WorldWideScience

Sample records for behavioral sequence analysis

  1. 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...

  2. 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 ...

  3. Sequence analysis on microcomputers.

    Science.gov (United States)

    Cannon, G C

    1987-10-02

    Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further

  4. Analysis of radionuclide behavior in a BWR Mark-II containment under severe accident management condition in low pressure sequence

    International Nuclear Information System (INIS)

    Funayama, Kyoko; Kajimoto, Mitsuhiro; Nagayoshi, Takuji; Tanaka, Nobuo

    1999-01-01

    In the Level 2 PSA program at INS/NUPEC, MELCOR1.8.3 is extensively applied to analyze radionuclide behavior of dominant sequences. In addition, the revised source terms provided in the NUREG-1465 report have been also discussed to examine the potential of the radionuclides release to the environment in the conventional siting criteria. In the present study, characteristics of source terms to the environment were examined comparing with results by the Hypothetical Accident (LOCA), NUREG-1465 and MELCOR1.8.3. calculation for a typical BWR with a Mark-II containment in order to assure conservatives of the Hypothetical Accident in Japan. Release fractions of iodine to the environment for the Hypothetical Accident and NUREG-1465, which used engineering models for predicting radionuclide behaviors, were about 10 -4 and 10 -6 of core inventory, respectively, while the best estimate MELCOR1.8.3 code predicted 10 -9 of iodine to the environment. The present study showed that the engineering models in the Hypothetical Accident or NUREG-1465 have large conservatives to estimate source term of iodine to the environment. (author)

  5. Image analysis for DNA sequencing

    International Nuclear Information System (INIS)

    Palaniappan, K.; Huang, T.S.

    1991-01-01

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

  6. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

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

  7. 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

  8. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

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

    2006-01-01

    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......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...... inositol-anchored proteins....

  9. Countercontrol in behavior analysis.

    Science.gov (United States)

    Delprato, Dennis J

    2002-01-01

    Countercontrol is a functional class of behavior that is part of Skinner's analysis of social behavior. Countercontrol refers to behavioral episodes comprised of socially mediated aversive controlling conditions and escape or avoidance responses that do not reinforce, and perhaps even punish, controllers' responses. This paper suggests that neglect of countercontrol in modern behavior analysis is unfortunate because the concept applies to interpersonal and social relations the fundamental operant principle that human behavior is both controlled and controlling-humans are not passive and inflexible. Countercontrol is addressed here in terms of conceptual status, contemporary developments in behavior analysis, its importance in a behavior-analytic approach to freedom and cultural design, applications, and research. The main conclusion is that Skinner's formulation of counter-control is scientifically supported and worthy of increased prominence in behavior analysis.

  10. Countercontrol in behavior analysis

    OpenAIRE

    Delprato, Dennis J.

    2002-01-01

    Countercontrol is a functional class of behavior that is part of Skinner's analysis of social behavior. Countercontrol refers to behavioral episodes comprised of socially mediated aversive controlling conditions and escape or avoidance responses that do not reinforce, and perhaps even punish, controllers' responses. This paper suggests that neglect of countercontrol in modern behavior analysis is unfortunate because the concept applies to interpersonal and social relations the fundamental ope...

  11. Computational Analysis of Behavior.

    Science.gov (United States)

    Egnor, S E Roian; Branson, Kristin

    2016-07-08

    In this review, we discuss the emerging field of computational behavioral analysis-the use of modern methods from computer science and engineering to quantitatively measure animal behavior. We discuss aspects of experiment design important to both obtaining biologically relevant behavioral data and enabling the use of machine vision and learning techniques for automation. These two goals are often in conflict. Restraining or restricting the environment of the animal can simplify automatic behavior quantification, but it can also degrade the quality or alter important aspects of behavior. To enable biologists to design experiments to obtain better behavioral measurements, and computer scientists to pinpoint fruitful directions for algorithm improvement, we review known effects of artificial manipulation of the animal on behavior. We also review machine vision and learning techniques for tracking, feature extraction, automated behavior classification, and automated behavior discovery, the assumptions they make, and the types of data they work best with.

  12. Zen and Behavior Analysis

    Science.gov (United States)

    Bass, Roger

    2010-01-01

    Zen's challenge for behavior analysis is to explain a repertoire that renders analysis itself meaningless--a result following not from scientific or philosophical arguments but rather from a unique verbal history generated by Zen's methods. Untying Zen's verbal knots suggests how meditation's and koans' effects on verbal behavior contribute to…

  13. 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.

  14. Behavior Analysis for Elderly

    NARCIS (Netherlands)

    Salah, A.A.; Kröse, B.J.A.; Cook, D.J.; Salah, A.A.; Kröse, B.J.A.; Cook, D.J.

    2015-01-01

    Ubiquitous computing, new sensor technologies, and increasingly available and accessible algorithms for pattern recognition and machine learning enable automatic analysis and modeling of human behavior in many novel ways. In this introductory paper of the 6th International Workshop on Human Behavior

  15. Behavior analysis in Brasil

    Directory of Open Access Journals (Sweden)

    João Cláudio Todorov

    2006-01-01

    Full Text Available The history of behavior analysis in Brazil began with the visit of Fred S. Keller as a FulbrightScholar to the University of São Paulo in 1961. Keller introduced Skinner works to the Brazilianpsychologists. His first assistant was Carolina Martuscelli Bori, then a social psychologistinfluenced by the work of Kurt Lewin. Initially guided by Keller, Carolina Bori was the majorforce in the diffusion of Behavior Analysis in Brazil, beginning with the psychology course ofthe University of Brasília, where the first course on Experimental Analysis of Behavior beganin August of 1964. Most of behavior analysts in Brazil today were students, directly or indirectly,of Carolina Bori. Several graduate programs throughout the country offer courses in behavioranalysis.

  16. Sequence analysis of Leukemia DNA

    Science.gov (United States)

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

    2018-03-01

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

  17. Positive Behavior Support and Applied Behavior Analysis

    Science.gov (United States)

    Johnston, J. M.; Foxx, R. M.; Jacobson, J. W.; Green, G.; Mulick, J. A.

    2006-01-01

    This article reviews the origins and characteristics of the positive behavior support (PBS) movement and examines those features in the context of the field of applied behavior analysis (ABA). We raise a number of concerns about PBS as an approach to delivery of behavioral services and its impact on how ABA is viewed by those in human services. We…

  18. Applied Behavior Analysis

    Science.gov (United States)

    Szapacs, Cindy

    2006-01-01

    Teaching strategies that work for typically developing children often do not work for those diagnosed with an autism spectrum disorder. However, teaching strategies that work for children with autism do work for typically developing children. In this article, the author explains how the principles and concepts of Applied Behavior Analysis can be…

  19. Invitation to Consumer Behavior Analysis

    Science.gov (United States)

    Foxall, Gordon R.

    2010-01-01

    This article presents an introduction to consumer behavior analysis by describing the Behavioral Perspective Model of consumer choice and showing how research has, first, confirmed this framework and, second, opened up behavior analysis and behavioral economics to the study of consumer behavior in natural settings. It concludes with a discussion…

  20. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

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

  1. Automated genome sequence analysis and annotation.

    Science.gov (United States)

    Andrade, M A; Brown, N P; Leroy, C; Hoersch, S; de Daruvar, A; Reich, C; Franchini, A; Tamames, J; Valencia, A; Ouzounis, C; Sander, C

    1999-05-01

    Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. The GeneQuiz system

  2. Applied Behavior Analysis in Education.

    Science.gov (United States)

    Cooper, John O.

    1982-01-01

    Applied behavioral analysis in education is expanding rapidly. This article describes the dimensions of applied behavior analysis and the contributions this technology offers teachers in the area of systematic applications, direct and daily measurement, and experimental methodology. (CJ)

  3. Sequence analysis by iterated maps, a review.

    Science.gov (United States)

    Almeida, Jonas S

    2014-05-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.

  4. Preliminary hazard analysis using sequence tree method

    International Nuclear Information System (INIS)

    Huang Huiwen; Shih Chunkuan; Hung Hungchih; Chen Minghuei; Yih Swu; Lin Jiinming

    2007-01-01

    A system level PHA using sequence tree method was developed to perform Safety Related digital I and C system SSA. The conventional PHA is a brainstorming session among experts on various portions of the system to identify hazards through discussions. However, this conventional PHA is not a systematic technique, the analysis results strongly depend on the experts' subjective opinions. The analysis quality cannot be appropriately controlled. Thereby, this research developed a system level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. Two major phases are included in this sequence tree based technique. The first phase uses a table to analyze each event in SAR Chapter 15 for a specific safety related I and C system, such as RPS. The second phase uses sequence tree to recognize what I and C systems are involved in the event, how the safety related systems work, and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. In the sequence tree, the defense-in-depth echelons, including Control echelon, Reactor trip echelon, ESFAS echelon, and Indication and display echelon, are arranged to construct the sequence tree structure. All the related I and C systems, include digital system and the analog back-up systems are allocated in their specific echelon. By this system centric sequence tree based analysis, not only preliminary hazard can be identified systematically, the vulnerability of the nuclear power plant can also be recognized. Therefore, an effective simplified D3 evaluation can be performed as well. (author)

  5. Moving Forward: Positive Behavior Support and Applied Behavior Analysis

    Science.gov (United States)

    Tincani, Matt

    2007-01-01

    A controversy has emerged about the relationship between positive behavior support and applied behavior analysis. Some behavior analysts suggest that positive behavior support and applied behavior analysis are the same (e.g., Carr & Sidener, 2002). Others argue that positive behavior support is harmful to applied behavior analysis (e.g., Johnston,…

  6. Information theory applications for biological sequence analysis.

    Science.gov (United States)

    Vinga, Susana

    2014-05-01

    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  7. Digital image sequence processing, compression, and analysis

    CERN Document Server

    Reed, Todd R

    2004-01-01

    IntroductionTodd R. ReedCONTENT-BASED IMAGE SEQUENCE REPRESENTATIONPedro M. Q. Aguiar, Radu S. Jasinschi, José M. F. Moura, andCharnchai PluempitiwiriyawejTHE COMPUTATION OF MOTIONChristoph Stiller, Sören Kammel, Jan Horn, and Thao DangMOTION ANALYSIS AND DISPLACEMENT ESTIMATION IN THE FREQUENCY DOMAINLuca Lucchese and Guido Maria CortelazzoQUALITY OF SERVICE ASSESSMENT IN NEW GENERATION WIRELESS VIDEO COMMUNICATIONSGaetano GiuntaERROR CONCEALMENT IN DIGITAL VIDEOFrancesco G.B. De NataleIMAGE SEQUENCE RESTORATION: A WIDER PERSPECTIVEAnil KokaramVIDEO SUMMARIZATIONCuneyt M. Taskiran and Edward

  8. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

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

  9. 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.

  10. Protein sequence analysis using Hewlett-Packard biphasic sequencing cartridges in an applied biosystems 473A protein sequencer.

    Science.gov (United States)

    Tang, S; Mozdzanowski, J; Anumula, K R

    1999-01-01

    Protein sequence analysis using an adsorptive biphasic sequencing cartridge, a set of two coupled columns introduced by Hewlett-Packard for protein sequencing by Edman degradation, in an Applied Biosystems 473A protein sequencer has been demonstrated. Samples containing salts, detergents, excipients, etc. (e.g., formulated protein drugs) can be easily analyzed using the ABI sequencer. Simple modifications to the ABI sequencer to accommodate the cartridge extend its utility in the analysis of difficult samples. The ABI sequencer solvents and reagents were compatible with the HP cartridge for sequencing. Sequence information up to ten residues can be easily generated by this nonoptimized procedure, and it is sufficient for identifying proteins by database search and for preparing a DNA probe for cloning novel proteins.

  11. Genome sequence and analysis of Lactobacillus helveticus

    Directory of Open Access Journals (Sweden)

    Paola eCremonesi

    2013-01-01

    Full Text Available The microbiological characterization of lactobacilli is historically well developed, but the genomic analysis is recent. Because of the widespread use of L. helveticus in cheese technology, information concerning the heterogeneity in this species is accumulating rapidly. Recently, the genome of five L. helveticus strains was sequenced to completion and compared with other genomically characterized lactobacilli. The genomic analysis of the first sequenced strain, L. helveticus DPC 4571, isolated from cheese and selected for its characteristics of rapid lysis and high proteolytic activity, has revealed a plethora of genes with industrial potential including those responsible for key metabolic functions such as proteolysis, lipolysis, and cell lysis. These genes and their derived enzymes can facilitate the production of cheese and cheese derivatives with potential for use as ingredients in consumer foods. In addition, L. helveticus has the potential to produce peptides with a biological function, such as angiotensin converting enzyme (ACE inhibitory activity, in fermented dairy products, demonstrating the therapeutic value of this species. A most intriguing feature of the genome of L. helveticus is the remarkable similarity in gene content with many intestinal lactobacilli. Comparative genomics has allowed the identification of key gene sets that facilitate a variety of lifestyles including adaptation to food matrices or the gastrointestinal tract.As genome sequence and functional genomic information continues to explode, key features of the genomes of L. helveticus strains continue to be discovered, answering many questions but also raising many new ones.

  12. Analysis of Malware behavior

    DEFF Research Database (Denmark)

    Pirscoveanu, Radu-Stefan; Hansen, Steven Strandlund; Larsen, Thor Mark Tampus

    2015-01-01

    and automatized manner. We have developed a distributed malware testing environment by extending Cuckoo Sandbox that was used to test an extensive number of malware samples and trace their behavioral data. The extracted data was used for the development of a novel type classification approach based on supervised...

  13. 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...

  14. Bayesian Correlation Analysis for Sequence Count Data.

    Directory of Open Access Journals (Sweden)

    Daniel Sánchez-Taltavull

    Full Text Available Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.

  15. A basic analysis toolkit for biological sequences

    Directory of Open Access Journals (Sweden)

    Siragusa Enrico

    2007-09-01

    Full Text Available Abstract This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at http://www.math.unipa.it/~raffaele/BATS/ under the GNU GPL.

  16. An analysis of sequence alignment: heuristic algorithms.

    Science.gov (United States)

    Bucak, I Ö; Uslan, V

    2010-01-01

    Sequence alignment becomes challenging with an increase in size and number of sequences. Finding optimal or near optimal solutions for sequence alignment is one of the most important operations in bioinformatics. This study aims to survey heuristics applied for the sequence alignment problem summarized in a time line.

  17. Whole genome sequence analysis of Mycobacterium suricattae

    KAUST Repository

    Dippenaar, Anzaan

    2015-10-21

    Tuberculosis occurs in various mammalian hosts and is caused by a range of different lineages of the Mycobacterium tuberculosis complex (MTBC). A recently described member, Mycobacterium suricattae, causes tuberculosis in meerkats (Suricata suricatta) in Southern Africa and preliminary genetic analysis showed this organism to be closely related to an MTBC pathogen of rock hyraxes (Procavia capensis), the dassie bacillus. Here we make use of whole genome sequencing to describe the evolution of the genome of M. suricattae, including known and novel regions of difference, SNPs and IS6110 insertion sites. We used genome-wide phylogenetic analysis to show that M. suricattae clusters with the chimpanzee bacillus, previously isolated from a chimpanzee (Pan troglodytes) in West Africa. We propose an evolutionary scenario for the Mycobacterium africanum lineage 6 complex, showing the evolutionary relationship of M. africanum and chimpanzee bacillus, and the closely related members M. suricattae, dassie bacillus and Mycobacterium mungi.

  18. Sequence analysis of putative swrW gene required for surfactant ...

    African Journals Online (AJOL)

    Serratia marcescens produces biosurfactant serrawettin, essential for its population migration behavior. Serrawettin W1 was revealed to be an antibiotic serratamolide that makes it significant for deoxyribonucleic acid (DNA) and protein sequence analysis. Four nucleotide and amino-acid sequences from local strains ...

  19. 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

  20. 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

  1. Multilocus sequence analysis of the family Halomonadaceae.

    Science.gov (United States)

    de la Haba, Rafael R; Márquez, M Carmen; Papke, R Thane; Ventosa, Antonio

    2012-03-01

    Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of

  2. BEHAVIOR ANALYSIS OF CONSUMER COMPLAINT

    Directory of Open Access Journals (Sweden)

    Andrie Prasetyo

    2016-05-01

    Full Text Available Complaining is one form of communication for consumers to express their dissatisfaction. Understanding the consumer complaint behavior is an important thing for businesses; however, it is not easy to do. The initial step in understanding this behavior of consumer complaints is to map consumers based on their behavior of complaints and analyze the factors that influence this. This study examines the complaint behavior of consumers in Cibubur who have experienced dissatisfaction with a product.  The objectives of this study are to map the consumer complaint behavior and identify its relationship with various factors such as consumer demographics, personality, attitude to businesses, attribution of the causes of dissatisfaction, and product attributes. A crosstab descriptive analysis method was used to map the consumers, while the Pearson correlation analysis methods was used to analyze consumer complaint behavioral relationships with various factors. The results of this study indicated that consumers in Cibubur based on their complaint behavior are classified into four groups: passive, voicers, irates and activist. The passive consumers dominate the category with a percentage of 49%.  The voicers, irates, and activist belong to the complaining type and are dominated by young women, with high levels of education and income. Keywords: consumer complaint behavior, product, crosstab, pearson correlation

  3. Time fluctuation analysis of forest fire sequences

    Science.gov (United States)

    Vega Orozco, Carmen D.; Kanevski, Mikhaïl; Tonini, Marj; Golay, Jean; Pereira, Mário J. G.

    2013-04-01

    Forest fires are complex events involving both space and time fluctuations. Understanding of their dynamics and pattern distribution is of great importance in order to improve the resource allocation and support fire management actions at local and global levels. This study aims at characterizing the temporal fluctuations of forest fire sequences observed in Portugal, which is the country that holds the largest wildfire land dataset in Europe. This research applies several exploratory data analysis measures to 302,000 forest fires occurred from 1980 to 2007. The applied clustering measures are: Morisita clustering index, fractal and multifractal dimensions (box-counting), Ripley's K-function, Allan Factor, and variography. These algorithms enable a global time structural analysis describing the degree of clustering of a point pattern and defining whether the observed events occur randomly, in clusters or in a regular pattern. The considered methods are of general importance and can be used for other spatio-temporal events (i.e. crime, epidemiology, biodiversity, geomarketing, etc.). An important contribution of this research deals with the analysis and estimation of local measures of clustering that helps understanding their temporal structure. Each measure is described and executed for the raw data (forest fires geo-database) and results are compared to reference patterns generated under the null hypothesis of randomness (Poisson processes) embedded in the same time period of the raw data. This comparison enables estimating the degree of the deviation of the real data from a Poisson process. Generalizations to functional measures of these clustering methods, taking into account the phenomena, were also applied and adapted to detect time dependences in a measured variable (i.e. burned area). The time clustering of the raw data is compared several times with the Poisson processes at different thresholds of the measured function. Then, the clustering measure value

  4. Statistical analysis of next generation sequencing data

    CERN Document Server

    Nettleton, Dan

    2014-01-01

    Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized med...

  5. SVAMP: Sequence variation analysis, maps and phylogeny

    KAUST Repository

    Naeem, Raeece

    2014-04-03

    Summary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima\\'s D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents. Availability and implementation: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp. © The Author 2014.

  6. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

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

    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 BAC clone derived genome sequence have been annotated using the Pre-Ensembl and Ensembl automated pipelines and made accessible through the Pre-Ensembl/Ensembl browsers. The current annotated genome assembly (Sscrofa9) was released with Ensembl 56 in September 2009. A revised assembly (Sscrofa10......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  7. Movement Pattern Analysis Based on Sequence Signatures

    Directory of Open Access Journals (Sweden)

    Seyed Hossein Chavoshi

    2015-09-01

    Full Text Available Increased affordability and deployment of advanced tracking technologies have led researchers from various domains to analyze the resulting spatio-temporal movement data sets for the purpose of knowledge discovery. Two different approaches can be considered in the analysis of moving objects: quantitative analysis and qualitative analysis. This research focuses on the latter and uses the qualitative trajectory calculus (QTC, a type of calculus that represents qualitative data on moving point objects (MPOs, and establishes a framework to analyze the relative movement of multiple MPOs. A visualization technique called sequence signature (SESI is used, which enables to map QTC patterns in a 2D indexed rasterized space in order to evaluate the similarity of relative movement patterns of multiple MPOs. The applicability of the proposed methodology is illustrated by means of two practical examples of interacting MPOs: cars on a highway and body parts of a samba dancer. The results show that the proposed method can be effectively used to analyze interactions of multiple MPOs in different domains.

  8. Behavioral Task Analysis

    Science.gov (United States)

    2010-01-01

    methods included task analysis as a critical phase in developing instruction and training. Mon- temerlo and Tennyson (1976) noted that from 1951 to 1976...designed. The trend in the U.S . Department of Defense toward extensive procedural documentation noted by Montemerlo and Tennyson (1976) has not...M. Gagne’ (Ed.), Psychological principles in system development (pp. 187-228). New York: Holt. Montemerlo, M. D., & Tennyson , M. E. (1975

  9. Efficient computational methods for sequence analysis of small RNAs

    OpenAIRE

    Cozen, Gozde

    2007-01-01

    With the discovery of small regulatory RNAs, there has been a tremendous increase in the number of RNA sequencing projects. Meanwhile, novel high-throughput sequencing technologies, which can sequence as much as 500000 small RNA sequences in one run, have emerged. The challenge of processing this rapidly growing data can be addressed by optimizing current analysis approaches for small RNA sequences. We present fast register-level methods for small RNA pairwise alignment and small RNA to genom...

  10. Noncoding sequence classification based on wavelet transform analysis: part I

    Science.gov (United States)

    Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

    2017-09-01

    DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

  11. Nonlinear analysis of river flow time sequences

    Science.gov (United States)

    Porporato, Amilcare; Ridolfi, Luca

    1997-06-01

    Within the field of chaos theory several methods for the analysis of complex dynamical systems have recently been proposed. In light of these ideas we study the dynamics which control the behavior over time of river flow, investigating the existence of a low-dimension deterministic component. The present article follows the research undertaken in the work of Porporato and Ridolfi [1996a] in which some clues as to the existence of chaos were collected. Particular emphasis is given here to the problem of noise and to nonlinear prediction. With regard to the latter, the benefits obtainable by means of the interpolation of the available time series are reported and the remarkable predictive results attained with this nonlinear method are shown.

  12. Sequencing small RNA: introduction and data analysis fundamentals.

    Science.gov (United States)

    Mehta, Jai Prakash

    2014-01-01

    Small RNAs are important transcriptional regulators within cells. With the advent of powerful Next Generation Sequencing platforms, sequencing small RNAs seems to be an obvious choice to understand their expression and its downstream effect. Additionally, sequencing provides an opportunity to identify novel and polymorphic miRNA. However, the biggest challenge is the appropriate data analysis pipeline, which is still in phase of active development by various academic groups. This chapter describes basic and advanced steps for small RNA sequencing analysis including quality control, small RNA alignment and quantification, differential expression analysis, novel small RNA identification, target prediction, and downstream analysis. We also provide a list of various resources for small RNA analysis.

  13. Project Report: Automatic Sequence Processor Software Analysis

    Science.gov (United States)

    Benjamin, Brandon

    2011-01-01

    The Mission Planning and Sequencing (MPS) element of Multi-Mission Ground System and Services (MGSS) provides space missions with multi-purpose software to plan spacecraft activities, sequence spacecraft commands, and then integrate these products and execute them on spacecraft. Jet Propulsion Laboratory (JPL) is currently is flying many missions. The processes for building, integrating, and testing the multi-mission uplink software need to be improved to meet the needs of the missions and the operations teams that command the spacecraft. The Multi-Mission Sequencing Team is responsible for collecting and processing the observations, experiments and engineering activities that are to be performed on a selected spacecraft. The collection of these activities is called a sequence and ultimately a sequence becomes a sequence of spacecraft commands. The operations teams check the sequence to make sure that no constraints are violated. The workflow process involves sending a program start command, which activates the Automatic Sequence Processor (ASP). The ASP is currently a file-based system that is comprised of scripts written in perl, c-shell and awk. Once this start process is complete, the system checks for errors and aborts if there are any; otherwise the system converts the commands to binary, and then sends the resultant information to be radiated to the spacecraft.

  14. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

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

  15. Empirical analysis of consumer behavior

    NARCIS (Netherlands)

    Huang, Yufeng

    2015-01-01

    This thesis consists of three essays in quantitative marketing, focusing on structural empirical analysis of consumer behavior. In the first essay, he investigates the role of a consumer's skill of product usage, and its imperfect transferability across brands, in her product choice. It shows that

  16. Time-clustering behavior of sharp fluctuation sequences in Chinese stock markets

    International Nuclear Information System (INIS)

    Yuan Ying; Zhuang Xintian; Liu Zhiying; Huang Weiqiang

    2012-01-01

    Sharp fluctuations (in particular, extreme fluctuations) of asset prices have a great impact on financial markets and risk management. Therefore, investigating the time dynamics of sharp fluctuation is a challenge in the financial fields. Using two different representations of the sharp fluctuations (inter-event times and series of counts), the time clustering behavior in the sharp fluctuation sequences of stock markets in China is studied with several statistical tools, including coefficient of variation, Allan Factor, Fano Factor as well as R/S (rescaled range) analysis. All of the empirical results indicate that the time dynamics of the sharp fluctuation sequences can be considered as a fractal process with a high degree of time-clusterization of the events. It can help us to get a better understanding of the nature and dynamics of sharp fluctuation of stock price in stock markets.

  17. Analysis and prediction of baculovirus promoter sequences.

    Science.gov (United States)

    Xing, Ke; Deng, Riqiang; Wang, Jinwen; Feng, Jinghua; Huang, Mingsong; Wang, Xunzhang

    2005-10-01

    Consensus patterns of baculovirus sequences upstream from the translational initiation sites have been analyzed and a web tool, Local Alignment Promoter Predictor (LAPP), for the prediction of baculovirus promoter sequences has also been developed. Potential consensus sequences, i.e., TCATTGT, TCTTGTA, CTCGTAA, TCCATTT and TCATT plus TCGT in approximately 30 bp spacing context, have been found in baculovirus promoter regions, in addition to well-characterized late and early promoter elements G/T/ATAAG and TATAA, which is accompanied about 30-bp downstream by a transcriptional initiation sequence CAGT or CATT. Promoter prediction is performed by a dynamic programming algorithm based on maximal segment pair measure with scores above some cutoff against each sequence in a refined promoter database. The algorithm was able to discriminate between promoter and non-promoter sequences in a test set of baculovirus sequences with prediction specificity and sensitivity superior to that using five other eukaryotic promoter recognition programs available on the Internet. A web server that implements the LAPP with continually updated promoter database is freely available at http://life.zsu.edu.cn/LAPP/.

  18. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Primers specific for CSRP3 were designed using known cDNA sequences of Bos taurus published in database with different accession numbers. Polymerase chain reaction (PCR) was performed and products were purified and sequenced. Sequence analysis and alignment were carried out using CLUSTAL W (1.83).

  19. Incident sequence analysis; event trees, methods and graphical symbols

    International Nuclear Information System (INIS)

    1980-11-01

    When analyzing incident sequences, unwanted events resulting from a certain cause are looked for. Graphical symbols and explanations of graphical representations are presented. The method applies to the analysis of incident sequences in all types of facilities. By means of the incident sequence diagram, incident sequences, i.e. the logical and chronological course of repercussions initiated by the failure of a component or by an operating error, can be presented and analyzed simply and clearly

  20. Computer-aided visualization and analysis system for sequence evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Chee, Mark S.; Wang, Chunwei; Jevons, Luis C.; Bernhart, Derek H.; Lipshutz, Robert J.

    2004-05-11

    A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

  1. Analysis of Neuronal Sequences Using Pairwise Biases

    Science.gov (United States)

    2015-08-27

    semantic memory (knowledge of facts) and implicit memory (e.g., how to ride a bike ). Evidence for the participation of the hippocampus in the formation of...very different from each other in many ways including duration and number of spikes. Still, these sequences share a similar trend in the general order...1 and 2 precede all other spikes in both s and s�). Many other sequences share this property with s and s�; in fact, we can completely characterize

  2. Rational Behavior Skills: A Teaching Sequence for Students with Emotional Disabilities.

    Science.gov (United States)

    Patton, Patricia Lucey

    1995-01-01

    Rational behavior training is a proactive teaching model concerned with helping students with behavior disorders or serious emotional disturbances develop rational thinking and appropriate social skills. Describes a seven-session sequence for teaching rational behavior skills in a middle school setting. Pre- and posttest data revealed significant…

  3. Behavioral economics and regulatory analysis.

    Science.gov (United States)

    Robinson, Lisa A; Hammitt, James K

    2011-09-01

    Behavioral economics has captured the interest of scholars and the general public by demonstrating ways in which individuals make decisions that appear irrational. While increasing attention is being focused on the implications of this research for the design of risk-reducing policies, less attention has been paid to how it affects the economic valuation of policy consequences. This article considers the latter issue, reviewing the behavioral economics literature and discussing its implications for the conduct of benefit-cost analysis, particularly in the context of environmental, health, and safety regulations. We explore three concerns: using estimates of willingness to pay or willingness to accept compensation for valuation, considering the psychological aspects of risk when valuing mortality-risk reductions, and discounting future consequences. In each case, we take the perspective that analysts should avoid making judgments about whether values are "rational" or "irrational." Instead, they should make every effort to rely on well-designed studies, using ranges, sensitivity analysis, or probabilistic modeling to reflect uncertainty. More generally, behavioral research has led some to argue for a more paternalistic approach to policy analysis. We argue instead for continued focus on describing the preferences of those affected, while working to ensure that these preferences are based on knowledge and careful reflection. © 2011 Society for Risk Analysis.

  4. Establishing a framework for comparative analysis of genome sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  5. Empirical analysis of consumer behavior

    OpenAIRE

    Huang, Yufeng

    2015-01-01

    This thesis consists of three essays in quantitative marketing, focusing on structural empirical analysis of consumer behavior. In the first essay, he investigates the role of a consumer's skill of product usage, and its imperfect transferability across brands, in her product choice. It shows that experienced consumers have higher but more specialized demand towards high-end products. The second essay investigates a consumer’s choice of considering a product before purchase. Because considera...

  6. Bioinformatic analysis of whole genome sequencing data

    OpenAIRE

    Maqbool, Khurram

    2014-01-01

    Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome. Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1,...

  7. [Tabular excel editor for analysis of aligned nucleotide sequences].

    Science.gov (United States)

    Demkin, V V

    2010-01-01

    Excel platform was used for transition of results of multiple aligned nucleotide sequences obtained using the BLAST network service to the form appropriate for visual analysis and editing. Two macros operators for MS Excel 2007 were constructed. The array of aligned sequences transformed into Excel table and processed using macros operators is more appropriate for analysis than initial html data.

  8. SEQUENCE ANALYSIS OF MATURASE K (MATK): A ...

    African Journals Online (AJOL)

    Global Journal

    The application and utilization of sequence data has been found very informative in the characterization and phylogenetic relationship of different crops species. This study aimed to use bioinformatics tools to characterize the. matK gene in some selected legumes with special reference to pigeon pea [cajanus cajan ...

  9. Evaluating the function of applied behavior analysis a bibliometric analysis.

    OpenAIRE

    Critchfield, Thomas S

    2002-01-01

    Analysis of scholarly citations involving behavioral journals reveals that, consistent with its mission, applied behavior analysis research frequently references the basic behavioral literature but, as some have suspected, exerts narrow scholarly influence.

  10. The Analysis of Human Behavior in Context

    Science.gov (United States)

    Sidman, Murray

    2004-01-01

    Does the name of the special interest group, "The Experimental Analysis of Human Behavior," imply that those who analyze the behavior of human animals must organize themselves apart from those who analyze the behavior of nonhuman animals? Is the use of nonhumans in experiments really not relevant to the analysis of the behavior of humans? If so,…

  11. Consolidating behavioral and neurophysiologic findings to explain the influence of contextual interference during motor sequence learning

    NARCIS (Netherlands)

    Wright, David; Verwey, Willem B.; Buchanen, John; Chen, Jing; Rhee, Joohyun; Immink, Maarten

    2016-01-01

    Motor sequence learning under high levels of contextual interference (CI) disrupts initial performance but supports delayed test and transfer performance when compared to learning under low CI. Integrating findings from early behavioral work and more recent experimental efforts that incorporated

  12. Google matrix analysis of DNA sequences.

    Science.gov (United States)

    Kandiah, Vivek; Shepelyansky, Dima L

    2013-01-01

    For DNA sequences of various species we construct the Google matrix [Formula: see text] of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scale-free networks as the World Wide Web (WWW). At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of [Formula: see text] is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scale-free features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.

  13. Google matrix analysis of DNA sequences.

    Directory of Open Access Journals (Sweden)

    Vivek Kandiah

    Full Text Available For DNA sequences of various species we construct the Google matrix [Formula: see text] of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scale-free networks as the World Wide Web (WWW. At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of [Formula: see text] is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scale-free features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.

  14. Positive Behavior Support and Applied Behavior Analysis: A Familial Alliance

    Science.gov (United States)

    Dunlap, Glen; Carr, Edward G.; Horner, Robert H.; Zarcone, Jennifer R.; Schwartz, Ilene

    2008-01-01

    Positive behavior support (PBS) emerged in the mid-1980s as an approach for understanding and addressing problem behaviors. PBS was derived primarily from applied behavior analysis (ABA). Over time, however, PBS research and practice has incorporated evaluative methods, assessment and intervention procedures, and conceptual perspectives associated…

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

    Directory of Open Access Journals (Sweden)

    Wadim L. Matochko

    2013-01-01

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

  16. Behavior analysis: the science of training.

    Science.gov (United States)

    Farhoody, Parvene

    2012-09-01

    Behavior analysis is a data-driven science dedicated to understanding the mechanisms of behavior. Applied behavior analysis is a branch of this scientific field that systematically applies scientific principles to real-world problems in an effort to improve quality of life. The use of the behavioral technology provides a way to teach human and nonhuman animals more effectively and efficiently and offers those using this technology increased success in achieving behavioral goals. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

    DEFF Research Database (Denmark)

    Svitashev, S.; Bryngelsson, T.; Vershinin, A.

    1994-01-01

    A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. In situ hybridization experiments showed dispersed organization of the sequences...

  18. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    In Pakistan, more than 10 million people are living with hepatitis C virus (HCV) with high morbidity and mortality. The aims of the present study are to report HCV core gene sequences from Pakistani population and perform their sequence comparison/phylogenetic analysis. The core gene of HCV has been cloned from six ...

  19. Cloning and sequence analysis of the Antheraea pernyi ...

    Indian Academy of Sciences (India)

    A genomic library was generated using HindIII and the positive clones were sequenced and analysed. The gp64 gene, encoding the baculovirus envelope protein GP64, was found in an insert. The nucleotide sequence analysis indicated that the AnpeNPV gp64 gene consists of a 1530 nucleotide open reading frame ...

  20. Sequence analysis corresponding to the PPE and PE proteins in ...

    Indian Academy of Sciences (India)

    Amino acid sequence analysis corresponding to the PPE proteins in H37Rv and CDC1551 strains of the Mycobacterium tuberculosis genomes resulted in the identification of a previously uncharacterized 225 amino acidresidue common region in 22 proteins. The pairwise sequence identities were as low as 18%.

  1. Biological sequence analysis: probabilistic models of proteins and nucleic acids

    National Research Council Canada - National Science Library

    Durbin, Richard

    1998-01-01

    ... analysis methods are now based on principles of probabilistic modelling. Examples of such methods include the use of probabilistically derived score matrices to determine the significance of sequence alignments, the use of hidden Markov models as the basis for profile searches to identify distant members of sequence families, and the inference...

  2. Effect of stacking sequence on the erosive wear behavior of jute and ...

    African Journals Online (AJOL)

    Effect of stacking sequence on the erosive wear behavior of jute and juteglass fabric reinforced epoxy composite. ... morphology of the eroded surface was examined by SEM.It is conclude from the study that the erosive wear behavior of natural fiber jute can be improved significantly by hybridizing with synthetic fiber glass.

  3. How behavioral economics can help to avoid 'The last mile problem' in whole genome sequencing.

    Science.gov (United States)

    Blumenthal-Barby, Jennifer S; McGuire, Amy L; Green, Robert C; Ubel, Peter A

    2015-01-01

    Failure to consider lessons from behavioral economics in the case of whole genome sequencing may cause us to run into the 'last mile problem' - the failure to integrate newly developed technology, on which billions of dollars have been invested, into society in a way that improves human behavior and decision-making.

  4. RNA Sequencing Analysis of Salivary Extracellular RNA.

    Science.gov (United States)

    Majem, Blanca; Li, Feng; Sun, Jie; Wong, David T W

    2017-01-01

    Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs. Using these invaluable technical tools, one can identify thousands of ncRNA species in saliva. These methods indicate that salivary exRNA provides an efficient medium for biomarker discovery of oral and systemic diseases.

  5. Strategy for the sequence analysis of heparin.

    Science.gov (United States)

    Liu, J; Desai, U R; Han, X J; Toida, T; Linhardt, R J

    1995-12-01

    The versatile biological activities of proteoglycans are mainly mediated by their glycosaminoglycan (GAG) components. Unlike proteins and nucleic acids, no satisfactory method for sequencing GAGs has been developed. This paper describes a strategy to sequence the GAG chains of heparin. Heparin, prepared from animal tissue, and processed by proteinases and endoglucuronidases, is 90% GAG heparin and 10% peptidoglycan heparin (containing small remnants of core protein). Raw porcine mucosal heparin was labelled on the amino termini of these core protein remnants with a hydrophobic, fluorescent tag [N-4-(6-dimethylamino-2-benzofuranyl) phenyl (NDBP)-isothiocyanate]. Enrichment of the NDBP-heparin using phenyl-Sepharose chromatography, followed by treatment with a mixture of heparin lyase I and III, resulted in a single NDBP-linkage region tetrasaccharide, which was characterized as deltaUAp(1-->3)-beta-D-Galp(1-->3)-beta-D-Galp(1-->4)-beta-Xylp -(1-->O-Ser-NDBP (deltaUAp is 4-deoxy-alpha-L-threo-hex-4-enopyranosyl uronic acid). Several NDBP-octasaccharides were isolated when NDBP-heparin was treated with only heparin lyase I. The structure of one of these NDBP-octasaccharides, deltaUAp2S(1-->4)-alpha-D-GlcNpAc(1-->4)-alpha-L-IdoAp (1-->4)-alpha-D-GlcNpAc6S(1-->4)-beta-D-GlcAp(1-->3)-beta-D- Galp(1-->3)-beta-D-Galp(1-->4)-beta-Xylp-(1-->O-Ser NDBP (S is sulphate, Ac is acetate), was determined by 1H-NMR and enzymatic methods. Enriched NDBP-heparin was treated with lithium hydroxide to release heparin, and the GAG chain was then labelled at xylose with 7-amino-1,3-naphthalene disulphonic acid (AGA). The resulting AGA-Xyl-heparin was sequenced on gradient PAGE using heparin lyase I and heparin lyase III. A predominant sequence in heparin at the protein core attachment site was deduced to be -D-GlcNp2S6S(or 6OH)(1-->4)-alpha-L-IdoAp2S-(1-->4)-alpha-D-GlcNp2S6S (or60H) (1-->4)-alpha-L-IdoAp2S(1-->4)-alpha-D-GlcNp2S6S( or 6OH)(1-->4)-alpha-L-IdoAp2S(1-->4)-alpha-D-GlcNpAc (1

  6. Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

    Directory of Open Access Journals (Sweden)

    Veli Mäkinen

    2014-03-01

    Full Text Available This special issue of Algorithms is dedicated to approaches to biological sequence analysis that have algorithmic novelty and potential for fundamental impact in methods used for genome research.

  7. Initial sequencing and comparative analysis of the mouse genome.

    Science.gov (United States)

    Waterston, Robert H; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R; Brown, Daniel G; Brown, Stephen D; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T; Church, Deanna M; Clamp, Michele; Clee, Christopher; Collins, Francis S; Cook, Lisa L; Copley, Richard R; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D; Deri, Justin; Dermitzakis, Emmanouil T; Dewey, Colin; Dickens, Nicholas J; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M; Eddy, Sean R; Elnitski, Laura; Emes, Richard D; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A; Flicek, Paul; Foley, Karen; Frankel, Wayne N; Fulton, Lucinda A; Fulton, Robert S; Furey, Terrence S; Gage, Diane; Gibbs, Richard A; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A; Green, Eric D; Gregory, Simon; Guigó, Roderic; Guyer, Mark; Hardison, Ross C; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B; Johnson, L Steven; Jones, Matthew; Jones, Thomas A; Joy, Ann; Kamal, Michael; Karlsson, Elinor K; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W James; Kirby, Andrew; Kolbe, Diana L; Korf, Ian; Kucherlapati, Raju S; Kulbokas, Edward J; Kulp, David; Landers, Tom; Leger, J P; Leonard, Steven; Letunic, Ivica; Levine, Rosie; Li, Jia; Li, Ming; Lloyd, Christine; Lucas, Susan; Ma, Bin; Maglott, Donna R; Mardis, Elaine R; Matthews, Lucy; Mauceli, Evan; Mayer, John H; McCarthy, Megan; McCombie, W Richard; McLaren, Stuart; McLay, Kirsten; McPherson, John D; Meldrim, Jim; Meredith, Beverley; Mesirov, Jill P; Miller, Webb; Miner, Tracie L; Mongin, Emmanuel; Montgomery, Kate T; Morgan, Michael; Mott, Richard; Mullikin, James C; Muzny, Donna M; Nash, William E; Nelson, Joanne O; Nhan, Michael N; Nicol, Robert; Ning, Zemin; Nusbaum, Chad; O'Connor, Michael J; Okazaki, Yasushi; Oliver, Karen; Overton-Larty, Emma; Pachter, Lior; Parra, Genís; Pepin, Kymberlie H; Peterson, Jane; Pevzner, Pavel; Plumb, Robert; Pohl, Craig S; Poliakov, Alex; Ponce, Tracy C; Ponting, Chris P; Potter, Simon; Quail, Michael; Reymond, Alexandre; Roe, Bruce A; Roskin, Krishna M; Rubin, Edward M; Rust, Alistair G; Santos, Ralph; Sapojnikov, Victor; Schultz, Brian; Schultz, Jörg; Schwartz, Matthias S; Schwartz, Scott; Scott, Carol; Seaman, Steven; Searle, Steve; Sharpe, Ted; Sheridan, Andrew; Shownkeen, Ratna; Sims, Sarah; Singer, Jonathan B; Slater, Guy; Smit, Arian; Smith, Douglas R; Spencer, Brian; Stabenau, Arne; Stange-Thomann, Nicole; Sugnet, Charles; Suyama, Mikita; Tesler, Glenn; Thompson, Johanna; Torrents, David; Trevaskis, Evanne; Tromp, John; Ucla, Catherine; Ureta-Vidal, Abel; Vinson, Jade P; Von Niederhausern, Andrew C; Wade, Claire M; Wall, Melanie; Weber, Ryan J; Weiss, Robert B; Wendl, Michael C; West, Anthony P; Wetterstrand, Kris; Wheeler, Raymond; Whelan, Simon; Wierzbowski, Jamey; Willey, David; Williams, Sophie; Wilson, Richard K; Winter, Eitan; Worley, Kim C; Wyman, Dudley; Yang, Shan; Yang, Shiaw-Pyng; Zdobnov, Evgeny M; Zody, Michael C; Lander, Eric S

    2002-12-05

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  8. Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis

    Science.gov (United States)

    Chen, C. H. Winston; Taranenko, N. I.; Golovlev, V. V.; Isola, N. R.; Allman, S. L.

    1998-03-01

    Rapid DNA sequencing and/or analysis is critically important for biomedical research. In the past, gel electrophoresis has been the primary tool to achieve DNA analysis and sequencing. However, gel electrophoresis is a time-consuming and labor-extensive process. Recently, we have developed and used laser desorption mass spectrometry (LDMS) to achieve sequencing of ss-DNA longer than 100 nucleotides. With LDMS, we succeeded in sequencing DNA in seconds instead of hours or days required by gel electrophoresis. In addition to sequencing, we also applied LDMS for the detection of DNA probes for hybridization LDMS was also used to detect short tandem repeats for forensic applications. Clinical applications for disease diagnosis such as cystic fibrosis caused by base deletion and point mutation have also been demonstrated. Experimental details will be presented in the meeting. abstract.

  9. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C

    2006-07-01

    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  10. Categorizing accident sequences in the external radiotherapy for risk analysis

    OpenAIRE

    Kim, Jonghyun

    2013-01-01

    Purpose This study identifies accident sequences from the past accidents in order to help the risk analysis application to the external radiotherapy. Materials and Methods This study reviews 59 accidental cases in two retrospective safety analyses that have collected the incidents in the external radiotherapy extensively. Two accident analysis reports that accumulated past incidents are investigated to identify accident sequences including initiating events, failure of safety measures, and co...

  11. Sequencing and Analysis of Neanderthal Genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Coop, Graham; Kudaravalli, Sridhar; Smith,Doug; Krause, Johannes; Alessi, Joe; Chen, Feng; Platt, Darren; Paabo,Svante; Pritchard, Jonathan K.; Rubin, Edward M.

    2006-06-13

    Recovery and analysis of multiple Neanderthal autosomalsequences using a metagenomic approach reveals that modern humans andNeanderthals split ~;400,000 years ago, without significant evidence ofsubsequent admixture.

  12. DNA Sequence Analysis in Clinical Medicine, Proceeding Cautiously

    Directory of Open Access Journals (Sweden)

    Moyra Smith

    2017-05-01

    Full Text Available Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications. In recent decades, exome sequencing has primarily been used in patient studies. Discussed in some detail, are important measures that have been developed to standardize variant calling and to assess pathogenicity of variants. Examples of cases where exome sequencing has facilitated diagnosis and led to improved medical management are presented. Whole genome sequencing and its clinical relevance are presented particularly in the context of analysis of nucleotide and structural genomic variants in large population studies and in certain patient cohorts. Applications involving analysis of cell free DNA in maternal blood for prenatal diagnosis of specific autosomal trisomies are reviewed. Applications of DNA sequencing to diagnosis and therapeutics of cancer are presented. Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived cell free DNA and exosomes that are present in body fluids. Insights gained into underlying pathogenetic mechanisms of certain complex common diseases, including schizophrenia, macular degeneration, neurodegenerative disease are presented. The relevance of different types of variants, rare, uncommon, and common to disease pathogenesis, and the continuum of causality, are addressed. Pharmogenetic variants detected by DNA sequence analysis are gaining in importance and are particularly relevant

  13. Improving Public Perception of Behavior Analysis.

    Science.gov (United States)

    Freedman, David H

    2016-05-01

    The potential impact of behavior analysis is limited by the public's dim awareness of the field. The mass media rarely cover behavior analysis, other than to echo inaccurate negative stereotypes about control and punishment. The media instead play up appealing but less-evidence-based approaches to problems, a key example being the touting of dubious diets over behavioral approaches to losing excess weight. These sorts of claims distort or skirt scientific evidence, undercutting the fidelity of behavior analysis to scientific rigor. Strategies for better connecting behavior analysis with the public might include reframing the field's techniques and principles in friendlier, more resonant form; pushing direct outcome comparisons between behavior analysis and its rivals in simple terms; and playing up the "warm and fuzzy" side of behavior analysis.

  14. Quantiprot - a Python package for quantitative analysis of protein sequences.

    Science.gov (United States)

    Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

    2017-07-17

    The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

  15. Genome sequencing and analysis conference grant

    Energy Technology Data Exchange (ETDEWEB)

    Venter, J.C. [ed.

    1995-10-01

    The 14 plenary session presentations focused on nematode; yeast; fruit fly; plants; mycobacteria; and man. In addition there were presentations on a variety of technical innovations including database developments and refinements, bioelectronic genesensors, computer-assisted multiplex techniques, and hybridization analysis with DNA chip technology. This document includes a list of exhibitors and abstracts of sessions.

  16. Analysis of Health Behavior Theories for Clustering of Health Behaviors.

    Science.gov (United States)

    Choi, Seung Hee; Duffy, Sonia A

    The objective of this article was to review the utility of established behavior theories, including the Health Belief Model, Theory of Reasoned Action, Theory of Planned Behavior, Transtheoretical Model, and Health Promotion Model, for addressing multiple health behaviors among people who smoke. It is critical to design future interventions for multiple health behavior changes tailored to individuals who currently smoke, yet it has not been addressed. Five health behavior theories/models were analyzed and critically evaluated. A review of the literature included a search of PubMed and Google Scholar from 2010 to 2016. Two hundred sixty-seven articles (252 studies from the initial search and 15 studies from the references of initially identified studies) were included in the analysis. Most of the health behavior theories/models emphasize psychological and cognitive constructs that can be applied only to one specific behavior at a time, thus making them not suitable to address multiple health behaviors. However, the Health Promotion Model incorporates "related behavior factors" that can explain multiple health behaviors among persons who smoke. Future multiple behavior interventions guided by the Health Promotion Model are necessary to show the utility and applicability of the model to address multiple health behaviors.

  17. Categorizing accident sequences in the external radiotherapy for risk analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Hyun [KEPCO International Nuclear Graduate School (KINGS), Ulsan (Korea, Republic of)

    2013-06-15

    This study identifies accident sequences from the past accidents in order to help the risk analysis application to the external radiotherapy. This study reviews 59 accidental cases in two retrospective safety analyses that have collected the incidents in the external radiotherapy extensively. Two accident analysis reports that accumulated past incidents are investigated to identify accident sequences including initiating events, failure of safety measures, and consequences. This study classifies the accidents by the treatments stages and sources of errors for initiating events, types of failures in the safety measures, and types of undesirable consequences and the number of affected patients. Then, the accident sequences are grouped into several categories on the basis of similarity of progression. As a result, these cases can be categorized into 14 groups of accident sequence. The result indicates that risk analysis needs to pay attention to not only the planning stage, but also the calibration stage that is committed prior to the main treatment process. It also shows that human error is the largest contributor to initiating events as well as to the failure of safety measures. This study also illustrates an event tree analysis for an accident sequence initiated in the calibration. This study is expected to provide sights into the accident sequences for the prospective risk analysis through the review of experiences.

  18. Categorizing accident sequences in the external radiotherapy for risk analysis.

    Science.gov (United States)

    Kim, Jonghyun

    2013-06-01

    This study identifies accident sequences from the past accidents in order to help the risk analysis application to the external radiotherapy. This study reviews 59 accidental cases in two retrospective safety analyses that have collected the incidents in the external radiotherapy extensively. Two accident analysis reports that accumulated past incidents are investigated to identify accident sequences including initiating events, failure of safety measures, and consequences. This study classifies the accidents by the treatments stages and sources of errors for initiating events, types of failures in the safety measures, and types of undesirable consequences and the number of affected patients. Then, the accident sequences are grouped into several categories on the basis of similarity of progression. As a result, these cases can be categorized into 14 groups of accident sequence. The result indicates that risk analysis needs to pay attention to not only the planning stage, but also the calibration stage that is committed prior to the main treatment process. It also shows that human error is the largest contributor to initiating events as well as to the failure of safety measures. This study also illustrates an event tree analysis for an accident sequence initiated in the calibration. This study is expected to provide sights into the accident sequences for the prospective risk analysis through the review of experiences.

  19. Cognition, behavior, and the experimental analysis of behavior

    OpenAIRE

    Shimp, Charles P.

    1984-01-01

    A case history illustrates how one research program in the experimental analysis of behavior evolved somewhat differently from the modal research program represented in this journal. A chief issue that seems to be responsible for this difference is the role attributed to theory in behavioral research: Skinner's views on the nature and function of theory and on the nature of observation combine to produce a certain kind of picture of behavior. The classic conception of reinforcement contingenc...

  20. Deep Sequencing Analysis of Nucleolar Small RNAs: Bioinformatics.

    Science.gov (United States)

    Bai, Baoyan; Laiho, Marikki

    2016-01-01

    Small RNAs (size 20-30 nt) of various types have been actively investigated in recent years, and their subcellular compartmentalization and relative concentrations are likely to be of importance to their cellular and physiological functions. Comprehensive data on this subset of the transcriptome can only be obtained by application of high-throughput sequencing, which yields data that are inherently complex and multidimensional, as sequence composition, length, and abundance will all inform to the small RNA function. Subsequent data analysis, hypothesis testing, and presentation/visualization of the results are correspondingly challenging. We have constructed small RNA libraries derived from different cellular compartments, including the nucleolus, and asked whether small RNAs exist in the nucleolus and whether they are distinct from cytoplasmic and nuclear small RNAs, the miRNAs. Here, we present a workflow for analysis of small RNA sequencing data generated by the Ion Torrent PGM sequencer from samples derived from different cellular compartments.

  1. Molecular cloning and sequence analysis of the cat myostatin gene ...

    African Journals Online (AJOL)

    ... MEF3, MTBF, PAX3, SMAD, HBOX, HOMF and TEAF motifs. Comparative analysis for some motifs showed both conservations and differences among cat, horse, porcine and human. Key words: Cat, myostatin 5'-regulatory region, molecular cloning, sequence analysis and comparison, transcription factor binding sites.

  2. Food Fish Identification from DNA Extraction through Sequence Analysis

    Science.gov (United States)

    Hallen-Adams, Heather E.

    2015-01-01

    This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

  3. An optimum analysis sequence for environmental gamma-ray spectrometry

    International Nuclear Information System (INIS)

    De la Torre, F.; Rios M, C.; Ruvalcaba A, M. G.; Mireles G, F.; Saucedo A, S.; Davila R, I.; Pinedo, J. L.

    2010-10-01

    This work aims to obtain an optimum analysis sequence for environmental gamma-ray spectroscopy by means of Genie 2000 (Canberra). Twenty different analysis sequences were customized using different peak area percentages and different algorithms for: 1) peak finding, and 2) peak area determination, and with or without the use of a library -based on evaluated nuclear data- of common gamma-ray emitters in environmental samples. The use of an optimum analysis sequence with certified nuclear information avoids the problems originated by the significant variations in out-of-date nuclear parameters of commercial software libraries. Interference-free gamma ray energies with absolute emission probabilities greater than 3.75% were included in the customized library. The gamma-ray spectroscopy system (based on a Ge Re-3522 Canberra detector) was calibrated both in energy and shape by means of the IAEA-2002 reference spectra for software intercomparison. To test the performance of the analysis sequences, the IAEA-2002 reference spectrum was used. The z-score and the reduced χ 2 criteria were used to determine the optimum analysis sequence. The results show an appreciable variation in the peak area determinations and their corresponding uncertainties. Particularly, the combination of second derivative peak locate with simple peak area integration algorithms provides the greater accuracy. Lower accuracy comes from the combination of library directed peak locate algorithm and Genie's Gamma-M peak area determination. (Author)

  4. An optimum analysis sequence for environmental gamma-ray spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    De la Torre, F.; Rios M, C.; Ruvalcaba A, M. G.; Mireles G, F.; Saucedo A, S.; Davila R, I.; Pinedo, J. L., E-mail: fta777@hotmail.co [Universidad Autonoma de Zacatecas, Centro Regional de Estudis Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico)

    2010-10-15

    This work aims to obtain an optimum analysis sequence for environmental gamma-ray spectroscopy by means of Genie 2000 (Canberra). Twenty different analysis sequences were customized using different peak area percentages and different algorithms for: 1) peak finding, and 2) peak area determination, and with or without the use of a library -based on evaluated nuclear data- of common gamma-ray emitters in environmental samples. The use of an optimum analysis sequence with certified nuclear information avoids the problems originated by the significant variations in out-of-date nuclear parameters of commercial software libraries. Interference-free gamma ray energies with absolute emission probabilities greater than 3.75% were included in the customized library. The gamma-ray spectroscopy system (based on a Ge Re-3522 Canberra detector) was calibrated both in energy and shape by means of the IAEA-2002 reference spectra for software intercomparison. To test the performance of the analysis sequences, the IAEA-2002 reference spectrum was used. The z-score and the reduced {chi}{sup 2} criteria were used to determine the optimum analysis sequence. The results show an appreciable variation in the peak area determinations and their corresponding uncertainties. Particularly, the combination of second derivative peak locate with simple peak area integration algorithms provides the greater accuracy. Lower accuracy comes from the combination of library directed peak locate algorithm and Genie's Gamma-M peak area determination. (Author)

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

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

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

  6. Long-range correlations in the fire sequences with Detrended Fluctuation Analysis

    Science.gov (United States)

    Zheng, H.; Song, W.

    2009-04-01

    Forest fires have been found to exhibit good power-law relation in the frequency-size distribution over many orders of magnitude in different countries, which identifies that forest fires behave as self-organized criticality (SOC). And in the temporal aspect, it is also found that the frequency-interval distributions of fires obey power-law with periodic fluctuations. The fire sequences cannot generally be described as Poisson point process, because the distribution of the occurrence times is not homogeneous and shows a clustering behavior. So the power-law distributions, the scaling behavior of the parameters are usually used to describe the sequence. Inter-event time series, the waiting-time between consecutive events, were studied in the similar earthquakes system in recent years, focusing on the distributions and the intrinsic mechanism. In order to find the long-range correlations of fire sequences, we analyzed the scaling behavior of the fires occurred in some places of Asia by means of the detrended fluctuation analysis (DFA), which provides the information of the scaling behavior and long-range characteristics in non-stationary time series. The scaling exponents, larger than 0.5, indicate the presence of persistent long-range correlations, while it performs white noise at 0.5. The detail fire data were investigated in several places, and with the different thresholds of the burned areas or losses. The result reveals the existence of long-range correlations in the fire interval sequences, and the scaling exponents are quite constant over several orders of magnitude. But the exponents are different from each other, possibly due to the orientation of the places we analyzed and other local influencing factors: human activity, weather, economic etc. Besides, the fire sequences of different types were studied in the same way, to find out the possible different long-range behaviors and their possible reasons. The results seem to be helpful to understand the

  7. High Throughput Plasmid Sequencing with Illumina and CLC Bio (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    Energy Technology Data Exchange (ETDEWEB)

    Athavale, Ajay

    2012-06-01

    Ajay Athavale (Monsanto) presents "High Throughput Plasmid Sequencing with Illumina and CLC Bio" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  8. Bioinformatics analysis of circulating cell-free DNA sequencing data.

    Science.gov (United States)

    Chan, Landon L; Jiang, Peiyong

    2015-10-01

    The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  9. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing

    Science.gov (United States)

    Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

    2015-01-01

    Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids. PMID:26115486

  10. Handbook of Applied Behavior Analysis

    Science.gov (United States)

    Fisher, Wayne W., Ed.; Piazza, Cathleen C., Ed.; Roane, Henry S., Ed.

    2011-01-01

    Describing the state of the science of ABA, this comprehensive handbook provides detailed information about theory, research, and intervention. The contributors are leading ABA authorities who present current best practices in behavioral assessment and demonstrate evidence-based strategies for supporting positive behaviors and reducing problem…

  11. Virtual environment for behavioral analysis of malware

    OpenAIRE

    KOVÁŘ, Jaroslav

    2013-01-01

    The goal of this bachelor thesis was to propose and implement a virtual environment for behavioral analysis of malware. Specifically with simulated network services. Subsequently was this environment applied to the analysis of several selected malware samples.

  12. Exact combinatorial reliability analysis of dynamic systems with sequence-dependent failures

    International Nuclear Information System (INIS)

    Xing Liudong; Shrestha, Akhilesh; Dai Yuanshun

    2011-01-01

    Many real-life fault-tolerant systems are subjected to sequence-dependent failure behavior, in which the order in which the fault events occur is important to the system reliability. Such systems can be modeled by dynamic fault trees (DFT) with priority-AND (pAND) gates. Existing approaches for the reliability analysis of systems subjected to sequence-dependent failures are typically state-space-based, simulation-based or inclusion-exclusion-based methods. Those methods either suffer from the state-space explosion problem or require long computation time especially when results with high degree of accuracy are desired. In this paper, an analytical method based on sequential binary decision diagrams is proposed. The proposed approach can analyze the exact reliability of non-repairable dynamic systems subjected to the sequence-dependent failure behavior. Also, the proposed approach is combinatorial and is applicable for analyzing systems with any arbitrary component time-to-failure distributions. The application and advantages of the proposed approach are illustrated through analysis of several examples. - Highlights: → We analyze the sequence-dependent failure behavior using combinatorial models. → The method has no limitation on the type of time-to-failure distributions. → The method is analytical and based on sequential binary decision diagrams (SBDD). → The method is computationally more efficient than existing methods.

  13. A Contextualized, Differential Sequence Mining Method to Derive Students' Learning Behavior Patterns

    Science.gov (United States)

    Kinnebrew, John S.; Loretz, Kirk M.; Biswas, Gautam

    2013-01-01

    Computer-based learning environments can produce a wealth of data on student learning interactions. This paper presents an exploratory data mining methodology for assessing and comparing students' learning behaviors from these interaction traces. The core algorithm employs a novel combination of sequence mining techniques to identify deferentially…

  14. Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes).

    Science.gov (United States)

    Johnson, Jennifer L; Wittgenstein, Helena; Mitchell, Sharon E; Hyma, Katie E; Temnykh, Svetlana V; Kharlamova, Anastasiya V; Gulevich, Rimma G; Vladimirova, Anastasiya V; Fong, Hiu Wa Flora; Acland, Gregory M; Trut, Lyudmila N; Kukekova, Anna V

    2015-01-01

    The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.

  15. Genotyping-By-Sequencing (GBS Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes.

    Directory of Open Access Journals (Sweden)

    Jennifer L Johnson

    Full Text Available The silver fox (Vulpes vulpes offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.

  16. Probabilistic Slow Features for Behavior Analysis

    NARCIS (Netherlands)

    Zafeiriou, Lazaros; Nicolaou, Mihalis A.; Zafeiriou, Stefanos; Nikitidis, Symeon; Pantic, Maja

    A recently introduced latent feature learning technique for time-varying dynamic phenomena analysis is the so-called slow feature analysis (SFA). SFA is a deterministic component analysis technique for multidimensional sequences that, by minimizing the variance of the first-order time derivative

  17. Learning slow features for behavior analysis

    NARCIS (Netherlands)

    Zafeiriou, Lazaros; Nicolaou, Mihalis A.; Zafeiriou, Stefanos; Nikitids, Symeon; Pantic, Maja

    2013-01-01

    A recently introduced latent feature learning technique for time varying dynamic phenomena analysis is the socalled Slow Feature Analysis (SFA). SFA is a deterministic component analysis technique for multi-dimensional sequences that by minimizing the variance of the first order time derivative

  18. Different behaviors of epidemic spreading in scale-free networks with identical degree sequence

    Energy Technology Data Exchange (ETDEWEB)

    Chu Xiangwei; Guan Jihong [School of Electronics and Information, Tongji University, 4800 Cao' an Road, Shanghai 201804 (China); Zhang Zhongzhi; Zhou Shuigeng [School of Computer Science, Fudan University, Shanghai 200433 (China); Li Mo, E-mail: zhangzz@fudan.edu.c, E-mail: jhguan@tongj.edu.c, E-mail: sgzhou@fudan.edu.c [Software School, Fudan University, Shanghai 200433 (China)

    2010-02-12

    Recently, the study of dynamical behaviors of the susceptible-infected (SI) disease model in complex networks, especially in Barabasi-Albert (BA) scale-free networks, has attracted much attention. Although some interesting phenomena have been observed, the formative reasons for those particular dynamical behaviors are still not well understood, despite the speculation that topological properties (for example the degree distribution) have a strong impact on epidemic spreading. In this paper, we study the evolution behaviors of epidemic spreading on a class of scale-free networks sharing identical degree sequence, and observe significantly different evolution behaviors in the whole family of networks. We show that the power-law degree distribution does not suffice to characterize the dynamical behaviors of disease diffusion on scale-free networks.

  19. De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae)

    Science.gov (United States)

    2014-01-01

    Background Anopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq). Methods To provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs). Results Approximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species. Conclusions Our data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis. PMID:25000941

  20. Emergence of good conduct, scaling and zipf laws in human behavioral sequences in an online world.

    Directory of Open Access Journals (Sweden)

    Stefan Thurner

    Full Text Available We study behavioral action sequences of players in a massive multiplayer online game. In their virtual life players use eight basic actions which allow them to interact with each other. These actions are communication, trade, establishing or breaking friendships and enmities, attack, and punishment. We measure the probabilities for these actions conditional on previous taken and received actions and find a dramatic increase of negative behavior immediately after receiving negative actions. Similarly, positive behavior is intensified by receiving positive actions. We observe a tendency towards antipersistence in communication sequences. Classifying actions as positive (good and negative (bad allows us to define binary 'world lines' of lives of individuals. Positive and negative actions are persistent and occur in clusters, indicated by large scaling exponents α ~ 0.87 of the mean square displacement of the world lines. For all eight action types we find strong signs for high levels of repetitiveness, especially for negative actions. We partition behavioral sequences into segments of length n (behavioral 'words' and 'motifs' and study their statistical properties. We find two approximate power laws in the word ranking distribution, one with an exponent of κ ~ -1 for the ranks up to 100, and another with a lower exponent for higher ranks. The Shannon n-tuple redundancy yields large values and increases in terms of word length, further underscoring the non-trivial statistical properties of behavioral sequences. On the collective, societal level the timeseries of particular actions per day can be understood by a simple mean-reverting log-normal model.

  1. Molecular cloning, sequence analysis and structure prediction of the ...

    African Journals Online (AJOL)

    Molecular cloning, sequence analysis and structure prediction of the related to b 0,+ amino acid transporter (rBAT) in Cyprinus carpio L. ... The amplified product was 2370 bp, including a 42 bp 5'-untranslated region, a 288 bp 3'-untranslated region, and a 2040 bp open reading frame (ORF), which encoded 679 amino acids ...

  2. Sequence analysis corresponding to the PPE and PE proteins in ...

    Indian Academy of Sciences (India)

    Unknown

    AB repeats; Mycobacterium tuberculosis genome; PE-PPE domain; PPE, PE proteins; sequence analysis; surface antigens. J. Biosci. | Vol. ... bacterium tuberculosis genomes resulted in the identification of a previously uncharacterized 225 amino acid- ...... Vega Lopez F, Brooks L A, Dockrell H M, De Smet K A,. Thompson ...

  3. Sequence analysis corresponding to the PPE and PE proteins in ...

    Indian Academy of Sciences (India)

    Unknown

    Amino acid sequence analysis corresponding to the PE proteins resulted in the identification of tandem repeats comprising 41–43 amino acid ..... Q9RAP8. Leptospira interrogans serovar ictero- haemorrhagiae-B. ORFC protein. 5. P71003. Bacillus subtilis-B. Hypothetical 49⋅4 kDa protein. 5. ALL2941. Anabaena sp.

  4. Sequence symmetry analysis in pharmacovigilance and pharmacoepidemiologic studies

    DEFF Research Database (Denmark)

    Lai, Edward Chia Cheng; Pratt, Nicole; Hsieh, Cheng Yang

    2017-01-01

    Sequence symmetry analysis (SSA) is a method for detecting adverse drug events by utilizing computerized claims data. The method has been increasingly used to investigate safety concerns of medications and as a pharmacovigilance tool to identify unsuspected side effects. Validation studies have i...

  5. Inter simple sequence repeat analysis of genetic diversity of five ...

    African Journals Online (AJOL)

    This paper studied the genetic diversity of five cultivated pepper species using inter simple sequence repeat (ISSR) analysis. The amplicons of 13 out of 15 designed primers were stable polymorphic and therefore were used as genetic biomarkers. 135 total clear bands were obtained, of which 102 were polymorphic bands ...

  6. Molecular cloning, expression analysis and sequence prediction of ...

    African Journals Online (AJOL)

    CCAAT/enhancer-binding protein beta as an essential transcriptional factor, regulates the differentiation of adipocytes and the deposition of fat. Herein, we cloned the whole open reading frame (ORF) of bovine C/EBPβ gene and analyzed its putative protein structures via DNA cloning and sequence analysis. Then, the ...

  7. Sequence analysis of mitochondrial 16S ribosomal RNA gene ...

    Indian Academy of Sciences (India)

    Unknown

    Sequence analysis of mitochondrial 16S ribosomal RNA gene fragment from seven mosquito species. YOGESH S SHOUCHE* and MILIND S PATOLE. National Center for Cell Science, Pune University Campus, Pune 411 007, India. *Corresponding author (Fax, 91-20-5672259; Email, yogesh@nccs.res.in). Mosquitoes are ...

  8. Phylogenetic relationships of Malassezia species based on multilocus sequence analysis.

    Science.gov (United States)

    Castellá, Gemma; Coutinho, Selene Dall' Acqua; Cabañes, F Javier

    2014-01-01

    Members of the genus Malassezia are lipophilic basidiomycetous yeasts, which are part of the normal cutaneous microbiota of humans and other warm-blooded animals. Currently, this genus consists of 14 species that have been characterized by phenetic and molecular methods. Although several molecular methods have been used to identify and/or differentiate Malassezia species, the sequencing of the rRNA genes and the chitin synthase-2 gene (CHS2) are the most widely employed. There is little information about the β-tubulin gene in the genus Malassezia, a gene has been used for the analysis of complex species groups. The aim of the present study was to sequence a fragment of the β-tubulin gene of Malassezia species and analyze their phylogenetic relationship using a multilocus sequence approach based on two rRNA genes (ITS including 5.8S rRNA and D1/D2 region of 26S rRNA) together with two protein encoding genes (CHS2 and β-tubulin). The phylogenetic study of the partial β-tubulin gene sequences indicated that this molecular marker can be used to assess diversity and identify new species. The multilocus sequence analysis of the four loci provides robust support to delineate species at the terminal nodes and could help to estimate divergence times for the origin and diversification of Malassezia species.

  9. Software for rapid time dependent ChIP-sequencing analysis (TDCA).

    Science.gov (United States)

    Myschyshyn, Mike; Farren-Dai, Marco; Chuang, Tien-Jui; Vocadlo, David

    2017-11-25

    Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically

  10. The SCALE criticality safety analysis sequences: Status and future directions

    International Nuclear Information System (INIS)

    Parks, C.V.

    1993-01-01

    The Standardized Computer Analyses for Licensing Evaluation (SCALE) code system. Was originally conceived and developed in the late 1970s for the US Nuclear Regulatory Commission. The goal was to provide easy-to-use, yet accurate, analysis capabilities for use in evaluating the criticality safety, shielding, and heat transfer aspects of transportation packages for radioactive material. The Criticality Safety Analysis Sequences (CSAS) for SCALE were developed to ''automate'' problem-dependent cross-section and material processing prior to execution of the wellestablished XSDRNPM or KENO codes for calculation of k eff . The criticality analysis sequences provided in SCALE-4 are summarized. The SCALE system continues to be maintained and enhanced by staff of the Computing Applications Division at Oak Ridge National Laboratory (ORNL). The purpose of this paper is to discuss recent work to improve system portability and user interfaces and to provide information on ongoing work to enhance the analysis capabilities

  11. Complete genome sequence analysis of chicken astrovirus isolate from India.

    Science.gov (United States)

    Patel, Amrutlal K; Pandit, Ramesh J; Thakkar, Jalpa R; Hinsu, Ankit T; Pandey, Vinod C; Pal, Joy K; Prajapati, Kantilal S; Jakhesara, Subhash J; Joshi, Chaitanya G

    2017-03-01

    Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and "white chicks" condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens. Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein. The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5'-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3'-UTR which harboured two corona virus stem loop II like "s2m" motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74-98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.

  12. Phylogeny and classification of Dickeya based on multilocus sequence analysis.

    Science.gov (United States)

    Marrero, Glorimar; Schneider, Kevin L; Jenkins, Daniel M; Alvarez, Anne M

    2013-09-01

    Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.

  13. Toward the globalization of behavior analysis.

    Science.gov (United States)

    Malott, Maria E

    2004-01-01

    Globalization could facilitate the long-term growth of behavior analysis, and although progress has been made, much yet needs to be done. Given the scarcity of resources, it is suggested that we draw from successes in the development of behavior analysis and establish behavioral programs around the world that embrace research, education, and practice as a focus of systematic globalization efforts. The strategy would require the implementation of cultural contingencies that support initiation and long-term program expansion. For program initiation, contingencies are needed to place pioneer behavior analysts in university units that would be unlikely to start a behavioral program otherwise. The task of these pioneers would be to build a critical mass that would multiply behavior-analytic repertoires, obtain research funding, conduct publishable research, and establish applied settings. For long-term program development, the field should expand internationally as it continues building the infrastructure needed to accelerate the demand for behavioral programs in higher education, scholarly work in behavior analysis, behavior analysts in existing jobs, and behavioral technology in the market place.

  14. Construction of an integrated database to support genomic sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, W.; Overbeek, R.

    1994-11-01

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  15. Analysis of Sequence Diagram Layout in Advanced UML Modelling Tools

    Directory of Open Access Journals (Sweden)

    Ņikiforova Oksana

    2016-05-01

    Full Text Available System modelling using Unified Modelling Language (UML is the task that should be solved for software development. The more complex software becomes the higher requirements are stated to demonstrate the system to be developed, especially in its dynamic aspect, which in UML is offered by a sequence diagram. To solve this task, the main attention is devoted to the graphical presentation of the system, where diagram layout plays the central role in information perception. The UML sequence diagram due to its specific structure is selected for a deeper analysis on the elements’ layout. The authors research represents the abilities of modern UML modelling tools to offer automatic layout of the UML sequence diagram and analyse them according to criteria required for the diagram perception.

  16. Evolutionary analysis of hepatitis C virus gene sequences from 1953

    Science.gov (United States)

    Gray, Rebecca R.; Tanaka, Yasuhito; Takebe, Yutaka; Magiorkinis, Gkikas; Buskell, Zelma; Seeff, Leonard; Alter, Harvey J.; Pybus, Oliver G.

    2013-01-01

    Reconstructing the transmission history of infectious diseases in the absence of medical or epidemiological records often relies on the evolutionary analysis of pathogen genetic sequences. The precision of evolutionary estimates of epidemic history can be increased by the inclusion of sequences derived from ‘archived’ samples that are genetically distinct from contemporary strains. Historical sequences are especially valuable for viral pathogens that circulated for many years before being formally identified, including HIV and the hepatitis C virus (HCV). However, surprisingly few HCV isolates sampled before discovery of the virus in 1989 are currently available. Here, we report and analyse two HCV subgenomic sequences obtained from infected individuals in 1953, which represent the oldest genetic evidence of HCV infection. The pairwise genetic diversity between the two sequences indicates a substantial period of HCV transmission prior to the 1950s, and their inclusion in evolutionary analyses provides new estimates of the common ancestor of HCV in the USA. To explore and validate the evolutionary information provided by these sequences, we used a new phylogenetic molecular clock method to estimate the date of sampling of the archived strains, plus the dates of four more contemporary reference genomes. Despite the short fragments available, we conclude that the archived sequences are consistent with a proposed sampling date of 1953, although statistical uncertainty is large. Our cross-validation analyses suggest that the bias and low statistical power observed here likely arise from a combination of high evolutionary rate heterogeneity and an unstructured, star-like phylogeny. We expect that attempts to date other historical viruses under similar circumstances will meet similar problems. PMID:23938759

  17. Caldwell University's Department of Applied Behavior Analysis.

    Science.gov (United States)

    Reeve, Kenneth F; Reeve, Sharon A

    2016-05-01

    Since 2004, faculty members at Caldwell University have developed three successful graduate programs in Applied Behavior Analysis (i.e., PhD, MA, non-degree programs), increased program faculty from two to six members, developed and operated an on-campus autism center, and begun a stand-alone Applied Behavior Analysis Department. This paper outlines a number of strategies used to advance these initiatives, including those associated with an extensive public relations campaign. We also outline challenges that have limited our programs' growth. These strategies, along with a consideration of potential challenges, might prove useful in guiding academicians who are interested in starting their own programs in behavior analysis.

  18. A general sequence processing and analysis program for protein engineering.

    Science.gov (United States)

    Stafford, Ryan L; Zimmerman, Erik S; Hallam, Trevor J; Sato, Aaron K

    2014-10-27

    Protein engineering projects often amass numerous raw DNA sequences, but no readily available software combines sequence processing and activity correlation required for efficient lead identification. XLibraryDisplay is an open source program integrated into Microsoft Excel for Windows that automates batch sequence processing via a simple step-by-step, menu-driven graphical user interface. XLibraryDisplay accepts any DNA template which is used as a basis for trimming, filtering, translating, and aligning hundreds to thousands of sequences (raw, FASTA, or Phred PHD file formats). Key steps for library characterization through lead discovery are available including library composition analysis, filtering by experimental data, graphing and correlating to experimental data, alignment to structural data extracted from PDB files, and generation of PyMOL visualization scripts. Though larger data sets can be handled, the program is best suited for analyzing approximately 10 000 or fewer leads or naïve clones which have been characterized using Sanger sequencing and other experimental approaches. XLibraryDisplay can be downloaded for free from sourceforge.net/projects/xlibrarydisplay/ .

  19. Translational Behavior Analysis and Practical Benefits

    Science.gov (United States)

    Pilgrim, Carol

    2011-01-01

    In his article, Critchfield ("Translational Contributions of the Experimental Analysis of Behavior," "The Behavior Analyst," v34, p3-17, 2011) summarizes a previous call (Mace & Critchfield, 2010) for basic scientists to reexamine the inspiration for their research and turn increasingly to translational approaches. Interestingly, rather than…

  20. Now and next-generation sequencing techniques: future of sequence analysis using cloud computing.

    Science.gov (United States)

    Thakur, Radhe Shyam; Bandopadhyay, Rajib; Chaudhary, Bratati; Chatterjee, Sourav

    2012-01-01

    Advances in the field of sequencing techniques have resulted in the greatly accelerated production of huge sequence datasets. This presents immediate challenges in database maintenance at datacenters. It provides additional computational challenges in data mining and sequence analysis. Together these represent a significant overburden on traditional stand-alone computer resources, and to reach effective conclusions quickly and efficiently, the virtualization of the resources and computation on a pay-as-you-go concept (together termed "cloud computing") has recently appeared. The collective resources of the datacenter, including both hardware and software, can be available publicly, being then termed a public cloud, the resources being provided in a virtual mode to the clients who pay according to the resources they employ. Examples of public companies providing these resources include Amazon, Google, and Joyent. The computational workload is shifted to the provider, which also implements required hardware and software upgrades over time. A virtual environment is created in the cloud corresponding to the computational and data storage needs of the user via the internet. The task is then performed, the results transmitted to the user, and the environment finally deleted after all tasks are completed. In this discussion, we focus on the basics of cloud computing, and go on to analyze the prerequisites and overall working of clouds. Finally, the applications of cloud computing in biological systems, particularly in comparative genomics, genome informatics, and SNP detection are discussed with reference to traditional workflows.

  1. Now And Next Generation Sequencing Techniques: Future of Sequence Analysis using Cloud Computing

    Directory of Open Access Journals (Sweden)

    Radhe Shyam Thakur

    2012-12-01

    Full Text Available Advancements in the field of sequencing techniques resulted in the huge sequenced data to be produced at a very faster rate. It is going cumbersome for the datacenter to maintain the databases. Data mining and sequence analysis approaches needs to analyze the databases several times to reach any efficient conclusion. To cope with such overburden on computer resources and to reach efficient and effective conclusions quickly, the virtualization of the resources and computation on pay as you go concept was introduced and termed as cloud computing. The datacenter’s hardware and software is collectively known as cloud which when available publicly is termed as public cloud. The datacenter’s resources are provided in a virtual mode to the clients via a service provider like Amazon, Google and Joyent which charges on pay as you go manner. The workload is shifted to the provider which is maintained by the required hardware and software upgradation. The service provider manages it by upgrading the requirements in the virtual mode. Basically a virtual environment is created according to the need of the user by taking permission from datacenter via internet, the task is performed and the environment is deleted after the task is over. In this discussion, we are focusing on the basics of cloud computing, the prerequisites and overall working of clouds. Furthermore, briefly the applications of cloud computing in biological systems, especially in comparative genomics, genome informatics and SNP detection with reference to traditional workflow are discussed.

  2. SEQUENCING AND SEQUENCE ANALYSIS OF MYOSTATIN GENE IN THE EXON 1 OF THE CAMEL (CAMELUS DROMEDARIUS

    Directory of Open Access Journals (Sweden)

    M. G. SHAH, A. S. QURESHI1, M. REISSMANN2 AND H. J. SCHWARTZ3

    2006-10-01

    Full Text Available Myostatin, also called growth differentiation factor-8 (GDF-8, is a member of the mammalian growth transforming family (TGF-beta superfamily, which is expressed specifically in developing an adult skeletal muscle. Muscular hypertrophy allele (mh allele in the double muscle breeds involved mutation within the myostatin gene. Genomic DNA was isolated from the camel hair using NucleoSpin Tissue kit. Two animals of each of the six breeds namely, Marecha, Dhatti, Larri, Kohi, Sakrai and Cambelpuri were used for sequencing. For PCR amplification of the gene, a primer pair was designed from homolog regions of already published sequences of farm animals from GenBank. Results showed that camel myostatin possessed more than 90% homology with that of cattle, sheep and pig. Camel formed separate cluster from the pig in spite of having high homology (98% and showed 94% homology with cattle and sheep as reported in literature. Sequence analysis of the PCR amplified part of exon 1 (256 bp of the camel myostatin was identical among six camel breeds.

  3. Infrared thermal facial image sequence registration analysis and verification

    Science.gov (United States)

    Chen, Chieh-Li; Jian, Bo-Lin

    2015-03-01

    To study the emotional responses of subjects to the International Affective Picture System (IAPS), infrared thermal facial image sequence is preprocessed for registration before further analysis such that the variance caused by minor and irregular subject movements is reduced. Without affecting the comfort level and inducing minimal harm, this study proposes an infrared thermal facial image sequence registration process that will reduce the deviations caused by the unconscious head shaking of the subjects. A fixed image for registration is produced through the localization of the centroid of the eye region as well as image translation and rotation processes. Thermal image sequencing will then be automatically registered using the two-stage genetic algorithm proposed. The deviation before and after image registration will be demonstrated by image quality indices. The results show that the infrared thermal image sequence registration process proposed in this study is effective in localizing facial images accurately, which will be beneficial to the correlation analysis of psychological information related to the facial area.

  4. Multilocus sequence analysis of Treponema denticola strains of diverse origin

    Science.gov (United States)

    2013-01-01

    Background The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA) of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. Results The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC) were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA) to 8.9% (dnaN). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain) using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. Conclusions Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic analysis of T

  5. Multilocus sequence analysis of Treponema denticola strains of diverse origin

    Directory of Open Access Journals (Sweden)

    Mo Sisu

    2013-02-01

    Full Text Available Abstract Background The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. Results The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA to 8.9% (dnaN. Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. Conclusions Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic

  6. Automated sequence analysis of atmospheric oxidation pathways: SEQUENCE version 1.0

    Directory of Open Access Journals (Sweden)

    T. M. Butler

    2009-10-01

    Full Text Available An algorithm for the sequential analysis of the atmospheric oxidation of chemical species using output from a photochemical model is presented. Starting at a "root species", the algorithm traverses all possible reaction sequences which consume this species, and lead, via intermediate products, to final products. The algorithm keeps track of the effects of all of these reactions on their respective reactants and products. Upon completion, the algorithm has built a detailed picture of the effects of the oxidation of the root species on its chemical surroundings. The output of the algorithm can be used to determine product yields, radical recycling fractions, and ozone production potentials of arbitrary chemical species.

  7. A stochastic model for EEG microstate sequence analysis.

    Science.gov (United States)

    Gärtner, Matthias; Brodbeck, Verena; Laufs, Helmut; Schneider, Gaby

    2015-01-01

    The analysis of spontaneous resting state neuronal activity is assumed to give insight into the brain function. One noninvasive technique to study resting state activity is electroencephalography (EEG) with a subsequent microstate analysis. This technique reduces the recorded EEG signal to a sequence of prototypical topographical maps, which is hypothesized to capture important spatio-temporal properties of the signal. In a statistical EEG microstate analysis of healthy subjects in wakefulness and three stages of sleep, we observed a simple structure in the microstate transition matrix. It can be described with a first order Markov chain in which the transition probability from the current state (i.e., map) to a different map does not depend on the current map. The resulting transition matrix shows a high agreement with the observed transition matrix, requiring only about 2% of mass transport (1/2 L1-distance). In the second part, we introduce an extended framework in which the simple Markov chain is used to make inferences on a potential underlying time continuous process. This process cannot be directly observed and is therefore usually estimated from discrete sampling points of the EEG signal given by the local maxima of the global field power. Therefore, we propose a simple stochastic model called sampled marked intervals (SMI) model that relates the observed sequence of microstates to an assumed underlying process of background intervals and thus, complements approaches that focus on the analysis of observable microstate sequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Congruence analysis of point clouds from unstable stereo image sequences

    Directory of Open Access Journals (Sweden)

    C. Jepping

    2014-06-01

    Full Text Available This paper deals with the correction of exterior orientation parameters of stereo image sequences over deformed free-form surfaces without control points. Such imaging situation can occur, for example, during photogrammetric car crash test recordings where onboard high-speed stereo cameras are used to measure 3D surfaces. As a result of such measurements 3D point clouds of deformed surfaces are generated for a complete stereo sequence. The first objective of this research focusses on the development and investigation of methods for the detection of corresponding spatial and temporal tie points within the stereo image sequences (by stereo image matching and 3D point tracking that are robust enough for a reliable handling of occlusions and other disturbances that may occur. The second objective of this research is the analysis of object deformations in order to detect stable areas (congruence analysis. For this purpose a RANSAC-based method for congruence analysis has been developed. This process is based on the sequential transformation of randomly selected point groups from one epoch to another by using a 3D similarity transformation. The paper gives a detailed description of the congruence analysis. The approach has been tested successfully on synthetic and real image data.

  9. CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

    Directory of Open Access Journals (Sweden)

    Charalambos Chrysostomou

    2015-01-01

    Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

  10. Influence of the stacking sequence of layers on the mechanical behavior of polymeric composite cylinders

    International Nuclear Information System (INIS)

    Carvalho, Osni de

    2006-01-01

    This work evaluated experimentally the influence of the stacking sequence of layers symmetrical and asymmetrical on the mechanical behavior of polymeric composite cylinders. For so much, two open-ended cylinders groups were manufactured by filament winding process, which had different stacking sequence related to the laminate midplane, characterizing symmetrical and asymmetrical laminates. The composite cylinders were made with epoxy matrix and carbon fiber as reinforcement. For evaluation of the mechanical strength, the cylinders were tested hydrostatically, which consisted of internal pressurization in a hydrostatic device through the utilization of a fluid until the cylinders burst. Additionally, were compared the strains and failure modes between the cylinders groups. The utilization of a finite element program allowed to conclude that this tool, very used in design, does not get to identify tensions in the fiber direction in each composite layer, as well as interlaminar shear stress, that appears in the cylinders with asymmetrical stacking sequence. The tests results showed that the stacking sequence had influence in the mechanical behavior of the composite cylinders, favoring the symmetrical construction. (author)

  11. Frame to Frame Diffeomorphic Motion Analysis from Echocardiographic Sequences

    OpenAIRE

    Zhang, Zhijun; Sahn, David; Song, Xubo

    2011-01-01

    International audience; Quantitative motion analysis from echocardiography is an important yet challenging problem. We develop a motion estimation algorithm for echocardiographic image sequences based on diffeomorphic image registration in which the velocity field is spatiotemporally smooth. The novelty of this work is that instead of optimizing a functional of velocity field which consists of similarity metrics between a reference image to each of the following images (\\textitfirst-to-follow...

  12. The sequence and analysis of Trypanosoma brucei chromosome II

    OpenAIRE

    El-Sayed, Najib M. A.; Ghedin, Elodie; Song, Jinming; MacLeod, Annette; Bringaud, Frederic; Larkin, Christopher; Wanless, David; Peterson, Jeremy; Hou, Lihua; Taylor, Sonya; Tweedie, Alison; Biteau, Nicolas; Khalak, Hanif G.; Lin, Xiaoying; Mason, Tanya

    2003-01-01

    We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-couple...

  13. Analyzing Dyadic Data Using Grid-Sequence Analysis: Interdyad Differences in Intradyad Dynamics.

    Science.gov (United States)

    Brinberg, Miriam; Ram, Nilam; Hülür, Gizem; Brick, Timothy R; Gerstorf, Denis

    2017-12-15

    Spouses are proximal contexts for and influence each other's behaviors, particularly in old age. In this article, we forward an integrated approach that merges state space grid methods adapted from the dynamic systems literature with sequence analysis methods adapted from molecular biology into a "grid-sequence" method for studying interdyad differences in intradyad dynamics. Using dyadic data from 108 older couples (MAge = 75.18 years) with six within-day emotion and activity reports over 7 days, we illustrate how grid-sequence analysis can be used to identify a taxonomy of dyads with different emotion dynamics. Results provide a basis for measuring a set of dyad-level variables that capture dynamic equilibrium, daily routines, and interdyad differences. Specifically, we identified four groups of dyads who differed in how their moment-to-moment happiness was organized, with some evidence that these patterns were related to dyad-level differences in agreement on amount of time spent with partner and in subjective health. Methodologically, grid-sequence analysis extends the toolbox of techniques for analysis of dyadic experience sampling data. Substantively, we identify patterns of dyad-level microdynamics that may serve as new markers of risk/protective factors and potential points for intervention in older adults' proximal context.

  14. Sequence length variation, indel costs, and congruence in sensitivity analysis

    DEFF Research Database (Denmark)

    Aagesen, Lone; Petersen, Gitte; Seberg, Ole

    2005-01-01

    The behavior of two topological and four character-based congruence measures was explored using different indel treatments in three empirical data sets, each with different alignment difficulties. The analyses were done using direct optimization within a sensitivity analysis framework in which...

  15. Analysis on Response of Dynamic Systems to Pulse Sequences Excitation

    Directory of Open Access Journals (Sweden)

    Xie Lili

    2009-07-01

    Full Text Available Near-fault ground motions with long-period pulses can place severe demands on structures near an active fault. These pulse-type ground motions can be represented by pulse sequences with simple shapes. Half-sinusoidal pulse sequences are used to approximate recorded ground motions and dynamic responses of SDOF system under the excitation of these pulse sequences are studied. Four cases are considered: (1 variation in duration of successor sub-pulse; (2 variation in duration of predecessor sub-pulse; (3 variation in amplitude of successor sub-pulse; and (4 variation in amplitude of predecessor sub-pulse. The corresponding acceleration, velocity and displacement response spectra of these pulse sequences are studied. The analysis on SDOF system shows that in some cases the responses are strongly affected by the changes of duration and/or amplitude of the sub-pulse. The study can be useful to understand the influences of sub-pulse in the near-fault pulse-type ground motions.

  16. Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

    Science.gov (United States)

    Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

  17. Environmental impact analysis for the main accidental sequences of ignitor

    International Nuclear Information System (INIS)

    Carpignano, A.; Francabandiera, S.; Vella, R.; Zucchetti, M.

    1996-01-01

    A safety analysis study has been applied to the Ignitor machine using Probabilistic Safety Assessment. The main initiating events have been identified, and accident sequences have been studied by means of traditional methods such as Failure Mode and Effect Analysis (FMEA), Fault Trees (FT) and Event Trees (ET). The consequences of the radioactive environmental releases have been assessed in terms of Effective Dose Equivalent (EDEs) to the Most Exposed Individuals (MEI) of the chosen site, by means of a population dose code. Results point out the low enviromental impact of the machine. 13 refs., 1 fig., 3 tabs

  18. INTERVIEW GUIDELINE FOR FUNCTIONAL BEHAVIOR ANALYSIS IN TRANSSEXUAL PERSONS

    Directory of Open Access Journals (Sweden)

    José Miguel Rodríguez Molina

    2013-05-01

    Full Text Available Transsexuality is an emerging phenomenon. There are therefore few psychological assessment tools for it. The purpose of this article is to show the professional clinical psychology and social intervention community a tool that could facilitate this task. We begin with a brief introduction to the phenomenon of transsexuality and psychological assessment in this field, which almost always concentrates on diagnosis or other variables, generally personality (personality traits, depression, anxiety, etc.. Then we approach the main problems found in a transsexual person during the transition. These problems are a potential or real source of psychological conflict. After this we briefly describe behavioral assessment which has been quite forgotten in this area. Finally, we propose a new instrument for this assessment. The main result is the Interview Guideline for Functional Behavior Sequence Analysis (FBSA. We conclude that there is a need for more behavior assessment in this field.

  19. Nicotinamide-NAD sequence: redox process and related behavior, behavior and properties of intermediate and final products

    International Nuclear Information System (INIS)

    Elving, P.J.; Schmakel, C.O.; Santhanam, K.S.V.

    1976-01-01

    Illustrations of the application of analytical chemical techniques to the study of chemical phenomena are given. In particular, electrochemical techniques and methodology and, to a lesser extent, spectrophotometry were used to investigate the solution behavior, adsorption, redox processes including coupled chemical reactions, and allied aspects of biologically significant compounds and of their intermediate and final redox products, e.g., the behavior of the free radicals produced by initial one-electron processes. This approach is illustrated by the consideration of the behavior in aqueous and nonaqueous media of a sequence of compounds ranging from nicotinamide (3-carbamoylpyridine) to NAD + and NADP + ; the latter compounds function as coenzymes for the pyridinoproteins which are principal components in the Krebs citric acid cycle and in the electron transport chain in biological redox reactions. The discussion is presented under the following section headings: interpretation of electrochemical behavior; mechanistic patterns; kinetic aspects of charge-transfer and chemical reactions; correlation with theoretically calculated parameters; and, mechanisms of biological oxidation-reduction reactions. The use of pulse radiolysis, chronopotentiometric, and cyclic voltammetric methods in studies on free radical dimerization rates is reviewed in the discussion of the kinetic aspects of charge-transfer and chemical reactions. (188 references)

  20. Multifractal analysis of 2001 Mw 7 . 7 Bhuj earthquake sequence in Gujarat, Western India

    Science.gov (United States)

    Aggarwal, Sandeep Kumar; Pastén, Denisse; Khan, Prosanta Kumar

    2017-12-01

    The 2001 Mw 7 . 7 Bhuj mainshock seismic sequence in the Kachchh area, occurring during 2001 to 2012, has been analyzed using mono-fractal and multi-fractal dimension spectrum analysis technique. This region was characterized by frequent moderate shocks of Mw ≥ 5 . 0 for more than a decade since the occurrence of 2001 Bhuj earthquake. The present study is therefore important for precursory analysis using this sequence. The selected long-sequence has been investigated first time for completeness magnitude Mc 3.0 using the maximum curvature method. Multi-fractal Dq spectrum (Dq ∼ q) analysis was carried out using effective window-length of 200 earthquakes with a moving window of 20 events overlapped by 180 events. The robustness of the analysis has been tested by considering the magnitude completeness correction term of 0.2 to Mc 3.0 as Mc 3.2 and we have tested the error in the calculus of Dq for each magnitude threshold. On the other hand, the stability of the analysis has been investigated down to the minimum magnitude of Mw ≥ 2 . 6 in the sequence. The analysis shows the multi-fractal dimension spectrum Dq decreases with increasing of clustering of events with time before a moderate magnitude earthquake in the sequence, which alternatively accounts for non-randomness in the spatial distribution of epicenters and its self-organized criticality. Similar behavior is ubiquitous elsewhere around the globe, and warns for proximity of a damaging seismic event in an area. OS: Please confirm math roman or italics in abs.

  1. Targeted DNA methylation analysis by next-generation sequencing.

    Science.gov (United States)

    Masser, Dustin R; Stanford, David R; Freeman, Willard M

    2015-02-24

    The role of epigenetic processes in the control of gene expression has been known for a number of years. DNA methylation at cytosine residues is of particular interest for epigenetic studies as it has been demonstrated to be both a long lasting and a dynamic regulator of gene expression. Efforts to examine epigenetic changes in health and disease have been hindered by the lack of high-throughput, quantitatively accurate methods. With the advent and popularization of next-generation sequencing (NGS) technologies, these tools are now being applied to epigenomics in addition to existing genomic and transcriptomic methodologies. For epigenetic investigations of cytosine methylation where regions of interest, such as specific gene promoters or CpG islands, have been identified and there is a need to examine significant numbers of samples with high quantitative accuracy, we have developed a method called Bisulfite Amplicon Sequencing (BSAS). This method combines bisulfite conversion with targeted amplification of regions of interest, transposome-mediated library construction and benchtop NGS. BSAS offers a rapid and efficient method for analysis of up to 10 kb of targeted regions in up to 96 samples at a time that can be performed by most research groups with basic molecular biology skills. The results provide absolute quantitation of cytosine methylation with base specificity. BSAS can be applied to any genomic region from any DNA source. This method is useful for hypothesis testing studies of target regions of interest as well as confirmation of regions identified in genome-wide methylation analyses such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing, and methylated DNA immunoprecipitation sequencing.

  2. Signal analysis of behavioral and molecular cycles

    Science.gov (United States)

    Levine, Joel D; Funes, Pablo; Dowse, Harold B; Hall, Jeffrey C

    2002-01-01

    Background Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities. Results We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase. Conclusion Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed. PMID:11825337

  3. Signal analysis of behavioral and molecular cycles

    Directory of Open Access Journals (Sweden)

    Dowse Harold B

    2002-01-01

    Full Text Available Abstract Background Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities. Results We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase. Conclusion Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed.

  4. Analysis of integrated human papillomavirus type 16 DNA in cervical cancers: amplification of viral sequences together with cellular flanking sequences.

    Science.gov (United States)

    Wagatsuma, M; Hashimoto, K; Matsukura, T

    1990-01-01

    We have isolated four clones of integrated human papillomavirus type 16 (HPV-16) DNA from four different primary cervical cancer specimens. All clones were found to be monomeric or dimeric forms of HPV-16 DNA with cellular flanking sequences at both ends. Analysis of the viral sequences in these clones showed that E6/E7 open reading frames and the long control region were conserved and that no region specific for the integration was detected. Analysis of the cellular flanking sequences revealed no significant homology with any known human DNA sequences, except Alu sequences, and no homology among the clones, indicating no cellular sequence specific for the integration. By probing with single-copy cellular flanking sequences from the clones, it was demonstrated that the integrated HPV-16 DNAs, with different sizes in the same specimens, shared the same cellular flanking sequences at the ends. Furthermore, it was shown that the viral sequences together with cellular flanking sequences were amplified. The possible process of viral integration into cell chromosomes in cervical cancer is discussed. Images PMID:2153245

  5. Laban Movement Analysis towards Behavior Patterns

    Science.gov (United States)

    Santos, Luís; Dias, Jorge

    This work presents a study about the use of Laban Movement Analysis (LMA) as a robust tool to describe human basic behavior patterns, to be applied in human-machine interaction. LMA is a language used to describe and annotate dancing movements and is divided in components [1]: Body, Space, Shape and Effort. Despite its general framework is widely used in physical and mental therapy [2], it has found little application in the engineering domain. Rett J. [3] proposed to implement LMA using Bayesian Networks. However LMA component models have not yet been fully implemented. A study on how to approach behavior using LMA is presented. Behavior is a complex feature and movement chain, but we believe that most basic behavior primitives can be discretized in simple features. Correctly identifying Laban parameters and the movements the authors feel that good patterns can be found within a specific set of basic behavior semantics.

  6. Toward applied behavior analysis of life aloft

    Science.gov (United States)

    Brady, J. V.

    1990-01-01

    This article deals with systems at multiple levels, at least from cell to organization. It also deals with learning, decision making, and other behavior at multiple levels. Technological development of a human behavioral ecosystem appropriate to space environments requires an analytic and synthetic orientation, explicitly experimental in nature, dictated by scientific and pragmatic considerations, and closely approximating procedures of established effectiveness in other areas of natural science. The conceptual basis of such an approach has its roots in environmentalism which has two main features: (1) knowledge comes from experience rather than from innate ideas, divine revelation, or other obscure sources; and (2) action is governed by consequences rather than by instinct, reason, will, beliefs, attitudes or even the currently fashionable cognitions. Without an experimentally derived data base founded upon such a functional analysis of human behavior, the overgenerality of "ecological systems" approaches render them incapable of ensuring the successful establishment of enduring space habitats. Without an experimentally derived function account of individual behavioral variability, a natural science of behavior cannot exist. And without a natural science of behavior, the social sciences will necessarily remain in their current status as disciplines of less than optimal precision or utility. Such a functional analysis of human performance should provide an operational account of behavior change in a manner similar to the way in which Darwin's approach to natural selection accounted for the evolution of phylogenetic lines (i.e., in descriptive, nonteleological terms). Similarly, as Darwin's account has subsequently been shown to be consonant with information obtained at the cellular level, so too should behavior principles ultimately prove to be in accord with an account of ontogenetic adaptation at a biochemical level. It would thus seem obvious that the most

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

    Data.gov (United States)

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

  8. Pan-Cancer Analysis of Genomic Sequencing Among the Elderly.

    Science.gov (United States)

    Wahl, Daniel R; Nguyen, Paul L; Santiago, Maria; Yousefi, Kasra; Davicioni, Elai; Shumway, Dean A; Speers, Corey; Mehra, Rohit; Feng, Felix Y; Osborne, Joseph R; Spratt, Daniel E

    2017-07-15

    We hypothesized that elderly patients might have age-specific genetic abnormalities yet be underrepresented in currently available sequencing repositories, which could limit the effect of sequencing efforts for this population. Leveraging The Cancer Genome Atlas (TCGA) data portal, 9 tumor types were analyzed. The frequency distribution of cancer by age was determined and compared with Surveillance, Epidemiology, and End Results data. Using the estimated median somatic mutational frequency of each tumor type, the samples needed beyond TCGA to detect a 10% mutational frequency were calculated. Microarray data from a separate prospective cohort were obtained from primary prostatectomy samples to determine whether elderly-specific transcriptomic alterations could be identified. Of the 5236 TCGA samples, 73% were from patients aged elderly patients with cancer were likely to harbor age-specific molecular abnormalities, we accessed transcriptomic data from a separate, larger database of >2000 prostate cancer samples. That analysis revealed significant differences in the expression of 10 genes in patients aged ≥70 years compared with those Elderly patients have been underrepresented in genomic sequencing studies. Our data suggest the presence of elderly-specific molecular alterations. Further dedicated efforts to understand the biology of cancer among the elderly will be important moving forward. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Linear discriminant analysis of character sequences using occurrences of words

    KAUST Repository

    Dutta, Subhajit

    2014-02-01

    Classification of character sequences, where the characters come from a finite set, arises in disciplines such as molecular biology and computer science. For discriminant analysis of such character sequences, the Bayes classifier based on Markov models turns out to have class boundaries defined by linear functions of occurrences of words in the sequences. It is shown that for such classifiers based on Markov models with unknown orders, if the orders are estimated from the data using cross-validation, the resulting classifier has Bayes risk consistency under suitable conditions. Even when Markov models are not valid for the data, we develop methods for constructing classifiers based on linear functions of occurrences of words, where the word length is chosen by cross-validation. Such linear classifiers are constructed using ideas of support vector machines, regression depth, and distance weighted discrimination. We show that classifiers with linear class boundaries have certain optimal properties in terms of their asymptotic misclassification probabilities. The performance of these classifiers is demonstrated in various simulated and benchmark data sets.

  10. Planarian homeobox genes: cloning, sequence analysis, and expression.

    Science.gov (United States)

    Garcia-Fernàndez, J; Baguñà, J; Saló, E

    1991-01-01

    Freshwater planarians (Platyhelminthes, Turbellaria, and Tricladida) are acoelomate, triploblastic, unsegmented, and bilaterally symmetrical organisms that are mainly known for their ample power to regenerate a complete organism from a small piece of their body. To identify potential pattern-control genes in planarian regeneration, we have isolated two homeobox-containing genes, Dth-1 and Dth-2 [Dugesia (Girardia) tigrina homeobox], by using degenerate oligonucleotides corresponding to the most conserved amino acid sequence from helix-3 of the homeodomain. Dth-1 and Dth-2 homeodomains are closely related (68% at the nucleotide level and 78% at the protein level) and show the conserved residues characteristic of the homeodomains identified to data. Similarity with most homeobox sequences is low (30-50%), except with Drosophila NK homeodomains (80-82% with NK-2) and the rodent TTF-1 homeodomain (77-87%). Some unusual amino acid residues specific to NK-2, TTF-1, Dth-1, and Dth-2 can be observed in the recognition helix (helix-3) and may define a family of homeodomains. The deduced amino acid sequences from the cDNAs contain, in addition to the homeodomain, other domains also present in various homeobox-containing genes. The expression of both genes, detected by Northern blot analysis, appear slightly higher in cephalic regions than in the rest of the intact organism, while a slight increase is detected in the central period (5 days) or regeneration. Images PMID:1714599

  11. Integrated visual analysis of protein structures, sequences, and feature data.

    Science.gov (United States)

    Stolte, Christian; Sabir, Kenneth S; Heinrich, Julian; Hammang, Christopher J; Schafferhans, Andrea; O'Donoghue, Seán I

    2015-01-01

    To understand the molecular mechanisms that give rise to a protein's function, biologists often need to (i) find and access all related atomic-resolution 3D structures, and (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures. To streamline these processes we recently developed Aquaria, a resource offering unprecedented access to protein structure information based on an all-against-all comparison of SwissProt and PDB sequences. In this work, we provide a requirements analysis for several frequently occuring tasks in molecular biology and describe how design choices in Aquaria meet these requirements. Finally, we show how the interface can be used to explore features of a protein and gain biologically meaningful insights in two case studies conducted by domain experts. The user interface design of Aquaria enables biologists to gain unprecedented access to molecular structures and simplifies the generation of insight. The tasks involved in mapping sequence features onto structures can be conducted easier and faster using Aquaria.

  12. Determining physical constraints in transcriptional initiationcomplexes using DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Shultzaberger, Ryan K.; Chiang, Derek Y.; Moses, Alan M.; Eisen,Michael B.

    2007-07-01

    Eukaryotic gene expression is often under the control ofcooperatively acting transcription factors whose binding is limited bystructural constraints. By determining these structural constraints, wecan understand the "rules" that define functional cooperativity.Conversely, by understanding the rules of binding, we can inferstructural characteristics. We have developed an information theory basedmethod for approximating the physical limitations of cooperativeinteractions by comparing sequence analysis to microarray expressiondata. When applied to the coordinated binding of the sulfur amino acidregulatory protein Met4 by Cbf1 and Met31, we were able to create acombinatorial model that can correctly identify Met4 regulatedgenes.

  13. Effect of sequence on the ionization behavior of a series of amphiphilic polypeptides.

    Science.gov (United States)

    Fowler, Michael; Siddique, Bushra; Duhamel, Jean

    2013-04-09

    The behavior of five polypeptides made of hydrophilic and pH-responsive aspartic acid (Asp) and hydrophobic phenylalanine (Phe), which had been prepared by stitching together short well-defined sequences of Asp and Phe, was studied as a function of pH. The effect of pH on these polypeptides referred to as (Asp3Phe1)n, (Asp2Phe1)n, (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n varied dramatically depending on their constituting sequence. The more hydrophobic polypeptides (Asp1Phe2)n and (Asp1Phe3)n behaved as if the Asp's were isolated from each other and showed an apparent pKa (pKa(app)) that remained constant with level of ionization (α = [Asp(-)]/[Asp]total) and equaled 5.4 and 6.4, respectively. The more hydrophilic polypeptides (Asp3Phe1)n and (Asp2Phe1)n behaved like weak polyacids showing a linear increase in pKa(app) with increasing α. The pKa(app) of (Asp1Phe1)n showed a trend as a function of α intermediate between the Asp-rich and Phe-rich polypeptides, behaving as if the Asp's were isolated at low α values (0.35). The effect that α, and thus the charge density of the polypeptides, had on the collapse and aggregation of the polypeptides was characterized by conducting static light scattering and fluorescence measurements. Static light scattering measurements demonstrated that all polypeptides precipitated and aggregated in solution at a critical charge density of 0.2. Fluorescence measurements with pyrene indicated that this behavior was due to the formation of Phe aggregates in water. Together, these experiments provide a complete description of how pH affects the behavior of a series of unique amphiphilic polypeptides designed with a well-defined sequence.

  14. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

    OpenAIRE

    Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Yang, Tuxi; Wei, Anzhi

    2017-01-01

    Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence re...

  15. Streaming Support for Data Intensive Cloud-Based Sequence Analysis

    Science.gov (United States)

    Issa, Shadi A.; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J.; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

    2013-01-01

    Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation. PMID:23710461

  16. Next-Generation Sequence Analysis of Cancer Xenograft Models

    Science.gov (United States)

    Rossello, Fernando J.; Tothill, Richard W.; Britt, Kara; Marini, Kieren D.; Falzon, Jeanette; Thomas, David M.; Peacock, Craig D.; Marchionni, Luigi; Li, Jason; Bennett, Samara; Tantoso, Erwin; Brown, Tracey; Chan, Philip; Martelotto, Luciano G.; Watkins, D. Neil

    2013-01-01

    Next-generation sequencing (NGS) studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC), a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations. PMID:24086345

  17. Next-generation sequence analysis of cancer xenograft models.

    Directory of Open Access Journals (Sweden)

    Fernando J Rossello

    Full Text Available Next-generation sequencing (NGS studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC, a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.

  18. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and phylogenetic ..... Tree was generated by Neighbor joining algorithm. Boot strap values are shown ... Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence ...

  19. A novel method for comparative analysis of DNA sequences by Ramanujan-Fourier transform.

    Science.gov (United States)

    Yin, Changchuan; Yin, Xuemeng E; Wang, Jiasong

    2014-12-01

    Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity. However, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-free computational method for sequence analysis based on Ramanujan-Fourier transform (RFT), in which complete information of DNA sequences is retained. We represent DNA sequences as four binary indicator sequences and apply RFT on the indicator sequences to convert them into frequency domain. The Euclidean distance of the complete RFT coefficients of DNA sequences are used as similarity measures. To address the different lengths of RFT coefficients in Euclidean space, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data. Thus, the DNA sequences are compared in the same dimensional frequency space without information loss. We demonstrate the usefulness of the proposed method by presenting experimental results on hierarchical clustering of genes and genomes. The proposed method opens a new channel to biological sequence analysis, classification, and structural module identification.

  20. Behavior Analysis of Elderly using Topic Models

    NARCIS (Netherlands)

    Rieping, K.; Englebienne, G.; Kröse, B.

    2014-01-01

    This paper describes two new topic models for the analysis of human behavior in homes that are equipped with sensor networks. The models are based on Latent Dirichlet Allocation (LDA) topic models and can detect patterns in sensor data in an unsupervised manner. LDA-Gaussian, the first variation of

  1. Applied Behavior Analysis: Beyond Discrete Trial Teaching

    Science.gov (United States)

    Steege, Mark W.; Mace, F. Charles; Perry, Lora; Longenecker, Harold

    2007-01-01

    We discuss the problem of autism-specific special education programs representing themselves as Applied Behavior Analysis (ABA) programs when the only ABA intervention employed is Discrete Trial Teaching (DTT), and often for limited portions of the school day. Although DTT has many advantages to recommend its use, it is not well suited to teach…

  2. Behavior analysis and neuroscience: Complementary disciplines.

    Science.gov (United States)

    Donahoe, John W

    2017-05-01

    Behavior analysis and neuroscience are disciplines in their own right but are united in that both are subfields of a common overarching field-biology. What most fundamentally unites these disciplines is a shared commitment to selectionism, the Darwinian mode of explanation. In selectionism, the order and complexity observed in nature are seen as the cumulative products of selection processes acting over time on a population of variants-favoring some and disfavoring others-with the affected variants contributing to the population on which future selections operate. In the case of behavior analysis, the central selection process is selection by reinforcement; in neuroscience it is natural selection. The two selection processes are inter-related in that selection by reinforcement is itself the product of natural selection. The present paper illustrates the complementary nature of behavior analysis and neuroscience through considering their joint contributions to three central problem areas: reinforcement-including conditioned reinforcement, stimulus control-including equivalence classes, and memory-including reminding and remembering. © 2017 Society for the Experimental Analysis of Behavior.

  3. Consumer Behavior Analysis of Green Food

    OpenAIRE

    Chao Luo; Guangrong Tong; Yang Pan; Sha Yang

    2015-01-01

    This study uses empirical research methods, based on detailed analysis of the food transaction big data. It use descriptive statistical method to analyze the current situation of cognitive and behavioral characteristics of the green food and it conducted data mining of factors affecting consumer buying green food. Multiple linear regression analysis have shown that the price factor is an important factor affecting consumer buying green food, next are food quality and health awareness and prod...

  4. Analysis of the interaction between experimental and applied behavior analysis.

    Science.gov (United States)

    Virues-Ortega, Javier; Hurtado-Parrado, Camilo; Cox, Alison D; Pear, Joseph J

    2014-01-01

    To study the influences between basic and applied research in behavior analysis, we analyzed the coauthorship interactions of authors who published in JABA and JEAB from 1980 to 2010. We paid particular attention to authors who published in both JABA and JEAB (dual authors) as potential agents of cross-field interactions. We present a comprehensive analysis of dual authors' coauthorship interactions using social networks methodology and key word analysis. The number of dual authors more than doubled (26 to 67) and their productivity tripled (7% to 26% of JABA and JEAB articles) between 1980 and 2010. Dual authors stood out in terms of number of collaborators, number of publications, and ability to interact with multiple groups within the field. The steady increase in JEAB and JABA interactions through coauthors and the increasing range of topics covered by dual authors provide a basis for optimism regarding the progressive integration of basic and applied behavior analysis. © Society for the Experimental Analysis of Behavior.

  5. An Analysis of Loss of Offsite Power Sequence for the Severe Accident Analysis Database (II)

    Energy Technology Data Exchange (ETDEWEB)

    Park, Soo Yong; Kim, Dong Ha

    2006-12-15

    This report contains analysis methodologies and calculation results of loss of offsite sequences for the severe accident analysis database system. The Korean standard nuclear power plant has been selected as a reference plant. Based on the probabilistic safety analysis of the corresponding plant, Twelve accident scenarios, which was predicted to have more than 10-10 /ry occurrence frequency, have been analyzed as base cases for the loss of offsite sequence database. The functions of the severe accident analysis database system will be to make a diagnosis of the accident by some input information from the plant symptoms, to search a corresponding scenario, and finally to provide the user phenomenological information based on the pre-analyzed results. The MAAP 4.06 calculation results of loss of offsite sequence in this report will be utilized as input data of the severe accident analysis database system. This report updates and complements a previously published Technical Report.

  6. Recognition of long-term behaviors by parsing sequences of short-term actions with a stochastic regular grammar

    NARCIS (Netherlands)

    Sanromà, G.; Burghouts, G.J.; Schutte, K.

    2012-01-01

    Human behavior understanding from visual data has applications such as threat recognition. A lot of approaches are restricted to limited time actions, which we call short-term actions. Long-term behaviors are sequences of short-term actions that are more extended in time. Our hypothesis is that they

  7. Collaborative Approach to Network Behavior Analysis

    Science.gov (United States)

    Rehak, Martin; Pechoucek, Michal; Grill, Martin; Bartos, Karel; Celeda, Pavel; Krmicek, Vojtech

    Network Behavior Analysis techniques are designed to detect intrusions and other undesirable behavior in computer networks by analyzing the traffic statistics. We present an efficient framework for integration of anomaly detection algorithms working on the identical input data. This framework is based on high-speed network traffic acquisition subsystem and on trust modeling, a well-established set of techniques from the multi-agent system field. Trust-based integration of algorithms results in classification with lower error rate, especially in terms of false positives. The presented framework is suitable for both online and offline processing, and introduces a relatively low computational overhead compared to deployment of isolated anomaly detection algorithms.

  8. Multilocus sequence analysis for Leishmania braziliensis outbreak investigation.

    Directory of Open Access Journals (Sweden)

    Mariel A Marlow

    2014-02-01

    Full Text Available With the emergence of leishmaniasis in new regions around the world, molecular epidemiological methods with adequate discriminatory power, reproducibility, high throughput and inter-laboratory comparability are needed for outbreak investigation of this complex parasitic disease. As multilocus sequence analysis (MLSA has been projected as the future gold standard technique for Leishmania species characterization, we propose a MLSA panel of six housekeeping gene loci (6pgd, mpi, icd, hsp70, mdhmt, mdhnc for investigating intraspecific genetic variation of L. (Viannia braziliensis strains and compare the resulting genetic clusters with several epidemiological factors relevant to outbreak investigation. The recent outbreak of cutaneous leishmaniasis caused by L. (V. braziliensis in the southern Brazilian state of Santa Catarina is used to demonstrate the applicability of this technique. Sequenced fragments from six genetic markers from 86 L. (V. braziliensis strains from twelve Brazilian states, including 33 strains from Santa Catarina, were used to determine clonal complexes, genetic structure, and phylogenic networks. Associations between genetic clusters and networks with epidemiological characteristics of patients were investigated. MLSA revealed epidemiological patterns among L. (V. braziliensis strains, even identifying strains from imported cases among the Santa Catarina strains that presented extensive homogeneity. Evidence presented here has demonstrated MLSA possesses adequate discriminatory power for outbreak investigation, as well as other potential uses in the molecular epidemiology of leishmaniasis.

  9. Sequencing Infrastructure Investments under Deep Uncertainty Using Real Options Analysis

    Directory of Open Access Journals (Sweden)

    Nishtha Manocha

    2018-02-01

    Full Text Available The adaptation tipping point and adaptation pathway approach developed to make decisions under deep uncertainty do not shed light on which among the multiple available pathways should be chosen as the preferred pathway. This creates the need to extend these approaches by means of suitable tools that can help sequence actions and subsequently enable the outlining of relevant policies. This paper presents two sequencing approaches, namely, the “Build to Target” and “Build Up” approach, to aid in sub-selecting a set of preferred pathways. Both approaches differ in the levels of flexibility they offer. They are exemplified by means of two case studies wherein the Net Present Valuation and the Real Options Analysis are employed as selection criterions. The results demonstrate the benefit of these two approaches when used in conjunction with the adaptation pathways and show how the pathways selected by means of a Build to Target approach generally have a value greater than, or at least the same as, the pathways selected by the Build Up approach. Further, this paper also demonstrates the capacity of Real Options to quantify and capture the economic value of flexibility, which cannot be done by traditional valuation approaches such as Net Present Valuation.

  10. BNL severe accident sequence experiments and analysis program

    International Nuclear Information System (INIS)

    Greene, G.A.; Ginsberg, T.; Tutu, N.K.

    1985-01-01

    Analyses of LWR degraded core accidents require mathematical characterization of two major sources of pressure and temperature loading on the reactor containment buildings: (1) steam generation from core debris-water thermal interactions and (2) molten core-concrete interactions. Experiments are in progress at BNL in support of analytical model development related to aspects of the above containment loading mechanisms. The work supports development and evaluation of the CORCON, MARCH, CONTAIN and MEDICI computer under development at other NRC-contractor laboratories. The thermal-hydraulic behavior of hot debris located within the reactor core region upon sudden introduction of cooling water is being investigated in a joint experimental and analytical program. This work supports development and evaluation of the SCDAP computer code being developed at EG and G to characterize in-vessel severe core damage accident sequences. Progress is described in the two areas of: 1) core debris thermal-hydraulic phenomenology and 2) heat transfer in core-concrete interactions

  11. How Has Applied Behavior Analysis and Behavior Therapy Changed?: An Historical Analysis of Journals

    Science.gov (United States)

    O'Donohue, William; Fryling, Mitch

    2007-01-01

    Applied behavior analysis and behavior therapy are now nearly a half century old. It is interesting to ask if and how these disciplines have changed over time, particularly regarding some of their key internal controversies (e.g., role of cognitions). We examined the first five years and the 2000-2004 five year period of the "Journal of Applied…

  12. Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing.

    Science.gov (United States)

    Kiyosawa, Hidenori; Okumura, Akio; Okui, Saya; Ushida, Chisato; Kawai, Gota

    2015-08-01

    In order to find novel structured small RNAs, next-generation sequencing was applied to small RNA fractions with lengths ranging from 40 to 140 nt and secondary structure-based clustering was performed. Sequences of structured RNAs were effectively clustered and analyzed by secondary structure. Although more than 99% of the obtained sequences were known RNAs, 16 candidate mouse structured small non-coding RNAs (MsncRs) were isolated. Based on these results, the merits of secondary structure-based analysis are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Human factors review for Severe Accident Sequence Analysis (SASA)

    International Nuclear Information System (INIS)

    Krois, P.A.; Haas, P.M.; Manning, J.J.; Bovell, C.R.

    1984-01-01

    The paper will discuss work being conducted during this human factors review including: (1) support of the Severe Accident Sequence Analysis (SASA) Program based on an assessment of operator actions, and (2) development of a descriptive model of operator severe accident management. Research by SASA analysts on the Browns Ferry Unit One (BF1) anticipated transient without scram (ATWS) was supported through a concurrent assessment of operator performance to demonstrate contributions to SASA analyses from human factors data and methods. A descriptive model was developed called the Function Oriented Accident Management (FOAM) model, which serves as a structure for bridging human factors, operations, and engineering expertise and which is useful for identifying needs/deficiencies in the area of accident management. The assessment of human factors issues related to ATWS required extensive coordination with SASA analysts. The analysis was consolidated primarily to six operator actions identified in the Emergency Procedure Guidelines (EPGs) as being the most critical to the accident sequence. These actions were assessed through simulator exercises, qualitative reviews, and quantitative human reliability analyses. The FOAM descriptive model assumes as a starting point that multiple operator/system failures exceed the scope of procedures and necessitates a knowledge-based emergency response by the operators. The FOAM model provides a functionally-oriented structure for assembling human factors, operations, and engineering data and expertise into operator guidance for unconventional emergency responses to mitigate severe accident progression and avoid/minimize core degradation. Operators must also respond to potential radiological release beyond plant protective barriers. Research needs in accident management and potential uses of the FOAM model are described. 11 references, 1 figure

  14. Arguments for a Cluster Analysis of Nasal Consonant Sequences of ...

    African Journals Online (AJOL)

    Bantu language scholars, have among other things, debated over the issue of whether nasal and consonant sequences (NC sequences) in various Bantu languages should be considered as clusters or single segments (prenasalised stops). This paper examines these sequences as they occur in Sukwa nouns. Sukwa is a ...

  15. Design and Analysis of Single-Cell Sequencing Experiments

    NARCIS (Netherlands)

    Grün, Dominic; van Oudenaarden, Alexander

    2015-01-01

    Recent advances in single-cell sequencing hold great potential for exploring biological systems with unprecedented resolution. Sequencing the genome of individual cells can reveal somatic mutations and allows the investigation of clonal dynamics. Single-cell transcriptome sequencing can elucidate

  16. Chimera: construction of chimeric sequences for phylogenetic analysis

    NARCIS (Netherlands)

    Leunissen, J.A.M.

    2003-01-01

    Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output

  17. Sequence analysis of cereal sucrose synthase genes and isolation ...

    African Journals Online (AJOL)

    SERVER

    2007-10-18

    Oct 18, 2007 ... sequencing of sucrose synthase gene fragment from sor- ghum using primers designed at their conserved exons. MATERIALS AND METHODS. Multiple sequence alignment. Sucrose synthase gene sequences of various cereals like rice, maize, and barley were accessed from NCBI Genbank database.

  18. Analysis of expressed sequence tags derived from inflorescence ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-02

    Nov 2, 2009 ... genetically distant organisms. Clones could be isolated and partially sequenced by the thousands with the improvements in DNA sequencing technology. High- throughput DNA sequencing has greatly reduced both the cost and time involved in obtaining large ESTs data sets. There are several applications ...

  19. Accident Sequence Evaluation Program: Human reliability analysis procedure

    International Nuclear Information System (INIS)

    Swain, A.D.

    1987-02-01

    This document presents a shortened version of the procedure, models, and data for human reliability analysis (HRA) which are presented in the Handbook of Human Reliability Analysis With emphasis on Nuclear Power Plant Applications (NUREG/CR-1278, August 1983). This shortened version was prepared and tried out as part of the Accident Sequence Evaluation Program (ASEP) funded by the US Nuclear Regulatory Commission and managed by Sandia National Laboratories. The intent of this new HRA procedure, called the ''ASEP HRA Procedure,'' is to enable systems analysts, with minimal support from experts in human reliability analysis, to make estimates of human error probabilities and other human performance characteristics which are sufficiently accurate for many probabilistic risk assessments. The ASEP HRA Procedure consists of a Pre-Accident Screening HRA, a Pre-Accident Nominal HRA, a Post-Accident Screening HRA, and a Post-Accident Nominal HRA. The procedure in this document includes changes made after tryout and evaluation of the procedure in four nuclear power plants by four different systems analysts and related personnel, including human reliability specialists. The changes consist of some additional explanatory material (including examples), and more detailed definitions of some of the terms. 42 refs

  20. Accident Sequence Evaluation Program: Human reliability analysis procedure

    Energy Technology Data Exchange (ETDEWEB)

    Swain, A.D.

    1987-02-01

    This document presents a shortened version of the procedure, models, and data for human reliability analysis (HRA) which are presented in the Handbook of Human Reliability Analysis With emphasis on Nuclear Power Plant Applications (NUREG/CR-1278, August 1983). This shortened version was prepared and tried out as part of the Accident Sequence Evaluation Program (ASEP) funded by the US Nuclear Regulatory Commission and managed by Sandia National Laboratories. The intent of this new HRA procedure, called the ''ASEP HRA Procedure,'' is to enable systems analysts, with minimal support from experts in human reliability analysis, to make estimates of human error probabilities and other human performance characteristics which are sufficiently accurate for many probabilistic risk assessments. The ASEP HRA Procedure consists of a Pre-Accident Screening HRA, a Pre-Accident Nominal HRA, a Post-Accident Screening HRA, and a Post-Accident Nominal HRA. The procedure in this document includes changes made after tryout and evaluation of the procedure in four nuclear power plants by four different systems analysts and related personnel, including human reliability specialists. The changes consist of some additional explanatory material (including examples), and more detailed definitions of some of the terms. 42 refs.

  1. Functional analysis of verbal behavior: a brief review.

    Science.gov (United States)

    Plavnick, Joshua B; Normand, Matthew P

    2013-01-01

    A variation of the preintervention functional analysis of problem behavior has recently been extended to identify the function of verbal behavior emitted by children with autism. Recent research suggests that a functional analysis of verbal behavior might be beneficial in evaluating previous instruction and guiding the selection of future educational targets and instructional procedures. The present paper reviews previous literature on the functional analysis of verbal behavior and identifies avenues for future research. © Society for the Experimental Analysis of Behavior.

  2. Computer code (WETBERAN) for wet sequence behavior of radioactive nuclides in LWR plant at accident conditions

    International Nuclear Information System (INIS)

    Shimooke, T.; Kobayashi, K.; Sato, S.

    1985-01-01

    The WETBERAN code has been developed to simulate the isotopic- and time-dependent behaviors of fission products (FP) which leak through the multiple paths of liquid and gas flows within LWR plant under accident conditions. In this code, emphasis is put on the phenomena pertinent to the presence of water. The TMI, SL-1 and Ginna accidents were analyzed to show the code capability. The TMI 40 day analysis gave detailed information of FP behaviors, both leaking from and remaining in the plant, and proved effectiveness of the network model describing the multiple leakage paths. The SL-1 analysis was made to study halogen reduction by water, which cannot be taken into account by CORRAL. The Ginna analysis was to check the iodine transport by droplets usually generated by primary water flashing at SG tube rupture

  3. Discrete-Trial Functional Analysis and Functional Communication Training with Three Adults with Intellectual Disabilities and Problem Behavior

    Science.gov (United States)

    Chezan, Laura C.; Drasgow, Erik; Martin, Christian A.

    2014-01-01

    We conducted a sequence of two studies on the use of discrete-trial functional analysis and functional communication training. First, we used discrete-trial functional analysis (DTFA) to identify the function of problem behavior in three adults with intellectual disabilities and problem behavior. Results indicated clear patterns of problem…

  4. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

    OpenAIRE

    Ebhardt, H. Alexander; Tsang, Herbert H.; Dai, Denny C.; Liu, Yifeng; Bostan, Babak; Fahlman, Richard P.

    2009-01-01

    Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous...

  5. 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. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  6. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development.

    Science.gov (United States)

    Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Yang, Tuxi; Wei, Anzhi

    2017-12-01

    Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence repeat markers for identification of Zanthoxylum. In total, we predicted 45,057 unigenes and 22,212 protein coding sequences, approximately 90% of which showed significant similarities to known proteins in databases. Phylogenetic analysis indicated that Zanthoxylum is relatively recent and estimated to have diverged from Citrus ca. 36.5-37.7 million years ago. We also detected a whole-genome duplication event in Zanthoxylum that occurred 14 million years ago. We found no protein coding sequences that were significantly under positive selection by Ka/Ks. Simple sequence repeat analysis divided 31 Zanthoxylum cultivars and landraces into three major groups. This Zanthoxylum reference transcriptome provides crucial information for the evolutionary study of the Zanthoxylum genus and the Rutaceae family, and facilitates the establishment of more effective Zanthoxylum breeding programs.

  7. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

    Science.gov (United States)

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

  8. Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

    Directory of Open Access Journals (Sweden)

    Tingcai Cheng

    Full Text Available The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG and posterior silk gland (PSG. Three sericin genes (sericin 1, sericin 2, and sericin 3 were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25 were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs and 361 insertion-deletions (INDELs were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.

  9. Saving the world by teaching behavior analysis: A behavioral systems approach

    OpenAIRE

    Malott, Richard W.; Vunovich, Pamela L.; Boettcher, William; Groeger, Corina

    1995-01-01

    This article presents a behavioral systems approach to organizational design and applies that approach to the teaching of behavior analysis. This systems approach consists of three components: goal-directed systems design, behavioral systems engineering, and performance management. This systems approach is applied to the Education Board and Teaching Behavior Analysis Special Interest Group of the Association for Behavior Analysis, with a conclusion that we need to emphasize the recruitment of...

  10. Functional Analysis of Behavior and Its Clinical Application

    OpenAIRE

    Kaasim Fatih Yavuz; Furkan Bahadir Alptekin

    2017-01-01

    Many approaches to psychology and psychiatry have tried to explain behaviors etiologically. Functional contextualism, followed by radical behaviorism, and its application functional analysis of behavior can be considered as an alternative to mainstream approaches. Functional analysis, in analyzing a particular behavior, takes into account the context in which behavior itself present and suggests that it focus on contextual factors that influence behavior in the direction of learning principle...

  11. On the relation between applied behavior analysis and positive behavioral support.

    Science.gov (United States)

    Carr, James E; Sidener, Tina M

    2002-01-01

    Anderson and Freeman (2000) recently defined positive behavioral support (PBS) as a systematic approach to the delivery of clinical and educational services that is rooted in behavior analysis. However, the recent literature contains varied definitions of PBS as well as discrepant notions regarding the relation between applied behavior analysis and PBS. After summarizing common definitional characteristics of PBS from the literature, we conclude that PBS is comprised almost exclusively of techniques and values originating in applied behavior analysis. We then discuss the relations between applied behavior analysis and PBS that have been proposed in the literature. Finally, we discuss possible implications of considering PBS a field separate from applied behavior analysis.

  12. Database-driven primary analysis of raw sequencing data

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to methods for identifying the source of a biological sequence containing sample from raw sequencing reads. The method may be used to identify the source of unknown DNA and can be used for diagnostic, biodefense, food safety and quality, and hygiene applications....... In another aspect the invention relates to a database of reference sequences which can be used in the method of the invention....

  13. Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

    Science.gov (United States)

    Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

    2016-08-15

    Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Feature Extraction From DNA Sequences by Multifractal Analysis

    National Research Council Canada - National Science Library

    Zhang, H

    2001-01-01

    This paper presents feature extraction and estimation of multifractal measures of DNA sequences using a multifractal methodology and demonstrates a new scheme for identifying biological functionality...

  15. Sequence and expression analysis of gaps in human chromosome 20

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Seemann, Stefan; Mang, Yuan

    2012-01-01

    /or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing......The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and...

  16. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  17. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

    DEFF Research Database (Denmark)

    Worning, Peder; Jensen, Lars Juhl; Nelson, K. E.

    2000-01-01

    The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters......, which brings independent evidence for the lateral gene transfer in the genome of T.maritima, The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms...

  18. An Analysis of Medium Loss of Coolant Sequence for the Severe Accident Analysis DB

    Energy Technology Data Exchange (ETDEWEB)

    Park, Soo Yong; Song, Yong Mann

    2007-12-15

    This report contains analysis methodologies and calculation results of medium loss of Coolant sequences for the severe accident analysis database system. The Korean standard nuclear power plant has been selected as a reference plant. Based on the probabilistic safety analysis of the corresponding plant, 10 accident scenarios, which was predicted to have more than 10{sup -10} /ry occurrence frequency, have been analyzed as base cases for the medium loss of Coolant sequence database. The functions of the severe accident analysis database system will be to make a diagnosis of the accident by some input information from the plant symptoms, to search a corresponding scenario, and finally to provide the user phenomenological information based on the pre-analyzed results. The MAAP 4.06 calculation results in this report will be utilized as input data of the severe accident analysis database system.

  19. An Analysis of Large Loss of Coolant Sequence for the Severe Accident Analysis DB

    Energy Technology Data Exchange (ETDEWEB)

    Park, Soo Yong; Song, Yong Mann

    2007-12-15

    This report contains analysis methodologies and calculation results of Large loss of Coolant sequences for the severe accident analysis database system. The Korean standard nuclear power plant has been selected as a reference plant. Based on the probabilistic safety analysis of the corresponding plant, 14 accident scenarios, which was predicted to have more than 10{sup -10} /ry occurrence frequency, have been analyzed as base cases for the Large loss of Coolant sequence database. The functions of the severe accident analysis database system will be to make a diagnosis of the accident by some input information from the plant symptoms, to search a corresponding scenario, and finally to provide the user phenomenological information based on the pre-analyzed results. The MAAP 4.06 calculation results in this report will be utilized as input data of the severe accident analysis database system.

  20. An Analysis of Small Loss of Coolant Sequence for the Severe Accident Analysis Database

    Energy Technology Data Exchange (ETDEWEB)

    Park, Soo Yong; Song, Yong Mann

    2007-12-15

    This report contains analysis methodologies and calculation results of small loss of Coolant sequences for the severe accident analysis database system. The Korean standard nuclear power plant has been selected as a reference plant. Based on the probabilistic safety analysis of the corresponding plant, 10 accident scenarios, which was predicted to have more than 10{sup -9} /ry occurrence frequency, have been analyzed as base cases for the small loss of Coolant sequence database. The functions of the severe accident analysis database system will be to make a diagnosis of the accident by some input information from the plant symptoms, to search a corresponding scenario, and finally to provide the user phenomenological information based on the pre-analyzed results. The MAAP 4.06 calculation results in this report will be utilized as input data of the severe accident analysis database system.

  1. Sequence and comparative analysis of Leuconostoc dairy bacteriophages.

    Science.gov (United States)

    Kot, Witold; Hansen, Lars H; Neve, Horst; Hammer, Karin; Jacobsen, Susanne; Pedersen, Per D; Sørensen, Søren J; Heller, Knut J; Vogensen, Finn K

    2014-04-17

    Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc mesenteroides or Leuconostoc pseudomesenteroides strains. The phages have dsDNA genomes with sizes ranging from 25.7 to 28.4 kb. Comparative genomics analysis helped classify the 9 phages into two classes, which correlates with the host species. High percentage of similarity within the classes on both nucleotide and protein levels was observed. Genome comparison also revealed very high conservation of the overall genomic organization between the classes. The genes were organized in functional modules responsible for replication, packaging, head and tail morphogenesis, cell lysis and regulation and modification, respectively. No lysogeny modules were detected. To our knowledge this report provides the first comparative genomic work done on Leuconostoc dairy phages. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)

    Science.gov (United States)

    Niu, Jianfeng; Hu, Haiyan; Hu, Songnian; Wang, Guangce; Peng, Guang; Sun, Song

    2010-01-01

    In 2008, a green tide broke out before the sailing competition of the 29th Olympic Games in Qingdao. The causative species was determined to be Enteromorpha prolifera ( Ulva prolifera O. F. Müller), a familiar green macroalga along the coastline of China. Rapid accumulation of a large biomass of floating U. prolifera prompted research on different aspects of this species. In this study, we constructed a nonnormalized cDNA library from the thalli of U. prolifera and acquired 10 072 high-quality expressed sequence tags (ESTs). These ESTs were assembled into 3 519 nonredundant gene groups, including 1 446 clusters and 2 073 singletons. After annotation with the nr database, a large number of genes were found to be related with chloroplast and ribosomal protein, GO functional classification showed 1 418 ESTs participated in photosynthesis and 1 359 ESTs were responsible for the generation of precursor metabolites and energy. In addition, rather comprehensive carbon fixation pathways were found in U. prolifera using KEGG. Some stress-related and signal transduction-related genes were also found in this study. All the evidences displayed that U. prolifera had substance and energy foundation for the intense photosynthesis and the rapid proliferation. Phylogenetic analysis of cytochrome c oxidase subunit I revealed that this green-tide causative species is most closely affiliated to Pseudendoclonium akinetum (Ulvophyceae).

  3. The sequence and analysis of a Chinese pig genome

    Directory of Open Access Journals (Sweden)

    Fang Xiaodong

    2012-11-01

    Full Text Available Abstract Background The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP, as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome. Results Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes. Conclusion Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

  4. The sequence and analysis of Trypanosoma brucei chromosome II

    Science.gov (United States)

    El-Sayed, Najib M. A.; Ghedin, Elodie; Song, Jinming; MacLeod, Annette; Bringaud, Frederic; Larkin, Christopher; Wanless, David; Peterson, Jeremy; Hou, Lihua; Taylor, Sonya; Tweedie, Alison; Biteau, Nicolas; Khalak, Hanif G.; Lin, Xiaoying; Mason, Tanya; Hannick, Linda; Caler, Elisabet; Blandin, Gaëlle; Bartholomeu, Daniella; Simpson, Anjana J.; Kaul, Samir; Zhao, Hong; Pai, Grace; Aken, Susan Van; Utterback, Teresa; Haas, Brian; Koo, Hean L.; Umayam, Lowell; Suh, Bernard; Gerrard, Caroline; Leech, Vanessa; Qi, Rong; Zhou, Shiguo; Schwartz, David; Feldblyum, Tamara; Salzberg, Steven; Tait, Andrew; Turner, C. Michael R.; Ullu, Elisabetta; White, Owen; Melville, Sara; Adams, Mark D.; Fraser, Claire M.; Donelson, John E.

    2003-01-01

    We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational ‘hot’ and ‘cold’ regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events. PMID:12907728

  5. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Tarek

    2011-04-18

    Apr 18, 2011 ... 3056 Afr. J. Biotechnol. Table 1. DNA sequence of the primers tested. Name. Sequence. Accession no. ... The lack of contaminating genomic DNA was checked out by monitoring negative polymerase chain ..... variation between human and chimpanzee. Genome Res. 15: 1344-. 1356. Pomies P, Louis HA, ...

  6. Sequencing and analysis of an Irish human genome.

    LENUS (Irish Health Repository)

    Tong, Pin

    2010-01-01

    Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a population of interest due to its relative geographical isolation and genetic impact on further populations, we extend the above studies through the generation of 11-fold coverage of the first Irish human genome sequence.

  7. Illumina-based de novotranscriptome sequencing and analysis of ...

    Indian Academy of Sciences (India)

    ZHONGXIAN XU

    2017-12-18

    Dec 18, 2017 ... Next-generation sequencing technique is an efficient method for generating an enormous amount of sequence data that can represent a large number of genes and their expression levels. In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland.

  8. Sequence stratigraphy and structural analysis of the Emi field ...

    African Journals Online (AJOL)

    Highstand system tract and transgressive system tract were identified within the depositional sequences. Marker shales, characterized by index fossils Haplophramoides-24 and Bolivina-46, were used to date the key bounding surfaces with the aid of the Niger Delta chronostratigraphic chart. Ages assigned to the sequence ...

  9. CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

    Science.gov (United States)

    Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

    2017-05-15

    B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

  10. A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

    Science.gov (United States)

    Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

    2012-10-01

    One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. An auditory display tool for DNA sequence analysis.

    Science.gov (United States)

    Temple, Mark D

    2017-04-24

    DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorithms are logically designed from the simple through to the more complex. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. Codons may also be parsed degenerately into 20 notes with respect to the genetic code. Lastly nucleotide pairs can be parsed as two separate frames or codons can be parsed as three reading frames giving rise to multiple streams of audio. The most informative sonification algorithm reads the DNA sequence as codons in three reading frames to produce three concurrent streams of audio in an auditory display. This approach is advantageous since start and stop codons in either frame have a direct affect to start or stop the audio in that frame, leaving the other frames unaffected. Using these methods, DNA sequences such as open reading frames or repetitive DNA sequences can be distinguished from one another. These sonification tools are available through a webpage interface in which an input DNA sequence can be processed in real time to produce an auditory display playable directly within the browser. The potential of this approach as an analytical tool is discussed with reference to auditory displays derived from test sequences including simple nucleotide sequences, repetitive DNA sequences and coding or non-coding genes. This study presents a proof-of-concept that some properties of a DNA sequence can be identified through sonification alone and argues for their inclusion within the toolkit of DNA sequence browsers as an adjunct to existing visual and analytical tools.

  12. Strategies to Position Behavior Analysis as the Contemporary Science of What Works in Behavior Change

    OpenAIRE

    Smith, Julie M.

    2015-01-01

    The negative perception of behavior analysis by the public, and conveyed in mass media, is well-recognized by the professional community of behavior analysts. Several strategies for correcting this perception have been deployed in the field by organizational behavior management practitioners, in particular, with encouraging results. These strategies include (a) reframing behaviorism in a more resonant format, (b) pushing direct outcome comparisons between behavior analysis and its rivals, and...

  13. Identification and sequence analysis of Tapasin gene in guinea fowl

    Directory of Open Access Journals (Sweden)

    Varuna P. Panicker

    2014-12-01

    Full Text Available Aim: An attempt has been made to identify and study the nucleotide sequence variability in exon 5 - exon 6 regions of guinea fowl Tapasin gene. Materials and Methods: Blood samples were collected from randomly selected birds (12 guinea fowl birds and Tapasin gene amplified using chicken specific primers designed from GenBank submitted sequences. Polymerase chain reaction conditions were standardized so as get only single amplicons. Obtained products were then cloned and sequenced; sequences were then analyzed using suitable software. Results: Amplicon size of the Tapasin gene in guinea fowl was same as reported in chicken with areas of transitions and transversions. The sequence variations reported in these coding sequences might have influence in the protein structure, which may be correlated with the increased immune status of the bird when compared with chicken breeds. Conclusion: Since Tapasin gene is an immunologically important gene, which plays an important role in the immune status of the bird. Sequence variations in the gene can be correlated with the altered immune status of the bird.

  14. T-pattern analysis for the study of temporal structure of animal and human behavior: a comprehensive review.

    Science.gov (United States)

    Casarrubea, M; Jonsson, G K; Faulisi, F; Sorbera, F; Di Giovanni, G; Benigno, A; Crescimanno, G; Magnusson, M S

    2015-01-15

    A basic tenet in the realm of modern behavioral sciences is that behavior consists of patterns in time. For this reason, investigations of behavior deal with sequences that are not easily perceivable by the unaided observer. This problem calls for improved means of detection, data handling and analysis. This review focuses on the analysis of the temporal structure of behavior carried out by means of a multivariate approach known as T-pattern analysis. Using this technique, recurring sequences of behavioral events, usually hard to detect, can be unveiled and carefully described. T-pattern analysis has been successfully applied in the study of various aspects of human or animal behavior such as behavioral modifications in neuro-psychiatric diseases, route-tracing stereotypy in mice, interaction between human subjects and animal or artificial agents, hormonal-behavioral interactions, patterns of behavior associated with emesis and, in our laboratories, exploration and anxiety-related behaviors in rodents. After describing the theory and concepts of T-pattern analysis, this review will focus on the application of the analysis to the study of the temporal characteristics of behavior in different species from rodents to human beings. This work could represent a useful background for researchers who intend to employ such a refined multivariate approach to the study of behavior. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Event Sequence Analysis of the Air Intelligence Agency Information Operations Center Flight Operations

    National Research Council Canada - National Science Library

    Larsen, Glen

    1998-01-01

    This report applies Event Sequence Analysis, methodology adapted from aircraft mishap investigation, to an investigation of the performance of the Air Intelligence Agency's Information Operations Center (IOC...

  16. Sequence analysis of Schmallenberg virus genomes detected in Hungary.

    Science.gov (United States)

    Fehér, Enikő; Marton, Szilvia; Tóth, Ádám György; Ursu, Krisztina; Wernike, Kerstin; Beer, Martin; Dán, Ádám; Bányai, Krisztián

    2017-12-01

    Since its emergence near the German-Dutch border in 2011, Schmallenberg virus (SBV) has been identified in many European countries. In this study, we determined the complete coding sequence of seven Hungarian SBV genomes to expand our knowledge about the genetic diversity of circulating field strains. The samples originated from the first case, an aborted cattle fetus without malformation collected in 2012, and from the blood samples of six adult cattle in 2014. The Hungarian SBV sequences shared ≥99.3% nucleotide (nt) and ≥97.8% amino acid (aa) identity with each other, and ≥98.9 nt and ≥96.7% aa identity with reference strains. Although phylogenetic analyses showed low resolution in general, the M sequences of cattle and sheep origin SBV strains seemed to cluster on different branches. Both common and unique mutation sites were observed in different groups of sequences that might help understanding the evolution of emerging SBV strains.

  17. simple sequence repeat (SSR) markers in genetic analysis of

    African Journals Online (AJOL)

    Yomi

    2012-08-28

    1998). Cross- species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15:1275-1287.

  18. USE OF NEXT-GENERATION SEQUENCING FOR GENOMIC ANALYSIS IN COMPLEX DISEASES

    OpenAIRE

    Sana, Maria Elena

    2013-01-01

    Since the early 1990s, Sanger method has been the gold standard methodology for sequencing analysis of DNA. Next-generation sequencing (NGS) approaches revolutionized the field of genomics over the last 5 years. These new sequencing technologies make feasible the direct and cost-effective sequencing of genomes at unprecedented scale and speed. Furthermore, the applications of these technologies are wide-spread and have been developed to explore the complex biological systems, among which RNA ...

  19. Cloning and sequence analysis of lily and tobacco guanylate kinases.

    Science.gov (United States)

    Kumar, V

    2000-03-01

    Guanylate kinase is an essential enzyme in the nucleotide biosynthetic pathway, catalyzing the reversible transfer of the terminal phosphoryl group of ATP to GMP or dGMP. This enzyme has been well studied from several organisms and many structural and functional details have been characterized. Animal GMP kinases have also been implicated in signal transduction pathways. However, the corresponding role by plant derived GMP kinases remains to be elucidated. Full-length cDNA clones encoding enzymatically active guanylate kinases were isolated from cDNA libraries of lily and tobacco. Lily cDNA is predicted to encode a 392-amino acid protein with a molecular mass of 43.1 kDa and carries amino- and carboxy- terminal extensions of the guanylate kinase (GK)-like domain. But tobacco cDNA is predicted to encode a smaller protein of 297-amino acids with a molecular mass of 32.7 kDa. The amino acid residues known to participate in the catalytic activity of functionally characterized GMP kinases, are also conserved in GK domains of LGK-1 and NGK-1. The GK domains of NGK-1, LGK-1 and previously characterized AGK-1 from Arabidopsis exhibit 74-84% identity, whereas their N- and C-terminal domains are more divergent with amino acid conservation in the order of 48-55%. Phylogenetic analysis on the deduced amino acid sequences reveals that NGK-1 and LGK-1 form one distinct subgroup along with AGK-1 and AGK-2 homologues from Arabidopsis. Isolation of GMP kinases from diverse plant species like lily and tobacco adds a new dimension in understanding their role in cell signaling pathways that are associated with plant growth and development.

  20. Genome sequence and analysis of the tuber crop potato

    DEFF Research Database (Denmark)

    Xu, X.; Pan, S.; Cheng, S.

    2011-01-01

    and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade...... contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop....

  1. Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

    Directory of Open Access Journals (Sweden)

    Hideyuki Tamaki

    Full Text Available BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1, after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.

  2. Acceptance-Enhanced Behavior Therapy (AEBT) for Trichotillomania and Chronic Skin Picking: Exploring the Effects of Component Sequencing

    Science.gov (United States)

    Flessner, Christopher A.; Busch, Andrew M.; Heideman, Paul W.; Woods, Douglas W.

    2008-01-01

    This pilot study examined the utility of acceptance-enhanced behavior therapy (AEBT) for trichotillomania (TTM) and chronic skin picking (CSP) and the impact of altering treatment sequence on overall treatment efficacy. Participants referred to a TTM and CSP specialty clinic were assessed by an independent evaluator within separate, nonconcurrent,…

  3. First fungal genome sequence from Africa: A preliminary analysis

    Directory of Open Access Journals (Sweden)

    Rene Sutherland

    2012-01-01

    Full Text Available Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists

  4. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-01-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  5. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-05-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  6. Behavioral satiety sequence: an experimental model for studying feeding behavior Sequência comportamental de saciedade: um modelo experimental para o estudo do comportamento alimentar

    Directory of Open Access Journals (Sweden)

    Lisiane dos Santos Oliveira

    2011-08-01

    Full Text Available Feeding behavior is controlled by interactions between psychobiological and physiological systems. In rats, there is a sequence in the feeding behavior that is characterized by similar movements at the beginning and end of a meal, known as the behavioral satiety sequence. In the sequence, eating is followed by grooming and other activities, and ends with resting. The objective of this systematic review is to evaluate the use of the behavioral satiety sequence as an experimental model for the study of feeding behavior. A systematic search of the electronic databases MedLine, Lilacs, SciELO, Cochrane Library and PubMed was done from November 2007 to January 2008, using combinations of the keywords "behavioral," "satiety" and "sequence". Ninety articles were found and, of these, fifteen articles were selected for the review. The studies demonstrated the efficacy of using behavioral satiety sequence to evaluate the effects of some types of manipulations on feeding behavior. With this study method it was also possible to observe different factors that can interfere with feeding behavior, such as sedation, malaise or intake inhibition, by increasing satiety. Behavioral satiety sequence offers solid tools for gaining a better understanding of how treatment can influence feeding behavior.O comportamento alimentar é controlado por interações entre sistemas psicobiológicos e fisiológicos. Em ratos, existe uma sequência no comportamento alimentar que é caracterizada por movimentos similares no início e no término de uma refeição, conhecida como sequência comportamental de saciedade. Na sequência, o ato de comer é seguido pela limpeza e outra atividades, terminando com o descanso. O objetivo dessa revisão sistemática é avaliar o uso da sequência comportamental de saciedade como um modelo experimental para o estudo do comportamento alimentar. Uma busca sistemática das bases de dados MedLine, Lilacs, SciELO, Biblioteca Cochrane e PubMed foi

  7. Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum transcriptome.

    Directory of Open Access Journals (Sweden)

    Silvan Oulion

    Full Text Available BACKGROUND: The basally divergent phylogenetic position of amphioxus (Cephalochordata, as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae. RESULTS: Starting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode. Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp. Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species. CONCLUSION: We obtained a high-quality amphioxus (B. lanceolatum reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation

  8. An Objective Comparison of Applied Behavior Analysis and Organizational Behavior Management Research

    Science.gov (United States)

    Culig, Kathryn M.; Dickinson, Alyce M.; McGee, Heather M.; Austin, John

    2005-01-01

    This paper presents an objective review, analysis, and comparison of empirical studies targeting the behavior of adults published in Journal of Applied Behavior Analysis (JABA) and Journal of Organizational Behavior Management (JOBM) between 1997 and 2001. The purpose of the comparisons was to identify similarities and differences with respect to…

  9. Exome Sequence Analysis of 14 Families With High Myopia

    DEFF Research Database (Denmark)

    Kloss, Bethany A.; Tompson, Stuart W.; Whisenhunt, Kristina N.

    2017-01-01

    Purpose: To identify causal gene mutations in 14 families with autosomal dominant (AD) high myopia using exome sequencing. Methods: Select individuals from 14 large Caucasian families with high myopia were exome sequenced. Gene variants were filtered to identify potential pathogenic changes. Sang...... implicated in the pathogenesis of AD high myopia. This study provides new genes for consideration in the pathogenesis of high myopia, and may aid in the development of genetic profiling of those at greatest risk for attendant ocular morbidities of this disorder.......Purpose: To identify causal gene mutations in 14 families with autosomal dominant (AD) high myopia using exome sequencing. Methods: Select individuals from 14 large Caucasian families with high myopia were exome sequenced. Gene variants were filtered to identify potential pathogenic changes. Sanger...... sequencing was used to confirm variants in original DNA, and to test for disease cosegregation in additional family members. Candidate genes and chromosomal loci previously associated with myopic refractive error and its endophenotypes were comprehensively screened. Results: In 14 high myopia families, we...

  10. Combining text mining and sequence analysis to discover protein functional regions.

    Science.gov (United States)

    Eskin, E; Agichtein, E

    2004-01-01

    Recently presented protein sequence classification models can identify relevant regions of the sequence. This observation has many potential applications to detecting functional regions of proteins. However, identifying such sequence regions automatically is difficult in practice, as relatively few types of information have enough annotated sequences to perform this analysis. Our approach addresses this data scarcity problem by combining text and sequence analysis. First, we train a text classifier over the explicit textual annotations available for some of the sequences in the dataset, and use the trained classifier to predict the class for the rest of the unlabeled sequences. We then train a joint sequence text classifier over the text contained in the functional annotations of the sequences, and the actual sequences in this larger, automatically extended dataset. Finally, we project the classifier onto the original sequences to determine the relevant regions of the sequences. We demonstrate the effectiveness of our approach by predicting protein sub-cellular localization and determining localization specific functional regions of these proteins.

  11. Laser desorption mass spectrometry for DNA analysis and sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, C.H.; Taranenko, N.I.; Tang, K.; Allman, S.L.

    1995-03-01

    Laser desorption mass spectrometry has been considered as a potential new method for fast DNA sequencing. Our approach is to use matrix-assisted laser desorption to produce parent ions of DNA segments and a time-of-flight mass spectrometer to identify the sizes of DNA segments. Thus, the approach is similar to gel electrophoresis sequencing using Sanger`s enzymatic method. However, gel, radioactive tagging, and dye labeling are not required. In addition, the sequencing process can possibly be finished within a few hundred microseconds instead of hours and days. In order to use mass spectrometry for fast DNA sequencing, the following three criteria need to be satisfied. They are (1) detection of large DNA segments, (2) sensitivity reaching the femtomole region, and (3) mass resolution good enough to separate DNA segments of a single nucleotide difference. It has been very difficult to detect large DNA segments by mass spectrometry before due to the fragile chemical properties of DNA and low detection sensitivity of DNA ions. We discovered several new matrices to increase the production of DNA ions. By innovative design of a mass spectrometer, we can increase the ion energy up to 45 KeV to enhance the detection sensitivity. Recently, we succeeded in detecting a DNA segment with 500 nucleotides. The sensitivity was 100 femtomole. Thus, we have fulfilled two key criteria for using mass spectrometry for fast DNA sequencing. The major effort in the near future is to improve the resolution. Different approaches are being pursued. When high resolution of mass spectrometry can be achieved and automation of sample preparation is developed, the sequencing speed to reach 500 megabases per year can be feasible.

  12. Translational Research: It's Not 1960s Behavior Analysis

    Science.gov (United States)

    Poling, Alan; Edwards, Timothy L.

    2011-01-01

    The authors find Critchfield's article ("Translational Contributions of the Experimental Analysis of Behavior," "The Behavior Analyst," v34, p3-17, 2011) scholarly, clear, and insightful. In it, Critchfield provides an excellent overview of translational research in behavior analysis and suggests several general strategies for increasing the…

  13. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, D.M.; Bolund, Lars; As part of the Chinese Human Genome Sequencing Consortium, E.T.A.L.

    2006-01-01

    chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well...... as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion...

  14. Behavior Analysis Usage with Behavior Tures Adoption for Malicious Code Detection on JAVASCRIPT Scenarios Example

    Directory of Open Access Journals (Sweden)

    Y. M. Tumanov

    2010-03-01

    Full Text Available The article offers the method of malicious JavaScript code detection, based on behavior analysis. Conceptions of program behavior, program state, an algorithm of malicious code detection are described.

  15. Applied behavior analysis: understanding and changing behavior in the community-a representative review.

    Science.gov (United States)

    Luyben, Paul D

    2009-01-01

    Applied behavior analysis, a psychological discipline, has been characterized as the science of behavior change (Chance, 2006). Research in applied behavior analysis has been published for approximately 40 years since the initial publication of the Journal of Applied Behavior Analysis in 1968. The field now encompasses a wide range of human behavior. Although much of the published research centers on problem behaviors that occur in schools and among people with disabilities, a substantial body of knowledge has emerged in community settings. This article provides a review of the behavioral community research published in the Journal of Applied Behavior Analysis as representative of this work, including research in the areas of home and family, health, safety, community involvement and the environment, recreation and sports, crime and delinquency, and organizations. In the interest of space, research in schools and with people with disabilities has been excluded from this review.

  16. Universality in voting behavior: an empirical analysis

    Science.gov (United States)

    Chatterjee, Arnab; Mitrović, Marija; Fortunato, Santo

    2013-01-01

    Election data represent a precious source of information to study human behavior at a large scale. In proportional elections with open lists, the number of votes received by a candidate, rescaled by the average performance of all competitors in the same party list, has the same distribution regardless of the country and the year of the election. Here we provide the first thorough assessment of this claim. We analyzed election datasets of 15 countries with proportional systems. We confirm that a class of nations with similar election rules fulfill the universality claim. Discrepancies from this trend in other countries with open-lists elections are always associated with peculiar differences in the election rules, which matter more than differences between countries and historical periods. Our analysis shows that the role of parties in the electoral performance of candidates is crucial: alternative scalings not taking into account party affiliations lead to poor results.

  17. SmashCell: A software framework for the analysis of single-cell amplified genome sequences

    DEFF Research Database (Denmark)

    Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen

    2010-01-01

    SUMMARY: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes however is far more complicated than the analysis of those...

  18. cDNA sequence and tissue expression analysis of glucokinase from ...

    African Journals Online (AJOL)

    Yomi

    2012-01-10

    Jan 10, 2012 ... (Rattus norvegicus) were 98.1, 96.8, 80.3 and 79.8%, respectively. Phylogenetic analysis based on GK amino acid sequences. Phylogenetic analysis among eight fish species, eleven endothermic species and one amphibian species based on glucokinase amino acid sequences is shown in Figure. 3.

  19. Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Neumann, Pavel; Novák, Petr; Jiang, J.

    2010-01-01

    Roč. 26, č. 1797 (2010), s. 2101-2108 ISSN 1367-4803 R&D Projects: GA AV ČR KJB500960802; GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : next-generation sequencing * satellite repeats * K-mer analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.877, year: 2010

  20. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  1. Analysis of B-genome derived simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    A study was conducted to investigate the genetic variability between 40 Musa genotypes maintained at the Musa germplasm collection of the International Institute for Tropical Agriculture, Ibadan using nine B-genome derived simple sequence repeat (SSR) markers. The nine primers produced reproducible and discrete ...

  2. Cloning and sequence analysis of the Antheraea pernyi ...

    Indian Academy of Sciences (India)

    The genome size of AnpeNPV is estimated at 128 kb. ... A genomic library was generated using HindIII and the positive clones were sequenced and analysed. ... Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, People's Republic of China; School of Agricultural Science and Technology, ...

  3. Characterisation and Next-generation Sequencing Analysis of Unknown Arboviruses

    Science.gov (United States)

    2012-09-01

    incapacitating illness, lack of adequate control measures, and the ease of production of large quantities of virus. Characterisation by sequencing is...ability to induce a fatal or seriously incapacitating illness, the lack of adequate control measures, and the ease of production of large...Location Family Neutralising antibody detected Culex annulirostris (mosquito) DPP1163 1987 Darwin, NT Rhabdoviridae Cattle, buffalo

  4. Illumina-based de novo transcriptome sequencing and analysis of ...

    Indian Academy of Sciences (India)

    2017-12-18

    Dec 18, 2017 ... In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI ...

  5. Whole-genome sequence-based analysis of thyroid function

    DEFF Research Database (Denmark)

    Taylor, Peter N.; Porcu, Eleonora; Chew, Shelby

    2015-01-01

    Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N = 2,287). Using additional whole-genome seque...

  6. POSA: perl objects for DNA sequencing data analysis

    NARCIS (Netherlands)

    Aerts, J.A.; Jungerius, B.J.; Groenen, M.A.M.

    2004-01-01

    Background - Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide

  7. POSA : Perl objects for DNA sequencing data analysis

    NARCIS (Netherlands)

    Aerts, JA; Jungerius, BJ; Groenen, MA

    2004-01-01

    Background: Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide

  8. DNA sequence and prokaryotic expression analysis of vitellogenin ...

    African Journals Online (AJOL)

    In this study, the DNA sequence of vitellogenin from Antheraea pernyi (Ap-Vg) was identified and its functional domain (30-740 aa, Ap-Vg-1) was expressed in Escherichia coli BL21 (DE3) cells. The recombinant Ap-Vg-1 proteins were purified and used for antibody preparation. The results showed that the intact DNA ...

  9. Illumina-based de novo transcriptome sequencing and analysis

    Indian Academy of Sciences (India)

    In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant ...

  10. A deep sequencing analysis of transcriptomes and the development ...

    Indian Academy of Sciences (India)

    Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3–39.8 million paired-end reads with 73 bp lengths were generated. The pooled reads from the ...

  11. Sequence analysis of mitochondrial 16S ribosomal RNA gene ...

    Indian Academy of Sciences (India)

    Mosquitoes are vectors for the transmission of many human pathogens that include viruses, nematodes and protozoa. For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. Recently, molecular taxonomic techniques have been utilized for this purpose. Sequence ...

  12. A bibliometric analysis of global research on genome sequencing ...

    African Journals Online (AJOL)

    The results show that disease and protein related researches were the leading research focuses, and comparative genomics and evolution related research had strong potential in the near future. Key words: Genome sequencing, research trend, scientometrics, science citation index expanded (SCI-Expanded), word cluster ...

  13. Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences

    Directory of Open Access Journals (Sweden)

    Katelyn eBrandt

    2016-05-01

    Full Text Available Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends towards a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode.

  14. Sequence analysis of mitochondrial 16S ribosomal RNA gene

    Indian Academy of Sciences (India)

    Mosquitoes are vectors for the transmission of many human pathogens that include viruses, nematodes and protozoa. For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. Recently, molecular taxonomic techniques have been utilized for this purpose. Sequence ...

  15. Sequencing and Gene Expression Analysis of Leishmania tropica LACK Gene.

    Science.gov (United States)

    Hammoudeh, Nour; Kweider, Mahmoud; Abbady, Abdul-Qader; Soukkarieh, Chadi

    2014-01-01

    Leishmania Homologue of receptors for Activated C Kinase (LACK) antigen is a 36-kDa protein, which provokes a very early immune response against Leishmania infection. There are several reports on the expression of LACK through different life-cycle stages of genus Leishmania, but only a few of them have focused on L.tropica. The present study provides details of the cloning, DNA sequencing and gene expression of LACK in this parasite species. First, several local isolates of Leishmania parasites were typed in our laboratory using PCR technique to verify of Leishmania parasite species. After that, LACK gene was amplified and cloned into a vector for sequencing. Finally, the expression of this molecule in logarithmic and stationary growth phase promastigotes, as well as in amastigotes, was evaluated by Reverse Transcription-PCR (RT-PCR) technique. The typing result confirmed that all our local isolates belong to L.tropica. LACK gene sequence was determined and high similarity was observed with the sequences of other Leishmania species. Furthermore, the expression of LACK gene in both promastigotes and amastigotes forms was confirmed. Overall, the data set the stage for future studies of the properties and immune role of LACK gene products.

  16. Cloning and sequence analysis of the defective in anther ...

    African Journals Online (AJOL)

    To clone the defective in anther dehiscence1 (DAD1) gene fragment of Chinese kale, about 700 bp product was obtained by PCR amplification using Chinese kale genomic DNA as the template and a pair of specific primers designed according to the conserved sequence of DAD1 genes of Arabidopsis thaliana and ...

  17. A Bibliometric Analysis of Global Research on Genome Sequencing ...

    African Journals Online (AJOL)

    YSHo

    This study was carried out to evaluate the global scientific production of genome sequencing research to assess the characteristics of the research performances and the research tendencies. Data were obtained from Science Citation Index Expanded database during 1991-2010. Conventional methods including document ...

  18. Sequencing and phylogenetic analysis of Herpes simplex virus type ...

    African Journals Online (AJOL)

    For determination of the genetic relationship of HSV-2 glycoprotein G gene (gG) in Iran with those in other countries, DNA fragment of 1100 bp corresponding to gG from six HSV-2 strains have been isolated from human infected sera samples in Iran, it was amplified in PCR system and was sequenced for determining ...

  19. Molecular cloning and sequence analysis of the cat myostatin gene ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... TEAF. TEA/ATTS DNA binding domain factors. TEAD.01. TEA domain-containing factors, transcriptional enhancer factors 1, 3,. 4, 5. -1129/-1117(-) transcription factor binding sites located in the cat myostatin gene upstream sequence. According to previous works, we focused on analyzing and discussing.

  20. Molecular cloning, expression analysis and sequence prediction of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-28

    Nov 28, 2011 ... Besides, one basic leucine zipper domain (bZIP) in amino acid area from 274 to 337 was found, concurring with the main characteristic of C/EBPs. Homologous comparison of the amino acid sequences from C/EBPβ cloned in this study and those from different species indicated C/EBPβ gene of Qinchuan ...

  1. Sequence and comparative analysis of Leuconostoc dairy bacteriophages

    DEFF Research Database (Denmark)

    Kot, Witold; Hansen, Lars Henrik; Neve, Horst

    2014-01-01

    Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc...

  2. Cloning and sequence analysis of the Antheraea pernyi ...

    Indian Academy of Sciences (India)

    Unknown

    Goldbach R W and Vlak J M 1999 Sequence and organiza- tion of the Spodoptera exigua multicapsid nucleopolyhedro- virus genome; J. Gen. Virol. 80 3289–3304. Jakubowska A, Oers M M, Cory J S, Ziemnick J and Vlak J M. 2005 European Leucoma salicis NPV is closely related to. North American Orgyia pseudotsugata ...

  3. Development of a component Monte Carlo program for accident sequence analysis to apply for reprocessing facility

    International Nuclear Information System (INIS)

    Nomura, Yasushi; Tamaki, Hitoshi

    1997-01-01

    In consideration of application for reprocessing facility, where a variety of causal events such as equipment failure and human error might occur, and the event progression would take place with relatively substantial time delay before getting to the accident stage, a component Monte Carlo program for accident sequence analysis has been developed to pursue chronologically the probabilistic behavior of each component failure and repair in an exact manner. In comparison with analytical formulation and its calculated results, this Monte Carlo technique is shown to predict a reasonable result. Then, taking an example for a sample problem from a German reprocessing facility model, an accident sequence of red-oil explosion in a plutonium evaporator is analyzed to give a comprehensive interpretation about statistic variation range and computer time elapsed for random walk history calculations. Furthermore, to discuss about its applicability for the practical case of plant system with complex component constitution, a possibility of drastic speed-up of computation is shown by parallelization of the computer program. (author)

  4. Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine.

    Science.gov (United States)

    Granberg, F; Bálint, Á; Belák, S

    2016-04-01

    Next-generation sequencing (NGS), also referred to as deep, high-throughput or massively parallel sequencing, is a powerful new tool that can be used for the complex diagnosis and intensive monitoring of infectious disease in veterinary medicine. NGS technologies are also being increasingly used to study the aetiology, genomics, evolution and epidemiology of infectious disease, as well as host-pathogen interactions and other aspects of infection biology. This review briefly summarises recent progress and achievements in this field by first introducing a range of novel techniques and then presenting examples of NGS applications in veterinary infection biology. Various work steps and processes for sampling and sample preparation, sequence analysis and comparative genomics, and improving the accuracy of genomic prediction are discussed, as are bioinformatics requirements. Examples of sequencing-based applications and comparative genomics in veterinary medicine are then provided. This review is based on novel references selected from the literature and on experiences of the World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.

  5. Network Analysis of Sequence-Function Relationships and Exploration of Sequence Space of TEM β-Lactamases.

    Science.gov (United States)

    Zeil, Catharina; Widmann, Michael; Fademrecht, Silvia; Vogel, Constantin; Pleiss, Jürgen

    2016-05-01

    The Lactamase Engineering Database (www.LacED.uni-stuttgart.de) was developed to facilitate the classification and analysis of TEM β-lactamases. The current version contains 474 TEM variants. Two hundred fifty-nine variants form a large scale-free network of highly connected point mutants. The network was divided into three subnetworks which were enriched by single phenotypes: one network with predominantly 2be and two networks with 2br phenotypes. Fifteen positions were found to be highly variable, contributing to the majority of the observed variants. Since it is expected that a considerable fraction of the theoretical sequence space is functional, the currently sequenced 474 variants represent only the tip of the iceberg of functional TEM β-lactamase variants which form a huge natural reservoir of highly interconnected variants. Almost 50% of the variants are part of a quartet. Thus, two single mutations that result in functional enzymes can be combined into a functional protein. Most of these quartets consist of the same phenotype, or the mutations are additive with respect to the phenotype. By predicting quartets from triplets, 3,916 unknown variants were constructed. Eighty-seven variants complement multiple quartets and therefore have a high probability of being functional. The construction of a TEM β-lactamase network and subsequent analyses by clustering and quartet prediction are valuable tools to gain new insights into the viable sequence space of TEM β-lactamases and to predict their phenotype. The highly connected sequence space of TEM β-lactamases is ideally suited to network analysis and demonstrates the strengths of network analysis over tree reconstruction methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  6. XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.

    Science.gov (United States)

    Frank, Daniel N

    2008-10-07

    Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects. XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; 123) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file. XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.

  7. XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data

    Directory of Open Access Journals (Sweden)

    Frank Daniel N

    2008-10-01

    Full Text Available Abstract Background Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects. Results XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI. Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly, perform BLAST (Basic Local Alignment and Search Tool; 123 searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file. Conclusion XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.

  8. Addressing challenges in the production and analysis of illumina sequencing data.

    Science.gov (United States)

    Kircher, Martin; Heyn, Patricia; Kelso, Janet

    2011-07-29

    Advances in DNA sequencing technologies have made it possible to generate large amounts of sequence data very rapidly and at substantially lower cost than capillary sequencing. These new technologies have specific characteristics and limitations that require either consideration during project design, or which must be addressed during data analysis. Specialist skills, both at the laboratory and the computational stages of project design and analysis, are crucial to the generation of high quality data from these new platforms. The Illumina sequencers (including the Genome Analyzers I/II/IIe/IIx and the new HiScan and HiSeq) represent a widely used platform providing parallel readout of several hundred million immobilized sequences using fluorescent-dye reversible-terminator chemistry. Sequencing library quality, sample handling, instrument settings and sequencing chemistry have a strong impact on sequencing run quality. The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses. We discuss here some of the factors that influence the frequency and severity of these problems and provide solutions for circumventing these. Further, we present a set of general principles for good analysis practice that enable problems with sequencing runs to be identified and dealt with.

  9. Addressing challenges in the production and analysis of illumina sequencing data

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2011-07-01

    Full Text Available Abstract Advances in DNA sequencing technologies have made it possible to generate large amounts of sequence data very rapidly and at substantially lower cost than capillary sequencing. These new technologies have specific characteristics and limitations that require either consideration during project design, or which must be addressed during data analysis. Specialist skills, both at the laboratory and the computational stages of project design and analysis, are crucial to the generation of high quality data from these new platforms. The Illumina sequencers (including the Genome Analyzers I/II/IIe/IIx and the new HiScan and HiSeq represent a widely used platform providing parallel readout of several hundred million immobilized sequences using fluorescent-dye reversible-terminator chemistry. Sequencing library quality, sample handling, instrument settings and sequencing chemistry have a strong impact on sequencing run quality. The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses. We discuss here some of the factors that influence the frequency and severity of these problems and provide solutions for circumventing these. Further, we present a set of general principles for good analysis practice that enable problems with sequencing runs to be identified and dealt with.

  10. Behavior analysis and the growth of behavioral pharmacology

    OpenAIRE

    Laties, Victor G.

    2003-01-01

    Psychologists, particularly those influenced by the work of B. F. Skinner, played a major part in the development of behavioral pharmacology in the 1950s and 1960s. Revolutionary changes in pharmacology and psychiatry, including the discovery of powerful therapeutic agents such as chlorpromazine and reserpine, had produced a surge of interest in drug research. Pharmaceutical companies began hiring psychologists with operant conditioning backgrounds so as to compete successfully in the search ...

  11. Dynamic Behavior Analysis via Structured Rank Minimization

    NARCIS (Netherlands)

    Georgakis, Christos; Panagakis, Yannis; Pantic, Maja

    2017-01-01

    Human behavior and affect is inherently a dynamic phenomenon involving temporal evolution of patterns manifested through a multiplicity of non-verbal behavioral cues including facial expressions, body postures and gestures, and vocal outbursts. A natural assumption for human behavior modeling is

  12. The sequence and analysis of duplication rich human chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J; Han, C; Gordon, L A; Terry, A; Prabhakar, S; She, X; Xie, G; Hellsten, U; Chan, Y M; Altherr, M; Couronne, O; Aerts, A; Bajorek, E; Black, S; Blumer, H; Branscomb, E; Brown, N; Bruno, W J; Buckingham, J; Callen, D F; Campbell, C S; Campbell, M L; Campbell, E W; Caoile, C; Challacombe, J F; Chasteen, L A; Chertkov, O; Chi, H C; Christensen, M; Clark, L M; Cohn, J D; Denys, M; Detter, J C; Dickson, M; Dimitrijevic-Bussod, M; Escobar, J; Fawcett, J J; Flowers, D; Fotopulos, D; Glavina, T; Gomez, M; Gonzales, E; Goodstein, D; Goodwin, L A; Grady, D L; Grigoriev, I; Groza, M; Hammon, N; Hawkins, T; Haydu, L; Hildebrand, C E; Huang, W; Israni, S; Jett, J; Jewett, P B; Kadner, K; Kimball, H; Kobayashi, A; Krawczyk, M; Leyba, T; Longmire, J L; Lopez, F; Lou, Y; Lowry, S; Ludeman, T; Manohar, C F; Mark, G A; McMurray, K L; Meincke, L J; Morgan, J; Moyzis, R K; Mundt, M O; Munk, A C; Nandkeshwar, R D; Pitluck, S; Pollard, M; Predki, P; Parson-Quintana, B; Ramirez, L; Rash, S; Retterer, J; Ricke, D O; Robinson, D; Rodriguez, A; Salamov, A; Saunders, E H; Scott, D; Shough, T; Stallings, R L; Stalvey, M; Sutherland, R D; Tapia, R; Tesmer, J G; Thayer, N; Thompson, L S; Tice, H; Torney, D C; Tran-Gyamfi, M; Tsai, M; Ulanovsky, L E; Ustaszewska, A; Vo, N; White, P S; Williams, A L; Wills, P L; Wu, J; Wu, K; Yang, J; DeJong, P; Bruce, D; Doggett, N A; Deaven, L; Schmutz, J; Grimwood, J; Richardson, P; Rokhsar, D S; Eichler, E E; Gilna, P; Lucas, S M; Myers, R M; Rubin, E M; Pennacchio, L A

    2005-04-06

    Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes, and 3 RNA pseudogenes. These genes include metallothionein, cadherin, and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. While the segmental duplications of chromosome 16 are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events likely to have had an impact on the evolution of primates and human disease susceptibility.

  13. mitoSAVE: mitochondrial sequence analysis of variants in Excel.

    Science.gov (United States)

    King, Jonathan L; Sajantila, Antti; Budowle, Bruce

    2014-09-01

    The mitochondrial genome (mtGenome) contains genetic information amenable to numerous applications such as medical research, population and evolutionary studies, and human identity testing. However, inconsistent nomenclature assignment makes haplotype comparison difficult and can lead to false exclusion of potentially useful profiles. Massively Parallel Sequencing (MPS) is a platform for sequencing large datasets and potentially whole populations with relative ease. However, the data generated are not easily parsed and interpreted. With this in mind, mitoSAVE has been developed to enable fast conversion of Variant Call Format (VCF) files. mitoSAVE is an Excel-based workbook that converts data within the VCF into mtDNA haplotypes using phylogenetically-established nomenclature as well as rule-based alignments consistent with current forensic standards. mitoSAVE is formatted for human mitochondrial genome; however, it can easily be adapted to support other reasonably small genomes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  14. Sequence analysis of the Legionella micdadei groELS operon

    DEFF Research Database (Denmark)

    Hindersson, P; Høiby, N; Bangsborg, Jette Marie

    1991-01-01

    A 2.7 kb DNA fragment encoding the 60 kDa common antigen (CA) and a 13 kDa protein of Legionella micdadei was sequenced. Two open reading frames of 57,677 and 10,456 Da were identified, corresponding to the heat shock proteins GroEL and GroES, respectively. Typical -35, -10, and Shine-Dalgarno heat...

  15. Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants.

    Science.gov (United States)

    Ayliffe, M A; Scott, N S; Timmis, J N

    1998-06-01

    A wide-ranging examination of plastid (pt)DNA sequence homologies within higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion with methylation-sensitive restriction enzymes and Southern analysis was used to distinguish plastid and nuclear DNA in order to assess the extent of variability of promiscuous sequences within and between plant species. Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum (tobacco), and Chenopodium quinoa, showed homogenity of these sequences, while intraspecific sequence variation was observed among different cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum aestivum (wheat). Hypervariability of plastid sequence homologies was identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta vulgaris (beet), in which individual plants were shown to possess a unique spectrum of nuclear sequences with ptDNA homology. This hypervariability apparently extended to somatic variation in B. vulgaris. No sequences with ptDNA homology were identified by this method in the nuclear genome of Arabidopsis thaliana.

  16. OPTSDNA: Performance evaluation of an efficient distributed bioinformatics system for DNA sequence analysis.

    Science.gov (United States)

    Khan, Mohammad Ibrahim; Sheel, Chotan

    2013-01-01

    Storage of sequence data is a big concern as the amount of data generated is exponential in nature at several locations. Therefore, there is a need to develop techniques to store data using compression algorithm. Here we describe optimal storage algorithm (OPTSDNA) for storing large amount of DNA sequences of varying length. This paper provides performance analysis of optimal storage algorithm (OPTSDNA) of a distributed bioinformatics computing system for analysis of DNA sequences. OPTSDNA algorithm is used for storing various sizes of DNA sequences into database. DNA sequences of different lengths were stored by using this algorithm. These input DNA sequences are varied in size from very small to very large. Storage size is calculated by this algorithm. Response time is also calculated in this work. The efficiency and performance of the algorithm is high (in size calculation with percentage) when compared with other known with sequential approach.

  17. Functions of Research in Radical Behaviorism for the Further Development of Behavior Analysis

    Science.gov (United States)

    Leigland, Sam

    2010-01-01

    The experimental analysis of behavior began as an inductively oriented, empirically based scientific field. As the field grew, its distinctive system of science--radical behaviorism--grew with it. The continuing growth of the empirical base of the field has been accompanied by the growth of the literature on radical behaviorism and its…

  18. A model of the statistical power of comparative genome sequence analysis.

    OpenAIRE

    Sean R Eddy

    2005-01-01

    Comparative genome sequence analysis is powerful, but sequencing genomes is expensive. It is desirable to be able to predict how many genomes are needed for comparative genomics, and at what evolutionary distances. Here I describe a simple mathematical model for the common problem of identifying conserved sequences. The model leads to some useful rules of thumb. For a given evolutionary distance, the number of comparative genomes needed for a constant level of statistical stringency in identi...

  19. MiSeq: A Next Generation Sequencing Platform for Genomic Analysis.

    Science.gov (United States)

    Ravi, Rupesh Kanchi; Walton, Kendra; Khosroheidari, Mahdieh

    2018-01-01

    MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

  20. Learning and production of movement sequences: Behavioral, neurophysiological, and modelling perspectives.

    NARCIS (Netherlands)

    Rhodes, Bradley J.; Bullock, Daniel; Verwey, Willem B.; Averbeck, Bruno B.; Page, Michael P.A.

    2004-01-01

    A wave of recent behavioral studies has generated a new wealth of parametric observations about serial order behavior. What was a trickle of neurophysiological studies has grown to a steady stream of probes of neural sites and mechanisms underlying sequential behavior. Moreover, simulation models of

  1. Deep Sequencing Analysis of the Ixodes ricinus Haemocytome.

    Directory of Open Access Journals (Sweden)

    Michalis Kotsyfakis

    2015-05-01

    Full Text Available Ixodes ricinus is the main tick vector of the microbes that cause Lyme disease and tick-borne encephalitis in Europe. Pathogens transmitted by ticks have to overcome innate immunity barriers present in tick tissues, including midgut, salivary glands epithelia and the hemocoel. Molecularly, invertebrate immunity is initiated when pathogen recognition molecules trigger serum or cellular signalling cascades leading to the production of antimicrobials, pathogen opsonization and phagocytosis. We presently aimed at identifying hemocyte transcripts from semi-engorged female I. ricinus ticks by mass sequencing a hemocyte cDNA library and annotating immune-related transcripts based on their hemocyte abundance as well as their ubiquitous distribution.De novo assembly of 926,596 pyrosequence reads plus 49,328,982 Illumina reads (148 nt length from a hemocyte library, together with over 189 million Illumina reads from salivary gland and midgut libraries, generated 15,716 extracted coding sequences (CDS; these are displayed in an annotated hyperlinked spreadsheet format. Read mapping allowed the identification and annotation of tissue-enriched transcripts. A total of 327 transcripts were found significantly over expressed in the hemocyte libraries, including those coding for scavenger receptors, antimicrobial peptides, pathogen recognition proteins, proteases and protease inhibitors. Vitellogenin and lipid metabolism transcription enrichment suggests fat body components. We additionally annotated ubiquitously distributed transcripts associated with immune function, including immune-associated signal transduction proteins and transcription factors, including the STAT transcription factor.This is the first systems biology approach to describe the genes expressed in the haemocytes of this neglected disease vector. A total of 2,860 coding sequences were deposited to GenBank, increasing to 27,547 the number so far deposited by our previous transcriptome studies

  2. A Markovian analysis of bacterial genome sequence constraints

    Directory of Open Access Journals (Sweden)

    Aaron D. Skewes

    2013-08-01

    Full Text Available The arrangement of nucleotides within a bacterial chromosome is influenced by numerous factors. The degeneracy of the third codon within each reading frame allows some flexibility of nucleotide selection; however, the third nucleotide in the triplet of each codon is at least partly determined by the preceding two. This is most evident in organisms with a strong G + C bias, as the degenerate codon must contribute disproportionately to maintaining that bias. Therefore, a correlation exists between the first two nucleotides and the third in all open reading frames. If the arrangement of nucleotides in a bacterial chromosome is represented as a Markov process, we would expect that the correlation would be completely captured by a second-order Markov model and an increase in the order of the model (e.g., third-, fourth-…order would not capture any additional uncertainty in the process. In this manuscript, we present the results of a comprehensive study of the Markov property that exists in the DNA sequences of 906 bacterial chromosomes. All of the 906 bacterial chromosomes studied exhibit a statistically significant Markov property that extends beyond second-order, and therefore cannot be fully explained by codon usage. An unrooted tree containing all 906 bacterial chromosomes based on their transition probability matrices of third-order shares ∼25% similarity to a tree based on sequence homologies of 16S rRNA sequences. This congruence to the 16S rRNA tree is greater than for trees based on lower-order models (e.g., second-order, and higher-order models result in diminishing improvements in congruence. A nucleotide correlation most likely exists within every bacterial chromosome that extends past three nucleotides. This correlation places significant limits on the number of nucleotide sequences that can represent probable bacterial chromosomes. Transition matrix usage is largely conserved by taxa, indicating that this property is likely

  3. Analysis of next-generation sequencing data using Galaxy.

    Science.gov (United States)

    Blankenberg, Daniel; Hillman-Jackson, Jennifer

    2014-01-01

    The extraordinary throughput of next-generation sequencing (NGS) technology is outpacing our ability to analyze and interpret the data. This chapter will focus on practical informatics methods, strategies, and software tools for transforming NGS data into usable information through the use of a web-based platform, Galaxy. The Galaxy interface is explored through several different types of example analyses. Instructions for running one's own Galaxy server on local hardware or on cloud computing resources are provided. Installing new tools into a personal Galaxy instance is also demonstrated.

  4. Analysis of consumer behavior at chocolate purchase

    Directory of Open Access Journals (Sweden)

    Dagmar Kozelová

    2014-02-01

    Full Text Available At food purchase consumer is affected by several factors. In this work analysis of consumer behavior at chocolate purchase was performed involving 277 respondents. Statistical testing of results was performed by Chi - Square statistic, correlations have been tested with use of the Cramer's coefficient. It was found, that 86% of respondents consume chocolate. Factors affecting respondents at purchase were recommendations of friends, acquaintances (32%, brand of chocolate (24%, price (16%, personal experience (12%, health restrictions and allergies (11%. Less important factors when choosing chocolates are flavor (4%, nutritional quality (3%, country of origin (2% and chocolate packaging (1%. In the consumption of chocolate moderate correlation among various categories of economic activity of respondents was confirmed. Chocolate was consumed mainly by respondents whose monthly income ranges from 801 to 1001 €. We found that consumers prefer milk chocolate followed by dark and white at the end. In terms of gender the most commonly was chocolate consumed by women, once to three times a week. The same frequency of chocolate consumption dominates at the categories of students and employee. Expenses frequently spent to buy chocolates were from 1-3 € per week by young people (18-23 years and middle age generation of people (46-55 years. Normal 0 21 false false false CS JA X-NONE

  5. The spread of behavior analysis to the applied fields 1

    OpenAIRE

    Fraley, Lawrence E.

    1981-01-01

    This paper reviews the status of applied behavioral science as it exists in the various behavioral fields and considers the role of the Association for Behavior Analysis in serving those fields. The confounding effects of the traditions of psychology are discussed. Relevant issues are exemplified in the fields of law, communications, psychology, and education, but broader generalization is implied.

  6. Context, Cognition, and Biology in Applied Behavior Analysis.

    Science.gov (United States)

    Morris, Edward K.

    Behavior analysts are having their professional identities challenged by the roles that cognition and biology are said to play in the conduct and outcome of applied behavior analysis and behavior therapy. For cogniphiliacs, cognition and biology are central to their interventions because cognition and biology are said to reflect various processes,…

  7. A retrospective appreciation of Willard Day's contributions to radical behaviorism and the analysis of verbal behavior

    Science.gov (United States)

    Moore, Jay

    1991-01-01

    Willard Day's contributions to radical behaviorism are grouped under three headings: (a) an emphasis on the distinction between radical and methodological behaviorism; (b) an emphasis on the interpretation, rather than the prediction and control, of behavior; and (c) an emphasis on the analysis of verbal behavior as a natural, ongoing phenomenon. The paper suggests that the contributions above are listed in ascending order of significance. PMID:22477632

  8. Behavioral Research Data Analysis with R

    CERN Document Server

    Li, Yuelin

    2012-01-01

    This book is written for behavioral scientists who want to consider adding R to their existing set of statistical tools, or want to switch to R as their main computation tool. The authors aim primarily to help practitioners of behavioral research make the transition to R. The focus is to provide practical advice on some of the widely-used statistical methods in behavioral research, using a set of notes and annotated examples. This book will also help beginners learn more about statistics and behavioral research. These are statistical techniques used by psychologists who do research on human su

  9. Multinomial analysis of behavior: statistical methods.

    Science.gov (United States)

    Koster, Jeremy; McElreath, Richard

    2017-01-01

    Behavioral ecologists frequently use observational methods, such as instantaneous scan sampling, to record the behavior of animals at discrete moments in time. We develop and apply multilevel, multinomial logistic regression models for analyzing such data. These statistical methods correspond to the multinomial character of the response variable while also accounting for the repeated observations of individuals that characterize behavioral datasets. Correlated random effects potentially reveal individual-level trade-offs across behaviors, allowing for models that reveal the extent to which individuals who regularly engage in one behavior also exhibit relatively more or less of another behavior. Using an example dataset, we demonstrate the estimation of these models using Hamiltonian Monte Carlo algorithms, as implemented in the RStan package in the R statistical environment. The supplemental files include a coding script and data that demonstrate auxiliary functions to prepare the data, estimate the models, summarize the posterior samples, and generate figures that display model predictions. We discuss possible extensions to our approach, including models with random slopes to allow individual-level behavioral strategies to vary over time and the need for models that account for temporal autocorrelation. These models can potentially be applied to a broad class of statistical analyses by behavioral ecologists, focusing on other polytomous response variables, such as behavior, habitat choice, or emotional states.

  10. In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak; Minovitsky, Simon; Visel,Axel; Dubchak, Inna; Holt, Amy; Lewis, Keith D.; Plajzer-Frick, Ingrid; Akiyama, Jennifer; De Val, Sarah; Afzal, Veena; Black, Brian L.; Couronne, Olivier; Eisen, Michael B.; Rubin, Edward M.

    2006-02-01

    The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of the human genome.

  11. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    NARCIS (Netherlands)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F.; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We

  12. Sequence analysis of the mitochondrial genomes from Dutch pedigrees with Leber hereditary optic neuropathy

    NARCIS (Netherlands)

    Howell, Neil; Oostra, Roelof-Jan; Bolhuis, Piet A.; Spruijt, Liesbeth; Clarke, Lorne A.; Mackey, David A.; Preston, Gwen; Herrnstadt, Corinna

    2003-01-01

    The complete mitochondrial DNA (mtDNA) sequences for 63 Dutch pedigrees with Leber hereditary optic neuropathy (LHON) were determined, 56 of which carried one of the classic LHON mutations at nucleotide (nt) 3460, 11778, or 14484. Analysis of these sequences indicated that there were several

  13. High-Throughput Analysis of DNA Break-Induced Chromosome Rearrangements by Amplicon Sequencing.

    Science.gov (United States)

    Brown, Alexander J; Al-Soodani, Aneesa T; Saul, Miles; Her, Stephanie; Garcia, Juan C; Ramsden, Dale A; Her, Chengtao; Roberts, Steven A

    2018-01-01

    The mechanistic understanding of how DNA double-strand breaks (DSB) are repaired is rapidly advancing in part due to the advent of inducible site-specific break model systems as well as the employment of next-generation sequencing (NGS) technologies to sequence repair junctions at high depth. Unfortunately, the sheer volume of data produced by these methods makes it difficult to analyze the structure of repair junctions manually or with other general-purpose software. Here, we describe methods to produce amplicon libraries of DSB repair junctions for sequencing, to map the sequencing reads, and then to use a robust, custom python script, Hi-FiBR, to analyze the sequence structure of mapped reads. The Hi-FiBR analysis processes large data sets quickly and provides information such as number and type of repair events, size of deletion, size of insertion and inserted sequence, microhomology usage, and whether mismatches are due to sequencing error or biological effect. The analysis also corrects for common alignment errors generated by sequencing read mapping tools, allowing high-throughput analysis of DSB break repair fidelity to be accurately conducted regardless of which suite of NGS analysis software is available. © 2018 Elsevier Inc. All rights reserved.

  14. Cloning and sequence analysis of H. contortus HC58cDNA gene ...

    African Journals Online (AJOL)

    Phylogenetic analysis revealed close evolutionary proximity of the protein sequence to counterpart sequences in the cathepsin B like proteases, suggesting that HC58cDNA was a member of the papain family. Keywords:Haemonchus contortus, HC58cDNA, cathepsin B like protease, papain family. Kenya Veterinarian Vol.

  15. Functional Analysis of Behavior and Its Clinical Application

    Directory of Open Access Journals (Sweden)

    Kaasim Fatih Yavuz

    2017-08-01

    Full Text Available Many approaches to psychology and psychiatry have tried to explain behaviors etiologically. Functional contextualism, followed by radical behaviorism, and its application functional analysis of behavior can be considered as an alternative to mainstream approaches. Functional analysis, in analyzing a particular behavior, takes into account the context in which behavior itself present and suggests that it focus on contextual factors that influence behavior in the direction of learning principles. These factors are environment in which a particular behavior occurs, internal/external stimuli, and consequences of that behavior. In this review, we will first explain the topographic analysis that focuses on the shape and features of behavior and the structural analysis that reveals the time, duration, frequency, intensity, deficit or excess, and will discuss the existing differences between these and functional analysis. Then the learning principles, habituation, respondent conditioning, operant conditioning, social learning and derived relational response will be briefly explained. And after functional analysis of behavior and its clinical examples will be focused. Taken together, these three analyzes can create an objective and useful background in clinical practice and research processes –independent of theoretical approaches. [JCBPR 2017; 6(2.000: 88-94

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

    Directory of Open Access Journals (Sweden)

    Wang Jintu

    2011-04-01

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

  17. Negative reinforcement in applied behavior analysis: an emerging technology.

    OpenAIRE

    Iwata, B A

    1987-01-01

    Although the effects of negative reinforcement on human behavior have been studied for a number of years, a comprehensive body of applied research does not exist at this time. This article describes three aspects of negative reinforcement as it relates to applied behavior analysis: behavior acquired or maintained through negative reinforcement, the treatment of negatively reinforced behavior, and negative reinforcement as therapy. A consideration of research currently being done in these area...

  18. The sequence and analysis of duplication rich human chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-08-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  19. The Sequence and Analysis of Duplication Rich Human Chromosome 16

    Science.gov (United States)

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-01-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  20. Massively parallel sequencing and analysis of the Necator americanus transcriptome.

    Directory of Open Access Journals (Sweden)

    Cinzia Cantacessi

    2010-05-01

    Full Text Available The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses.A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%, proteinase inhibitors (7.8% or calcium-binding EF-hand proteins (6.7%. Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%, oxidative phosphorylation (63% and/or proteases (60%; most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins or amino acid metabolism (e.g., asparagine t-RNA synthetase.This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human

  1. Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.

    Science.gov (United States)

    Petkovic, Sonja; Badelt, Stefan; Block, Stephan; Flamm, Christoph; Delcea, Mihaela; Hofacker, Ivo; Müller, Sabine

    2015-07-01

    Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to the emergence of functional diversity and increasing complexity of regulatory RNAs in early life. We have previously engineered a variant of the hairpin ribozyme that shows how ribozymes may have circularized or extended their own length by forming concatemers. Using the Vienna RNA package, we now optimized this hairpin ribozyme variant and selected four different RNA sequences that were expected to circularize more efficiently or form longer concatemers upon transcription. (Two-dimensional) PAGE analysis confirms that (i) all four selected ribozymes are catalytically active and (ii) high yields of cyclic species are obtained. AFM imaging in combination with RNA structure prediction enabled us to calculate the distributions of monomers and self-concatenated dimers and trimers. Our results show that computationally optimized molecules do form reasonable amounts of trimers, which has not been observed for the original system so far, and we demonstrate that the combination of theoretical prediction, biochemical and physical analysis is a promising approach toward accurate prediction of ribozyme behavior and design of ribozymes with predefined functions. © 2015 Petkovic et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  2. Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering

    DEFF Research Database (Denmark)

    Busk, Peter Kamp

    2017-01-01

    Large collections of protein sequences with divergent sequences are tedious to analyze for understanding their phylogenetic or structure-function relation. Peptide Pattern Recognition is an algorithm that was developed to facilitate this task but the previous version does only allow a limited...... number of sequences as input. I implemented Peptide Pattern Recognition as a multithread software designed to handle large numbers of sequences and perform analysis in a reasonable time frame. Benchmarking showed that the new implementation of Peptide Pattern Recognition is twenty times faster than...... the previous implementation on a small protein collection with 673 MAP kinase sequences. In addition, the new implementation could analyze a large protein collection with 48,570 Glycosyl Transferase family 20 sequences without reaching its upper limit on a desktop computer. Peptide Pattern Recognition...

  3. Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane

    Science.gov (United States)

    Vettore, André L.; da Silva, Felipe R.; Kemper, Edson L.; Souza, Glaucia M.; da Silva, Aline M.; Ferro, Maria Inês T.; Henrique-Silva, Flavio; Giglioti, Éder A.; Lemos, Manoel V.F.; Coutinho, Luiz L.; Nobrega, Marina P.; Carrer, Helaine; França, Suzelei C.; Bacci, Maurício; Goldman, Maria Helena S.; Gomes, Suely L.; Nunes, Luiz R.; Camargo, Luis E.A.; Siqueira, Walter J.; Van Sluys, Marie-Anne; Thiemann, Otavio H.; Kuramae, Eiko E.; Santelli, Roberto V.; Marino, Celso L.; Targon, Maria L.P.N.; Ferro, Jesus A.; Silveira, Henrique C.S.; Marini, Danyelle C.; Lemos, Eliana G.M.; Monteiro-Vitorello, Claudia B.; Tambor, José H.M.; Carraro, Dirce M.; Roberto, Patrícia G.; Martins, Vanderlei G.; Goldman, Gustavo H.; de Oliveira, Regina C.; Truffi, Daniela; Colombo, Carlos A.; Rossi, Magdalena; de Araujo, Paula G.; Sculaccio, Susana A.; Angella, Aline; Lima, Marleide M.A.; de Rosa, Vicente E.; Siviero, Fábio; Coscrato, Virginia E.; Machado, Marcos A.; Grivet, Laurent; Di Mauro, Sonia M.Z.; Nobrega, Francisco G.; Menck, Carlos F.M.; Braga, Marilia D.V.; Telles, Guilherme P.; Cara, Frank A.A.; Pedrosa, Guilherme; Meidanis, João; Arruda, Paulo

    2003-01-01

    To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged. PMID:14613979

  4. Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.

    Science.gov (United States)

    Vettore, André L; da Silva, Felipe R; Kemper, Edson L; Souza, Glaucia M; da Silva, Aline M; Ferro, Maria Inês T; Henrique-Silva, Flavio; Giglioti, Eder A; Lemos, Manoel V F; Coutinho, Luiz L; Nobrega, Marina P; Carrer, Helaine; França, Suzelei C; Bacci Júnior, Mauricio; Goldman, Maria Helena S; Gomes, Suely L; Nunes, Luiz R; Camargo, Luis E A; Siqueira, Walter J; Van Sluys, Marie-Anne; Thiemann, Otavio H; Kuramae, Eiko E; Santelli, Roberto V; Marino, Celso L; Targon, Maria L P N; Ferro, Jesus A; Silveira, Henrique C S; Marini, Danyelle C; Lemos, Eliana G M; Monteiro-Vitorello, Claudia B; Tambor, José H M; Carraro, Dirce M; Roberto, Patrícia G; Martins, Vanderlei G; Goldman, Gustavo H; de Oliveira, Regina C; Truffi, Daniela; Colombo, Carlos A; Rossi, Magdalena; de Araujo, Paula G; Sculaccio, Susana A; Angella, Aline; Lima, Marleide M A; de Rosa Júnior, Vicente E; Siviero, Fábio; Coscrato, Virginia E; Machado, Marcos A; Grivet, Laurent; Di Mauro, Sonia M Z; Nobrega, Francisco G; Menck, Carlos F M; Braga, Marilia D V; Telles, Guilherme P; Cara, Frank A A; Pedrosa, Guilherme; Meidanis, João; Arruda, Paulo

    2003-12-01

    To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.

  5. Vocational behavior analysis in psychology students

    Directory of Open Access Journals (Sweden)

    María Estrella LÓPEZ PÉREZ

    2014-06-01

    Full Text Available Introduction. The European Higher Education Area (EHEA is supporting gain relevance of vocational guidance into the frame of University Education. In order to a better planning of this guidance we need to know his contents evaluating student vocational interests of each center. The aim of the study is to analyze the indicators of Psychology students vocational behavior and his evolution and comparing those results with data of another students population. Methodology. The 329 psychology students participants from the University of Salamanca (248 in the second year and 81 in the fifth answered the questionnaire of university biodata (Rocabert, 2005. In all cases we took a significance level of ? = 0.05 carrying out samples comparison tests using U de Mann-Whitney techniques and contingency analysis. Results: The present study found significant differences between second and fifth psychology grade students and with general university population data collected by Rocabert, Descals and Gomez (2007. In general, psychology students begin their degrees with a high level interest and motivated; they are making decisions based on the academic specialty they want to work in. However, for last year students group (fith year students we detected a lower satisfaction in their studies, more difficulties in deciding what they want to do and a greater demand of information in order to choose the advisablest option for them. Conclusions. Despite the high motivation of psychology students, the nearer is his integration into the job market the higher is the need of guidance to help them to take decisions concerning specialization or the professional world.

  6. Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses.

    Science.gov (United States)

    Yanagisawa, Hironobu; Tomita, Reiko; Katsu, Koji; Uehara, Takuya; Atsumi, Go; Tateda, Chika; Kobayashi, Kappei; Sekine, Ken-Taro

    2016-03-07

    The presence of high molecular weight double-stranded RNA (dsRNA) within plant cells is an indicator of infection with RNA viruses as these possess genomic or replicative dsRNA. DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing) analysis has been shown to be capable of detecting unknown viruses. We postulated that a combination of DECS analysis and next-generation sequencing (NGS) would improve detection efficiency and usability of the technique. Here, we describe a model case in which we efficiently detected the presumed genome sequence of Blueberry shoestring virus (BSSV), a member of the genus Sobemovirus, which has not so far been reported. dsRNAs were isolated from BSSV-infected blueberry plants using the dsRNA-binding protein, reverse-transcribed, amplified, and sequenced using NGS. A contig of 4,020 nucleotides (nt) that shared similarities with sequences from other Sobemovirus species was obtained as a candidate of the BSSV genomic sequence. Reverse transcription (RT)-PCR primer sets based on sequences from this contig enabled the detection of BSSV in all BSSV-infected plants tested but not in healthy controls. A recombinant protein encoded by the putative coat protein gene was bound by the BSSV-antibody, indicating that the candidate sequence was that of BSSV itself. Our results suggest that a combination of DECS analysis and NGS, designated here as "DECS-C," is a powerful method for detecting novel plant viruses.

  7. Data Analysis of Sequences and qPCR for Microbial Communities during Algal Blooms

    Science.gov (United States)

    A training opportunity is open to a highly microbial-research-motivated student to conduct sequence analysis, explore novel genes and metabolic pathways, validate resultant findings using qPCR/RT-qPCR and summarize the findings

  8. On Misconceptions about Behavior Analysis among University Students and Teachers

    Science.gov (United States)

    Arntzen, Erik; Lokke, Jon; Lokke, Gunn; Eilertsen, Dag-Erik

    2010-01-01

    Students frequently show misconceptions regarding scientific psychology in general and basic concepts in behavior analysis in particular. We wanted to replicate the study by Lamal (1995) and to expand the study by including some additional statements. In the current study, the focus was on misconceptions about behavior analysis held by…

  9. Seismically induced accident sequence analysis of the advanced test reactor

    International Nuclear Information System (INIS)

    Khericha, S.T.; Henry, D.M.; Ravindra, M.K.; Hashimoto, P.S.; Griffin, M.J.; Tong, W.H.; Nafday, A.M.

    1991-01-01

    A seismic probabilistic risk assessment (PRA) was performed for the Department of Energy (DOE) Advanced Test Reactor (ATR) as part of the external events analysis. The risk from seismic events to the fuel in the core and in the fuel storage canal was evaluated. The key elements of this paper are the integration of seismically induced internal flood and internal fire, and the modeling of human error rates as a function of the magnitude of earthquake. The systems analysis was performed by EG ampersand G Idaho, Inc. and the fragility analysis and quantification were performed by EQE International, Inc. (EQE)

  10. Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer

    Science.gov (United States)

    2015-09-01

    Assay Kits respectively on the Qubit 2.0 Fluorometer (Life Technologies). The BioRad Experion Automated Electrophoresis System RNA kit was used to...AWARD NUMBER: W81XWH-14-1-0080 TITLE: Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer. PRINCIPAL INVESTIGATOR...Aug 2015 4. TITLE AND SUBTITLE Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer. 5a. CONTRACT NUMBER 5b. GRANT

  11. Microscopic Analysis and Modeling of Airport Surface Sequencing, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Although a number of airportal surface models exist and have been successfully used for analysis of airportal operations, only recently has it become possible to...

  12. Microscopic Analysis and Modeling of Airport Surface Sequencing, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The complexity and interdependence of operations on the airport surface motivate the need for a comprehensive and detailed, yet flexible and validated analysis and...

  13. BioMatriX: Sequence analysis, structure visualization, phylogenetics ...

    African Journals Online (AJOL)

    bmx-biomatrix.blogspot.com) developed for biological science community to augment scientific research regarding genomics, proteomics, phylogenetics and linkage analysis in one platform. BioMatriX offers multi-functional services to perform ...

  14. Secure distributed genome analysis for GWAS and sequence comparison computation

    Science.gov (United States)

    2015-01-01

    Background The rapid increase in the availability and volume of genomic data makes significant advances in biomedical research possible, but sharing of genomic data poses challenges due to the highly sensitive nature of such data. To address the challenges, a competition for secure distributed processing of genomic data was organized by the iDASH research center. Methods In this work we propose techniques for securing computation with real-life genomic data for minor allele frequency and chi-squared statistics computation, as well as distance computation between two genomic sequences, as specified by the iDASH competition tasks. We put forward novel optimizations, including a generalization of a version of mergesort, which might be of independent interest. Results We provide implementation results of our techniques based on secret sharing that demonstrate practicality of the suggested protocols and also report on performance improvements due to our optimization techniques. Conclusions This work describes our techniques, findings, and experimental results developed and obtained as part of iDASH 2015 research competition to secure real-life genomic computations and shows feasibility of securely computing with genomic data in practice. PMID:26733307

  15. Sequence analysis of L RNA of Lassa virus

    International Nuclear Information System (INIS)

    Vieth, Simon; Torda, Andrew E.; Asper, Marcel; Schmitz, Herbert; Guenther, Stephan

    2004-01-01

    The L RNA of three Lassa virus strains originating from Nigeria, Ghana/Ivory Coast, and Sierra Leone was sequenced and the data subjected to structure predictions and phylogenetic analyses. The L gene products had 2218-2221 residues, diverged by 18% at the amino acid level, and contained several conserved regions. Only one region of 504 residues (positions 1043-1546) could be assigned a function, namely that of an RNA polymerase. Secondary structure predictions suggest that this domain is very similar to RNA-dependent RNA polymerases of known structure encoded by plus-strand RNA viruses, permitting a model to be built. Outside the polymerase region, there is little structural data, except for regions of strong alpha-helical content and probably a coiled-coil domain at the N terminus. No evidence for reassortment or recombination during Lassa virus evolution was found. The secondary structure-assisted alignment of the RNA polymerase region permitted a reliable reconstruction of the phylogeny of all negative-strand RNA viruses, indicating that Arenaviridae are most closely related to Nairoviruses. In conclusion, the data provide a basis for structural and functional characterization of the Lassa virus L protein and reveal new insights into the phylogeny of negative-strand RNA viruses

  16. Robust Recognition of Specific Human Behaviors in Crowded Surveillance Video Sequences

    Directory of Open Access Journals (Sweden)

    Shin'ichi Satoh

    2010-01-01

    Full Text Available We describe a method that can detect specific human behaviors even in crowded surveillance video scenes. Our developed system recognizes specific behaviors based on the trajectories created by detecting and tracking people in a video. It detects people using an HOG descriptor and SVM classifier, and it tracks the regions by calculating the two-dimensional color histograms. Our system identifies several specific human behaviors, such as running and meeting, by analyzing the similarities to the reference trajectory of each behavior. Verification techniques such as backward tracking and calculating optical flows contributed to robust recognition. Comparative experiments showed that our system could track people more robustly than a baseline tracking algorithm even in crowded scenes. Our system precisely identified specific behaviors and achieved first place for detecting running people in the TRECVID 2009 Surveillance Event Detection Task.

  17. Control of automated behavior: insights from the discrete sequence production task

    Science.gov (United States)

    Abrahamse, Elger L.; Ruitenberg, Marit F. L.; de Kleine, Elian; Verwey, Willem B.

    2013-01-01

    Work with the discrete sequence production (DSP) task has provided a substantial literature on discrete sequencing skill over the last decades. The purpose of the current article is to provide a comprehensive overview of this literature and of the theoretical progress that it has prompted. We start with a description of the DSP task and the phenomena that are typically observed with it. Then we propose a cognitive model, the dual processor model (DPM), which explains performance of (skilled) discrete key-press sequences. Key features of this model are the distinction between a cognitive processor and a motor system (i.e., motor buffer and motor processor), the interplay between these two processing systems, and the possibility to execute familiar sequences in two different execution modes. We further discuss how this model relates to several related sequence skill research paradigms and models, and we outline outstanding questions for future research throughout the paper. We conclude by sketching a tentative neural implementation of the DPM. PMID:23515430

  18. Discerning the Fatigue Crack Growth Behavior of API X65 Steels Under Sequence Loading

    Directory of Open Access Journals (Sweden)

    N. I. I. Mansor

    Full Text Available Abstract This paper presents the effect of sequence loading on fatigue crack growth of API X65 steel tested in room temperature. Most of pipeline steels are subjected to wide spectrum of loading during the length of service. Influence of load history effect can cause a trickier assessment to the fatigue behaviour. The objective of this study is to determine the fatigue crack growth behaviour under sequence loading. The material used in this study is X65 steel grade, broadly used in transporting the oil and gas. The constant amplitude loading under mode-I loading and stress ratio of 0.1 and 0.7 are investigate. The effects of sequence load are presents by the two-level block loading. The retardation effect is more intense for block sequence loading. At least about 9.7x104 delayed numbers of cycles was observed which is two times longer compared to constant amplitude loading. The load sequence was suggested affected by retardation consequently delayed the crack growth. It was further observed an increase of overload load ratio consequently resulted a crack grows faster about 18%. It was concluded a lengthy in crack growth was associated with the delay cycles suggesting that the fatigue life depends mainly on size of delay zone and compressive residual stress near the crack tip.

  19. Spatio-temporal analysis of aftershock sequences in terms of Non Extensive Statistical Physics.

    Science.gov (United States)

    Chochlaki, Kalliopi; Vallianatos, Filippos

    2017-04-01

    Earth's seismicity is considered as an extremely complicated process where long-range interactions and fracturing exist (Vallianatos et al., 2016). For this reason, in order to analyze it, we use an innovative methodological approach, introduced by Tsallis (Tsallis, 1988; 2009), named Non Extensive Statistical Physics. This approach introduce a generalization of the Boltzmann-Gibbs statistical mechanics and it is based on the definition of Tsallis entropy Sq, which maximized leads the the so-called q-exponential function that expresses the probability distribution function that maximizes the Sq. In the present work, we utilize the concept of Non Extensive Statistical Physics in order to analyze the spatiotemporal properties of several aftershock series. Marekova (Marekova, 2014) suggested that the probability densities of the inter-event distances between successive aftershocks follow a beta distribution. Using the same data set we analyze the inter-event distance distribution of several aftershocks sequences in different geographic regions by calculating non extensive parameters that determine the behavior of the system and by fitting the q-exponential function, which expresses the degree of non-extentivity of the investigated system. Furthermore, the inter-event times distribution of the aftershocks as well as the frequency-magnitude distribution has been analyzed. The results supports the applicability of Non Extensive Statistical Physics ideas in aftershock sequences where a strong correlation exists along with memory effects. References C. Tsallis, Possible generalization of Boltzmann-Gibbs statistics, J. Stat. Phys. 52 (1988) 479-487. doi:10.1007/BF01016429 C. Tsallis, Introduction to nonextensive statistical mechanics: Approaching a complex world, 2009. doi:10.1007/978-0-387-85359-8. E. Marekova, Analysis of the spatial distribution between successive earthquakes in aftershocks series, Annals of Geophysics, 57, 5, doi:10.4401/ag-6556, 2014 F. Vallianatos, G

  20. Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikos; Vinther, Jeppe

    2015-01-01

    time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data...

  1. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.

    Science.gov (United States)

    Ebhardt, H Alexander; Tsang, Herbert H; Dai, Denny C; Liu, Yifeng; Bostan, Babak; Fahlman, Richard P

    2009-05-01

    Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3' micro RNA uridine extensions and 5' micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5' deletions and 3' uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.

  2. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.

    Directory of Open Access Journals (Sweden)

    Morgan Kullberg

    Full Text Available BACKGROUND: We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human, lagomorphs (rabbit, rodents (rat and mouse, artiodactyls (cow, carnivorans (dog and proboscideans (elephant. METHODOLOGY/PRINCIPAL FINDINGS: We have produced 2000 ESTs (1.2 mega bases from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. CONCLUSIONS: The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.

  3. A base composition analysis of natural patterns for the preprocessing of metagenome sequences.

    Science.gov (United States)

    Bonham-Carter, Oliver; Ali, Hesham; Bastola, Dhundy

    2013-01-01

    On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy. We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code.

  4. Establishment of screening technique for mutant cell and analysis of base sequence in the mutation

    International Nuclear Information System (INIS)

    Sofuni, Toshio; Nomi, Takehiko; Yamada, Masami; Masumura, Kenichi

    2000-01-01

    This research project aimed to establish an easy and quick detection method for radiation-induced mutation using molecular-biological techniques and an effective analyzing method for the molecular changes in base sequence. In this year, Spi mutants derived from γ-radiation exposed mouse were analyzed by PCR method and DNA sequence method. Male transgenic mice were exposed to γ-ray at 5,10, 50 Gy and the transgene was taken out from the genome DNA from the spleen in vivo packaging method. Spi mutant plaques were obtained by infecting the recovered phage to E. coli. Sequence analysis for the mutants was made using ALFred DNA sequencer and SequiTherm TM Long-Red Cycle sequencing kit. Sequence analysis was carried out for 41 of 50 independent Spi mutants obtained. The deletions were classified into 4 groups; Group 1 included 15 mutants that were characterized with a large deletion (43 bp-10 kb) with a short homologous sequence. Group 2 included 11 mutants of a large deletion having no homologous sequence at the connecting region. Group 3 included 11 mutants having a short deletion of less than 20 bp, which occurred in the non-repetitive sequence of gam gene and possibly caused by oxidative breakage of DNA or recombination of DNA fragment produced by the breakage. Group 4 included 4 mutants having deletions as short as 20 bp or less in the repetitive sequence of gam gene, resulting in an alteration of the reading frame. Thus, the synthesis of Gam protein was terminated by the appearance of TGA between code 13 and 14 of redB gene, leading to inactivation of gam gene and redBA gene. These results indicated that most of Spi mutants had a deletion in red/gam region and the deletions in more than half mutants occurred in homologous sequences as short as 8 bp. (M.N.)

  5. The BsaHI restriction-modification system: Cloning, sequencing and analysis of conserved motifs

    Directory of Open Access Journals (Sweden)

    Roberts Richard J

    2008-05-01

    Full Text Available Abstract Background Restriction and modification enzymes typically recognise short DNA sequences of between two and eight bases in length. Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC. Results The DNA sequences of the genes for the BsaHI methyltransferase, bsaHIM, and restriction endonuclease, bsaHIR, have been determined (GenBank accession #EU386360, cloned and expressed in E. coli. Both the restriction endonuclease and methyltransferase enzymes share significant similarity with a group of 6 other enzymes comprising the restriction-modification systems HgiDI and HgiGI and the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP restriction-modification systems. A sequence alignment of these homologues shows that their amino acid sequences are largely conserved and highlights several motifs of interest. We target one such conserved motif, reading SPERRFD, at the C-terminal end of the bsaHIR gene. A mutational analysis of these amino acids indicates that the motif is crucial for enzymatic activity. Sequence alignment of the methyltransferase gene reveals a short motif within the target recognition domain that is conserved among enzymes recognising the same sequences. Thus, this motif may be used as a diagnostic tool to define the recognition sequences of the cytosine C5 methyltransferases. Conclusion We have cloned and sequenced the BsaHI restriction and modification enzymes. We have identified a region of the R. BsaHI enzyme that is crucial for its activity. Analysis of the amino acid sequence of the BsaHI methyltransferase enzyme led us to propose two new motifs that can be used in the diagnosis of the recognition sequence of the cytosine C5-methyltransferases.

  6. [Sequence analysis of ITS2 and CO1 genes of Paragonimus harinasutai].

    Science.gov (United States)

    Qian, Bao-zhen; Sugiyama, H; Waikagul, J; Zhu, Zhi-hang

    2006-04-30

    To identify Paragonimus harinasutai from Ninghai, Zhejiang Province, China. Metacercariae were collected from the crabs Sinopotamon chekiangenes in Xixi village of Ninghai County for ITS2 sequence analysis, CO1 sequence analysis and endonuclease BsaHI and StuI analysis by PCR-RFLP. Results The fingerprintings of PCR-RFLP were virtually same to the isolate from Thailand (Nakorn-nayok). The ITS2 sequence with 366 bp and CO1 sequence with 390 bp of the metacercariae collected from Ninghai revealed a nucleotide identity 95.6% and 89.5% respectively to the Thai isolate. The study confirmed that Paragonimus harinasutai is present in Ninghai, China, with certain variation on molecular biology in comparison to the Thai isolate.

  7. De novo structural modeling and computational sequence analysis ...

    African Journals Online (AJOL)

    Jane

    2011-07-25

    Jul 25, 2011 ... Our study was aimed towards computational proteomic analysis and 3D structural modeling of this novel bacteriocin protein encoded by the earlier aforementioned gene. Different bioinformatics tools and machine learning techniques were used for protein structural classification. De novo protein modeling ...

  8. Inter Simple Sequence Repeat (ISSR) analysis of wild and cultivated ...

    African Journals Online (AJOL)

    ONOS

    2010-08-09

    Aug 9, 2010 ... ed through interspecific hybridization of Asian and African rice, formed a cluster with Asian rice. Generally cultivated and wild species clearly observed to have separated groups in both UPGMA and neighbor joining analysis. The two methods showed almost the same tree topology with similar groupings ...

  9. Simple sequence repeat (SSR) markers analysis of genetic diversity ...

    African Journals Online (AJOL)

    hope&shola

    2012-04-24

    Apr 24, 2012 ... eight groups according to the k-means cluster analysis based on seed quality characters. There were significant differences among different groups (P< 0.01). The characteristics of each group were as follows; group 1: yellow seed with high oil and protein content, group 2: yellow seed with low oil and high ...

  10. Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences.

    Science.gov (United States)

    Pariset, Lorraine; Chillemi, Giovanni; Bongiorni, Silvia; Romano Spica, Vincenzo; Valentini, Alessio

    2009-06-01

    Microarrays produce a measurement of gene expression based on the relative measures of dye intensities that correspond to the amount of target RNA. This technology is fast developing and its application is expanding from Homo sapiens to a wide number of species, where enough information on sequences and annotations exist. Anyway, the number of species for which a dedicated platform exists is not high. The use of heterologous array hybridization, screening for gene expression in one species using an array developed for another one, is still quite frequent, even though cross-species microarray hybridization has raised many arguments. Some methods which are high throughput and do not rely on knowledge of the DNA/RNA sequence exist, namely serial analysis of gene expression (SAGE), Massively Parallel Signature Sequencing (MPSS) and deep sequencing of full transcriptome. Although very powerful, particularly the latter, they are still quite costly and cumbersome methods. In some species where genome sequences are largely unknown, several anonymous sequences are deposited in gene banks as a result of Expressed Sequence Tags (ESTs) sequencing projects. The ESTs databases represent a valuable knowledge that can be exploited with some bioinformatic effort to build species-specific microarrays. We present here a method of high-density in situ synthesized microarrays starting from available EST sequences in, Ovis aries. Our data indicate that the method is very efficient and can be easily extended to other species of which genetic sequences are present in public databases, but neglected so far with advanced devices like microarrays. As a perspective, the approach can be applied also to species of which no sequences are available to date, thanks to high-throughput deep sequencing methods.

  11. Experimental analysis of precursors to severe problem behavior.

    Science.gov (United States)

    Fritz, Jennifer N; Iwata, Brian A; Hammond, Jennifer L; Bloom, Sarah E

    2013-01-01

    Some individuals engage in both mild and severe forms of problem behavior. Research has shown that when mild behaviors precede severe behaviors (i.e., the mild behaviors serve as precursors), they can (a) be maintained by the same source of reinforcement as severe behavior and (b) reduce rates of severe behavior observed during assessment. In Study 1, we developed an objective checklist to identify precursors via videotaped trials for 16 subjects who engaged in problem behavior and identified at least 1 precursor for every subject. In Study 2, we conducted separate functional analyses of precursor and severe problem behaviors for 8 subjects, and obtained correspondence between outcomes in 7 cases. In Study 3, we evaluated noncontingent reinforcement schedule thinning plus differential reinforcement of alternative behavior to reduce precursors, increase appropriate behavior, and maintain low rates of severe behavior during 3 treatment analyses for 2 subjects. Results showed that this treatment strategy was effective for behaviors maintained by positive and negative reinforcement. © Society for the Experimental Analysis of Behavior.

  12. Analysis of Multiple Genomic Sequence Alignments: A Web Resource, Online Tools, and Lessons Learned From Analysis of Mammalian SCL Loci

    Science.gov (United States)

    Chapman, Michael A.; Donaldson, Ian J.; Gilbert, James; Grafham, Darren; Rogers, Jane; Green, Anthony R.; Göttgens, Berthold

    2004-01-01

    Comparative analysis of genomic sequences is becoming a standard technique for studying gene regulation. However, only a limited number of tools are currently available for the analysis of multiple genomic sequences. An extensive data set for the testing and training of such tools is provided by the SCL gene locus. Here we have expanded the data set to eight vertebrate species by sequencing the dog SCL locus and by annotating the dog and rat SCL loci. To provide a resource for the bioinformatics community, all SCL sequences and functional annotations, comprising a collation of the extensive experimental evidence pertaining to SCL regulation, have been made available via a Web server. A Web interface to new tools specifically designed for the display and analysis of multiple sequence alignments was also implemented. The unique SCL data set and new sequence comparison tools allowed us to perform a rigorous examination of the true benefits of multiple sequence comparisons. We demonstrate that multiple sequence alignments are, overall, superior to pairwise alignments for identification of mammalian regulatory regions. In the search for individual transcription factor binding sites, multiple alignments markedly increase the signal-to-noise ratio compared to pairwise alignments. PMID:14718377

  13. Cloning and sequence analysis of hyaluronoglucosaminidase (nagH gene of Clostridium chauvoei

    Directory of Open Access Journals (Sweden)

    Saroj K. Dangi

    2017-09-01

    Full Text Available Aim: Blackleg disease is caused by Clostridium chauvoei in ruminants. Although virulence factors such as C. chauvoei toxin A, sialidase, and flagellin are well characterized, hyaluronidases of C. chauvoei are not characterized. The present study was aimed at cloning and sequence analysis of hyaluronoglucosaminidase (nagH gene of C. chauvoei. Materials and Methods: C. chauvoei strain ATCC 10092 was grown in ATCC 2107 media and confirmed by polymerase chain reaction (PCR using the primers specific for 16-23S rDNA spacer region. nagH gene of C. chauvoei was amplified and cloned into pRham-SUMO vector and transformed into Escherichia cloni 10G cells. The construct was then transformed into E. cloni cells. Colony PCR was carried out to screen the colonies followed by sequencing of nagH gene in the construct. Results: PCR amplification yielded nagH gene of 1143 bp product, which was cloned in prokaryotic expression system. Colony PCR, as well as sequencing of nagH gene, confirmed the presence of insert. Sequence was then subjected to BLAST analysis of NCBI, which confirmed that the sequence was indeed of nagH gene of C. chauvoei. Phylogenetic analysis of the sequence showed that it is closely related to Clostridium perfringens and Clostridium paraputrificum. Conclusion: The gene for virulence factor nagH was cloned into a prokaryotic expression vector and confirmed by sequencing.

  14. EventThread: Visual Summarization and Stage Analysis of Event Sequence Data.

    Science.gov (United States)

    Guo, Shunan; Xu, Ke; Zhao, Rongwen; Gotz, David; Zha, Hongyuan; Cao, Nan

    2018-01-01

    Event sequence data such as electronic health records, a person's academic records, or car service records, are ordered series of events which have occurred over a period of time. Analyzing collections of event sequences can reveal common or semantically important sequential patterns. For example, event sequence analysis might reveal frequently used care plans for treating a disease, typical publishing patterns of professors, and the patterns of service that result in a well-maintained car. It is challenging, however, to visually explore large numbers of event sequences, or sequences with large numbers of event types. Existing methods focus on extracting explicitly matching patterns of events using statistical analysis to create stages of event progression over time. However, these methods fail to capture latent clusters of similar but not identical evolutions of event sequences. In this paper, we introduce a novel visualization system named EventThread which clusters event sequences into threads based on tensor analysis and visualizes the latent stage categories and evolution patterns by interactively grouping the threads by similarity into time-specific clusters. We demonstrate the effectiveness of EventThread through usage scenarios in three different application domains and via interviews with an expert user.

  15. Escalation research: providing new frontiers for applying behavior analysis to organizational behavior.

    Science.gov (United States)

    Goltz, S M

    2000-01-01

    Decision fiascoes such as escalation of commitment, the tendency of decision makers to "throw good money after bad," can have serious consequences for organizations and are therefore of great interest in applied research. This paper discusses the use of behavior analysis in organizational behavior research on escalation. Among the most significant aspects of behavior-analytic research on escalation is that it has indicated that both the patterns of outcomes that decision makers have experienced for past decisions and the patterns of responses that they make are critical for understanding escalation. This research has also stimulated the refinement of methods by researchers to better assess decision making and the role reinforcement plays in it. Finally, behavior-analytic escalation research has not only indicated the utility of reinforcement principles for predicting more complex human behavior but has also suggested some additional areas for future exploration of decision making using behavior analysis.

  16. An approach to modeling operator's cognitive behavior using artificial intelligence techniques in emergency operating event sequences

    International Nuclear Information System (INIS)

    Cheon, Se Woo; Sur, Sang Moon; Lee, Yong Hee; Park, Young Taeck; Moon, Sang Joon

    1994-01-01

    Computer modeling of an operator's cognitive behavior is a promising approach for the purpose of human factors study and man-machine systems assessment. In this paper, the states of the art in modeling operator behavior and the current status in developing an operator's model (MINERVA - NPP) are presented. The model is constructed as a knowledge-based system of a blackboard framework and is simulated based on emergency operating procedures

  17. The scale analysis sequence for LWR fuel depletion

    International Nuclear Information System (INIS)

    Hermann, O.W.; Parks, C.V.

    1991-01-01

    The SCALE (Standardized Computer Analyses for Licensing Evaluation) code system is used extensively to perform away-from-reactor safety analysis (particularly criticality safety, shielding, heat transfer analyses) for spent light water reactor (LWR) fuel. Spent fuel characteristics such as radiation sources, heat generation sources, and isotopic concentrations can be computed within SCALE using the SAS2 control module. A significantly enhanced version of the SAS2 control module, which is denoted as SAS2H, has been made available with the release of SCALE-4. For each time-dependent fuel composition, SAS2H performs one-dimensional (1-D) neutron transport analyses (via XSDRNPM-S) of the reactor fuel assembly using a two-part procedure with two separate unit-cell-lattice models. The cross sections derived from a transport analysis at each time step are used in a point-depletion computation (via ORIGEN-S) that produces the burnup-dependent fuel composition to be used in the next spectral calculation. A final ORIGEN-S case is used to perform the complete depletion/decay analysis using the burnup-dependent cross sections. The techniques used by SAS2H and two recent applications of the code are reviewed in this paper. 17 refs., 5 figs., 5 tabs

  18. MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

    Directory of Open Access Journals (Sweden)

    Daniel H Huson

    2016-06-01

    Full Text Available There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.

  19. Automated regional behavioral analysis for human brain images.

    Science.gov (United States)

    Lancaster, Jack L; Laird, Angela R; Eickhoff, Simon B; Martinez, Michael J; Fox, P Mickle; Fox, Peter T

    2012-01-01

    Behavioral categories of functional imaging experiments along with standardized brain coordinates of associated activations were used to develop a method to automate regional behavioral analysis of human brain images. Behavioral and coordinate data were taken from the BrainMap database (http://www.brainmap.org/), which documents over 20 years of published functional brain imaging studies. A brain region of interest (ROI) for behavioral analysis can be defined in functional images, anatomical images or brain atlases, if images are spatially normalized to MNI or Talairach standards. Results of behavioral analysis are presented for each of BrainMap's 51 behavioral sub-domains spanning five behavioral domains (Action, Cognition, Emotion, Interoception, and Perception). For each behavioral sub-domain the fraction of coordinates falling within the ROI was computed and compared with the fraction expected if coordinates for the behavior were not clustered, i.e., uniformly distributed. When the difference between these fractions is large behavioral association is indicated. A z-score ≥ 3.0 was used to designate statistically significant behavioral association. The left-right symmetry of ~100K activation foci was evaluated by hemisphere, lobe, and by behavioral sub-domain. Results highlighted the classic left-side dominance for language while asymmetry for most sub-domains (~75%) was not statistically significant. Use scenarios were presented for anatomical ROIs from the Harvard-Oxford cortical (HOC) brain atlas, functional ROIs from statistical parametric maps in a TMS-PET study, a task-based fMRI study, and ROIs from the ten "major representative" functional networks in a previously published resting state fMRI study. Statistically significant behavioral findings for these use scenarios were consistent with published behaviors for associated anatomical and functional regions.

  20. Time-clustering behavior in the sequence of the aftershocks of the Al-Hoceima (Morocco 24 February 2004 earthquake

    Directory of Open Access Journals (Sweden)

    L. Telesca

    2009-12-01

    Full Text Available The time dynamics of the aftershock sequence of the Al-Hoceima (Morocco earthquake of 24 February 2004 has been investigated. The sequence of the occurrence times of the events with threshold magnitude Mth≥3.2 is characterized by a time-clustering behavior, identified using different fractal methods (Fano Factor, Allan Factor, Count-based Periodogram, well suited to reveal scaling features in point processes. The obtained results not only show the presence of memory phenomena and correlation structures in the Al-Hoceima aftershocks, but also furnish quantitatively the estimate of the magnitude of such correlation by means of the estimate of the scaling exponent α.

  1. Descriptive analysis of the verbal behavior of a therapist: a known-group validity analysis of the putative behavioral functions involved in clinical interaction.

    Science.gov (United States)

    Virues-Ortega, Javier; Montaño-Fidalgo, Montserrat; Froján-Parga, María Xesús; Calero-Elvira, Ana

    2011-12-01

    This study analyzes the interobserver agreement and hypothesis-based known-group validity of the Therapist's Verbal Behavior Category System (SISC-INTER). The SISC-INTER is a behavioral observation protocol comprised of a set of verbal categories representing putative behavioral functions of the in-session verbal behavior of a therapist (e.g., discriminative, reinforcing, punishing, and motivational operations). The complete therapeutic process of a clinical case of an individual with marital problems was recorded (10 sessions, 8 hours), and data were arranged in a temporal sequence using 10-min periods. Hypotheses based on the expected performance of the putative behavioral functions portrayed by the SISC-INTER codes across prevalent clinical activities (i.e., assessing, explaining, Socratic method, providing clinical guidance) were tested using autoregressive integrated moving average (ARIMA) models. Known-group validity analyses provided support to all hypotheses. The SISC-INTER may be a useful tool to describe therapist-client interaction in operant terms. The utility of reliable and valid protocols for the descriptive analysis of clinical practice in terms of verbal behavior is discussed. Copyright © 2011. Published by Elsevier Ltd.

  2. Applied behavior analysis: behavior management of children with autism spectrum disorders in dental environments.

    Science.gov (United States)

    Hernandez, Purnima; Ikkanda, Zachary

    2011-03-01

    There are a limited number of studies addressing behavior management techniques and procedural modifications that dentists can use to treat people with an autism spectrum disorder (ASD). The authors conducted a search of the dental and behavioral analytic literature to identify management techniques that address problem behaviors exhibited by children with ASDs in dental and other health-related environments. Applied behavior analysis (ABA) is a science in which procedures are based on the principles of behavior through systematic experimentation. Clinicians have used ABA procedures successfully to modify socially significant behaviors of people with ASD. Basic behavior management techniques currently used in dentistry may not encourage people with cognitive and behavioral disabilities, such as ASD, to tolerate simple in-office dental procedures consistently. Instead, dental care providers often are required to use advanced behavior management techniques to complete simple in-office procedures such as prophylaxis, sealant placement and obtaining radiographs. ABA procedures can be integrated in the dental environment to manage problem behaviors often exhibited by children with an ASD. The authors found no evidence-based procedural modifications that address the behavioral characteristics and problematic behaviors of children with an ASD in a dental environment. Further research in this area should be conducted. Knowledge and in-depth understanding of behavioral principles is essential when a dentist is concerned with modifying behaviors. Using ABA procedures can help dentists manage problem behaviors effectively and systematically when performing routine dental treatment. Being knowledgeable about each patient's behavioral characteristics and the parents' level of involvement is important in the successful integration of the procedures and reduction of in-office time.

  3. Analysis of sequence variability in the CART gene in relation to obesity in a Caucasian population

    Directory of Open Access Journals (Sweden)

    Hercberg Serge

    2005-04-01

    Full Text Available Abstract Background Cocaine and amphetamine regulated transcript (CART is an anorectic neuropeptide located principally in hypothalamus. CART has been shown to be involved in control of feeding behavior, but a direct relationship with obesity has not been established. The aim of this study was to evaluate the effect of polymorphisms within the CART gene with regards to a possible association with obesity in a Caucasian population. Results Screening of the entire gene as well as a 3.7 kb region of 5' upstream sequence revealed 31 SNPs and 3 rare variants ; 14 of which were subsequently genotyped in 292 French morbidly obese subjects and 368 controls. Haplotype analysis suggested an association with obesity which was found to be mainly due to SNP-3608T>C (rs7379701 (p = 0.009. Genotyping additional cases and controls also of European Caucasian origin supported further this possible association between the CART SNP -3608T>C T allele and obesity (global p-value = 0.0005. Functional studies also suggested that the SNP -3608T>C could modulate nuclear protein binding. Conclusion CART SNP -3608T>C may possibly contribute to the genetic risk for obesity in the Caucasian population. However confirmation of the importance of the role of the CART gene in energy homeostasis and obesity will require investigation and replication in further populations.

  4. Time for behavioral political economy? An analysis of articles in behavioral economics

    OpenAIRE

    Berggren, Niclas

    2011-01-01

    This study analyzes leading research in behavioral economics to see whether it contains advocacy of paternalism and whether it addresses the potential cognitive limitations and biases of the policymakers who are going to implement paternalist policies. The findings reveal that 20.7% of the studied articles in behavioral economics propose paternalist policy action and that 95.5% of these do not contain any analysis of the cognitive ability of policymakers. This suggests that behavioral politic...

  5. Multifractal analysis of DNA sequences using a novel chaos-game representation

    Science.gov (United States)

    Gutiérrez, J. M.; Rodríguez, M. A.; Abramson, G.

    2001-11-01

    We present a generalization of the standard chaos-game representation method introduced by Jeffrey. To this aim, a DNA symbolic sequence is mapped onto a singular measure on the attractor of a particular IFS model, which is a perfect statistical representation of the sequence. A multifractal analysis of the resulting measure is introduced and an interpretation of singularities in terms of mutual information and redundancy (statistical dependence) among subsequence symbols within the DNA sequence is provided. The multifractal spectrum is also shown to be more sensitive for detecting dependence structures within the DNA sequence than the averaged contribution given by redundancy. This method presents several advantages with respect to other representations such as walks or interfaces, which may introduce spurious effects. In contrast with the results obtained by other standard methods, here we note that no general statement can be made on the influence of coding and non-coding content on the correlation length of a given sequence.

  6. Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences.

    Science.gov (United States)

    Mandell, Kathleen E; Vallone, Peter M; Owczarzy, Richard; Riccelli, Peter V; Benight, Albert S

    2006-06-15

    Melting curves and circular dichroism spectra were measured for a number of DNA dumbbell and linear molecules containing dinucleotide repeat sequences of different lengths. To study effects of different sequences on the melting and spectroscopic properties, six DNA dumbbells whose stems contain the central sequences (AA)(10), (AC)(10), (AG)(10), (AT)(10), (GC)(10), and (GG)(10) were prepared. These represent the minimal set of 10 possible dinucleotide repeats. To study effects of dinucleotide repeat length, dumbbells with the central sequences (AG)(n), n = 5 and 20, were prepared. Control molecules, dumbbells with a random central sequence, (RN)(n), n = 5, 10, and 20, were also prepared. The central sequence of each dumbbell was flanked on both sides by the same 12 base pairs and T(4) end-loops. Melting curves were measured by optical absorbance and differential scanning calorimetry in solvents containing 25, 55, 85, and 115 mM Na(+). CD spectra were collected from 20 to 45 degrees C and [Na(+)] from 25 to 115 mM. The spectral database did not reveal any apparent temperature dependence in the pretransition region. Analysis of the melting thermodynamics evaluated as a function of Na(+) provided a means for quantitatively estimating the counterion release with melting for the different sequences. Results show a very definite sequence dependence, indicating the salt-dependent properties of duplex DNA are also sequence dependent. Linear DNA molecules containing the (AG)(n) and (RN)(n), sequences, n = 5, 10, 20, and 30, were also prepared and studied. The linear DNA molecules had the exact sequences of the dumbbell stems. That is, the central repeat sequence in each linear duplex was flanked on both sides by the same 12-bp sequence. Melting and CD studies were also performed on the linear DNA molecules. Comparison of results obtained for the same sequences in dumbbell and linear molecular environments reveals several interesting features of the interplay between

  7. Saving the world by teaching behavior analysis: a behavioral systems approach.

    Science.gov (United States)

    Malott, R W; Vunovich, P L; Boettcher, W; Groeger, C

    1995-01-01

    This article presents a behavioral systems approach to organizational design and applies that approach to the teaching of behavior analysis. This systems approach consists of three components: goal-directed systems design, behavioral systems engineering, and performance management. This systems approach is applied to the Education Board and Teaching Behavior Analysis Special Interest Group of the Association for Behavior Analysis, with a conclusion that we need to emphasize the recruitment of students and the placement and maintenance of alumni. This systems approach is also applied at the scale of the individual faculty member running a university-based training system and is seen to generate special approaches to textbook preparation, undergraduate research, colloquium and conference attendance, career counseling, preparation for graduate examinations, graduate training and graduate seminars, and classroom alternatives to the traditional lecture.

  8. Pretense and Peer Behavior: an Intersectoral Analysis

    Science.gov (United States)

    Fein, Greta G.; And Others

    1982-01-01

    Children between the ages of 19 and 41 months were videotaped with a peer in a standardized playroom for four 15-minute sessions in order to examine a developmental model describing the relation between changes in pretense (pretend play, transformations, and communications) and changes in peer-oriented social behavior. (MP)

  9. FROM THE BEHAVIORAL ANALYSIS TO POST-BEHAVIORALISM: HISTORY OF PARADIGM

    Directory of Open Access Journals (Sweden)

    M. I. Bogachev

    2017-01-01

    Full Text Available Article is devoted to the review of formation and decline of behavioralism paradigm in political science. The author begins the analysis with critical consideration of the scientific concepts preceding emergence of modernist empiricism within which there is a behavioral analysis. Further the researcher traces formation behaviorism in the social disciplines: formation model in psychology, release of the theory out of limits of pure psychology and transferring ideas in sociology and political science. The author analyzes inquiries to the scientific theory by behavioralism. He opens the principles of behavioralism as paradigm in political science. The author presents the conceptual and contextual factors promoting recession of popularity behavioralism in political science and submits methodological restrictions approach. The author states the main claims of critics to this research approach and explains the reasons decline this paradigm. At the same time the methodological reflection of behavioralism which has followed recession of his popularity is reflected in work. The author opens the principles of the new methodological direction – post-behavioralism and the position of modern representatives of the behavioral analysis.

  10. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing

    Directory of Open Access Journals (Sweden)

    del Viso Florencia

    2012-11-01

    Full Text Available Abstract Background Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify the causative mutation for a given phenotype. In models like Xenopus tropicalis, an incomplete and occasionally incorrect genome assembly compounds this problem. To facilitate cloning of X. tropicalis mutants identified in forward genetic screens, we sought to combine bulk segregant analysis and exome sequencing into a single step. Results Here we report the first use of exon capture sequencing to identify mutations in a non-mammalian, vertebrate model. We demonstrate that bulk segregant analysis coupled with exon capture sequencing is not only able to identify causative mutations but can also generate linkage information, facilitate the assembly of scaffolds, identify misassembles, and discover thousands of SNPs for fine mapping. Conclusion Exon capture sequencing and bulk segregant analysis is a rapid, inexpensive method to clone mutants identified in forward genetic screens. With sufficient meioses, this method can be generalized to any model system with a genome assembly, polished or unpolished, and in the latter case, it also provides many critical genomic resources.

  11. An Annotated Bibliography of Verbal Behavior Scholarship Published Outside of The Analysis of Verbal Behavior: 2014.

    Science.gov (United States)

    Carr, James E; Nosik, Melissa R; Lechago, Sarah A; Phillips, Lauren

    2015-06-01

    This annotated bibliography summarizes journal articles on verbal behavior published outside of The Analysis of Verbal Behavior, the primary journal for scholarship in this area. Seventeen such articles were published in 2014 and are annotated as a resource for practitioners, researchers, and educators.

  12. An Annotated Bibliography of Verbal Behavior Articles Published outside of "The Analysis of Verbal Behavior": 2015

    Science.gov (United States)

    Lechago, Sarah A.; Phillips, Lauren A.

    2016-01-01

    An annotated bibliography is provided that summarizes journal articles on verbal behavior published outside of "The Analysis of Verbal Behavior" in 2015, the primary journal for scholarship in this area. Thirty such articles were identified and annotated as a resource for practitioners, researchers, and educators.

  13. An Annotated Bibliography of Verbal Behavior Articles Published Outside of The Analysis of Verbal Behavior: 2015.

    Science.gov (United States)

    Lechago, Sarah A; Phillips, Lauren A

    2016-06-01

    An annotated bibliography is provided that summarizes journal articles on verbal behavior published outside of The Analysis of Verbal Behavior in 2015, the primary journal for scholarship in this area. Thirty such articles were identified and annotated as a resource for practitioners, researchers, and educators.

  14. An Annotated Bibliography of Verbal Behavior Scholarship Published outside of "The Analysis of Verbal Behavior": 2014

    Science.gov (United States)

    Carr, James E.; Nosik, Melissa R.; Lechago, Sarah A.; Phillips, Lauren

    2015-01-01

    This annotated bibliography summarizes journal articles on verbal behavior published outside of "The Analysis of Verbal Behavior," the primary journal for scholarship in this area. Seventeen such articles were published in 2014 and are annotated as a resource for practitioners, researchers, and educators.

  15. An Annotated Bibliography of Verbal Behavior Articles Published outside of "The Analysis of Verbal Behavior: 2016"

    Science.gov (United States)

    Lechago, Sarah A.; Jackson, Rachel E.; Oda, Fernanda S.

    2017-01-01

    An annotated bibliography is provided that summarizes journal articles on verbal behavior published outside of "The Analysis of Verbal Behavior" in 2016, the primary journal for scholarship in this area. Thirty-seven such articles were identified and annotated as a resource for practitioners, researchers, and educators.

  16. Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis

    Directory of Open Access Journals (Sweden)

    Arias Covadonga

    2007-06-01

    Full Text Available Abstract Background The ciliate protozoan Ichthyophthirius multifiliis (Ich is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of this parasite has been lacking. To study gene expression involved in Ich pathogenesis and virulence, our goal was to generate expressed sequence tags (ESTs for the development of a powerful microarray platform for the analysis of global gene expression in this species. Here, we initiated a project to sequence and analyze over 10,000 ESTs. Results We sequenced 10,368 EST clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate. Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons. These unique sequences represent over two million base pairs (~10% of Plasmodium falciparum genome, a phylogenetically related protozoan. BLASTX searches produced 2,518 significant (E-value -5 hits and further Gene Ontology (GO analysis annotated 1,008 of these genes. The ESTs were analyzed comparatively against the genomes of the related protozoa Tetrahymena thermophila and P. falciparum, allowing putative identification of additional genes. All the EST sequences were deposited by dbEST in GenBank (GenBank: EG957858–EG966289. Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents a significant proportion of the Ich transcriptome, and provides a material basis for the development of microarrays useful for gene expression studies concerning Ich development, pathogenesis, and virulence.

  17. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

    DEFF Research Database (Denmark)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

    2014-01-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease d...

  18. A genome-wide analysis of FRT-like sequences in the human genome.

    Science.gov (United States)

    Shultz, Jeffry L; Voziyanova, Eugenia; Konieczka, Jay H; Voziyanov, Yuri

    2011-03-23

    Efficient and precise genome manipulations can be achieved by the Flp/FRT system of site-specific DNA recombination. Applications of this system are limited, however, to cases when target sites for Flp recombinase, FRT sites, are pre-introduced into a genome locale of interest. To expand use of the Flp/FRT system in genome engineering, variants of Flp recombinase can be evolved to recognize pre-existing genomic sequences that resemble FRT and thus can serve as recombination sites. To understand the distribution and sequence properties of genomic FRT-like sites, we performed a genome-wide analysis of FRT-like sites in the human genome using the experimentally-derived parameters. Out of 642,151 identified FRT-like sequences, 581,157 sequences were unique and 12,452 sequences had at least one exact duplicate. Duplicated FRT-like sequences are located mostly within LINE1, but also within LTRs of endogenous retroviruses, Alu repeats and other repetitive DNA sequences. The unique FRT-like sequences were classified based on the number of matches to FRT within the first four proximal bases pairs of the Flp binding elements of FRT and the nature of mismatched base pairs in the same region. The data obtained will be useful for the emerging field of genome engineering.

  19. A genome-wide analysis of FRT-like sequences in the human genome.

    Directory of Open Access Journals (Sweden)

    Jeffry L Shultz

    2011-03-01

    Full Text Available Efficient and precise genome manipulations can be achieved by the Flp/FRT system of site-specific DNA recombination. Applications of this system are limited, however, to cases when target sites for Flp recombinase, FRT sites, are pre-introduced into a genome locale of interest. To expand use of the Flp/FRT system in genome engineering, variants of Flp recombinase can be evolved to recognize pre-existing genomic sequences that resemble FRT and thus can serve as recombination sites. To understand the distribution and sequence properties of genomic FRT-like sites, we performed a genome-wide analysis of FRT-like sites in the human genome using the experimentally-derived parameters. Out of 642,151 identified FRT-like sequences, 581,157 sequences were unique and 12,452 sequences had at least one exact duplicate. Duplicated FRT-like sequences are located mostly within LINE1, but also within LTRs of endogenous retroviruses, Alu repeats and other repetitive DNA sequences. The unique FRT-like sequences were classified based on the number of matches to FRT within the first four proximal bases pairs of the Flp binding elements of FRT and the nature of mismatched base pairs in the same region. The data obtained will be useful for the emerging field of genome engineering.

  20. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.

    Science.gov (United States)

    Brenner, S; Johnson, M; Bridgham, J; Golda, G; Lloyd, D H; Johnson, D; Luo, S; McCurdy, S; Foy, M; Ewan, M; Roth, R; George, D; Eletr, S; Albrecht, G; Vermaas, E; Williams, S R; Moon, K; Burcham, T; Pallas, M; DuBridge, R B; Kirchner, J; Fearon, K; Mao, J; Corcoran, K

    2000-06-01

    We describe a novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 microm diameter microbeads. After constructing a microbead library of DNA templates by in vitro cloning, we assembled a planar array of a million template-containing microbeads in a flow cell at a density greater than 3x10(6) microbeads/cm2. Sequences of the free ends of the cloned templates on each microbead were then simultaneously analyzed using a fluorescence-based signature sequencing method that does not require DNA fragment separation. Signature sequences of 16-20 bases were obtained by repeated cycles of enzymatic cleavage with a type IIs restriction endonuclease, adaptor ligation, and sequence interrogation by encoded hybridization probes. The approach was validated by sequencing over 269,000 signatures from two cDNA libraries constructed from a fully sequenced strain of Saccharomyces cerevisiae, and by measuring gene expression levels in the human cell line THP-1. The approach provides an unprecedented depth of analysis permitting application of powerful statistical techniques for discovery of functional relationships among genes, whether known or unknown beforehand, or whether expressed at high or very low levels.

  1. Genetic mutation analysis of human gastric adenocarcinomas using ion torrent sequencing platform.

    Directory of Open Access Journals (Sweden)

    Zhi Xu

    Full Text Available Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7% in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.

  2. galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

    Science.gov (United States)

    Nilsson, R Henrik; Larsson, Karl-Henrik; Ursing, Björn M

    2004-06-12

    The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable. A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

  3. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

    Directory of Open Access Journals (Sweden)

    Chuming Chen

    2011-04-01

    Full Text Available The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs, each selected from a Representative Proteome Group (RPG containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55 most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains and annotation information (93% of experimentally characterized proteins. All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization.

  4. DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis.

    Science.gov (United States)

    Erlich, Yaniv; Chang, Kenneth; Gordon, Assaf; Ronen, Roy; Navon, Oron; Rooks, Michelle; Hannon, Gregory J

    2009-07-01

    Next-generation sequencers have sufficient power to analyze simultaneously DNAs from many different specimens, a practice known as multiplexing. Such schemes rely on the ability to associate each sequence read with the specimen from which it was derived. The current practice of appending molecular barcodes prior to pooling is practical for parallel analysis of up to many dozen samples. Here, we report a strategy that permits simultaneous analysis of tens of thousands of specimens. Our approach relies on the use of combinatorial pooling strategies in which pools rather than individual specimens are assigned barcodes. Thus, the identity of each specimen is encoded within the pooling pattern rather than by its association with a particular sequence tag. Decoding the pattern allows the sequence of an original specimen to be inferred with high confidence. We verified the ability of our encoding and decoding strategies to accurately report the sequence of individual samples within a large number of mixed specimens in two ways. First, we simulated data both from a clone library and from a human population in which a sequence variant associated with cystic fibrosis was present. Second, we actually pooled, sequenced, and decoded identities within two sets of 40,000 bacterial clones comprising approximately 20,000 different artificial microRNAs targeting Arabidopsis or human genes. We achieved greater than 97% accuracy in these trials. The strategies reported here can be applied to a wide variety of biological problems, including the determination of genotypic variation within large populations of individuals.

  5. DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis

    Science.gov (United States)

    Erlich, Yaniv; Chang, Kenneth; Gordon, Assaf; Ronen, Roy; Navon, Oron; Rooks, Michelle; Hannon, Gregory J.

    2009-01-01

    Next-generation sequencers have sufficient power to analyze simultaneously DNAs from many different specimens, a practice known as multiplexing. Such schemes rely on the ability to associate each sequence read with the specimen from which it was derived. The current practice of appending molecular barcodes prior to pooling is practical for parallel analysis of up to many dozen samples. Here, we report a strategy that permits simultaneous analysis of tens of thousands of specimens. Our approach relies on the use of combinatorial pooling strategies in which pools rather than individual specimens are assigned barcodes. Thus, the identity of each specimen is encoded within the pooling pattern rather than by its association with a particular sequence tag. Decoding the pattern allows the sequence of an original specimen to be inferred with high confidence. We verified the ability of our encoding and decoding strategies to accurately report the sequence of individual samples within a large number of mixed specimens in two ways. First, we simulated data both from a clone library and from a human population in which a sequence variant associated with cystic fibrosis was present. Second, we actually pooled, sequenced, and decoded identities within two sets of 40,000 bacterial clones comprising approximately 20,000 different artificial microRNAs targeting Arabidopsis or human genes. We achieved greater than 97% accuracy in these trials. The strategies reported here can be applied to a wide variety of biological problems, including the determination of genotypic variation within large populations of individuals. PMID:19447965

  6. The effect of the number of condensed phases modeled on aerosol behavior during an induced steam generator tube rupture sequence

    International Nuclear Information System (INIS)

    Bixler, N.E.; Schaperow, J.H.

    1998-06-01

    VICTORIA is a mechanistic computer code designed to analyze fission product behavior within a nuclear reactor coolant system (RCS) during a severe accident. It provides detailed predictions of the release of radioactive and nonradioactive materials from the reactor core and transport and deposition of these materials within the RCS. A recently completed independent peer review of VICTORIA, while confirming the overall adequacy of the code, recommended a number of modeling improvements. One of these recommendations, to model three rather than a single condensed phase, is the focus of the work reported here. The recommendation has been implemented as an option so that either a single or three condensed phases can be treated. Both options have been employed in the study of fission product behavior during an induced steam generator tube rupture sequence. Differences in deposition patterns and mechanisms predicted using these two options are discussed

  7. Manometer Behavior Analysis using CATHENA, RELAP and GOTHIC Codes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yang Hoon; Han, Kee Soo; Moon, Bok Ja; Jang, Misuk [Nuclear Engineering Service and Solution Co. Ltd., Daejeon (Korea, Republic of)

    2014-05-15

    In this presentation, simple thermal hydraulic behavior is analyzed using three codes to show the possibility of using alternative codes. We established three models of simple u-tube manometer using three different codes. CATHENA (Canadian Algorithm for Thermal hydraulic Network Analysis), RELAP (Reactor Excursion and Leak Analysis Program), GOTHIC (Generation of Thermal Hydraulic Information for Containments) are used for this analysis. CATHENA and RELAP are widely used codes for the analysis of system behavior of CANDU and PWR. And GOTHIC code also has been widely used for the analysis of thermal hydraulic behavior in the containment system. In this paper, the internal behavior of u-tube manometer was analyzed using 3 codes, CATHENA, RELAP and GOTHIC. The general transient behavior is similar among 3 codes. However, the behavior simulated using GOTHIC shows some different trend compared with the results from the other 2 codes at the end of the transient. It would be resulted from the use of different physical model in GOTHIC, which is specialized for the multi-phase thermal hydraulic behavior analysis of containment system unlike the other two codes.

  8. Manometer Behavior Analysis using CATHENA, RELAP and GOTHIC Codes

    International Nuclear Information System (INIS)

    Kim, Yang Hoon; Han, Kee Soo; Moon, Bok Ja; Jang, Misuk

    2014-01-01

    In this presentation, simple thermal hydraulic behavior is analyzed using three codes to show the possibility of using alternative codes. We established three models of simple u-tube manometer using three different codes. CATHENA (Canadian Algorithm for Thermal hydraulic Network Analysis), RELAP (Reactor Excursion and Leak Analysis Program), GOTHIC (Generation of Thermal Hydraulic Information for Containments) are used for this analysis. CATHENA and RELAP are widely used codes for the analysis of system behavior of CANDU and PWR. And GOTHIC code also has been widely used for the analysis of thermal hydraulic behavior in the containment system. In this paper, the internal behavior of u-tube manometer was analyzed using 3 codes, CATHENA, RELAP and GOTHIC. The general transient behavior is similar among 3 codes. However, the behavior simulated using GOTHIC shows some different trend compared with the results from the other 2 codes at the end of the transient. It would be resulted from the use of different physical model in GOTHIC, which is specialized for the multi-phase thermal hydraulic behavior analysis of containment system unlike the other two codes

  9. QTL analysis by sequencing of Water Use Efficiency (WUE) in potato

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Sønderkær, Mads; Sørensen, Kirsten Kørup

    2013-01-01

    The traditional approach to potato breeding, the classical “mate and phenotype” approach is relatively costly and because phenotyping and growth capacity is limited, this are being slowly replaced by Marker Assisted Selection (MAS) breeding schemes. MAS is based on the presence of DNA polymorphic.......sparsipilum), phenotyped for water use efficiency. This population has also previously been phenotyped for the total glycoalkaloid (TGA) content....... and time consuming process. Here, a novel method for Quantitative Trait Locus (QTL) analysis has been developed, that allows for development of specific markers by use of genomic sequence reads and the recently published reference genome sequence for potato. Prior to sequencing the mapping population...

  10. An Evaluation of a High-Probability Instructional Sequence to Increase Acceptance of Food and Decrease Inappropriate Behavior in Children with Pediatric Feeding Disorders

    Science.gov (United States)

    Patel, Meeta R.; Reed, Gregory K.; Piazza, Cathleen C.; Bachmeyer, Melainie H.; Layer, Stacy A.; Pabico, Ryan S.

    2006-01-01

    We evaluated the effects of escape extinction with and without a high-probability (high-p) instructional sequence on food acceptance and inappropriate behavior for children diagnosed with feeding problems. The high-p sequence consisted of three presentations of a response that was similar topographically (i.e., presentations of an empty nuk[R],…

  11. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

    OpenAIRE

    Lam, Ernest T; Hastie, Alex; Lin, Chin; Ehrlich, Dean; Das, Somes K; Austin, Michael D; Deshpande, Paru; Cao, Han; Nagarajan, Niranjan; Xiao, Ming; Kwok, Pui-Yan

    2012-01-01

    We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4...

  12. Automated sequence analysis and editing software for HIV drug resistance testing.

    Science.gov (United States)

    Struck, Daniel; Wallis, Carole L; Denisov, Gennady; Lambert, Christine; Servais, Jean-Yves; Viana, Raquel V; Letsoalo, Esrom; Bronze, Michelle; Aitken, Sue C; Schuurman, Rob; Stevens, Wendy; Schmit, Jean Claude; Rinke de Wit, Tobias; Perez Bercoff, Danielle

    2012-05-01

    Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. To develop an automated sequence analysis and editing software to support high throughput automated sequencing. The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Analysis of price behavior in lazy $-game

    Science.gov (United States)

    Kiniwa, Jun; Koide, Takeshi; Sandoh, Hiroaki

    2009-09-01

    A non-cooperative iterated multiagent game, called a minority game, and its variations have been extensively studied in this decade. To increase its market similarity, a -game was presented by observing the current and the next agent’s payoffs. However, since the -game is defined as an offline game, it is difficult to simulate it in practice. So we propose a new online version of the -game, called a lazy -game, and analyze the price behavior of the game. First, we reveal the condition of a bubble phenomenon in the lazy -game. Next, we investigate the price behavior in the lazy -game and show that there are some upper/lower bounds of the price as long as both the buyers group and the sellers group are nonempty. Then, we consider the similarity between the lazy -game and the -game. Finally, we present some simulation results.

  14. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.

    Science.gov (United States)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta; Mikkelsen, Martin; Johansen, Peter; Børsting, Claus; Morling, Niels

    2014-08-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.

  15. Cultural Materialism and Behavior Analysis: Common Problems and Radical Solutions

    Science.gov (United States)

    Harris, Marvin

    2007-01-01

    This article presents a transcribed audio recording of the invited address the author gave to Sigrid Glenn on the relations between cultural materialism and radical behaviorism at the 12th annual conference of the Association for Behavior Analysis in Milwaukee, Wisconsin on May 23rd, 1986. In his address, the author emphasizes that the necessity…

  16. Citation Analysis of Skinner's "Verbal Behavior:" 1984-2004

    Science.gov (United States)

    Dymond, S.; O'Hora, D.; Whelan, R.; O'Donovan, A.

    2006-01-01

    The present study undertook an updated citation analysis of Skinner's (1957) "Verbal Behavior". All articles that cited "Verbal Behavior" between 1984 and 2004 were recorded and content analyzed into one of five categories; four empirical and one nonempirical. Of the empirical categories, studies that employed a verbal operant from Skinner's…

  17. Business communication and communicative behavior: analysis of foreign approach

    OpenAIRE

    Biryuk, M.

    2014-01-01

    This paper sets out the analysis of business communication focused at the aspects of communicative behavior. Business communication is considered to be fundamental in business, as a collaborative activity.We study personal features as the barriers to overcome the gaps of mutual understanding and the role of communicative behavior as an important element at every step in the business communication model.

  18. Role of Communication Networks in Behavioral Systems Analysis

    Science.gov (United States)

    Houmanfar, Ramona; Rodrigues, Nischal Joseph; Smith, Gregory S.

    2009-01-01

    This article provides an overview of communication networks and the role of verbal behavior in behavioral systems analysis. Our discussion highlights styles of leadership in the design and implementation of effective organizational contingencies that affect ways by which coordinated work practices are managed. We draw upon literature pertaining to…

  19. Animal Research in the "Journal of Applied Behavior Analysis"

    Science.gov (United States)

    Edwards, Timothy L.; Poling, Alan

    2011-01-01

    This review summarizes the 6 studies with nonhuman animal subjects that have appeared in the "Journal of Applied Behavior Analysis" and offers suggestions for future research in this area. Two of the reviewed articles described translational research in which pigeons were used to illustrate and examine behavioral phenomena of applied significance…

  20. B. F. Skinner's Contributions to Applied Behavior Analysis

    Science.gov (United States)

    Morris, Edward K.; Smith, Nathaniel G.; Altus, Deborah E.

    2005-01-01

    Our paper reviews and analyzes B. F. Skinner's contributions to applied behavior analysis in order to assess his role as the field's originator and founder. We found, first, that his contributions fall into five categorizes: the style and content of his science, his interpretations of typical and atypical human behavior, the implications he drew…

  1. A Preliminary Analysis of a Behavioral Classrooms Needs Assessment

    Science.gov (United States)

    Leaf, Justin B.; Leaf, Ronald; McCray, Cynthia; Lamkins, Carol; Taubman, Mitchell; McEachin, John; Cihon, Joseph H.

    2016-01-01

    Today many special education classrooms implement procedures based upon the principles of Applied Behavior Analysis (ABA) to establish educationally relevant skills and decrease aberrant behaviors. However, it is difficult for school staff and consultants to evaluate the implementation of various components of ABA and general classroom set up. In…

  2. Applied Behavior Analysis: Current Myths in Public Education

    Science.gov (United States)

    Fielding, Cheryl; Lowdermilk, John; Lanier, Lauren L.; Fannin, Abigail G.; Schkade, Jennifer L.; Rose, Chad A.; Simpson, Cynthia G.

    2013-01-01

    The effective use of behavior management strategies and related policies continues to be a debated issue in public education. Despite overwhelming evidence espousing the benefits of the implementation of procedures derived from principles based on the science of applied behavior analysis (ABA), educators often indicate many common misconceptions…

  3. Emerging Themes in the Functional Analysis of Problem Behavior.

    Science.gov (United States)

    Carr, Edward G.

    1994-01-01

    The successful application of functional analysis to problem behavior suggests the need to examine: additional functional properties of behavior involving social avoidance, biological reinforcement, and respondent conditioning; the role of context (including social factors and biological factors); and the multidimensional character of assessment…

  4. Translational Contributions of the Experimental Analysis of Behavior

    Science.gov (United States)

    Critchfield, Thomas S.

    2011-01-01

    It has been argued that to increase societal impact behavioral researchers must do more to address problems of obvious practical importance. The basic science wing of behavior analysis has been described as especially detached from this goal, but is it really necessary that basic science demonstrate social relevance? If so, why hasn't this…

  5. Seismic behavior analysis of piled drums

    International Nuclear Information System (INIS)

    Aoki, H.; Kosaka, T.; Mizushina, T.; Shimizu, M.; Uji, S.; Tsuchiya, H.

    1987-01-01

    In general, low level radioactive waste is packed in drums and stored in a warehouse being piled vertically, or laid horizontally. To observe the behavior of piled drums during an earthquake, an experimental study was reported. The experimental study is limited by the vibrating platform capacity. To carry out these tests up to the supporting limit is not recommended, in view of the vibrating platform curing as well as the operators' security. It is very useful to develop the analytical method for simulating the behavior of the drums. In this report, a computer program of piled drum's dynamic motion is shown, and the analytical result is referred to the experimental result. From the result of experiment on piled drums, the sliding effect has been found to be very important for the stability of drum, and the rocking motion observed, showing a little acceleration is less than the static estimated value. Behavior of piled drums is a complex phenomena comprising of sliding, rocking and jumping

  6. ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

    Directory of Open Access Journals (Sweden)

    Aldert Zomer

    Full Text Available High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.

  7. TRENDS [Transport and Retention of Nuclides in Dominant Sequences]: A code for modeling iodine behavior in containment during severe accidents

    International Nuclear Information System (INIS)

    Weber, C.F.; Beahm, E.C.; Kress, T.S.; Daish, S.R.; Shockley, W.E.

    1989-01-01

    The ultimate aim of a description of iodine behavior in severe LWR accidents is a time-dependent accounting of iodine species released into containment and to the environment. Factors involved in the behavior of iodine can be conveniently divided into four general categories: (1) initial release into containment, (2) interaction of iodine species in containment not directly involving water pools, (3) interaction of iodine species in, or with, water pools, and (4) interaction with special systems such as ice condensers or gas treatment systems. To fill the large gaps in knowledge and to provide a means for assaying the iodine source term, this program has proceeded along two paths: (1) Experimental studies of the chemical behavior of iodine under containment conditions. (2) Development of TRENDS (Transport and Retention of Nuclides in Dominant Sequences), a computer code for modeling the behavior of iodine in containment and its release from containment. The main body of this report consists of a description of TRENDS. These two parts to the program are complementary in that models within TRENDS use data that were produced in the experimental program; therefore, these models are supported by experimental evidence that was obtained under conditions expected in severe accidents. 7 refs., 1 fig., 2 tabs

  8. Towards high-throughput phenotyping of complex patterned behaviors in rodents: focus on mouse self-grooming and its sequencing.

    Science.gov (United States)

    Kyzar, Evan; Gaikwad, Siddharth; Roth, Andrew; Green, Jeremy; Pham, Mimi; Stewart, Adam; Liang, Yiqing; Kobla, Vikrant; Kalueff, Allan V

    2011-12-01

    Increasingly recognized in biological psychiatry, rodent self-grooming is a complex patterned behavior with evolutionarily conserved cephalo-caudal progression. While grooming is traditionally assessed by the latency, frequency and duration, its sequencing represents another important domain sensitive to various experimental manipulations. Such behavioral complexity requires novel objective approaches to quantify rodent grooming, in addition to time-consuming and highly variable manual observation. The present study combined modern behavior-recognition video-tracking technologies (CleverSys, Inc.) with manual observation to characterize in-depth spontaneous (novelty-induced) and artificial (water-induced) self-grooming in adult male C57BL/6J mice. We specifically focused on individual episodes of grooming (paw licking, head washing, body/leg washing, and tail/genital grooming), their duration and transitions between episodes. Overall, the frequency, duration and transitions detected using the automated approach significantly correlated with manual observations (R=0.51-0.7, pgrooming, also indicating that behavior-recognition tools can be applied to characterize both the amount and sequential organization (patterning) of rodent grooming. Together with further refinement and methodological advancement, this approach will foster high-throughput neurophenotyping of grooming, with multiple applications in drug screening and testing of genetically modified animals. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Applying behavior analysis to school violence and discipline problems: Schoolwide positive behavior support

    Science.gov (United States)

    Anderson, Cynthia M.; Kincaid, Donald

    2005-01-01

    School discipline is a growing concern in the United States. Educators frequently are faced with discipline problems ranging from infrequent but extreme problems (e.g., shootings) to less severe problems that occur at high frequency (e.g., bullying, insubordination, tardiness, and fighting). Unfortunately, teachers report feeling ill prepared to deal effectively with discipline problems in schools. Further, research suggests that many commonly used strategies, such as suspension, expulsion, and other reactive strategies, are not effective for ameliorating discipline problems and may, in fact, make the situation worse. The principles and technology of behavior analysis have been demonstrated to be extremely effective for decreasing problem behavior and increasing social skills exhibited by school children. Recently, these principles and techniques have been applied at the level of the entire school, in a movement termed schoolwide positive behavior support. In this paper we review the tenets of schoolwide positive behavior support, demonstrating the relation between this technology and applied behavior analysis. PMID:22478439

  10. Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library.

    Science.gov (United States)

    Zhou, Qiongqiong; Sun, Wenjuan; Liu, Xiyan; Wang, Xiliang; Xiao, Yuncai; Bi, Dingren; Yin, Jingdong; Shi, Deshi

    2016-01-01

    Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis. Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression. This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes provides the necessary foundation for

  11. The Analysis of Verbal Behavior: a Status Update.

    Science.gov (United States)

    Luke, Molli M; Carr, James E

    2015-10-01

    We analyzed past volumes of The Analysis of Verbal Behavior (TAVB) to provide a comprehensive status update after 30 years of publication. Data on TAVB's content, frequent contributors, and scholarly impact suggest a healthy state of the journal.

  12. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

    KAUST Repository

    Doan, Ryan

    2012-02-17

    BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse\\'s genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

  13. Assessing randomness and complexity in human motion trajectories through analysis of symbolic sequences.

    Science.gov (United States)

    Peng, Zhen; Genewein, Tim; Braun, Daniel A

    2014-01-01

    Complexity is a hallmark of intelligent behavior consisting both of regular patterns and random variation. To quantitatively assess the complexity and randomness of human motion, we designed a motor task in which we translated subjects' motion trajectories into strings of symbol sequences. In the first part of the experiment participants were asked to perform self-paced movements to create repetitive patterns, copy pre-specified letter sequences, and generate random movements. To investigate whether the degree of randomness can be manipulated, in the second part of the experiment participants were asked to perform unpredictable movements in the context of a pursuit game, where they received feedback from an online Bayesian predictor guessing their next move. We analyzed symbol sequences representing subjects' motion trajectories with five common complexity measures: predictability, compressibility, approximate entropy, Lempel-Ziv complexity, as well as effective measure complexity. We found that subjects' self-created patterns were the most complex, followed by drawing movements of letters and self-paced random motion. We also found that participants could change the randomness of their behavior depending on context and feedback. Our results suggest that humans can adjust both complexity and regularity in different movement types and contexts and that this can be assessed with information-theoretic measures of the symbolic sequences generated from movement trajectories.

  14. Assessing randomness and complexity in human motion trajectories through analysis of symbolic sequences

    Directory of Open Access Journals (Sweden)

    Zhen ePeng

    2014-03-01

    Full Text Available Complexity is a hallmark of intelligent behavior consisting both of regular patterns and random variation. To quantitatively assess the complexity and randomness of human motion, we designed a motor task in which we translated subjects' motion trajectories into strings of symbol sequences. In the first part of the experiment participants were asked to perform self-paced movements to create repetitive patterns, copy pre-specified letter sequences, and generate random movements. To investigate whether the degree of randomness can be manipulated, in the second part of the experiment participants were asked to perform unpredictable movements in the context of a pursuit game, where they received feedback from an online Bayesian predictor guessing their next move. We analyzed symbol sequences representing subjects' motion trajectories with five common complexity measures: predictability, compressibility, approximate entropy, Lempel-Ziv complexity, as well as effective measure complexity. We found that subjects’ self-created patterns were the most complex, followed by drawing movements of letters and self-paced random motion. We also found that participants could change the randomness of their behavior depending on context and feedback. Our results suggest that humans can adjust both complexity and regularity in different movement types and contexts and that this can be assessed with information-theoretic measures of the symbolic sequences generated from movement trajectories.

  15. Positive Behavioral Interventions and Support as Behavior Analysis in Practice: Why Is This Even Controversial?

    Science.gov (United States)

    Jarmolowicz, David P; Tetreault, Allison S

    2015-05-01

    The inclusion of Positive Behavioral Intervention and Supports as a type of applied behavior analysis has often spurred considerable controversy. This controversy seems related to at least three areas of contention: measurement issues, views on aversive control, and the overall target of treatment. The present paper discusses these three areas in light of Horner and Sugai's target article and the current state of the field of applied behavior analysis. In the end, the authors are left wondering why this is even an ongoing controversy.

  16. Relational classification in behavior analysis and ecological psychology

    OpenAIRE

    Viklund, Johan Sten

    2017-01-01

    Master i læring i komplekse systemer The thesis discusses relational classification in behavior analysis and ecological psychology. First, relational classification within behavior analysis is discussed in a theoretical article. The article aims to technically define the distinction between structure and function. The definition endeavors to be (a) in line with previous usage, (b) pay homage to the idea that different yet continuous functional levels can be studied in their own right, and ...

  17. Relational classification in behavior analysis and ecological psychology

    OpenAIRE

    Viklund, Johan Sten

    2017-01-01

    The thesis discusses relational classification in behavior analysis and ecological psychology. First, relational classification within behavior analysis is discussed in a theoretical article. The article aims to technically define the distinction between structure and function. The definition endeavors to be (a) in line with previous usage, (b) pay homage to the idea that different yet continuous functional levels can be studied in their own right, and (c) be empirically accountable. The phil...

  18. In silico analysis of 3'-end-processing signals in Aspergillus oryzae using expressed sequence tags and genomic sequencing data.

    Science.gov (United States)

    Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

    2011-06-01

    To investigate 3'-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3'-untranslated region (3' UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3' UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3' UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15-30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3'-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3'-end-processing signals are similar to those in yeast and plants, some notable differences exist between them.

  19. Molecular characterization, sequence analysis and tissue expression of a porcine gene – MOSPD2

    Directory of Open Access Journals (Sweden)

    Yang Jie

    2017-01-01

    Full Text Available The full-length cDNA sequence of a porcine gene, MOSPD2, was amplified using the rapid amplification of cDNA ends method based on a pig expressed sequence tag sequence which was highly homologous to the coding sequence of the human MOSPD2 gene. Sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 491 amino acids that has high homology with the motile sperm domain-containing protein 2 (MOSPD2 of five species: horse (89%, human (90%, chimpanzee (89%, rhesus monkey (89% and mouse (85%; thus, it could be defined as a porcine MOSPD2 gene. This novel porcine gene was assigned GeneID: 100153601. This gene is structured in 15 exons and 14 introns as revealed by computer-assisted analysis. The phylogenetic analysis revealed that the porcine MOSPD2 gene has a closer genetic relationship with the MOSPD2 gene of horse. Tissue expression analysis indicated that the porcine MOSPD2 gene is generally and differentially expressed in the spleen, muscle, skin, kidney, lung, liver, fat and heart. Our experiment is the first to establish the primary foundation for further research on the porcine MOSPD2 gene.

  20. Sequence and phylogenetic analysis of chicken anaemia virus obtained from backyard and commercial chickens in Nigeria.

    Science.gov (United States)

    Oluwayelu, D O; Todd, D; Olaleye, O D

    2008-12-01

    This work reports the first molecular analysis study of chicken anaemia virus (CAV) in backyard chickens in Africa using molecular cloning and sequence analysis to characterize CAV strains obtained from commercial chickens and Nigerian backyard chickens. Partial VP1 gene sequences were determined for three CAVs from commercial chickens and for six CAV variants present in samples from a backyard chicken. Multiple alignment analysis revealed that the 6% and 4% nucleotide diversity obtained respectively for the commercial and backyard chicken strains translated to only 2% amino acid diversity for each breed. Overall, the amino acid composition of Nigerian CAVs was found to be highly conserved. Since the partial VP1 gene sequence of two backyard chicken cloned CAV strains (NGR/CI-8 and NGR/CI-9) were almost identical and evolutionarily closely related to the commercial chicken strains NGR-1, and NGR-4 and NGR-5, respectively, we concluded that CAV infections had crossed the farm boundary.

  1. A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis.

    Science.gov (United States)

    Young, Brian; King, Jonathan L; Budowle, Bruce; Armogida, Luigi

    2017-01-01

    Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.

  2. Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

    Science.gov (United States)

    Sato, Shusei; Hirakawa, Hideki; Isobe, Sachiko; Fukai, Eigo; Watanabe, Akiko; Kato, Midori; Kawashima, Kumiko; Minami, Chiharu; Muraki, Akiko; Nakazaki, Naomi; Takahashi, Chika; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Yamada, Manabu; Tsuruoka, Hisano; Sasamoto, Shigemi; Tabata, Satoshi; Aizu, Tomoyuki; Toyoda, Atsushi; Shin-i, Tadasu; Minakuchi, Yohei; Kohara, Yuji; Fujiyama, Asao; Tsuchimoto, Suguru; Kajiyama, Shin'ichiro; Makigano, Eri; Ohmido, Nobuko; Shibagaki, Nakako; Cartagena, Joyce A.; Wada, Naoki; Kohinata, Tsutomu; Atefeh, Alipour; Yuasa, Shota; Matsunaga, Sachihiro; Fukui, Kiichi

    2011-01-01

    The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ∼95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/. PMID:21149391

  3. A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Aditi Sengupta

    2016-03-01

    Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

  4. Identification and sequence analysis of grain softness protein in selected wheat, rye and triticale.

    Science.gov (United States)

    Kharrazi, M A S; Bobojonov, V

    2012-08-16

    Grain softness protein (GSP) is an important protein for overcoming milling and grain defenses in the innate immunity systems of cereals. The objective of this study was to evaluate and understand GSP sequences in selected wheat, rye and triticale. Using sequences for this gene from a sequence database, we performed clustering analysis to compare the sequences obtained from 3 germplasms with other studied sequences for GSP. The maximum difference between the Hirmand GSP genotype in wheat and the database sequences was 23% in EF109396 and EF109399. Most amino acid variation between the GSP sequences involved the same amino acids. The Nikita rye GSP gene showed 64% identity with DQ269918 and AY667063. The isoelectric point in the GSP of wheat and Lasko triticale was significantly higher than that of rye GSP. In addition, parameters such as optical density, grand average of hydrophobicity, percentage of hydrophobicity and hydrophilic amino acids, and number of alpha helices and beta sheets in GSP were similar in wheat and triticale but not in wheat and rye.

  5. Texture analysis of common renal masses in multiple MR sequences for prediction of pathology

    Science.gov (United States)

    Hoang, Uyen N.; Malayeri, Ashkan A.; Lay, Nathan S.; Summers, Ronald M.; Yao, Jianhua

    2017-03-01

    This pilot study performs texture analysis on multiple magnetic resonance (MR) images of common renal masses for differentiation of renal cell carcinoma (RCC). Bounding boxes are drawn around each mass on one axial slice in T1 delayed sequence to use for feature extraction and classification. All sequences (T1 delayed, venous, arterial, pre-contrast phases, T2, and T2 fat saturated sequences) are co-registered and texture features are extracted from each sequence simultaneously. Random forest is used to construct models to classify lesions on 96 normal regions, 87 clear cell RCCs, 8 papillary RCCs, and 21 renal oncocytomas; ground truths are verified through pathology reports. The highest performance is seen in random forest model when data from all sequences are used in conjunction, achieving an overall classification accuracy of 83.7%. When using data from one single sequence, the overall accuracies achieved for T1 delayed, venous, arterial, and pre-contrast phase, T2, and T2 fat saturated were 79.1%, 70.5%, 56.2%, 61.0%, 60.0%, and 44.8%, respectively. This demonstrates promising results of utilizing intensity information from multiple MR sequences for accurate classification of renal masses.

  6. Isolation and sequence analysis of a cDNA clone encoding the fifth complement component

    DEFF Research Database (Denmark)

    Lundwall, Åke B; Wetsel, Rick A; Kristensen, Torsten

    1985-01-01

    clone of 1.85 kilobase pairs was isolated. Hybridization of the mixed-sequence probe to the complementary strand of the plasmid insert and sequence analysis by the dideoxy method predicted the expected protein sequence of C5a (positions 1-12), amino-terminal to the anticipated priming site. The sequence......We have used available protein sequence data for the anaphylatoxin (C5a) portion of the fifth component of human complement (residues 19-25) to synthesize a mixed-sequence oligonucleotide probe. The labeled oligonucleotide was then used to screen a human liver cDNA library, and a single candidate cDNA...... obtained further predicted an arginine-rich sequence (RPRR) immediately upstream of the N-terminal threonine of C5a, indicating that the promolecule form of C5 is synthesized with a beta alpha-chain orientation as previously shown for pro-C3 and pro-C4. The C5 cDNA clone was sheared randomly by sonication...

  7. Multivariable modeling and multivariate analysis for the behavioral sciences

    CERN Document Server

    Everitt, Brian S

    2009-01-01

    Multivariable Modeling and Multivariate Analysis for the Behavioral Sciences shows students how to apply statistical methods to behavioral science data in a sensible manner. Assuming some familiarity with introductory statistics, the book analyzes a host of real-world data to provide useful answers to real-life issues.The author begins by exploring the types and design of behavioral studies. He also explains how models are used in the analysis of data. After describing graphical methods, such as scatterplot matrices, the text covers simple linear regression, locally weighted regression, multip

  8. A graph theoretic approach to the analysis of DNA sequencing data.

    Science.gov (United States)

    Berno, A J

    1996-02-01

    The analysis of data from automated DNA sequencing instruments has been a limiting factor in the development of new sequencing technology. A new base-calling algorithm that is intended to be independent of any particular sequencing technology has been developed and shown to be effective with data from the Applied Biosystems 373 sequencing system. This algorithm makes use of a nonlinear deconvolution filter to detect likely oligomer events and a graph theoretic editing strategy to find the subset of those events that is most likely to correspond to the correct sequence. Metrics evaluating the quality and accuracy of the resulting sequence are also generated and have been shown to be predictive of measured error rates. Compared to the Applied Biosystems Analysis software, this algorithm generates 18% fewer insertion errors, 80% more deletion errors, and 4% fewer mismatches. The tradeoff between different types of errors can be controlled through a secondary editing step that inserts or deletes base calls depending on their associated confidence values.

  9. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

    Directory of Open Access Journals (Sweden)

    Samuel V Angiuoli

    Full Text Available The widespread popularity of genomic applications is threatened by the "bioinformatics bottleneck" resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly.We present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2, which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes and costs associated with different microbial genomics applications. While all 16S analyses completed on a single-CPU desktop in under three hours, microbial genome and metagenome analyses utilized multi-CPU support of up to 120 CPUs on Amazon EC2, where each analysis completed in under 24 hours for less than $60. Representative datasets were used to estimate maximum data throughput on different cluster sizes and to compare costs between EC2 and comparable local grid servers.Although bioinformatics requirements for microbial genomics depend on dataset characteristics and the analysis protocols applied, our results suggests that smaller sequencing facilities (up to three Roche/454 or one Illumina GAIIx sequencer invested in 16S rRNA amplicon sequencing

  10. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

    Science.gov (United States)

    Angiuoli, Samuel V; White, James R; Matalka, Malcolm; White, Owen; Fricke, W Florian

    2011-01-01

    The widespread popularity of genomic applications is threatened by the "bioinformatics bottleneck" resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly. We present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS) sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2), which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes and costs associated with different microbial genomics applications. While all 16S analyses completed on a single-CPU desktop in under three hours, microbial genome and metagenome analyses utilized multi-CPU support of up to 120 CPUs on Amazon EC2, where each analysis completed in under 24 hours for less than $60. Representative datasets were used to estimate maximum data throughput on different cluster sizes and to compare costs between EC2 and comparable local grid servers. Although bioinformatics requirements for microbial genomics depend on dataset characteristics and the analysis protocols applied, our results suggests that smaller sequencing facilities (up to three Roche/454 or one Illumina GAIIx sequencer) invested in 16S rRNA amplicon sequencing, microbial single

  11. A Conceptual Framework for the Analysis of Risk and Problem Behaviors: The Case of Adolescent Sexual Behavior

    Science.gov (United States)

    Guilamo-Ramos; Vincent; Jaccard, James; Dittus, Patricia; Gonzalez, Bernardo; Bouris, Alida

    2008-01-01

    A framework for the analysis of adolescent problem behaviors was explicated that draws on five major theories of human behavior. The framework emphasizes intentions to perform behaviors and factors that influence intentions as well as moderate the impact of intentions on behavior. The framework was applied to the analysis of adolescent sexual risk…

  12. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

    Directory of Open Access Journals (Sweden)

    Lalucat Jorge

    2010-04-01

    Full Text Available Abstract Background The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. Description The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI. Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. Conclusions The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://www.uib.es/microbiologiaBD/Welcome.html. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer

  13. Strategies for exome and genome sequence data analysis in disease-gene discovery projects.

    Science.gov (United States)

    Robinson, Peter N; Krawitz, P; Mundlos, S

    2011-08-01

    In whole-exome sequencing (WES), target capture methods are used to enrich the sequences of the coding regions of genes from fragmented total genomic DNA, followed by massively parallel, 'next-generation' sequencing of the captured fragments. Since its introduction in 2009, WES has been successfully used in several disease-gene discovery projects, but the analysis of whole-exome sequence data can be challenging. In this overview, we present a summary of the main computational strategies that have been applied to identify novel disease genes in whole-exome data, including intersect filters, the search for de novo mutations, and the application of linkage mapping or inference of identity-by-descent (IBD) in family studies. © 2011 John Wiley & Sons A/S.

  14. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing.

    Science.gov (United States)

    González, Roberto; Zato, Carolina; Benito, Rocío; Bajo, Javier; Hernández, Jesús M; De Paz, Juan F; Vera, Vicente; Corchado, Juan M

    2012-12-01

    Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  15. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing

    Directory of Open Access Journals (Sweden)

    González Roberto

    2012-12-01

    Full Text Available Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  16. Capillary electrophoresis fragment analysis and clone sequencing in detection of dynamic mutations of spinocerebellar ataxia

    Directory of Open Access Journals (Sweden)

    Yuan-yuan CHEN

    2018-04-01

    Full Text Available Objective To estimate the accuracy and stability of capillary electrophoresis fragment analysis and clone sequencing in detecting dynamic mutations of spinocerebellar ataxia (SCA. Methods Capillary electrophoresis fragment analysis and clone sequencing were used in detecting trinucleotide repeated sequence of 14 SCA patients (3 cases of SCA2, 2 cases of SCA7, 7 cases of SCA8 and 2 cases of SCA17. Results Capillary electrophoresis fragment analysis of 3 SCA2 cases showed the expanded cytosine-adenine-guanine (CAG repeats were 31, 30 and 32, and the copy numbers of 3 clone sequencing for 3 colonies in each case were 37/40/40, 37/38/39 and 38/39/40 respectively. Capillary electrophoresis fragment analysis of 2 SCA7 cases showed the expanded CAG repeats were 57 and 34, and the copy numbers of repeats were 69, 74, 75 in 3 colonies of one case, and was 45 in the other case. For the 7 SCA8 cases with the expanded cytosine-thymine-adenine (CTA/cytosine-thymine-guanine (CTG repeats of 99, 111, 104, 92, 89, 104 and 75, the results of clone sequencing were 97, 116, 104, 90, 90, 102 and 76 respectively. For 2 SCA17 cases with the short/expanded CAG repeats of 37/50 and 36/45, the results of clone sequencing were 51/50/52 and 45/44 for 3 and 2 colonies. Conclusions Although the higher mobility of polymerase chain reaction (PCR products containing dynamic mutation in the capillary electrophoresis fragment analysis might cause the deviation for analysis of copy numbers, the deviation was predictable and the results were repeatable. The clone sequencing results showed obvious instability, especially for SCA2 and SCA7 genes, which might owing to their simple CAG repeats. Consequently, clone sequencing is not suited for detection of dynamic mutation, not to mention the quantitative criteria of dynamic mutation sequencing. DOI: 10.3969/j.issn.1672-6731.2018.03.008

  17. Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus.

    Science.gov (United States)

    Liu, Wen-Chun; Lin, Chih-Peng; Cheng, Chun-Pei; Ho, Cheng-Hsun; Lan, Kuo-Lun; Cheng, Ji-Hong; Yen, Chia-Jui; Cheng, Pin-Nan; Wu, I-Chin; Li, I-Chen; Chang, Bill Chia-Han; Tseng, Vincent S; Chiu, Yen-Cheng; Chang, Ting-Tsung

    2016-01-01

    Hepatitis B virus (HBV) quasispecies are crucial in the pathogenesis of chronic liver disease. Next-generation sequencing (NGS) is powerful for identifying viral quasispecies. To improve mapping quality and single nucleotide variant (SNV) calling accuracy in the NGS analysis of HBV, we compared different mapping references, including the sample-specific reference sequence, same genotype sequences and different genotype sequences, according to the sample. Real Illumina HBV datasets from 86 patients, and simulated datasets from 158 HBV strains in the GenBank database, were used to assess mapping quality. SNV calling accuracy was evaluated using different mapping references to align Real Illumina datasets from a single HBV clone. Using the sample-specific reference sequence as a mapping reference produced the largest number of mappable reads and coverages. With a different genotype mapping reference, the consensus sequence derived from the Real Illumina datasets of the single HBV clone showed 21 false SNV callings in polymerase and surface genes, the regions most divergent between the mapping reference and this HBV clone. A ~6 % coverage of most of these false SNVs was yielded even with a same genotype mapping reference, but none with the sample-specific reference sequence. Using sample-specific reference sequences as a mapping reference in NGS analysis optimized mapping quality and the SNV calling accuracy for HBV quasispecies.

  18. Statistical power analysis for the behavioral sciences

    National Research Council Canada - National Science Library

    Cohen, Jacob

    1988-01-01

    ... offers a unifying framework and some new data-analytic possibilities. 2. A new chapter (Chapter 11) considers some general topics in power analysis in more integrted form than is possible in the earlier...

  19. Statistical power analysis for the behavioral sciences

    National Research Council Canada - National Science Library

    Cohen, Jacob

    1988-01-01

    .... A chapter has been added for power analysis in set correlation and multivariate methods (Chapter 10). Set correlation is a realization of the multivariate general linear model, and incorporates the standard multivariate methods...

  20. New insights on co- and post-seismic deformation and slip behavior associated with the Mw7.8 2016 Pedernales, Ecuador earthquake and its aftershock sequence

    Science.gov (United States)

    Soto-Cordero, L.; Nealy, J. L.; Meltzer, A.; Agurto-Detzel, H.; Alvarado, A. P.; Beck, S. L.; Benz, H.; Bergman, E. A.; Charvis, P.; Font, Y.; Hayes, G. P.; Hernandez, S.; Hoskins, M.; Leon Rios, S.; Lynner, C.; Regnier, M. M.; Rietbrock, A.; Stachnik, J. C.; Yeck, W. L.

    2017-12-01

    On April 16, 2016, a Mw7.8 earthquake, associated with oblique subduction of the Nazca Plate under South America, ruptured a segment approximately 130x100km in the region north of the intersection of the Carnegie ridge with the Ecuador subduction zone. The rupture coincides with the rupture area of the Mw7.8 1942 earthquake. To characterize the aftershock sequence, we analyze seismic data recorded by 30 stations from April 17, 2016 to May 8, 2017; 11 stations belong to Ecuador's national network and 19 are part of a PASSCAL temporary deployment. We apply a kurtosis detector to obtain automatic P- and S-wave picks. Earthquake locations, magnitudes, and regional moment tensors are obtained using the U.S. Geological Survey National Earthquake Information Center (NEIC) processing system. We also determine calibrated relocations using the Hypocentroidal Decomposition approach for a subset of events for which we combine phase readings from local and temporary PASSCAL stations with regional and teleseismic phase readings from the NEIC. In contrast with other earthquake relocation approaches, this method evaluates absolute location uncertainties for each event in the cluster, which allows us to more confidently assess the relationships between mainshock slip and aftershock activity. We find the aftershock sequence is characterized by a series of event clusters that predominantly surround the main rupture patches. However, the aftershocks extend beyond the mainshock rupture area, covering a region approximately 250x100km. Aftershocks north of the 2016 rupture fall in the rupture area of the Mw7.7 1958 earthquake. The southernmost region of elevated seismicity occurs south of a region of low coupling where the Carnegie ridge meets the subduction zone. The characterization of this sequence allows a detailed spatial and temporal analysis of the rupture processes, stress patterns and slip behavior during this earthquake sequence in Ecuador subduction zone.

  1. Analysis Of Segmental Duplications In The Pig Genome Based On Next-Generation Sequencing

    DEFF Research Database (Denmark)

    Fadista, João; Bendixen, Christian

    extensively studied in other organisms, its analysis in pig has been hampered by the lack of a complete pig genome assembly. By measuring the depth of coverage of Illumina whole-genome shotgun sequencing reads of the Tabasco animal aligned to the latest pig genome assembly (Sus scrofa 10 – based also...... on Tabasco), led us to the detection of a high-resolution map of segmental duplications in the pig genome. Comparing these segments with four other Duroc animals sequenced at our institute, supplied the resources needed to describe the first genome-wide and systematic analysis of segmental duplications...

  2. Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements

    Directory of Open Access Journals (Sweden)

    Temple Matthew H

    2007-03-01

    Full Text Available Abstract Background Completion of the human genome sequence along with other species allows for greater understanding of the biochemical mechanisms and processes that govern healthy as well as diseased states. The large size of the genome sequences has made them difficult to study using traditional methods. There are many studies focusing on the protein coding sequences, however, not much is known about the function of non-coding regions of the genome. It has been demonstrated that parts of the non-coding region play a critical role as gene regulatory elements. Enhancers that regulate transcription processes have been found in intergenic regions. Furthermore, it is observed that regulatory elements found in non-coding regions are highly conserved across different species. However, the analysis of these regulatory elements is not as straightforward as it may first seem. The development of a centralized resource that allows for the quick and easy retrieval of non-coding sequences from multiple species and is capable of handing multi-gene queries is critical for the analysis of non-coding sequences. Here we describe the development of a web-based non-coding sequence retrieval system. Results This paper presents a Non-Coding Sequences Retrieval System (NCSRS. The NCSRS is a web-based bioinformatics tool that performs fast and convenient retrieval of non-coding and coding sequences from multiple species related to a specific gene or set of genes. This tool has compiled resources from multiple sources into one easy to use and convenient web based interface. With no software installation necessary, the user needs only internet access to use this tool. Conclusion The unique features of this tool will be very helpful for those studying gene regulatory elements that exist in non-coding regions. The web based application can be accessed on the internet at: http://cell.rutgers.edu/ncsrs/.

  3. Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

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    Inês C Conceição

    Full Text Available BACKGROUND: Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. METHODOLOGY/PRINCIPAL FINDINGS: We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes. CONCLUSIONS: The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1 the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2 the high

  4. Facies analysis and sequence stratigraphy of the Eocene successions, east Beni Suef area, eastern Desert, Egypt

    Science.gov (United States)

    Saber, Shaban G.; Salama, Yasser F.

    2017-11-01

    Three Eocene stratigraphic successions east of the Beni Suef area are described and measured. These successions are made up of four rock units that are from base to top: Qarara (upper Lutetian), El Fashn (Bartonian), Beni Suef, and Maadi (Priabonian) formations. A detailed facies and sequence analysis unravels the stratigraphic framework and constructs a depositional model for the Middle-Upper Eocene succession. Ten microfacies types were grouped into four facies associations on a homoclinal ramp that compose the Upper Lutetian-Priabonian succession exposed in the east Beni Suef area. The depositional environment varied from a shallow to deep ramp setting. Four third-order depositional sequences were identified in the studied sections. The sequence boundaries are paleosoil horizons that can be traced throughout the entire outcrop area. Missing biozones are also evidence of the sequence boundaries. The history of these sequences mirrors the eustatic sea-level changes and the local tectonics in the region. Each sequence comprises facies associations that make up lowstand and/or transgressive and highstand systems tracts. The lowstand systems tract (LST) deposits are mainly sandstone facies and in Sequences 3 and 4 at Gabal Abyiad and Gabal Homret Shaibun respectively. The transgressive systems tract (TST) of Sequence 1 is dominated by nummulitic facies at Gabal Diya. The shale, mudstone and wackestone facies with planktic foraminifera and echinoids dominate the TST of Sequences 2 and 3 at Gabal Abyiad and Gabal Homret Shaibun respectively. The highstand systems tract (HST) of the studied sections is characterized by benthic foraminifera and bryozoan wackestone and packstone facies.

  5. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Science.gov (United States)

    Liu, Hongliang; Wang, Tingting; Wang, Jinke; Quan, Fusheng; Zhang, Yong

    2013-01-01

    Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology. Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51%) unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17%) unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes. The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  6. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Hongliang Liu

    Full Text Available Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology.Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51% unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17% unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes.The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  7. Behavioral Finances versus Technical and Fundamental Analysis

    Directory of Open Access Journals (Sweden)

    Ion Stancu

    2007-01-01

    Full Text Available Although the field of modern finance has progressed impressively, it is still hard to explain on a scientific basis why people behave nonrationally when dealing with money. The classic finance assumes people rationalize and optimize their financial decisions. Behavioral Finance adds the importance of what investors should do and complements the mantra of classic finance with what people actually do, in terms of economic decisions. The new field of Neuroeconomy investigates the subtle and profound interactions within the human brain when faced with uncertainties of an economic decision. The most basic psychological traits of human being (fear, anger, greed and altruism stamp an indelible mark on our decisions about money. The intellect (understanding a situation, reason (long term consequences of the contemplated action and emotion (the judge of the course of action are all intercorrelated resorts behind human decision making.

  8. Dual-tracer PET using generalized factor analysis of dynamic sequences.

    Science.gov (United States)

    El Fakhri, Georges; Trott, Cathryn M; Sitek, Arkadiusz; Bonab, Ali; Alpert, Nathaniel M

    2013-12-01

    With single-photon emission computed tomography, simultaneous imaging of two physiological processes relies on discrimination of the energy of the emitted gamma rays, whereas the application of dual-tracer imaging to positron emission tomography (PET) imaging has been limited by the characteristic 511-keV emissions. To address this limitation, we developed a novel approach based on generalized factor analysis of dynamic sequences (GFADS) that exploits spatio-temporal differences between radiotracers and applied it to near-simultaneous imaging of 2-deoxy-2-[(18)F]fluoro-D-glucose (FDG) (brain metabolism) and (11)C-raclopride (D2) with simulated human data and experimental rhesus monkey data. We show theoretically and verify by simulation and measurement that GFADS can separate FDG and raclopride measurements that are made nearly simultaneously. The theoretical development shows that GFADS can decompose the studies at several levels: (1) It decomposes the FDG and raclopride study so that they can be analyzed as though they were obtained separately. (2) If additional physiologic/anatomic constraints can be imposed, further decomposition is possible. (3) For the example of raclopride, specific and nonspecific binding can be determined on a pixel-by-pixel basis. We found good agreement between the estimated GFADS factors and the simulated ground truth time activity curves (TACs), and between the GFADS factor images and the corresponding ground truth activity distributions with errors less than 7.3 ± 1.3 %. Biases in estimation of specific D2 binding and relative metabolism activity were within 5.9 ± 3.6 % compared to the ground truth values. We also evaluated our approach in simultaneous dual-isotope brain PET studies in a rhesus monkey and obtained accuracy of better than 6 % in a mid-striatal volume, for striatal activity estimation. Dynamic image sequences acquired following near-simultaneous injection of two PET radiopharmaceuticals can be separated

  9. A probabilistic cell model in background corrected image sequences for single cell analysis

    Directory of Open Access Journals (Sweden)

    Fieguth Paul

    2010-10-01

    Full Text Available Abstract Background Methods of manual cell localization and outlining are so onerous that automated tracking methods would seem mandatory for handling huge image sequences, nevertheless manual tracking is, astonishingly, still widely practiced in areas such as cell biology which are outside the influence of most image processing research. The goal of our research is to address this gap by developing automated methods of cell tracking, localization, and segmentation. Since even an optimal frame-to-frame association method cannot compensate and recover from poor detection, it is clear that the quality of cell tracking depends on the quality of cell detection within each frame. Methods Cell detection performs poorly where the background is not uniform and includes temporal illumination variations, spatial non-uniformities, and stationary objects such as well boundaries (which confine the cells under study. To improve cell detection, the signal to noise ratio of the input image can be increased via accurate background estimation. In this paper we investigate background estimation, for the purpose of cell detection. We propose a cell model and a method for background estimation, driven by the proposed cell model, such that well structure can be identified, and explicitly rejected, when estimating the background. Results The resulting background-removed images have fewer artifacts and allow cells to be localized and detected more reliably. The experimental results generated by applying the proposed method to different Hematopoietic Stem Cell (HSC image sequences are quite promising. Conclusion The understanding of cell behavior relies on precise information about the temporal dynamics and spatial distribution of cells. Such information may play a key role in disease research and regenerative medicine, so automated methods for observation and measurement of cells from microscopic images are in high demand. The proposed method in this paper is capable

  10. Dual-Tracer PET Using Generalized Factor Analysis of Dynamic Sequences

    Science.gov (United States)

    Fakhri, Georges El; Trott, Cathryn M.; Sitek, Arkadiusz; Bonab, Ali; Alpert, Nathaniel M.

    2013-01-01

    Purpose With single-photon emission computed tomography, simultaneous imaging of two physiological processes relies on discrimination of the energy of the emitted gamma rays, whereas the application of dual-tracer imaging to positron emission tomography (PET) imaging has been limited by the characteristic 511-keV emissions. Procedures To address this limitation, we developed a novel approach based on generalized factor analysis of dynamic sequences (GFADS) that exploits spatio-temporal differences between radiotracers and applied it to near-simultaneous imaging of 2-deoxy-2-[18F]fluoro-D-glucose (FDG) (brain metabolism) and 11C-raclopride (D2) with simulated human data and experimental rhesus monkey data. We show theoretically and verify by simulation and measurement that GFADS can separate FDG and raclopride measurements that are made nearly simultaneously. Results The theoretical development shows that GFADS can decompose the studies at several levels: (1) It decomposes the FDG and raclopride study so that they can be analyzed as though they were obtained separately. (2) If additional physiologic/anatomic constraints can be imposed, further decomposition is possible. (3) For the example of raclopride, specific and nonspecific binding can be determined on a pixel-by-pixel basis. We found good agreement between the estimated GFADS factors and the simulated ground truth time activity curves (TACs), and between the GFADS factor images and the corresponding ground truth activity distributions with errors less than 7.3±1.3 %. Biases in estimation of specific D2 binding and relative metabolism activity were within 5.9±3.6 % compared to the ground truth values. We also evaluated our approach in simultaneous dual-isotope brain PET studies in a rhesus monkey and obtained accuracy of better than 6 % in a mid-striatal volume, for striatal activity estimation. Conclusions Dynamic image sequences acquired following near-simultaneous injection of two PET radiopharmaceuticals

  11. Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons.

    Science.gov (United States)

    Diaz de Arce, Alexander J; Noderer, William L; Wang, Clifford L

    2018-01-25

    The initiation of mRNA translation from start codons other than AUG was previously believed to be rare and of relatively low impact. More recently, evidence has suggested that as much as half of all translation initiation utilizes non-AUG start codons, codons that deviate from AUG by a single base. Furthermore, non-AUG start codons have been shown to be involved in regulation of expression and disease etiology. Yet the ability to gauge expression based on the sequence of a translation initiation site (start codon and its flanking bases) has been limited. Here we have performed a comprehensive analysis of translation initiation sites that utilize non-AUG start codons. By combining genetic-reporter, cell-sorting, and high-throughput sequencing technologies, we have analyzed the expression associated with all possible variants of the -4 to +4 positions of non-AUG translation initiation site motifs. This complete motif analysis revealed that 1) with the right sequence context, certain non-AUG start codons can generate expression comparable to that of AUG start codons, 2) sequence context affects each non-AUG start codon differently, and 3) initiation at non-AUG start codons is highly sensitive to changes in the flanking sequences. Complete motif analysis has the potential to be a key tool for experimental and diagnostic genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. The development of human behavior analysis techniques

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jung Woon; Lee, Yong Hee; Park, Geun Ok; Cheon, Se Woo; Suh, Sang Moon; Oh, In Suk; Lee, Hyun Chul; Park, Jae Chang

    1997-07-01

    In this project, which is to study on man-machine interaction in Korean nuclear power plants, we developed SACOM (Simulation Analyzer with a Cognitive Operator Model), a tool for the assessment of task performance in the control rooms using software simulation, and also develop human error analysis and application techniques. SACOM was developed to assess operator`s physical workload, workload in information navigation at VDU workstations, and cognitive workload in procedural tasks. We developed trip analysis system including a procedure based on man-machine interaction analysis system including a procedure based on man-machine interaction analysis and a classification system. We analyzed a total of 277 trips occurred from 1978 to 1994 to produce trip summary information, and for 79 cases induced by human errors time-lined man-machine interactions. The INSTEC, a database system of our analysis results, was developed. The MARSTEC, a multimedia authoring and representation system for trip information, was also developed, and techniques for human error detection in human factors experiments were established. (author). 121 refs., 38 tabs., 52 figs.

  13. Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.

    Directory of Open Access Journals (Sweden)

    Jaeyoung Choi

    2017-12-01

    Full Text Available The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012 was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H. annosum has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of H. annosum genome sequences were aligned with those of previously sequenced H. irregulare TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of H. annosum were aligned against the genome sequences of H. irregulare, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two Heterobasidion spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.

  14. A preliminary analysis of a behavioral classrooms needs assessment

    Directory of Open Access Journals (Sweden)

    Justin B. Leaf

    2016-12-01

    Full Text Available Today many special education classrooms implement procedures based upon the principles of Applied Behavior Analysis (ABA to establish educationally relevant skills and decrease aberrant behaviors. However, it is difficult for school staff and consultants to evaluate the implementation of various components of ABA and general classroom set up. In the present study we developed the Behavioral Classroom Needs Assessment as a tool to measure the quality of implementation of principles derived from ABA, teaching, and classroom set up in special education classrooms. Experiment 1 evaluated the reliability of two observers using the Behavioral Classroom Needs Assessment during 128 different observations across 68 different special education classrooms. An Intraclass Correlation Coefficient and Cronbach Alpha Analysis were utilized to determine reliability, and the results showed a high f of reliability across the 40 questions of the assessment. Experiment 2 compared the quality of intervention using the Behavioral Classroom Needs Assessment in five classrooms who received behavioral consultation and five classrooms that did not receive behavioral consultation. The results showed an improvement in the scores on the Behavioral Classroom Needs Assessment for those classrooms in which consultation occurred.

  15. A Preliminary Analysis of a Behavioral Classrooms Needs Assessment

    Directory of Open Access Journals (Sweden)

    Justin B. LEAF

    2016-12-01

    Full Text Available Today many special education classrooms implement procedures based upon the principles of Applied Behavior Analysis (ABA to establish educationally relevant skills and decrease aberrant behaviors. However, it is difficult for school staff and consultants to evaluate the implementation of various components of ABA and general classroom set up. In the present study we developed the Behavioral Classroom Needs Assessment as a tool to measure the quality of implementation of principles derived from ABA, teaching, and classroom set up in special education classrooms. Experiment 1 evaluated the reliability of two observers using the Behavioral Classroom Needs Assessment during 128 different observations across 68 different special education classrooms. An Intraclass Correlation Coefficient and Cronbach Alpha Analysis were utilized to determine reliability, and the results showed a high f of reliability across the 40 questions of the assessment. Experiment 2 compared the quality of intervention using the Behavioral Classroom Needs Assessment in five classrooms who received behavioral consultation and five classrooms that did not receive behavioral consultation. The results showed an improvement in the scores on the Behavioral Classroom Needs Assessment for those classrooms in which consultation occurred.

  16. Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis.

    Science.gov (United States)

    Goldfeder, Rachel L; Wall, Dennis P; Khoury, Muin J; Ioannidis, John P A; Ashley, Euan A

    2017-10-15

    Most human diseases have underlying genetic causes. To better understand the impact of genes on disease and its implications for medicine and public health, researchers have pursued methods for determining the sequences of individual genes, then all genes, and now complete human genomes. Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then computationally reordered and analyzed, enables fast and affordable sequencing of full human genomes. As the price of sequencing continues to decline, more and more individuals are having their genomes sequenced. This may facilitate better population-level disease subtyping and characterization, as well as individual-level diagnosis and personalized treatment and prevention plans. In this review, we describe several massively parallel high-throughput DNA sequencing technologies and their associated strengths, limitations, and error modes, with a focus on applications in epidemiologic research and precision medicine. We detail the methods used to computationally process and interpret sequence data to inform medical or preventative action. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Swimming behavior of zebrafish is accurately classified by direct modeling and behavioral space analysis

    Science.gov (United States)

    Feng, Ruopei; Chemla, Yann; Gruebele, Martin

    Larval zebrafish is a popular organism in the search for the correlation between locomotion behavior and neural pathways because of their highly stereotyped and temporally episodic swimming motion. This correlation is usually investigated using electrophysiological recordings of neural activities in partially immobilized fish. Seeking for a way to study animal behavior without constraints or intruding electrodes, which can in turn modify their behavior, our lab has introduced a parameter-free approach which allows automated classification of the locomotion behaviors of freely swimming fish. We looked into several types of swimming bouts including free swimming and two modes of escape responses and established a new classification of these behaviors. Combined with a neurokinematic model, our analysis showed the capability to probe intrinsic properties of the underlying neural pathways of freely swimming larval zebrafish by inspecting swimming movies only.

  18. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags

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    Moerman Donald G

    2008-07-01

    Full Text Available Abstract Background We have applied a high-throughput pyrosequencing technology for transcriptome profiling of Caenorhabditis elegans in its first larval stage. Using this approach, we have generated a large amount of data for expressed sequence tags, which provides an opportunity for the discovery of putative novel transcripts and alternative splice variants that could be developmentally specific to the first larval stage. This work also demonstrates the successful and efficient application of a next generation sequencing methodology. Results We have generated over 30 million bases of novel expressed sequence tags from first larval stage worms utilizing high-throughput sequencing technology. We have shown that approximately 14% of the newly sequenced expressed sequence tags map completely or partially to genomic regions where there are no annotated genes or splice variants and therefore, imply that these are novel genetic structures. Expressed sequence tags, which map to intergenic (around 1000 and intronic regions (around 580, may represent novel transcribed regions, such as unannotated or unrecognized small protein-coding or non-protein-coding genes or splice variants. Expressed sequence tags, which map across intron-exon boundaries (around 300, indicate possible alternative splice sites, while expressed sequence tags, which map near the ends of known transcripts (around 600, suggest extension of the coding or untranslated regions. We have also discovered that intergenic and intronic expressed sequence tags, which are well conserved across different nematode species, are likely to represent non-coding RNAs. Lastly, we have incorporated available serial analysis of gene expression data generated from first larval stage worms, in order to predict novel transcripts that might be specifically or predominantly expressed in the first larval stage. Conclusion We have demonstrated the use of a high-throughput sequencing methodology to efficiently

  19. A strategic stakeholder approach for addressing further analysis requests in whole genome sequencing research.

    Science.gov (United States)

    Thornock, Bradley Steven O

    2016-01-01

    Whole genome sequencing (WGS) can be a cost-effective and efficient means of diagnosis for some children, but it also raises a number of ethical concerns. One such concern is how researchers derive and communicate results from WGS, including future requests for further analysis of stored sequences. The purpose of this paper is to think about what is at stake, and for whom, in any solution that is developed to deal with such requests. To accomplish this task, this paper will utilize stakeholder theory, a common method used in business ethics. Several scenarios that connect stakeholder concerns and WGS will also posited and analyzed. This paper concludes by developing criteria composed of a series of questions that researchers can answer in order to more effectively address requests for further analysis of stored sequences.

  20. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis.

    Directory of Open Access Journals (Sweden)

    Li-Hui Zuo

    Full Text Available Elm (Ulmus has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections separated by a pair of inverted repeats (IRs. The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137-145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA+, trnL-TAA-, rpoC1-, rpl2-, ndhA-, ycf1, rps12-, rps12+, trnA-TGC+, trnA-TGC-, trnV-TAC-, trnI-GAT+, and trnI-GAT were shared among all five species. The intron of ycf1 was the longest (5,675bp while that of trnF-AAA was the smallest (53bp. All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be

  1. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis.

    Science.gov (United States)

    Zuo, Li-Hui; Shang, Ai-Qin; Zhang, Shuang; Yu, Xiao-Yue; Ren, Ya-Chao; Yang, Min-Sheng; Wang, Jin-Mao

    2017-01-01

    Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137-145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA+, trnL-TAA-, rpoC1-, rpl2-, ndhA-, ycf1, rps12-, rps12+, trnA-TGC+, trnA-TGC-, trnV-TAC-, trnI-GAT+, and trnI-GAT) were shared among all five species. The intron of ycf1 was the longest (5,675bp) while that of trnF-AAA was the smallest (53bp). All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be confirmed with a

  2. A Behavioral Analysis of Morality and Value.

    Science.gov (United States)

    Hocutt, Max

    2013-01-01

    Morality has long been conceived as divinely instituted, so otherworldly, rules meant not to describe or explain behavior but to guide it towards an absolute good. The philosophical formulation of this theory by Plato was later grafted onto Christian thought by Augustine and Aquinas. The equally ancient theory of the Greek sophist Protagoras (that the good is relative to personal preferences and morality to man-made social customs) was forgotten until revived in the 18th and 19th centuries by such empiricists as David Hume and J. S. Mill. Then it was dismissed again in the 20th century by G. E. Moore and W. D. Ross as naturalistic fallacy, that is, conflation of what is with what ought to be. However, those who took this dismissive attitude themselves made the reverse mistake of conflating what ideally ought to be with what actually is. In other words, they mistook ideals for actualities. As B. F. Skinner (1971) said in Beyond Freedom and Dignity , sorting things out requires behaviorist parsing of the good (the personally reinforcing) and duty (the socially reinforced).

  3. Essays to the application of behavioral economic concepts to the analysis of health behavior

    OpenAIRE

    Panidi, Ksenia

    2012-01-01

    In this thesis I apply the concepts of Behavioral Economics to the analysis of the individual health care behavior. In the first chapter I provide a theoretical explanation of the link between loss aversion and health anxiety leading to infrequent preventive testing. In the second chapter I analyze this link empirically based on the general population questionnaire study. In the third chapter I theoretically explore the effects of motivational crowding-in and crowding-out induced by external ...

  4. Essays on the Application of Behavioral Economic Concepts to the Analysis of Health Behavior.

    OpenAIRE

    Panidi, Ksenia

    2012-01-01

    In this thesis I apply the concepts of Behavioral Economics to the analysis of the individual health care behavior. In the first chapter I provide a theoretical explanation of the link between loss aversion and health anxiety leading to infrequent preventive testing. In the second chapter I analyze this link empirically based on the general population questionnaire study. In the third chapter I theoretically explore the effects of motivational crowding-in and crowding-out induced by external ...

  5. Antibody V and C domain sequence, structure, and interaction analysis with special reference to IMGT®.

    Science.gov (United States)

    Alamyar, Eltaf; Giudicelli, Véronique; Duroux, Patrice; Lefranc, Marie-Paule

    2014-01-01

    IMGT(®), the international ImMunoGeneTics information system(®) (http://www.imgt.org), created in 1989 (Centre National de la Recherche Scientifique, Montpellier University), is acknowledged as the global reference in immunogenetics and immunoinformatics. The accuracy and the consistency of the IMGT(®) data are based on IMGT-ONTOLOGY which bridges the gap between genes, sequences, and three-dimensional (3D) structures. Thus, receptors, chains, and domains are characterized with the same IMGT(®) rules and standards (IMGT standardized labels, IMGT gene and allele nomenclature, IMGT unique numbering, IMGT Collier de Perles), independently from the molecule type (genomic DNA, complementary DNA, transcript, or protein) or from the species. More particularly, IMGT(®) tools and databases provide a highly standardized analysis of the immunoglobulin (IG) or antibody and T cell receptor (TR) V and C domains. IMGT/V-QUEST analyzes the V domains of IG or TR rearranged nucleotide sequences, integrates the IMGT/JunctionAnalysis and IMGT/Automat tools, and provides IMGT Collier de Perles. IMGT/HighV-QUEST analyzes sequences from high-throughput sequencing (HTS) (up to 150,000 sequences per batch) and performs statistical analysis on up to 450,000 results, with the same resolution and high quality as IMGT/V-QUEST online. IMGT/DomainGapAlign analyzes amino acid sequences of V and C domains and IMGT/3Dstructure-DB and associated tools provide information on 3D structures, contact analysis, and paratope/epitope interactions. These IMGT(®) tools and databases, and the IMGT/mAb-DB interface with access to therapeutical antibody data, provide an invaluable help for antibody engineering and antibody humanization.

  6. Gestural overlap of stop-consonant sequences: Evidence from analysis and synthesis

    Science.gov (United States)

    Zhao, Sherry; Stevens, Kenneth N.

    2003-04-01

    This study uses an analysis-by-synthesis approach to discover possible principles governing the coordination of oral and laryngeal articulators in the production of English stop-consonant sequences. Individual recordings were made of two male and two female native American-English speakers reading phrases which include voiced and voiceless stop consonants in word-initial (V#CV) and word-final (VC#V) positions, as well as in VC#CV stop-stop consonant sequences. Articulatory timing estimates were made based on analyzing acoustic data including formant movements, closure durations, release bursts, and spectrum shape at low frequencies. Based on the gestural estimates, the same consonant sequences were generated using HLsyn, a quasiarticulatory synthesizer. The synthetic utterances were acoustically and perceptually compared to the actual utterances in order to verify and refine the articulatory timing estimates from which possible principles could be derived. Preliminary results agree with earlier findings of more overlapping of oral gestures in sequences with front-to-back order of place of articulation than those with back-to-front order [Chitoran, Goldstein, and Byrd, Lab. Phonology 7, 419-448 (2002)]. Furthermore, overlapping of laryngeal gestures is suggested by the smaller acoustical loss at the glottis in vowels after voiced-voiceless sequences than voiceless-voiceless sequences.

  7. Sequence analysis and genetic diversity of five new Indian isolates of cucumber mosaic virus.

    Science.gov (United States)

    Kumar, S; Gautam, K K; Raj, S K

    2015-12-01

    Cucumber mosaic virus (CMV) is an important virus since it causes severe losses to many economically important crops worldwide. Five new isolates of CMV were isolated from naturally infected Hippeastrum hybridum, Dahlia pinnata, Hemerocallis fulva, Acorus calamus and Typhonium trilobatum plants, all exhibiting severe leaf mosaic symptoms. For molecular identification and sequence analyses, the complete coat protein (CP) gene of these isolates was amplified by RT-PCR. The resulting amplicons were cloned and sequenced and isolates were designated as HH (KP698590), DP (JF682239), HF (KP698589), AC (KP698588) and TT (JX570732). For study of genetic diversity among these isolates, the sequence data were analysed by BLASTn, multiple alignment and generating phylogenetic trees along with the respective sequences of other CMV isolates available in GenBank Database were done. The isolates under study showed 82-99% sequence diversity among them at nucleotide and amino acid levels; however they showed close relationships with CMV isolates of subgroup IB. In alignment analysis of amino acid sequences of HH and AC isolates, we have found fifteen and twelve unique substitutions, compared to HF, DP and TT isolates, suggesting the cause of high genetic diversity.

  8. Characterization of squid enolase mRNA: sequence analysis, tissue distribution, and axonal localization.

    Science.gov (United States)

    Chun, J T; Gioio, A E; Crispino, M; Giuditta, A; Kaplan, B B

    1995-08-01

    Enolase is a glycolytic enzyme whose amino acid sequence is highly conserved across a wide range of animal species. In mammals, enolase is known to be a dimeric protein composed of distinct but closely related subunits: alpha (non-neuronal), beta (muscle-specific), and gamma (neuron-specific). However, little information is available on the primary sequence of enolase in invertebrates. Here we report the isolation of two overlapping cDNA clones and the putative primary structure of the enzyme from the squid (Loligo pealii) nervous system. The composite sequence of those cDNA clones is 1575 bp and contains the entire coding region (1302 bp), as well as 66 and 207 bp of 5' and 3' untranslated sequence, respectively. Cross-species comparison of enolase primary structure reveals that squid enolase shares over 70% sequence identity to vertebrate forms of the enzyme. The greatest degree of sequence similarity was manifest to the alpha isoform of the human homologue. Results of Northern analysis revealed a single 1.6 kb mRNA species, the relative abundance of which differs approximately 10-fold between various tissues. Interestingly, evidence derived from in situ hybridization and polymerase chain reaction experiments indicate that the mRNA encoding enolase is present in the squid giant axon.

  9. Sequencing and phylogenetic analysis of partial CXCR2 gene of Murrah buffalo

    Directory of Open Access Journals (Sweden)

    S. A. Wani

    2014-05-01

    Full Text Available Aim: Present study was carried out to sequence and phylogenetic analysis of CXCR2 gene of Murrah buffalo. Materials and Methods: For the present investigation, from a group of forty eight Murrah buffaloes (Bubalus bubalis, blood samples were collected randomly from eight animals, out of which four were healthy and four were mastitic. Results: The amplification of Interleukin-8B (IL-8B receptor gene target sequence was carried out using the primer pair in an optimized polymerase chain reaction. Partial sequencing of IL-8B receptor gene of Bubalus bubalis (Murrah has been done successfully. The sequences of IL-8B receptor gene showed 99% homology to that of Bos indicus × Bos taurus, 98% to that of Bos taurus, 97% to that of Ovis aries, 93% to that of Sus scrofa, 92% to that of Equus caballus and 90% to that of Felis catus. Conclusion: From the present study it can be concluded that the PCR amplification procedure for target region of IL-8B receptor gene yielding 459 bp products has been standardized, which yielded consistent and specific amplification. Amplification of partial IL-8B receptor gene (exon 2- 459 bp using self designed primers specific for cattle ortholog sequence signifies that the locus is conserved in cattle and buffaloes. In phylogenetic tree, the target sequence of IL-8B receptor gene of Bubalus bubalis were found to be more closely related to Bos indicus × Bos Taurus and Bos taurus than to Ovis aries and Sus scrofa.

  10. Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.

    Science.gov (United States)

    Jordan, Michael R; Kearney, Mary; Palmer, Sarah; Shao, Wei; Maldarelli, Frank; Coakley, Eoin P; Chappey, Colombe; Wanke, Christine; Coffin, John M

    2010-09-01

    To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity. Copyright 2010 Elsevier B.V. All rights reserved.

  11. Estimation of physiological parameters using knowledge-based factor analysis of dynamic nuclear medicine image sequences

    International Nuclear Information System (INIS)

    Yap, J.T.; Chen, C.T.; Cooper, M.

    1995-01-01

    The authors have previously developed a knowledge-based method of factor analysis to analyze dynamic nuclear medicine image sequences. In this paper, the authors analyze dynamic PET cerebral glucose metabolism and neuroreceptor binding studies. These methods have shown the ability to reduce the dimensionality of the data, enhance the image quality of the sequence, and generate meaningful functional images and their corresponding physiological time functions. The new information produced by the factor analysis has now been used to improve the estimation of various physiological parameters. A principal component analysis (PCA) is first performed to identify statistically significant temporal variations and remove the uncorrelated variations (noise) due to Poisson counting statistics. The statistically significant principal components are then used to reconstruct a noise-reduced image sequence as well as provide an initial solution for the factor analysis. Prior knowledge such as the compartmental models or the requirement of positivity and simple structure can be used to constrain the analysis. These constraints are used to rotate the factors to the most physically and physiologically realistic solution. The final result is a small number of time functions (factors) representing the underlying physiological processes and their associated weighting images representing the spatial localization of these functions. Estimation of physiological parameters can then be performed using the noise-reduced image sequence generated from the statistically significant PCs and/or the final factor images and time functions. These results are compared to the parameter estimation using standard methods and the original raw image sequences. Graphical analysis was performed at the pixel level to generate comparable parametric images of the slope and intercept (influx constant and distribution volume)

  12. CPSS: a computational platform for the analysis of small RNA deep sequencing data.

    Science.gov (United States)

    Zhang, Yuanwei; Xu, Bo; Yang, Yifan; Ban, Rongjun; Zhang, Huan; Jiang, Xiaohua; Cooke, Howard J; Xue, Yu; Shi, Qinghua

    2012-07-15

    Next generation sequencing (NGS) techniques have been widely used to document the small ribonucleic acids (RNAs) implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analysing the enormous datasets from small RNA deep sequencing approach. Herein, we present a novel web server, CPSS (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. Small RNA NGS data can be submitted to this server with analysis results being returned in two parts: (i) annotation analysis, which provides the most comprehensive analysis for small RNA transcriptome, including length distribution and genome mapping of sequencing reads, small RNA quantification, prediction of novel miRNAs, identification of differentially expressed miRNAs, piwi-interacting RNAs and other non-coding small RNAs between paired samples and detection of miRNA editing and modifications and (ii) functional analysis, including prediction of miRNA targeted genes by multiple tools, enrichment of gene ontology terms, signalling pathway involvement and protein-protein interaction analysis for the predicted genes. CPSS, a ready-to-use web server that integrates most functions of currently available bioinformatics tools, provides all the information wanted by the majority of users from small RNA deep sequencing datasets. CPSS is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/db/cpss/index.html or http://mcg.ustc.edu.cn/sdap1/cpss/index.html.

  13. Behavioral economic analysis of demand for fuel in North America.

    Science.gov (United States)

    Reed, Derek D; Partington, Scott W; Kaplan, Brent A; Roma, Peter G; Hursh, Steven R

    2013-01-01

    Emerging research clearly indicates that human behavior is contributing to climate change, notably, the use of fossil fuels as a form of energy for everyday behaviors. This dependence on oil in North America has led to assertions that the current level of demand is the social equivalent to an "addiction." The purpose of this study was to apply behavioral economic demand curves-a broadly applicable method of evaluating relative reinforcer efficacy in behavioral models of addiction-to North American oil consumption to examine whether such claims of oil addiction are warranted. Toward this end, we examined government data from the United States and Canada on per capita energy consumption for transportation and oil prices between 1995 and 2008. Our findings indicate that consumption either persisted or simultaneously increased despite sharp increases in oil price per barrel over the past decade. © Society for the Experimental Analysis of Behavior.

  14. Hunting down frame shifts: Ecological analysis of diverse functional gene sequences

    Directory of Open Access Journals (Sweden)

    Michal eStrejcek

    2015-11-01

    Full Text Available Functional gene ecological analyses using amplicon sequencing can be challenging as translated sequences are often burdened with shifted reading frames. The aim of this work was to evaluate several bioinformatics tools designed to correct errors which arise during sequencing in an effort to reduce the number of frame-shifts (FS. Genes encoding for alpha subunits of biphenyl (bphA and benzoate (benA dioxygenases were used as model sequences. FrameBot, a FS correction tool, was able to reduce the number of detected FS to zero. However, up to 43.1% of sequences were discarded by FrameBot as non-specific targets. Therefore, we proposed a de novo mode of FrameBot for FS correction, which works on a similar basis as common chimera identifying platforms and is not dependent on reference sequences. By nature of FrameBot de novo design, it is crucial to provide it with data as error free as possible. We tested the ability of several publicly available correction tools to decrease the number of errors in the data sets. The combination of Maximum Expected Error (MEE filtering and single linkage pre-clustering (SLP proved the most efficient read procession. Applying FrameBot de novo on the processed data enabled analysis of BphA sequences with minimal losses of potentially functional sequences not homologous to those previously known. This experiment also demonstrated the extensive diversity of dioxygenases in soil. A script which performs FrameBot de novo is presented in the supplementary material to the study and the tool was implemented into FunGene Pipeline available at http://fungene.cme.msu.edu/FunGenePipeline/ and https://github.com/rdpstaff/Framebot.

  15. Phylogenetic analysis of lack gene sequences for 22 Chinese Leishmania isolates.

    Science.gov (United States)

    Zhang, Chun-Ying; Zhou, Juan; Ding, Bin; Lu, Xiao-Jun; Xiao, Yu-Ling; Hu, Xiao-Su; Ma, Ying

    2013-07-01

    The phylogenetic relationships between Chinese Leishmania strains were investigated using lack (Leishmania homolog of receptors for activated protein kinase C) gene sequences, and the power of this gene was assessed for understanding the epidemiology and population genetics of Leishmania. The lack gene sequences from Leishmania isolates were sequenced after polymerase chain reaction (PCR) amplification. Sequence alignment was performed and a phylogenetic tree was created using the MEGA 5.0 software program. Sequences of 850 bp were analyzed for each of the Leishmania strains collected from different locations in China, and minor differences in sequences were noted between the strains. Four distinct groups formed according to differences in the sequences of the lack gene. Group I consisted of 12 isolates from Shandong, Xinjiang, Gansu and Sichuan. These strains are part of the Leishmania donovani complex and are pathogenic to humans and canines. Group II included six isolates from Xinjiang and a reference strain, Leishmania turanica. Group III contained two isolates (one from a sand fly in Xinjiang and one from a rodent in Inner Mongolia) and they were identified as Leishmania gerbilli. Finally, group IV contained a strain from a sand fly in Xinjiang and a strain from a lizard in Inner Mongolia, and these strains were found to be Sauroleishmania. The Chinese Leishmania isolates formed four groups based on differences in the sequences of the lack gene, and this result is consistent with previous studies. Phylogenetic analysis suggests that the Leishmania isolates from China are more complicated than previously thought. There is consensus between genetic clustering and identification using classical methods, which means that the lack gene yields polymorphic information that could be used for genotyping Leishmania isolates. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Estimation of a Killer Whale (Orcinus orca Population's Diet Using Sequencing Analysis of DNA from Feces.

    Directory of Open Access Journals (Sweden)

    Michael J Ford

    Full Text Available Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%. Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population's summer diet.

  17. Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia radiculosa

    Science.gov (United States)

    J. D. Tang; A. D. Perkins; T. S. Sonstegard; S. G. Schroeder; S. C. Burgess; S. V. Diehl

    2012-01-01

    The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment...

  18. Formative Research on the Simplifying Conditions Method (SCM) for Task Analysis and Sequencing.

    Science.gov (United States)

    Kim, YoungHwan; Reigluth, Charles M.

    The Simplifying Conditions Method (SCM) is a set of guidelines for task analysis and sequencing of instructional content under the Elaboration Theory (ET). This article introduces the fundamentals of SCM and presents the findings from a formative research study on SCM. It was conducted in two distinct phases: design and instruction. In the first…

  19. Molecular cloning and sequence analysis of VP6 gene of giant ...

    African Journals Online (AJOL)

    Jane

    2011-10-24

    Oct 24, 2011 ... G), and the major structural protein of inner capsid particles (ICP), and also specific antigen of mucosa immunization that mediate specific immunological reaction. In this report, sequence analysis of VP6 gene of giant panda rotavirus was carried out. Full-length VP6 gene encoding for ICP of giant panda.

  20. Phylogenetic analysis of 23S rRNA gene sequences of some ...

    African Journals Online (AJOL)

    The phylogenetic relationships among thirteen Rhizobium leguminosarum bv. viciae isolates collected from various geographical regions were studied by analysis of the 23S rRNA sequences. The average of genetic distance among the studied isolates was very narrow (ranged from 0.00 to 0.04) and the studied isolates ...

  1. Genome-based exome sequencing analysis identifies GYG1, DIS3L ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 6. Genome-based exome sequencing analysis identifies GYG1, DIS3L and DDRGK1 are associated with myocardial infarction in Koreans. JI-YOUNG LEE SANGHOON MOON YUN KYOUNG KIM SANG-HAK LEE BOK-SOO LEE MIN-YOUNG PARK JEONG EUY PARK ...

  2. Multilocus Sequence Analysis for Typing Leptospira interrogans and Leptospira kirschneri▿ †

    Science.gov (United States)

    Leon, Albertine; Pronost, Stéphane; Fortier, Guillaume; Andre-Fontaine, Geneviève; Leclercq, Roland

    2010-01-01

    Fifty-three strains belonging to the pathogenic species Leptospira interrogans and Leptospira kirschneri were analyzed by multilocus sequence analysis. The species formed two distinct branches. In the L. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. Genogroups and serogroups were superimposed but not strictly. PMID:19955271

  3. Multilocus Sequence Analysis for Typing Leptospira interrogans and Leptospira kirschneri▿ †

    OpenAIRE

    Leon, Albertine; Pronost, Stéphane; Fortier, Guillaume; Andre-Fontaine, Geneviève; Leclercq, Roland

    2009-01-01

    Fifty-three strains belonging to the pathogenic species Leptospira interrogans and Leptospira kirschneri were analyzed by multilocus sequence analysis. The species formed two distinct branches. In the L. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. Genogroups and serogroups were superimposed but not strictly.

  4. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools.

    Science.gov (United States)

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikolaos; Vinther, Jeppe

    2015-01-01

    RNA structure-probing data can improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. In recent years, massive parallel sequencing has dramatically improved the throughput of RNA structure probing experiments, but at the same time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data, we have made a collection of tools, which allow raw sequencing reads to be converted to normalized probing values using different published strategies. In addition, we also provide tools for visualization of the probing data in the UCSC Genome Browser and for converting RNA coordinates to genomic coordinates and vice versa. The collection is implemented as functions in the R statistical environment and as tools in the Galaxy platform, making them easily accessible for the scientific community. We demonstrate the usefulness of the collection by applying it to the analysis of sequencing-based hydroxyl radical probing data and comparing different normalization strategies. © 2015 Elsevier Inc. All rights reserved.

  5. Sequence analysis of putative swrW gene required for surfactant ...

    African Journals Online (AJOL)

    owner

    2012-07-17

    Jul 17, 2012 ... Sequence analysis of putative swrW gene required for surfactant serrawettin W1 production from Serratia marcescens. Monabel May N. Apao*, Franco G. Teves and Ma. Reina Suzette B. Madamba. Department of Biological Sciences, College of Science and Mathematics, MSU-Iligan Institute of Technology, ...

  6. Phylogenetic analysis of 23S rRNA gene sequences of some ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-08-31

    Aug 31, 2016 ... The phylogenetic relationships among thirteen Rhizobium leguminosarum bv. viciae isolates collected from various geographical regions were studied by analysis of the 23S rRNA sequences. The average of genetic distance among the studied isolates was very narrow (ranged from 0.00 to 0.04) and the ...

  7. Analysis of common SHOX gene sequence variants and ∼4.9-kb ...

    Indian Academy of Sciences (India)

    [Solc R., Hirschfeldova K., Kebrdlova V. and Baxova A. 2014 Analysis of common SHOX gene sequence variants and ∼4.9-kb PAR1 deletion in ISS patients. J. Genet. 93, 505–508]. Introduction. Defects of the SHOX gene (short stature homeobox- containing gene), localized in the pseudoautosomal region 1. (PAR1) have ...

  8. Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among ...

    African Journals Online (AJOL)

    Yazun Bashir Jarrar

    2017-11-26

    Nov 26, 2017 ... Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among Jordanian volunteers. Yazun Bashir Jarrar, Ayat Ahmed Balasmeh and Wassan Jarrar. Department of Pharmacy, College of Pharmacy, AlZaytoonah University of Jordan, Amman, Jordan. ABSTRACT. The present study aimed to identify ...

  9. ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data.

    NARCIS (Netherlands)

    Zomer, A.L.; Burghout, P.J.; Bootsma, H.J.; Hermans, P.W.M.; Hijum, S.A.F.T. van

    2012-01-01

    High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon

  10. Weighted symbolic analysis of human behavior for event detection

    Science.gov (United States)

    Rosani, A.; Boato, G.; De Natale, F. G. B.

    2013-03-01

    Automatic video analysis and understanding has become a high interest research topic, with applications to video browsing, content-based video indexing, and visual surveillance. However, the automation of this process is still a challenging task, due to clutters produced by low-level processing operations. This common problem can be solved by embedding signi cant contextual information into the data, as well as using simple syntactic approaches to perform the matching between actual sequences and models. In this context we propose a novel framework that employs a symbolic representation of complex activities through sequences of atomic actions based on a weighted Context-Free Grammar.

  11. Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing.

    Science.gov (United States)

    Miller, Marisa E; Liberatore, Katie L; Kianian, Shahryar F

    2017-07-28

    Plant organellar genomes contain large, repetitive elements that may undergo pairing or recombination to form complex structures and/or sub-genomic fragments. Organellar genomes also exist in admixtures within a given cell or tissue type (heteroplasmy), and an abundance of subtypes may change throughout development or when under stress (sub-stoichiometric shifting). Next-generation sequencing (NGS) technologies are required to obtain deeper understanding of organellar genome structure and function. Traditional sequencing studies use several methods to obtain organellar DNA: (1) If a large amount of starting tissue is used, it is homogenized and subjected to differential centrifugation and/or gradient purification. (2) If a smaller amount of tissue is used (i.e., if seeds, material, or space is limited), the same process is performed as in (1), followed by whole-genome amplification to obtain sufficient DNA. (3) Bioinformatics analysis can be used to sequence the total genomic DNA and to parse out organellar reads. All these methods have inherent challenges and tradeoffs. In (1), it may be difficult to obtain such a large amount of starting tissue; in (2), whole-genome amplification could introduce a sequencing bias; and in (3), homology between nuclear and organellar genomes could interfere with assembly and analysis. In plants with large nuclear genomes, it is advantageous to enrich for organellar DNA to reduce sequencing costs and sequence complexity for bioinformatics analyses. Here, we compare a traditional differential centrifugation method with a fourth method, an adapted CpG-methyl pulldown approach, to separate the total genomic DNA into nuclear and organellar fractions. Both methods yield sufficient DNA for NGS, DNA that is highly enriched for organellar sequences, albeit at different ratios in mitochondria and chloroplasts. We present the optimization of these methods for wheat leaf tissue and discuss major advantages and disadvantages of each approach in

  12. Context based computational analysis and characterization of ARS consensus sequences (ACS of Saccharomyces cerevisiae genome

    Directory of Open Access Journals (Sweden)

    Vinod Kumar Singh

    2016-09-01

    Full Text Available Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS requires an essential consensus sequence (ACS for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC denoted as ORC-ACS and non-replicating ACS sequences (nrACS, that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.

  13. Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis.

    Science.gov (United States)

    Forsythe, Stephen J; Dickins, Benjamin; Jolley, Keith A

    2014-12-16

    Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the organism. This paper presents the application of Next Generation Sequencing (NGS) to Cronobacter which has led to the establishment of the Cronobacter PubMLST genome and sequence definition database (http://pubmlst.org/cronobacter/) containing over 1000 isolates with metadata along with the recognition of specific clonal lineages linked to neonatal meningitis and adult infections Whole genome sequencing and multilocus sequence typing (MLST) has supports the formal recognition of the genus Cronobacter composed of seven species to replace the former single species Enterobacter sakazakii. Applying the 7-loci MLST scheme to 1007 strains revealed 298 definable sequence types, yet only C. sakazakii clonal complex 4 (CC4) was principally associated with neonatal meningitis. This clonal lineage has been confirmed using ribosomal-MLST (51-loci) and whole genome-MLST (1865 loci) to analyse 107 whole genomes via the Cronobacter PubMLST database. This database has enabled the retrospective analysis of historic cases and outbreaks following re-identification of those strains. The Cronobacter PubMLST database offers a central, open access, reliable sequence-based repository for researchers. It has the capacity to create new analysis schemes 'on the fly', and to integrate metadata (source, geographic distribution, clinical presentation). It is also expandable and adaptable to changes in taxonomy, and able to support the development of reliable detection methods of use to industry and regulatory authorities. Therefore it meets the WHO (2004) request for the establishment of a typing scheme for this emergent bacterial pathogen. Whole genome sequencing has additionally shown a range

  14. Animal research in the Journal of Applied Behavior Analysis.

    Science.gov (United States)

    Edwards, Timothy L; Poling, Alan

    2011-01-01

    This review summarizes the 6 studies with nonhuman animal subjects that have appeared in the Journal of Applied Behavior Analysis and offers suggestions for future research in this area. Two of the reviewed articles described translational research in which pigeons were used to illustrate and examine behavioral phenomena of applied significance (say-do correspondence and fluency), 3 described interventions that changed animals' behavior (self-injury by a baboon, feces throwing and spitting by a chimpanzee, and unsafe trailer entry by horses) in ways that benefited the animals and the people in charge of them, and 1 described the use of trained rats that performed a service to humans (land-mine detection). We suggest that each of these general research areas merits further attention and that the Journal of Applied Behavior Analysis is an appropriate outlet for some of these publications.

  15. Masking as an effective quality control method for next-generation sequencing data analysis.

    Science.gov (United States)

    Yun, Sajung; Yun, Sijung

    2014-12-13

    Next generation sequencing produces base calls with low quality scores that can affect the accuracy of identifying simple nucleotide variation calls, including single nucleotide polymorphisms and small insertions and deletions. Here we compare the effectiveness of two data preprocessing methods, masking and trimming, and the accuracy of simple nucleotide variation calls on whole-genome sequence data from Caenorhabditis elegans. Masking substitutes low quality base calls with 'N's (undetermined bases), whereas trimming removes low quality bases that results in a shorter read lengths. We demonstrate that masking is more effective than trimming in reducing the false-positive rate in single nucleotide polymorphism (SNP) calling. However, both of the preprocessing methods did not affect the false-negative rate in SNP calling with statistical significance compared to the data analysis without preprocessing. False-positive rate and false-negative rate for small insertions and deletions did not show differences between masking and trimming. We recommend masking over trimming as a more effective preprocessing method for next generation sequencing data analysis since masking reduces the false-positive rate in SNP calling without sacrificing the false-negative rate although trimming is more commonly used currently in the field. The perl script for masking is available at http://code.google.com/p/subn/. The sequencing data used in the study were deposited in the Sequence Read Archive (SRX450968 and SRX451773).

  16. Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment

    Directory of Open Access Journals (Sweden)

    Rachael eDoherty

    2014-05-01

    Full Text Available Recent advances made in omics technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS and more recently whole genome bisulfite sequencing (WGBS have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed.

  17. sRNAnalyzer—a flexible and customizable small RNA sequencing data analysis pipeline

    Science.gov (United States)

    Kim, Taek-Kyun; Baxter, David; Scherler, Kelsey; Gordon, Aaron; Fong, Olivia; Etheridge, Alton; Galas, David J.

    2017-01-01

    Abstract Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline—sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/. PMID:29069500

  18. sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline.

    Science.gov (United States)

    Wu, Xiaogang; Kim, Taek-Kyun; Baxter, David; Scherler, Kelsey; Gordon, Aaron; Fong, Olivia; Etheridge, Alton; Galas, David J; Wang, Kai

    2017-12-01

    Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline-sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Analysis of plant microbe interactions in the era of next generation sequencing technologies

    Directory of Open Access Journals (Sweden)

    Claudia eKnief

    2014-05-01

    Full Text Available Next generation sequencing (NGS technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the pant associated microbiota to demonstrate the worth of the new methods.

  20. Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia.

    Science.gov (United States)

    Chao, Q J; Li, Y D; Geng, X X; Zhang, L; Dai, X; Zhang, X; Li, J; Zhang, H J

    2014-04-14

    This is the first report of a complete mitochondrial genome sequence from Himalayan marmot (Marmota himalayana, class Marmota). We determined the M. himalayana mitochondrial (mt) genome sequence by using long-PCR methods and a primer-walking sequencing strategy with genus-specific primers. The complete mt genome of M. himalayana was 16,443 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (CR). Gene order and orientation were identical to those in mt genomes of most vertebrates. The heavy strand showed an overall A+T content of 63.49%. AT and GC skews for the mt genome of the M. himalayana were 0.012 and -0.300, respectively, indicating a nucleotide bias against T and G. The control region was 997 bp in size and displayed some unusual features, including absence of repeated motifs and two conserved sequence blocks (CSB2 and CSB3), which is consistent with observations from two other rodent species, Sciurus vulgaris and Myoxus glis. Phylogenetic analysis of complete mt DNA sequences without the control region including 30 taxa of Rodentia was performed with Maximum-Likelihood (ML) and Bayesian Inference (BI) methods and provided strong support for Sciurognathi polyphyly and Hystricognathi monophyly. This analysis also provided evidence that M. himalayana mt DNA was closely related to that from Sciurus vulgaris (Sciuridae) and was similar to mt DNA from Myoxus glis.