekker, S.; Mathur, S.; Mosser, B.; Verner, G.A.; Bonanno, A.; Buzasi, D.L.; Campante, T.L.; Elsworth, Y.P.; Hale, S.J.; Kallinger, T.; Silva Aguirre, V.; Chaplin, W.J.; de Ridder, J.; Garcia, R.A.; Appourchaux, T.; Frandsen, S.; Houdek, G.; Molenda-Żakowicz, J.; Monteiro, M.J.P.F.G.; Christensen-Dalsgaard, J.; Gilliland, R.L.; Kawaler, S.D.; Kjeldsen, H.; Broomhall, A.M.; Corsaro, E.; Salabert, D.; Sanderfer, D.T.; Seader, S.E.; Smith, J.C.

    2011-01-01

    We have analyzed solar-like oscillations in ~1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power (νmax), the large frequency separation (Δν), and oscillation

  11. mapDamage: testing for damage patterns in ancient DNA sequences.

    Science.gov (United States)

    Ginolhac, Aurelien; Rasmussen, Morten; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2011-08-01

    Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences. The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems.

  12. Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer

    Science.gov (United States)

    Feliubadaló, Lídia; Tonda, Raúl; Gausachs, Mireia; Trotta, Jean-Rémi; Castellanos, Elisabeth; López-Doriga, Adriana; Teulé, Àlex; Tornero, Eva; del Valle, Jesús; Gel, Bernat; Gut, Marta; Pineda, Marta; González, Sara; Menéndez, Mireia; Navarro, Matilde; Capellá, Gabriel; Gut, Ivo; Serra, Eduard; Brunet, Joan; Beltran, Sergi; Lázaro, Conxi

    2017-01-01

    Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes. PMID:28050010

  13. HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing.

    Science.gov (United States)

    Chimukangara, Benjamin; Varyani, Bhavini; Shamu, Tinei; Mutsvangwa, Junior; Manasa, Justen; White, Elizabeth; Chimbetete, Cleophas; Luethy, Ruedi; Katzenstein, David

    2017-05-01

    HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls.

    Directory of Open Access Journals (Sweden)

    Yi-Juan Hu

    2016-05-01

    Full Text Available Next-generation sequencing of DNA provides an unprecedented opportunity to discover rare genetic variants associated with complex diseases and traits. However, the common practice of first calling underlying genotypes and then treating the called values as known is prone to false positive findings, especially when genotyping errors are systematically different between cases and controls. This happens whenever cases and controls are sequenced at different depths, on different platforms, or in different batches. In this article, we provide a likelihood-based approach to testing rare variant associations that directly models sequencing reads without calling genotypes. We consider the (weighted burden test statistic, which is the (weighted sum of the score statistic for assessing effects of individual variants on the trait of interest. Because variant locations are unknown, we develop a simple, computationally efficient screening algorithm to estimate the loci that are variants. Because our burden statistic may not have mean zero after screening, we develop a novel bootstrap procedure for assessing the significance of the burden statistic. We demonstrate through extensive simulation studies that the proposed tests are robust to a wide range of differential sequencing qualities between cases and controls, and are at least as powerful as the standard genotype calling approach when the latter controls type I error. An application to the UK10K data reveals novel rare variants in gene BTBD18 associated with childhood onset obesity. The relevant software is freely available.

  15. Testing statistical significance scores of sequence comparison methods with structure similarity

    NARCIS (Netherlands)

    Hulsen, T.; Vlieg, J. de; Leunissen, J.A.M.; Groenen, P.M.

    2006-01-01

    BACKGROUND: In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical s

  16. Testing statistical significance scores of sequence comparison methods with structure similarity

    NARCIS (Netherlands)

    Hulsen, T.; Vlieg, de J.; Leunissen, J.A.M.; Groenen, P.

    2006-01-01

    Background - In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical

  17. Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions

    Directory of Open Access Journals (Sweden)

    Ivone U. S. Leong

    2014-06-01

    Full Text Available Sudden cardiac death in people between the ages of 1–40 years is a devastating event and is frequently caused by several heritable cardiac disorders. These disorders include cardiac ion channelopathies, such as long QT syndrome, catecholaminergic polymorphic ventricular tachycardia and Brugada syndrome and cardiomyopathies, such as hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy. Through careful molecular genetic evaluation of DNA from sudden death victims, the causative gene mutation can be uncovered, and the rest of the family can be screened and preventative measures implemented in at-risk individuals. The current screening approach in most diagnostic laboratories uses Sanger-based sequencing; however, this method is time consuming and labour intensive. The development of massively parallel sequencing has made it possible to produce millions of sequence reads simultaneously and is potentially an ideal approach to screen for mutations in genes that are associated with sudden cardiac death. This approach offers mutation screening at reduced cost and turnaround time. Here, we will review the current commercially available enrichment kits, massively parallel sequencing (MPS platforms, downstream data analysis and its application to sudden cardiac death in a diagnostic environment.

  18. Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test.

    Science.gov (United States)

    Shum, Bennett O V; Henner, Ilya; Belluoccio, Daniele; Hinchcliffe, Marcus J

    2017-07-01

    The sensitivity and specificity of next-generation sequencing laboratory developed tests (LDTs) are typically determined by an analyte-specific approach. Analyte-specific validations use disease-specific controls to assess an LDT's ability to detect known pathogenic variants. Alternatively, a methods-based approach can be used for LDT technical validations. Methods-focused validations do not use disease-specific controls but use benchmark reference DNA that contains known variants (benign, variants of unknown significance, and pathogenic) to assess variant calling accuracy of a next-generation sequencing workflow. Recently, four whole-genome reference materials (RMs) from the National Institute of Standards and Technology (NIST) were released to standardize methods-based validations of next-generation sequencing panels across laboratories. We provide a practical method for using NIST RMs to validate multigene panels. We analyzed the utility of RMs in validating a novel newborn screening test that targets 70 genes, called NEO1. Despite the NIST RM variant truth set originating from multiple sequencing platforms, replicates, and library types, we discovered a 5.2% false-negative variant detection rate in the RM truth set genes that were assessed in our validation. We developed a strategy using complementary non-RM controls to demonstrate 99.6% sensitivity of the NEO1 test in detecting variants. Our findings have implications for laboratories or proficiency testing organizations using whole-genome NIST RMs for testing. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  19. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

    Science.gov (United States)

    Hu, Hao; Roach, Jared C; Coon, Hilary; Guthery, Stephen L; Voelkerding, Karl V; Margraf, Rebecca L; Durtschi, Jacob D; Tavtigian, Sean V; Shankaracharya; Wu, Wilfred; Scheet, Paul; Wang, Shuoguo; Xing, Jinchuan; Glusman, Gustavo; Hubley, Robert; Li, Hong; Garg, Vidu; Moore, Barry; Hood, Leroy; Galas, David J; Srivastava, Deepak; Reese, Martin G; Jorde, Lynn B; Yandell, Mark; Huff, Chad D

    2014-07-01

    High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.

  20. Sequence-dependent stability test of a left-handed β-helix motif.

    Science.gov (United States)

    Hayre, Natha R; Singh, Rajiv R P; Cox, Daniel L

    2012-03-21

    The left-handed β-helix (LHBH) is an intriguing, rare structural pattern in polypeptides that has been implicated in the formation of amyloid aggregates. We used accurate all-atom replica-exchange molecular dynamics (REMD) simulations to study the relative stability of diverse sequences in the LHBH conformation. Ensemble-average coordinates from REMD served as a scoring criterion to identify sequences and threadings optimally suited to the LHBH, as in a fold recognition paradigm. We examined the repeatability of our REMD simulations, finding that single simulations can be reliable to a quantifiable extent. We find expected behavior for the positive and negative control cases of a native LHBH and intrinsically disordered sequences, respectively. Polyglutamine and a designed hexapeptide repeat show remarkable affinity for the LHBH motif. A structural model for misfolded murine prion protein was also considered, and showed intermediate stability under the given conditions. Our technique is found to be an effective probe of LHBH stability, and promises to be scalable to broader studies of this and potentially other novel or rare motifs. The superstable character of the designed hexapeptide repeat suggests theoretical and experimental follow-ups.

  1. Development and Psychometric Properties of the Taiwan Odd-Even Number Sequencing Test: A Nonalphabetic Measure of Working Memory.

    Science.gov (United States)

    Chen, Yen-Ting; Peng, Chung-Yu; Hua, Mau-Sun; Liu, Chen-Chung; Chen, Hsin-Yi; Hwu, Hai-Gwo

    2016-05-09

    Alphabetic working memory (WM) tests, such as the Wechsler Adult Intelligence Scale-III and IV Letter Number Sequencing, are not appropriate for nonalphabetic cultures. This study examined the psychometric properties of the Taiwan Odd-Even Number Sequencing Test (TOENST) and identified representative norms. The TOENST and other mental screening tasks were administered to 300 randomly selected healthy participants, 32 purposive sampling patients with schizophrenia, and 32 quota sampling controls. To investigate reliability and validity, a subset of the 300 healthy participants was randomly selected to receive a second TOENST (n = 30) or conventional WM tests (n = 42). The split-half reliability of the TOENST ranged from 0.69 to 0.95, and its test-retest reliability was 0.75. Criterion validity was demonstrated by significant correlations with conventional WM measures (all p < .05, except semantic verbal fluency), and construct validity was demonstrated by significant correlations with aging (main effect, F10,259 = 10.99, p < .001). Normative data were established, and performance was significantly associated with age and education. TOENST scores of patients with schizophrenia were significantly lower and correlated with frontal lobe tests, but not demographical or clinical characteristics. The TOENST has adequate psychometric properties and clinical utility and is as a viable alternative WM task for nonalphabetic cultures.

  2. Association testing for next-generation sequencing data using score statistics

    DEFF Research Database (Denmark)

    Skotte, Line; Korneliussen, Thorfinn Sand; Albrechtsen, Anders

    2012-01-01

    of genotype calls into account have been proposed; most require numerical optimization which for large-scale data is not always computationally feasible. We show that using a score statistic for the joint likelihood of observed phenotypes and observed sequencing data provides an attractive approach...... computationally feasible due to the use of score statistics. As part of the joint likelihood, we model the distribution of the phenotypes using a generalized linear model framework, which works for both quantitative and discrete phenotypes. Thus, the method presented here is applicable to case-control studies...

  3. Accelerating Gene Discovery by Phenotyping Whole-Genome Sequenced Multi-mutation Strains and Using the Sequence Kernel Association Test (SKAT.

    Directory of Open Access Journals (Sweden)

    Tiffany A Timbers

    2016-08-01

    Full Text Available Forward genetic screens represent powerful, unbiased approaches to uncover novel components in any biological process. Such screens suffer from a major bottleneck, however, namely the cloning of corresponding genes causing the phenotypic variation. Reverse genetic screens have been employed as a way to circumvent this issue, but can often be limited in scope. Here we demonstrate an innovative approach to gene discovery. Using C. elegans as a model system, we used a whole-genome sequenced multi-mutation library, from the Million Mutation Project, together with the Sequence Kernel Association Test (SKAT, to rapidly screen for and identify genes associated with a phenotype of interest, namely defects in dye-filling of ciliated sensory neurons. Such anomalies in dye-filling are often associated with the disruption of cilia, organelles which in humans are implicated in sensory physiology (including vision, smell and hearing, development and disease. Beyond identifying several well characterised dye-filling genes, our approach uncovered three genes not previously linked to ciliated sensory neuron development or function. From these putative novel dye-filling genes, we confirmed the involvement of BGNT-1.1 in ciliated sensory neuron function and morphogenesis. BGNT-1.1 functions at the trans-Golgi network of sheath cells (glia to influence dye-filling and cilium length, in a cell non-autonomous manner. Notably, BGNT-1.1 is the orthologue of human B3GNT1/B4GAT1, a glycosyltransferase associated with Walker-Warburg syndrome (WWS. WWS is a multigenic disorder characterised by muscular dystrophy as well as brain and eye anomalies. Together, our work unveils an effective and innovative approach to gene discovery, and provides the first evidence that B3GNT1-associated Walker-Warburg syndrome may be considered a ciliopathy.

  4. Omnibus test for change detection in a time sequence of polarimetric SAR data

    DEFF Research Database (Denmark)

    Nielsen, Allan Aasbjerg; Conradsen, Knut; Skriver, Henning

    2016-01-01

    Based on an omnibus likelihood ratio test statistic for the equality of several variance-covariance matrices following the complex Wishart distribution with an associated p-value and a factorization of this test statistic, change analysis in a (short) time series of multilook, polarimetric SAR data...

  5. Genetic evaluation and testing for hereditary forms of cancer in the era of next-generation sequencing

    Institute of Scientific and Technical Information of China (English)

    Christine Stanislaw; Yuan Xue; William R Wilcox

    2016-01-01

    The introduction of next-generation sequencing (NGS) technology in testing for hereditary cancer susceptibility allows testing of multiple cancer susceptibility genes simultaneously. While there are many potential benefits to utilizing this technology in the hereditary cancer clinic, including efficiency of time and cost, there are also important limitations that must be considered. The best panel for the given clinical situation should be selected to minimize the number of variants of unknown significance. The inclusion in panels of low penetrance or newly identified genes without specific actionability can be problematic for interpretation. Genetic counselors are an essential part of the hereditary cancer risk assessment team, helping the medical team select the most appropriate test and interpret the often complex results. Genetic counselors obtain an extended family history, counsel patients on the available tests and the potential implications of results for themselves and their family members (pre-test counseling), explain to patients the implications of the test results (post-test counseling), and assist in testing family members at risk.

  6. Spanish Multicenter Normative Studies (NEURONORMA Project): norms for verbal span, visuospatial span, letter and number sequencing, trail making test, and symbol digit modalities test.

    Science.gov (United States)

    Peña-Casanova, Jordi; Quiñones-Ubeda, Sonia; Quintana-Aparicio, María; Aguilar, Miquel; Badenes, Dolors; Molinuevo, José Luis; Torner, Laura; Robles, Alfredo; Barquero, María Sagrario; Villanueva, Clara; Antúnez, Carmen; Martínez-Parra, Carlos; Frank-García, Anna; Sanz, Azucena; Fernández, Manuel; Alfonso, Verónica; Sol, Josep M; Blesa, Rafael

    2009-06-01

    As part of the Spanish Multicenter Normative Studies (NEURONORMA project), we provide age- and education-adjusted norms for the following instruments: verbal span (digits), visuospatial span (Corsi's test), letter-number sequencing (WAIS-III), trail making test, and symbol digit modalities test. The sample consists of 354 participants who are cognitively normal, community-dwelling, and age ranging from 50 to 90 years. Tables are provided to convert raw scores to age-adjusted scaled scores. These were further converted into education-adjusted scaled scores by applying regression-based adjustments. The current norms should provide clinically useful data for evaluating elderly Spanish people. These data may be of considerable use for comparisons with other normative studies. Limitations of these normative data are mainly related to the techniques of recruitment and stratification employed.

  7. Beyond the Main Sequence: Testing the accuracy of stellar masses predicted by the PARSEC evolutionary tracks

    CERN Document Server

    Ghezzi, Luan

    2015-01-01

    Characterizing the physical properties of exoplanets, and understanding their formation and orbital evolution requires precise and accurate knowledge of the physical properties of their host stars. Accurately measuring stellar mass is particularly important because the masses of host stars likely influence planet occurrence and the architectures of planetary systems observed today. Single main-sequence stars typically have masses estimated from evolutionary tracks, which generally provide accurate results due to their extensive empirical calibration. However, the validity of this method for subgiants and giants has been called into question, with suggestions that the evolutionary models could contain systematic errors that would cause mass estimates of these evolved stars to be overestimated. We investigate these concerns using a sample of 59 benchmark evolved stars with model-independent masses (from binary systems or asteroseismology) obtained from the extant literature. We find very good agreement between ...

  8. BEYOND THE MAIN SEQUENCE: TESTING THE ACCURACY OF STELLAR MASSES PREDICTED BY THE PARSEC EVOLUTIONARY TRACKS

    Energy Technology Data Exchange (ETDEWEB)

    Ghezzi, Luan; Johnson, John Asher, E-mail: lghezzi@cfa.harvard.edu [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2015-10-20

    Characterizing the physical properties of exoplanets and understanding their formation and orbital evolution requires precise and accurate knowledge of their host stars. Accurately measuring stellar masses is particularly important because they likely influence planet occurrence and the architectures of planetary systems. Single main-sequence stars typically have masses estimated from evolutionary tracks, which generally provide accurate results due to their extensive empirical calibration. However, the validity of this method for subgiants and giants has been called into question by recent studies, with suggestions that the masses of these evolved stars could have been overestimated. We investigate these concerns using a sample of 59 benchmark evolved stars with model-independent masses (from binary systems or asteroseismology) obtained from the literature. We find very good agreement between these benchmark masses and the ones estimated using evolutionary tracks. The average fractional difference in the mass interval ∼0.7–4.5 M{sub ⊙} is consistent with zero (−1.30 ± 2.42%), with no significant trends in the residuals relative to the input parameters. A good agreement between model-dependent and -independent radii (−4.81 ± 1.32%) and surface gravities (0.71 ± 0.51%) is also found. The consistency between independently determined ages for members of binary systems adds further support for the accuracy of the method employed to derive the stellar masses. Taken together, our results indicate that determination of masses of evolved stars using grids of evolutionary tracks is not significantly affected by systematic errors, and is thus valid for estimating the masses of isolated stars beyond the main sequence.

  9. Final Scientific/Technical Report to the U.S. Department of Energy on NOVA's Einstein's Big Idea (Project title: E-mc2, A Two-Hour Television Program on NOVA)

    Energy Technology Data Exchange (ETDEWEB)

    Susanne Simpson

    2007-05-07

    Executive Summary A woman in the early 1700s who became one of Europe’s leading interpreters of mathematics and a poor bookbinder who became one of the giants of nineteenth-century science are just two of the pioneers whose stories NOVA explored in Einstein’s Big Idea. This two-hour documentary premiered on PBS in October 2005 and is based on the best-selling book by David Bodanis, E=mc2: A Biography of the World’s Most Famous Equation. The film and book chronicle the scientific challenges and discoveries leading up to Einstein’s startling conclusion that mass and energy are one, related by the formula E = mc2.

  10. The Click Test: A Novel Tool to Quantify the Age-Related Decline of Fast Motor Sequencing of the Thumb.

    Science.gov (United States)

    Bodranghien, Florian; Mahé, Helene; Baude, Benjamin; Manto, Mario U; Busegnies, Yves; Camut, Stéphane; Habas, Christophe; Marien, Peter; de Marco, Giovanni; van Dun, Kim

    2017-05-10

    The thumb plays a critical role for manual tasks during the activities of daily life and the incidence of neurological or musculoskeletal disorders affecting the voluntary movements of the thumb is high in the elderly. There is currently no tool to assess repetitive motor sequencing of the thumb during ageing. To report a novel procedure (the Click Test) assessing the effects of ageing on fast motor sequencing of the thumb. Healthy subjects (n = 252; mean age +/- SD: 49.76 +/- 19.97 years; range: 19-89 years; F/M: 151/101) were asked to perform fast repeated flexion/extension movements of the thumb using a mechanical counter. Motor performances (assessed by the number of clicks during 3 time periods: 15, 30 and 45 sec), significantly decreased as a function of age for both the dominant (age effect; p < 0.0001 for 15, 30 and 45 sec) and the non-dominant hand (p < 0.0001 for 15, 30 and 45 sec). The number of clicks was significantly higher in males (gender effect; p < 0.001) and was higher on the dominant side as compared to the non-dominant side (handedness effect: p < 0.001). The Click Test is characterized by high repeatability (coefficients of variation from 3.20 to 4.47%), excellent intra-rater reliability (intra-class coefficients ICC ranging from 0.89 to 0.98), high inter-rater reproducibility (Pearson's product correlation ranging from 0.85 to 0.96), high internal consistency (Cronbach alpha coefficient = 0.95) and is highly correlated in terms of relative performances with the box and block test and the 9-hole peg test (positive linear correlation with the results of the box and block test: p < 0.001 for 15, 30 and 45 sec for both the dominant and the non-dominant hand; negative linear correlation with the results of the 9-hole peg test: p < 0.001 for 15, 30 and 45 sec for both the dominant and the non-dominant hand). The Click Test is an entirely novel and very low cost tool to reliably discriminate the ageing effects upon the performances during fast

  11. Genetic testing of Korean familial hypercholesterolemia using whole-exome sequencing.

    Directory of Open Access Journals (Sweden)

    Soo Min Han

    Full Text Available Familial hypercholesterolemia (FH is a genetic disorder with an increased risk of early-onset coronary artery disease. Although some clinically diagnosed FH cases are caused by mutations in LDLR, APOB, or PCSK9, mutation detection rates and profiles can vary across ethnic groups. In this study, we aimed to provide insight into the spectrum of FH-causing mutations in Koreans. Among 136 patients referred for FH, 69 who met Simon Broome criteria with definite family history were enrolled. By whole-exome sequencing (WES analysis, we confirmed that the 3 known FH-related genes accounted for genetic causes in 23 patients (33.3%. A substantial portion of the mutations (19 of 23 patients, 82.6% resulted from 17 mutations and 2 copy number deletions in LDLR gene. Two mutations each in the APOB and PCSK9 genes were verified. Of these anomalies, two frameshift deletions in LDLR and one mutation in PCSK9 were identified as novel causative mutations. In particular, one novel mutation and copy number deletion were validated by co-segregation in their relatives. This study confirmed the utility of genetic diagnosis of FH through WES.

  12. Realizing a Rasch measurement through instructionally- sequenced domains of test items.

    Science.gov (United States)

    Schulz, E. Matthew

    2016-11-01

    This paper presents results from a project in which instructionally-sequenced domains were defined for purposes of constructing measures that that conform to an ideal in Guttman scaling and Rasch measurement. A fundamental idea in these measurement systems is that every person higher on the measurement scale can do everything that lower-level persons can do, plus at least one more thing. This idea has had limited application in educational measurement due to the stochastic nature of item response data and the sheer number of items needed to obtain reliable measures. However, it has been shown by Schulz, Lee, and Mullen [1] that this ideal can be can be realized at a higher level of abstraction - when items within a content strand are aggregated into a small number of domains that are ordered in instructional timing and difficulty. The present paper shows how this was done, and the results, in an achievement level setting project for the 2007 Grade 12 NAEP Economics Assessment.

  13. The congruency sequence effect 3.0: a critical test of conflict adaptation.

    Directory of Open Access Journals (Sweden)

    Wout Duthoo

    Full Text Available Over the last two decades, the congruency sequence effect (CSE -the finding of a reduced congruency effect following incongruent trials in conflict tasks- has played a central role in advancing research on cognitive control. According to the influential conflict-monitoring account, the CSE reflects adjustments in selective attention that enhance task focus when needed, often termed conflict adaptation. However, this dominant interpretation of the CSE has been called into question by several alternative accounts that stress the role of episodic memory processes: feature binding and (stimulus-response contingency learning. To evaluate the notion of conflict adaptation in accounting for the CSE, we construed versions of three widely used experimental paradigms (the colour-word Stroop, picture-word Stroop and flanker task that effectively control for feature binding and contingency learning. Results revealed that a CSE can emerge in all three tasks. This strongly suggests a contribution of attentional control to the CSE and highlights the potential of these unprecedentedly clean paradigms for further examining cognitive control.

  14. Design and validation of a next generation sequencing assay for hereditary BRCA1 and BRCA2 mutation testing

    Directory of Open Access Journals (Sweden)

    Hyunseok P. Kang

    2016-06-01

    Full Text Available Hereditary breast and ovarian cancer syndrome, caused by a germline pathogenic variant in the BRCA1 or BRCA2 (BRCA1/2 genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs, short insertions and deletions (indels, and copy-number variants (CNVs, also known as large rearrangements with zero errors over a 114-sample validation set consisting of samples from cell lines and deidentified patient samples, including 36 samples with BRCA1/2pathogenic germline mutations.

  15. Testing Scaling Relations for Solar-like Oscillations from the Main Sequence to Red Giants Using Kepler Data

    DEFF Research Database (Denmark)

    Huber, D.; Bedding, T.R.; Stello, D.;

    2011-01-01

    We have analyzed solar-like oscillations in ~1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power (νmax), the large frequency separation (Δν...... an offset particularly for unevolved stars, suggesting that an additional physical dependency is necessary to fully reproduce the observed amplitudes. We investigate correlations between amplitudes and stellar activity, and find evidence that the effect of amplitude suppression is most pronounced...... for subgiant stars. Finally, we test the location of the cool edge of the instability strip in the Hertzsprung-Russell diagram using solar-like oscillations and find the detections in the hottest stars compatible with a domain of hybrid stochastically excited and opacity driven pulsation....

  16. TESTING SCALING RELATIONS FOR SOLAR-LIKE OSCILLATIONS FROM THE MAIN SEQUENCE TO RED GIANTS USING KEPLER DATA

    Energy Technology Data Exchange (ETDEWEB)

    Huber, D.; Bedding, T. R.; Stello, D. [Sydney Institute for Astronomy (SIfA), School of Physics, University of Sydney, NSW 2006 (Australia); Hekker, S. [Astronomical Institute ' Anton Pannekoek' , University of Amsterdam, Science Park 904, 1098 XH Amsterdam (Netherlands); Mathur, S. [High Altitude Observatory, NCAR, P.O. Box 3000, Boulder, CO 80307 (United States); Mosser, B. [LESIA, CNRS, Universite Pierre et Marie Curie, Universite Denis, Diderot, Observatoire de Paris, 92195 Meudon cedex (France); Verner, G. A.; Elsworth, Y. P.; Hale, S. J.; Chaplin, W. J. [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Bonanno, A. [INAF Osservatorio Astrofisico di Catania (Italy); Buzasi, D. L. [Eureka Scientific, 2452 Delmer Street Suite 100, Oakland, CA 94602-3017 (United States); Campante, T. L. [Centro de Astrofisica da Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Kallinger, T. [Department of Physics and Astronomy, University of British Columbia, Vancouver (Canada); Silva Aguirre, V. [Max-Planck-Institut fuer Astrophysik, Karl-Schwarzschild-Str. 1, 85748 Garching (Germany); De Ridder, J. [Instituut voor Sterrenkunde, K.U.Leuven (Belgium); Garcia, R. A. [Laboratoire AIM, CEA/DSM-CNRS, Universite Paris 7 Diderot, IRFU/SAp, Centre de Saclay, 91191, Gif-sur-Yvette (France); Appourchaux, T. [Institut d' Astrophysique Spatiale, UMR 8617, Universite Paris Sud, 91405 Orsay Cedex (France); Frandsen, S. [Danish AsteroSeismology Centre (DASC), Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C (Denmark); Houdek, G., E-mail: dhuber@physics.usyd.edu.au [Institute of Astronomy, University of Vienna, 1180 Vienna (Austria); and others

    2011-12-20

    We have analyzed solar-like oscillations in {approx}1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power ({nu}{sub max}), the large frequency separation ({Delta}{nu}), and oscillation amplitudes. We show that the difference of the {Delta}{nu}-{nu}{sub max} relation for unevolved and evolved stars can be explained by different distributions in effective temperature and stellar mass, in agreement with what is expected from scaling relations. For oscillation amplitudes, we show that neither (L/M){sup s} scaling nor the revised scaling relation by Kjeldsen and Bedding is accurate for red-giant stars, and demonstrate that a revised scaling relation with a separate luminosity-mass dependence can be used to calculate amplitudes from the main sequence to red giants to a precision of {approx}25%. The residuals show an offset particularly for unevolved stars, suggesting that an additional physical dependency is necessary to fully reproduce the observed amplitudes. We investigate correlations between amplitudes and stellar activity, and find evidence that the effect of amplitude suppression is most pronounced for subgiant stars. Finally, we test the location of the cool edge of the instability strip in the Hertzsprung-Russell diagram using solar-like oscillations and find the detections in the hottest stars compatible with a domain of hybrid stochastically excited and opacity driven pulsation.

  17. Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq

    Directory of Open Access Journals (Sweden)

    Manabu Nakayama

    2017-03-01

    Full Text Available Autoinflammatory diseases occupy one of a group of primary immunodeficiency diseases that are generally thought to be caused by mutation of genes responsible for innate immunity, rather than by acquired immunity. Mutations related to autoinflammatory diseases occur in 12 genes. For example, low-level somatic mosaic NLRP3 mutations underlie chronic infantile neurologic, cutaneous, articular syndrome (CINCA, also known as neonatal-onset multisystem inflammatory disease (NOMID. In current clinical practice, clinical genetic testing plays an important role in providing patients with quick, definite diagnoses. To increase the availability of such testing, low-cost high-throughput gene-analysis systems are required, ones that not only have the sensitivity to detect even low-level somatic mosaic mutations, but also can operate simply in a clinical setting. To this end, we developed a simple method that employs two-step tailed PCR and an NGS system, MiSeq platform, to detect mutations in all coding exons of the 12 genes responsible for autoinflammatory diseases. Using this amplicon sequencing system, we amplified a total of 234 amplicons derived from the 12 genes with multiplex PCR. This was done simultaneously and in one test tube. Each sample was distinguished by an index sequence of second PCR primers following PCR amplification. With our procedure and tips for reducing PCR amplification bias, we were able to analyze 12 genes from 25 clinical samples in one MiSeq run. Moreover, with the certified primers designed by our short program—which detects and avoids common SNPs in gene-specific PCR primers—we used this system for routine genetic testing. Our optimized procedure uses a simple protocol, which can easily be followed by virtually any office medical staff. Because of the small PCR amplification bias, we can analyze simultaneously several clinical DNA samples with low cost and can obtain sufficient read numbers to detect a low level of

  18. Optimal sequencing during category learning: Testing a dual-learning systems perspective.

    Science.gov (United States)

    Noh, Sharon M; Yan, Veronica X; Bjork, Robert A; Maddox, W Todd

    2016-10-01

    Recent studies demonstrate that interleaving the exemplars of different categories, rather than blocking exemplars by category, can enhance inductive learning-the ability to categorize new exemplars-presumably because interleaving affords discriminative contrasts between exemplars from different categories. Consistent with this view, other studies have demonstrated that decreasing between-category similarity and increasing within-category variability can eliminate or even reverse the interleaving benefit. We tested another hypothesis, one based on the dual-learning systems framework-namely, that the optimal schedule for learning categories should depend on an interaction of the cognitive system that mediates learning and the structure of the particular category being learned. Blocking should enhance rule-based category learning, which is mediated by explicit, hypothesis-testing processes, whereas interleaving should enhance information-integration category learning, which is mediated by an implicit, procedural-based learning system. Consistent with this view, we found a crossover interaction between schedule (blocked vs. interleaved) and category structure (rule-based vs. information-integration). Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Next generation sequencing for preimplantation genetic testing of blastocysts aneuploidies in women of different ages

    Directory of Open Access Journals (Sweden)

    Krzysztof Lukaszuk

    2015-12-01

    Full Text Available Most of the current preimplantation genetic screening of aneuploidies tests are based on the low quality and low density comparative genomic hybridization arrays. The results are based on fewer than 2,700 probes. Our main outcome was the association of aneuploidy rates and the women’s age. Between August–December 2013, 198 blastocysts from women (mean age 36.3+-4.6 undergoing in vitro fertilization underwent routine trophectoderm biopsy. NGS was performed on Ion Torrent PGM (Life Technologies. The results were analyzed in five age groups (<31, 31–35, 36–38, 39–40 and >40. 85 blastocysts were normal according to NGS results. The results in the investigated groups were (% of normal blastocyst in each group: <31 (41.9%, 31–35 (47.6%, 36–38 (47.8%, 39–40 (37.7% and >40 (38.5%. Our study suggests that NGS PGD is applicable for routine preimplantation genetic testing. It allows also for easy customization of the procedure for each individual patient making personalized diagnostics a reality.

  20. Practical Experience of the Application of a Weighted Burden Test to Whole Exome Sequence Data for Obesity and Schizophrenia.

    Science.gov (United States)

    Curtis, David

    2016-01-01

    For biological and statistical reasons it makes sense to combine information from variants at the level of the gene. One may wish to give more weight to variants which are rare and those that are more likely to affect function. A combined weighting scheme, implemented in the SCOREASSOC program, was applied to whole exome sequence data for 1392 subjects with schizophrenia and 982 with obesity from the UK10K project. Results conformed fairly well with null hypothesis expectations and no individual gene was strongly implicated. However, a number of the higher ranked genes appear plausible candidates as being involved in one or other phenotype and may warrant further investigation. These include MC4R, NLGN2, CRP, DONSON, GTF3A, IL36B, ADCYAP1R1, ARSA, DLG1, SIK2, SLAIN1, UBE2Q2, ZNF507, CRHR1, MUSK, NSF, SNORD115, GDF3 and HIBADH. Some individual variants in these genes have different frequencies between cohorts and could be genotyped in additional subjects. For other genes, there is a general excess of variants at many different sites so attempts at replication would be more difficult. Overall, the weighted burden test provides a convenient method for using sequence data to highlight genes of interest.

  1. Testing Scaling Relations for Solar-Like Oscillations from the Main Sequence to Red Giants using Kepler Data

    CERN Document Server

    Huber, D; Stello, D; Hekker, S; Mathur, S; Mosser, B; Verner, G A; Bonanno, A; Buzasi, D L; Campante, T L; Elsworth, Y P; Hale, S J; Kallinger, T; Aguirre, V Silva; Chaplin, W J; De Ridder, J; Garcia, R A; Appourchaux, T; Frandsen, S; Houdek, G; Molenda-Zakowicz, J; Monteiro, M J P F G; Christensen-Dalsgaard, J; Gilliland, R L; Kawaler, S D; Kjeldsen, H; Broomhall, A M; Corsaro, E; Salabert, D; Sanderfer, D T; Seader, S E; Smith, J C

    2011-01-01

    We have analyzed solar-like oscillations in ~1700 stars observed by the Kepler Mission, spanning from the main-sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power (nu_max), the large frequency separation (Delta_nu) and oscillation amplitudes. We show that the difference of the Delta_nu-nu_max relation for unevolved and evolved stars can be explained by different distributions in effective temperature and stellar mass, in agreement with what is expected from scaling relations. For oscillation amplitudes, we show that neither (L/M)^s scaling nor the revised scaling relation by Kjeldsen & Bedding (2011) are accurate for red-giant stars, and demonstrate that a revised scaling relation with a separate luminosity-mass dependence can be used to calculate amplitudes from the main-sequence to red-giants to a precision of ~25%. The residuals show an offset particularly for unevolved stars, suggesting that an additional physical dependency ...

  2. Research on lock-in thermography for aerospace materials of nondestructive test based on image sequence processing

    Science.gov (United States)

    Liu, Junyan; Dai, Jingmin; Wang, Yang

    2008-11-01

    IR Lock in thermography is an active thermography technology based on thermal wave signal processing, especially, it has many advantages for nondestructive test of composite materials and compound structure application and has been applied on aerospace, automotive, mechanics and electric fields. In lock in thermography, given sufficient time for periodic heating, the surface temperature will evolve periodically in a sinusoidal pattern form the transient state to the steady state. In this paper, the principle of lock in thermography is introduced and the heat transferring process is analyzed by the sinusoidal variation heating flow transferred in materials by means of FEM method. In experiment, the modulating optical stimulation is applied to sample, and image sequences are collected by Jade MWIR 550 FPA IR camera. The digital filter algorithm which is Savitzky-Golay digital smoothness filters is used to remove the effects of high frequency noise. A phase image at the frequency of periodic heating can be calculated using a Fourier transform of the periodic heating frequency in transient state for defect detection. The IR lock in thermography processing software is developed by using of visual C++ programmed based image sequence collected. The experimental results show that the developed system reached up to high level of conventional steady state Lock in method.

  3. Acceptability of, and Information Needs Regarding, Next-Generation Sequencing in People Tested for Hereditary Cancer: A Qualitative Study.

    Science.gov (United States)

    Meiser, Bettina; Storey, Ben; Quinn, Veronica; Rahman, Belinda; Andrews, Lesley

    2016-04-01

    Next generation sequencing (NGS) for patients at risk of hereditary cancer syndromes can also identify non-cancer related mutations, as well as variants of unknown significance. This study aimed to determine what benefits and shortcomings patients perceive in relation to NGS, as well as their interest and information preferences in regards to such testing. Eligible patients had previously received inconclusive results from clinical mutation testing for cancer susceptibility. Semi-structured telephone interviews were subjected to qualitative analysis guided by the approach developed by Miles and Huberman. The majority of the 19 participants reported they would be interested in panel/genomic testing. Advantages identified included that it would enable better preparation and allow implementation of individualized preventative strategies, with few disadvantages mentioned. Almost all participants said they would want all results, not just those related to their previous diagnosis. Participants felt that a face-to-face discussion supplemented by an information booklet would be the best way to convey information and achieve informed consent. All participants wanted their information stored and reviewed in accordance with new developments. Although the findings indicate strong interest among these individuals, it seems that the consent process, and the interpretation and communication of results will be areas that will require revision to meet the needs of patients.

  4. Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida; Albrechtsen, Anders

    2013-01-01

    A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Next Generation Sequencing (NGS) data. However......, estimates of frequency spectra from NGS data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the value of the statistic among genomic regions....

  5. 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

    Science.gov (United States)

    Cunningham, Kevin J.; Robinson, Edward

    2017-07-18

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

  6. Tests of Sunspot Number Sequences: 4. Discontinuities Around 1946 in Various Sunspot Number and Sunspot-Group-Number Reconstructions

    Science.gov (United States)

    Lockwood, M.; Owens, M. J.; Barnard, L.

    2016-11-01

    We use five test data series to search for, and quantify, putative discontinuities around 1946 in five different annual-mean sunspot-number or sunspot-group-number data sequences. The data series tested are the original and new versions of the Wolf/Zürich/International sunspot number composite [R_{{ISNv1}} and R_{{ISNv2}}] (respectively Clette et al. in Adv. Space Res. 40, 919, 2007 and Clette et al. in The Solar Activity Cycle 35, Springer, New York, 2015); the corrected version of R ISNv1 proposed by Lockwood, Owens, and Barnard ( J. Geophys. Res. 119, 5193, 2014a) [R C]; the new "backbone" group-number composite proposed by Svalgaard and Schatten ( Solar Phys. 291, 2016) [R_{{BB}}]; and the new group-number composite derived by Usoskin et al. ( Solar Phys. 291, 2016) [R_{{UEA}}]. The test data series used are the group-number [NG] and total sunspot area [A G] from the Royal Observatory, Greenwich/Royal Greenwich Observatory (RGO) photoheliographic data; the Ca K index from the recent re-analysis of Mount Wilson Observatory (MWO) spectroheliograms in the Calcium ii K ion line; the sunspot-group-number from the MWO sunspot drawings [N_{{MWO}}]; and the dayside ionospheric F2-region critical frequencies measured by the Slough ionosonde [foF2]. These test data all vary in close association with sunspot numbers, in some cases non-linearly. The tests are carried out using both the before-and-after fit-residual comparison method and the correlation method of Lockwood, Owens, and Barnard, applied to annual mean data for intervals iterated to minimise errors and to eliminate uncertainties associated with the precise date of the putative discontinuity. It is not assumed that the correction required is by a constant factor, nor even linear in sunspot number. It is shown that a non-linear correction is required by RC, R_{BB}, and R_{{ISNv1}}, but not by R_{{ISNv2}} or R_{{UEA}}. The five test datasets give very similar results in all cases. By multiplying the probability

  7. A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes.

    Science.gov (United States)

    Haridas, Sajeet; Breuill, Colette; Bohlmann, Joerg; Hsiang, Tom

    2011-09-01

    We offer a guide to de novo genome assembly using sequence data generated by the Illumina platform for biologists working with fungi or other organisms whose genomes are less than 100Mb in size. The guide requires no familiarity with sequencing assembly technology or associated computer programs. It defines commonly used terms in genome sequencing and assembly; provides examples of assembling short-read genome sequence data for four strains of the fungus Grosmannia clavigera using four assembly programs; gives examples of protocols and software; and presents a commented flowchart that extends from DNA preparation for submission to a sequencing center, through to processing and assembly of the raw sequence reads using freely available operating systems and software.

  8. Beyond BRAF(V600): clinical mutation panel testing by next-generation sequencing in advanced melanoma.

    Science.gov (United States)

    Siroy, Alan E; Boland, Genevieve M; Milton, Denái R; Roszik, Jason; Frankian, Silva; Malke, Jared; Haydu, Lauren; Prieto, Victor G; Tetzlaff, Michael; Ivan, Doina; Wang, Wei-Lien; Torres-Cabala, Carlos; Curry, Jonathan; Roy-Chowdhuri, Sinchita; Broaddus, Russell; Rashid, Asif; Stewart, John; Gershenwald, Jeffrey E; Amaria, Rodabe N; Patel, Sapna P; Papadopoulos, Nicholas E; Bedikian, Agop; Hwu, Wen-Jen; Hwu, Patrick; Diab, Adi; Woodman, Scott E; Aldape, Kenneth D; Luthra, Rajyalakshmi; Patel, Keyur P; Shaw, Kenna R; Mills, Gordon B; Mendelsohn, John; Meric-Bernstam, Funda; Kim, Kevin B; Routbort, Mark J; Lazar, Alexander J; Davies, Michael A

    2015-02-01

    The management of melanoma has evolved owing to improved understanding of its molecular drivers. To augment the current understanding of the prevalence, patterns, and associations of mutations in this disease, the results of clinical testing of 699 advanced melanoma patients using a pan-cancer next-generation sequencing (NGS) panel of hotspot regions in 46 genes were reviewed. Mutations were identified in 43 of the 46 genes on the panel. The most common mutations were BRAFV600 (36%), NRAS (21%), TP53 (16%), BRAFNon-V600 (6%), and KIT (4%). Approximately one-third of melanomas had >1 mutation detected, and the number of mutations per tumor was associated with melanoma subtype. Concurrent TP53 mutations were the most frequent events in tumors with BRAFV600 and NRAS mutations. Melanomas with BRAFNon-V600mutations frequently harbored concurrent NRAS mutations (18%), which were rare in tumors with BRAFV600 mutations (1.6%). The prevalence of BRAFV600 and KIT mutations were significantly associated with melanoma subtypes, and BRAFV600 and TP53 mutations were significantly associated with cutaneous primary tumor location. Multiple potential therapeutic targets were identified in metastatic unknown primary and cutaneous melanomas that lacked BRAFV600 and NRAS mutations. These results enrich our understanding of the patterns and clinical associations of oncogenic mutations in melanoma.

  9. Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity.

    Science.gov (United States)

    Costa, Marta D; Cherni, Lotfi; Fernandes, Verónica; Freitas, Fernando; Ammar El Gaaied, Amel Ben; Pereira, Luísa

    2009-04-01

    Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.

  10. Test Feasibility of Next-Generation Sequencing Assays in Clinical Mutation Detection of Small Biopsy and Fine Needle Aspiration Specimens.

    Science.gov (United States)

    Zheng, Gang; Tsai, Harrison; Tseng, Li-Hui; Illei, Peter; Gocke, Christopher D; Eshleman, James R; Netto, George; Lin, Ming-Tseh

    2016-05-01

    To evaluate preanalytic factors contributing to failure of next-generation sequencing (NGS) assays. AmpliSeq Cancer Hotspot Panel was conducted in 1,121 of 1,152 formalin-fixed paraffin-embedded tissues submitted to a clinical laboratory, including 493 small biopsy or fine needle aspiration (FNA) specimens (44%) and 25 metastatic bone specimens (2.2%). Single nucleotide mutations and/or insertion/deletion mutations were detected in 702 specimens. Thirty-eight specimens (3.4%) were reported as "no results" due to NGS assay failure. Higher failure rates were observed in specimens submitted for lung cancer panel and melanoma panel (3.1% and 3.7% vs 1.0% colorectal cancer panel), metastatic bone specimens (36% vs 2.6% nonbone specimens), referred specimens (5.0% vs 1.8% in-house specimens), and small biopsy and FNA specimens (5.8% and 3.1% vs 0.7% resection/excision specimens). Test feasibility was higher in in-house specimens than referred specimens (99.1% vs 96.9% in resection specimens, 94.4% vs 87.3% in small biopsy specimens, and 94.3% vs 58.8% in FNA specimens). NGS assays demonstrated clinical utility in solid tumor specimens, including those taken by biopsy or FNA. Preanalytic factors identified by this study that may contribute to NGS assay failure highlight the need for pathologists to revisit tissue processing protocols in order to better optimize cancer mutational profiling. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. 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.

  12. Heart Failure in an Infant With Pierre Robin Sequence: Is There a Diagnostic Test to Aid in Treatment Planning and Monitoring?

    Science.gov (United States)

    Biskup, Nataliya; Francis, Stacey H

    2015-11-01

    This case report describes an infant with Pierre Robin sequence who was managed conservatively until he presented at 4 months of age with right-sided heart failure. This rare clinical presentation displays the physiologic response to chronic respiratory obstruction and the acid-base disturbances, which become evident on metabolic panel and blood gas. We suggest that these tests can be added to the workup, especially in conservatively managed infants, to help predict which infants may fail conservative treatment and to avoid the rare complication of heart failure in infants with Pierre Robin sequence.

  13. Antimicrobial susceptibility determined by the E test, Löwenstein-Jensen proportion, and DNA sequencing methods among Mycobacterium tuberculosis isolates discrepancies, preliminary results

    Directory of Open Access Journals (Sweden)

    Maria Inês Moura Freixo

    2004-02-01

    Full Text Available Mycobacterium tuberculosis strains resistant to streptomycin (SM, isoniazid (INH, and/or rifampin (RIF as determined by the conventional Löwenstein-Jensen proportion method (LJPM were compared with the E test, a minimum inhibitory concentration susceptibility method. Discrepant isolates were further evaluated by BACTEC and by DNA sequence analyses for mutations in genes most often associated with resistance to these drugs (rpsL, katG, inhA, and rpoB. Preliminary discordant E test results were seen in 75% of isolates resistant to SM and in 11% to INH. Discordance improved for these two drugs (63% for SM and none for INH when isolates were re-tested but worsened for RIF (30%. Despite good agreement between phenotypic results and sequencing analyses, wild type profiles were detected on resistant strains mainly for SM and INH. It should be aware that susceptible isolates according to molecular methods might contain other mechanisms of resistance. Although reproducibility of the LJPM susceptibility method has been established, variable E test results for some M. tuberculosis isolates poses questions regarding its reproducibility particularly the impact of E test performance which may vary among laboratories despite adherence to recommended protocols. Further studies must be done to enlarge the evaluated samples and looked possible mutations outside of the hot spot sequenced gene among discrepant strains.

  14. Finding the needle in the haystack: differentiating "identical" twins in paternity testing and forensics by ultra-deep next generation sequencing.

    Science.gov (United States)

    Weber-Lehmann, Jacqueline; Schilling, Elmar; Gradl, Georg; Richter, Daniel C; Wiehler, Jens; Rolf, Burkhard

    2014-03-01

    Monozygotic (MZ) twins are considered being genetically identical, therefore they cannot be differentiated using standard forensic DNA testing. Here we describe how identification of extremely rare mutations by ultra-deep next generation sequencing can solve such cases. We sequenced DNA from sperm samples of two twins and from a blood sample of the child of one twin. Bioinformatics analysis revealed five single nucleotide polymorphisms (SNPs) present in the twin father and the child, but not in the twin uncle. The SNPs were confirmed by classical Sanger sequencing. Our results give experimental evidence for the hypothesis that rare mutations will occur early after the human blastocyst has split into two, the origin of twins, and that such mutations will be carried on into somatic tissue and the germline. The method provides a solution to solve paternity and forensic cases involving monozygotic twins as alleged fathers or originators of DNA traces.

  15. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

    Directory of Open Access Journals (Sweden)

    Kuraku Shigehiro

    2011-06-01

    Full Text Available Abstract Background In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA family, whose members are mostly single-exon. Results Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family. Conclusions Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.

  16. Genome Sequence of a Candidate World Health Organization Reference Strain of Zika Virus for Nucleic Acid Testing

    Science.gov (United States)

    Trösemeier, Jan-Hendrik; Musso, Didier; Blümel, Johannes; Thézé, Julien; Pybus, Oliver G.

    2016-01-01

    We report here the sequence of a candidate reference strain of Zika virus (ZIKV) developed on behalf of the World Health Organization (WHO). The ZIKV reference strain is intended for use in nucleic acid amplification (NAT)-based assays for the detection and quantification of ZIKV RNA. PMID:27587826

  17. 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 th...

  18. Testing between UG-Based and Problem-Solving Models of L2A: Developmental Sequence Data.

    Science.gov (United States)

    Schwartz, Bonnie D.

    1992-01-01

    A novel approach is examined for using developmental sequence data for deciding between Universal Grammar-based and problem solving models of adult nonnative grammatical development. Results support the Universal Grammar-based model of nonnative language acquisition. (19 references) (Author/LB)

  19. 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

    of costs. The priority pathogens reported by respondents reflected the key drivers for NGS use (high burden disease and ‘high profile’ pathogens). The performance of and participation in PT was perceived as important by most respondents. The wide range of sequencing and bioinformatics practices reported...

  20. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    Full Text Available Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads. Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I. Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II. Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR

  1. High-precision dating and correlation of ice, marine and terrestrial sequences spanning Heinrich Event 3: Testing mechanisms of interhemispheric change using New Zealand ancient kauri (Agathis australis)

    Science.gov (United States)

    Turney, Chris S. M.; Palmer, Jonathan; Bronk Ramsey, Christopher; Adolphi, Florian; Muscheler, Raimund; Hughen, Konrad A.; Staff, Richard A.; Jones, Richard T.; Thomas, Zoë A.; Fogwill, Christopher J.; Hogg, Alan

    2016-04-01

    Robustly testing hypotheses of geographic synchroneity of abrupt and extreme change during the late Pleistocene (60,000 to 11,650 years ago) requires a level of chronological precision often lacking in ice, marine and terrestrial sequences. Here we report a bidecadally-resolved New Zealand kauri (Agathis australis) tree-ring sequence spanning two millennia that preserves a record of atmospheric radiocarbon (14C) during ice-rafted debris event Heinrich Event 3 (HE3) in the North Atlantic and Antarctic Isotope Maximum 4 (AIM4) in the Southern Hemisphere. Using 14C in the marine Cariaco Basin and 10Be preserved in Greenland ice, the kauri 14C sequence allows us to precisely align sequences across this period. We observe no significant difference between atmospheric and marine 14C records during HE3, suggesting no stratification of surface waters and collapse in Atlantic Meridional Overturning Circulation (AMOC). Instead our results support recent evidence for a weakened AMOC across at least two millennia of the glacial period. Our work adds to a growing body of literature confirming that Heinrich events are not the cause of stadial cooling and suggests changes in the AMOC were not the primary driver of antiphase temperature trends between the hemispheres. Decadally-resolved 14C in ancient kauri offers a powerful new (and complementary) approach to polar ice core CH4 alignment for testing hypotheses of abrupt and extreme climate change.

  2. Side-to-side range of movement variability in variants of the median and radial neurodynamic test sequences in asymptomatic people.

    Science.gov (United States)

    Stalioraitis, Vaidas; Robinson, Kim; Hall, Toby

    2014-08-01

    Side-to-side discrepancy in range of motion (ROM) during upper limb neurodynamic testing is used in part to identify abnormal peripheral nerve mechanosensitivity and is one of three factors to consider in determining a positive test. Large side-to-side variability is reported for some variants of the upper limb neurodynamic test sequences, however discrepancies for other test variants are unknown. Hence the purpose of this study was to evaluate side-to-side discrepancy in elbow flexion ROM during two variants of upper limb neurodynamic test sequence for the median and radial nerves. 51 asymptomatic subjects (26 females, mean age 29.69 years) were evaluated. A uniaxial electrogoniometer was used to measure elbow flexion ROM at onset of resistance (R1) and onset of discomfort (P1) during the median and radial neurodynamic tests on each side. Reliability was determined by testing 20 subjects twice and was found to be good (ICC greater than 0.88 and SEM less than 4.02°). There was no significant difference in mean ROM between sides. Lower-bound scores indicate that intra-individual, inter-limb differences of more than 15° for the median nerve and 11° for the radial nerve exceeds the range of normal ROM asymmetry on neurodynamic testing at R1 and P1. Correlation of ROM between limbs was significant with R(2) values of 0.62 and 0.85 for the median and radial nerves respectively. These finding provide clinicians with information regarding normal side-to-side variability in ROM during two commonly used variants of neurodynamic tests.

  3. On the phi-divergence test statistics for the change point problem in a sequence of exponentially distributed random variables

    CERN Document Server

    Apostolos, Batsidis; Leandro, Pardo; Konstantinos, Zografos

    2011-01-01

    Recently Batsidis et al. (2011) have presented a new procedure based on divergence measures for testing the hypothesis of the existence of a change point in exponential populations. A simulation study was carried out using the asymptotic critical points obtained from the asymptotic distribution of the new test statistics introduced. The main purpose of this paper is to use the behavior of the test statistics introduced in the cited paper of Batsidis et al. (2011) using simulated critical points.

  4. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Science.gov (United States)

    França, Luís; Simões, Catarina; Taborda, Marco; Diogo, Catarina; da Costa, Milton S

    2015-01-01

    Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  5. Could test length or order affect scores on letter number sequencing of the WAIS-III and WMS-III? Ruling out effects of fatigue.

    Science.gov (United States)

    Tulsky, D S; Zhu, J

    2000-11-01

    The Letter Number Sequencing subtest of the WAIS-III and WMS-III was administered at the end of the standardization edition of the WMS-III. It was not administered as part of the WAIS-III standardization battery. Nevertheless, the subtest was included in the published version of the WAIS-III. This study examines differences between examinees administered the Letter Number Sequencing subtest at three different times during a psychological battery: (1) as part of the published battery, (2) as part of the WMS-III when the WMS-III was administered as the first test in a sequence, and (3) as part of the WMS-III standardization when the WAIS-III was administered immediately preceding the WMS-III. The participants were 372 examinees ( n = 124 in each condition) who were matched on key demographic variables. A repeated measures MANOVA yielded no difference in subtest scores when administered in any of these conditions. The results show no evidence of fatigue or ordering effects on the Letter Number Sequencing subtest.

  6. Using a Sequence Homology-Based Predictive Strategy to Address Current Demands for Focused Toxicity Testing in Ecological Risk Assessment

    Science.gov (United States)

    The lack of resources available for comprehensive toxicity testing, international interest in limiting the quantity of animals used in testing, and a mounting list of anthropogenic chemicals produced world-wide have led to the exploration of innovative means for identifying chemi...

  7. Targeted sequencing identifies a novel SH2D1A pathogenic variant in a Chinese family: Carrier screening and prenatal genetic testing

    Science.gov (United States)

    Chen, Yi-Yao; Li, Shu-Yuan; Zhang, Lan-Lan; Shen, Ying-Hua; Chang, Chun-Xin; Xiang, Yu-Qian; Huang, He-Feng; Xu, Chen-Ming

    2017-01-01

    X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family. Next-generation sequencing (NGS)-based multigene panel was used in carrier screening of the pregnant woman. Variants of immunodeficiency related genes were analyzed and prioritized. Candidate variant was verified by using Sanger sequencing. The possible influence of the identified variant was evaluated through RNA assay. Amniocentesis, karyotyping, and Sanger sequencing were performed for prenatal testing. We identified a novel de novo frameshift SH2D1A pathogenic variant (c.251_255delTTTCA) in the pregnant carrier. Peripheral blood RNA assay indicated that the mutant transcript could escape nonsense-mediated mRNA decay (NMD) and might encode a C-terminal truncated protein. Information of the variant led to success prenatal diagnosis of the fetus. In conclusion, our study clarified the genetic diagnosis and altered disease prevention for a pregnant carrier of XLP1. PMID:28231257

  8. Discordant results between fetal karyotyping and non-invasive prenatal testing by maternal plasma sequencing in a case of uniparental disomy 21 due to trisomic rescue.

    Science.gov (United States)

    Pan, Min; Li, Fa Tao; Li, Yan; Jiang, Fu Man; Li, Dong Zhi; Lau, Tze Kin; Liao, Can

    2013-06-01

    Uniparental disomy (UPD) is an uncommon chromosome condition, but UPD involving chromosome 21 is rarely reported. We reported here a case who had first trimester screening test for Down syndrome, chorionic villus sampling for fetal karyotyping, quantitative fluorescence polymerase chain reaction (QF-PCR), as well as non-invasive prenatal testing (NIPT) by maternal plasma sequencing. There were discordant results between fetal karyotyping and NIPT due to UPD 21combined with confined placental mosaicism of trisomy 21. This demonstrated that it is possible to detect placental mosaicism by NIPT, but further studies are required to confirm its sensitivity. Therefore, all positive NIPT results must be confirmed by conventional invasive test and karyotyping. QF-PCR has the additional benefit in diagnosing UPD.

  9. The optimal sequence and selection of screening test items to predict fall risk in older disabled women: the Women's Health and Aging Study.

    Science.gov (United States)

    Lamb, Sarah E; McCabe, Chris; Becker, Clemens; Fried, Linda P; Guralnik, Jack M

    2008-10-01

    Falls are a major cause of disability, dependence, and death in older people. Brief screening algorithms may be helpful in identifying risk and leading to more detailed assessment. Our aim was to determine the most effective sequence of falls screening test items from a wide selection of recommended items including self-report and performance tests, and to compare performance with other published guidelines. Data were from a prospective, age-stratified, cohort study. Participants were 1002 community-dwelling women aged 65 years old or older, experiencing at least some mild disability. Assessments of fall risk factors were conducted in participants' homes. Fall outcomes were collected at 6 monthly intervals. Algorithms were built for prediction of any fall over a 12-month period using tree classification with cross-set validation. Algorithms using performance tests provided the best prediction of fall events, and achieved moderate to strong performance when compared to commonly accepted benchmarks. The items selected by the best performing algorithm were the number of falls in the last year and, in selected subpopulations, frequency of difficulty balancing while walking, a 4 m walking speed test, body mass index, and a test of knee extensor strength. The algorithm performed better than that from the American Geriatric Society/British Geriatric Society/American Academy of Orthopaedic Surgeons and other guidance, although these findings should be treated with caution. Suggestions are made on the type, number, and sequence of tests that could be used to maximize estimation of the probability of falling in older disabled women.

  10. Study of HIV-1 subtypes in serodiscordant couples attending an integrated counselling and testing centre in Mumbai using heteroduplex mobility analysis and DNA sequencing

    Directory of Open Access Journals (Sweden)

    Mehta P

    2010-01-01

    Full Text Available Aims: To determine the prevalent subtypes of HIV-1 in serodiscordant couples. Setting: Integrated Counselling and Testing Centre (ICTC, Department of Microbiology. Study Design: Prospective pilot study. Participants: Thirty HIV-1 serodiscordant couples. Inclusion Criteria: a Documentation of HIV-1 infection in one partner and seronegative status in the other, current history of continued unprotected sexual activity within the partnership, demonstration that they have been in a partnership for at least 1 year and are not currently on highly active antiretroviral therapy HAART; b willingness of both partners to provide written informed consent including consent to continued couple counselling for 3 months. Materials and Methods: HIV-1 subtyping was carried out by heteroduplex mobility analysis (HMA by amplifying env region; and DNA sequencing by amplifying gag region. Results: HIV-1 env gene was amplified successfully in 10/30 samples; gag gene, in 25/30 samples; and both env and gag gene were amplified successfully in 5/30 samples. HIV-1 subtype C was detected from 21 samples; subtype B, from 7; and subtype A, from 2. Sample from 1 positive partner was detected as subtype C by env HMA and subtype B by gag sequencing. Conclusion: HIV-1 subtype C was found to be the predominant subtype of HIV-1 in serodiscordant couples attending our ICTC, followed by HIV-1 subtype B and HIV-1 subtype A, respectively. DNA sequencing was found to be the most reliable method for determining the subtypes of HIV-1.

  11. Research, Development and Testing of a Fault-Tolerant FPGA-Based Sequencer for CubeSat Launching Applications

    Science.gov (United States)

    2013-03-01

    ABBREVIATIONS 2-D Two-Dimensional 3-D Three-Dimensional AES Advanced Encryption Standard AIAA American Institute of Aeronautics and Astronautics APIC ... transition from combinational to sequential logic, method of power-on configuration, and the transition from a test experiment to practical application... breakdown of particular approaches. The particular advantages and disadvantages of scrubbing, TMR, quadded logic, TIR, and QFDR were presented. Initially

  12. SEVENTY TWO-HOUR RAT PANCREAS PRESERVATION USING PERELUOROCHEMICAL

    Institute of Scientific and Technical Information of China (English)

    洪鹤群; 漆原贵; 土肥雪彦

    1994-01-01

    SEVENTYTWO-HOURRATPANCREASPRESER-VATIONUSINGPERELUOROCHEMICALHongHequn(洪鹤群)(DepartmentofSurgery,RuijingHospital,SSMU,Shanghai...

  13. Two-hour evaluation of renal function in the elderly

    OpenAIRE

    Maria do Carmo B. Sammartino Benarab; Yara Marcondes Machado Castiglia; Pedro Thadeu Galvão Vianna; José Reinaldo Cerqueira Braz

    2005-01-01

    JUSTIFICATIVA E OBJETIVOS: Os idosos têm diminuição progressiva da função renal e os hipertensos, maior risco de lesão renal adicional no intra-operatório. Avalia-se a função renal pela depuração da creatinina, com débito urinário de 24 horas, para diluir o erro de possível volume vesical residual (VVR). O objetivo deste trabalho foi avaliar a função renal pré-operatória de idosos hipertensos e não-hipertensos, com débito urinário de duas horas, utilizando aparelho de ultra-som portátil para ...

  14. Reviewing 741 patients records in two hours with FASTVISU

    OpenAIRE

    2015-01-01

    The secondary use of electronic health records opens up new perspectives. They provide researchers with structured data and unstructured data, including free text reports. Many applications been developed to leverage knowledge from free-text reports, but manual review of documents is still a complex process.

  15. 分布式环境下基于多UIO的测试序列生成方法%Multiple UIO-based test sequence generation for distributed systems

    Institute of Scientific and Technical Information of China (English)

    刘文宇; 曾红卫; 缪淮扣

    2008-01-01

    In developing distributed systems, conformance testing is required to determine whether an implementation under test (IUT) conforms to its specification. With distributed test architectures involving multiple remote testers, testing approaches may become more complicated because of issues known as controllability and observability problems. Based on a finite state machine (FSM) representation of the system's specification, this paper proposes a new method to generate a test sequence utilizing multiple UIO sequences. The method is essentially guided by the way of minimizing the use of external coordination messages and input/output operations. Experiments are given to evaluate the proposed method.

  16. Study on stacking sequence on the flexural properties of basalt/carbon/epoxy hybrid composites using test and finite element analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, S. H.; Lee, J. I.; Rhee, K. Y. [Kyung Hee University, Yongin (Korea, Republic of); Choi, C. R. [ELSOLTEC Inc., Yongin (Korea, Republic of)

    2015-05-15

    Basalt fiber is widely used in various industries and several studies have been carried out to understand the mechanical behavior of basalt fiber reinforced composites. However, few studies have been made to specifically investigate the mechanical properties of basalt/carbon hybrid composites. In this study, the effect of stacking sequence on the flexural properties of carbon/basalt/epoxy hybrid composites was investigated in order to verify the reliability of this composite model. Two types of carbon/basalt/epoxy hybrid composites with a sandwich form were fabricated: basalt skin-carbon core (BSCC) composites and carbon skin-basalt core (CSBC) composites. After fabrication flexural tests and finite element method (FEM) were conducted. FEM results of flexural analysis are compared with experimental results. A FEA analysis model has been successfully developed in order to predict flexural behavior of basalt/carbon/epoxy hybrid composites. The simulation using the FEA model produces a similar flexural strength to that obtained from the experiment. Therefore, the developed FEA model in general will be highly useful for the prediction of stacking sequence of basalt/carbon/ epoxy hybrid composites for several industrial applications.

  17. Application of whole-exome sequencing to direct the specific functional testing and diagnosis of rare inherited bleeding disorders in patients from the Öresund Region, Scandinavia.

    Science.gov (United States)

    Leinøe, Eva; Zetterberg, Eva; Kinalis, Savvas; Østrup, Olga; Kampmann, Peter; Norström, Eva; Andersson, Nadine; Klintman, Jenny; Qvortrup, Klaus; Nielsen, Finn Cilius; Rossing, Maria

    2017-07-27

    Rare inherited bleeding disorders (IBD) are a common cause of bleeding tendency. To ensure a correct diagnosis, specialized laboratory analyses are necessary. This study reports the results of an upfront diagnostic strategy using targeted whole exome sequencing. In total, 156 patients with a significant bleeding assessment tool score participated in the study, of which a third had thrombocytopenia. Eighty-seven genes specifically associated with genetic predisposition to bleeding were analysed by whole exome sequencing. Variants were classified according to the five-tier scheme. We identified 353 germline variants. Eight patients (5%) harboured a known pathogenic variant. Of the 345 previously unknown variants, computational analyses predicted 99 to be significant. Further filtration according to the Mendelian inheritance pattern, resulted in 59 variants being predicted to be clinically significant. Moreover, 34% (20/59) were assigned as novel class 4 or 5 variants upon targeted functional testing. A class 4 or 5 variant was identified in 30% of patients with thrombocytopenia (14/47) versus 11% of patients with a normal platelet count (12/109) (P < 0·01). An IBD diagnosis has a major clinical impact. The genetic investigations detailed here extricated our patients from a diagnostic conundrum, thus demonstrating that continuous optimization of the diagnostic work-up of IBD is of great benefit. © 2017 The Authors. British Journal of Haematology published by John Wiley & Sons Ltd.

  18. A theoretical-experimental proposal, in teaching sequences about intermolecular interactions on teaching chemistry using varations of the test of adulteration in gasline and urucum dyes

    Directory of Open Access Journals (Sweden)

    Ademir de Souza Pereira

    2012-09-01

    Full Text Available This paper reports presents the results of a research developed with students of the high school in the Dourados, Mato Grosso do Sul, with the objective of proposing a theoretical-experimental teaching sequences, potentially significant, approaching the theme Intermolecular Interactions. The teaching sequence was developed with 44 students of the last year of the high school, with the duration of 9 classes of 50 minutes. The methodology presents the characteristics of the qualitative research, being based on David Ausubel's theoretical. We used, as advance organizer, the test determination of the ethanol content in gasoline, adapting, along the experiments, to the use of the natural dyes of the urucum seeds communly used through the region the research was done. The instruments used to collect the information was through the use of questionnaires and observations of the classes. At the end 32 students presented arguments, developing in each stage, as well as in participation, as in classroom discussion, evidencing the evolution conceptual on the process of significant learning.

  19. Test

    DEFF Research Database (Denmark)

    Bendixen, Carsten

    2014-01-01

    Bidrag med en kortfattet, introducerende, perspektiverende og begrebsafklarende fremstilling af begrebet test i det pædagogiske univers.......Bidrag med en kortfattet, introducerende, perspektiverende og begrebsafklarende fremstilling af begrebet test i det pædagogiske univers....

  20. Sequence-modified primers for the differential RT-PCR detection of Andean potato latent and Andean potato mild mosaic viruses in quarantine tests.

    Science.gov (United States)

    Koenig, Renate; Ziebell, Heiko

    2014-05-01

    To enable the differential PCR detection of Andean potato latent virus (APLV) and Andean potato mild mosaic virus (APMMV) strains, sense primers were designed that correspond to regions directly upstream of the coat protein genes. Their differentiating power was increased by A->C or T->C replacements in their 3'-terminal parts. Together with the broad-specificity antisense primer EM3, primer AL-a-mod3C detected all APLV strains tested, but none of the APMMV strains. Primer AM-a-mod4C yielded PCR products with all APMMV preparations, but also with some APLV preparations. Sequence analysis revealed that this was not due to a lack of primer specificity, but to the sensitive detection of contaminating APMMV in some of our APLV preparations.

  1. Exploiting RNA-sequencing data from the porcine testes to identify the key genes involved in spermatogenesis in Large White pigs.

    Science.gov (United States)

    Song, Huibin; Zhu, Lihua; Li, Yan; Ma, Changping; Guan, Kaifeng; Xia, Xuanyan; Li, Fenge

    2015-12-01

    Mammalian testis development and spermatogenesis play critical roles in male fertility. However, little genomic information is available for porcine sexually mature and immature testis. Presently, we detected approximately 76% of previously annotated genes that were expressed in the porcine testes by RNA sequencing. Taking an FDR of 0.001 and a |log2Ratio| of 1 as cutoffs, 10,095 genes were significantly differentially expressed between two stages, including 242 spermatogenesis-associated genes. These genes were significantly enriched to GO BP terms concerning spermatogenesis, male gamete generation, developmental process and sexual reproduction; to the KEEG pathways, including focal adhesion, ECM-receptor interaction, and phagosome. 186 extended transcripts, 1273 alternative splicing events and 2846 SNPs were detected in spermatogenesis-associated DEGs. Two PIWIL4 SNPs were successfully validated and suggested to be the potential molecular markers for semen quality. This study will help identify the specific genes and isoforms that are active in porcine spermatogenesis and sexual maturity.

  2. A scoping study to explore the cost-effectiveness of next-generation sequencing compared with traditional genetic testing for the diagnosis of learning disabilities in children.

    Science.gov (United States)

    Beale, Sophie; Sanderson, Diana; Sanniti, Anna; Dundar, Yenal; Boland, Angela

    2015-06-01

    Learning disability (LD) is a serious and lifelong condition characterised by the impairment of cognitive and adaptive skills. Some cases of LD with unidentified causes may be linked to genetic factors. Next-generation sequencing (NGS) techniques are new approaches to genetic testing that are expected to increase diagnostic yield. This scoping study focused on the diagnosis of LD in children and the objectives were to describe current pathways that involve the use of genetic testing; collect stakeholder views on the changes in service provision that would need to be put in place before NGS could be used in clinical practice; describe the new systems and safeguards that would need to be put in place before NGS could be used in clinical practice; and explore the cost-effectiveness of using NGS compared with conventional genetic testing. A research advisory group was established. This group provided ongoing support by e-mail and telephone through the lifetime of the study and also contributed face-to-face through a workshop. A detailed review of published studies and reports was undertaken. In addition, information was collected through 33 semistructured interviews with key stakeholders. NGS techniques consist of targeted gene sequencing, whole-exome sequencing (WES) and whole-genome sequencing (WGS). Targeted gene panels, which are the least complex, are in their infancy in clinical settings. Some interviewees thought that during the next 3-5 years targeted gene panels would be superseded by WES. If NGS technologies were to be fully introduced into clinical practice in the future a number of factors would need to be overcome. The main resource-related issues pertaining to service provision are the need for additional computing capacity, more bioinformaticians, more genetic counsellors and also genetics-related training for the public and a wide range of staff. It is also considered that, as the number of children undergoing genetic testing increases, there will be an

  3. Brain histamine depletion enhances the behavioural sequences complexity of mice tested in the open-field: Partial reversal effect of the dopamine D2/D3 antagonist sulpiride.

    Science.gov (United States)

    Santangelo, Andrea; Provensi, Gustavo; Costa, Alessia; Blandina, Patrizio; Ricca, Valdo; Crescimanno, Giuseppe; Casarrubea, Maurizio; Passani, M Beatrice

    2017-02-01

    Markers of histaminergic dysregulation were found in several neuropsychiatric disorders characterized by repetitive behaviours, thoughts and stereotypies. We analysed the effect of acute histamine depletion by means of i. c.v. injections of alpha-fluoromethylhistidine, a blocker of histidine decarboxylase, on the temporal organization of motor sequences of CD1 mice behaviour in the open-field test. An ethogram encompassing 9 behavioural components was employed. Durations and frequencies were only slightly affected by treatments. However, as revealed by multivariate t-pattern analysis, histamine depletion was associated with a striking increase in the number of behavioural patterns. We found 42 patterns of different composition occurring, on average, 520.90 ± 50.23 times per mouse in the histamine depleted (HD) group, whereas controls showed 12 different patterns occurring on average 223.30 ± 20.64 times. Exploratory and grooming behaviours clustered separately, and the increased pattern complexity involved exclusively exploratory patterns. To test the hypothesis of a histamine-dopamine interplay on behavioural pattern phenotype, non-sedative doses of the D2/D3 antagonist sulpiride (12.5-25-50 mg/kg) were additionally administered to different groups of HD mice. Sulpiride counterbalanced the enhancement of exploratory patterns of different composition, but it did not affect the mean number of patterns at none of the doses used. Our results provide new insights on the role of histamine on repetitive behavioural sequences of freely moving mice. Histamine deficiency is correlated with a general enhancement of pattern complexity. This study supports a putative involvement of histamine in the pathophysiology of tics and related disorders.

  4. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  5. Testing of sequences by simulation

    CERN Document Server

    Iványi, Antal

    2010-01-01

    Let $\\xi$ be a random integer vector, having uniform distribution \\[\\mathbf{P} \\{\\xi = (i_1,i_2,...,i_n) = 1/n^n \\} \\ \\hbox{for} \\ 1 \\leq i_1,i_2,...,i_n\\leq n.\\] A realization $(i_1,i_2,...,i_n)$ of $\\xi$ is called \\textit{good}, if its elements are different. We present algorithms \\textsc{Linear}, \\textsc{Backward}, \\textsc{Forward}, \\textsc{Tree}, \\textsc{Garbage}, \\textsc{Bucket} which decide whether a given realization is good. We analyse the number of comparisons and running time of these algorithms using simulation gathering data on all possible inputs for small values of $n$ and generating random inputs for large values of $n$.

  6. Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance.

    Directory of Open Access Journals (Sweden)

    Gabriel Minarik

    Full Text Available The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods.Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied.Using a z score value of 3 as the cut-off, 98.11%-100% (104-106/106 specificity and 100% (24/24 sensitivity and 99.06%-100% (105-106/106 specificity and 100% (24/24 sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly--p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively.Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide.

  7. Diagnosis for choroideremia in a large Chinese pedigree by next-generation sequencing (NGS) and non-invasive prenatal testing (NIPT)

    Science.gov (United States)

    Zhu, Li; Cheng, Jingliang; Zhou, Boxu; Wei, Chunli; Yang, Weichan; Jiang, Dong; Ijaz, Iqra; Tan, Xiaojun; Chen, Rui; Fu, Junjiang

    2017-01-01

    To develop an effective strategy to isolate and use cell-free fetal DNA (cffDNA) for the combined use of next-generation sequencing (NGS) for diagnosing choroideremia and non-invasive prenatal testing (NIPT) for Y chromosome determination, a large Chinese family with an X-linked recessive disease, choroideremia, was recruited. Cell-free DNA was extracted from maternal plasma, and SRY polymerase chain reaction amplification was performed using NIPT. Sanger sequencing was subsequently used for fetal amniotic fluid DNA verification. A nonsense mutation (c.C799T:p.R267X) of the CHM gene on the X chromosome of the proband (IV:7) and another 5 males with choroideremia were detected, while 3 female carriers with no symptoms were also identified. The fetus (VI:7) was identified as female from the cffDNA, and the same heterozygous nonsense mutation present in her mother was also confirmed. At one and a half years of age, the female baby did not present with any associated symptoms of choroideremia. Therefore, cffDNA was successfully used for the combined use of NGS for diagnosing choroideremia in a large Chinese pedigree, and NIPT for Y chromosome determination. This approach should result in a markedly increased use of prenatal diagnosis and improvement, and more sophisticated clinical management of diseases in China and other developing countries. The establishment of a highly accurate method for prenatal gene diagnosis will allow for more reliable gene diagnosis, improved genetic counseling, and personalized clinical management of our patients. PMID:28098911

  8. 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...

  9. Investigation of Clostridium difficile interspecies relatedness using multilocus sequence typing, multilocus variable-number tandem-repeat analysis and antimicrobial susceptibility testing.

    Science.gov (United States)

    Rodriguez, C; Avesani, V; Taminiau, B; Van Broeck, J; Brévers, B; Delmée, M; Daube, G

    2015-12-01

    Multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA) and antimicrobial susceptibility were performed on 37 animal and human C. difficile isolates belonging to 15 different PCR-ribotypes in order to investigate the relatedness of human and animal isolates and to identify possible transmission routes. MLVA identified a total of 21 different types while MLST only distinguished 12 types. Identical C. difficile strains were detected in the same animal species for PCR-ribotypes 014, 078, UCL 16U and UCL 36, irrespective of their origin or the isolation date. Non clonal strains were found among different hosts; however, a high genetic association between pig and cattle isolates belonging to PCR-ribotype 078 was revealed. MLVA also showed genetic differences that clearly distinguished human from animal strains. For a given PCR-ribotype, human and animal strains presented a similar susceptibility to the antimicrobials tested. All strains were susceptible to vancomycin, metronidazole, chloramphenicol and rifampicin, while PCR-ribotypes 078, UCL 5a, UCL 36 and UCL 103 were associated with erythromycin resistance. The data suggest a wide dissemination of clones at hospitals and breeding-farms or a contamination at the slaughterhouse, but less probability of interspecies transmission. However, further highly discriminatory genotyping methods are necessary to elucidate interspecies and zoonotic transmission of C. difficile.

  10. Motivations for undertaking DNA sequencing-based non-invasive prenatal testing for fetal aneuploidy: a qualitative study with early adopter patients in Hong Kong.

    Directory of Open Access Journals (Sweden)

    Huso Yi

    Full Text Available BACKGROUND: A newly introduced cell-free fetal DNA sequencing based non-invasive prenatal testing (DNA-NIPT detects Down syndrome with sensitivity of 99% at early gestational stage without risk of miscarriage. Attention has been given to its public health implications; little is known from consumer perspectives. This qualitative study aimed to explore women's motivations for using, and perceptions of, DNA-NIPT in Hong Kong. METHODS AND FINDINGS: In-depth interviews were conducted with 45 women who had undertaken DNA-NIPT recruited by purposive sampling based on socio-demographic and clinical characteristics. The sample included 31 women identified as high-risk from serum and ultrasound based Down syndrome screening (SU-DSS. Thematic narrative analysis examined informed-decision making of the test and identified the benefits and needs. Women outlined a number of reasons for accessing DNA-NIPT: reducing the uncertainty associated with risk probability-based results from SU-DSS, undertaking DNA-NIPT as a comprehensive measure to counteract risk from childbearing especially at advanced age, perceived predictive accuracy and absence of risk of harm to fetus. Accounts of women deemed high-risk or not high-risk are distinctive in a number of respects. High-risk women accessed DNA-NIPT to get a clearer idea of their risk. This group perceived SU-DSS as an unnecessary and confusing procedure because of its varying, protocol-dependent detection rates. Those women not deemed high-risk, in contrast, undertook DNA-NIPT for psychological assurance and to reduce anxiety even after receiving the negative result from SU-DSS. CONCLUSIONS: DNA-NIPT was regarded positively by women who chose this method of screening over the routine, less expensive testing options. Given its perceived utility, health providers need to consider whether DNA-NIPT should be offered as part of universal routine care to women at high-risk for fetal aneuploidy. If this is the case, then

  11. 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...

  12. Performance assessment of the GenoType MTBDRsl test and DNA sequencing for detection of second-line and ethambutol drug resistance among patients infected with multidrug-resistant Mycobacterium tuberculosis.

    Science.gov (United States)

    Huang, Wei-Lun; Chi, Ting-Lin; Wu, Mei-Hua; Jou, Ruwen

    2011-07-01

    The GenoType MTBDRsl test and DNA sequencing were used to rapidly detect second-line drug- and ethambutol (EMB)-resistant Mycobacterium tuberculosis. The ability of these two assays to detect the presence of mutations associated with resistance to fluoroquinolones (FLQ), aminoglycosides/cyclic peptide (AG/CP), and EMB in the gyrA, rrs, and embB genes (for the GenoType MTBDRsl test) and gyrA, gyrB, rrs, eis, embC, embA, embB, and embR genes (for DNA sequencing) was compared to that of conventional agar proportion drug susceptibility testing (DST). We evaluated 234 multidrug-resistant (MDR) M. tuberculosis isolates. The two molecular methods had high levels of specificity (95.8 to 100%). The sensitivities for FLQ resistance detection for both methods were 85.1%. For AG (kanamycin [KM] and amikacin [AM]) and CP (capreomycin CAP]), the sensitivities of resistance detection using the GenoType MTBDRsl test were 43.2%, 84.2%, and 71.4%, respectively, while with the inclusion of an extra gene, eis, in sequencing, the sensitivity reached 70.3% for detection of KM resistance. The sensitivities of EMB resistance detection were 56.2% and 90.7% with the GenoType MTBDRsl test and sequencing, respectively. We found that the GenoType MTBDRsl test can rapidly detect resistance to FLQ, CAP, and AM. The accuracy of the GenoType MTBDRsl test for the detection of FLQ and AM resistance was comparable to that of conventional DST; however, the test was less accurate for the detection of KM and EMB resistance and demonstrated a poor predictive value for CAP resistance. We recommend including new alleles consisting of the eis promoter and embB genes in molecular analysis. However, conventional DST is necessary to rule out false-negative results from molecular assays.

  13. Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II

    Directory of Open Access Journals (Sweden)

    Karen W. Hughes

    2015-06-01

    Full Text Available Gymnopus dichrous exists in the southern Appalachians (USA as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II. F1 ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F1 heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%. The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F1 fruitbodies showed no recombinant haplotypes within the ITS + LSU span and clones derived from P1 homozygotes were identical to the P1 parent. Thus, chimeric sequences are likely an artifact of the PCR-cloning process and not a consequence of natural recombination events found in nature, nor are they due to hidden existing variation within the ribosomal repeat. Chimeras and PCR-induced mutations are common in cloned PCR products and may result in incorrect sequence information in public databases.

  14. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  15. 在带OCL约束的状态图下测试线索的自动生成%Test sequence automate generation from state diagram with OCL constraints

    Institute of Scientific and Technical Information of China (English)

    曾一; 徐攀登; 柴艳欣; 邹明; 丁娜

    2011-01-01

    提出一种带OCL约束的状态图测试线索的自动生成方法.该方法自动解析类图和带OCL约束的状态图的XML模型文件,获取相应的状态节点邻接表,再结合状态对一事件约束集合生成带OCL约束的测试线索.实例研究表明,通过OCL约束冲突判断可避免不可行测试线索的生成,减少测试用例数目,达到降低测试成本的目的.实验结果证明了该方法的可行性和有效性.%This paper proposed an effective generation approach to test sequence from state diagram with OCL constraints. It acquired constitute corresponding adjacency list of state nodes by automatically analyzing XML model file of class diagram &state diagram with OCL constraints. Then, generated test sequence with OCL constraints based on state adjacency list & StatusCouple-Event set. The case research indicated that, the generation of infeasible testing sequence could be avoided through OCL restrict conflict judgement, and that it could effectively reduce the number of test case, so as to achieve the objective of reducing the test cost. This method was verified to be feasible and effective by experimental results.

  16. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

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

  17. Ingestão de glutamina e maltodextrina duas horas no pré-operatório imediato melhora a sensibilidade à insulina pós-operatória: estudo aleatório, duplo-cego e controlado Ingestion of glutamine and maltodextrin two hours preoperatively improves insulin sensitivity after surgery: a randomized, double blind, controlled trial

    Directory of Open Access Journals (Sweden)

    Diana Borges Dock-Nascimento

    2012-12-01

    randomly divided into three groups: conventional fasting (fasting group, and two groups receiving two different diets, eight hours (400ml and two hours before induction of anesthesia (200ml: carbohydrate (CHO group (12.5% dextrinomaltose and the glutamine (GLN group (12.5% dextrinomaltose and 40 and 10g of glutamine, respectively. Blood samples were collected pre and postoperatively. RESULTS: Twenty-eight patients completed the study. No pulmonary complication occurred. Gastric residual volume was similar between groups (p = 0.95. Postoperatively, all patients from the fasting group had abnormal glucose (> 110mg/dl, this abnormality being of 50% when compared to the CHO group (p = 0.14, and of 22.2% when compared to the GLN group (p = 0.01. All patients who had the fasting period shortened (CHO + GLN had normal postoperative insulin, contrasting with 66.7% in the fasted group (p = 0.02. The abnormal sensitivity to insulin postoperatively rose from 32.1% to 46.4% of cases (p = 0.24, and it occurred in only 11.1% of patients in GLN group when compared to 55.5% in the fasting group (p = 0.02. CONCLUSION: the abbreviation of preoperative fasting for two hours with dextrinomaltose and glutamine improves insulin sensitivity in patients undergoing elective laparoscopic cholecystectomy.

  18. 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...... the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56...... MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types...

  19. Matters Needing Attention in the Installation of Zero Sequence Current Transformer and Its Test Method%零序电流互感器安装注意事项及试验方法

    Institute of Scientific and Technical Information of China (English)

    初家祥

    2016-01-01

    In this paper, combined with the operating requirements of small resistance grounding system in 110kV total voltage transformer substation of Baotou Steel Corp, through connecting the zero sequence current transformer in primary cable by the protection device, the zero sequence current is extracted, the specific method of installation and inspection of the zero sequence current transformer is proposed and the problems should be paid attention to in the installation and the test of zero sequence current transformer are cleared to avoid the large measurement error of zero sequence current and the system grounding fault, protect refuse operation and override trip to ensure that the zero sequence current transformer really play a role.%本文结合包钢新体系110kV总降压变电站小电阻接地系统运行要求,保护装置通过在一次电缆安装外接零序电流互感器,来提取零序电流,提出一套规范零序电流互感器安装及检验方法,同时明确安装及零序电流互感器试验中须注意的问题,以避免产生较大的零序电流测量误差以及系统发生接地故障、保护拒动及越级跳闸等问题,确保零序电流互感器真正发挥作用。

  20. Feasibility and diagnostic accuracy of Ecg-gated SPECT myocardial perfusion imaging by a two-hour protocol: The Myofast study;Faisabilite et precision diagnostique d'un protocole de scintigraphie myocardique synchronisee a l'ECG en deux heures: l'etude Myofast

    Energy Technology Data Exchange (ETDEWEB)

    Dunet, V.; Costo, S.; Sabatier, R.; Grollier, G.; Bouvard, G.; Agostini, D. [CHU Cote-de-Nacre, Service de medecine nucleaire, 14 - Caen (France)

    2010-04-15

    Aim of the study: To assess the feasibility of early stress and rest myocardial perfusion and function study using a fast {sup 99m}Tc-tetrofosmin gated-SPECT protocol in patients with known coronary artery disease. Materials and methods: Forty-three patients (pts) (37 M, 6 F, mean age 63.8 +- 9.8 years) underwent a {sup 99m}Tc-Tetrofosmin gated-SPECT (Axis Picker-Philips) myocardial study and a coronary angiography (C.A.) within 3 months. Images were acquired (LEHR, eight bins, 40 sec per image) after injection of {sup 99m}Tc-tetrofosmin (200 to 380 MBq) early (15 min) post-stress (36 dipyridamole, two dobutamine and five ergo-metric stress), and at rest after {sup 99m}Tc-tetrofosmin reinjection (600 to 1150 MBq), in a total time not exceeding 2 hours. Processing was performed with Q.G.S. software using the 17-segment model. Pathological study was defined as a summed difference score (SDS) greater than or equal to 4 4, a fixed defect with summed rest score greater than or equal to 4 and/or L.V. dysfunction defined as myocardial stunning (variation between stress and rest L.V.E.F. greater than or equal to 4 5%), stress L.V.E.F. less than or equal to 45% or rest L.V.E.F. less than or equal to 40%. Results were compared with C.A., and stenosis greater than or equal to 4 50% was considered as significant. Results: For 100% the quality of SPECT imaging was good or excellent. For six patients gating was impossible because of arrhythmia. The overall sensitivity, specificity and accuracy were 95%, 50%, and 91%, respectively. The concordance between gated SPECT and C.A. was moderate (kappa = 0.45, S.E. = 0.15). Interestingly, early-gated acquisition permitted to underline left ventricular dysfunction in 11 cases (30%), of whom eight had poly vascular disease. Stunning was detected in six of 37 cases (16%), of whom six had poly vascular disease. Conclusion: A one-day two-hour {sup 99m}Tc-tetrofosmin gated-SPECT protocol to assess left ventricular perfusion and function is

  1. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seq...uence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  2. Improving Adequacy of Small Biopsy and Fine-Needle Aspiration Specimens for Molecular Testing by Next-Generation Sequencing in Patients With Lung Cancer: A Quality Improvement Study at Dartmouth-Hitchcock Medical Center.

    Science.gov (United States)

    Padmanabhan, Vijayalakshmi; Steinmetz, Heather B; Rizzo, Elizabeth J; Erskine, Amber J; Fairbank, Tamara L; de Abreu, Francine B; Tsongalis, Gregory J; Tafe, Laura J

    2017-03-01

    - At our medical center, cytopathologists perform rapid on-site evaluation for specimen adequacy of fine-needle aspiration and touch imprint of needle core biopsy lung cancer samples. Two years ago the molecular diagnostics laboratory at our institution changed to next-generation sequencing using the Ion Torrent PGM and the 50-gene AmpliSeq Cancer Hotspot Panel v2 for analyzing mutations in a 50-gene cancer hot spot panel. This was associated with a dramatic fall in adequacy rate (68%). - To improve the adequacy rate to at least 90% for molecular testing using next-generation sequencing for all specimens collected by rapid on-site evaluation by the cytology laboratory. - After baseline data on adequacy rate of cytology specimens with rapid on-site evaluation for molecular testing had been collected, 2 changes were implemented. Change 1 concentrated all the material in one block but did not produce desired results; change 2, in addition, faced the block only once with unstained slides cut up front for molecular testing. Data were collected in an Excel spreadsheet and adequacy rate was assessed. - Following process changes 1 and 2 we reached our goal of at least 90% adequacy rate for molecular testing by next-generation sequencing on samples collected by rapid on-site evaluation including computed tomography-guided needle core biopsies (94%; 17 of 18) and fine-needle aspiration samples (94%; 30 of 32). - This study focused on factors that are controllable in a pathology department and on maximizing use of scant tissue. Optimizing the adequacy of the specimen available for molecular tests avoids the need for a second procedure to obtain additional tissue.

  3. A abreviação do jejum pré-operatório para duas horas com carboidratos aumenta o risco anestésico? ¿La Reducción del ayuno preoperatorio en dos horas con carbohidratos aumenta el riesgo anestésico? Does abbreviation of preoperative fasting to two hours with carbohydrates increase the anesthetic risk?

    Directory of Open Access Journals (Sweden)

    Kátia Gomes Bezerra de Oliveira

    2009-10-01

    procedimiento quirúrgico. La recolección de datos fue prospectiva sin que los profesionales del servicio lo supieran. Se observó el tiempo de ayuno preoperatorio y las complicaciones anestésicas relacionadas con el corto tiempo de ayuno (broncoaspiración. RESULTADOS: Se evaluaron 375 pacientes, siendo de ellos 174 hombres (un 46,4% y 201 mujeres (un 53,6%, entre 18 y 90 años de edad. El tiempo promedio de ayuno preoperatorio fue de cuatro horas, variando de 2 a 20 horas. No se registró ningún caso de broncoaspiración durante los procedimientos. El tiempo de ayuno fue mayor (p BACKGROUND AND OBJECTIVES: The objective of the present study was to evaluate the incidence of possible anesthetic complications related with the abbreviation of preoperative fasting to two hours with a solution of 12.5% dextrinomaltose within the ACERTO (from the Portuguese for Acceleration of Total Postoperative Recovery project. METHODS: All patients undergoing different types of digestive tract and abdominal wall surgeries within a new protocol of perioperative conducts, established by the ACERTO project, between August 2005 and December 2007 were evaluated. All patients received oral nutritional supplementation (12.5% dextrinomaltose six and two hours before the procedure. Data were collected prospectively without the knowledge of the professionals in the department. The length of preoperative fasting and anesthetic complications related with the short fasting time (pulmonary aspiration were recorded. RESULTS: Three hundred and seventy five patients, 174 male (46.4% and 201 female (53.6%, ages 18 to 90 years, were evaluated. The mean preoperative fasting time was four hours, ranging from two to 20 hours. Pulmonary aspiration was not observed during the procedures. The length of fasting was longer (p < 0.01 when combined anesthesia (blockade + general was used. CONCLUSIONS: Adopting the multidisciplinary preoperative measures of the ACERTO project was not associated with any preoperative

  4. Testing the companion hypothesis for the origin of the X-ray emission from intermediate-mass main-sequence stars

    CERN Document Server

    Stelzer, B; Micela, G; Hubrig, S

    2006-01-01

    There is no straightforward explanation for intrinsic X-ray emission from intermediate-mass main-sequence stars. Therefore the observed emission is often interpreted in terms of (hypothesized) late-type magnetically active companion stars. We use Chandra imaging observations to spatially resolve in X-rays a sample of main-sequence B-type stars with recently discovered companions at arcsecond separation. We find that all spatially resolved companions are X-ray emitters, but seven out of eleven intermediate-mass stars are also X-ray sources. If this emission is interpreted in terms of additional sub-arcsecond or spectroscopic companions, this implies a high multiplicity of B-type stars. Firm results on B star multiplicity pending, the alternative, that B stars produce intrinsic X-rays, can not be discarded. The appropriate scenario in this vein is might be a magnetically confined wind, as suggested for the X-ray emission of the magnetic Ap star IQ Aur. However, the only Ap star in the Chandra sample is not dete...

  5. Evaluation of Mutational Testing of Preneoplastic Barrett's Mucosa by Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Endoscopic Samples for Detection of Concurrent Dysplasia and Adenocarcinoma in Barrett's Esophagus.

    Science.gov (United States)

    Del Portillo, Armando; Lagana, Stephen M; Yao, Yuan; Uehara, Takeshi; Jhala, Nirag; Ganguly, Tapan; Nagy, Peter; Gutierrez, Jorge; Luna, Aesis; Abrams, Julian; Liu, Yang; Brand, Randall; Sepulveda, Jorge L; Falk, Gary W; Sepulveda, Antonia R

    2015-07-01

    Barrett's intestinal metaplasia (BIM) may harbor genomic mutations before the histologic appearance of dysplasia and cancer and requires frequent surveillance. We explored next-generation sequencing to detect mutations with the analytical sensitivity required to predict concurrent high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC) in patients with Barrett's esophagus by testing nonneoplastic BIM. Formalin-fixed, paraffin-embedded (FFPE) routine biopsy or endoscopic mucosal resection samples from 32 patients were tested: nonprogressors to HGD or EAC (BIM-NP) with BIM, who never had a diagnosis of dysplasia or EAC (N = 13); progressors to HGD or EAC (BIM-P) with BIM and a worse diagnosis of HGD or EAC (N = 15); and four BIM-negative samples. No mutations were detected in the BIM-NP (0 of 13) or BIM-negative samples, whereas the BIM-P samples had mutations in 6 (75%) of 8 cases in TP53, APC, and CDKN2A (P = 0.0005), detected in samples with as low as 20% BIM. We found that next-generation sequencing from routine FFPE nonneoplastic Barrett's esophagus samples can detect multiple mutations in minute areas of BIM with high analytical sensitivity. Next-generation sequencing panels for detection of TP53 and possibly combined mutations in other genes, such as APC and CDKN2A, may be useful in the clinical setting to improve dysplasia and cancer surveillance in patients with Barrett's esophagus.

  6. Molecular clock hypothesis testing based on mitochondrial cytochrome b gene sequence of subfamily bovinae%以牛亚科家畜线粒体细胞色素b基因全序列检验分子钟假说

    Institute of Scientific and Technical Information of China (English)

    耿荣庆; 王兰萍; 常洪; 冀德君; 李永红; 常春芳

    2011-01-01

    To provide some objective data for accepting or refusing molecular clock hypothesis, non-parameter test method was employed based on mitochondrial cytochrome b gene sequence of six species of subfamily bovinae. The complete cytochrome b gene was 1 140 bp in length for all six bovine species and there was a little difference in base composition between species. Transition was the dominant base substitution model and the ratio of transition to transversion was 5.4. The testing results of relative evolution rate based on nucleotide sequences and amino acid sequences showed that molecular clock hypothesis was accepted absolutely within bovine species. The evolution of only a few sequences refused molecular clock hypothesis and evolution of most sequencesaccepted it among the species. It was easier to refuse molecular clock hypothesis based on the testing result from nucleotide sequence than the result from amino acid sequence. There was no obvious correlation between accepting or refusing molecular clock hypothesis and genetic distance between tested species. Molecular clock existed in some species. There was no nucleotide sequence or amino acid sequence varying in an absolutely stable rate in long evolution, and molecular clock was not unicersal.%在测定牛亚科家畜6个物种线粒体细胞色素b(Cyt b)基因全序列的基础上,以非参数检验法检验分子钟假说,提出肯定或否定分子钟假说的部分客观资料.结果表明,6个牛种的Cyt b基因全序列长度都是1140bp,牛种间序列的碱基组成差异较小,碱基替代以转换为主,转换/颠换比为5.4.基于核苷酸序列和氨基酸相对速率检验结果表明,牛种内序列的进化全部接受分子钟假说;牛种问大多数序列的进化接受分子钟假说,少数序列的进化拒绝分子钟假说.与基于氨基酸序列的检验结果相比较,基于核苷酸序列的检验结果更易于拒绝分子钟假说.进而推论,接受或者拒绝分子钟假说与所

  7. A CAPS test allowing a rapid distinction of Penicillium expansum among fungal species collected on grape berries, inferred from the sequence and secondary structure of the mitochondrial SSU-rRNA.

    Science.gov (United States)

    Garcia, Carole; La Guerche, Stéphane; Mouhamadou, Bello; Férandon, Cyril; Labarère, Jacques; Blancard, Dominique; Darriet, Philippe; Barroso, Gérard

    2006-10-01

    Penicillium expansum is a fungal species highly damageable for the postharvest conservation of numerous fruits. In vineyards, this fungus is sometimes isolated from grape berries where its presence may lead to the production of geosmin, a powerful earthy odorant, which can impair grapes and wines aromas. However, the discrimination of P. expansum from related fungi is difficult because it is based on ambiguous phenotypic characters and/or expensive and time-consuming molecular tests. In this context, the complete sequences and secondary structures of Penicillium expansum and Penicillium thomii mitochondrial SSU-rRNAs were achieved and compared with those of two other phylogenetically related Ascomycota: Penicillium chrysogenum and Emericella nidulans. The comparison has shown a high conservation in size and sequence of the core and of the variable domains (more than 80% of nt identity) of the four SSU-rRNAs, arguing for a close phylogenetic relationship between these four species of the Trichocomaceae family. Large (from 10 to 18 nt) inserted/deleted (indel) sequences were evidenced in the V1, V5 and V6 variable domains. The size variations (10 to 18 nt) of the V1 indel sequence allowed the distinction of the four species; the V5 indel (15 nt) was specifically recovered in E. nidulans; the V6 indel (16 nt), shared by the three Penicillium species, was lacking in E. nidulans. A couple of conserved primers (UI/R2) were defined to generate a PCR product containing the V1 to V5 variable domains. This product contained the two regions of the four SSU-rRNAs showing the highest rates of nt substitutions, namely the V2 variable domain and, surprisingly, a helix (H17) of the core. The H17 sequence was shown to specifically possess in P. expansum a recognition site for the ClaI restriction endonuclease. Hence, this enzyme generates a digestion pattern of the PCR product with two bands (350 bp+500 bp), specific to P. expansum and easily separable by agarose gel

  8. A test of the asteroseismic numax scaling relation for solar-like oscillations in main-sequence and sub-giant stars

    CERN Document Server

    Coelho, H R; Basu, S; Serenelli, A; Miglio, A; Reese, D R

    2015-01-01

    Large-scale analyses of stellar samples comprised of cool, solar-like oscillators now commonly utilize the so-called asteroseismic scaling relations to estimate fundamental stellar properties. In this paper we present a test of the scaling relation for the global asteroseismic parameter $\

  9. The Distances to Open Clusters from Main-Sequence Fitting. V. Extension of Color Calibration and Test using Cool and Metal-Rich Stars in NGC 6791

    CERN Document Server

    An, Deokkeun; Pinsonneault, Marc H; Lee, Jae-Woo

    2015-01-01

    We extend our effort to calibrate stellar isochrones in the Johnson-Cousins ($BVI_C$) and the 2MASS ($JHK_s$) filter systems based on observations of well-studied open clusters. Using cool main-sequence (MS) stars in Praesepe, we define empirical corrections to the Lejeune et al. color-effective temperature ($T_{\\rm eff}$) relations down to $T_{\\rm eff} \\sim 3600$ K, complementing our previous work based on the Hyades and the Pleiades. We apply empirically corrected isochrones to existing optical and near-infrared photometry of cool ($T_{\\rm eff} \\leq 5500$ K) and metal-rich ([Fe/H]$=+0.37$) MS stars in NGC 6791. The current methodology relies on an assumption that color-$T_{\\rm eff}$ corrections are independent of metallicity, but we find that estimates of color-excess and distance from color-magnitude diagrams with different color indices converge on each other at the precisely known metallicity of the cluster. Along with a satisfactory agreement with eclipsing binary data in the cluster, we view the improv...

  10. Characterization and potential of three temperature ranges for hydrogen fermentation of cellulose by means of activity test and 16s rRNA sequence analysis.

    Science.gov (United States)

    Gadow, Samir I; Jiang, Hongyu; Li, Yu-You

    2016-06-01

    A series of standardized activity experiments were performed to characterize three different temperature ranges of hydrogen fermentation from different carbon sources. 16S rRNA sequences analysis showed that the bacteria were close to Enterobacter genus in the mesophilic mixed culture (MMC) and Thermoanaerobacterium genus in the thermophilic and hyper-thermophilic mixed cultures (TMC and HMC). The MMC was able to utilize the glucose and cellulose to produce methane gas within a temperature range between 25 and 45 °C and hydrogen gas from 35 to 60°C. While, the TMC and HMC produced only hydrogen gas at all temperature ranges and the highest activity of 521.4mlH2/gVSSd was obtained by TMC. The thermodynamic analysis showed that more energy is consumed by hydrogen production from cellulose than from glucose. The experimental results could help to improve the economic feasibility of cellulosic biomass energy using three-phase technology to produce hythane.

  11. Rotating Massive Main-Sequence Stars II: Simulating a Population of LMC early B-type Stars as a Test of Rotational Mixing

    CERN Document Server

    Brott, Ines; Hunter, Ian; de Koter, Alex; Langer, Norbert; Dufton, Philip L; Cantiello, Matteo; Trundle, Carrie; Lennon, Danny J; de Mink, Selma E; Yoon, Sung-Chul; Anders, Peter

    2011-01-01

    Rotational mixing in massive stars is a widely applied concept, with far reaching consequences for stellar evolution. Nitrogen surface abundances for a large and homogeneous sample of massive B-type stars in the LMC were obtained by the VLT-FLAMES Survey of Massive Stars. This sample is the first covering a broad range of projected stellar rotational velocities, with a large enough sample of high quality data to allow for a statistically significant analysis. We use the sample to provide the first rigorous test of the theory of rotational mixing in massive stars. We calculated a grid of stellar evolution models, using the FLAMES sample to calibrate some of the uncertain mixing processes. We developed a new population-synthesis code, which uses this grid to simulate a large population of stars with masses, ages and rotational velocity distributions consistent with those from the FLAMES sample. The synthesized population is then filtered by the selection effects in the observed sample, to enable a direct compar...

  12. Incidental Sequence Learning across the Lifespan

    Science.gov (United States)

    Weiermann, Brigitte; Meier, Beat

    2012-01-01

    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

  13. 线粒体D-loop序列变异与东方鲀属鱼类系统发育%PHYLOGENETIC RELATIONSHIPS OF THE GENUS TAKIFUGU (TETRAODONTIFORMES, TETRAODONTIDAE) TESTED BY mtDNA D-LOOP REGION SEQUENCE VARIATIONS

    Institute of Scientific and Technical Information of China (English)

    张玉波; 甘小妮; 何舜平

    2009-01-01

    The pufferfishes of the genus Takifugu are East Asian fish, mainly distribute along the coastal region in western part of the Sea of Japan and the East China. This genus is attached more and more importance to researchers, for Takifugu rubripes, which is one species in it, has been a new model fish in the post-genomic era. The details of the phylogenetic relationships within the genus remain unresolved. In the present paper, mitochondrial D-loop sequences of 11 species of the genus Takifugu were determined and analyzed to test the present phylogenetic hypotheses. The sequence saturation analysis was inferred from the shape of the trend line, which indicated that the sequence was unsaturated and could be used in the following phylogenetic analysis. After alignment, the sequence compositions and variations were analyzed by using MEGA 3 software. There were 841 sites, among which 395 sites were variable, and 267 were informative. There was significant difference in base compositional bias between the ingroup and the outgroup species. The uncorrected p-distance matrix obtained from the analysis of the alignment of all D-loop sequences showed that the relationships among the different species were closely. Neighbor-joining, Maximum Parsimony, Maximum Likelihood and Bayesian methods were employed for phylogenetics analysis, respectively. Due to the SH test about the phylogeny hypothesis, we chose the Bayesian tree as our best tree in this paper. The Bayesian tree has described a more clearly phylogeny and the analysis also has pointed out the basal species in the genus. The results indicate that the genus form a monophyletic groups, with the sister group consisted by T. oblongus and T. alboplumbeus is the basal group of the genus. Our results also show some confusion about the taxonomy in the genus, according to the data and combined analysis with the morphological characters, we suppose some species are in fact synonymous in this genus, which suggest that the taxonomy

  14. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  15. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_seq...uence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  16. 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.

  17. High-precision Radio and Infrared Astrometry of LSPM J1314+1320AB. II. Testing Pre-main-sequence Models at the Lithium Depletion Boundary with Dynamical Masses

    Science.gov (United States)

    Dupuy, Trent J.; Forbrich, Jan; Rizzuto, Aaron; Mann, Andrew W.; Aller, Kimberly; Liu, Michael C.; Kraus, Adam L.; Berger, Edo

    2016-08-01

    We present novel tests of pre-main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of 92.8 ± 0.6 M Jup (0.0885 ± 0.0006 M ⊙) and 91.7 ± 1.0 M Jup (0.0875 ± 0.0010 M ⊙) and a parallactic distance of 17.249 ± 0.013 pc. We find component luminosities consistent with the system being coeval at 80.8 ± 2.5 Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first test of the theoretical lithium depletion boundary using ultracool dwarfs of known mass. However, we find that the evolutionary model-derived average effective temperature (2950 ± 5 K) is 180 K hotter than that given by a spectral type-{T}{eff} relation based on BT-Settl models (2770 ± 100 K). We suggest that the dominant source of this discrepancy is model radii being too small by ≈13%. In a test mimicking the typical application of models by observers, we derive masses on the H-R diagram using luminosity and BT-Settl temperature. The estimated masses are lower by {46}-19+16 % (2.0σ) than we measure dynamically and would imply that this is a system of ≈50 M Jup brown dwarfs, highlighting the large systematic errors possible in H-R diagram properties. This is the first time masses have been measured for ultracool (≥M6) dwarfs displaying spectral signatures of low gravity. Based on features in the infrared, LSPM J1314+1320AB appears to have higher gravity than typical Pleiades and AB Dor members, opposite the expectation given its younger age. The components of LSPM J1314+1320AB are now the nearest, lowest mass pre-main-sequence stars with direct mass measurements. Data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the

  18. High-Precision Radio and Infrared Astrometry of LSPM J1314+1320AB - II: Testing Pre--Main-Sequence Models at the Lithium Depletion Boundary with Dynamical Masses

    CERN Document Server

    Dupuy, Trent J; Rizzuto, Aaron; Mann, Andrew W; Aller, Kimberly; Liu, Michael C; Kraus, Adam L; Berger, Edo

    2016-01-01

    We present novel tests of pre$-$main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of our Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of $0.0885\\pm0.0006$ $M_{\\odot}$ and $0.0875\\pm0.0010$ $M_{\\odot}$ and a parallactic distance of $17.249\\pm0.013$ pc. We also derive component luminosities that are consistent with the system being coeval at an age of $80.8\\pm2.5$ Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first time the theoretical lithium depletion boundary has been tested with ultracool dwarfs of known mass. However, we find that the average evolutionary model-derived effective temperature ($2950\\pm5$ K) is 180 K hotter than we derive from a spectral type$-$$T_{\\rm eff}$ relation based on BT-Settl models ($2770\\pm100$ K). We suggest that the dominant source of this discrepancy is mod...

  19. 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...

  20. Coordinate cytokine regulatory sequences

    Science.gov (United States)

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

    2005-05-10

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

  1. Experimental investigation of an RNA sequence space

    Science.gov (United States)

    Lee, Youn-Hyung; Dsouza, Lisa; Fox, George E.

    1993-12-01

    Modern rRNAs are the historic consequence of an ongoing evolutionary exploration of a sequence space. These extant sequences belong to a special subset of the sequence space that is comprised only of those primary sequences that can validly perform the biological function(s) required of the particular RNA. If it were possible to readily identify all such valid sequences, stochastic predictions could be made about the relative likelihood of various evolutionary pathways available to an RNA. Herein an experimental system which can assess whether a particular sequence is likely to have validity as a eubacterial 5S rRNA is described. A total of ten naturally occurring, and hence known to be valid, sequences and two point mutants of unknown validity were used to test the usefulness of the approach. Nine of the ten valid sequences tested positive whereas both mutants tested as clearly defective. The tenth valid sequence gave results that would be interpreted as reflecting a borderline status were the answer not known. These results demonstrate that it is possible to experimentally determine which sequences in local regions of the sequence space are potentially valid 5S rRNAs. This approach will allow direct study of the constraints governing RNA evolution and allow inquiry into how the last common ancestor of extant life apparently came to have very complex ribosomal RNAs that subsequently were very conserved.

  2. Two Hours of Teamwork Training Improves Teamwork in Simulated Cardiopulmonary Arrest Events.

    Science.gov (United States)

    Mahramus, Tara L; Penoyer, Daleen A; Waterval, Eugene M E; Sole, Mary L; Bowe, Eileen M

    2016-01-01

    Teamwork during cardiopulmonary arrest events is important for resuscitation. Teamwork improvement programs are usually lengthy. This study assessed the effectiveness of a 2-hour teamwork training program. A prospective, pretest/posttest, quasi-experimental design assessed the teamwork training program targeted to resident physicians, nurses, and respiratory therapists. Participants took part in a simulated cardiac arrest. After the simulation, participants and trained observers assessed perceptions of teamwork using the Team Emergency Assessment Measure (TEAM) tool (ratings of 0 [low] to 4 [high]). A debriefing and 45 minutes of teamwork education followed. Participants then took part in a second simulated cardiac arrest scenario. Afterward, participants and observers assessed teamwork. Seventy-three team members participated-resident physicians (25%), registered nurses (32%), and respiratory therapists (41%). The physicians had significantly less experience on code teams (P teamwork scores were 2.57 to 2.72. Participants' mean (SD) scores on the TEAM tool for the first and second simulations were 3.2 (0.5) and 3.7 (0.4), respectively (P teamwork educational intervention resulted in improved perceptions of teamwork behaviors. Participants reported interactions with other disciplines, teamwork behavior education, and debriefing sessions were beneficial for enhancing the program.

  3. One-two hour scale evolution of the inner magnetospheric plasma

    Science.gov (United States)

    Yamauchi, Masatoshi; Dandouras, Iannis; Reme, Henri; Lundin, Rickard

    2013-04-01

    In the inner magnetosphere inside the geosynchronous orbit, energy-latitude patterns of trapped low-energy ring current ions (eastward drifting energy domain of less than 5 keV) are normally north-south symmetric because these ions are bouncing between southern and northern hemispheres with short bouncing periods (only about 10 minutes for 100 eV proton and 1 minutes for 10 keV protons at L=4). Therefore, for inner magnetospheric phenomena with longer time scale than few tens minutes, one can ignore the hemispheric difference when examining temporal changes of the ion distribution at a fixed latitude (or L value) and longitude. This fact gives an advantage to Cluster that has relatively quick perigee traversals and nearly north-south symmetric orbits, i.e., along nearly the same longitude (longitudinal difference between inbound and outbound is less than 1-2 hours) during 2001-2006. Therefore, any significant asymmetry in the ion energy-latitude pattern observed during the Cluster perigee traversals during 2001-2006 means a temporal effect such as ion energization, transport, or loss, with the time scale of order of an hour. After removing traversals in which ion data are severely contaminated by the radiation belt particles (about one third of all traversals), e took statistics the inbound-outbound asymmetry of the ion population and its energy-latitude patterns at low energy (less than several keV) for the remaining 494 perigee traversals of Cluster spacecraft 4 during 2001-2006. As the baseline, we considered the following two ion populations that are commonly found in Cluster data: (1) Wedge-like energy-latitude structure at sub-keV range. (2) Similar to the wedge-like structure but dispersion is weak (nearly vertical in the spectrogram) and the energy range extends from the about 10 keV to sub-keV (Yamauchi et al., 2006). For both types, the asymmetric cases are observed more frequently than the symmetric cases at all local time. The excess of the asymmetric case is reasonable for the second type that is most frequently observed at post-midnight because at this population is most likely related to the substorm injection. However, the excess of the asymmetric case for the wedge-like structure (first type) is unexpected because it is formed after long-time drift with slow drifting velocity. The peak local time for the asymmetric wedge-like structure is morning, whereas symmetric case is peaked at prenoon.

  4. 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.

  5. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  6. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-04-25

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

  7. Understanding Laboratory Tests

    Science.gov (United States)

    ... and Drug Administration (FDA) regulates the development and marketing of all laboratory tests that use test kits ... are of great interest in cancer medicine because research suggests that levels of ... sequencing methods are being developed to provide gene mutation profiles ...

  8. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  9. Concept For Generation Of Long Pseudorandom Sequences

    Science.gov (United States)

    Wang, C. C.

    1990-01-01

    Conceptual very-large-scale integrated (VLSI) digital circuit performs exponentiation in finite field. Algorithm that generates unusually long sequences of pseudorandom numbers executed by digital processor that includes such circuits. Concepts particularly advantageous for such applications as spread-spectrum communications, cryptography, and generation of ranging codes, synthetic noise, and test data, where usually desirable to make pseudorandom sequences as long as possible.

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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....

  15. Quantitative biostratigraphy and species evolutionary se-quence

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Introduction of species evolutionary sequence into the quantitative biostratigraphy is a significant work, either for studying biologic evolution or for making stratigraphic correlation and reconstructing geologic history. The quantitative biostratigraphy is to determine biostratigraphic event sequences by using probabilistic analysis. The evolutionary sequence systematics can efficiently ascertain species evolutionary sequences. Two methods have been proposed to determine the sequence of species-disappearance events: (1) species extinction events can be closed by last occurrence events using quantitative biostratigraphic analysis; (2) the duration of a species may be approximately replaced by the duration of its parent species. To combine these two methods for determining the sequence of species disappearance is the best way up to now. A consulting standard sequence that consists of the speciation sequence of Permian waagenophylloid corals and the biostratigraphic event sequence of other important fossils in Permian is used as an example. The group spearman rank-correlation test is used to test the consulting standard sequence by comparing four types of calculations and two kinds of sequences and to find abnormal events. Based on the found abnormal events in the test, the consulting standard sequence is revised to deal with different conditions. Sequences of speciation and species-disappearance, and species duration are determined. Application of species evolutionary sequence to quantitative biostratigraphy can largely improve the quality of biostratigraphic event sequence. In stratigraphic correlation, furthermore, event sequences have higher precision than range biozones.

  16. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  17. 46 CFR 160.041-5 - Inspections and tests.

    Science.gov (United States)

    2010-10-01

    ... temperature of 150 °F. for one hour and then to a temperature of 30 °F. below zero for one hour. There shall... one foot of water for a period of two hours. At the end of this period the container shall be removed.... Four cartons from each container tested shall be submerged under a head of one foot of water for...

  18. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  19. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  20. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca

    2014-05-01

    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 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 and occur in formulae simultaneously with the latter.

  1. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu

    2012-01-01

    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  2. 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

  3. Randomness in Sequence Evolution Increases over Time.

    Directory of Open Access Journals (Sweden)

    Guangyu Wang

    Full Text Available The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution.

  4. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

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

    Science.gov (United States)

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

    2009-03-01

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

  6. FAMSA: Fast and accurate multiple sequence alignment of huge protein families

    Science.gov (United States)

    Deorowicz, Sebastian; Debudaj-Grabysz, Agnieszka; Gudyś, Adam

    2016-01-01

    Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms, such as Clustal Omega or MAFFT for datasets exceeding a few thousand sequences. Quality does not compromise on time or memory requirements, which are an order of magnitude lower than those in the existing solutions. For example, a family of 415519 sequences was analyzed in less than two hours and required no more than 8 GB of RAM. FAMSA is available for free at http://sun.aei.polsl.pl/REFRESH/famsa. PMID:27670777

  7. Multiplexed microsatellite recovery using massively parallel sequencing.

    Science.gov (United States)

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

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  8. Locomotor sequence learning in visually guided walking.

    Science.gov (United States)

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

    2016-04-01

    Voluntary limb modifications must be integrated with basic walking patterns during visually guided walking. In this study we tested whether voluntary gait modifications can become more automatic with practice. We challenged walking control by presenting visual stepping targets that instructed subjects to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence-nonspecific learning during walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 yr,n= 20) could learn a specific sequence of step lengths over 300 training steps. Younger children (age 6-10 yr,n= 8) had lower baseline performance, but their magnitude and rate of sequence learning were the same compared with those of older children (11-16 yr,n= 10) and healthy adults. In addition, learning capacity may be more limited at faster walking speeds. To our knowledge, this is the first study to demonstrate that spatial sequence learning can be integrated with a highly automatic task such as walking. These findings suggest that adults and children use implicit knowledge about the sequence to plan and execute leg movement during visually guided walking.

  9. Hardware bitstream sequence recognizer

    OpenAIRE

    Karpin, Oleksandr; Sokil, Volodymyr

    2009-01-01

    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  10. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  11. DNA sequencing by CE.

    Science.gov (United States)

    Karger, Barry L; Guttman, András

    2009-06-01

    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 multiCE 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 were only possible with the advent of modern sequencing technologies that were 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 breakneck 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 CE in DNA sequencing based in part of several of our articles in this journal.

  12. Sequencing the maize genome.

    Science.gov (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  13. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  14. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

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

  15. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    OpenAIRE

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  16. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  17. Pitfalls in genetic testing

    DEFF Research Database (Denmark)

    Djémié, Tania; Weckhuysen, Sarah; von Spiczak, Sarah

    2016-01-01

    BACKGROUND: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying...

  18. Combinatorial Testing for VDM

    DEFF Research Database (Denmark)

    Larsen, Peter Gorm; Lausdahl, Kenneth; Battle, Nick

    2010-01-01

    by forgotten preconditions as well as broken invariants and post-conditions. Trace definitions are defined as regular expressions describing possible sequences of operation calls, and are conceptually similar to UML sequence diagrams. In this paper we present a tool enabling test automation based on VDM traces...

  19. 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.

  20. GASP: Gapped Ancestral Sequence Prediction for proteins

    Directory of Open Access Journals (Sweden)

    Shields Denis C

    2004-09-01

    Full Text Available Abstract Background The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel events or sequence fragments. Results Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction, for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. Conclusions GASP (Gapped Ancestral Sequence Prediction will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.

  1. GASP: Gapped Ancestral Sequence Prediction for proteins.

    Science.gov (United States)

    Edwards, Richard J; Shields, Denis C

    2004-09-06

    The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.

  2. 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.

  3. The double main sequence of Omega Centauri

    CERN Document Server

    Bedin, L R

    2004-01-01

    Recent, high precision photometry of Omega Centauri, the biggest Galactic globular cluster, has been obtained with Hubble Space Telescope. The color magnitude diagram reveals an unexpected bifurcation of colors in the main sequence (MS). The newly found double MS, the multiple turnoffs and subgiant branches, and other sequences discovered in the past along the red giant branch of this cluster add up to a fascinating but frustrating puzzle. Among the possible explanations for the blue main sequence an anomalous overabundance of helium is suggested. The hypothesis will be tested with a set of FLAMES@VLT data we have recently obtained (ESO DDT program), and with forthcoming ACS@HST images.

  4. Tests on the directional elements of zero-sequence power of 110 kV line for Yamzho Yumco Pumped Storage Station under the load condition%羊湖电厂110 kV线路零序功率 方向元件带负荷试验

    Institute of Scientific and Technical Information of China (English)

    戴雪梅; 尹晓霞

    2001-01-01

    按绝对值比较原理构成的零序功率方向元件,在零序电流方向保护中应用极为广泛。在常规的模拟调试中难以直接模拟出运行状态下接地故障时的零序电流和零序电压,因此要正确判断零序功率方向元件接线的正确与否,应在带负荷状态下,用负荷电流通过人为改变保护用的电流互感器和电压互感器二次回路的接线方式,来达到试验目的。%:The directional element of zero-sequence power, as a judgment element, is made in accordance with the absolute value comparison principle and is widely applied in the direction protection of zero-sequence current. In the routine simulation tests, it is difficult to simulate directly the zero-sequence current and voltage under the operation condition during earthing failure. In order to judge accurately the correctness of the connection of directional elements of zero-sequence power, the tests should be made under load condition. In this way, we can use load current to change the protective current transformer and potential transformer to reach the test objective.

  5. Space Suit Portable Life Support System (PLSS) 2.0 Unmanned Vacuum Environment Testing

    Science.gov (United States)

    Watts, Carly; Vogel, Matthew

    2016-01-01

    For the first time in more than 30 years, an advanced space suit Portable Life Support System (PLSS) design was operated inside a vacuum chamber representative of the flight operating environment. The test article, PLSS 2.0, was the second system-level integrated prototype of the advanced PLSS design, following the PLSS 1.0 Breadboard that was developed and tested throughout 2011. Whereas PLSS 1.0 included five technology development components with the balance the system simulated using commercial-off-the-shelf items, PLSS 2.0 featured first generation or later prototypes for all components less instrumentation, tubing and fittings. Developed throughout 2012, PLSS 2.0 was the first attempt to package the system into a flight-like representative volume. PLSS 2.0 testing included an extensive functional evaluation known as Pre-Installation Acceptance (PIA) testing, Human-in-the-Loop testing in which the PLSS 2.0 prototype was integrated via umbilicals to a manned prototype space suit for 19 two-hour simulated EVAs, and unmanned vacuum environment testing. Unmanned vacuum environment testing took place from 1/9/15-7/9/15 with PLSS 2.0 located inside a vacuum chamber. Test sequences included performance mapping of several components, carbon dioxide removal evaluations at simulated intravehicular activity (IVA) conditions, a regulator pressure schedule assessment, and culminated with 25 simulated extravehicular activities (EVAs). During the unmanned vacuum environment test series, PLSS 2.0 accumulated 378 hours of integrated testing including 291 hours of operation in a vacuum environment and 199 hours of simulated EVA time. The PLSS prototype performed nominally throughout the test series, with two notable exceptions including a pump failure and a Spacesuit Water Membrane Evaporator (SWME) leak, for which post-test failure investigations were performed. In addition to generating an extensive database of PLSS 2.0 performance data, achievements included requirements and

  6. 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...

  7. Scope and Sequence.

    Science.gov (United States)

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  8. Evolution of DNA sequencing

    National Research Council Canada - National Science Library

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-01-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted...

  9. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  10. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.

    2014-01-01

    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  11. Gomphid DNA sequence data

    Data.gov (United States)

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

  12. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan

    2014-12-01

    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  13. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    million cases and up to 2.7 million A whole chromosome shotgun sequencing strategy was used to deaths from malaria each year. The mortality levels are...deaths from malaria each year. The mortality levels are greatest in determine the genome sequence of P. falciparum clone 3D7. This sub-Saharan Africa...aminolevulinic acid dehydratase. Cura . Genet. 40, 391-398 (2002). 15. Lasonder, E. et al Analysis of the Plasmodium falciparum proteome by high-accuracy mass

  14. Biological sequence analysis

    DEFF Research Database (Denmark)

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

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

  15. Genome sequencing conference II

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  16. 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.

  17. CEQATR Thermal Test Overview

    Science.gov (United States)

    Balusek, Alan R.

    2009-01-01

    A thermal test overview of the Constellation Environmental Qualification and Acceptance Test Requirement (CEQATR) is presented. The contents include: 1) CEQATR Thermal Test Overview; 2) CxP Environments; 3) CEQATR Table 1.2-1; 4) Levels of Assembly; 5) Definitions for Levels of Assembly; 6) Hardware Applicability; 7) CEQATR Thermal-Related Definitions; 8) Requirements for unit-level thermal testing; 9) Requirements for major assembly level thermal testing; 10) General thermal testing requirements; 11) General thermal cycle, thermal vacuum profiles; 12) Test tolerances; 13) Vacuum vs Ambient; 14) Thermal Gradient; 15) Sequence of Testing; 16) Alternative Strategies; 17) Protoflight; 18) Halt/Hass; 19) Humidity; and 20) Tailoring.

  18. Pitfalls in genetic testing

    DEFF Research Database (Denmark)

    Djémié, Tania; Weckhuysen, Sarah; von Spiczak, Sarah;

    2016-01-01

    BACKGROUND: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying...... mutations. METHODS: We sent out a survey to 16 genetic centers performing SCN1A testing. RESULTS: We collected data on 28 mutations initially missed using Sanger sequencing. All patients were falsely reported as SCN1A mutation-negative, both due to technical limitations and human errors. CONCLUSION: We...

  19. Timing issues in distributed testing

    Institute of Scientific and Technical Information of China (English)

    HUANG Chuan-dong; JIANG Fan

    2007-01-01

    The objective of conformance testing is to determine whether an implementation under test (IUT) conforms to its specification. In distributed test architecture where there are multiple remote testers, the objective can be complicated by the fact that testers may encounter controllability and observability problems during the application of a test sequence. A certain amount of work has been done in the area of generating test sequence that is free from these problems. However, few researchers investigate them from the aspect of test execution. This work studies the test execution phase when test sequences are applied to the implementation and it is pointed out that controllability and observability problems can be resolved if and only if the test system implements some timing constraints. When determining these constraints, the dynamic time information during test is taken into account, which reduces the test execution time and improves test efficiency further.

  20. Testing of the Sunstove Organization`s Sunstove Solar Oven

    Energy Technology Data Exchange (ETDEWEB)

    Moss, T.A.

    1997-03-01

    A Sunstove Organization`s Sunstove was tested at Sandia`s Solar Thermal Test Facility. It was instrumented with five type K thermocouples to determine warm-up rates when empty and when a pot containing two liters of water was placed inside. It reached inside air temperatures above 115{degrees}C (240{degrees}F). It heated two liters of water from room temperature to 80{degrees}C (175{degrees}F) in about two hours. Observations were made on the cooling and reheating rates during a cloud passage. The adverse effects of wind on the operation of the solar oven were also noted.

  1. Differential correlation for sequencing data.

    Science.gov (United States)

    Siska, Charlotte; Kechris, Katerina

    2017-01-19

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from -omics studies. Most DC methods have only been tested with microarrays and other platforms producing continuous and Gaussian-like data. Sequencing data is in the form of counts, often modeled with a negative binomial distribution making it difficult to apply standard correlation metrics. We have developed an R package for identifying DC called Discordant which uses mixture models for correlations between features and the Expectation Maximization (EM) algorithm for fitting parameters of the mixture model. Several correlation metrics for sequencing data are provided and tested using simulations. Other extensions in the Discordant package include additional modeling for different types of differential correlation, and faster implementation, using a subsampling routine to reduce run-time and address the assumption of independence between molecular feature pairs. With simulations and breast cancer miRNA-Seq and RNA-Seq data, we find that Spearman's correlation has the best performance among the tested correlation methods for identifying differential correlation. Application of Spearman's correlation in the Discordant method demonstrated the most power in ROC curves and sensitivity/specificity plots, and improved ability to identify experimentally validated breast cancer miRNA. We also considered including additional types of differential correlation, which showed a slight reduction in power due to the additional parameters that need to be estimated, but more versatility in applications. Finally, subsampling within the EM algorithm considerably decreased run-time with negligible effect on performance. A new method and R package called Discordant is presented for identifying differential correlation with sequencing data. Based on comparisons with different correlation metrics, this study suggests Spearman's correlation is appropriate for sequencing data

  2. Multiple sequence alignment accuracy and evolutionary distance estimation.

    Science.gov (United States)

    Rosenberg, Michael S

    2005-11-23

    Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic position of the additional sequence relative to the first pair changes the accuracy of the initial pair's alignment as well as their estimated evolutionary distance. The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other). Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences. The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.

  3. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    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.

  4. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

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

  5. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

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

  6. Movement sequencing in Huntington disease.

    Science.gov (United States)

    Georgiou-Karistianis, Nellie; Long, Jeffrey D; Lourens, Spencer G; Stout, Julie C; Mills, James A; Paulsen, Jane S

    2014-08-01

    To examine longitudinal changes in movement sequencing in prodromal Huntington's disease (HD) participants (795 prodromal HD; 225 controls) from the PREDICT-HD study. Prodromal HD participants were tested over seven annual visits and were stratified into three groups (low, medium, high) based on their CAG-Age Product (CAP) score, which indicates likely increasing proximity to diagnosis. A cued movement sequence task assessed the impact of advance cueing on response initiation and execution via three levels of advance information. Compared to controls, all CAP groups showed longer initiation and movement times across all conditions at baseline, demonstrating a disease gradient for the majority of outcomes. Across all conditions, the high CAP group had the highest mean for baseline testing, but also demonstrated an increase in movement time across the study. For initiation time, the high CAP group showed the highest mean baseline time across all conditions, but also faster decreasing rates of change over time. With progress to diagnosis, participants may increasingly use compensatory strategies, as evidenced by faster initiation. However, this occurred in conjunction with slowed execution times, suggesting a decline in effectively accessing control processes required to translate movement into effective execution.

  7. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  8. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr

    2015-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar\\'e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular $S$-matrix. This leads to the identifi...

  9. Gelada vocal sequences follow Menzerath's linguistic law.

    Science.gov (United States)

    Gustison, Morgan L; Semple, Stuart; Ferrer-I-Cancho, Ramon; Bergman, Thore J

    2016-05-10

    Identifying universal principles underpinning diverse natural systems is a key goal of the life sciences. A powerful approach in addressing this goal has been to test whether patterns consistent with linguistic laws are found in nonhuman animals. Menzerath's law is a linguistic law that states that, the larger the construct, the smaller the size of its constituents. Here, to our knowledge, we present the first evidence that Menzerath's law holds in the vocal communication of a nonhuman species. We show that, in vocal sequences of wild male geladas (Theropithecus gelada), construct size (sequence size in number of calls) is negatively correlated with constituent size (duration of calls). Call duration does not vary significantly with position in the sequence, but call sequence composition does change with sequence size and most call types are abbreviated in larger sequences. We also find that intercall intervals follow the same relationship with sequence size as do calls. Finally, we provide formal mathematical support for the idea that Menzerath's law reflects compression-the principle of minimizing the expected length of a code. Our findings suggest that a common principle underpins human and gelada vocal communication, highlighting the value of exploring the applicability of linguistic laws in vocal systems outside the realm of language.

  10. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

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

  11. USING LABORATORY TESTS TO PREDICT OXIDATION IN TODAY'S ENGINES

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    Laboratory bench tests are used to predict lubricant performance in modern engines. The evolution of ASTM (American Society of Testing and Materials) engine Sequence tests and associated laboratory bench tests is reviewed. Several oxidation screening tests are described. Correlation of oxidation screening tests with ASTM Sequence Ⅲ high temperature oxidation engine test is addressed, using both European and ASTM reference oils. Modification of the oxidation screening test methods is attempted in order to improve the correlation as the Sequencetest method evolves.

  12. Complete dataset for 2-treatment, 2-sequence, 2-period efavirenz bioequivalence study conducted with nightly dosing

    Directory of Open Access Journals (Sweden)

    Manuel Ibarra

    2016-06-01

    Full Text Available The efavirenz pharmacokinetic raw data presented in this article was obtained in an average bioequivalence study between a local brand and Stocrin (Merck Sharp & Dohme, purchased from Australia, batch H009175, expiration date November 2013. Dose was administered at night (9:00 p.m. two hours after food intake. Fourteen healthy subjects, 8 women and 6 men, completed the study. For each subject, 15 data points until 96 h post-administration are included. Subject demographic characteristics and sequences of administration are provided along with individual pharmacokinetic profiles of efavirenz obtained for both formulations after a single oral dose of 600 mg. This data provides information in support of the research article “Sex-by-formulation interaction assessed through a bioequivalence study of efavirenz tablets” [1].

  13. Complete dataset for 2-treatment, 2-sequence, 2-period efavirenz bioequivalence study conducted with nightly dosing.

    Science.gov (United States)

    Ibarra, Manuel; Magallanes, Laura; Lorier, Marianela; Vázquez, Marta; Fagiolino, Pietro

    2016-06-01

    The efavirenz pharmacokinetic raw data presented in this article was obtained in an average bioequivalence study between a local brand and Stocrin (Merck Sharp & Dohme, purchased from Australia, batch H009175, expiration date November 2013). Dose was administered at night (9:00 p.m.) two hours after food intake. Fourteen healthy subjects, 8 women and 6 men, completed the study. For each subject, 15 data points until 96 h post-administration are included. Subject demographic characteristics and sequences of administration are provided along with individual pharmacokinetic profiles of efavirenz obtained for both formulations after a single oral dose of 600 mg. This data provides information in support of the research article "Sex-by-formulation interaction assessed through a bioequivalence study of efavirenz tablets" [1].

  14. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2012-01-01

    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  15. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

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

  16. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

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

  17. Biological sequence analysis

    DEFF Research Database (Denmark)

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

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

  18. Characterization of minisatellites in Arabidopsis thaliana with sequence similarity to the human minisatellite core sequence.

    Science.gov (United States)

    Tourmente, S; Deragon, J M; Lafleuriel, J; Tutois, S; Pélissier, T; Cuvillier, C; Espagnol, M C; Picard, G

    1994-08-25

    A strategy based on random PCR amplification was used to isolate new repetitive elements of Arabidopsis thaliana. One of the random PCR product analyzed by this approach contained a tandem repetitive minisatellite sequence composed of 33 bp repeated units. The genomic locus corresponding to this PCR product was isolated by screening a lambda genomic library. New related loci were also isolated from the genomic library by screening with a 14 mer oligonucleotide representing a region conserved among the different repeated units. Alignment of the consensus sequence for each minisatellite locus allowed the definition of an Arabidopsis thaliana core sequence that shows strong sequence similarities with the human core sequence and with the generalized recombination signal Chi of Escherichia coli. The minisatellites were tested for their ability to detect polymorphism, and their chromosomal position was established.

  19. The "muffin test"--an alternative to the oral glucose tolerance test for detecting impaired glucose tolerance.

    Science.gov (United States)

    Traub, Michael L; Jain, Akas; Maslow, Bat-Sheva; Pal, Lubna; Stein, Daniel T; Santoro, Nanette; Freeman, Ruth

    2012-01-01

    The aim of this study was to compare the effectiveness of the "muffin test" (MT) with that of the oral glucose tolerance test (OGTT) in diagnosing impaired glucose tolerance (IGT). This is a cross-sectional study in a single academic institution. The participants were 73 women aged 42 to 58 years, less than 36 months after menopause, recruited for the Kronos Early Estrogen Prevention Study Trial. After a 10-hour fasting blood draw, the participants were provided a muffin and a beverage. Two-hour glucose levels were assessed. A subset underwent metabolic testing consisting of an OGTT (n = 12) and a mixed-meal tolerance test (n = 10). The main outcome measures were the prevalence of IGT and 2-hour glucose measurements after each testing method. Two-hour glucose levels were linearly related to fasting values by multivariable linear regression. This association was exaggerated in overweight (body mass index, 25 kg/m2) women (coefficient, 1.43; P 0.05); 2-hour glucose levels after OGTT were slightly lower than after the mixed-meal tolerance test (P < 0.05). The prevalence of IGT was 11% (8 of 73). Fasting plasma glucose alone would have missed 63% of cases (five of eight cases). The MT demonstrated 100% sensitivity and specificity for diagnosing IGT compared with the gold standard OGTT. This small pilot study should be confirmed in a larger prospective group of participants.

  20. Generalized Mignotte Sequences and Software Watermarking

    Directory of Open Access Journals (Sweden)

    Hedley Morris

    2009-12-01

    Full Text Available Dynamic Graph Watermarking (DGW is vulnerable to attack. We propose the use of a multiple secret sharing scheme to improve the robustness of DGW. We propose using Mignotte Sequences as the way to create the watermark shares needed by the method. The new scheme is suitable for inclusion in the SandMark test program. All necessary algorithms are identified.

  1. 厚尾相依序列均值多变点 ANOVA 型检验%An ANOVA-type test for multiple change points in the mean of heavy-tailed dependent sequence

    Institute of Scientific and Technical Information of China (English)

    吕会琴; 赵文芝; 赵蕊

    2016-01-01

    In order to study multiple breaks detection of mean in heavy-tailed dependent se-quence,under the null hypothesis of no change against the alternative hypothesis of multiple change points,an ANOVA-type test statistic is proposed.Then the limiting distribution of the test statistic under the null hypothesis and the consistence of the test statistic is obtained re-spectively.Finally,the results of Monte Carlo is shown to support the argument.%为了研究厚尾相依序列均值的多变点检验问题,在厚尾相依随机变量序列原假设无变点与备择假设存在多个变点的假设检验下,提出 ANOVA 型的检验统计量。分别得到在原假设下统计量的极限分布,并对统计量的一致性检验进行推导证明。最后通过数值模拟验证了该方法的有效性。

  2. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples

    DEFF Research Database (Denmark)

    Wikman, Friedrik; Lu, Ming-Lan; Andersen, Thomas Thykjær;

    2000-01-01

    available chip and describes a method to increase the specificity of the chip. Methods: DNA from 140 human bladder tumors was extracted and subjected to a multiplex-PCR before loading onto the p53 GeneChip from Affymetrix. The same samples were previously sequenced by manual dideoxy sequencing. In addition......Background: Testing for mutations of the TP53 gene in tumors is a valuable predictor for disease outcome in certain cancers, but the time and cost of conventional sequencing limit its use. The present study compares traditional sequencing with the much faster microarray sequencing on a commercially...

  3. 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....

  4. 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.

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    Wilm Andreas

    2010-05-01

    Full Text Available 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 N2 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.

  7. Memory for sequences of events impaired in typical aging

    Science.gov (United States)

    Allen, Timothy A.; Morris, Andrea M.; Stark, Shauna M.; Fortin, Norbert J.

    2015-01-01

    Typical aging is associated with diminished episodic memory performance. To improve our understanding of the fundamental mechanisms underlying this age-related memory deficit, we previously developed an integrated, cross-species approach to link converging evidence from human and animal research. This novel approach focuses on the ability to remember sequences of events, an important feature of episodic memory. Unlike existing paradigms, this task is nonspatial, nonverbal, and can be used to isolate different cognitive processes that may be differentially affected in aging. Here, we used this task to make a comprehensive comparison of sequence memory performance between younger (18–22 yr) and older adults (62–86 yr). Specifically, participants viewed repeated sequences of six colored, fractal images and indicated whether each item was presented “in sequence” or “out of sequence.” Several out of sequence probe trials were used to provide a detailed assessment of sequence memory, including: (i) repeating an item from earlier in the sequence (“Repeats”; e.g., ABADEF), (ii) skipping ahead in the sequence (“Skips”; e.g., ABDDEF), and (iii) inserting an item from a different sequence into the same ordinal position (“Ordinal Transfers”; e.g., AB3DEF). We found that older adults performed as well as younger controls when tested on well-known and predictable sequences, but were severely impaired when tested using novel sequences. Importantly, overall sequence memory performance in older adults steadily declined with age, a decline not detected with other measures (RAVLT or BPS-O). We further characterized this deficit by showing that performance of older adults was severely impaired on specific probe trials that required detailed knowledge of the sequence (Skips and Ordinal Transfers), and was associated with a shift in their underlying mnemonic representation of the sequences. Collectively, these findings provide unambiguous evidence that the

  8. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa

    2015-09-01

    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  9. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compared...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight di...fference exist when compared to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  10. Sequencing of aromatase inhibitors

    OpenAIRE

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  11. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan

    1989-01-01

    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  12. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  13. Sequencing BPS spectra

    Science.gov (United States)

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

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  14. Image sequence analysis

    CERN Document Server

    1981-01-01

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

  15. The Galaxy End Sequence

    Science.gov (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  16. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  17. Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'

    Directory of Open Access Journals (Sweden)

    Wang Tianming

    2008-09-01

    Full Text Available Abstract Background Many proposed statistical measures can efficiently compare protein sequence to further infer protein structure, function and evolutionary information. They share the same idea of using k-word frequencies of protein sequences. Given a protein sequence, the information on its related protein sequences hasn't been used for protein sequence comparison until now. This paper proposed a scheme to construct protein 'sequence space' which was associated with protein sequences related to the given protein, and the performances of statistical measures were compared when they explored the information on protein 'sequence space' or not. This paper also presented two statistical measures for protein: gre.k (generalized relative entropy and gsm.k (gapped similarity measure. Results We tested statistical measures based on protein 'sequence space' or not with three data sets. This not only offers the systematic and quantitative experimental assessment of these statistical measures, but also naturally complements the available comparison of statistical measures based on protein sequence. Moreover, we compared our statistical measures with alignment-based measures and the existing statistical measures. The experiments were grouped into two sets. The first one, performed via ROC (Receiver Operating Curve analysis, aims at assessing the intrinsic ability of the statistical measures to discriminate and classify protein sequences. The second set of the experiments aims at assessing how well our measure does in phylogenetic analysis. Based on the experiments, several conclusions can be drawn and, from them, novel valuable guidelines for the use of protein 'sequence space' and statistical measures were obtained. Conclusion Alignment-based measures have a clear advantage when the data is high redundant. The more efficient statistical measure is the novel gsm.k introduced by this article, the cos.k followed. When the data becomes less redundant, gre

  18. Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images

    Institute of Scientific and Technical Information of China (English)

    Yusei Kobori; Satoshi Mizuta

    2016-01-01

    Graphical representation of DNA sequences is one of the most popular techniques for alignment-free sequence comparison. Here, we propose a new method for the feature extraction of DNA sequences represented by binary images, by estimating the similarity between DNA sequences using the frequency histograms of local bitmap patterns of images. Our method shows linear time complexity for the length of DNA sequences, which is practical even when long sequences, such as whole genome sequences, are compared. We tested five distance measures for the estimation of sequence similarities, and found that the histogram intersection and Manhattan distance are the most appropriate ones for phylogenetic analyses.

  19. Inferring phylogenies from RAD sequence data.

    Directory of Open Access Journals (Sweden)

    Benjamin E R Rubin

    Full Text Available Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD to sequence restriction-site associated DNA (RAD--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively. RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in

  20. Inferring phylogenies from RAD sequence data.

    Science.gov (United States)

    Rubin, Benjamin E R; Ree, Richard H; Moreau, Corrie S

    2012-01-01

    Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD)--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which sufficient

  1. Processing Aftershock Sequences Using Waveform Correlation

    Science.gov (United States)

    Resor, M. E.; Procopio, M. J.; Young, C. J.; Carr, D. B.

    2008-12-01

    For most event monitoring systems, the objective is to keep up with the flow of incoming data, producing a bulletin with some modest, relatively constant, time delay after present time, often a period of a few hours or less. Because the association problem scales exponentially and not linearly with the number of detections, a dramatic increase in seismicity due to an aftershock sequence can easily cause the bulletin delay time to increase dramatically. In some cases, the production of a bulletin may cease altogether, until the automatic system can catch up. For a nuclear monitoring system, the implications of such a delay could be dire. Given the expected similarity between a mainshock and aftershocks, it has been proposed that waveform correlation may provide a powerful means to simultaneously increase the efficiency of processing aftershock sequences, while also lowering the detection threshold and improving the quality of the event solutions. However, many questions remain unanswered. What are the key parameters for achieving the best correlations between waveforms (window length, filtering, etc.), and are they sequence-dependent? What is the overall percentage of similar events in an aftershock sequence, i.e. what is the maximum level of efficiency that a waveform correlation could be expected to achieve? Finally, how does this percentage of events vary among sequences? Using data from the aftershock sequence for the December 26, 2004 Mw 9.1 Sumatra event, we investigate these issues by building and testing a prototype waveform correlation event detection system that automatically expands its library of known events as new signatures are indentified in the aftershock sequence (by traditional signal detection and event processing). Our system tests all incoming data against this dynamic library, thereby identify any similar events before traditional processing takes place. In the region surrounding the Sumatra event, the NEIC EDR contains 4997 events in the 9

  2. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  3. Extended Logistic Chaotic Sequence and Its Performance Analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xuefeng; FAN Jiulun

    2007-01-01

    In order to improve performance and security of image encryption algorithm effectively based on chaotic sequences, an extended chaotic sequence generating method is presented based on logistic chaotic system using Bernstein form Bezier curve generating algorithm. In order to test the pseudorandom performance of the extended chaotic sequence, we also analyze random performance, autocorrelation performance, and balance performance of the extended chaotic sequence. Simulation results show that the extended chaotic sequence generated using our method is pseudorandom and its correlation performance and balance performance are good. As an application, we apply the extended chaotic sequence in image encryption algorithm, the simulation results show that the performance of the encrypted image using our method is better than that using logistic chaotic sequence.

  4. Evaluation, au laboratoire, du pouvoir dispersant d'une huile pour moteurs à essence et relation avec les résultats obtenus dans la séquence VE Laboratory Evaluation of the Dispersive Power of Gazoline Engines Oils and Relation with Sequence Ve Test Results

    Directory of Open Access Journals (Sweden)

    Hipeaux J. C.

    2006-11-01

    200°C, à l'aide de boues provenant d'une huile ayant été préalablement vieillie sur moteur Ford Pinto 2,3 l et d'eau (tableaux 4 et 6, fig. 3. On trace alors la courbe Mérite dispersant résiduel(MDR en fonction du temps d'oxydation (fig. 5 et 12. Cette courbe a la même allure que celle décrite dans la séquence VE (fig. 1. Le tracé des courbes MDR en fonction de la cotation moteur moyenne en boues VE (Average Engine Sludge Deposit (AES permet de discriminer clairement les huiles bonnes ou mauvaises en Séquence VE. À partir de 96 h d'oxydation, dans l'essai OXYDISP (fig. 9 et de 48 h dans l'essai POTDISP (fig. 14, nous sommes en présence de deux familles de produits : les produits qui conservent leur MDR et qui obtiennent un mérite boueségal ou supérieur à 9, dans la Séquence VE et les produits qui perdent leur MDR et qui ont tous des mérites inférieurs à 9 dans la même séquence. Les méthodes OXYDISP et POTDISP permettent également de différencier des huiles de niveaux API différents (niveaux SE, SF et SG (fig. 16 et 17. Evaluating the dispersive power of an oil for gasoline engines is included in international specifications such as the ones issued by the Committee of Common Market Automobile Constructors (CCMC and the American Petroleum Institute (API. This evaluation is the result of lengthy, severe and costly testing in engines on a test bench. These tests are performed in Mercedes M102E (CCMC levels G4 and G5 and Ford Pinto 2. 31 (API levels SG and SH engines. The cost of these tests requires the laboratory use of reliable preselection tests. The more often used test for evaluating the dispersive power of a motor oil is the spottest. It is performed in the presence of pollutants coming from an used Diesel motor oil (Tables 1 and 4, Fig. 2. However, some additive technologies that give good results for this test give poor results during engine testing (Table 2. During the VE Sequence lasting for 288 hr, the oil is subjected to different

  5. Inferring short-range linkage information from sequencing chromatograms.

    Directory of Open Access Journals (Sweden)

    Bastian Beggel

    Full Text Available Direct Sanger sequencing of viral genome populations yields multiple ambiguous sequence positions. It is not straightforward to derive linkage information from sequencing chromatograms, which in turn hampers the correct interpretation of the sequence data. We present a method for determining the variants existing in a viral quasispecies in the case of two nearby ambiguous sequence positions by exploiting the effect of sequence context-dependent incorporation of dideoxynucleotides. The computational model was trained on data from sequencing chromatograms of clonal variants and was evaluated on two test sets of in vitro mixtures. The approach achieved high accuracies in identifying the mixture components of 97.4% on a test set in which the positions to be analyzed are only one base apart from each other, and of 84.5% on a test set in which the ambiguous positions are separated by three bases. In silico experiments suggest two major limitations of our approach in terms of accuracy. First, due to a basic limitation of Sanger sequencing, it is not possible to reliably detect minor variants with a relative frequency of no more than 10%. Second, the model cannot distinguish between mixtures of two or four clonal variants, if one of two sets of linear constraints is fulfilled. Furthermore, the approach requires repetitive sequencing of all variants that might be present in the mixture to be analyzed. Nevertheless, the effectiveness of our method on the two in vitro test sets shows that short-range linkage information of two ambiguous sequence positions can be inferred from Sanger sequencing chromatograms without any further assumptions on the mixture composition. Additionally, our model provides new insights into the established and widely used Sanger sequencing technology. The source code of our method is made available at http://bioinf.mpi-inf.mpg.de/publications/beggel/linkageinformation.zip.

  6. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

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

  7. The learning of two similar complex movement sequences: does practice insulate a sequence from interference?

    Science.gov (United States)

    Panzer, Stefan; Shea, Charles H

    2008-12-01

    Panzer et al. [Panzer, S., Wilde, H., & Shea, C. H. (2006). The learning of two similar complex movement sequences: Proactive and retroactive effects on learning. Journal of Motor Behavior, 38, 60-70] found evidence to indicate that the memory state(s) underpinning the production of a movement sequence that was practiced for one day was essentially "overwritten" when another similar sequence was subsequently practiced on the next day. An interference paradigm was used to determine if additional practice on the first sequence would insulate it from retroactive interference arising from learning a new similar sequence. Participants produced the sequences by moving a lever with their right arm/hand to sequentially presented target locations. The experimental group practiced one 16-element movement sequence (S1) for two consecutive days. A second 16-element sequence (S2) was practiced on Day 3. The sequence practiced on Day 3 was created by switching the positions of 2 of 16 elements in the sequence practiced on the first day. Control groups received either two days of practice on S1 or one day of practice on S2. Contrary to our earlier findings (Panzer, Wilde, & Shea, 2006) of strong retroactive interference when S1 was only practiced for one day, we found no evidence of retroactive interference when S1 was practiced for two days prior to the switch to S2 practice. Interestingly, but also contrary to our earlier findings, we found the learning of S2 was facilitated by the prior practice of S1. This proactive facilitation was observed in S2 acquisition and on the S2 retention test.

  8. Cognitive processing in new and practiced discrete keying sequences

    Directory of Open Access Journals (Sweden)

    Willem B Verwey

    2010-07-01

    Full Text Available This study addresses the role of cognitive control in the initiation and execution of familiar and unfamiliar movement sequences. To become familiar with two movement sequences participants first practiced two discrete key press sequences by responding to two fixed series of 6 key specific stimuli. In the ensuing test phase they executed these two familiar and also two unfamiliar keying sequences while there was a two-third chance a tone was presented together with one randomly selected key specific stimulus in each sequence. In the counting condition of the test phase participants counted the low pitched (i.e., target tones. By and large the results support the dual processor model in which the prime role of the cognitive processor shifts from executing to initiating sequences while the gradual development of motor chunks allows a motor processor to execute the sequences. Yet, the results extend this simple model by suggesting that with little practice sequence execution is based also on some non-cognitive (perhaps associative learning mechanism and, for some participants, on the use of explicit sequence knowledge. Also, after extensive practice the cognitive processor appears to still contribute to slower responses. The occurrence of long interkey intervals was replicated suggesting that fixed 6-key sequences include several motor chunks. Yet, no indication was found that the cognitive processor is responsible for concatenating these chunks.

  9. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

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

  10. Lessons from whole-exome sequencing in MODYX families

    DEFF Research Database (Denmark)

    Dusatkova, Petra; Fang, Mingyan; Pruhova, Stepanka

    2014-01-01

    We report the first results from whole-exome sequencing performed in families with Maturity-Onset Diabetes of the Young without a known genetic cause of diabetes (MODYX). This next generation sequencing technique pointed out that routine testing of MODY needs constant awareness and regular re...

  11. Efficient Probability Sequences

    Science.gov (United States)

    2014-08-18

    forecasting systems, including memorylessness and increasing discrimination. These results suggest tests for efficiency and remedial interventions for...properties of e cient forecasting systems including memorylessness and increasing discrimination. These results suggest tests for e ciency and remedial...0. A large literature discusses the advantages and disadvantages of various scor - 5 DRMI WORKING PAPER Regnier August 18, 2014 ing functions. Some

  12. Transforming clinical microbiology with bacterial genome sequencing.

    Science.gov (United States)

    Didelot, Xavier; Bowden, Rory; Wilson, Daniel J; Peto, Tim E A; Crook, Derrick W

    2012-09-01

    Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

  13. ANGSD: Analysis of Next Generation Sequencing Data.

    Science.gov (United States)

    Korneliussen, Thorfinn Sand; Albrechtsen, Anders; Nielsen, Rasmus

    2014-11-25

    High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd . The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

  14. 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.

  15. Spaces of Ideal Convergent Sequences

    Directory of Open Access Journals (Sweden)

    M. Mursaleen

    2014-01-01

    Full Text Available In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ=Mk. We also examine some topological properties of the resulting sequence spaces.

  16. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  17. The Galaxy End Sequence

    CERN Document Server

    Eales, Stephen; Smith, Matthew; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2016-01-01

    A common assumption is that galaxies fall in two distinct regions on a plot of specific star-formation rate (SSFR) versus galaxy stellar mass: a star-forming Galaxy Main Sequence (GMS) and a separate region of `passive' or `red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus being a fair representation of the Universe at the end of 12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the `red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather t...

  18. Rapid Polymer Sequencer

    Science.gov (United States)

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

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  19. Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing.

    Science.gov (United States)

    Cao, Minh Duc; Ganesamoorthy, Devika; Elliott, Alysha G; Zhang, Huihui; Cooper, Matthew A; Coin, Lachlan J M

    2016-07-26

    The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance profile identification. Using four culture isolate samples, as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 min of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 h. While strain identification with multi-locus sequence typing required more than 15x coverage to generate confident assignments, our novel gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.

  20. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  1. Application of wavelet transform in runoff sequence analysis

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A wavelet transform is applied to runoff analysis to obtain the composition of the runoff sequence and to forecast future runoff. An observed runoff sequence is firstly decomposed and reconstructed by wavelet transform and its expanding tendency is derived. Then, the runoff sequence is forecasted by the back propagation artificial neural networks (BPANN) and by a wavelet transform combined with BPANN. The earlier researches seldom involve the problem of how to choose wavelet function, which is important and cannot be ignored when the wavelet transform is used. With application of the developed approach to the analysis of runoff sequence, several kinds of wavelet functions have been tested.

  2. The sequence of learning cycle activities in high school chemistry

    Science.gov (United States)

    Abraham, Michael R.; Renner, John W.

    The sequence of the three phases of two high school learning cycles in chemistry was altered in order to: (I ) give insights into the factors which account for the success of the learning cycle, (2) serve as an indirect test of the association between Piaget's theory and the learning cycle, and (3) to compare the learning cycle with traditional instruction. Each of the six sequences (one n o d and five altered) was studied with content and atritudc measures. The outcomes of the study supported the contention that the normal learning cycle sequence is the optimum sequence for achievement of content knowledge.

  3. Cryptographic pseudo-random sequences from the chaotic Hénon map

    Indian Academy of Sciences (India)

    Madhekar Suneel

    2009-10-01

    A scheme for pseudo-random binary sequence generation based on the two-dimensional discrete-time Hénon map is proposed. Properties of the proposed sequences pertaining to linear complexity, linear complexity profile, correlation and auto-correlation are investigated. All these properties of the sequences suggest a strong resemblance to random sequences. Results of statistical testing of the sequences are found encouraging. An estimate of the keyspace size is presented.

  4. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  5. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  6. Musical Sequences in Comics

    Directory of Open Access Journals (Sweden)

    Kieron Michael Brown

    2013-11-01

    Full Text Available Critical attention paid to the media of music and comics has historically focused on parallels between the temporal rhythm and pacing of music and the implied rhythm and temporality of comics (Eisner 2008, Godek 2007. Recent attention has begun to focus on both comics’ potential to represent the character of music (Whitted 2011 and the effects of musical images and themes on comics’ narratology (Peters 2013.    I suggest that analyses of comics that combine the traditional interplay of image and word with the use of elements of musical notation are able to shed further light on each of these areas, via the connotations and conventions of symbols pulled exclusively from the realms of music, and their integration with the other elements of the page in sequence.

  7. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  8. Problem-Solving Test: Pyrosequencing

    Science.gov (United States)

    Szeberenyi, Jozsef

    2013-01-01

    Terms to be familiar with before you start to solve the test: Maxam-Gilbert sequencing, Sanger sequencing, gel electrophoresis, DNA synthesis reaction, polymerase chain reaction, template, primer, DNA polymerase, deoxyribonucleoside triphosphates, orthophosphate, pyrophosphate, nucleoside monophosphates, luminescence, acid anhydride bond,…

  9. Intake of Protein Plus Carbohydrate during the First Two Hours after Exhaustive Cycling Improves Performance the following Day.

    Science.gov (United States)

    Rustad, Per I; Sailer, Manuela; Cumming, Kristoffer T; Jeppesen, Per B; Kolnes, Kristoffer J; Sollie, Ove; Franch, Jesper; Ivy, John L; Daniel, Hannelore; Jensen, Jørgen

    2016-01-01

    Intake of protein immediately after exercise stimulates protein synthesis but improved recovery of performance is not consistently observed. The primary aim of the present study was to compare performance 18 h after exhaustive cycling in a randomized diet-controlled study (175 kJ·kg(-1) during 18 h) when subjects were supplemented with protein plus carbohydrate or carbohydrate only in a 2-h window starting immediately after exhaustive cycling. The second aim was to investigate the effect of no nutrition during the first 2 h and low total energy intake (113 kJ·kg(-1) during 18 h) on performance when protein intake was similar. Eight endurance-trained subjects cycled at 237±6 Watt (~72% VO2max) until exhaustion (TTE) on three occasions, and supplemented with 1.2 g carbohydrate·kg(-1)·h(-1) (CHO), 0.8 g carbohydrate + 0.4 g protein·kg(-1)·h(-1) (CHO+PRO) or placebo without energy (PLA). Intake of CHO+PROT increased plasma glucose, insulin, and branch chained amino acids, whereas CHO only increased glucose and insulin. Eighteen hours later, subjects performed another TTE at 237±6 Watt. TTE was increased after intake of CHO+PROT compared to CHO (63.5±4.4 vs 49.8±5.4 min; pintake of CHO+PROT compared to an isocaloric amount of carbohydrate during the first 2 h post exercise. Intake of a similar amount of protein but less carbohydrate during the 18 h recovery period reduced performance.

  10. Functional evidence of persistent airway obstruction in rats following a two-hour inhalation exposure to methyl isocyanate

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, M.A.; Fitzgerald, S.; Menache, M.G.; Costa, D.L.; Bucher, J.R.

    1987-06-01

    Pulmonary function was assessed in male, F344 rats 1,2,4,7 and 13 weeks after a single 2-hr exposure to 0, 3, 10, or 30 ppm methyl isocyanate. No significant changes were observed in the rats exposed to 3 ppm through 13 weeks. Diffusing capacity (DL/sub co/), quasistatic lung compliance, and homogeneity of ventilation, as determined by multibreath nitrogen washout, were depressed in the rats exposed to 10 and 30 ppm by 1 week after exposure. None of the rats exposed to 30 ppm survived beyond 1 week. By 13 weeks, dramatic increases in lung volumes were observed in the rats exposed to 10 ppm, while DL/sub co/ and lung compliance were only mildly affected. However, volume-specific DL/sub co/ and compliance were depressed in the rats exposed to 10 ppm, suggesting that lung hyperinflation or other compensatory means of increasing lung size occurred in response to the methyl isocyanate-induced lung lesion. This group also exhibited increased expiratory times during tidal breathing and severely impaired distribution of ventilated air. Collectively, these results suggest the development and likely progression of a severe, obstructive airway lesion with associated gas trapping, and the existence of a pronounced concentration-response relationship between 3 and 10 ppm methyl isocyanate exposures.

  11. “Setenta y dos horas en Londres 38” / “Seventy-Two Hours in London 38”

    Directory of Open Access Journals (Sweden)

    Patricio Rivas

    2006-12-01

    Full Text Available Based on direct references to his past in Chile—during Pinochet's dictatorship—the author presents a heart-rending testimony of the tortures and ill-treats he had to endure during the military repression.

  12. Graft function based on two hours peak level monitoring of cyclosporine A during the first six months of renal transplantation.

    Science.gov (United States)

    Hami, Maryam; Naghibi, Massih; Mojahedi, Mohammad Javad; Sharifipour, Farzaneh; Shakeri, Mohammad Taghi

    2012-11-01

    Inadequate cyclosporine blood levels may cause acute rejection in transplanted renal graft, and its increase is accompanied with graft toxicity. Cyclosporine has variable bioavailability and pharmacokinetics among patients at different times after transplantation. In this study, we compared the effects of cyclosporine blood levels (trough versus 2-hour peak, C2) on renal graft function during the first six months after transplantation in order to find better methods for drug levels assessment in our patients. We studied 50 patients who received grafts at Mashhad transplant centers from October 2006 to May 2007. Drug levels were monitored seven times during the study; in each assessment, more than 80% of the patients did not reach the therapeutic C2 levels. There was no significant correlation between age, sex, times of transplantation and acute rejection with drug C2 levels. There was no difference between graft function in patients with therapeutic C2 level and those with inadequate C2 levels. However, we found a significant correlation between trough levels and acute rejection (P transplantation was the drug dosage significantly higher in patients with therapeutic C2 level than that in other patients (P >0.05). Apparently, peak levels were not a suitable method in drug monitoring in our patients, or peak levels might have occurred at a different time (like 1.5 or 3 or 4 h after ingestion of the drug) in our population. Based on this study, trough level may be a better method of evaluation of cyclosporine effects on renal allografts than 2-h peak levels in our patients.

  13. Sequence variability of Campylobacter temperate bacteriophages

    Directory of Open Access Journals (Sweden)

    Ng Lai-King

    2008-03-01

    Full Text Available Abstract Background Prophages integrated within the chromosomes of Campylobacter jejuni isolates have been demonstrated very recently. Prior work with Campylobacter temperate bacteriophages, as well as evidence from prophages in other enteric bacteria, suggests these prophages might have a role in the biology and virulence of the organism. However, very little is known about the genetic variability of Campylobacter prophages which, if present, could lead to differential phenotypes in isolates carrying the phages versus those that do not. As a first step in the characterization of C. jejuni prophages, we investigated the distribution of prophage DNA within a C. jejuni population assessed the DNA and protein sequence variability within a subset of the putative prophages found. Results Southern blotting of C. jejuni DNA using probes from genes within the three putative prophages of the C. jejuni sequenced strain RM 1221 demonstrated the presence of at least one prophage gene in a large proportion (27/35 of isolates tested. Of these, 15 were positive for 5 or more of the 7 Campylobacter Mu-like phage 1 (CMLP 1, also designated Campylobacter jejuni integrated element 1, or CJIE 1 genes tested. Twelve of these putative prophages were chosen for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence. Structural and sequence variability, including short insertions, deletions, and allele replacements, were found within the prophage genomes, some of which would alter the protein products of the ORFs involved. No insertions of novel genes were detected within the sequenced regions. The 12 prophages and RM 1221 had a % G+C very similar to C. jejuni sequenced strains, as well as promoter regions characteristic of C. jejuni. None of the putative prophages were successfully induced and propagated, so it is not known if they were functional or

  14. Image encryption using random sequence generated from generalized information domain

    Science.gov (United States)

    Xia-Yan, Zhang; Guo-Ji, Zhang; Xuan, Li; Ya-Zhou, Ren; Jie-Hua, Wu

    2016-05-01

    A novel image encryption method based on the random sequence generated from the generalized information domain and permutation-diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security.

  15. NARX neural networks for sequence processing tasks

    OpenAIRE

    Hristev, Eugen

    2012-01-01

    This project aims at researching and implementing a neural network architecture system for the NARX (Nonlinear AutoRegressive with eXogenous inputs) model, used in sequence processing tasks and particularly in time series prediction. The model can fallback to different types of architectures including time-delay neural networks and multi layer perceptron. The NARX simulator tests and compares the different architectures for both synthetic and real data, including the time series o...

  16. Generalisation of new sequence knowledge depends on response modality.

    Directory of Open Access Journals (Sweden)

    Clive R Rosenthal

    Full Text Available New visuomotor skills can guide behaviour in novel situations. Prior studies indicate that learning a visuospatial sequence via responses based on manual key presses leads to effector- and response-independent knowledge. Little is known, however, about the extent to which new sequence knowledge can generalise, and, thereby guide behaviour, outside of the manual response modality. Here, we examined whether learning a visuospatial sequence either via manual (key presses, without eye movements, oculomotor (obligatory eye movements, or perceptual (covert reorienting of visuospatial attention responses supported generalisation to direct and indirect tests administered either in the same (baseline conditions or a novel response modality (transfer conditions with respect to initial study. Direct tests measured the use of conscious knowledge about the studied sequence, whereas the indirect tests did not ostensibly draw on the study phase and measured response priming. Oculomotor learning supported the use of conscious knowledge on the manual direct tests, whereas manual learning supported generalisation to the oculomotor direct tests but did not support the conscious use of knowledge. Sequence knowledge acquired via perceptual responses did not generalise onto any of the manual tests. Manual, oculomotor, and perceptual sequence learning all supported generalisation in the baseline conditions. Notably, the manual baseline condition and the manual to oculomotor transfer condition differed in the magnitude of general skill acquired during the study phase; however, general skill did not predict performance on the post-study tests. The results demonstrated that generalisation was only affected by the responses used to initially code the visuospatial sequence when new knowledge was applied to a novel response modality. We interpret these results in terms of response-effect distinctiveness, the availability of integrated effector- and motor-plan based

  17. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system.

    Science.gov (United States)

    Schloss, Patrick D; Jenior, Matthew L; Koumpouras, Charles C; Westcott, Sarah L; Highlander, Sarah K

    2016-01-01

    Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina's MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3-V5, V1-V3, V1-V5, V1-V6, and V1-V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1-V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina's MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.

  18. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

    Directory of Open Access Journals (Sweden)

    Patrick D. Schloss

    2016-03-01

    Full Text Available Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina’s MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3–V5, V1–V3, V1–V5, V1–V6, and V1–V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1–V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina’s MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.

  19. The application of nucleic acid sequence?based amplification,real?time PCR and GM test in invasive aspergillosis diagnosis%核酸序列依赖性扩增、Real?time PCR及GM试验诊断侵袭性曲霉菌感染的临床应用评价

    Institute of Scientific and Technical Information of China (English)

    王立朋; 鲍翠霞; 于丽梅; 张晓录; 于威娟; 张霞; 李玮; 黄葆华; 李杰

    2015-01-01

    Objective To study the diagnostic performance of nucleic acid sequence?based amplification ( NASBA) assay,real?time PCR and GM test in detecting invasive aspergillosis for clinical diagnosis.Methods Blood samples from 80 patients at a high risk for IA were collected during from November 2013 to June 2014.These patients were categorized as 8 proven IA,26 probable IA, and 46 non?IA according to the 2008 revised definitions of EORTC/MSG.Blood samples were tested by NASBA,real?time PCR and GM test and their diagnostic parameters were calculated,respectively.Result The sensitivity of NASBA,real?time PCR and GM test was 76.47%,67.65% and 52.94%,while their specificity was 80.43%,89.13%,80.43%,respectively.The efficiency of various com?binations of tests was also evaluated.Perfect specificity (100%) and positive predictive value (100%) were achieved by combining NASBA and real?time PCR as a serial testing.A combination of NASBA and real?time PCR as a parallel testing was the most sensitive (94.12%).Conclusion The sensitivity and specificity of NASBA and real?time PCR were superior to GM test.Combination of these assays could be particularly useful in specific clinical situations.%目的 核酸序列依赖性扩增 ( nucleic acid sequence?based amplification,NASBA)、Real?time PCR及GM试验在侵袭性曲霉菌感染中的诊断价值. 方法 收集2013年11月~2014年6月临床上曲霉菌感染高危病患的血液标本80例,并根据EORTC/MSG诊断标准分为确诊组8例,拟诊组26例,非感染组46例,分别利用NASBA、real?time PCR及GM试验进行检测,计算3种方法的诊断指标并分析评价. 结果 NASBA、real?time PCR及GM试验3种方法的灵敏度分别为76.47%、67.65%、52.94%,特异度分别为80.43%、89.13%、80.43%. 联合诊断结果显示,NASBA与real?time PCR串联方案有最好的特异度 (100%)及阳性预测值(100%);NASBA与real?time PCR并联方案则最为灵敏(94.12%). 结论 NASBA用于诊断IA最为敏感,而real?time PCR

  20. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

    Science.gov (United States)

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-07

    Genetic analyses play a central role in infectious disease research. Massively parallelized "mechanical cloning" and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure--from nucleic acid extraction to sequencing--should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.

  1. Cladistic analysis of anuran POMC sequences.

    Science.gov (United States)

    Alrubaian, Jasem; Danielson, Phillip; Walker, David; Dores, Robert M

    2002-03-01

    Procedures for performing cladistic analyses can provide powerful tools for understanding the evolution of neuropeptide and polypeptide hormone coding genes. These analyses can be done on either amino acid data sets or nucleotide data sets and can utilize several different algorithms that are dependent on distinct sets of operating assumptions and constraints. In some cases, the results of these analyses can be used to gauge phylogenetic relationships between taxa. Selecting the proper cladistic analysis strategy is dependent on the taxonomic level of analysis and the rate of evolution within the orthologous genes being evaluated. For example, previous studies have shown that the amino acid sequence of proopiomelanocortin (POMC), the common precursor for the melanocortins and beta-endorphin, can be used to resolve phylogenetic relationships at the class and order level. This study tested the hypothesis that POMC sequences could be used to resolve phylogenetic relationships at the family taxonomic level. Cladistic analyses were performed on amphibian POMC sequences characterized from the marine toad, Bufo marinus (family Bufonidae; this study), the spadefoot toad, Spea multiplicatus (family Pelobatidae), the African clawed frog, Xenopus laevis (family Pipidae) and the laughing frog, Rana ridibunda (family Ranidae). In these analyses the sequence of Australian lungfish POMC was used as the outgroup. The analyses were done at the amino acid level using the maximum parsimony algorithm and at the nucleotide level using the maximum likelihood algorithm. For the anuran POMC genes, analysis at the nucleotide level using the maximum likelihood algorithm generated a cladogram with higher bootstrap values than the maximum parsimony analysis of the POMC amino acid data set. For anuran POMC sequences, analysis of nucleotide sequences using the maximum likelihood algorithm would appear to be the preferred strategy for resolving phylogenetic relationships at the family taxonomic

  2. Sequence-Based Identification of Aerobic Actinomycetes

    Science.gov (United States)

    Patel, Jean Baldus; Wallace, Richard J.; Brown-Elliott, Barbara A.; Taylor, Tony; Imperatrice, Carol; Leonard, Deborah G. B.; Wilson, Rebecca W.; Mann, Linda; Jost, Kenneth C.; Nachamkin, Irving

    2004-01-01

    We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis. PMID:15184431

  3. 40 CFR 86.1330-90 - Test sequence; general requirements.

    Science.gov (United States)

    2010-07-01

    ... that particular engine. (ii) Inlet depression and exhaust backpressure shall be set with the engine operating at rated speed and wide open throttle, except for the case of inlet depression for naturally... location at which the inlet depression and exhaust backpressure is measured shall be specified by...

  4. 40 CFR 92.124 - Test sequence; general requirements.

    Science.gov (United States)

    2010-07-01

    ... restrictions which would be seen in use in a representative application. (ii) Inlet depression and exhaust.... (iii) The locations at which the inlet depression and exhaust backpressure are measured shall...

  5. Solid phase sequencing of biopolymers

    Science.gov (United States)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  6. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  7. 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

  8. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  9. 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.

  10. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    Liang Chen

    2014-09-01

    In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked and low-power-low-sychrotron-peaked blazars. Because most blazars have similar size of emission region, theoretical blazar sequence implies that the break of Spectral Energy Distribution (SED) is a cooling break in nature.

  11. 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.

  12. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  13. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  14. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  15. 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.

  16. Mechanisms of protein sequence divergence and incompatibility.

    Directory of Open Access Journals (Sweden)

    Alon Wellner

    Full Text Available Alignments of orthologous protein sequences convey a complex picture. Some positions are utterly conserved whilst others have diverged to variable degrees. Amongst the latter, many are non-exchangeable between extant sequences. How do functionally critical and highly conserved residues diverge? Why and how did these exchanges become incompatible within contemporary sequences? Our model is phosphoglycerate kinase (PGK, where lysine 219 is an essential active-site residue completely conserved throughout Eukaryota and Bacteria, and serine is found only in archaeal PGKs. Contemporary sequences tested exhibited complete loss of function upon exchanges at 219. However, a directed evolution experiment revealed that two mutations were sufficient for human PGK to become functional with serine at position 219. These two mutations made position 219 permissive not only for serine and lysine, but also to a range of other amino acids seen in archaeal PGKs. The identified trajectories that enabled exchanges at 219 show marked sign epistasis - a relatively small loss of function with respect to one amino acid (lysine versus a large gain with another (serine, and other amino acids. Our findings support the view that, as theoretically described, the trajectories underlining the divergence of critical positions are dominated by sign epistatic interactions. Such trajectories are an outcome of rare mutational combinations. Nonetheless, as suggested by the laboratory enabled K219S exchange, given enough time and variability in selection levels, even utterly conserved and functionally essential residues may change.

  17. Sublinear Time Motif Discovery from Multiple Sequences

    Directory of Open Access Journals (Sweden)

    Yunhui Fu

    2013-10-01

    Full Text Available In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 ... gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 ... bm of G, every character, bi, is probabilistically generated, such that the probability for bi ≠ gi is at most α. We develop two new randomized algorithms and one new deterministic algorithm. They make advancements in the following aspects: (1 The algorithms are much faster than those before. Our algorithms can even run in sublinear time. (2 They can handle any motif pattern. (3 The restriction for the alphabet size is a lower bound of four. This gives them potential applications in practical problems, since gene sequences have an alphabet size of four. (4 All algorithms have rigorous proofs about their performances. The methods developed in this paper have been used in the software implementation. We observed some encouraging results that show improved performance for motif detection compared with other software.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rauzy, Antoine B., E-mail: Antoine.Rauzy@lix.polytechnique.f [LIX-CNRS, Computer Science, Ecole Polytechnique, 91128 Palaiseau Cedex (France)

    2011-07-15

    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.

  19. Three-Distance Sequences with Three Symbols

    OpenAIRE

    SAKAMOTO, Kuniko

    2003-01-01

    We will show that every $3$ dimensional cutting sequence is a three-distance sequence, and there are uncountable many periodic or aperiodic three-distance sequences (with $3$-symbols) which are not $3$ dimensional cutting sequences.

  20. NSIT: novel sequence identification tool.

    Directory of Open Access Journals (Sweden)

    Benjarath Pupacdi

    Full Text Available Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2-5 Mb of such sequences and estimated that the human pan-genome contains as high as 19-40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed NSIT (Novel Sequence Identification Tool, a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African, YH (Asian, and NA12878 (European de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires [Formula: see text]2GB of RAM and 1.5-2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence

  1. Self-assembled magnetic bead biosensor for measuring bacterial growth and antimicrobial susceptibility testing.

    Science.gov (United States)

    Kinnunen, Paivo; McNaughton, Brandon H; Albertson, Theodore; Sinn, Irene; Mofakham, Sima; Elbez, Remy; Newton, Duane W; Hunt, Alan; Kopelman, Raoul

    2012-08-20

    Bacterial antibiotic resistance is one of the major concerns of modern healthcare worldwide, and the development of rapid, growth-based, antimicrobial susceptibility tests is key for addressing it. The cover image shows a self-assembled asynchronous magnetic bead rotation (AMBR) biosensor developed for rapid detection of bacterial growth. Using the biosensors, the minimum inhibitory concentration of a clinical E. coli isolate can be measured within two hours, where currently tests take 6-24 hours. A 16-well prototype is also constructed for simple and robust observation of the self-assembled AMBR biosensors.

  2. ICDS database: interrupted CoDing sequences in prokaryotic genomes.

    Science.gov (United States)

    Perrodou, Emmanuel; Deshayes, Caroline; Muller, Jean; Schaeffer, Christine; Van Dorsselaer, Alain; Ripp, Raymond; Poch, Olivier; Reyrat, Jean-Marc; Lecompte, Odile

    2006-01-01

    Unrecognized frameshifts, in-frame stop codons and sequencing errors lead to Interrupted CoDing Sequence (ICDS) that can seriously affect all subsequent steps of functional characterization, from in silico analysis to high-throughput proteomic projects. Here, we describe the Interrupted CoDing Sequence database containing ICDS detected by a similarity-based approach in 80 complete prokaryotic genomes. ICDS can be retrieved by species browsing or similarity searches via a web interface (http://www-bio3d-igbmc.u-strasbg.fr/ICDS/). The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. Furthermore, to facilitate the experimental characterization of ICDS, we propose optimized primers for re-sequencing purposes. The database will be regularly updated with additional data from ongoing sequenced genomes. Our strategy has been validated by three independent tests: (i) ICDS prediction on a benchmark of artificially created frameshifts, (ii) comparison of predicted ICDS and results obtained from the comparison of the two genomic sequences of Bacillus licheniformis strain ATCC 14580 and (iii) re-sequencing of 25 predicted ICDS of the recently sequenced genome of Mycobacterium smegmatis. This allows us to estimate the specificity and sensitivity (95 and 82%, respectively) of our program and the efficiency of primer determination.

  3. Testing? Testing? In Literature?

    Science.gov (United States)

    Purves, Alan C.

    The assumptions behind secondary school literature course tests--whether asking students to recall aspects of literary works, to relate literary works to each other, or to analyze unfamiliar literary works--are open to question. They fail to acknowledge some of the most important aspects of literature which, if properly taught, should provide a…

  4. Test Under Test

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    China’s national college entrance examination, regarded as a make-or-break test by many students, leaves much to be desired “We’ve bribed the exam supervisors, paying each one 20,000 yuan. They will make everything go smooth during the exams,” Li Feng, a teacher from No.2 High School in

  5. Using Layer Recurrent Neural Network to Generate Pseudo Random Number Sequences

    Directory of Open Access Journals (Sweden)

    Veena Desai

    2012-03-01

    Full Text Available Pseudo Random Numbers (PRNs are required for many cryptographic applications. This paper proposes a new method for generating PRNs using Layer Recurrent Neural Network (LRNN. The proposed technique generates PRNs from the weight matrix obtained from the layer weights of the LRNN. The LRNN random number generator (RNG uses a short keyword as a seed and generates a long sequence as a pseudo PRN sequence. The number of bits generated in the PRN sequence depends on the number of neurons in the input layer of the LRNN. The generated PRN sequence changes, with a change in the training function of the LRNN .The sequences generated are a function of the keyword, initial state of network and the training function. In our implementation the PRN sequences have been generated using 3 training functions: 1Scaled Gradient Descent 2Levenberg-Marquartz (TRAINLM and 3 TRAINBGF. The generated sequences are tested for randomness using ENT and NIST test suites. The ENT test can be applied for sequences of small size. NIST has 16 tests to test random numbers. The LRNN generated PRNs pass in 11 tests, show no observations for 4 tests, and fail in 1 test when subjected to NIST .This paper presents the test results for random number sequence ranging from 25 bits to 1000 bits, generated using LRNN.

  6. Test plan :

    Energy Technology Data Exchange (ETDEWEB)

    Dwyer, Stephen F.

    2013-05-01

    This test plan is a document that provides a systematic approach to the planned testing of rooftop structures to determine their actual load carrying capacity. This document identifies typical tests to be performed, the responsible parties for testing, the general feature of the tests, the testing approach, test deliverables, testing schedule, monitoring requirements, and environmental and safety compliance.

  7. Exome Sequencing in Fetuses with Structural Malformations

    Directory of Open Access Journals (Sweden)

    Fiona L. Mackie

    2014-07-01

    Full Text Available Prenatal diagnostic testing is a rapidly advancing field. An accurate diagnosis of structural anomalies and additional abnormalities in fetuses with structural anomalies is important to allow “triage” and designation of prognosis. This will allow parents to make an informed decision relating to the pregnancy. This review outlines the current tests used in prenatal diagnosis, focusing particularly on “new technologies” such as exome sequencing. We demonstrate the utility of exome sequencing above that of conventional karyotyping and Chromosomal Microarray (CMA alone by outlining a recent proof of concept study investigating 30 parent-fetus trios where the fetus is known to have a structural anomaly. This may allow the identification of pathological gene anomalies and consequently improved prognostic profiling, as well as excluding anomalies and distinguishing between de novo and inherited mutations, in order to estimate the recurrence risk in future pregnancies. The potential ethical dilemmas surrounding exome sequencing are also considered, and the future of prenatal genetic diagnosis is discussed.

  8. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.

  9. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  10. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  11. Gambling strategies for random sequences

    OpenAIRE

    George Davie

    2010-01-01

    There is a general consensus that it is not possible to gamble successfully against a random se-quence. This consensus is based on results from probability theory that all gambling systems arein some sense futile and the idea that at any stage of the sequence, the next outcome is entirelyunpredictable.

  12. Sequence conserved for subcellular localization

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2002-01-01

    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  13. Bayesian analysis of binary sequences

    Science.gov (United States)

    Torney, David C.

    2005-03-01

    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  14. 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.

  15. Thyroid Tests

    Science.gov (United States)

    ... calories and how fast your heart beats. Thyroid tests check how well your thyroid is working. They ... thyroid diseases such as hyperthyroidism and hypothyroidism. Thyroid tests include blood tests and imaging tests. Blood tests ...

  16. Pinworm test

    Science.gov (United States)

    Oxyuriasis test; Enterobiasis test; Tape test ... diagnose this infection is to do a tape test. The best time to do this is in ... lay their eggs at night. Steps for the test are: Firmly press the sticky side of a ...

  17. 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

  18. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn

    2010-01-01

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  19. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen

    2008-01-01

    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

  20. Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

    Directory of Open Access Journals (Sweden)

    Pietro Liò

    Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

  1. Sequence Matching Analysis for Curriculum Development

    Directory of Open Access Journals (Sweden)

    Liem Yenny Bendatu

    2015-06-01

    Full Text Available Many organizations apply information technologies to support their business processes. Using the information technologies, the actual events are recorded and utilized to conform with predefined model. Conformance checking is an approach to measure the fitness and appropriateness between process model and actual events. However, when there are multiple events with the same timestamp, the traditional approach unfit to result such measures. This study attempts to develop a sequence matching analysis. Considering conformance checking as the basis of this approach, this proposed approach utilizes the current control flow technique in process mining domain. A case study in the field of educational process has been conducted. This study also proposes a curriculum analysis framework to test the proposed approach. By considering the learning sequence of students, it results some measurements for curriculum development. Finally, the result of the proposed approach has been verified by relevant instructors for further development.

  2. Tactical Maneuvering Using Immunized Sequence Selection

    Science.gov (United States)

    Kaneshige, John; KrishnaKumar, K.; Shung, Felix

    2003-01-01

    This paper describes a tactical maneuvering system that uses an artificial immune system based approach for selecting maneuver sequences. This approach combines the problem solving abilities of genetic algorithms with the memory retention characteristics of an immune system. Of significant importance here is the fact that the tactical maneuvering system can make time-critical decisions to accomplish near-term objectives within a dynamic environment. These objectives can be received from a human operator, autonomous executive, or various flight planning specialists. Simulation tests were performed using a high performance military aircraft model. Results demonstrate the potential of using immunized sequence selection in order to accomplish tactical maneuvering objectives ranging from flying to a location while avoiding unforeseen obstacles, to performing relative positioning in support of air combat maneuvering.

  3. Web Navigation Sequences Automation in Modern Websites

    Science.gov (United States)

    Montoto, Paula; Pan, Alberto; Raposo, Juan; Bellas, Fernando; López, Javier

    Most today’s web sources are designed to be used by humans, but they do not provide suitable interfaces for software programs. That is why a growing interest has arisen in so-called web automation applications that are widely used for different purposes such as B2B integration, automated testing of web applications or technology and business watch. Previous proposals assume models for generating and reproducing navigation sequences that are not able to correctly deal with new websites using technologies such as AJAX: on one hand existing systems only allow recording simple navigation actions and, on the other hand, they are unable to detect the end of the effects caused by an user action. In this paper, we propose a set of new techniques to record and execute web navigation sequences able to deal with all the complexity existing in AJAX-based web sites. We also present an exhaustive evaluation of the proposed techniques that shows very promising results.

  4. Tritium pellet injection sequences for TFTR

    Energy Technology Data Exchange (ETDEWEB)

    Houlberg, W.A.; Milora, S.L.; Attenberger, S.E.; Singer, C.E.; Schmidt, G.L.

    1983-01-01

    Tritium pellet injection into neutral deuterium, beam heated deuterium plasmas in the Tokamak Fusion Test Reactor (TFTR) is shown to be an attractive means of (1) minimizing tritium use per tritium discharge and over a sequence of tritium discharges; (2) greatly reducing the tritium load in the walls, limiters, getters, and cryopanels; (3) maintaining or improving instantaneous neutron production (Q); (4) reducing or eliminating deuterium-tritium (D-T) neutron production in non-optimized discharges; and (5) generally adding flexibility to the experimental sequences leading to optimal Q operation. Transport analyses of both compression and full-bore TFTR plasmas are used to support the above observations and to provide the basis for a proposed eight-pellet gas gun injector for the 1986 tritium experiments.

  5. Image-based temporal alignment of echocardiographic sequences

    Science.gov (United States)

    Danudibroto, Adriyana; Bersvendsen, Jørn; Mirea, Oana; Gerard, Olivier; D'hooge, Jan; Samset, Eigil

    2016-04-01

    Temporal alignment of echocardiographic sequences enables fair comparisons of multiple cardiac sequences by showing corresponding frames at given time points in the cardiac cycle. It is also essential for spatial registration of echo volumes where several acquisitions are combined for enhancement of image quality or forming larger field of view. In this study, three different image-based temporal alignment methods were investigated. First, a method based on dynamic time warping (DTW). Second, a spline-based method that optimized the similarity between temporal characteristic curves of the cardiac cycle using 1D cubic B-spline interpolation. Third, a method based on the spline-based method with piecewise modification. These methods were tested on in-vivo data sets of 19 echo sequences. For each sequence, the mitral valve opening (MVO) time was manually annotated. The results showed that the average MVO timing error for all methods are well under the time resolution of the sequences.

  6. QUASAR--scoring and ranking of sequence-structure alignments.

    Science.gov (United States)

    Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

    2005-12-15

    Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

  7. Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Sae-Won Han

    Full Text Available Recent advance in sequencing technology has enabled comprehensive profiling of genetic alterations in cancer. We have established a targeted sequencing platform using next-generation sequencing (NGS technology for clinical use, which can provide mutation and copy number variation data. NGS was performed with paired-end library enriched with exons of 183 cancer-related genes. Normal and tumor tissue pairs of 60 colorectal adenocarcinomas were used to test feasibility. Somatic mutation and copy number alteration were analyzed. A total of 526 somatic non-synonymous sequence variations were found in 113 genes. Among these, 278 single nucleotide variations were 232 different somatic point mutations. 216 SNV were 79 known single nucleotide polymorphisms in the dbSNP. 32 indels were 28 different indel mutations. Median number of mutated gene per tumor was 4 (range 0-23. Copy number gain (>X2 fold was found in 65 genes in 40 patients, whereas copy number loss (sequencing platform using NGS technology is feasible for clinical use and provides comprehensive genetic alteration data.

  8. Controls on sequence development and preservation offshore Namibia: Implications for sequence stratigraphic models and hydrocarbon prediction

    Energy Technology Data Exchange (ETDEWEB)

    Bagguley, J.G. [Oxford Brookes Univ., Oxford (United Kingdom); Prosser, S. [Saga Petroleum, Sandvika (Norway)

    1996-12-31

    Regional seismic interpretation of the passive margin offshore Namibia has enabled a sequence stratigraphic framework to be established for this previously under-studied region. Within this framework potential hydrocarbon plays, for example the location of source, seal and reservoir rocks can be pinpointed. The history of sequence stratigraphic models suggests that the passive margin offshore Namibia should provide an ideal setting for applying and testing sequence stratigraphic concepts. Results from this study however suggest that alongside the documented controls in sequence stratigraphy (i.e. tectonics, eustacy and sediment flux), additional factors act to influence sequence development and preservation along this margin. Detailed seismic interpretation of the post rift section of the Namibian margin has led to the identification of a member of erosional and depositional events; for example, charmers, canyons and slumps. Seismic facies analysis allows causative mechanisms to be inferred for the different geometries observed. In addition, the recognition of characteristic seismic facies enables reservoir and non-reservoir targets to be identified, thus aiding the prediction of potential hydrocarbon plays. Backstripping studies provide further information as to the evolution of the Namibian margin. For example, estimates can be made regarding changes in the rates of tectonics and sedimentation and the relative importance of these factors on the development of the margin can be assessed.

  9. Controls on sequence development and preservation offshore Namibia: Implications for sequence stratigraphic models and hydrocarbon prediction

    Energy Technology Data Exchange (ETDEWEB)

    Bagguley, J.G. (Oxford Brookes Univ., Oxford (United Kingdom)); Prosser, S. (Saga Petroleum, Sandvika (Norway))

    1996-01-01

    Regional seismic interpretation of the passive margin offshore Namibia has enabled a sequence stratigraphic framework to be established for this previously under-studied region. Within this framework potential hydrocarbon plays, for example the location of source, seal and reservoir rocks can be pinpointed. The history of sequence stratigraphic models suggests that the passive margin offshore Namibia should provide an ideal setting for applying and testing sequence stratigraphic concepts. Results from this study however suggest that alongside the documented controls in sequence stratigraphy (i.e. tectonics, eustacy and sediment flux), additional factors act to influence sequence development and preservation along this margin. Detailed seismic interpretation of the post rift section of the Namibian margin has led to the identification of a member of erosional and depositional events; for example, charmers, canyons and slumps. Seismic facies analysis allows causative mechanisms to be inferred for the different geometries observed. In addition, the recognition of characteristic seismic facies enables reservoir and non-reservoir targets to be identified, thus aiding the prediction of potential hydrocarbon plays. Backstripping studies provide further information as to the evolution of the Namibian margin. For example, estimates can be made regarding changes in the rates of tectonics and sedimentation and the relative importance of these factors on the development of the margin can be assessed.

  10. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

    Directory of Open Access Journals (Sweden)

    Bram Vrancken

    2016-01-01

    Full Text Available Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™ with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure—from nucleic acid extraction to sequencing—should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.

  11. Inaudible functional MRI using a truly mute gradient echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Marcar, V.L. [University of Zurich, Department of Psychology, Neuropsychology, Treichlerstrasse 10, 8032 Zurich (Switzerland); Girard, F. [GE Medical Systems SA, 283, rue de la Miniere B.P. 34, 78533 Buc Cedex (France); Rinkel, Y.; Schneider, J.F.; Martin, E. [University Children' s Hospital, Neuroradiology and Magnetic Resonance, Department of Diagnostic Imaging, Steinwiesstrasse 75, 8032 Zurich (Switzerland)

    2002-11-01

    We performed functional MRI experiments using a mute version of a gradient echo sequence on adult volunteers using either a simple visual stimulus (flicker goggles: 4 subjects) or an auditory stimulus (music: 4 subjects). Because the mute sequence delivers fewer images per unit time than a fast echo planar imaging (EPI) sequence, we explored our data using a parametric ANOVA test and a non-parametric Wilcoxon-Mann-Whitney test in addition to performing a cross-correlation analysis. All three methods were in close agreement regarding the location of the BOLD contrast signal change. We demonstrated that, using appropriate statistical analysis, functional MRI using an MR sequence that is acoustically inaudible to the subject is feasible. Furthermore compared with the ''silent'' event-related procedures involving an EPI protocol, our mGE protocol compares favourably with respect to experiment time and the BOLD signal. (orig.)

  12. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

  13. Pseudo-random sequence generator based on the generalized Henon map

    Institute of Scientific and Technical Information of China (English)

    ZHENG Fan; TIAN Xiao-jian; SONG Jing-yi; LI Xue-yan

    2008-01-01

    By analysis and comparison of several chaotic systems that are applied to generate pseudo-random sequence, the generalized Henon map is proposed as a pseudo-random sequence generator. A new algorithm is created to solve the problem of non-uniform distribution of the sequence generated by the generalized Henon map. First, move the decimal point of elements in the sequence to the right; then, cut off the integer; and finally, quantify it into a binary sequence. Statistical test, security analysis, and the application of image encryption have strongly supported the good random statistical characteristics, high linear complexity, large key space, and great sensitivity of the binary sequence.

  14. Application of noninvasive fetal trisomy testing based on massively parallel sequencing for the detection of chromosomal deletions and duplications%基于大规模平行测序的无创检测技术在胎儿染色体缺失或重复检测中的应用

    Institute of Scientific and Technical Information of China (English)

    文思敏; 隗伏冰; 何怡; 徐婉芳; 谢润桂; 张晓燕; 刘彦慧; 熊符

    2014-01-01

    Objective To assess the value of noninvasive fetal trisomy testing based on massively parallel sequencing for the detection of chromosomal deletions and duplications.Methods Peripheral venous blood was taken from pregnant women with a high risk.Free fetal DNA in maternal plasma was used for library construction and subjected to massively parallel sequencing.Positive results were validated by traditional karyotype analysisor array-CGH.Phenotype of the fetus was observed through pathological evaluation.Results Thirteenout of 629 cases were suspected to harbor chromosomal aberrations,which included 9 aneuploid cases and 4 structural abnormalities.The latter included one case with dup(18q) (14.35 Mb),del(18q) (21.34 Mb),one with dup(3q) (35 Mb) and two with dup(7q) (7.0 Mb).Among these,dup(18q) (14.35 Mb),del(18q) (21.34 Mb) and dup (3q)(35 Mb) were confirmed by karyotype analysis and pathological evaluation.However,the two cases with dup(7q) were validated by karyotype analysis and array-CGH as false positives.The phenotype with the fetus also presented as normal.Conclusion The introduction of maternal plasma sequencing for prenatal testing could dramatically improve the efficiency for detecting large,partial (> 10 Mb) chromosomal deletions and duplications.%目的 探讨大规模平行测序的无创基因产前检测技术在染色体缺失或重复检测中的应用.方法 选择产前筛查疑为高危的孕妇629人,应用大规模平行测序的无创基因产前检测技术对孕妇外周血血浆中胎儿游离DNA进行分析,对检出可疑缺失或重复者应用侵入性技术取样和传统核型分析或分子生物学技术进行验证,并随访至胎儿引产或出生,对于签订知情同意书者进行引产胎儿尸体解剖.结果 在629位高危孕妇中,检出13例染色体异常.其中9例为非整倍体,4例结构异常.4例结构异常中,例1为dup(18q)(14.35 Mb),del(18q)(21.34 Mb),例2为dup(3q)(35Mb),两例分别经脐静脉血和羊水

  15. DNA sequence analysis of newly formed telomeres in yeast.

    Science.gov (United States)

    Wang, S S; Pluta, A F; Zakian, V A

    1989-01-01

    A plasmid can be maintained in linear form in baker's yeast if it bears telomeric sequences at each end. Linear plasmids bearing cloned telomeric C4A4 repeats at one end (test end) and a natural DNA terminus with approximately 300 bps of C4A2 repeats at the other or control end were introduced by transformation into yeast. Test-end termini of 28 to 112 bps supported telomere formation. During telomere formation, C4A2 repeats were often transferred to test-end termini. To determine in greater detail the fate of test-end sequences on these plasmids after propagation in yeast, test-end telomeres were subcloned into E. coli and sequenced. DNA sequencing established a number of points about the molecular events involved in telomere formation in yeast. The results suggest that there are at least two mechanisms for telomere formation in yeast. One is mediated by a recombination event that requires neither a long stretch of homology nor the RAD52 gene product. The other mechanism is by addition of C1-3A repeats to the termini of linear DNA molecules. The telomeric sequence required to support C1-3A addition need not be at the very end of a molecule for telomere formation.

  16. 九种鲱科鱼类线粒体DNA细胞色素b基因相对速率测试及分歧时间估计%Phylogenetic analysis and relative-rate test of nine Clupeidae fishes ( Osteichthyes: Clupeiformes) inferred from cytochrome b gene sequence of mitochondrial DNA

    Institute of Scientific and Technical Information of China (English)

    程起群; 卢大儒

    2006-01-01

    对鲱科9种鱼类的线粒体细胞色素b(cytb)基因序列进行综合分析.结果表明:(1)用NeighbourJoining(NJ)法构建的分子系统树显示盖纹沙丁鱼属的3种鱼类形成一个单系类群,鲱属2种鱼类形成一个单系类群,它们的bootstrap支持率均为100%.金色小沙丁鱼和短体小沙丁鱼形成一个单系类群,在NJ树中的支持率达到或超过50%.欧洲黍鲱与太平洋鲱和大西洋鲱是单系起源,其bootstrap支持率高达100%.系统发育结果还支持沙丁鱼属鱼类与盖纹沙丁鱼属鱼类是单系类群,支持率分别为87%和95%.但单系类群Ⅰ(包括大西洋鲱、太平洋鲱、欧洲黍鲱)和单系类群Ⅱ(包括欧洲沙丁鱼、加州沙丁鱼、南美拟沙丁鱼、斑点盖纹沙丁鱼)之间的系统发育关系尚不明确,因为它们之间的支持率很低.(2)dN/dS的比值显著的小于1(Ztest),提示由于功能限制,cytb基因受到强烈的负选择作用.(3)基于Tajima的1D和2D相对速率测试表明,分子钟假说在鲱科鱼类中是成立的;鲱科鱼类的分歧时间是0.12至13.45百万年间.%Phylogenetic analysis and relative- rate test of 9 Clupeidae fishes were performed using the cytochrome b(cytb) gene sequence data. Based on Kimura-2-Parameter(K2P) distance, bootstrapped NJ tree ( 1000 replicates) was generated from these 9 cytb gene sequences of Clupeidae fishes. Three species of genus Sardinops are monophyletic group, 2 species of genus Clupea are monophyletic group, and their bootstrap values are both 100%. Sardinella aurita and Sardinella maderensis are monophyletic group, their bootstrap value reached or exceed 50%. Sprattus sprattus which is a species of genus Sprattus, has a monophyletic origin with genus Clupea, their bootstrap value was 100%. The number of synonymous nucleotide substitution per synonymous site (dS) and the number of nonsynonymous nucleotide substitution per nonsynonymous site (dN) of cytb gene among Clupeidae fishes were calculated

  17. A Criterion for Regular Sequences

    Indian Academy of Sciences (India)

    D P Patil; U Storch; J Stückrad

    2004-05-01

    Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .

  18. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-05-19

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

  19. Tracking of Individuals in Very Long Video Sequences

    DEFF Research Database (Denmark)

    Fihl, Preben; Corlin, Rasmus; Park, Sangho

    2006-01-01

    In this paper we present an approach for automatically detecting and tracking humans in very long video sequences. The detection is based on background subtraction using a multi-mode Codeword method. We enhance this method both in terms of representation and in terms of automatically updating...... the background allowing for handling gradual and rapid changes. Tracking is conducted by building appearance-based models and matching these over time. Tests show promising detection and tracking results in a ten hour video sequence....

  20. Statistical design and analysis of RNA sequencing data.

    Science.gov (United States)

    Auer, Paul L; Doerge, R W

    2010-06-01

    Next-generation sequencing technologies are quickly becoming the preferred approach for characterizing and quantifying entire genomes. Even though data produced from these technologies are proving to be the most informative of any thus far, very little attention has been paid to fundamental design aspects of data collection and analysis, namely sampling, randomization, replication, and blocking. We discuss these concepts in an RNA sequencing framework. Using simulations we demonstrate the benefits of collecting replicated RNA sequencing data according to well known statistical designs that partition the sources of biological and technical variation. Examples of these designs and their corresponding models are presented with the goal of testing differential expression.

  1. Thermal-Aware Soc Test Scheduling with Test Set Partitioning and Interleaving

    OpenAIRE

    2007-01-01

    High temperature has become a major problem for system-on-chip testing. In order to reduce the test application time while keeping the temperatures of the cores under test within safe ranges, a thermal-aware test scheduling technique is required. This paper presents an approach to minimize the test application time and, at the same time, prevent the temperatures of cores under test going beyond given limits. We employ test set partitioning to divide test sets into shorter test sequences, and ...

  2. Challenges and opportunities for next-generation sequencing in companion diagnostics.

    Science.gov (United States)

    Lin, Erick; Chien, Jeremy; Ong, Frank S; Fan, Jian-Bing

    2015-02-01

    The rapid decline in sequencing costs has allowed next-generation sequencing (NGS) assays, previously ubiquitous only in research laboratories, to begin making inroads into molecular diagnostics. Genotypic assays - DNA sequencing - include whole genome sequencing, whole exome sequencing, focused assays that target only a handful of genes. Phenotypic assays comprise a broader spectrum of options and can query a variety of epigenetic modifications of DNA (such as ChIP-seq, bisulfite sequencing, DNase-I hypersensitivity site-sequencing, Formaldehyde-Assisted Isolation of Regulatory Elements-sequencing, etc.) that regulate gene expression-related processes or gene expression (RNA-sequencing) itself. To date, the US FDA has only cleared 12 DNA-based companion diagnostic tests, all in cancer. Although challenges exist for NGS in companion diagnostics, the wide-ranging capabilities of NGS offer extraordinary opportunities for the development and implementation of NGS-based companion diagnostics to probe oncogenes, tumor suppressor genes and cancer-enabling genes.

  3. DIME: a novel framework for de novo metagenomic sequence assembly.

    Science.gov (United States)

    Guo, Xuan; Yu, Ning; Ding, Xiaojun; Wang, Jianxin; Pan, Yi

    2015-02-01

    The recently developed next generation sequencing platforms not only decrease the cost for metagenomics data analysis, but also greatly enlarge the size of metagenomic sequence datasets. A common bottleneck of available assemblers is that the trade-off between the noise of the resulting contigs and the gain in sequence length for better annotation has not been attended enough for large-scale sequencing projects, especially for the datasets with low coverage and a large number of nonoverlapping contigs. To address this limitation and promote both accuracy and efficiency, we develop a novel metagenomic sequence assembly framework, DIME, by taking the DIvide, conquer, and MErge strategies. In addition, we give two MapReduce implementations of DIME, DIME-cap3 and DIME-genovo, on Apache Hadoop platform. For a systematic comparison of the performance of the assembly tasks, we tested DIME and five other popular short read assembly programs, Cap3, Genovo, MetaVelvet, SOAPdenovo, and SPAdes on four synthetic and three real metagenomic sequence datasets with various reads from fifty thousand to a couple million in size. The experimental results demonstrate that our method not only partitions the sequence reads with an extremely high accuracy, but also reconstructs more bases, generates higher quality assembled consensus, and yields higher assembly scores, including corrected N50 and BLAST-score-per-base, than other tools with a nearly theoretical speed-up. Results indicate that DIME offers great improvement in assembly across a range of sequence abundances and thus is robust to decreasing coverage.

  4. Test Anxiety

    Science.gov (United States)

    ... I Help Someone Who's Being Bullied? Volunteering Test Anxiety KidsHealth > For Teens > Test Anxiety Print A A ... with their concentration or performance. What Is Test Anxiety? Test anxiety is actually a type of performance ...

  5. Pregnancy Tests

    Science.gov (United States)

    ... Us Home A-Z Health Topics Pregnancy tests Pregnancy tests > A-Z Health Topics Pregnancy test fact ... To receive Publications email updates Enter email Submit Pregnancy tests If you think you may be pregnant , ...

  6. Coombs test

    Science.gov (United States)

    Direct antiglobulin test; Indirect antiglobulin test; Anemia - hemolytic ... No special preparation is necessary for this test. ... There are 2 types of the Coombs test: Direct Indirect The direct ... that are stuck to the surface of red blood cells. Many diseases ...

  7. Ham test

    Science.gov (United States)

    Acid hemolysin test; Paroxysmal nocturnal hemoglobinuria - Ham test; PNH - Ham test ... BJ. In: Chernecky CC, Berger BJ, eds. Laboratory Tests and Diagnostic Procedures . 6th ed. Philadelphia, PA: Elsevier ...

  8. ISIS Individualized Support In Sequencing

    NARCIS (Netherlands)

    Drachsler, Hendrik; Hummel, Hans

    2007-01-01

    Drachsler, H., & Hummel, H. G. K. (2007). ISIS Individualized Support In Sequencing. Presentation given during the PIP meeting on March 22, 2007. Open University of the Netherlands: Heerlen, The Netherlands.

  9. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  10. Classification of Base Sequences (+1,

    Directory of Open Access Journals (Sweden)

    Dragomir Ž. Ðoković

    2010-01-01

    Full Text Available Base sequences BS(+1, are quadruples of {±1}-sequences (;;;, with A and B of length +1 and C and D of length n, such that the sum of their nonperiodic autocor-relation functions is a -function. The base sequence conjecture, asserting that BS(+1, exist for all n, is stronger than the famous Hadamard matrix conjecture. We introduce a new definition of equivalence for base sequences BS(+1, and construct a canonical form. By using this canonical form, we have enumerated the equivalence classes of BS(+1, for ≤30. As the number of equivalence classes grows rapidly (but not monotonically with n, the tables in the paper cover only the cases ≤13.

  11. Pythagorean Triples from Harmonic Sequences.

    Science.gov (United States)

    DiDomenico, Angelo S.; Tanner, Randy J.

    2001-01-01

    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  12. Overview of Sequence Data Formats.

    Science.gov (United States)

    Zhang, Hongen

    2016-01-01

    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  13. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou

    2013-01-01

    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

  14. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  15. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples

    DEFF Research Database (Denmark)

    Wikman, Friedrik; Lu, Ming-Lan; Andersen, Thomas Thykjær

    2000-01-01

    of mutation calling without mathematical correction to be low. This problem was solved by regarding each chip position as a separate entity with its own noise and threshold characteristics. The use of background plus 2 SD as the cutoff improved the specificity from 0.34 to 0.86 at the cost of a reduced......Background: Testing for mutations of the TP53 gene in tumors is a valuable predictor for disease outcome in certain cancers, but the time and cost of conventional sequencing limit its use. The present study compares traditional sequencing with the much faster microarray sequencing on a commercially...

  16. Diversifying microRNA sequence and function.

    Science.gov (United States)

    Ameres, Stefan L; Zamore, Phillip D

    2013-08-01

    MicroRNAs (miRNAs) regulate the expression of most genes in animals, but we are only now beginning to understand how they are generated, assembled into functional complexes and destroyed. Various mechanisms have now been identified that regulate miRNA stability and that diversify miRNA sequences to create distinct isoforms. The production of different isoforms of individual miRNAs in specific cells and tissues may have broader implications for miRNA-mediated gene expression control. Rigorously testing the many discrepant models for how miRNAs function using quantitative biochemical measurements made in vivo and in vitro remains a major challenge for the future.

  17. Analysis of simple sequence repeats markers derived from Phytophthora sojae expressed sequence tags

    Institute of Scientific and Technical Information of China (English)

    ZHU Zhendong; HUO Yunlong; WANG Xiaoming; HUANG Junbin; WU Xiaofei

    2004-01-01

    Five thousand and eight hundred publicly available expressed sequence tags (ESTs) of Phytophthora sojae were electronically searched and 415 simple sequence repeats (SSRs) were identified in 369 ESTs. The average density of SSRs was one SSR per 8.9 kb of EST sequence screened. The most frequent repeats were trinucleotide repeats (50.1%) and the least frequent were tetranucleotide repeats (8.2%). Forty primer pairs were designed and tested on 5 strains of P. sojae. Thirty-three primer pairs had successful PCR amplifications. Of the 33 functional primer pairs, 28 primer pairs produced characteristic SSR bands of the expected size, and 15 primer pairs (45.5%) detected polymorphism among 5 tested strains of P. sojae. Based on the polymorphisms detected with 20 EST-SSR markers, the 5 tested strains of P. sojae were clustered into 3 groups. In this study, the SSR markers of P. sojae were developed for the first time. These markers could be useful for identification, genetic variation study, and molecular mapping of P. sojae and its relative species.

  18. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the B

  19. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  20. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    Science.gov (United States)

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.

  1. Impaired picture sequencing ability in children with premature birth.

    Science.gov (United States)

    Chuthapisith, Jariya; Jantarapagdee, Kakanang; Roongpraiwan, Rawiwan; Nunnarumit, Pracha

    2014-07-01

    Children born preterm are at increased risk for executive dysfunction, which affects learning outcomes. Picture sequencing ability is considered as executive function (EF) that requires skills in working memory and organizing the pictures. Children born preterm might have difficulties in these skills. The present study aimed to develop practical Picture Sequencing test (PS test) and examine the sequencing ability in preterm children comparing with term children. The PS test was developed to assess the child's ability to arrange pictures into a sequence. It consisted of three conditions, which were daily activities, social interaction routines, and feeling expressions. Each story had four cartoon styles cards. The child had to rearrange picture cards into the correct sequence positions. Thirty preterm children aged five to six years with gestational ages of 32 weeks and birth weights of < 1,500 grams, and thirty-five term children matched age, gender child 's education, parental education, and socioeconomic status were performed the PS test. The total scores were compared between the preterm group and the term group. The PS test scores on the daily activities domain of the preterm and term group were 18 and 25 (p = 0.03), respectively. The scores on the social interaction routines domain ofthe preterm and term group were 20 and 28 (p = 0.01) and the scores on the feeling expression domain were 18.5 and25 (p = 0.03), respectively. There was no significant correlation between perinatal complications and the PS test scores. The preterm children with IQs in the average range showed impairment in sequencing ability compared with the term children. The results underline the need for follow-up care with more comprehensive assessment of EF.

  2. Detecting overlapping coding sequences in virus genomes

    Directory of Open Access Journals (Sweden)

    Brown Chris M

    2006-02-01

    Full Text Available Abstract Background Detecting new coding sequences (CDSs in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret – especially within overlapping genes; and viruses often employ non-canonical translational mechanisms – e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites – which can conceal potentially coding open reading frames (ORFs. Results In a previous paper we introduced a new statistic – MLOGD (Maximum Likelihood Overlapping Gene Detector – for detecting and analysing overlapping CDSs. Here we present (a an improved MLOGD statistic, (b a greatly extended suite of software using MLOGD, (c a database of results for 640 virus sequence alignments, and (d a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment. Conclusion MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs – in particular overlapping or short CDSs – and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at http://guinevere.otago.ac.nz/mlogd.html.

  3. Whole-exome/genome sequencing and genomics.

    Science.gov (United States)

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  4. SNP calling by sequencing pooled samples

    Directory of Open Access Journals (Sweden)

    Raineri Emanuele

    2012-09-01

    performance of snape to that of other packages. Conclusions We present a software which helps in calling SNPs in pooled samples: it has good power while retaining a low false discovery rate (FDR. The method also provides the posterior probability that a SNP is segregating and the full posterior distribution of f for every SNP. In order to test the behaviour of our software, we generated (through simulated coalescence artificial genomes and computed the effect of a pooled sequencing protocol, followed by SNP calling. In this setting, snape has better power and False Discovery Rate (FDR than the comparable packages samtools, PoPoolation, Varscan : for N = 50 chromosomes, snape has power ≈ 35%and FDR ≈ 2.5%. snape is available at http://code.google.com/p/snape-pooled/ (source code and precompiled binaries.

  5. Earthquake Tests of Reinforced Concrete Frames

    DEFF Research Database (Denmark)

    Skjærbæk, P. S.; Nielsen, Søren R.K.; Kirkegaard, Poul Henning

    1996-01-01

    the equilibrium state. Afterwards the test structure is subjected to the three strong ground motion oscillations where the two first sequences are followed by a free decay test. No free decay test was performed after the third earthquake due to collapse of the test structure during the third strong motion...

  6. Earthquake Tests of Reinforced Concrete Frames

    DEFF Research Database (Denmark)

    Skjærbæk, P. S.; Nielsen, Søren R.K.; Kirkegaard, Poul Henning

    1997-01-01

    the equilibrium state. Afterwards the test structure is subjected to the three strong ground motion oscillations where the two first sequences are followed by a free decay test. No free decay test was performed after the third earthquake due to collapse of the test structure during the third strong motion...

  7. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  8. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  9. Sequence-dependent nucleosome positioning.

    Science.gov (United States)

    Chung, Ho-Ryun; Vingron, Martin

    2009-03-13

    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  10. Noncontinuously binding loop-out primers for avoiding problematic DNA sequences in PCR and sanger sequencing.

    Science.gov (United States)

    Sumner, Kelli; Swensen, Jeffrey J; Procter, Melinda; Jama, Mohamed; Wooderchak-Donahue, Whitney; Lewis, Tracey; Fong, Michael; Hubley, Lindsey; Schwarz, Monica; Ha, Youna; Paul, Eleri; Brulotte, Benjamin; Lyon, Elaine; Bayrak-Toydemir, Pinar; Mao, Rong; Pont-Kingdon, Genevieve; Best, D Hunter

    2014-09-01

    We present a method in which noncontinuously binding (loop-out) primers are used to exclude regions of DNA that typically interfere with PCR amplification and/or analysis by Sanger sequencing. Several scenarios were tested using this design principle, including M13-tagged PCR primers, non-M13-tagged PCR primers, and sequencing primers. With this technique, a single oligonucleotide is designed in two segments that flank, but do not include, a short region of problematic DNA sequence. During PCR amplification or sequencing, the problematic region is looped-out from the primer binding site, where it does not interfere with the reaction. Using this method, we successfully excluded regions of up to 46 nucleotides. Loop-out primers were longer than traditional primers (27 to 40 nucleotides) and had higher melting temperatures. This method allows the use of a standardized PCR protocol throughout an assay, keeps the number of PCRs to a minimum, reduces the chance for laboratory error, and, above all, does not interrupt the clinical laboratory workflow.

  11. Peptide based diagnostics: are random-sequence peptides more useful than tiling proteome sequences?

    Science.gov (United States)

    Navalkar, Krupa Arun; Johnston, Stephan Albert; Stafford, Phillip

    2015-02-01

    Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.

  12. Radiation resistance of sequencing chips for in situ life detection.

    Science.gov (United States)

    Carr, Christopher E; Rowedder, Holli; Lui, Clarissa S; Zlatkovsky, Ilya; Papalias, Chris W; Bolander, Jarie; Myers, Jason W; Bustillo, James; Rothberg, Jonathan M; Zuber, Maria T; Ruvkun, Gary

    2013-06-01

    Life beyond Earth may be based on RNA or DNA if such life is related to life on Earth through shared ancestry due to meteoritic exchange, such as may be the case for Mars, or if delivery of similar building blocks to habitable environments has biased the evolution of life toward utilizing nucleic acids. In this case, in situ sequencing is a powerful approach to identify and characterize such life without the limitations or expense of returning samples to Earth, and can monitor forward contamination. A new semiconductor sequencing technology based on sensing hydrogen ions released during nucleotide incorporation can enable massively parallel sequencing in a small, robust, optics-free CMOS chip format. We demonstrate that these sequencing chips survive several analogues of space radiation at doses consistent with a 2-year Mars mission, including protons with solar particle event-distributed energy levels and 1 GeV oxygen and iron ions. We find no measurable impact of irradiation at 1 and 5 Gy doses on sequencing quality nor on low-level hardware characteristics. Further testing is required to study the impacts of soft errors as well as to characterize performance under neutron and gamma irradiation and at higher doses, which would be expected during operation in environments with significant trapped energetic particles such as during a mission to Europa. Our results support future efforts to use in situ sequencing to test theories of panspermia and/or whether life has a common chemical basis.

  13. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

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

  14. Transgressive Surface as Sequence Boundary

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Analysis of the four cases of the sequence boundary (SB)-transgressive surface (TS) relation in nature shows that applying transgressive surfaces as sequence boundaries has the following merits: it improves the methodology of stratigraphic subdivision; the position of transgressive surface in a sea level curve is relatively fixed; the transgressive surface is a transforming surface of the stratal structure; in platforms or ramps, the transgressive surface is the only choice for determining the sequence boundary; the transgressive surface is a readily recognized physical surface reflected by seismic records in seismostratigraphy. The paper reaches a conclusion that to delineate a SB in terms of the TS is theoretically and practically better than to delineate it between highstand and lowstand sediments as has been done traditionally.

  15. On the base sequence conjecture

    CERN Document Server

    Djokovic, Dragomir Z

    2010-01-01

    Let BS(m,n) denote the set of base sequences (A;B;C;D), with A and B of length m and C and D of length n. The base sequence conjecture (BSC) asserts that BS(n+1,n) exist (i.e., are non-empty) for all n. This is known to be true for n <= 36 and when n is a Golay number. We show that it is also true for n=37 and n=38. It is worth pointing out that BSC is stronger than the famous Hadamard matrix conjecture. In order to demonstrate the abundance of base sequences, we have previously attached to BS(n+1,n) a graph Gamma_n and computed the Gamma_n for n <= 27. We now extend these computations and determine the Gamma_n for n=28,...,35. We also propose a conjecture describing these graphs in general.

  16. Test Madness

    Science.gov (United States)

    Hedrick, Wanda B., Ed.

    2007-01-01

    There's accountability and then there's the testing craze an iatrogenic practice that undermines real learning. Hedrick documents the negative effects of testing, giving teachers another weapon in their arsenal against mindless preparation for high-stakes tests.

  17. Pharmacogenomic Testing

    Science.gov (United States)

    ... what you want to learn. Search form Search Pharmacogenomic testing You are here Home Testing & Services Testing ... people avoid harmful reactions to medication. What Is Pharmacogenomics? Did you ever wonder why a medicine doesn' ...

  18. Predictive Testing

    Science.gov (United States)

    ... your family Plan for the future Insurance and financial planning Transition for children Emergency preparedness Testing & Services Testing ... Support Genetic Disease Information Find a Support Group Financial Planning Who Should I Tell? Genetic Testing & Counseling Compensation ...

  19. Laboratory Tests

    Science.gov (United States)

    Laboratory tests check a sample of your blood, urine, or body tissues. A technician or your doctor ... compare your results to results from previous tests. Laboratory tests are often part of a routine checkup ...

  20. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  1. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake

    2006-01-01

    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  2. Novor: real-time peptide de novo sequencing software.

    Science.gov (United States)

    Ma, Bin

    2015-11-01

    De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract ᅟ.

  3. The Nature of Red-Sequence Cluster Spiral Galaxies

    Science.gov (United States)

    Kashur, Lane; Barkhouse, Wayne; Sultanova, Madina; Kalawila Vithanage, Sandanuwa; Archer, Haylee; Foote, Gregory; Mathew, Elijah; Rude, Cody; Lopez-Cruz, Omar

    2017-01-01

    Preliminary analysis of the red-sequence galaxy population from a sample of 57 low-redshift galaxy clusters observed using the KPNO 0.9m telescope and 74 clusters from the WINGS dataset, indicates that a small fraction of red-sequence galaxies have a morphology consistent with spiral systems. For spiral galaxies to acquire the color of elliptical/S0s at a similar luminosity, they must either have been stripped of their star-forming gas at an earlier epoch, or contain a larger than normal fraction of dust. To test these ideas we have compiled a sample of red-sequence spiral galaxies and examined their infrared properties as measured by 2MASS, WISE, Spitzer, and Herschel. These IR data allows us to estimate the amount of dust in each of our red-sequence spiral galaxies. We compare the estimated dust mass in each of these red-sequence late-type galaxies with spiral galaxies located in the same cluster field but having colors inconsistent with the red-sequence. We thus provide a statistical measure to discriminate between purely passive spiral galaxy evolution and dusty spirals to explain the presence of these late-type systems in cluster red-sequences.

  4. Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering

    Science.gov (United States)

    Anand, Santosh; Mangano, Eleonora; Barizzone, Nadia; Bordoni, Roberta; Sorosina, Melissa; Clarelli, Ferdinando; Corrado, Lucia; Martinelli Boneschi, Filippo; D’Alfonso, Sandra; De Bellis, Gianluca

    2016-01-01

    Sequencing large number of individuals, which is often needed for population genetics studies, is still economically challenging despite falling costs of Next Generation Sequencing (NGS). Pool-seq is an alternative cost- and time-effective option in which DNA from several individuals is pooled for sequencing. However, pooling of DNA creates new problems and challenges for accurate variant call and allele frequency (AF) estimation. In particular, sequencing errors confound with the alleles present at low frequency in the pools possibly giving rise to false positive variants. We sequenced 996 individuals in 83 pools (12 individuals/pool) in a targeted re-sequencing experiment. We show that Pool-seq AFs are robust and reliable by comparing them with public variant databases and in-house SNP-genotyping data of individual subjects of pools. Furthermore, we propose a simple filtering guideline for the removal of spurious variants based on the Kolmogorov-Smirnov statistical test. We experimentally validated our filters by comparing Pool-seq to individual sequencing data showing that the filters remove most of the false variants while retaining majority of true variants. The proposed guideline is fairly generic in nature and could be easily applied in other Pool-seq experiments. PMID:27670852

  5. Novor: Real-Time Peptide de Novo Sequencing Software

    Science.gov (United States)

    Ma, Bin

    2015-11-01

    De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data.

  6. PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences.

    Directory of Open Access Journals (Sweden)

    Ryuji J Machida

    Full Text Available BACKGROUND: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. METHODOLOGY/PRINCIPAL FINDINGS: A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. CONCLUSIONS/SIGNIFICANCE: Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.

  7. KERNEL WORDS AND GAP SEQUENCE OF THE TRIBONACCI SEQUENCE

    Institute of Scientific and Technical Information of China (English)

    Yuke HUANG; Zhiying WEN

    2016-01-01

    In this paper, we investigate the factor properties and gap sequence of the Tri-bonacci sequence, the fixed point of the substitution σ(a, b, c) = (ab, ac, a). Let ωp be the p-th occurrence of ω and Gp(ω) be the gap between ωp and ωp+1. We introduce a notion of kernel for each factor ω, and then give the decomposition of the factor ω with respect to its kernel. Using the kernel and the decomposition, we prove the main result of this paper:for each factorω, the gap sequence{Gp(ω)}p≥1 is the Tribonacci sequence over the alphabet{G1(ω), G2(ω), G4(ω)}, and the expressions of gaps are determined completely. As an appli-cation, for each factorω and p∈N, we determine the position ofωp. Finally we introduce a notion of spectrum for studying some typical combinatorial properties, such as power, overlap and separate of factors.

  8. Sequences and series involving the sequence of composite numbers

    Directory of Open Access Journals (Sweden)

    Panayiotis Vlamos

    2002-01-01

    Full Text Available Denoting by pn and cn the nth prime number and the nth composite number, respectively, we prove that both the sequence (xnn≥1, defined by xn=∑k=1n (ck+1−ck / k−pn / n, and the series ∑n=1∞ (pcn−cpn / npn are convergent.

  9. Automated Search-Based Robustness Testing for Autonomous Vehicle Software

    National Research Council Canada - National Science Library

    Betts, Kevin M; Petty, Mikel D

    2016-01-01

    .... Search-based testing techniques were used to automatically generate test cases, consisting of initial conditions and fault sequences, intended to challenge the control software more than test cases...

  10. Randomization tests

    CERN Document Server

    Edgington, Eugene

    2007-01-01

    Statistical Tests That Do Not Require Random Sampling Randomization Tests Numerical Examples Randomization Tests and Nonrandom Samples The Prevalence of Nonrandom Samples in Experiments The Irrelevance of Random Samples for the Typical Experiment Generalizing from Nonrandom Samples Intelligibility Respect for the Validity of Randomization Tests Versatility Practicality Precursors of Randomization Tests Other Applications of Permutation Tests Questions and Exercises Notes References Randomized Experiments Unique Benefits of Experiments Experimentation without Mani

  11. Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean

    Science.gov (United States)

    Sherman-Broyles, Sue; Bombarely, Aureliano; Grimwood, Jane; Schmutz, Jeremy; Doyle, Jeff

    2014-01-01

    Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful because they are increasingly easier to obtain. Complete plastome sequences allow us to detect rare rearrangements and test the tempo of sequence evolution. Chloroplast sequences are generally considered a nuisance to be kept to a minimum in bacterial artificial chromosome libraries. Here, we sequenced two bacterial artificial chromosomes per species to generate complete plastome sequences from seven species. The plastome sequences from Glycine syndetika and six other perennial Glycine species are similar in arrangement and gene content to the previously published soybean plastome. Repetitive sequences were detected in high frequencies as in soybean, but further analysis showed that repeat sequence numbers are inflated. Previous chloroplast-based phylogenetic trees for perennial Glycine were incongruent with nuclear gene–based phylogenetic trees. We tested whether the hypothesis of introgression was supported by the complete plastomes. Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast “capture.” PMID:25155272

  12. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

    Science.gov (United States)

    Spielman, Stephanie J; Wilke, Claus O

    2015-01-01

    We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve.

  13. Next-generation sequencing and large genome assemblies.

    Science.gov (United States)

    Henson, Joseph; Tischler, German; Ning, Zemin

    2012-06-01

    The next-generation sequencing (NGS) revolution has drastically reduced time and cost requirements for sequencing of large genomes, and also qualitatively changed the problem of assembly. This article reviews the state of the art in de novo genome assembly, paying particular attention to mammalian-sized genomes. The strengths and weaknesses of the main sequencing platforms are highlighted, leading to a discussion of assembly and the new challenges associated with NGS data. Current approaches to assembly are outlined and the various software packages available are introduced and compared. The question of whether quality assemblies can be produced using short-read NGS data alone, or whether it must be combined with more expensive sequencing techniques, is considered. Prospects for future assemblers and tests of assembly performance are also discussed.

  14. A new parameterized algorithm for rapid peptide sequencing.

    Directory of Open Access Journals (Sweden)

    Yinglei Song

    Full Text Available De novo sequencing is an important computational approach to determining the amino acid sequence of a peptide with tandem mass spectrometry (MS/MS. Most of the existing approaches use a graph model to describe a spectrum and the sequencing is performed by computing the longest antisymmetric path in the graph. The task is often computationally intensive since a given MS/MS spectrum often contains noisy data, missing mass peaks, or post translational modifications/mutations. This paper develops a new parameterized algorithm that can efficiently compute the longest antisymmetric partial path in an extended spectrum graph that is of bounded path width. Our testing results show that this algorithm can efficiently process experimental spectra and provide sequencing results of high accuracy.

  15. Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Winston Chen, C.H.; Taranenko, N.I.; Zhu, Y.F.; Chung, C.N.; Allman, S.L.

    1997-03-01

    Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Snager`s enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. The preliminary results indicate laser mass spectrometry can possibly be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

  16. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  17. Convergence of Fuzzy Set Sequences

    Institute of Scientific and Technical Information of China (English)

    FENG Yu-hu

    2002-01-01

    There are more than one mode of convergence with respect to the fuzzy set sequences. In this paper,common six modes of convergence and their relationships are discussed. These six modes are convergence in uniform metric D, convergence in separable metric Dp or D*p, 1 ≤ p <∞, convergence in level set, strong convergence in level set and weak convergence. Suitable counterexamples are given. The necessary and sufficient conditions of convergence in uniform metric D are described. Some comme nts on the convergence of LRfuzzy number sequences are represented.

  18. Reduced representation sequencing: a success in maize and a promise for other plant genomes.

    Science.gov (United States)

    Barbazuk, W Brad; Bedell, Joseph A; Rabinowicz, Pablo D

    2005-08-01

    Plant, and particularly cereal genomes, are challenging to sequence due to their large size and high repetitive DNA content. Gene-enrichment strategies are alternative or complementary approaches to complete genome sequencing that yield, rapidly and inexpensively, useful sequence data from large and complex genomes. The maize genome is large (2.7 Gbp) and contains large amounts of conserved repetitive elements. Furthermore, the high allelic diversity found between maize inbred lines may necessitate sequencing several inbred lines in order to recover the maize "gene pool". Two gene-enrichment approaches, methylation filtration (MF) and high C(o)t (HC) sequencing have been tested in maize and their ability to sample the gene space has been examined. Combined with other genomic sequencing strategies, gene-enriched genomic sequencing is a practical way to examine the maize gene pool, to order and orient the genic sequences on the genome, and to enable investigation of gene content of other complex plant genomes.

  19. NICMOS FOM Operation Test

    Science.gov (United States)

    Noll, Keith

    2001-07-01

    This test verifies the FOM's mechanical operation. A 7 x 1 grid of points will be made by moving the FOM in steps of 6.5 from -20 to +19 arcsec relative to the 0 position {-36 to +3 relative to the default NIC3 FOM position of +16 arcsec}. We also have an additional FOM position at the default NIC3 position. These exposures all use the F166N filter. At the end of this sequence we will take F222M exposures at three additional FOM positions, the default position {+16 arcsec relative to the center point of the FOM mechanical range} and +/- 2 arcsec. This is to test for vignetting. Prerequisites for this test are cool down to nominal operating temperature {cold and stable, near the expected final temperature set point, but not necessarily the final temperature set point} and the filter wheel minifunctional and the filter wheel tests {proposals 8944 and 8972}.

  20. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

    Science.gov (United States)

    Pruitt, Kim D; Tatusova, Tatiana; Maglott, Donna R

    2007-01-01

    NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2,879,860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.

  1. A Mission Control Architecture for robotic lunar sample return as field tested in an analogue deployment to the sudbury impact structure

    Science.gov (United States)

    Moores, John E.; Francis, Raymond; Mader, Marianne; Osinski, G. R.; Barfoot, T.; Barry, N.; Basic, G.; Battler, M.; Beauchamp, M.; Blain, S.; Bondy, M.; Capitan, R.-D.; Chanou, A.; Clayton, J.; Cloutis, E.; Daly, M.; Dickinson, C.; Dong, H.; Flemming, R.; Furgale, P.; Gammel, J.; Gharfoor, N.; Hussein, M.; Grieve, R.; Henrys, H.; Jaziobedski, P.; Lambert, A.; Leung, K.; Marion, C.; McCullough, E.; McManus, C.; Neish, C. D.; Ng, H. K.; Ozaruk, A.; Pickersgill, A.; Preston, L. J.; Redman, D.; Sapers, H.; Shankar, B.; Singleton, A.; Souders, K.; Stenning, B.; Stooke, P.; Sylvester, P.; Tornabene, L.

    2012-12-01

    A Mission Control Architecture is presented for a Robotic Lunar Sample Return Mission which builds upon the experience of the landed missions of the NASA Mars Exploration Program. This architecture consists of four separate processes working in parallel at Mission Control and achieving buy-in for plans sequentially instead of simultaneously from all members of the team. These four processes were: science processing, science interpretation, planning and mission evaluation. science processing was responsible for creating products from data downlinked from the field and is organized by instrument. Science Interpretation was responsible for determining whether or not science goals are being met and what measurements need to be taken to satisfy these goals. The Planning process, responsible for scheduling and sequencing observations, and the Evaluation process that fostered inter-process communications, reporting and documentation assisted these processes. This organization is advantageous for its flexibility as shown by the ability of the structure to produce plans for the rover every two hours, for the rapidity with which Mission Control team members may be trained and for the relatively small size of each individual team. This architecture was tested in an analogue mission to the Sudbury impact structure from June 6-17, 2011. A rover was used which was capable of developing a network of locations that could be revisited using a teach and repeat method. This allowed the science team to process several different outcrops in parallel, downselecting at each stage to ensure that the samples selected for caching were the most representative of the site. Over the course of 10 days, 18 rock samples were collected from 5 different outcrops, 182 individual field activities - such as roving or acquiring an image mosaic or other data product - were completed within 43 command cycles, and the rover travelled over 2200 m. Data transfer from communications passes were filled to 74

  2. FAST - FREEDOM ASSEMBLY SEQUENCING TOOL PROTOTYPE

    Science.gov (United States)

    Borden, C. S.

    1994-01-01

    FAST is a project management tool designed to optimize the assembly sequence of Space Station Freedom. An appropriate assembly sequence coordinates engineering, design, utilization, transportation availability, and operations requirements. Since complex designs tend to change frequently, FAST assesses the system level effects of detailed changes and produces output metrics that identify preferred assembly sequences. FAST incorporates Space Shuttle integration, Space Station hardware, on-orbit operations, and programmatic drivers as either precedence relations or numerical data. Hardware sequencing information can either be input directly and evaluated via the "specified" mode of operation or evaluated from the input precedence relations in the "flexible" mode. In the specified mode, FAST takes as its input a list of the cargo elements assigned to each flight. The program determines positions for the cargo elements that maximize the center of gravity (c.g.) margin. These positions are restricted by the geometry of the cargo elements and the location of attachment fittings both in the orbiter and on the cargo elements. FAST calculates every permutation of cargo element location according to its height, trunnion fitting locations, and required intercargo element spacing. Each cargo element is tested in both its normal and reversed orientation (rotated 180 degrees). The best solution is that which maximizes the c.g. margin for each flight. In the flexible mode, FAST begins with the first flight and determines all feasible combinations of cargo elements according to mass, volume, EVA, and precedence relation constraints. The program generates an assembly sequence that meets mass, volume, position, EVA, and precedence constraints while minimizing the total number of Shuttle flights required. Issues associated with ground operations, spacecraft performance, logistics requirements and user requirements will be addressed in future versions of the model. FAST is written in C

  3. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  4. RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.

    Directory of Open Access Journals (Sweden)

    Simon H Tausch

    Full Text Available The assembly of viral or endosymbiont genomes from Next Generation Sequencing (NGS data is often hampered by the predominant abundance of reads originating from the host organism. These reads increase the memory and CPU time usage of the assembler and can lead to misassemblies.We developed RAMBO-K (Read Assignment Method Based On K-mers, a tool which allows rapid and sensitive removal of unwanted host sequences from NGS datasets. Reaching a speed of 10 Megabases/s on 4 CPU cores and a standard hard drive, RAMBO-K is faster than any tool we tested, while showing a consistently high sensitivity and specificity across different datasets.RAMBO-K rapidly and reliably separates reads from different species without data preprocessing. It is suitable as a straightforward standard solution for workflows dealing with mixed datasets. Binaries and source code (java and python are available from http://sourceforge.net/projects/rambok/.

  5. PCR master mixes harbour murine DNA sequences. Caveat emptor!

    Directory of Open Access Journals (Sweden)

    Philip W Tuke

    Full Text Available BACKGROUND: XMRV is the most recently described retrovirus to be found in Man, firstly in patients with prostate cancer (PC and secondly in 67% of patients with chronic fatigue syndrome (CFS and 3.7% of controls. Both disease associations remain contentious. Indeed, a recent publication has concluded that "XMRV is unlikely to be a human pathogen". Subsequently related but different polytropic MLV (pMLV sequences were also reported from the blood of 86.5% of patients with CFS. and 6.8% of controls. Consequently we decided to investigate blood donors for evidence of XMRV/pMLV. METHODOLOGY/PRINCIPAL FINDINGS: Testing of cDNA prepared from the whole blood of 80 random blood donors, generated gag PCR signals from two samples (7C and 9C. These had previously tested negative for XMRV by two other PCR based techniques. To test whether the PCR mix was the source of these sequences 88 replicates of water were amplified using Invitrogen Platinum Taq (IPT and Applied Biosystems Taq Gold LD (ABTG. Four gag sequences (2D, 3F, 7H, 12C were generated with the IPT, a further sequence (12D by ABTG re-amplification of an IPT first round product. Sequence comparisons revealed remarkable similarities between these sequences, endogeous MLVs and the pMLV sequences reported in patients with CFS. CONCLUSIONS/SIGNIFICANCE: Methodologies for the detection of viruses highly homologous to endogenous murine viruses require special caution as the very reagents used in the detection process can be a source of contamination and at a level where it is not immediately apparent. It is suggested that such contamination is likely to explain the apparent presence of pMLV in CFS.

  6. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

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

  7. Instruction Sequences for Computer Science

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2012-01-01

    This book demonstrates that the concept of an instruction sequence offers a novel and useful viewpoint on issues relating to diverse subjects in computer science. Selected issues relating to well-known subjects from the theory of computation and the area of computer architecture are rigorously

  8. Single-primer fluorescent sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, J.L.; Morgan, C.A.; Middendorf, L.R.; Grone, D.L.; Brumbaugh, J.A.

    1987-05-01

    Modified linker arm oligonucleotides complementary to standard M13 priming sites were synthesized, labelled with either one, two, or three fluoresceins, and purified by reverse-phase HPLC. When used as primers in standard dideoxy M13 sequencing with /sup 32/P-dNTPs, normal autoradiographic patterns were obtained. To eliminate the radioactivity, direct on-line fluorescence detection was achieved by the use of a scanning 10 mW Argon laser emitting 488 nm light. Fluorescent bands were detected directly in standard 0.2 or 0.35 mm thick polyacrylamide gels at a distance of 24 cm from the loading wells by a photomultiplier tube filtered at 520 nm. Horizontal and temporal location of each band was displayed by computer as a band in real time, providing visual appearance similar to normal 4-lane autoradiograms. Using a single primer labelled with two fluoresceins, sequences of between 500 and 600 bases have been read in a single loading with better than 98% accuracy; up to 400 bases can be read reproducibly with no errors. More than 50 sequences have been determined by this method. This approach requires only 1-2 ug of cloned template, and produces continuous sequence data at about one band per minute.

  9. Multifractal analyses of music sequences

    Science.gov (United States)

    Su, Zhi-Yuan; Wu, Tzuyin

    2006-09-01

    Multifractal analysis is applied to study the fractal property of music. In this paper, a method is proposed to transform both the melody and rhythm of a music piece into individual sets of distributed points along a one-dimensional line. The structure of the musical composition is thus manifested and characterized by the local clustering pattern of these sequences of points. Specifically, the local Hölder exponent and the multifractal spectrum are calculated for the transformed music sequences according to the multifractal formalism. The observed fluctuations of the Hölder exponent along the music sequences confirm the non-uniformity feature in the structures of melodic and rhythmic motions of music. Our present result suggests that the shape and opening width of the multifractal spectrum plot can be used to distinguish different styles of music. In addition, a characteristic curve is constructed by mapping the point sequences converted from the melody and rhythm of a musical work into a two-dimensional graph. Each different pieces of music has its own unique characteristic curve. This characteristic curve, which also exhibits a fractal trait, unveils the intrinsic structure of music.

  10. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

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

    2002-01-01

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

  11. Farey Sequences and Resistor Networks

    Indian Academy of Sciences (India)

    Sameen Ahmed Khan

    2012-05-01

    In this article, we employ the Farey sequence and Fibonacci numbers to establish strict upper and lower bounds for the order of the set of equivalent resistances for a circuit constructed from equal resistors combined in series and in parallel. The method is applicable for networks involving bridge and non-planar circuits.

  12. Tissue tests

    NARCIS (Netherlands)

    Sonneveld, C.; Voogt, W.

    2009-01-01

    Tissue tests are widely used in horticulture practice and have in comparison with soil or substrate testing advantages as well disadvantages in comparison with soil testing. One of the main advantages of tissue tests is the certainty that analysed nutrients in plant tissues are really present in the

  13. Tissue tests

    NARCIS (Netherlands)

    Sonneveld, C.; Voogt, W.

    2009-01-01

    Tissue tests are widely used in horticulture practice and have in comparison with soil or substrate testing advantages as well disadvantages in comparison with soil testing. One of the main advantages of tissue tests is the certainty that analysed nutrients in plant tissues are really present in the

  14. Advanced sequencing technologies and their wider impact in microbiology.

    Science.gov (United States)

    Hall, Neil

    2007-05-01

    In the past 10 years, microbiology has undergone a revolution that has been driven by access to cheap high-throughput DNA sequencing. It was not long ago that the cloning and sequencing of a target gene could take months or years, whereas now this entire process has been replaced by a 10 min Internet search of a public genome database. There has been no single innovation that has initiated this rapid technological change; in fact, the core chemistry of DNA sequencing is the same as it was 30 years ago. Instead, progress has been driven by large sequencing centers that have incrementally industrialized the Sanger sequencing method. A side effect of this industrialization is that large-scale sequencing has moved out of small research labs, and the vast majority of sequence data is now generated by large genome centers. Recently, there have been advances in technology that will enable high-throughput genome sequencing to be established in research labs using bench-top instrumentation. These new technologies are already being used to explore the vast microbial diversity in the natural environment and the untapped genetic variation that can occur in bacterial species. It is expected that these powerful new methods will open up new questions to genomic investigation and will also allow high-throughput sequencing to be more than just a discovery exercise but also a routine assay for hypothesis testing. While this review will concentrate on microorganisms, many of the important arguments about the need to measure and understand variation at the species, population and ecosystem level will hold true for many other biological systems.

  15. Delineating relative homogeneous G+C domains in DNA sequences.

    Science.gov (United States)

    Li, W

    2001-10-03

    The concept of homogeneity of G+C content is always relative and subjective. This point is emphasized and quantified in this paper using a simple example of one sequence segmented into two subsequences. Whether the sequence is homogeneous or not can be answered by whether the two-subsequence model describes the DNA sequence better than the one-sequence model. There are at least three equivalent ways of looking at the 1-to-2 segmentation: Jensen-Shannon divergence measure, log likelihood ratio test, and model selection using Bayesian information criterion. Once a criterion is chosen, a DNA sequence can be recursively segmented into multiple domains. We use one subjective criterion called segmentation strength based on the Bayesian information criterion. Whether or not a sequence is homogeneous and how many domains it has depend on this criterion. We compare six different genome sequences (yeast S. cerevisiae chromosome III and IV, bacterium M. pneumoniae, human major histocompatibility complex sequence, longest contigs in human chromosome 21 and 22) by recursive segmentations at different strength criteria. Results by recursive segmentation confirm that yeast chromosome IV is more homogeneous than yeast chromosome III, human chromosome 21 is more homogeneous than human chromosome 22, and bacterial genomes may not be homogeneous due to short segments with distinct base compositions. The recursive segmentation also provides a quantitative criterion for identifying isochores in human sequences. Some features of our recursive segmentation, such as the possibility of delineating domain borders accurately, are superior to those of the moving-window approach commonly used in such analyses.

  16. Development of Multilocus Sequence Typing (MLST) for Mycoplasma synoviae.

    Science.gov (United States)

    El-Gazzar, Mohamed; Ghanem, Mostafa; McDonald, Kristina; Ferguson-Noel, Naola; Raviv, Ziv; Slemons, Richard D

    2017-03-01

    Mycoplasma synoviae (MS) is a poultry pathogen that has had an increasing incidence and economic impact over the past few years. Strain identification is necessary for outbreak investigation, infection source identification, and facilitating prevention and control as well as eradication efforts. Currently, a segment of the variable lipoprotein hemagglutinin A (vlhA) gene (420 bp) is the only target that is used for MS strain identification. A major limitation of this assay is that colonality of typed samples can only be inferred if their vlhA sequences are identical; however, if their sequences are different, the degree of relatedness is uncertain. In this study we propose a multilocus sequence typing (MLST) assay to further refine MS strain identification. After initial screening of 24 housekeeping genes as potential targets, seven genes were selected for the MLST assay. An internal segment (450-711 bp) from each of the seven genes was successfully amplified and sequenced from 58 different MS strains and field isolates (n = 30) or positive clinical samples (n = 28). The collective sequence of all seven gene segments (3960 bp total) was used for MS sequence typing. The 58 tested MS samples were typed into 30 different sequence types using the MLST assay and, coincidentally, all the samples were typed into 30 sequence types using the vlhA assay. However, the phylogenetic tree generated using the MLST data was more congruent to the epidemiologic information than was the tree generated by the vlhA assay. We suggest that the newly developed MLST assay and the vlhA assay could be used in tandem for MS typing. The MLST assay will be a valuable and more reliable tool for MS sequence typing, providing better understanding of the epidemiology of MS infection. This in turn will aid disease prevention, control, and eradication efforts.

  17. A blackberry (Rubus L. expressed sequence tag library for the development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Main Dorrie S

    2008-06-01

    Full Text Available Abstract Background The recent development of novel repeat-fruiting types of blackberry (Rubus L. cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR, and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars. Results A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products. Conclusion This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.

  18. The Toothpick Sequence and Other Sequences from Cellular Automata

    CERN Document Server

    Applegate, David; Sloane, N J A

    2010-01-01

    A two-dimensional arrangement of toothpicks is constructed by the following iterative procedure. At stage 1, place a single toothpick of length 1 on a square grid, aligned with the y-axis. At each subsequent stage, for every exposed toothpick end, place an orthogonal toothpick centered at that end. The resulting structure has a fractal-like appearance. We will analyze the toothpick sequence, which gives the total number of toothpicks after n steps. We also study several related sequences that arise from enumerating active cells in cellular automata. Some unusual recurrences appear: a typical example is that instead of the Fibonacci recurrence, which we may write as a(2+i) = a(i) + a(i+1), we set n = 2^k+i (0 = 0} (1+x^{2^k-1}+2x^{2^k}) and variations thereof.

  19. Algebraic divisibility sequences over function fields

    CERN Document Server

    Ingram, Patrick; Silverman, Joseph H; Stange, Katherine E; Streng, Marco

    2011-01-01

    We study the existence of primes and of primitive divisors in classical divisibility sequences defined over function fields. Under various hypotheses, we prove that Lucas sequences and elliptic divisibility sequences over function fields defined over number fields contain infinitely many irreducible elements. We also prove that an elliptic divisibility sequence over a function field has only finitely many terms lacking a primitive divisor.

  20. The Feasibility of a Diagnostic Media Test System Model.

    Science.gov (United States)

    Rapp, Alfred V.

    Research investigated the feasibility of a diagnostic media test system. Two distinct tests were developed for sixth grade and university populations, each having: 1) a main phase with three specific teaching sequences, one for each media form; 2) test items for each teaching sequence; and 3) a validation phase with one teaching sequence…