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Sample records for vector magnetogram sequences

  1. Forecasting Coronal Mass Ejections from Vector Magnetograms

    Science.gov (United States)

    Falconer, D. A.; Moore, R. L.; Gary, G. A.; Six, N. Frank (Technical Monitor)

    2002-01-01

    In a 17 vector magnetogram study of 12 bipolar active regions (Falconer, Moore, & Gary, 2002, ApJ in press), we correlated four quantitative global magnetic measures with the Coronal Mass Ejections (CME) productivity of the active region. The global measures included a measure of active region size, the total magnetic flux phi and three measures of an active region global nonpotentiality 1) the net current (I (sub N)), 2) the length of the strong-shear, strong-field main neutral line (L(sub SS)) and 3) and the normalized twist (alpha = muIN/PHI). The CME productivity was determined from YOHKOH/SXT observations, Geostationary Operational Environmental Satellite (GOES), and when possible Solar and Heliospheric Observatory/Large Angle and Spectrometric Coronagraph Experiment (SOHO/LASCO) observations within 12 days of the day of the magnetogram. We found that the three measures of global nonpotentiality (I(sub N), L(sub SS), alpha) were all well correlated (greater than 99% confidence level) with an active region's CME productivity. The sample size was to small to confirm if there was a statistical significant correlation of the globally nonscientist measures with future CME activity (i.e. from the date of the magnetogram forward). We are doubling our sample, and will report on the statistical significance of global nonpotentiality as a predictor of future CME productivity. The new active regions are all from the first year of the upgraded MSFC vector magnetograms. This work, is funded by NSF through the Space Weather Program, by NASA through the Living with the Star, Targeted Research and Technology, and by NASA Solar Physics Supporting Research and Technology Program. The upgrade to the MSFC vector magnetograph was supported by the High Energy Solar Spectroscopic Imager (HESSI) mission.

  2. Software for Interactively Visualizing Solar Vector Magnetograms of ...

    Indian Academy of Sciences (India)

    Astr. (2008) 29, 107–111. Software for Interactively Visualizing Solar Vector Magnetograms of Udaipur Solar Observatory ... tion and analysis software have been developed to make the data processing pipeline user-friendly and less ... The straight and symmetric telescope design is used to avoid instrumental polarization ...

  3. Off disk-center potential field calculations using vector magnetograms

    Science.gov (United States)

    Venkatakrishnan, P.; Gary, G. Allen

    1989-01-01

    A potential field calculation for off disk-center vector magnetograms that uses all the three components of the measured field is investigated. There is neither any need for interpolation of grid points between the image plane and the heliographic plane nor for an extension or a truncation to a heliographic rectangle. Hence, the method provides the maximum information content from the photospheric field as well as the most consistent potential field independent of the viewing angle. The introduction of polarimetric noise produces a less tolerant extrapolation procedure than using the line-of-sight extrapolation, but the resultant standard deviation is still small enough for the practical utility of this method.

  4. Software for Interactively Visualizing Solar Vector Magnetograms of ...

    Indian Academy of Sciences (India)

    The retrieval of vector fields from the imaging spectro-polarimetric observational data requires a substantial amount of computer post-processing. The GUI-based data reduction and analysis software have been developed to make the data processing pipeline user-friendly and less time-consuming. In this paper we describe ...

  5. Prediction of Coronal Mass Ejections From Vector Magnetograms: Quantitative Measures as Predictors

    Science.gov (United States)

    Falconer, D. A.; Moore, R. L.; Gary, G. A.; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    We derived two quantitative measures of an active region's global nonpotentiality from the region's vector magnetogram, 1) the net current (I(sub N)), and 2) the length of strong-shear, strong-field main neutral line (Lss), and used these two measures in a pilot study of the CME productivity of 4 active regions. We compared the global nonpotentiality measures to the active regions' CME productivity determined from GOES and Yohkoh/SXT observations. We found that two of the active regions were highly globally nonpotential and were CME productive, while the other two active regions had little global nonpotentiality and produced no CMEs. At the Fall 2000 AGU, we reported on an expanded study (12 active regions and 17 magnetograms) in which we evaluated four quantitative global measures of an active region's magnetic field and compared these measures with the CME productivity. The four global measures (all derived from MSFC vector magnetograms) included our two previous measures (I(sub N) and L(sub ss)) as well as two new ones, the total magnetic flux (PHI) (a measure of an active region's size), and the normalized twist (alpha (bar)= muIN/PHI). We found that the three quantitative measures of global nonpotentiality (I(sub N), L(sub ss), alpha (bar)) were all well correlated (greater than 99% confidence level) with an active region's CME productivity within plus or minus 2 days of the day of the magnetogram. We will now report on our findings of how good our quantitative measures are as predictors of active-region CME productivity, using only CMEs that occurred after the magnetogram. We report the preliminary skill test of these quantitative measures as predictors. We compare the CME prediction success of our quantitative measures to the CME prediction success based on an active region's past CME productivity. We examine the cases of the handful of false positive and false negatives to look for improvements to our predictors. This work is funded by NSF through the Space

  6. Solar Flare Prediction Model with Three Machine-learning Algorithms using Ultraviolet Brightening and Vector Magnetograms

    Science.gov (United States)

    Nishizuka, N.; Sugiura, K.; Kubo, Y.; Den, M.; Watari, S.; Ishii, M.

    2017-02-01

    We developed a flare prediction model using machine learning, which is optimized to predict the maximum class of flares occurring in the following 24 hr. Machine learning is used to devise algorithms that can learn from and make decisions on a huge amount of data. We used solar observation data during the period 2010-2015, such as vector magnetograms, ultraviolet (UV) emission, and soft X-ray emission taken by the Solar Dynamics Observatory and the Geostationary Operational Environmental Satellite. We detected active regions (ARs) from the full-disk magnetogram, from which ˜60 features were extracted with their time differentials, including magnetic neutral lines, the current helicity, the UV brightening, and the flare history. After standardizing the feature database, we fully shuffled and randomly separated it into two for training and testing. To investigate which algorithm is best for flare prediction, we compared three machine-learning algorithms: the support vector machine, k-nearest neighbors (k-NN), and extremely randomized trees. The prediction score, the true skill statistic, was higher than 0.9 with a fully shuffled data set, which is higher than that for human forecasts. It was found that k-NN has the highest performance among the three algorithms. The ranking of the feature importance showed that previous flare activity is most effective, followed by the length of magnetic neutral lines, the unsigned magnetic flux, the area of UV brightening, and the time differentials of features over 24 hr, all of which are strongly correlated with the flux emergence dynamics in an AR.

  7. High-Resolution Vector Magnetograms of the Sun's Poles from Hinode: Flux Distributions and Global Coronal Modeling

    Science.gov (United States)

    Petrie, Gordon

    2017-01-01

    The Sun's polar fields play a leading role in structuring the large-scale solar atmosphere and in determining the interplanetary magnetic field. They are also believed to supply the seed field for the subsequent solar activity cycle. However, present-day synoptic observations do not have sufficient spatial resolution or sensitivity to diagnose accurately the high-latitude magnetic vector field. The high spatial resolution and sensitivity of the full-Stokes observations from the Hinode Solar Optical Telescope Spectro-Polarimeter, observing the poles long-term, allows us to build up a detailed picture of the Cycle 24 polar field reversal, including the changing latitude distribution of the high-latitude flux, and to study the effect on global coronal field models. The Hinode observations provide detailed information on the dominant facular-scale magnetic structure of the polar fields, and their field inclination and flux distribution. Hybrid synoptic magnetograms are constructed from Hinode polar measurements and full-disk magnetograms from the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectro-Magnetograph (VSM), and coronal potential field models are calculated. Loss of effective spatial resolution at the highest latitudes presents complications. Possible improvements to synoptic polar data are discussed.

  8. First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

    Science.gov (United States)

    Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

    2014-01-01

    Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.

  9. Solar Wind Simulations from the Sun to Earth Using a Data-Driven, MHD Model and Characteristically-Consistent Boundary Conditions Derived from SDO/HMI Vector Magnetograms

    Science.gov (United States)

    Yalim, M. S.; Pogorelov, N.; Liu, Y.; Hu, Q.; Wu, S. T.

    2016-12-01

    The solar wind (SW) emerging from the Sun is the main driving mechanism of solar events which may lead to geomagnetic storms that are the primary causes of space weather disturbances that affect the magnetic environment of Earth and may have hazardous effects on the space-borne and ground-based technological systems as well as human health. Therefore, accurate modeling of the SW is very important to understand the underlying mechanisms of such storms. We have developed a data-driven, magnetohydrodynamic (MHD) model of the global solar corona which utilizes characteristic boundary conditions implemented within the Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) - a collection of problem oriented routines incorporated into the Chombo adaptive mesh refinement framework developed at Lawrence Berkeley National Laboratory. Our global solar corona model can be driven by both time-dependent and Carrington-rotation averaged vector magnetogram synoptic map data obtained by the Solar Dynamics Observatory/Helioseismic and Magnetic Imager (SDO/HMI) and the horizontal velocity data on the photosphere obtained by applying the Differential Affine Velocity Estimator for Vector Magnetograms method on the HMI-observed vector magnetic fields. In this study, we will present the results of three-dimensional global simulations of SW propagation from the Sun to Earth by using our global solar corona and inner heliosphere models and validate our results using spacecraft data at 1 AU.

  10. Plasma Motions and Turbulent Magnetic Diffusivity of Active Region AR 12158 Using a Minimum Energy Functional and Non-Force-Free Reconstructions of Vector Magnetograms

    Science.gov (United States)

    Tremblay, Benoit; Vincent, Alain

    2017-01-01

    We present a generalization of the resistive minimum-energy fit (MEF-R: Tremblay and Vincent, Solar Phys. 290, 437, 2015) for non-force-free (NFF) magnetic fields. In MEF-R, an extremum principle is used to infer two-dimensional maps of plasma motions [boldsymbol{v}(x,y)] and magnetic eddy diffusivity [η _{eddy}(x,y)] at the photosphere. These reconstructions could be used as boundary conditions in data-driven simulations or in data assimilation. The algorithm is validated using the analytical model of a resistive expanding spheromak by Rakowski, Laming, and Lyutikov ( Astrophys. J. 730, 30, 2011). We study the flaring Active Region AR 12158 using a series of magnetograms and Dopplergrams provided by the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO). The results are discussed for a non-force-free magnetic-field reconstruction [boldsymbol{B}_{NFF}] (Hu and Dasgupta in Solar Phys. 247, 87, 2008). We found that the vertical plasma velocities [vz(x,y)] inferred using MEF-R are very similar to the observed Doppler velocities [vr(x,y)]. Finally, we study the potential spatial correlation between microturbulent velocities and significant values of η_{eddy}(x,y).

  11. Figaro: a novel statistical method for vector sequence removal

    Science.gov (United States)

    White, James Robert; Roberts, Michael; Yorke, James A.; Pop, Mihai

    2009-01-01

    Motivation Sequences produced by automated Sanger sequencing machines frequently contain fragments of the cloning vector on their ends. Software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment—information often omitted from public databases. Furthermore, the clipping coordinates themselves are missing or incorrectly reported. As an example, within the ~1.24 billion shotgun sequences deposited in the NCBI Trace Archive, as many as ~735 million (~60%) lack vector clipping information. Correct clipping information is essential to scientists attempting to validate, improve and even finish the increasingly large number of genomes released at a ‘draft’ quality level. Results We present here Figaro, a novel software tool for identifying and removing the vector from raw sequence data without prior knowledge of the vector sequence. The vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics. We show that Figaro achieves 99.98% sensitivity when tested on ~1.5 million shotgun reads from Drosophila pseudoobscura. We further explore the impact of accurate vector trimming on the quality of whole-genome assemblies by re-assembling two bacterial genomes from shotgun sequences deposited in the Trace Archive. Designed as a module in large computational pipelines, Figaro is fast, lightweight and flexible. Availability Figaro is released under an open-source license through the AMOS package (http://amos.sourceforge.net/Figaro). PMID:18202027

  12. Generalized Vector-Valued Sequence Spaces Defined by Modulus Functions

    Directory of Open Access Journals (Sweden)

    Işik Mahmut

    2010-01-01

    Full Text Available We introduce the vector-valued sequence spaces , , and , and , using a sequence of modulus functions and the multiplier sequence of nonzero complex numbers. We give some relations related to these sequence spaces. It is also shown that if a sequence is strongly -Cesàro summable with respect to the modulus function then it is -statistically convergent.

  13. On Estimating Force-freeness Based on Observed Magnetograms

    Science.gov (United States)

    Zhang, X. M.; Zhang, M.; Su, J. T.

    2017-01-01

    It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such as limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.

  14. Standardized Metadata for Human Pathogen/Vector Genomic Sequences

    Science.gov (United States)

    Dugan, Vivien G.; Emrich, Scott J.; Giraldo-Calderón, Gloria I.; Harb, Omar S.; Newman, Ruchi M.; Pickett, Brett E.; Schriml, Lynn M.; Stockwell, Timothy B.; Stoeckert, Christian J.; Sullivan, Dan E.; Singh, Indresh; Ward, Doyle V.; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M.; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H.; Cuomo, Christina A.; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W. Florian; Giovanni, Maria; Henn, Matthew R.; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C.; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F.; Murphy, Cheryl I.; Myers, Garry; Neafsey, Daniel E.; Nelson, Karen E.; Nierman, William C.; Puzak, Julia; Rasko, David; Roos, David S.; Sadzewicz, Lisa; Silva, Joana C.; Sobral, Bruno; Squires, R. Burke; Stevens, Rick L.; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H.

    2014-01-01

    High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a

  15. Standardized metadata for human pathogen/vector genomic sequences.

    Directory of Open Access Journals (Sweden)

    Vivien G Dugan

    Full Text Available High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs, the Bioinformatics Resource Centers (BRCs for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID, part of the National Institutes of Health (NIH, informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI. The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will

  16. Memorizing binary vector sequences by a sparsely encoded network.

    Science.gov (United States)

    Baram, Y

    1994-01-01

    We present a neural network employing Hebbian storage and sparse internal coding, which is capable of memorizing and correcting sequences of binary vectors by association. A ternary version of the Kanerva memory, folded into a feedback configuration, is shown to perform the basic sequence memorization and regeneration function. The inclusion of lateral connections between the internal cells increases the network capacity considerably and facilitates the correction of individual input patterns and the detection of large errors. The introduction of higher delays in the transmission lines between the external input-output layer and the internal memory layer is shown to further improve the network's error correction capability.

  17. Tessellation of SoHO Magnetograms

    Indian Academy of Sciences (India)

    ... flux concentrations in solar and heliospheric observatory (SoHO) magnetograms. The mean absolute flux and size of the concentrations at the considered scale is found to be about 1.7 × 1018Mx and 5.2Mm for both polarities. The form of the flux distribution is characterized by a skewness of 3 = 4.9 and a kurtosis of 4, ...

  18. Tessellation of SoHO Magnetograms

    Indian Academy of Sciences (India)

    tribpo

    trations in solar and heliospheric observatory (SoHO) magnetograms. The mean absolute flux and size of the concentrations at the considered scale is found to be about 1.7 × 1018Mx and 5.2Mm for both polarities. The form of the flux distribution is characterized by a skewness of α3 = 4.9 and a kurtosis of α4, = 42.8. The fall ...

  19. Modeling the Global Coronal Field with Simulated Synoptic Magnetograms from L1 and L5

    Science.gov (United States)

    Petrie, G. J. D.; Bertello, L.; Pevtsov, A. A.

    2016-12-01

    In solar physics and space weather research, full-disk photospheric magnetograms are routinely used to map the full solar surface in near-real-time, and coronal field models are extrapolated from these data. One major shortcoming of this approach is that, at present, the magnetograms can only be taken from the Earth's direction. Thus data immediately eastward of the sub-Earth point in synoptic maps are around three weeks old, missing much active-region evolution and leading to inaccuracies in the models. A new magnetograph at L5 would update the synoptic maps at this critical location east of central meridian and would provide a more accurate, up-to-date picture of the global photospheric and coronal field. We demonstrate the value of L5 observations by simulating the construction of synoptic magnetograms from both L1 and L5 directions using past near-real-time data from two observatories: the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectromagnetograph (VSM) and Global Oscillation Network Group (GONG). We extrapolate potential-field source-surface (PFSS) coronal field models and compare their open-field and streamer distributions to coronal observations from the Solar Terrestrial Relations Observatory (STEREO) and the Solar Dynamics Observatory (SDO) Atmospheric Imaging Assembly (AIA).

  20. Forecasting Solar Flares Using Magnetogram-based Predictors and Machine Learning

    Science.gov (United States)

    Florios, Kostas; Kontogiannis, Ioannis; Park, Sung-Hong; Guerra, Jordan A.; Benvenuto, Federico; Bloomfield, D. Shaun; Georgoulis, Manolis K.

    2018-02-01

    We propose a forecasting approach for solar flares based on data from Solar Cycle 24, taken by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) mission. In particular, we use the Space-weather HMI Active Region Patches (SHARP) product that facilitates cut-out magnetograms of solar active regions (AR) in the Sun in near-realtime (NRT), taken over a five-year interval (2012 - 2016). Our approach utilizes a set of thirteen predictors, which are not included in the SHARP metadata, extracted from line-of-sight and vector photospheric magnetograms. We exploit several machine learning (ML) and conventional statistics techniques to predict flares of peak magnitude {>} M1 and {>} C1 within a 24 h forecast window. The ML methods used are multi-layer perceptrons (MLP), support vector machines (SVM), and random forests (RF). We conclude that random forests could be the prediction technique of choice for our sample, with the second-best method being multi-layer perceptrons, subject to an entropy objective function. A Monte Carlo simulation showed that the best-performing method gives accuracy ACC=0.93(0.00), true skill statistic TSS=0.74(0.02), and Heidke skill score HSS=0.49(0.01) for {>} M1 flare prediction with probability threshold 15% and ACC=0.84(0.00), TSS=0.60(0.01), and HSS=0.59(0.01) for {>} C1 flare prediction with probability threshold 35%.

  1. SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine.

    Science.gov (United States)

    Yang, Jianfeng; Ding, Xiaofan; Sun, Xing; Tsang, Shui-Ying; Xue, Hong

    2015-12-01

    Sequence alignment/map (SAM) formatted sequences [Li H, Handsaker B, Wysoker A et al., Bioinformatics 25(16):2078-2079, 2009.] have taken on a main role in bioinformatics since the development of massive parallel sequencing. However, because misalignment of sequences poses a significant problem in analysis of sequencing data that could lead to false positives in variant calling, the exclusion of misaligned reads is a necessity in analysis. In this regard, the multiple features of SAM-formatted sequences can be treated as vectors in a multi-dimension space to allow the application of a support vector machine (SVM). Applying the LIBSVM tools developed by Chang and Lin [Chang C-C, Lin C-J, ACM Trans Intell Syst Technol 2:1-27, 2011.] as a simple interface for support vector classification, the SAMSVM package has been developed in this study to enable misalignment filtration of SAM-formatted sequences. Cross-validation between two simulated datasets processed with SAMSVM yielded accuracies that ranged from 0.89 to 0.97 with F-scores ranging from 0.77 to 0.94 in 14 groups characterized by different mutation rates from 0.001 to 0.1, indicating that the model built using SAMSVM was accurate in misalignment detection. Application of SAMSVM to actual sequencing data resulted in filtration of misaligned reads and correction of variant calling.

  2. An enhanced method for sequence walking and paralog mining: TOPO® Vector-Ligation PCR

    Directory of Open Access Journals (Sweden)

    Davis Thomas M

    2010-03-01

    Full Text Available Abstract Background Although technological advances allow for the economical acquisition of whole genome sequences, many organisms' genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO® Vector-Ligation PCR (or TVL-PCR that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining. Findings TVL-PCR exploits the ligation efficiency of the pCR®4-TOPO® (Invitrogen, Carlsbad, California vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3' adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes. Conclusions TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.

  3. A note on the almost sure central limit theorems for the maxima of strongly dependent nonstationary Gaussian vector sequences

    Directory of Open Access Journals (Sweden)

    Xiang Zeng

    2016-06-01

    Full Text Available Abstract We prove some almost sure central limit theorems for the maxima of strongly dependent nonstationary Gaussian vector sequences under some mild conditions. The results extend the ASCLT to nonstationary Gaussian vector sequences and give substantial improvements for the weight sequence obtained by Lin et al. (Comput. Math. Appl. 62(2:635-640, 2011.

  4. Unifying and generating of space vector modulation sequences for multilevel converter

    DEFF Research Database (Denmark)

    Ma, Ke; Blaabjerg, Frede

    2014-01-01

    Space Vector Modulation (SVM) is a powerful method which enables some freedom to generate the modulation sequences and modify the performances of converter. However, in the multi-level converter structures, the number of switching state redundancies significantly increases, and the determination ...... on the discovered correlation and pattern, a general method for modulation sequences generating is proposed, and a series of new modulation sequences are deducted according to several easily applied rules.......Space Vector Modulation (SVM) is a powerful method which enables some freedom to generate the modulation sequences and modify the performances of converter. However, in the multi-level converter structures, the number of switching state redundancies significantly increases, and the determination...

  5. A series of bacterial co-expression vectors with rare-cutter recognition sequences.

    Science.gov (United States)

    Wakamori, Masatoshi; Umehara, Takashi; Yokoyama, Shigeyuki

    2010-11-01

    The bacterial co-expression method is a useful protein expression technique to reconstitute a hetero-oligomeric protein complex in vitro. However, during the plasmid subcloning for co-expression, unintended cleavage at the sequences of target cDNAs becomes more frequent as the number of DNA inserts increases. This problem also makes it difficult to change the combination of targeted proteins after preparing a certain co-expression construct. To avoid this problem, we have developed a series of bacterial co-expression vectors, in which each translation cassette can be subcloned at a set of rare-cutter restriction enzyme sites. We selected 9 different rare-cutter restriction enzymes that recognize a 7 or 8-base-pair sequence, and constructed 27 kinds of cloning vectors and 3 kinds of co-expression vectors, utilizing the rare-cutter recognition sequences as multi-cloning sites. Using this vector system, we co-expressed and co-purified a 7-subunit protein complex composed of the mammalian 26S proteasome regulatory subunits RPT1 to RPT6, and their associated factor, gankyrin. We verified the presence of all 7 subunits by western blotting, by taking advantage of the vector system in which the target proteins can be fused with a broad repertoire of epitope tags. Copyright 2010 Elsevier Inc. All rights reserved.

  6. Vectors

    DEFF Research Database (Denmark)

    Boeriis, Morten; van Leeuwen, Theo

    2017-01-01

    This article revisits the concept of vectors, which, in Kress and van Leeuwen’s Reading Images (2006), plays a crucial role in distinguishing between ‘narrative’, action-oriented processes and ‘conceptual’, state-oriented processes. The use of this concept in image analysis has usually focused...... on the most salient vectors, and this works well, but many images contain a plethora of vectors, which makes their structure quite different from the linguistic transitivity structures with which Kress and van Leeuwen have compared ‘narrative’ images. It can also be asked whether facial expression vectors...... should be taken into account in discussing ‘reactions’, which Kress and van Leeuwen link only to eyeline vectors. Finally, the question can be raised as to whether actions are always realized by vectors. Drawing on a re-reading of Rudolf Arnheim’s account of vectors, these issues are outlined...

  7. Complete genome sequence of a Klebsiella pneumoniae strain isolated from a known cotton insect boll vector

    Science.gov (United States)

    Klebsiella pneumoniae (associated with bacterial pneumonia) was previously isolated from Nezara viridula, a significant vector of cotton boll-rot pathogens. We provide the first annotated genome sequence of the cotton opportunistic strain K. pneumoniae 5-1. This data provides guidance to study the...

  8. A Shellcode Detection Method Based on Full Native API Sequence and Support Vector Machine

    Science.gov (United States)

    Cheng, Yixuan; Fan, Wenqing; Huang, Wei; An, Jing

    2017-09-01

    Dynamic monitoring the behavior of a program is widely used to discriminate between benign program and malware. It is usually based on the dynamic characteristics of a program, such as API call sequence or API call frequency to judge. The key innovation of this paper is to consider the full Native API sequence and use the support vector machine to detect the shellcode. We also use the Markov chain to extract and digitize Native API sequence features. Our experimental results show that the method proposed in this paper has high accuracy and low detection rate.

  9. Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus

    Directory of Open Access Journals (Sweden)

    Tsai Shih-Feng

    2007-12-01

    Full Text Available Abstract Background The mosquito, Armigeres subalbatus, mounts a distinctively robust innate immune response when infected with the nematode Brugia malayi, a causative agent of lymphatic filariasis. In order to mine the transcriptome for new insight into the cascade of events that takes place in response to infection in this mosquito, 6 cDNA libraries were generated from tissues of adult female mosquitoes subjected to immune-response activation treatments that lead to well-characterized responses, and from aging, naïve mosquitoes. Expressed sequence tags (ESTs from each library were produced, annotated, and subjected to comparative analyses. Results Six libraries were constructed and used to generate 44,940 expressed sequence tags, of which 38,079 passed quality filters to be included in the annotation project and subsequent analyses. All of these sequences were collapsed into clusters resulting in 8,020 unique sequence clusters or singletons. EST clusters were annotated and curated manually within ASAP (A Systematic Annotation Package for Community Analysis of Genomes web portal according to BLAST results from comparisons to Genbank, and the Anopheles gambiae and Drosophila melanogaster genome projects. Conclusion The resulting dataset is the first of its kind for this mosquito vector and provides a basis for future studies of mosquito vectors regarding the cascade of events that occurs in response to infection, and thereby providing insight into vector competence and innate immunity.

  10. Measurement Scale of the SOLIS Vector Spectromagnetograph

    Science.gov (United States)

    Jones, H. P.; Harvey, J. W.; Henney, C. J.; Keller, C. U.; Malanushenko, O. M.

    2004-05-01

    Longitudinal magnetograms obtained with the SOLIS Vector Spectromagnetograph (VSM) during a cross-calibration period are compared with similar data from the NASA/NSO Spectromagnetograph (SPM) at the NSO/Kitt Peak Vacuum Telescope as well as with SOHO/MDI and GONG magnetograms. The VSM began observations at the University of Arizona agricultural test site and collaborative observations were obtained with both the VSM and SPM from 2003 Aug 05 through 2003 Sep 21 when the SPM was officially retired. The VSM replaces the SPM and continues the 30-year NSO/Kitt Peak synoptic magnetogram record. Magnetograms are compared by equating histograms and, for selected examples, by pixel-by-pixel comparison of coregistered images. The VSM was not corrected for polarization crosstalk and was operated without fast guiding. Solar activity was at best moderate during this period. Over the range of observed fields, the VSM magnetograms show greatly improved sensitivity but are otherwise virtually identical with "raw" SPM magnetograms. GONG magnetograms are also closely comparable with the SPM while MDI flux values tend to be stronger by a factor of 1.2 - 1.4. Dependence of the results on seeing will be discussed. Partial funding for this work was provided through Solar and Heliospheric Research Supporting Research and Technology grants from NASA's Office of Space Sciences.

  11. Genome sequence of the tsetse fly (Glossina morsitans ): Vector of African trypanosomiasis

    KAUST Repository

    Watanabe, Junichi

    2014-04-24

    Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

  12. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

    DEFF Research Database (Denmark)

    Mirzadeh, Kiavash; Martinez, Virginia; Toddo, Stephen

    2015-01-01

    lie between the Shine-Dalgarno sequence and the start codon, they are an integral part of the translation initiation region. To identify the most optimal sequences, we devised a simple and inexpensive PCR-based step that generates sequence variants at the vector-coding sequence junction......Protein production in Escherichia coli is a fundamental activity for a large fraction of academic, pharmaceutical, and industrial research laboratories. Maximum production is usually sought, as this reduces costs and facilitates downstream purification steps. Frustratingly, many coding sequences...... are poorly expressed even when they are codon-optimized and expressed from vectors with powerful genetic elements. In this study, we show that poor expression can be caused by certain nucleotide sequences (e.g., cloning scars) at the junction between the vector and the coding sequence. Since these sequences...

  13. Recent patents involving virus nucleotide sequences; host defense, RNA silencing and expression vector strategies.

    Science.gov (United States)

    Ahmad, Tauqeer; AbouHaidar, Mounir; Hefferon, Kathleen L

    2011-12-01

    Improved knowledge of the molecular biology of viruses, including recent gains in virus sequence data analysis, has greatly contributed to recent innovations in medical diagnostics, therapeutics, drug development and other related areas. Virus sequences have been used for the development of vaccines and antiviral agents to block the spread of viral infections, as well as to target and battle chronic diseases such as cancer. Virus sequences are now routinely employed in a wide array of RNA silencing technologies. Viruses can also be engineered into expression vectors which in turn can be used as protein production platforms as well as delivery vehicles for gene therapies. This review article outlines a number of patents that have been recently issued with respect to virus sequence data and describes some of their biotechnological applications.

  14. Worldwide Magnetograms with Geomagnetic Components D, H, Z, or X, Y, and Z

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NOAA National Centers for Environmental Information (formerly National Geophysical Data Center) receives magnetograms from over 200 geomagnetic observatories....

  15. Magnetogram Forecast: An All-Clear Space Weather Forecasting System

    Science.gov (United States)

    Barghouty, Nasser; Falconer, David

    2015-01-01

    Solar flares and coronal mass ejections (CMEs) are the drivers of severe space weather. Forecasting the probability of their occurrence is critical in improving space weather forecasts. The National Oceanic and Atmospheric Administration (NOAA) currently uses the McIntosh active region category system, in which each active region on the disk is assigned to one of 60 categories, and uses the historical flare rates of that category to make an initial forecast that can then be adjusted by the NOAA forecaster. Flares and CMEs are caused by the sudden release of energy from the coronal magnetic field by magnetic reconnection. It is believed that the rate of flare and CME occurrence in an active region is correlated with the free energy of an active region. While the free energy cannot be measured directly with present observations, proxies of the free energy can instead be used to characterize the relative free energy of an active region. The Magnetogram Forecast (MAG4) (output is available at the Community Coordinated Modeling Center) was conceived and designed to be a databased, all-clear forecasting system to support the operational goals of NASA's Space Radiation Analysis Group. The MAG4 system automatically downloads nearreal- time line-of-sight Helioseismic and Magnetic Imager (HMI) magnetograms on the Solar Dynamics Observatory (SDO) satellite, identifies active regions on the solar disk, measures a free-energy proxy, and then applies forecasting curves to convert the free-energy proxy into predicted event rates for X-class flares, M- and X-class flares, CMEs, fast CMEs, and solar energetic particle events (SPEs). The forecast curves themselves are derived from a sample of 40,000 magnetograms from 1,300 active region samples, observed by the Solar and Heliospheric Observatory Michelson Doppler Imager. Figure 1 is an example of MAG4 visual output

  16. Identification of functionally diverse lipocalin proteins from sequence information using support vector machine.

    Science.gov (United States)

    Pugalenthi, Ganesan; Kandaswamy, Krishna Kumar; Suganthan, P N; Archunan, G; Sowdhamini, R

    2010-08-01

    Lipocalins are functionally diverse proteins that are composed of 120-180 amino acid residues. Members of this family have several important biological functions including ligand transport, cryptic coloration, sensory transduction, endonuclease activity, stress response activity in plants, odorant binding, prostaglandin biosynthesis, cellular homeostasis regulation, immunity, immunotherapy and so on. Identification of lipocalins from protein sequence is more challenging due to the poor sequence identity which often falls below the twilight zone. So far, no specific method has been reported to identify lipocalins from primary sequence. In this paper, we report a support vector machine (SVM) approach to predict lipocalins from protein sequence using sequence-derived properties. LipoPred was trained using a dataset consisting of 325 lipocalin proteins and 325 non-lipocalin proteins, and evaluated by an independent set of 140 lipocalin proteins and 21,447 non-lipocalin proteins. LipoPred achieved 88.61% accuracy with 89.26% sensitivity, 85.27% specificity and 0.74 Matthew's correlation coefficient (MCC). When applied on the test dataset, LipoPred achieved 84.25% accuracy with 88.57% sensitivity, 84.22% specificity and MCC of 0.16. LipoPred achieved better performance rate when compared with PSI-BLAST, HMM and SVM-Prot methods. Out of 218 lipocalins, LipoPred correctly predicted 194 proteins including 39 lipocalins that are non-homologous to any protein in the SWISSPROT database. This result shows that LipoPred is potentially useful for predicting the lipocalin proteins that have no sequence homologs in the sequence databases. Further, successful prediction of nine hypothetical lipocalin proteins and five new members of lipocalin family prove that LipoPred can be efficiently used to identify and annotate the new lipocalin proteins from sequence databases. The LipoPred software and dataset are available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/lipopred.htm.

  17. Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines

    Directory of Open Access Journals (Sweden)

    Seizi Someya

    2010-01-01

    Full Text Available Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs. We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homology-based prediction method to the annotated human genome database, H-invDB, we found that the true positive rate of prediction was improved.

  18. Field distribution of magnetograms from simulations of active region formation

    Science.gov (United States)

    Dacie, S.; van Driel-Gesztelyi, L.; Démoulin, P.; Linton, M. G.; Leake, J. E.; MacTaggart, D.; Cheung, M. C. M.

    2017-10-01

    Context. The evolution of the photospheric magnetic field distributions (probability densities) has previously been derived for a set of active regions. Photospheric field distributions are a consequence of physical processes that are difficult to determine from observations alone. Aims: We analyse simulated magnetograms from numerical simulations, which model the emergence and decay of active regions. These simulations have different experimental set-ups and include different physical processes, allowing us to investigate the relative importance of convection, magnetic buoyancy, magnetic twist, and braiding for flux emergence. Methods: We specifically studied the photospheric field distributions (probability densities found with a kernel density estimation analysis) and compared the results with those found from observations. Results: Simulations including convection most accurately reproduce the observed evolution of the photospheric field distributions during active region evolution. Conclusions: This indicates that convection may play an important role during the decay phase and also during the formation of active regions, particularly for low flux density values.

  19. Mi Gauss es su Gauss: Lessons from Cross-Calibrating 40 years of Full Disk Magnetograms

    Science.gov (United States)

    Werginz, Zachary; Munoz-Jaramillo, Andres; Martens, Petrus C.; Harvey, J. W.

    2017-08-01

    Full-disk line-of-sight magnetograms from the Kitt Peak Vacuum Telescope (KPVT) are a highly valuable, but underutilized, source of data for understanding long-term solar variability. Here we present the results of a project for obtaining a cross-callibrated series of magnetograms spanning 40 years including KPVT (512 and SPMG), SOHO/MDI and SDO/HMI magnetographs. The biggest challenge we face is empirically identifying a calibration factor and estimate of uncertainty between instruments with little temporal overlap.Here we propose a method that fragments magnetograms into spherical quadrangles bounded by latitudes and longitudes and calculates various information such as total area, mean flux density, and distance from disk center. Our main assumption is that the Sun does not change significantly over daily time periods.First a magnetogram to be calibrated is differentially rotated to match a reference magnetogram in time. Then the smaller magnetogram is interpolated into the larger one to account for sub-pixel heliographic coordinates. We then produce equally spaced bands of latitude and longitude determined from a fragmentation parameter. These are used to map out regions on each magnetogram that are expected to relay the same information. Our efforts to cross-calibrate lead to results that vary with fragmentation parameters, the difference in time of selected magnetograms, and distance from disk center.Given that this cross-callibrated series will be made publically available, we are looking for constructive criticism, suggestions, and feedback. Please join us in making these data as good as they can be.

  20. [PCR-RFLP and sequencing studies of malaria vectors (Diptera, Culicidae, Anopheles) in Kyrgyzstan].

    Science.gov (United States)

    Goriacheva, I I; Zvantsov, A B; Gordeev, M I; Bezzhonova, O V; Usenbaev, N T; Ezhov, M N

    2011-01-01

    The results of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, obtained after treatment of PCR-products with restriction endonuclease CfoI, could identify two members of the Anopheles maculipennis complex: An. maculipennis and An. artemievi. Treatment of amplification products with restriction endonuclease BsuI gave rise to fragment lengths of 192 and 218 bp, characteristic of An. artemievi, in the populations of the Talas (settlement of Kizil-Adyr, Kara-Bura District), Dzhelalabad (towns of Tashkumyr and Kara-Kul), and Osh (town of Gulcha, Alai District; village of Langar, Kara-Suisky District) Regions. After treatment of PCR-products with restriction endonuclease BstACI, fragment lengths of 292 and 150 bp, characteristic of An. messeae, were obtained for the mosquitoes of Issyk-Kul (town of Balykchi) and Naryn (settlement of Kochkorka, Kochkor District) Regions. To identify the molecular forms of An. superpictus, the investigators sequenced the amplification products obtained by PCR with 5.8S and 28S rRNA gene-specific primers. Analysis of the primary structure of the second internal transcribed spacer, by using the international databases, has indicated that molecular form X is prevalent in the study districts of Kyrgyzstan. The COI-COII region of the mitochondrial genome of the vector also underwent PCR-RFLP analysis. Three new haplotypes with restriction patterns of about 540, 420, 200, 150, 140 bp, about 540, 360, 280, 150, 140 bp, and about 580, 540, and 150, 140 bp have been identified along with the previously described haplotype X characterized by restriction products of 540, 420, 260, 150, and 140 bp in length.

  1. Delivery of Short Hairpin RNA Sequences by Using a Replication-Competent Avian Retroviral Vector

    OpenAIRE

    Bromberg-White, Jennifer L.; Webb, Craig P; Patacsil, Veronique S.; Miranti, Cindy K.; Williams, Bart O.; Holmen, Sheri L.

    2004-01-01

    While recent studies have demonstrated that retroviral vectors can be used to stably express short hairpin RNA (shRNA) to inhibit gene expression, these studies have utilized replication-defective retroviruses. We describe the creation of a replication-competent, Gateway-compatible retroviral vector capable of expressing shRNA that inhibits the expression of specific genes.

  2. Delivery of short hairpin RNA sequences by using a replication-competent avian retroviral vector.

    Science.gov (United States)

    Bromberg-White, Jennifer L; Webb, Craig P; Patacsil, Veronique S; Miranti, Cindy K; Williams, Bart O; Holmen, Sheri L

    2004-05-01

    While recent studies have demonstrated that retroviral vectors can be used to stably express short hairpin RNA (shRNA) to inhibit gene expression, these studies have utilized replication-defective retroviruses. We describe the creation of a replication-competent, Gateway-compatible retroviral vector capable of expressing shRNA that inhibits the expression of specific genes.

  3. Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing.

    Science.gov (United States)

    Cramaro, Wibke J; Hunewald, Oliver E; Bell-Sakyi, Lesley; Muller, Claude P

    2017-02-08

    Global warming and other ecological changes have facilitated the expansion of Ixodes ricinus tick populations. Ixodes ricinus is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular Borrelia burgdorferi (sensu lato), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the I. ricinus tick is necessary. To facilitate such studies, we recently published the first reference genome of this highly prevalent pathogen vector. Here, we further extend these studies by scaffolding and annotating the first reference genome by using ultra-long sequencing reads from third generation single molecule sequencing. In addition, we present the first genome size estimation for I. ricinus ticks and the embryo-derived cell line IRE/CTVM19. 235,953 contigs were integrated into 204,904 scaffolds, extending the currently known genome lengths by more than 30% from 393 to 516 Mb and the N50 contig value by 87% from 1643 bp to a N50 scaffold value of 3067 bp. In addition, 25,263 sequences were annotated by comparison to the tick's North American relative Ixodes scapularis. After (conserved) hypothetical proteins, zinc finger proteins, secreted proteins and P450 coding proteins were the most prevalent protein categories annotated. Interestingly, more than 50% of the amino acid sequences matching the homology threshold had 95-100% identity to the corresponding I. scapularis gene models. The sequence information was complemented by the first genome size estimation for this species. Flow cytometry-based genome size analysis revealed a haploid genome size of 2.65Gb for I. ricinus ticks and 3.80 Gb for the cell line. We present a first draft sequence map of the I. ricinus genome based on a PacBio-Illumina assembly. The I. ricinus genome was shown to be 26% (500 Mb) larger than the genome of its

  4. A CGMMV genome-replicon vector with partial sequences of coat protein gene efficiently expresses GFP in Nicotiana benthamiana.

    Science.gov (United States)

    Jailani, A Abdul Kader; Solanki, Vikas; Roy, Anirban; Sivasudha, T; Mandal, Bikash

    2017-04-02

    A highly infectious clone of Cucumber green mottle mosaic virus (CGMMV), a cucurbit-infecting tobamovirus was utilized for designing of gene expression vectors. Two versions of vector were examined for their efficacy in expressing the green fluorescent protein (GFP) in Nicotiana benthamiana. When the GFP gene was inserted at the stop codon of coat protein (CP) gene of the CGMMV genome without any read-through codon, systemic expression of GFP, as well as virion formation and systemic symptoms expression were obtained in N. benthamiana. The qRT-PCR analysis showed 23 fold increase of GFP over actin at 10days post inoculation (dpi), which increased to 45 fold at 14dpi and thereafter the GFP expression was significantly declined. Further, we show that when the most of the CP sequence is deleted retaining only the first 105 nucleotides, the shortened vector containing GFP in frame of original CP open reading frame (ORF) resulted in 234 fold increase of GFP expression over actin at 5dpi in N. benthamiana without the formation of virions and disease symptoms. Our study demonstrated that a simple manipulation of CP gene in the CGMMV genome while preserving the translational frame of CP resulted in developing a virus-free, rapid and efficient foreign protein expression system in the plant. The CGMMV based vectors developed in this study may be potentially useful for the production of edible vaccines in cucurbits. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

    Science.gov (United States)

    Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

    2017-06-17

    The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

  6. Suppression of leaky expression of adenovirus genes by insertion of microRNA-targeted sequences in the replication-incompetent adenovirus vector genome

    Directory of Open Access Journals (Sweden)

    Kahori Shimizu

    2014-01-01

    Full Text Available Leaky expression of adenovirus (Ad genes occurs following transduction with a conventional replication-incompetent Ad vector, leading to an induction of cellular immunity against Ad proteins and Ad protein-induced toxicity, especially in the late phase following administration. To suppress the leaky expression of Ad genes, we developed novel Ad vectors by incorporating four tandem copies of sequences with perfect complementarity to miR-122a or miR-142-3p into the 3′-untranslated region (UTR of the E2A, E4, or pIX gene, which were mainly expressed from the Ad vector genome after transduction. These Ad vectors easily grew to high titers comparable to those of a conventional Ad vector in conventional 293 cells. The leaky expression of these Ad genes in mouse organs was significantly suppressed by 2- to 100-fold, compared with a conventional Ad vector, by insertion of the miRNA-targeted sequences. Notably, the Ad vector carrying the miR-122a–targeted sequences into the 3′-UTR of the E4 gene expressed higher and longer-term transgene expression and more than 20-fold lower levels of all the Ad early and late genes examined in the liver than a conventional Ad vector. miR-122a–mediated suppression of the E4 gene expression in the liver significantly reduced the hepatotoxicity which an Ad vector causes via both adaptive and non-adaptive immune responses.

  7. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    Directory of Open Access Journals (Sweden)

    Xin Yi Ng

    2015-01-01

    Full Text Available This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM- LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity.

  8. Cloning vector

    Science.gov (United States)

    Guilfoyle, R.A.; Smith, L.M.

    1994-12-27

    A vector comprising a filamentous phage sequence containing a first copy of filamentous phage gene X and other sequences necessary for the phage to propagate is disclosed. The vector also contains a second copy of filamentous phage gene X downstream from a promoter capable of promoting transcription in a bacterial host. In a preferred form of the present invention, the filamentous phage is M13 and the vector additionally includes a restriction endonuclease site located in such a manner as to substantially inactivate the second gene X when a DNA sequence is inserted into the restriction site. 2 figures.

  9. Cloning vector

    Science.gov (United States)

    Guilfoyle, Richard A.; Smith, Lloyd M.

    1994-01-01

    A vector comprising a filamentous phage sequence containing a first copy of filamentous phage gene X and other sequences necessary for the phage to propagate is disclosed. The vector also contains a second copy of filamentous phage gene X downstream from a promoter capable of promoting transcription in a bacterial host. In a preferred form of the present invention, the filamentous phage is M13 and the vector additionally includes a restriction endonuclease site located in such a manner as to substantially inactivate the second gene X when a DNA sequence is inserted into the restriction site.

  10. Geometric Feature-Based Facial Expression Recognition in Image Sequences Using Multi-Class AdaBoost and Support Vector Machines

    Directory of Open Access Journals (Sweden)

    Joonwhoan Lee

    2013-06-01

    Full Text Available Facial expressions are widely used in the behavioral interpretation of emotions, cognitive science, and social interactions. In this paper, we present a novel method for fully automatic facial expression recognition in facial image sequences. As the facial expression evolves over time facial landmarks are automatically tracked in consecutive video frames, using displacements based on elastic bunch graph matching displacement estimation. Feature vectors from individual landmarks, as well as pairs of landmarks tracking results are extracted, and normalized, with respect to the first frame in the sequence. The prototypical expression sequence for each class of facial expression is formed, by taking the median of the landmark tracking results from the training facial expression sequences. Multi-class AdaBoost with dynamic time warping similarity distance between the feature vector of input facial expression and prototypical facial expression, is used as a weak classifier to select the subset of discriminative feature vectors. Finally, two methods for facial expression recognition are presented, either by using multi-class AdaBoost with dynamic time warping, or by using support vector machine on the boosted feature vectors. The results on the Cohn-Kanade (CK+ facial expression database show a recognition accuracy of 95.17% and 97.35% using multi-class AdaBoost and support vector machines, respectively.

  11. Acceleration of Convergence of a Vector Sequence by Reduced Rank Extrapolation.

    Science.gov (United States)

    1981-11-01

    iteration, x n vi ABSTRACT A new family of methods, called reduced rank extrap - olation, is developed for accelerating convergence of the sequence of...flow of air around aircraft and missiles, and the flux of neutrons in a nuclear reactor . Standard methods of setting up the iteration matrix A in

  12. MANGO - A Magnetogram Analysis Service for Enhancement of the Heliophysics Data Environment

    Science.gov (United States)

    Bargatze, L. F.

    2011-12-01

    The Heliophysics Data Environment Enhancement program supports efforts to integrate data services for conducting research of solar-terrestrial interactions. MANGO, Magnetogram Analysis for the Network of Geophysical Observatories, is a service that is directed at Heliophysics researchers interested in processing magnetic field data from ground magnetometers. Ground magnetograms are essential for monitoring the response of the magnetosphere to solar wind coupling. For instance, it is difficult to understand how spacecraft particle and field variations fit in context of activity throughout the global magnetospheric system without using ground magnetic field data. The MANGO service package allows one to decompose ground magnetic field variations and estimate the relative contributions from secular, diurnal, ring current, and auroral current systems. The MANGO service package leverages the SPASE metadata registries of the Virtual Magnetospheric Observatory (VMO) to compile a list of available magnetogram data products. Currently, MANGO provides access to over 900 data products from about 350 ground magnetic field stations located around the globe. The VMO SPASE Granule registry contains ~150,000 files that comprise the MANGO relevant data products. And, the VMO Granule registry count is steadily increasing as more data products are described and ingested. Data selection from the distributed network of stations is naturally aided by using a world map to display the set of observatories. The MANGO web site (http://mango.igpp.ucla.edu), plots stations on a map that have data products, which meet user-defined criteria based on time of observation, station location, time cadence, magnetometer chain, etc. Note that Many of the ground magnetogram and geomagnetic index data products relevant to the MANGO effort are only available from their data providers in formats that allow the data to be packed. The formats used, and there are many types, save time in file retrieval and

  13. RVMAB: Using the Relevance Vector Machine Model Combined with Average Blocks to Predict the Interactions of Proteins from Protein Sequences

    Directory of Open Access Journals (Sweden)

    Ji-Yong An

    2016-05-01

    Full Text Available Protein-Protein Interactions (PPIs play essential roles in most cellular processes. Knowledge of PPIs is becoming increasingly more important, which has prompted the development of technologies that are capable of discovering large-scale PPIs. Although many high-throughput biological technologies have been proposed to detect PPIs, there are unavoidable shortcomings, including cost, time intensity, and inherently high false positive and false negative rates. For the sake of these reasons, in silico methods are attracting much attention due to their good performances in predicting PPIs. In this paper, we propose a novel computational method known as RVM-AB that combines the Relevance Vector Machine (RVM model and Average Blocks (AB to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the AB feature representation on a Position Specific Scoring Matrix (PSSM, reducing the influence of noise using a Principal Component Analysis (PCA, and using a Relevance Vector Machine (RVM based classifier. We performed five-fold cross-validation experiments on yeast and Helicobacter pylori datasets, and achieved very high accuracies of 92.98% and 95.58% respectively, which is significantly better than previous works. In addition, we also obtained good prediction accuracies of 88.31%, 89.46%, 91.08%, 91.55%, and 94.81% on other five independent datasets C. elegans, M. musculus, H. sapiens, H. pylori, and E. coli for cross-species prediction. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM classifier on the yeast dataset. The experimental results demonstrate that our RVM-AB method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool. To facilitate extensive studies for future proteomics research, we developed

  14. Production of recombinant AAV vectors encoding insulin-like growth factor I is enhanced by interaction among AAV rep regulatory sequences

    Directory of Open Access Journals (Sweden)

    Dilley Robert

    2009-01-01

    Full Text Available Abstract Background Adeno-associated virus (AAV vectors are promising tools for gene therapy. Currently, their potential is limited by difficulties in producing high vector yields with which to generate transgene protein product. AAV vector production depends in part upon the replication (Rep proteins required for viral replication. We tested the hypothesis that mutations in the start codon and upstream regulatory elements of Rep78/68 in AAV helper plasmids can regulate recombinant AAV (rAAV vector production. We further tested whether the resulting rAAV vector preparation augments the production of the potentially therapeutic transgene, insulin-like growth factor I (IGF-I. Results We constructed a series of AAV helper plasmids containing different Rep78/68 start codon in combination with different gene regulatory sequences. rAAV vectors carrying the human IGF-I gene were prepared with these vectors and the vector preparations used to transduce HT1080 target cells. We found that the substitution of ATG by ACG in the Rep78/68 start codon in an AAV helper plasmid (pAAV-RC eliminated Rep78/68 translation, rAAV and IGF-I production. Replacement of the heterologous sequence upstream of Rep78/68 in pAAV-RC with the AAV2 endogenous p5 promoter restored translational activity to the ACG mutant, and restored rAAV and IGF-I production. Insertion of the AAV2 p19 promoter sequence into pAAV-RC in front of the heterologous sequence also enabled ACG to function as a start codon for Rep78/68 translation. The data further indicate that the function of the AAV helper construct (pAAV-RC, that is in current widespread use for rAAV production, may be improved by replacement of its AAV2 unrelated heterologous sequence with the native AAV2 p5 promoter. Conclusion Taken together, the data demonstrate an interplay between the start codon and upstream regulatory sequences in the regulation of Rep78/68 and indicate that selective mutations in Rep78/68 regulatory elements

  15. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine

    Directory of Open Access Journals (Sweden)

    Liu Guo-Ping

    2005-12-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are a group of short (~22 nt non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology. Results A set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information. Conclusion The local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.

  16. Three new shRNA expression vectors targeting the CYP3A4 coding sequence to inhibit its expression

    Directory of Open Access Journals (Sweden)

    Siyun Xu

    2014-10-01

    Full Text Available RNA interference (RNAi is useful for selective gene silencing. Cytochrome P450 3A4 (CYP3A4, which metabolizes approximately 50% of drugs in clinical use, plays an important role in drug metabolism. In this study, we aimed to develop a short hairpin RNA (shRNA to modulate CYP3A4 expression. Three new shRNAs (S1, S2 and S3 were designed to target the coding sequence (CDS of CYP3A4, cloned into a shRNA expression vector, and tested in different cells. The mixture of three shRNAs produced optimal reduction (55% in CYP3A4 CDS-luciferase activity in both CHL and HEK293 cells. Endogenous CYP3A4 expression in HepG2 cells was decreased about 50% at both mRNA and protein level after transfection of the mixture of three shRNAs. In contrast, CYP3A5 gene expression was not altered by the shRNAs, supporting the selectivity of CYP3A4 shRNAs. In addition, HepG2 cells transfected with CYP3A4 shRNAs were less sensitive to Ginkgolic acids, whose toxic metabolites are produced by CYP3A4. These results demonstrate that vector-based shRNAs could modulate CYP3A4 expression in cells through their actions on CYP3A4 CDS, and CYP3A4 shRNAs may be utilized to define the role of CYP3A4 in drug metabolism and toxicity.

  17. Sequence Analysis of Two Cryptic Plasmids from Bifidobacterium longum DJO10A and Construction of a Shuttle Cloning Vector

    Science.gov (United States)

    Lee, Ju-Hoon; O’Sullivan, Daniel J.

    2006-01-01

    Bifidobacterium longum DJO10A is a recent human isolate with probiotic characteristics and contains two plasmids, designated pDOJH10L and pDOJH10S. The complete sequences of both these plasmids have now been determined and consist of two circular DNA molecules of 10,073 and 3,661 bp, with G+C contents of 62.2% and 66.2%, respectively. Plasmid pDOJH10L is a cointegrate plasmid consisting of DNA regions exhibiting very high sequence identity to two other B. longum plasmids, pNAC2 (98%) and pKJ50 (96%), together with another region. Interestingly, the rolling circular replication (RCR) regions of both the pNAC2- and pKJ50-like plasmids were disrupted during the recombination event leading to a further recombination event to acquire a functional replicon. This consists of a new fused rep gene and an RCR-type ori consisting of a conserved DnaA box in an AT-rich region followed by four contiguous repeated sequences consistent with an iteron structure and an inverted repeat. The smaller pDOJH10S had no sequence similarity to any other characterized plasmid from bifidobacteria. In addition, it did not contain any features consistent with RCR, which is the replication mechanism proposed for all the bifidobacteria plasmids characterized to date. It did exhibit sequence similarity with several theta replication-related replication proteins from other gram-positive, high-G+C bacteria, with the closest match from a Rhodococcus rhodochrous plasmid, suggesting a theta mechanism of replication. S1 nuclease analysis of both plasmids in B. longum DJO10A revealed single-strand DNA intermediates for pDOJH10L, which is consistent for RCR, but none were detected for pDOJH10S. As the G+C content of pDOJH10S is similar to that of Rhodococcus rhodochrous (67%) and significantly higher than that of B. longum (60.1%), it may have been acquired through horizontal gene transfer from a Rhodococcus species, as both genera are members of the Actinomycetes and are intestinal inhabitants. An

  18. The functional role of S/MARs in episomal vectors as defined by the stress-induced destabilization profile of the vector sequences.

    Science.gov (United States)

    Giannakopoulos, Aristeidis; Stavrou, Eleana F; Zarkadis, Ioannis; Zoumbos, Nicholas; Thrasher, Adrian J; Athanassiadou, Aglaia

    2009-04-17

    The scaffold/matrix attachment regions (S/MARs) are chromosomal elements that participate in the formation of chromatin domains and have origin of replication support functions. Because of all these functions, in recent years, they have been used as part of episomal vectors for gene transfer. The S/MAR of the human beta-interferon gene has been shown to support efficient episome retention and transgene expression in various mammalian cells. In Jurkat and other cells, DNA plasmid vectors containing Epstein-Barr virus origin of replication (EBV OriP) and the EBV nuclear antigen-1 gene mediate prolonged episome retention in the host cell nucleus, which, however, diminishes over time. In order to enhance retention, we combined this system with an S/MAR element. Unexpectedly, this completely eliminated the capacity of episomes to replicate. Calculation of the stress-induced DNA duplex destabilization profile of the vectors suggested that the S/MAR element had created an increase in molecular stability at the OriP site that may have disturbed replicative potential. In contrast, introduction of an alternative initiation of replication region from the beta-globin gene locus, instead of EBV OriP and the EBV nuclear antigen-1 gene, restored replicative capacity and enhanced episome retention mediated by the S/MAR. These effects were associated with a destabilization profile at the initiation of replication region. These data demonstrate a correlation between S/MAR-mediated vector retention and the presence of an unstable duplex at a replication origin, in this particular setting. We consider that the calculation of stress-induced duplex destabilization may be an informative first step in the design of units that replicate extrachromosomally, particularly as the latter present a safer and, therefore, attractive alternative to integrating viral vectors for gene therapy applications.

  19. Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells.

    Science.gov (United States)

    Penaud-Budloo, Magalie; Lecomte, Emilie; Guy-Duché, Aurélien; Saleun, Sylvie; Roulet, Alain; Lopez-Roques, Céline; Tournaire, Benoît; Cogné, Benjamin; Léger, Adrien; Blouin, Véronique; Lindenbaum, Pierre; Moullier, Philippe; Ayuso, Eduard

    2017-06-01

    Recombinant adeno-associated viral (rAAV) vectors have proven excellent tools for the treatment of many genetic diseases and other complex diseases. However, the illegitimate encapsidation of DNA contaminants within viral particles constitutes a major safety concern for rAAV-based therapies. Moreover, the development of rAAV vectors for early-phase clinical trials has revealed the limited accuracy of the analytical tools used to characterize these new and complex drugs. Although most published data concerning residual DNA in rAAV preparations have been generated by quantitative PCR, we have developed a novel single-strand virus sequencing (SSV-Seq) method for quantification of DNA contaminants in AAV vectors produced in mammalian cells by next-generation sequencing (NGS). Here, we describe the adaptation of SSV-Seq for the accurate identification and quantification of DNA species in rAAV stocks produced in insect cells. We found that baculoviral DNA was the most abundant contaminant, representing less than 2.1% of NGS reads regardless of serotype (2, 8, or rh10). Sf9 producer cell DNA was detected at low frequency (≤0.03%) in rAAV lots. Advanced computational analyses revealed that (1) baculoviral sequences close to the inverted terminal repeats preferentially underwent illegitimate encapsidation, and (2) single-nucleotide variants were absent from the rAAV genome. The high-throughput sequencing protocol described here enables effective DNA quality control of rAAV vectors produced in insect cells, and is adapted to conform with regulatory agency safety requirements.

  20. [Creation of DNA vaccine vector based on codon-optimized gene of rabies virus glycoprotein (G protein) with consensus amino acid sequence].

    Science.gov (United States)

    Starodubova, E S; Kuzmenko, Y V; Latanova, A A; Preobrazhenskaya, O V; Karpov, V L

    2016-01-01

    An optimized design of the rabies virus glycoprotein (G protein) for use within DNA vaccines has been suggested. The design represents a territorially adapted antigen constructed taking into account glycoprotein amino acid sequences of the rabies viruses registered in the Russian Federation and the vaccine Vnukovo-32 strain. Based on the created consensus amino acid sequence, the nucleotide codon-optimized sequence of this modified glycoprotein was obtained and cloned into the pVAX1 plasmid (a vector of the last generation used in the creation of DNA vaccines). A twofold increase in this gene expression compared to the expression of the Vnukovo-32 strain viral glycoprotein gene in a similar vector was registered in the transfected cell culture. It has been demonstrated that the accumulation of modified G protein exceeds the number of the control protein synthesized using the plasmid with the Vnukovo-32 strain viral glycoprotein gene by 20 times. Thus, the obtained modified rabies virus glycoprotein can be considered to be a promising DNA vaccine antigen.

  1. DNA sequence characterisation and phylogeography of Lymnaea cousini and related species, vectors of fascioliasis in northern Andean countries, with description of L. meridensis n. sp. (Gastropoda: Lymnaeidae

    Directory of Open Access Journals (Sweden)

    Bargues M Dolores

    2011-07-01

    Full Text Available Abstract Background Livestock fascioliasis is a problem throughout Ecuador, Colombia and Venezuela, mainly in Andean areas where the disease also appears to affect humans. Transmission patterns and epidemiological scenarios of liver fluke infection have shown to differ according to the lymnaeid vector snail species involved. These Andean countries present the vectors Lymnaea cousini, L. bogotensis and L. ubaquensis, unknown in the rest of Latin America. An exhaustive combined haplotype study of these species is performed by means of DNA sequencing of the nuclear ribosomal 18S RNA gene, ITS-2 and ITS-1, and mitochondrial DNA cox1 gene. Results The conserved 5.8S rDNA sequence corroborated that no pseudogenes are involved in the numerous non-microsatellite/minisatellite-related indels appearing between the ITS-2 and ITS-1 sequences when comparing different L. cousini - L. bogotensis populations. Sequence analyses and phylogenetic reconstruction methods including other lymnaeid vector species show that (i L. bogotensis is a synonym of L. cousini, (ii L. ubaquensis is a synonym of Pseudosuccinea columella, and (iii populations of L. cousini hitherto known from Venezuelan highlands indeed belong to a new species for which the name L. meridensis n. sp. is proposed. This new species is described and a complete phenotypic differentiation provided. Conclusions ITS-2, ITS-1 and cox1 prove to be good markers for specimen classification and haplotype characterisation of these morphologically similar lymnaeids in endemic areas. Analysis of the 18S gene and phylogenetic reconstructions indicate that L. cousini and L. meridensis n. sp. cluster in an evolutionary line different from the one of P. columella, despite their external resemblance. This suggests an evolutionary phenotypic convergence related to similar environments and which has given rise to frequent specimen misclassification. Body size and phylogenetic relationships of L. meridensis n. sp. with

  2. New Approach to Fractal Approximation of Vector-Functions

    National Research Council Canada - National Science Library

    Igudesman, Konstantin; Davletbaev, Marsel; Shabernev, Gleb

    2015-01-01

      This paper introduces new approach to approximation of continuous vector-functions and vector sequences by fractal interpolation vector-functions which are multidimensional generalization of fractal...

  3. Enhancement of heterologous gene expression in Flammulina velutipes using polycistronic vectors containing a viral 2A cleavage sequence.

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    Yu-Ju Lin

    Full Text Available Agrobacterium tumefaciens-mediated transformation for edible mushrooms has been previously established. However, the enhancement of heterologous protein production and the expression of multi-target genes remains a challenge. In this study, heterologous protein expression in the enoki mushroom Flammulina velutipes was notably enhanced using 2A peptide-mediated cleavage to co-express multiple copies of single gene. The polycistronic expression vectors were constructed by connecting multi copies of the enhanced green fluorescent protein (egfp gene using 2A peptides derived from porcine teschovirus-1. The P2A peptides properly self-cleaved as shown by the formation of the transformants with antibiotic resistant capacity and exciting green fluorescence levels after introducing the vectors into F. velutipes mycelia. The results of western blot analysis, epifluorescent microscopy and EGFP production showed that heterologous protein expression in F. velutipes using the polycistronic strategy increased proportionally as the gene copy number increased from one to three copies. In contrast, much lower EGFP levels were detected in the F. velutipes transformants harboring four copies of the egfp gene due to mRNA instability. The polycistronic strategy using 2A peptide-mediated cleavage developed in this study can not only be used to express single gene in multiple copies, but also to express multiple genes in a single reading frame. It is a promising strategy for the application of mushroom molecular pharming.

  4. Cloning and Sequence Analysis of Recombinant Plasmodium vivax Merozoite Surface Protein 1 (PvMSP-142 kDa In pTZ57R/T Vector.

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    Hadi Mirahmadi

    2015-06-01

    Full Text Available Carboxy-terminal 42 kDa region of Plasmodium vivax merozoite surface protein-1 is considered as an important antigen in blood stage. Since, this region has been observed to be polymorphic among isolates of P. vivax, it is significant to survey on different regions of this antigen in various areas of the world.In the present study, the genetic diversity of cloned PvMSP-142 kDa gene from an Iranian patient is analyzed. Parasite DNA was extracted from a P. vivax - infected patient in Iran. The region of PvMSP-142 kDa was amplified by PCR, cloned into pTZ57R/T vector and then sequenced.Sequencing of cloned PvMSP-142 kDa gene clearly has a high degree of homology (95% with reference Sal-I sequence and also with the homogeneous sequences from some studied countries (97%. Thirty eight SNPs (single nucleotide polymorphism were identified in cloned PvMSP-142 kDa gene which the mutations had localized in the 33 kDa fragment (PvMSP-133 kDa, while there was nearly no variation in the 19 kDa fragment (PvMSP-119 kDa. 2 out of 38 mutations were found as to be novel haplotypes.High similarity of cloned PvMSP-142 kDa gene in comparison to reference sequence and other sequences could be beneficial as a remarkable molecular marker for serological diagnostic kits of P. vivax in malarious neighboring countries of Iran and around the world.

  5. Cloning and Sequence Analysis of Recombinant Plasmodium vivax Merozoite Surface Protein 1 (PvMSP-142 kDa) In pTZ57R/T Vector

    Science.gov (United States)

    MIRAHMADI, Hadi; SPOTIN, Adel; FALLAHI, Shirzad; TAGHIPOUR, Niloofar; TURKI, Habibollah; SEYYED TABAEI, Seyyed Javad

    2015-01-01

    Background: Carboxy-terminal 42 kDa region of Plasmodium vivax merozoite surface protein-1 is considered as an important antigen in blood stage. Since, this region has been observed to be polymorphic among isolates of P. vivax, it is significant to survey on different regions of this antigen in various areas of the world. Methods: In the present study, the genetic diversity of cloned PvMSP-142 kDa gene from an Iranian patient is analyzed. Parasite DNA was extracted from a P. vivax - infected patient in Iran. The region of PvMSP-142 kDa was amplified by PCR, cloned into pTZ57R/T vector and then sequenced. Results: Sequencing of cloned PvMSP-142 kDa gene clearly has a high degree of homology (95%) with reference Sal-I sequence and also with the homogeneous sequences from some studied countries (97%). Thirty eight SNPs (single nucleotide polymorphism) were identified in cloned PvMSP-142 kDa gene which the mutations had localized in the 33 kDa fragment (PvMSP-133 kDa), while there was nearly no variation in the 19 kDa fragment (PvMSP-119 kDa). 2 out of 38 mutations were found as to be novel haplotypes. Conclusion: High similarity of cloned PvMSP-142 kDa gene in comparison to reference sequence and other sequences could be beneficial as a remarkable molecular marker for serological diagnostic kits of P. vivax in malarious neighboring countries of Iran and around the world. PMID:26246817

  6. Checking Asymmetry of Magnetic Helicity Using Magnetograms with High Spatial and Temporal Resolution

    Science.gov (United States)

    Tian, Lirong; Zhu, C.; Alexander, D.

    2010-05-01

    In order to check if the helicity imbalance is robust between the leading and following polarities, found by Tian & Alexander, we use an improved technique, differential affline velocity estimator (DAVE), on series of MDI 1m and 96m line-of-sight magnetograms with spatial resolution of 0.6 and 2 arcsecs. respectively, to measure photospheric flow motions of an emerging active region: NOAA 10365 (S08). A better parameter of helicity density (Gθ) than GA is employed to calculate helicity injection rate of leading and following polarities. Our results display that the helicity injection rate of using MDI/1m data is 2 times larger than that of using MDI/ 96m data. The helicity injection rate is little affected by the size of apodizing window selected and the noise level (20 Gauss). However, it is improved so much due to decreasing time difference (up to Δt=10 mines) of two images tracked. The helicity injection rate of two polarities of the active region developed as roughly same step with flux emergence,and maintain its imbalance with more amount in the negative (leading) polarity over tracking period of three days, which is a similar development tendency no matter using MDI/1m data or MDI/96m data. These results reflect that the time difference of two tracking images is the most important factor affecting amount of helicity injection rate, while there is little relation with spatial resolution of data, the size of apodizing window, and the noise level. Therefore, it should be reliable to study the development of helicity injection rate and imbalanced relationship of two polarities when using MDI/96m data, though the amount calculated is two times smaller. Further test for MDI/96m data of ARs 8214 and 0656 confirm that the helicity imbalance indeed exists between the leading and following polarities.

  7. High-throughput sequencing as an effective approach in profiling small RNAs derived from a hairpin RNA expression vector in woody plants.

    Science.gov (United States)

    Zhao, Dongyan; Song, Guo-Qing

    2014-11-01

    Hairpin RNA (hpRNA)-mediated gene silencing has proved to be an efficient approach to develop virus-resistant transgenic plants. To characterize small RNA molecules (sRNAs) derived from an hpRNA expression vector in transgenic cherry rootstock plants, we conducted small RNA sequencing of (1) a transgenic rootstock containing an inverted repeat of the partial coat protein of Prunus necrotic ring spot virus (PNRSV-hpRNA); (2) a nontransgenic rootstock; and (3) a PNRSV-infected sweet cherry plant. Analysis of the PNRSV sRNA pools indicated that 24-nt (nucleotide) small interfering RNAs (siRNAs) were the most prevalent sRNAs in the transgenic rootstock whereas the most abundant sRNAs in the PNRSV-infected nontransgenic rootstock were 21-nt siRNAs. In addition, the 24-nt siRNAs of the PNRSV-hpRNA were more abundant on the sense strand than those on the antisense strand in the transgenic rootstock. In contrast, preference in generating PNRSV sRNAs, ranging from 19-nt to 30-nt for sense and antisense strands, was not distinct in the PNRSV-infected nontransgenic sweet cherry. Taken together, this is the first report on profiling hpRNA-derived sRNAs in woody plants using high-throughput sequencing technology, which is an efficient way to verify the presence/absence, the abundance, and the sequence features of certain sRNAs. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  8. Plasmodium-specific molecular assays produce uninterpretable results and non-Plasmodium spp. sequences in field-collected Anopheles vectors.

    Science.gov (United States)

    Harrison, Genelle F; Foley, Desmond H; Rueda, Leopoldo M; Melanson, Vanessa R; Wilkerson, Richard C; Long, Lewis S; Richardson, Jason H; Klein, Terry A; Kim, Heung-Chul; Lee, Won-Ja

    2013-12-01

    The Malaria Research and Reference Reagent Resource-recommended PLF/UNR/VIR polymerase chain reaction (PCR) was used to detect Plasmodium vivax in Anopheles spp. mosquitoes collected in South Korea. Samples that were amplified were sequenced and compared with known Plasmodium spp. by using the PlasmoDB.org Basic Local Alignment Search Tool/n and the National Center for Biotechnology Information Basic Local Alignment Search Tool/n tools. Results show that the primers PLF/UNR/VIR used in this PCR can produce uninterpretable results and non-specific sequences in field-collected mosquitoes. Three additional PCRs (PLU/VIV, specific for 18S small subunit ribosomal DNA; Pvr47, specific for a nuclear repeat; and GDCW/PLAS, specific for the mitochondrial marker, cytB) were then used to find a more accurate and interpretable assay. Samples that were amplified were again sequenced. The PLU/VIV and Pvr47 assays showed cross-reactivity with non-Plasmodium spp. and an arthropod fungus (Zoophthora lanceolata). The GDCW/PLAS assay amplified only Plasmodium spp. but also amplified the non-human specific parasite P. berghei from an Anopheles belenrae mosquito. Detection of P. berghei in South Korea is a new finding.

  9. Recognition of disturbances with specified morphology in time series. Part 1: Spikes on magnetograms of the worldwide INTERMAGNET network

    Science.gov (United States)

    Bogoutdinov, Sh. R.; Gvishiani, A. D.; Agayan, S. M.; Solovyev, A. A.; Kin, E.

    2010-11-01

    The International Real-time Magnetic Observatory Network (INTERMAGNET) is the world's biggest international network of ground-based observatories, providing geomagnetic data almost in real time (within 72 hours of collection) [Kerridge, 2001]. The observation data are rapidly transferred by the observatories participating in the program to regional Geomagnetic Information Nodes (GINs), which carry out a global exchange of data and process the results. The observations of the main (core) magnetic field of the Earth and its study are one of the key problems of geophysics. The INTERMAGNET system is the basis of monitoring the state of the Earth's magnetic field; therefore, the information provided by the system is required to be very reliable. Despite the rigid high-quality standard of the recording devices, they are subject to external effects that affect the quality of the records. Therefore, an objective and formalized recognition with the subsequent remedy of the anomalies (artifacts) that occur on the records is an important task. Expanding on the ideas of Agayan [Agayan et al., 2005] and Gvishiani [Gvishiani et al., 2008a; 2008b], this paper suggests a new algorithm of automatic recognition of anomalies with specified morphology, capable of identifying both physically- and anthropogenically-derived spikes on the magnetograms. The algorithm is constructed using fuzzy logic and, as such, is highly adaptive and universal. The developed algorithmic system formalizes the work of the expert-interpreter in terms of artificial intelligence. This ensures identical processing of large data arrays, almost unattainable manually. Besides the algorithm, the paper also reports on the application of the developed algorithmic system for identifying spikes at the INTERMAGNET observatories. The main achievement of the work is the creation of an algorithm permitting the almost unmanned extraction of spike-free (definitive) magnetograms from preliminary records. This automated

  10. Establishment of Sequence-Tagged Sites on 15q11-q13 by Alu-Vector PCR Cloning of Yac-Generated Fragments

    Directory of Open Access Journals (Sweden)

    W. S. Kim

    1996-01-01

    Full Text Available Angelman syndrome (AS is caused by the loss of function of undefined gene(s on human chromosome 15. The majority of subjects have deletions involving maternally-derived chromosome 15q II-q 13, and the shortest region of deletion overlap (SRO has been localized to the region between D15S10 and D15S113. In this study, yeast artificial chromosomes (YACs, 6G-D4, 9H-D2 and 37D-F9, mapping within the AS SRO, were isolated from the ICI Y AC library. Alu-vector PCR products were amplified from the YACs and from YACs A229A2 and A33FI 0 which had been obtained from the St. Louis Y AC library. The PCR products were cloned and sequenced, and three new sequence-tagged sites were generated within the AS SRO, facilitating the characterization of gene(s involved in the Angelman syndrome.

  11. PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein–Protein Interactions from Protein Sequences

    Science.gov (United States)

    Wang, Yanbin; You, Zhuhong; Li, Xiao; Chen, Xing; Jiang, Tonghai; Zhang, Jingting

    2017-01-01

    Protein–protein interactions (PPIs) are essential for most living organisms’ process. Thus, detecting PPIs is extremely important to understand the molecular mechanisms of biological systems. Although many PPIs data have been generated by high-throughput technologies for a variety of organisms, the whole interatom is still far from complete. In addition, the high-throughput technologies for detecting PPIs has some unavoidable defects, including time consumption, high cost, and high error rate. In recent years, with the development of machine learning, computational methods have been broadly used to predict PPIs, and can achieve good prediction rate. In this paper, we present here PCVMZM, a computational method based on a Probabilistic Classification Vector Machines (PCVM) model and Zernike moments (ZM) descriptor for predicting the PPIs from protein amino acids sequences. Specifically, a Zernike moments (ZM) descriptor is used to extract protein evolutionary information from Position-Specific Scoring Matrix (PSSM) generated by Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST). Then, PCVM classifier is used to infer the interactions among protein. When performed on PPIs datasets of Yeast and H. Pylori, the proposed method can achieve the average prediction accuracy of 94.48% and 91.25%, respectively. In order to further evaluate the performance of the proposed method, the state-of-the-art support vector machines (SVM) classifier is used and compares with the PCVM model. Experimental results on the Yeast dataset show that the performance of PCVM classifier is better than that of SVM classifier. The experimental results indicate that our proposed method is robust, powerful and feasible, which can be used as a helpful tool for proteomics research. PMID:28492483

  12. PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein-Protein Interactions from Protein Sequences.

    Science.gov (United States)

    Wang, Yanbin; You, Zhuhong; Li, Xiao; Chen, Xing; Jiang, Tonghai; Zhang, Jingting

    2017-05-11

    Protein-protein interactions (PPIs) are essential for most living organisms' process. Thus, detecting PPIs is extremely important to understand the molecular mechanisms of biological systems. Although many PPIs data have been generated by high-throughput technologies for a variety of organisms, the whole interatom is still far from complete. In addition, the high-throughput technologies for detecting PPIs has some unavoidable defects, including time consumption, high cost, and high error rate. In recent years, with the development of machine learning, computational methods have been broadly used to predict PPIs, and can achieve good prediction rate. In this paper, we present here PCVMZM, a computational method based on a Probabilistic Classification Vector Machines (PCVM) model and Zernike moments (ZM) descriptor for predicting the PPIs from protein amino acids sequences. Specifically, a Zernike moments (ZM) descriptor is used to extract protein evolutionary information from Position-Specific Scoring Matrix (PSSM) generated by Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST). Then, PCVM classifier is used to infer the interactions among protein. When performed on PPIs datasets of Yeast and H. Pylori, the proposed method can achieve the average prediction accuracy of 94.48% and 91.25%, respectively. In order to further evaluate the performance of the proposed method, the state-of-the-art support vector machines (SVM) classifier is used and compares with the PCVM model. Experimental results on the Yeast dataset show that the performance of PCVM classifier is better than that of SVM classifier. The experimental results indicate that our proposed method is robust, powerful and feasible, which can be used as a helpful tool for proteomics research.

  13. A new baseline for fascioliasis in Venezuela: lymnaeid vectors ascertained by DNA sequencing and analysis of their relationships with human and animal infection

    Science.gov (United States)

    2011-01-01

    Background Human and animal fascioliasis poses serious public health problems in South America. In Venezuela, livestock infection represents an important veterinary problem whereas there appear to be few human cases reported, most of which are passively detected in health centres. However, results of recent surveys suggest that the situation may be underestimated in particular areas. To obtain a baseline for future fascioliasis assessment, studies were undertaken by means of rDNA ITS-2 and ITS-1 and mtDNA cox1 sequencing to clarify the specific status of Venezuelan lymnaeids, their geographical distribution and fascioliasis transmission capacity, by comparison with other American countries and other continents. Results Results obtained completely change the lymnaeid scenario known so far. The relatively rich lymnaeid fauna of Venezuela has been proven to include (i) Lymnaea meridensis and L. neotropica as the only native members, (ii) L. cubensis and Pseudosuccinea columella introduced from the Caribbean area, and (iii) Galba truncatula and L. schirazensis introduced from the Old World. The absence of representatives of the stagnicoline and Radix groups is remarkable. Four species are fascioliasis vectors: G. truncatula, L. cubensis and L. neotropica, which have the capacity to give rise to human endemic areas, and P. columella, which is a source of animal infection and is responsible for the spread of disease. Vector capacity in the apparently highland endemic L. meridensis is to be confimed, although may be expected given its phylogenetic relationships. Similarly as elsewhere, the non-transmitting L. schirazensis has been confused with L. cubensis, also with G. truncatula and possibly with L. neotropica. Conclusions The new scenario leads to the re-opening of many disease aspects. In Venezuela, altitude appears to be the main factor influencing fascioliasis distribution. Human infection shows an altitude pattern similar to other Andean countries, although a

  14. Implication of respiratory syncytial virus (RSV) F transgene sequence heterogeneity observed in Phase 1 evaluation of MEDI-534, a live attenuated parainfluenza type 3 vectored RSV vaccine.

    Science.gov (United States)

    Yang, Chin-Fen; Wang, C Kathy; Malkin, Elissa; Schickli, Jeanne H; Shambaugh, Cindy; Zuo, Fengrong; Galinski, Mark S; Dubovsky, Filip; Tang, Roderick S

    2013-06-10

    MEDI-534 is the first live vectored RSV vaccine candidate to be evaluated in seronegative children. It consists of the bovine parainfluenza virus type 3 (PIV3) genome with substituted human PIV3 F and HN glycoproteins engineered to express RSV F protein. A Phase 1 study of 49 healthy RSV and PIV3 seronegative children 6 to <24 months of age demonstrated an acceptable safety profile at the following doses: 10(4), 10(5) and 10(6)TCID50. After 3 doses of MEDI-534 at 10(6)TCID50, administered at 0, 2 and 4 month intervals, 100% of subjects seroresponded to PIV3, whereas only 50% seroresponded to RSV. To investigate the discordance in seroresponse rates, the RSV F transgene and its flanking non-coding nucleotides were sequenced from shed virus recovered from the nasal washes of 24 MEDI-534-vaccinated children. Eleven out of 24 samples contained no nucleotide changes in the analyzed region. The other 13 samples contained mixtures of variant subpopulations. Fifty-five percent exhibited changes in the transcription termination poly A gene sequences of the upstream bPIV3N gene while 21% had variant subpopulations in the RSV F open reading frame that resulted in pre-mature stop codons. Both types of changes are expected to reduce RSV F expression. Evaluation of the administered vaccine by dual immunofluorescence staining showed ~2.5% variants with low or no RSV F expression while single nucleotide primer extension detected ~1% variation at nucleotide 2045 that resulted in a pre-mature translational termination at codon 85. An association between shedding of variants and lower RSV F serological response was observed but it was not possible to establish a definitive clinical significance due to the small number of subjects in this study. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. About vectors

    CERN Document Server

    Hoffmann, Banesh

    1975-01-01

    From his unusual beginning in ""Defining a vector"" to his final comments on ""What then is a vector?"" author Banesh Hoffmann has written a book that is provocative and unconventional. In his emphasis on the unresolved issue of defining a vector, Hoffmann mixes pure and applied mathematics without using calculus. The result is a treatment that can serve as a supplement and corrective to textbooks, as well as collateral reading in all courses that deal with vectors. Major topics include vectors and the parallelogram law; algebraic notation and basic ideas; vector algebra; scalars and scalar p

  16. Vector analysis

    CERN Document Server

    Newell, Homer E

    2006-01-01

    When employed with skill and understanding, vector analysis can be a practical and powerful tool. This text develops the algebra and calculus of vectors in a manner useful to physicists and engineers. Numerous exercises (with answers) not only provide practice in manipulation but also help establish students' physical and geometric intuition in regard to vectors and vector concepts.Part I, the basic portion of the text, consists of a thorough treatment of vector algebra and the vector calculus. Part II presents the illustrative matter, demonstrating applications to kinematics, mechanics, and e

  17. Elementary vectors

    CERN Document Server

    Wolstenholme, E Œ

    1978-01-01

    Elementary Vectors, Third Edition serves as an introductory course in vector analysis and is intended to present the theoretical and application aspects of vectors. The book covers topics that rigorously explain and provide definitions, principles, equations, and methods in vector analysis. Applications of vector methods to simple kinematical and dynamical problems; central forces and orbits; and solutions to geometrical problems are discussed as well. This edition of the text also provides an appendix, intended for students, which the author hopes to bridge the gap between theory and appl

  18. Characterization of constitutive and putative differentially expressed mRNAs by means of expressed sequence tags, differential display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR from the sand fly vector Lutzomyia longipalpis

    Directory of Open Access Journals (Sweden)

    JM Ramalho-Ortigão

    2001-01-01

    Full Text Available Molecular studies of insect disease vectors are of paramount importance for understanding parasite-vector relationship. Advances in this area have led to important findings regarding changes in vectors' physiology upon blood feeding and parasite infection. Mechanisms for interfering with the vectorial capacity of insects responsible for the transmission of diseases such as malaria, Chagas disease and dengue fever are being devised with the ultimate goal of developing transgenic insects. A primary necessity for this goal is information on gene expression and control in the target insect. Our group is investigating molecular aspects of the interaction between Leishmania parasites and Lutzomyia sand flies. As an initial step in our studies we have used random sequencing of cDNA clones from two expression libraries made from head/thorax and abdomen of sugar fed L. longipalpis for the identification of expressed sequence tags (EST. We applied differential display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR to characterize differentially expressed mRNA from sugar and blood fed insects, and, in one case, from a L. (V. braziliensis-infected L. longipalpis. We identified 37 cDNAs that have shown homology to known sequences from GeneBank. Of these, 32 cDNAs code for constitutive proteins such as zinc finger protein, glutamine synthetase, G binding protein, ubiquitin conjugating enzyme. Three are putative differentially expressed cDNAs from blood fed and Leishmania-infected midgut, a chitinase, a V-ATPase and a MAP kinase. Finally, two sequences are homologous to Drosophila melanogaster gene products recently discovered through the Drosophila genome initiative.

  19. Estimation of Motion Vector Fields

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    1993-01-01

    This paper presents an approach to the estimation of 2-D motion vector fields from time varying image sequences. We use a piecewise smooth model based on coupled vector/binary Markov random fields. We find the maximum a posteriori solution by simulated annealing. The algorithm generate sample...

  20. Vector analysis

    CERN Document Server

    Brand, Louis

    2006-01-01

    The use of vectors not only simplifies treatments of differential geometry, mechanics, hydrodynamics, and electrodynamics, but also makes mathematical and physical concepts more tangible and easy to grasp. This text for undergraduates was designed as a short introductory course to give students the tools of vector algebra and calculus, as well as a brief glimpse into these subjects' manifold applications. The applications are developed to the extent that the uses of the potential function, both scalar and vector, are fully illustrated. Moreover, the basic postulates of vector analysis are brou

  1. Solar Imagery - GONG (Magnetogram)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Global Oscillation Network Group (GONG) is a network of 6 globally-spaced solar observatories that the NOAA Space Weather Prediction Center uses to monitor the...

  2. Coordinate cytokine regulatory sequences

    Science.gov (United States)

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

    2005-05-10

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

  3. Vector geometry

    CERN Document Server

    Robinson, Gilbert de B

    2011-01-01

    This brief undergraduate-level text by a prominent Cambridge-educated mathematician explores the relationship between algebra and geometry. An elementary course in plane geometry is the sole requirement for Gilbert de B. Robinson's text, which is the result of several years of teaching and learning the most effective methods from discussions with students. Topics include lines and planes, determinants and linear equations, matrices, groups and linear transformations, and vectors and vector spaces. Additional subjects range from conics and quadrics to homogeneous coordinates and projective geom

  4. VECTOR INTEGRATION

    NARCIS (Netherlands)

    Thomas, E. G. F.

    2012-01-01

    This paper deals with the theory of integration of scalar functions with respect to a measure with values in a, not necessarily locally convex, topological vector space. It focuses on the extension of such integrals from bounded measurable functions to the class of integrable functions, proving

  5. New Approach to Fractal Approximation of Vector-Functions

    OpenAIRE

    Konstantin Igudesman; Marsel Davletbaev; Gleb Shabernev

    2014-01-01

    This paper introduces new approach to approximation of continuous vector-functions and vector sequences by fractal interpolation vector-functions which are multidimensional generalization of fractal interpolation functions. Best values of fractal interpolation vector-functions parameters are found. We give schemes of approximation of some sets of data and consider examples of approximation of smooth curves with different conditions.

  6. An introduction to vectors, vector operators and vector analysis

    CERN Document Server

    Joag, Pramod S

    2016-01-01

    Ideal for undergraduate and graduate students of science and engineering, this book covers fundamental concepts of vectors and their applications in a single volume. The first unit deals with basic formulation, both conceptual and theoretical. It discusses applications of algebraic operations, Levi-Civita notation, and curvilinear coordinate systems like spherical polar and parabolic systems and structures, and analytical geometry of curves and surfaces. The second unit delves into the algebra of operators and their types and also explains the equivalence between the algebra of vector operators and the algebra of matrices. Formulation of eigen vectors and eigen values of a linear vector operator are elaborated using vector algebra. The third unit deals with vector analysis, discussing vector valued functions of a scalar variable and functions of vector argument (both scalar valued and vector valued), thus covering both the scalar vector fields and vector integration.

  7. Vector velocimeter

    DEFF Research Database (Denmark)

    2012-01-01

    for generation of a reference beam, a detector system comprising a first detector arrangement arranged in such a way that the signal beam and the reference beam are incident upon the first detector arrangement with the reference beam propagating at an angle relative to a signal beam, and wherein the first......The present invention relates to a compact, reliable and low-cost vector velocimeter for example for determining velocities of particles suspended in a gas or fluid flow, or for determining velocity, displacement, rotation, or vibration of a solid surface, the vector velocimeter comprising a laser...... assembly for emission of a measurement beam for illumination of an object in a measurement volume with coherent light whereby a signal beam emanating from the object in the measurement volume is formed in response to illumination of the object by the measurement beam, a reference beam generator...

  8. Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes

    Science.gov (United States)

    2014-01-01

    Background Recently it has been shown that Ensifer adhaerens can be used as a plant transformation technology, transferring genes into several plant genomes when equipped with a Ti plasmid. For this study, we have sequenced the genome of Ensifer adhaerens OV14 (OV14) and compared it with those of Agrobacterium tumefaciens C58 (C58) and Sinorhizobium meliloti 1021 (1021); the latter of which has also demonstrated a capacity to genetically transform crop genomes, albeit at significantly reduced frequencies. Results The 7.7 Mb OV14 genome comprises two chromosomes and two plasmids. All protein coding regions in the OV14 genome were functionally grouped based on an eggNOG database. No genes homologous to the A. tumefaciens Ti plasmid vir genes appeared to be present in the OV14 genome. Unexpectedly, OV14 and 1021 were found to possess homologs to chromosomal based genes cited as essential to A. tumefaciens T-DNA transfer. Of significance, genes that are non-essential but exert a positive influence on virulence and the ability to genetically transform host genomes were identified in OV14 but were absent from the 1021 genome. Conclusions This study reveals the presence of homologs to chromosomally based Agrobacterium genes that support T-DNA transfer within the genome of OV14 and other alphaproteobacteria. The sequencing and analysis of the OV14 genome increases our understanding of T-DNA transfer by non-Agrobacterium species and creates a platform for the continued improvement of Ensifer-mediated transformation (EMT). PMID:24708309

  9. Origin and phylogeography of the Chagas disease main vector Triatoma infestans based on nuclear rDNA sequences and genome size.

    Science.gov (United States)

    Bargues, M D; Klisiowicz, D R; Panzera, F; Noireau, F; Marcilla, A; Perez, R; Rojas, M G; O'Connor, J E; Gonzalez-Candelas, F; Galvão, C; Jurberg, J; Carcavallo, R U; Dujardin, J P; Mas-Coma, S

    2006-01-01

    For about half of all Chagas disease cases T. infestans has been the responsible vector. Contributing to its genetic knowledge will increase our understanding of the capacity of geographic expansion and domiciliation of triatomines. Populations of all infestans subcomplex species, T. infestans, T. delpontei, T. platensis and T. melanosoma and the so-called T. infestans "dark morph", from many South American countries were studied. A total of 10 and 7 different ITS-2 and ITS-1 haplotypes, respectively, were found. The total intraspecific ITS-2 nucleotide variability detected in T. infestans is the highest hitherto known in triatomines. ITS-1 minisatellites, detected for the first time in triatomines, proved to be homologous and thus become useful markers. Calculations show that ITS-1 evolves 1.12-2.60 times faster than ITS-2. Despite all species analyzed presenting the same n=22 chromosome number, a large variation of the haploid DNA content was found, including a strikingly high DNA content difference between Andean and non-Andean specimens of T. infestans (mean reduction of 30%, with a maximum of up to 40%) and a correlation between presence/absence of minisatellites and larger/smaller genome size. Population genetics analysis of the eight composite haplotypes of T. infestans and net differences corroborate that there are clear differences between western and eastern populations (60%), and little genetic variation among populations (1.3%) and within populations (40%) within these two groups with migration rates larger than one individual per generation corresponding only to pairs of populations one from each of these groups. These values are indicative either of a large enough gene flow to prevent population differentiation by drift within each geographic area or a very recent spread, the latter hypothesis fitting available data better. Phylogenetic trees support a common ancestor for T. infestans and T. platensis, an origin of T. infestans in Bolivian highlands

  10. Vector description of nonlinear magnetization

    Energy Technology Data Exchange (ETDEWEB)

    Rysak, A. E-mail: rysak@tytan.umcs.lublin.pl; Korczak, S.Z

    2001-06-01

    The definition of the nonlinear magnetization, which is usually applied in investigating superconductors is discussed in this paper. The nonlinear magnetization of the superconductor, as the response to the alternating magnetic field, is a periodic time function and is determined by the sequence of complex numbers {chi}{sub n}={chi}{sub n}'+i{chi}{sub n}'', n=1,2,3,.... The sequence {chi}{sub n} is named harmonic susceptibility. Finding some limits in this definition we propose a new description, substituting the complex sequence {chi}{sub n} with the sequence of real covariant vectors. Such a definition of the nonlinear magnetization, allows to determine function M(t) of an investigated system for an arbitrary initial phase {theta}{sub o} of the inducing magnetic field H{sub ac}=h{sub ac} sin({omega}t+{theta}{sub o}). Vector description, in our opinion, is superior to the complex one in respect of explicitness, simplicity, and universality. Circular diagrams are used to illustrate the new vector description. We also show how the vectors of the harmonic susceptibility can be derived from both numeric calculations and experimental data.

  11. New recombinant serotypes of AAV vectors.

    Science.gov (United States)

    Gao, Guangping; Vandenberghe, Luk H; Wilson, James M

    2005-06-01

    AAV based vectors can achieve stable gene transfer with minimal vector related toxicities. AAV serotype 2 (AAV2) is the first AAV that was vectored for gene transfer applications. However, the restricted tissue tropism of AAV and its low transduction efficiency have limited its further development as vector. Recent studies using vectors derived from alternative AAV serotypes such as AAV1, 4, 5 and 6 have shown improved potency and broadened tropism of the AAV vector by packaging the same vector genome with different AAV capsids. In an attempt to search for potent AAV vectors with enhanced performance profiles, molecular techniques were employed for the detection and isolation of endogenous AAVs from a variety of human and non-human primate (NHP) tissues. A family of novel primate AAVs consisting of 110 non-redundant species of proviral sequences was discovered and turned to be prevalent in 18-19% of the tissues evaluated. Phylogenetic and functional analyses revealed that primate AAVs are segregated into clades based on phylogenetic relatedness. The members within a clade share functional and serological properties. Initial evaluation in mouse models of vectors based on these novel AAVs for tissue tropism and gene transfer potency led to the identification of some vector with improved gene transfer to different target tissues. Gene therapy treatment of several mouse and canine models with novel AAV vectors achieved long term phenotypic corrections. Vectors based on new primate AAVs could become the next generation of efficient gene transfer vehicles for various gene therapy applications.

  12. Propagating Gateway Vectors.

    Science.gov (United States)

    Reece-Hoyes, John S; Walhout, Albertha J M

    2018-01-02

    Generating stocks of Entry and Destination vectors for use in the Gateway recombinatorial cloning system requires transforming them into Escherichia coli strain DB3.1, where they can replicate because this strain is immune to the effects of the ccdB gene carried in the Gateway cassette. However, mutations in the ccdB gene can arise at low frequency, and these mutant plasmids will consequently allow growth of standard cloning strains of E. coli (e.g., DH5α). Therefore, after making new stocks of Gateway plasmids, their ability to grow in cloning strains of E. coli must be tested. This involves obtaining multiple stocks of vector, each arising from a single plasmid grown in a single DB3.1 bacterial colony, and transforming each stock into both DB3.1 and the preferred cloning strain of E. coli in a controlled fashion. Only vector stocks that effectively kill the standard cloning strain (i.e., no or few colonies are obtained after transformation) should be used in Gateway cloning reactions. The sequence can be performed in 3 d. © 2018 Cold Spring Harbor Laboratory Press.

  13. Sequential selection of random vectors under a sum constraint

    OpenAIRE

    Stanke, Mario

    2004-01-01

    We observe a sequence X1,X2,...,Xn of independent and identically distributed coordinatewise nonnegative d-dimensional random vectors. When a vector is observed it can either be selected or rejected but once made this decision is final. In each coordinate the sum of the selected vectors must not exceed a given constant. The problem is to find a selection policy that maximizes the expected number of selected vectors. For a general absolutely continuous distribution of t...

  14. Host and vector-dependent effects on the risk of germline transmission of AAV vectors.

    Science.gov (United States)

    Favaro, Patricia; Downey, Harre D; Zhou, J Shangzhen; Wright, J Fraser; Hauck, Bernd; Mingozzi, Federico; High, Katherine A; Arruda, Valder R

    2009-06-01

    The assessment of the risk of germline transmission of vector-coded sequences is critical for clinical translation of gene transfer strategies. We used rabbit models to analyze the risk of germline transmission of adeno-associated viral (AAV) vectors. Intravenous injection of AAV-2 or AAV-8 resulted in liver-mediated, long-term expression of therapeutic levels of human factor IX (hFIX) in a dose-dependent manner. In high-dose cohorts, AAV-8 resulted in twofold higher levels of circulating hFIX and of vector DNA in liver compared to AAV-2. Vector sequences were found in the semen of all rabbits. The kinetics of vector clearance from semen was dose- and time-dependent but serotype-independent. No late recurrence of AAV-8 sequences was found in the semen over several consecutive cycles of spermatogenesis. In a novel rabbit model, AAV-2 or AAV-8 sequences were detected in the semen of vasectomized animals that lack germ cells. Therefore, structures of the genitourinary (GU) tract, as well as the testis, contribute significantly to vector shedding in the semen. Collectively, data from these two models suggest that the risk of inadvertent germline transmission in males by AAV-8 vectors is low, similar to that of AAV-2, and that AAV dissemination to the semen is in part modulated by host-dependent factors.

  15. Vector Magnetic Fields and Electric Currents From the Imaging Vector Magnetograph

    Science.gov (United States)

    Li, Jing; van Ballegooijen, A. A.; Mickey, Don

    2009-02-01

    First, we describe a general procedure to produce high-quality vector magnetograms using the Imaging Vector Magnetograph (IVM) at Mees Solar Observatory. Two IVM effects are newly discussed and taken into account: (1) the central wavelength of the Fabry-Pérot is found to drift with time as a result of undiagnosed thermal or mechanical instabilities in the instrument; (2) the Stokes V-sign convention built into the IVM is found to be opposite to the conventional definition used in the study of radiative transfer of polarized radiation. At the spatial resolution 2'' × 2'', the Stokes Q, U, V uncertainty reaches ~1 × 10-3 to 5 × 10-4 in time-averaged data over 1 hr in the quiet Sun. When vector magnetic fields are inferred from the time-averaged Stokes spectral images of FeI 6302.5 Å, the resulting uncertainties are on the order of 10 G for the longitudinal fields (B par), 40 G for the transverse field strength (B bottom) and ~9° for the magnetic azimuth (phi). The magnetic field inversion used in this work is the "Triplet" code, which was developed and implemented in the IVM software package by the late B. J. LaBonte. The inversion code is described in detail in the Appendix. Second, we solve for the absolute value of the vertical electric current density, |Jz |, accounting for the above IVM problems, for two different active regions. One is a single sunspot region (NOAA 10001 observed on 2002 June 20) while the other is a more complex, quadrupolar region (NOAA10030 observed on 2002 July 15). We use a calculation that does not require disambiguation of 180° in the transverse field directions. The |Jz | uncertainty is on the order of ~7.0 mA m-2. The vertical current density increases with increasing vertical magnetic field. The rate of increase is about 1-2 times as large in the quadrupolar NOAA 10030 region as in the simple NOAA 10001, and it is more spatially variable over NOAA 10030 than over NOAA 10001.

  16. VectorBase

    Data.gov (United States)

    U.S. Department of Health & Human Services — VectorBase is a Bioinformatics Resource Center for invertebrate vectors. It is one of four Bioinformatics Resource Centers funded by NIAID to provide web-based...

  17. Custodial vector model

    DEFF Research Database (Denmark)

    Becciolini, Diego; Franzosi, Diogo Buarque; Foadi, Roshan

    2015-01-01

    We analyze the Large Hadron Collider (LHC) phenomenology of heavy vector resonances with a $SU(2)_L\\times SU(2)_R$ spectral global symmetry. This symmetry partially protects the electroweak S-parameter from large contributions of the vector resonances. The resulting custodial vector model spectrum...

  18. Insulated Foamy Viral Vectors

    Science.gov (United States)

    Browning, Diana L.; Collins, Casey P.; Hocum, Jonah D.; Leap, David J.; Rae, Dustin T.; Trobridge, Grant D.

    2016-01-01

    Retroviral vector-mediated gene therapy is promising, but genotoxicity has limited its use in the clinic. Genotoxicity is highly dependent on the retroviral vector used, and foamy viral (FV) vectors appear relatively safe. However, internal promoters may still potentially activate nearby genes. We developed insulated FV vectors, using four previously described insulators: a version of the well-studied chicken hypersensitivity site 4 insulator (650cHS4), two synthetic CCCTC-binding factor (CTCF)-based insulators, and an insulator based on the CCAAT box-binding transcription factor/nuclear factor I (7xCTF/NF1). We directly compared these insulators for enhancer-blocking activity, effect on FV vector titer, and fidelity of transfer to both proviral long terminal repeats. The synthetic CTCF-based insulators had the strongest insulating activity, but reduced titers significantly. The 7xCTF/NF1 insulator did not reduce titers but had weak insulating activity. The 650cHS4-insulated FV vector was identified as the overall most promising vector. Uninsulated and 650cHS4-insulated FV vectors were both significantly less genotoxic than gammaretroviral vectors. Integration sites were evaluated in cord blood CD34+ cells and the 650cHS4-insulated FV vector had fewer hotspots compared with an uninsulated FV vector. These data suggest that insulated FV vectors are promising for hematopoietic stem cell gene therapy. PMID:26715244

  19. Macro motion vector quantization

    Science.gov (United States)

    Lee, Yoon Y.; Woods, John W.

    1995-04-01

    A new algorithm is developed for reducing the bit rate required for motion vectors. This algorithm is a generalization of block matching motion estimation in which the search region is represented as a codebook of motion vectors. The new algorithm, called macro motion vector quantization (MMVQ), generalized our earlier MVQ by coding a group of motion vectors. The codebook is a set of macro motion vectors which represent the block locations of the small neighboring blocks in the previous frame. We develop an interative design algorithm for the codebook. Our experiments show that the variances of displaced frame differences (DFDs) are reduced significantly compared to block matching algorithm (BMA) with the macroblock size.

  20. Biosafety of onco-retroviral vectors.

    Science.gov (United States)

    VandenDriessche, Thierry; Collen, Désiré; Chuah, Marinee K L

    2003-12-01

    Extensive gene therapy studies in preclinical models and in clinical trials underscore the relative safety of onco-retroviral vectors. Up until recently, no adverse effects have been reported in nearly 2000 patients that were enrolled in gene therapy clinical trials involving onco-retroviral vectors. However, the main safety concern of using onco-retroviral vectors is related to the risk of malignant transformation following oncogene activation due to random onco-retroviral genomic integration. Based on primate studies, there is an apparent low risk of malignancy that is predominately associated with the occurrence of chronic retroviremia resulting from replication-competent retroviruses (RCR), particularly in immunosuppressed recipient hosts. However, in the latest packaging cell lines and vectors, the risk of RCR-generation has been drastically reduced, primarily by minimizing the homologous overlap between vector and helper sequences. Nevertheless, results from a recent preclinical study in mice and a clinical trial in patients suffering from SCID-X1 strongly suggest that onco-retroviral vectors devoid of RCR can contribute to lymphomagenesis by insertional activation of cellular oncogenes. The risk of inadvertent germline transmission of onco-retroviral vectors appears to be low, especially relative to the endogenous rate of germline insertion, which is known to occur naturally in the human population via transmission of endogenous retro-transposons. The strict dependency of onco-retroviral gene transfer on cell division is an important safety advantage that significantly limits the risks of horizontal transmission. Since improved onco-retroviral vectors or transduction protocols may result in an increased number of retroviral integrations per cell, this may concomitantly increase the risk of malignant transformation. The use of suicide genes, self-inactivating vectors and/or chromosomal insulators is, therefore, warranted to further enhance the safety features

  1. Implicit Real Vector Automata

    Directory of Open Access Journals (Sweden)

    Jean-François Degbomont

    2010-10-01

    Full Text Available This paper addresses the symbolic representation of non-convex real polyhedra, i.e., sets of real vectors satisfying arbitrary Boolean combinations of linear constraints. We develop an original data structure for representing such sets, based on an implicit and concise encoding of a known structure, the Real Vector Automaton. The resulting formalism provides a canonical representation of polyhedra, is closed under Boolean operators, and admits an efficient decision procedure for testing the membership of a vector.

  2. Inducing RNA interference in the arbovirus vector, Culicoides sonorensis

    Science.gov (United States)

    Biting midges in the genus Culicoides are important vectors of arboviral diseases, including Epizootic Hemorrhagic Disease, Bluetongue, and likely Schmallenberg, which cause significant economic burden worldwide. Research on these vectors has been hindered by the lack of a sequenced genome, the diff...

  3. Vectors and their applications

    CERN Document Server

    Pettofrezzo, Anthony J

    2005-01-01

    Geared toward undergraduate students, this text illustrates the use of vectors as a mathematical tool in plane synthetic geometry, plane and spherical trigonometry, and analytic geometry of two- and three-dimensional space. Its rigorous development includes a complete treatment of the algebra of vectors in the first two chapters.Among the text's outstanding features are numbered definitions and theorems in the development of vector algebra, which appear in italics for easy reference. Most of the theorems include proofs, and coordinate position vectors receive an in-depth treatment. Key concept

  4. Vector mesons in matter

    Indian Academy of Sciences (India)

    One consequence of the chiral restoration is the mixing of parity partners. We look for a possible signature of the mixing of vector and axial vector mesons in heavy-ion collisions. We suggest an experimental method for its observation. The dynamical evolution of the heavy-ion collision is described by a transport equation of ...

  5. Vector mesons in matter

    Indian Academy of Sciences (India)

    kfki.hu. Abstract. One consequence of the chiral restoration is the mixing of parity partners. We look for a possible signature of the mixing of vector and axial vector mesons in heavy- ion collisions. We suggest an experimental method for its ...

  6. Complex Polynomial Vector Fields

    DEFF Research Database (Denmark)

    Dias, Kealey

    The two branches of dynamical systems, continuous and discrete, correspond to the study of differential equations (vector fields) and iteration of mappings respectively. In holomorphic dynamics, the systems studied are restricted to those described by holomorphic (complex analytic) functions...... or meromorphic (allowing poles as singularities) functions. There already exists a well-developed theory for iterative holomorphic dynamical systems, and successful relations found between iteration theory and flows of vector fields have been one of the main motivations for the recent interest in holomorphic...... vector fields. Since the class of complex polynomial vector fields in the plane is natural to consider, it is remarkable that its study has only begun very recently. There are numerous fundamental questions that are still open, both in the general classification of these vector fields, the decomposition...

  7. Retrotransposon vectors for gene delivery in plants

    Directory of Open Access Journals (Sweden)

    Hou Yi

    2010-08-01

    Full Text Available Abstract Background Retrotransposons are abundant components of plant genomes, and although some plant retrotransposons have been used as insertional mutagens, these mobile genetic elements have not been widely exploited for plant genome manipulation. In vertebrates and yeast, retrotransposons and retroviruses are routinely altered to carry additional genes that are copied into complementary (cDNA through reverse transcription. Integration of cDNA results in gene delivery; recombination of cDNA with homologous chromosomal sequences can create targeted gene modifications. Plant retrotransposon-based vectors, therefore, may provide new opportunities for plant genome engineering. Results A retrotransposon vector system was developed for gene delivery in plants based on the Tnt1 element from Nicotiana tabacum. Mini-Tnt1 transfer vectors were constructed that lack coding sequences yet retain the 5' and 3' long terminal repeats (LTRs and adjacent cis sequences required for reverse transcription. The internal coding region of Tnt1 was replaced with a neomycin phosphotransferase gene to monitor replication by reverse transcription. Two different mini-Tnt1 s were developed: one with the native 5' LTR and the other with a chimeric 5' LTR that had the first 233 bp replaced by the CaMV 35 S promoter. After transfer into tobacco protoplasts, both vectors undergo retrotransposition using GAG and POL proteins provided in trans by endogenous Tnt1 elements. The transposition frequencies of mini-Tnt1 vectors are comparable with native Tnt1 elements, and like the native elements, insertion sites are within or near coding sequences. In this paper, we provide evidence that template switching occurs during mini-Tnt1 reverse transcription, indicating that multiple copies of Tnt1 mRNA are packaged into virus-like particles. Conclusions Our data demonstrate that mini-Tnt1 vectors can replicate efficiently in tobacco cells using GAG and POL proteins provided in trans by

  8. [Construction of human Bcl-6 3'UTR reporter vector and expression vector and their functional assessment].

    Science.gov (United States)

    Han, Bai-Yu; Cui, Han-Zhi; Yan, Xiang; Huang, Peng; Huang, Hua-Long; Fan, Zhong-Yi; Dou, Jing-Tao

    2015-10-01

    To observe the direct regulation of miR-127 on Bcl-6 and the effect of Bcl-6 in rescuing miR-127-induced cell cycle and cell growth inhibition. The 3'UTR and coding region of human bcl-6 gene were amplified by PCR and cloned into pcDNA3.0-Luc and pcDNA3.0-Flag vectors, respectively. Mutations were introduced into the seed sequences of the predicted miR-127 target sites within the Bcl-6 3'UTR using recombinant PCR. Luciferase assay was used to verify the direct targeted regulation of miR-127 on Bcl-6. In HepG2 cell models with overexpression or knockdown of miR-12, the changes of cell cycle and cell growth were investigated after transfection with the constructed vectors. The recombinant plasmids were successfully obtained as confirmed by double digestion and sequence identification. Luciferase assay showed that in 293T and HepG2 cells, miR-127 inhibited the activation of wild-type Bcl-6 3'UTR reporter vector but not mutated Bcl-6 3'UTR vector. Overexpression of miR-127 induced cell cycle arrest at G(2)/M phase and suppressed the growth of HepG2 cells, and these effects were reversed by Bcl-6 overexpression. We successfully cloned wild-type and mutated 3'UTR reporter vectors and expression vector of bcl-6 gene and confirmed their biological functions.

  9. Magnetic vector rotation in response to the energetic electron beam during a flare

    Science.gov (United States)

    Xu, Yan; Cao, Wenda; Kwangsu, Ahn; Jing, Ju; Liu, Chang; Chae, Jongchul; Huang, Nengyi; Deng, Na; Gary, Dale E.; Wang, Haimin

    2017-08-01

    As one of the most violent forms of eruption on the Sun, flares are believed to be powered by magnetic reconnection, by which stored magnetic energy is released. The fundamental physical processes involving the release, transfer and deposition of energy in multiple layers of the solar atmosphere have been studied extensively with significant progress. Taking advantage of recent developments in observing facilities, new phenomena are continually revealed, bringing new understanding of solar flares. Here we report the discovery of a transient rotation of vector magnetic fields associated with a flare observed by the 1.6-m New Solar Telescope at Big Bear Solar Observatory. After ruling out the possibility that the rotation is caused by line profile changes due to flare heating, our observation shows that the transverse field rotateded by about 12-20 degrees counterclockwise, and returned quickly to previous values after the flare ribbons swept through. More importantly, as a consequence of the rotation, the flare loops untwisted and became more potential. The vector magnetograms were obtained in the near infrared at 1560 nm, which is minimally affected by flare emission and no intensity profile change was detected. Therefore, we believe that these transient changes are real, and conclude the high energy electron beams play an crucial role in the field changes. A straightforward and instructive explanation is that the induced magnetic field of the electron beam superimposed on the pre-flare field leads to a transient rotation of the overall field.

  10. Vector SIMP dark matter

    Science.gov (United States)

    Choi, Soo-Min; Hochberg, Yonit; Kuflik, Eric; Lee, Hyun Min; Mambrini, Yann; Murayama, Hitoshi; Pierre, Mathias

    2017-10-01

    Strongly Interacting Massive Particles (SIMPs) have recently been proposed as light thermal dark matter relics. Here we consider an explicit realization of the SIMP mechanism in the form of vector SIMPs arising from an SU(2) X hidden gauge theory, where the accidental custodial symmetry protects the stability of the dark matter. We propose several ways of equilibrating the dark and visible sectors in this setup. In particular, we show that a light dark Higgs portal can maintain thermal equilibrium between the two sectors, as can a massive dark vector portal with its generalized Chern-Simons couplings to the vector SIMPs, all while remaining consistent with experimental constraints.

  11. Vector Difference Calculus

    Science.gov (United States)

    Schwalm, W. A.; Schwalm, M. K.; Giona, M.

    1998-03-01

    Space is filled with triangulating graph \\calG to serve as a quadrature grid. A discrete analog of the theory of differential forms is constructed using the associated simplical complex. The role of a basis for Λ^p at a point is played by the set of (p+1) -simplices containing a given vertex. Vector difference operations analogous to div, grad and curl, together with corresponding vector identities and exact difference analogs of the Stokes-type theorems, are obtained in terms of the boundary partial and coboundary d. Difference versions of the full vector Maxwell electromagnetic equations are analyzed on a random structure.

  12. [Sendai virus vector: vector development and its application to health care and biotechnology].

    Science.gov (United States)

    Iida, Akihiro

    2007-06-01

    Sendai virus (SeV) is an enveloped virus with a nonsegmented negative-strand RNA genome and a member of the paramyxovirus family. We have developed SeV vector which has shown a high efficiently of gene transfer and expression of foreign genes to a wide range of dividing and non-dividing mammalian cells and tissues. One of the characteristics of the vector is that the genome is located exclusively in the cytoplasm of infected cells and does not go through a DNA phase; thus there is no concern about unwanted integration of foreign sequences into chromosomal DNA. Therefore, this new class of "cytoplasmic RNA vector", an RNA vector with cytoplasmic expression, is expected to be a safer and more efficient viral vector than existing vectors for application to human therapy in various fields including gene therapy and vaccination. In this review, I describe development of Sendai virus vector, its application in the field of biotechnology and clinical application aiming to treat for a large number of diseases including cancer, cardiovascular disease, infectious diseases and neurologic disorders.

  13. GAP Land Cover - Vector

    Data.gov (United States)

    Minnesota Department of Natural Resources — This vector dataset is a detailed (1-acre minimum), hierarchically organized vegetation cover map produced by computer classification of combined two-season pairs of...

  14. Tagged Vector Contour (TVC)

    Data.gov (United States)

    Kansas Data Access and Support Center — The Kansas Tagged Vector Contour (TVC) dataset consists of digitized contours from the 7.5 minute topographic quadrangle maps. Coverage for the state is incomplete....

  15. Syngeneic AAV pseudo-vectors potentiates full vector transduction

    Science.gov (United States)

    An excessive amount of empty capsids are generated during regular AAV vector production process. These pseudo-vectors often remain in final vectors used for animal studies or clinical trials. The potential effects of these pseudo-vectors on AAV transduction have been a major concern. In the current ...

  16. Vector and axial vector mesons at finite temperature

    OpenAIRE

    mallik, S.; Sarkar, Sourav

    2002-01-01

    We consider the thermal correlation functions of vector and axial-vector currents and evaluate corrections to the vector and axial-vector meson pole terms to one loop in chiral perturbation theory. As expected, the pole positions do not shift to leading order in temperature. But the residues decrease with temperature.

  17. Extended Mixed Vector Equilibrium Problems

    Directory of Open Access Journals (Sweden)

    Mijanur Rahaman

    2014-01-01

    Full Text Available We study extended mixed vector equilibrium problems, namely, extended weak mixed vector equilibrium problem and extended strong mixed vector equilibrium problem in Hausdorff topological vector spaces. Using generalized KKM-Fan theorem (Ben-El-Mechaiekh et al.; 2005, some existence results for both problems are proved in noncompact domain.

  18. From population structure to genetically-engineered vectors: new ways to control vector-borne diseases?

    Science.gov (United States)

    Sparagano, O A E; De Luna, C J

    2008-07-01

    Epidemiological studies on vectors and the pathogens they can carry (such as Borrelia burgdorferi) are showing some correlations between infection rates and biodiversity highlighting the "dilution" effects on potential vectors. Meanwhile other studies comparing sympatric small rodent species demonstrated that rodent species transmitting more pathogens are parasitized by more ectoparasite species. Studies on population structure and size have also proven a difference on the intensity of the parasitic infection. Furthermore, preliminary results in genetic improvement in mosquitoes (genetic markers, sexing, and genetic sterilization) will also increase performance as it has already been shown in field applications in developing countries. Recent results have greatly improved the fitness of genetically-modified insects compared to wild type populations with new approaches such as the post-integration elimination of transposon sequences, stabilising any insertion in genetically-modified insects. Encouraging results using the Sterile Insect Technique highlighted some metabolism manipulation to avoid the viability of offspring from released parent insect in the wild. Recent studies on vector symbionts would also bring a new angle in vector control capabilities, while complete DNA sequencing of some arthropods could point out ways to block the deadly impact on animal and human populations. These new potential approaches will improve the levels of control or even in some cases would eradicate vector species and consequently the vector-borne diseases they can transmit. In this paper we review some of the population biology theories, biological control methods, and the genetic techniques that have been published in the last years that are recommended to control for vector-borne diseases.

  19. Bunyavirus-Vector Interactions

    Directory of Open Access Journals (Sweden)

    Kate McElroy Horne

    2014-11-01

    Full Text Available The Bunyaviridae family is comprised of more than 350 viruses, of which many within the Hantavirus, Orthobunyavirus, Nairovirus, Tospovirus, and Phlebovirus genera are significant human or agricultural pathogens. The viruses within the Orthobunyavirus, Nairovirus, and Phlebovirus genera are transmitted by hematophagous arthropods, such as mosquitoes, midges, flies, and ticks, and their associated arthropods not only serve as vectors but also as virus reservoirs in many cases. This review presents an overview of several important emerging or re-emerging bunyaviruses and describes what is known about bunyavirus-vector interactions based on epidemiological, ultrastructural, and genetic studies of members of this virus family.

  20. Free topological vector spaces

    OpenAIRE

    Gabriyelyan, Saak S.; Morris, Sidney A.

    2016-01-01

    We define and study the free topological vector space $\\mathbb{V}(X)$ over a Tychonoff space $X$. We prove that $\\mathbb{V}(X)$ is a $k_\\omega$-space if and only if $X$ is a $k_\\omega$-space. If $X$ is infinite, then $\\mathbb{V}(X)$ contains a closed vector subspace which is topologically isomorphic to $\\mathbb{V}(\\mathbb{N})$. It is proved that if $X$ is a $k$-space, then $\\mathbb{V}(X)$ is locally convex if and only if $X$ is discrete and countable. If $X$ is a metrizable space it is shown ...

  1. Matrix vector analysis

    CERN Document Server

    Eisenman, Richard L

    2005-01-01

    This outstanding text and reference applies matrix ideas to vector methods, using physical ideas to illustrate and motivate mathematical concepts but employing a mathematical continuity of development rather than a physical approach. The author, who taught at the U.S. Air Force Academy, dispenses with the artificial barrier between vectors and matrices--and more generally, between pure and applied mathematics.Motivated examples introduce each idea, with interpretations of physical, algebraic, and geometric contexts, in addition to generalizations to theorems that reflect the essential structur

  2. Scalar-vector bootstrap

    Energy Technology Data Exchange (ETDEWEB)

    Rejon-Barrera, Fernando [Institute for Theoretical Physics, University of Amsterdam,Science Park 904, Postbus 94485, 1090 GL, Amsterdam (Netherlands); Robbins, Daniel [Department of Physics, Texas A& M University,TAMU 4242, College Station, TX 77843 (United States)

    2016-01-22

    We work out all of the details required for implementation of the conformal bootstrap program applied to the four-point function of two scalars and two vectors in an abstract conformal field theory in arbitrary dimension. This includes a review of which tensor structures make appearances, a construction of the projectors onto the required mixed symmetry representations, and a computation of the conformal blocks for all possible operators which can be exchanged. These blocks are presented as differential operators acting upon the previously known scalar conformal blocks. Finally, we set up the bootstrap equations which implement crossing symmetry. Special attention is given to the case of conserved vectors, where several simplifications occur.

  3. Multithreading in vector processors

    Energy Technology Data Exchange (ETDEWEB)

    Evangelinos, Constantinos; Kim, Changhoan; Nair, Ravi

    2018-01-16

    In one embodiment, a system includes a processor having a vector processing mode and a multithreading mode. The processor is configured to operate on one thread per cycle in the multithreading mode. The processor includes a program counter register having a plurality of program counters, and the program counter register is vectorized. Each program counter in the program counter register represents a distinct corresponding thread of a plurality of threads. The processor is configured to execute the plurality of threads by activating the plurality of program counters in a round robin cycle.

  4. Nuclear rDNA pseudogenes in Chagas disease vectors: evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of North, Central and northern South America.

    Science.gov (United States)

    Bargues, M Dolores; Zuriaga, M Angeles; Mas-Coma, Santiago

    2014-01-01

    A pseudogene, paralogous to rDNA 5.8S and ITS-2, is described in Meccus dimidiata dimidiata, M. d. capitata, M. d. maculippenis, M. d. hegneri, M. sp. aff. dimidiata, M. p. phyllosoma, M. p. longipennis, M. p. pallidipennis, M. p. picturata, M. p. mazzottii, Triatoma mexicana, Triatoma nitida and Triatoma sanguisuga, covering North America, Central America and northern South America. Such a nuclear rDNA pseudogene is very rare. In the 5.8S gene, criteria for pseudogene identification included length variability, lower GC content, mutations regarding the functional uniform sequence, and relatively high base substitutions in evolutionary conserved sites. At ITS-2 level, criteria were the shorter sequence and large proportion of insertions and deletions (indels). Pseudogenic 5.8S and ITS-2 secondary structures were different from the functional foldings, different one another, showing less negative values for minimum free energy (mfe) and centroid predictions, and lower fit between mfe, partition function, and centroid structures. A complete characterization indicated a processed pseudogenic unit of the ghost type, escaping from rDNA concerted evolution and with functionality subject to constraints instead of evolving free by neutral drift. Despite a high indel number, low mutation number and an evolutionary rate similar to the functional ITS-2, that pseudogene distinguishes different taxa and furnishes coherent phylogenetic topologies with resolution similar to the functional ITS-2. The discovery of a pseudogene in many phylogenetically related species is unique in animals and allowed for an estimation of its palaeobiogeographical origin based on molecular clock data, inheritance pathways, evolutionary rate and pattern, and geographical spread. Additional to the technical risk to be considered henceforth, this relict pseudogene, designated as "ps(5.8S+ITS-2)", proves to be a valuable marker for specimen classification, phylogenetic analyses, and systematic

  5. Support Vector Components Analysis

    NARCIS (Netherlands)

    van der Ree, Michiel; Roerdink, Johannes; Phillips, Christophe; Garraux, Gaetan; Salmon, Eric; Wiering, Marco

    2017-01-01

    In this paper we propose a novel method for learning a distance metric in the process of training Support Vector Machines (SVMs) with the radial basis function kernel. A transformation matrix is adapted in such a way that the SVM dual objective of a classification problem is optimized. By using a

  6. Sesquilinear uniform vector integral

    Indian Academy of Sciences (India)

    1Faculty of Mathematics and Computer Science, University of Bucharest, Bucharest,. Academiei Str., 14, 010014, Romania. 2Technical University of Civil ... an integral of scalar functions with respect to vector measures, Dunford and his school introduced the spectral operators, thus founding the present operator theory (see ...

  7. Orthogonalisation of Vectors

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 3. Orthogonalisation of Vectors - Matrix Decomposition and Approximation Problems. Rajendra Bhatia. General Article Volume 5 ... Author Affiliations. Rajendra Bhatia1. Indian Statistical Institute 7, SJS Sansanwal Marg, New Delhi 110 016, India.

  8. Calculus with vectors

    CERN Document Server

    Treiman, Jay S

    2014-01-01

    Calculus with Vectors grew out of a strong need for a beginning calculus textbook for undergraduates who intend to pursue careers in STEM. fields. The approach introduces vector-valued functions from the start, emphasizing the connections between one-variable and multi-variable calculus. The text includes early vectors and early transcendentals and includes a rigorous but informal approach to vectors. Examples and focused applications are well presented along with an abundance of motivating exercises. All three-dimensional graphs have rotatable versions included as extra source materials and may be freely downloaded and manipulated with Maple Player; a free Maple Player App is available for the iPad on iTunes. The approaches taken to topics such as the derivation of the derivatives of sine and cosine, the approach to limits, and the use of "tables" of integration have been modified from the standards seen in other textbooks in order to maximize the ease with which students may comprehend the material. Additio...

  9. Vector-borne Infections

    Centers for Disease Control (CDC) Podcasts

    2011-04-18

    This podcast discusses emerging vector-borne pathogens, their role as prominent contributors to emerging infectious diseases, how they're spread, and the ineffectiveness of mosquito control methods.  Created: 4/18/2011 by National Center for Emerging Zoonotic and Infectious Diseases (NCEZID).   Date Released: 4/27/2011.

  10. The cHS4 Chromatin Insulator Reduces the Rate of Retroviral Vector-Mediated Gene Dysregulation Associated with Aberrant Vector Transcription.

    Science.gov (United States)

    Zhou, Xianyao; Liu, Qiujun; Wang, Da; Zhang, Xuemei; Emery, David W; Li, Chang L

    2017-01-01

    Integrating gammaretroviral vectors can dysregulate the expression of cellular genes through a variety of mechanisms, leading to genotoxicity and malignant transformation. Although most attention has focused on the activation of cellular genes by vector enhancers, aberrant fusion transcripts involving cellular gene sequences and vector promoters, vector splice elements, and vector transcription termination sequences have also been mechanistically associated with dysregulated expression of cellular genes. Chromatin insulators have emerged as an effective tool for reducing the frequency of vector-mediated genotoxicity and malignant transformation and have been shown to block the activation of cellular genes by vector enhancers. We report here evidence that flanking a gammaretroviral reporter vector with the cHS4 chromatin insulator also reduces the frequency of vector-mediated cellular gene dysregulation associated with aberrant vector transcripts, including vector transcription run-through and aberrant splicing. We demonstrate that the cHS4 element does not function to terminate transcription directly, implicating other mechanisms for this activity. © 2017 S. Karger AG, Basel.

  11. Efficient intracellular assembly of papillomaviral vectors.

    Science.gov (United States)

    Buck, Christopher B; Pastrana, Diana V; Lowy, Douglas R; Schiller, John T

    2004-01-01

    Although the papillomavirus structural proteins, L1 and L2, can spontaneously coassemble to form virus-like particles, currently available methods for production of L1/L2 particles capable of transducing reporter plasmids into mammalian cells are technically demanding and relatively low-yield. In this report, we describe a simple 293 cell transfection method for efficient intracellular production of papillomaviral-based gene transfer vectors carrying reporter plasmids. Using bovine papillomavirus type 1 (BPV1) and human papillomavirus type 16 as model papillomaviruses, we have developed a system for producing papillomaviral vector stocks with titers of several billion transducing units per milliliter. Production of these vectors requires both L1 and L2, and transduction can be prevented by papillomavirus-neutralizing antibodies. The stocks can be purified by an iodixanol (OptiPrep) gradient centrifugation procedure that is substantially more effective than standard cesium chloride gradient purification. Although earlier data had suggested a potential role for the viral early protein E2, we found that E2 protein expression did not enhance the intracellular production of BPV1 vectors. It was also possible to encapsidate reporter plasmids devoid of BPV1 DNA sequences. BPV1 vector production efficiency was significantly influenced by the size of the target plasmid being packaged. Use of 6-kb target plasmids resulted in BPV1 vector yields that were higher than those with target plasmids closer to the native 7.9-kb size of papillomavirus genomes. The results suggest that the intracellular assembly of papillomavirus structural proteins around heterologous reporter plasmids is surprisingly promiscuous and may be driven primarily by a size discrimination mechanism.

  12. MAR characteristic motifs mediate episomal vector in CHO cells.

    Science.gov (United States)

    Lin, Yan; Li, Zhaoxi; Wang, Tianyun; Wang, Xiaoyin; Wang, Li; Dong, Weihua; Jing, Changqin; Yang, Xianjun

    2015-04-01

    An ideal gene therapy vector should enable persistent transgene expression without limitations in safety and reproducibility. Recent researches' insight into the ability of chromosomal matrix attachment regions (MARs) to mediate episomal maintenance of genetic elements allowed the development of a circular episomal vector. Although a MAR-mediated engineered vector has been developed, little is known on which motifs of MAR confer this function during interaction with the host genome. Here, we report an artificially synthesized DNA fragment containing only characteristic motif sequences that served as an alternative to human beta-interferon matrix attachment region sequence. The potential of the vector to mediate gene transfer in CHO cells was investigated. The short synthetic MAR motifs were found to mediate episomal vector at a low copy number for many generations without integration into the host genome. Higher transgene expression was maintained for at least 4 months. In addition, MAR was maintained episomally and conferred sustained EGFP expression even in nonselective CHO cells. All the results demonstrated that MAR characteristic sequence-based vector can function as stable episomes in CHO cells, supporting long-term and effective transgene expression. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

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

  14. A mini binary vector series for plant transformation.

    Science.gov (United States)

    Xiang, C; Han, P; Lutziger, I; Wang, K; Oliver, D J

    1999-07-01

    A streamlined mini binary vector was constructed that is less than 1/2 the size of the pBIN19 backbone (3.5 kb). This was accomplished by eliminating over 5 kb of non-T-DNA sequences from the pBIN19 vector. The vector still retains all the essential elements required for a binary vector. These include a RK2 replication origin, the nptIII gene conferring kanamycin resistance in bacteria, both the right and left T-DNA borders, and a multiple cloning site (MCS) in between the T-DNA borders to facilitate cloning. Due to the reduced size, more unique restriction sites are available in the MCS, thus allowing more versatile cloning. Since the traF region was not included, it is not possible to mobilize this binary vector into Agrobacterium by triparental mating. This problem can be easily resolved by direct transformation. The mini binary vector has been demonstrated to successfully transform Arabidopsis plants. Based on this mini binary vector, a series of binary vectors were constructed for plant transformation.

  15. Helices and vector bundles

    CERN Document Server

    Rudakov, A N

    1990-01-01

    This volume is devoted to the use of helices as a method for studying exceptional vector bundles, an important and natural concept in algebraic geometry. The work arises out of a series of seminars organised in Moscow by A. N. Rudakov. The first article sets up the general machinery, and later ones explore its use in various contexts. As to be expected, the approach is concrete; the theory is considered for quadrics, ruled surfaces, K3 surfaces and P3(C).

  16. Anisotropic vector Preisach particle

    CERN Document Server

    Fuezi, J

    2000-01-01

    The static 2D vector magnetic behaviour of an anisotropic silicon iron sheet is modelled by a particle which depicts its space-averaged behaviour. The magnitude of magnetization is governed by a classical Preisach operator with the projection of field strength on the magnetization direction as input. Its orientation is determined by the equilibrium between the field strength orientation and the anisotropy of the sheet.

  17. What is a vector?

    Science.gov (United States)

    Morgan, Eric René; Booth, Mark; Norman, Rachel; Mideo, Nicole; McCallum, Hamish; Fenton, Andy

    2017-01-01

    Many important and rapidly emerging pathogens of humans, livestock and wildlife are ‘vector-borne’. However, the term ‘vector’ has been applied to diverse agents in a broad range of epidemiological systems. In this perspective, we briefly review some common definitions, identify the strengths and weaknesses of each and consider the functional differences between vectors and other hosts from a range of ecological, evolutionary and public health perspectives. We then consider how the use of designations can afford insights into our understanding of epidemiological and evolutionary processes that are not otherwise apparent. We conclude that from a medical and veterinary perspective, a combination of the ‘haematophagous arthropod’ and ‘mobility’ definitions is most useful because it offers important insights into contact structure and control and emphasizes the opportunities for pathogen shifts among taxonomically similar species with similar feeding modes and internal environments. From a population dynamics and evolutionary perspective, we suggest that a combination of the ‘micropredator’ and ‘sequential’ definition is most appropriate because it captures the key aspects of transmission biology and fitness consequences for the pathogen and vector itself. However, we explicitly recognize that the value of a definition always depends on the research question under study. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289253

  18. Lentiviral Vector Mediated Transgenesis.

    Science.gov (United States)

    Barde, Isabelle; Verp, Sonia; Offner, Sandra; Trono, Didier

    2011-03-01

    The genetic manipulation of rodents through the generation of fully transgenic animals or via the modification of selective cells or organs is a procedure of paramount importance for biomedical research, either to address fundamental questions or to develop preclinical models of human diseases. Lentiviral vectors occupy the front stage in this scene, as they can mediate the integration and stable expression of transgenes both in vitro and in vivo. Widely used to modify a variety of cells, including re-implantable somatic and embryonic stem cells, lentiviral vectors can also be directly administered in vivo, for instance in the brain. However, perhaps their most spectacular research application is in the generation of transgenic animals. Compared with the three-decade-old DNA pronuclear injection technique, lentivector-mediated transgenesis is simple, cheap, and highly efficient. Furthermore, it can take full advantage of the great diversity of lentiviral vectors developed for other applications, and thus allows for ubiquitous or tissue-specific or constitutive or externally controllable transgene expression, as well as RNAi-mediated gene knockdown. Curr. Protoc. Mouse Biol. 1:169-184. © 2011 by John Wiley & Sons, Inc. Copyright © 2011 John Wiley & Sons, Inc.

  19. Test of understanding of vectors: A reliable multiple-choice vector concept test

    Science.gov (United States)

    Barniol, Pablo; Zavala, Genaro

    2014-06-01

    In this article we discuss the findings of our research on students' understanding of vector concepts in problems without physical context. First, we develop a complete taxonomy of the most frequent errors made by university students when learning vector concepts. This study is based on the results of several test administrations of open-ended problems in which a total of 2067 students participated. Using this taxonomy, we then designed a 20-item multiple-choice test [Test of understanding of vectors (TUV)] and administered it in English to 423 students who were completing the required sequence of introductory physics courses at a large private Mexican university. We evaluated the test's content validity, reliability, and discriminatory power. The results indicate that the TUV is a reliable assessment tool. We also conducted a detailed analysis of the students' understanding of the vector concepts evaluated in the test. The TUV is included in the Supplemental Material as a resource for other researchers studying vector learning, as well as instructors teaching the material.

  20. Scalar - vector soliton fiber lasers

    CERN Document Server

    Wu, Zhichao; Li, Lei; Luo, Yiyang; Tang, Dingyuan; Shen, Deyuan; Tang, Ming; Fu, Songnian; Zhao, Luming

    2016-01-01

    Rapid progress in passively mode-locked fiber lasers is currently driven by the recent discovery of vector feature of mode-locking pulses, namely, the group velocity-locked vector solitons, the phase locked vector solitons, and the high-order vector solitons. Those vector solitons are fundamentally different from the previously known scalar solitons. Here, we report a fiber laser where the mode-locked pulse evolves as a vector soliton in the strong birefringent segment and is transformed into a regular scalar soliton after the polarizer within the laser cavity. The existence of solutions in a polarization-dependent cavity comprising a periodic combination of two distinct nonlinear waves is novel and likely to be applicable to various other nonlinear systems. For very large local birefringence, our laser approaches the working regime of vector soliton lasers, while it approaches scalar soliton fiber lasers under the conditions of very small birefringence.

  1. Construction and Application of Epitope- and Green Fluorescent Protein-Tagging Integration Vectors for Bacillus subtilis

    OpenAIRE

    Kaltwasser, Marcus; Wiegert, Thomas; Schumann, Wolfgang

    2002-01-01

    Here we describe the construction and application of six new tagging vectors allowing the fusion of two different types of tagging sequences, epitope and localization tags, to any Bacillus subtilis protein. These vectors are based on the backbone of pMUTIN2 and replace the lacZ gene with tagging sequences. Fusion of the tagging sequences occurs by PCR amplification of the 3′ terminal part of the gene of interest (about 300 bp), insertion into the tagging vector in such a way that a fusion pro...

  2. The Use of Chromatin Insulators to Improve the Expression and Safety of Integrating Gene Transfer Vectors

    Science.gov (United States)

    2011-01-01

    Abstract The therapeutic application of recombinant retroviruses and other integrating gene transfer vectors has been limited by problems of vector expression and vector-mediated genotoxicity. These problems arise in large part from the interactions between vector sequences and the genomic environment surrounding sites of integration. Strides have been made in overcoming both of these problems through the modification of deleterious vector sequences, the inclusion of better enhancers and promoters, and the use of alternative virus systems. However, these modifications often add other restrictions on vector design, which in turn can further limit therapeutic applications. As an alternative, several groups have been investigating a class of DNA regulatory elements known as chromatin insulators. These elements provide a means of blocking the interaction between an integrating vector and the target cell genome in a manner that is independent of the vector transgene, regulatory elements, or virus of origin. This review outlines the background, rationale, and evidence for using chromatin insulators to improve the expression and safety of gene transfer vectors. Also reviewed are topological factors that constrain the use of insulators in integrating gene transfer vectors, alternative sources of insulators, and the role of chromatin insulators as one of several components for optimal vector design. PMID:21247248

  3. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

    Directory of Open Access Journals (Sweden)

    Victor M. Bii

    2016-10-01

    Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

  4. Scalar and vector Galileons

    Science.gov (United States)

    Rodríguez, Yeinzon; Navarro, Andrés A.

    2017-03-01

    An alternative for the construction of fundamental theories is the introduction of Galileons. These are fields whose action leads to non higher than second-order equations of motion. As this is a necessary but not sufficient condition to make the Hamiltonian bounded from below, as long as the action is not degenerate, the Galileon construction is a way to avoid pathologies both at the classical and quantum levels. Galileon actions are, therefore, of great interest in many branches of physics, specially in high energy physics and cosmology. This proceedings contribution presents the generalities of the construction of both scalar and vector Galileons following two different but complimentary routes.

  5. Architecture and Vector Control

    DEFF Research Database (Denmark)

    von Seidlein, Lorenz; Knols, Bart GJ; Kirby, Matthew

    2012-01-01

    of vector-borne diseases have no access to electricity. Many houses in the hot, humid regions of Asia have adapted to the environment, they are built of porous materials and are elevated on stilts features which allow a comfortable climate even in the presence of bednets and screens. In contrast, many...... buildings in Africa and Asia in respect to their indoor climate characteristics and finally, show how state-of-the-art 3D modelling can predict climate characteristics and help to optimize buildings....

  6. Predicting Solar Flares Using SDO/HMI Vector Magnetic Data Product and Random Forest Algorithm

    Science.gov (United States)

    Liu, Chang; Deng, Na; Wang, Jason; Wang, Haimin

    2017-08-01

    Adverse space weather effects can often be traced to solar flares, prediction of which has drawn significant research interests. Many previous forecasting studies used physical parameters derived from photospheric line-of-sight field or ground-based vector field observations. The Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory produces full-disk vector magnetograms with continuous high-cadence, while flare prediction efforts utilizing this unprecedented data source are still limited. Here we report results of flare prediction using physical parameters provided by the Space-weather HMI Active Region Patches (SHARP) and related data products. We survey X-ray flares occurred from 2010 May to 2016 December, and categorize their source regions into four classes (B, C, M, and X) according to the maximum GOES magnitude of flares they generated. We then retrieve SHARP related parameters for each selected region at the beginning of its flare date to build a database. Finally, we train a machine-learning algorithm, called random forest (RF), to predict the occurrence of a certain class of flares in a given active region within 24 hours, evaluate the classifier performance using the 10-fold cross validation scheme, and characterize the results using standard performace metrics. Compared to previous works, our experiments indicate that using the HMI parameters and RF is a valid method for flare forecasting with fairly reasonable prediction performance. We also find that the total unsigned quantities of vertical current, current helicity, and flux near polarity inversion line are among the most important parameters for classifying flaring regions into different classes.

  7. Vector wave propagation method.

    Science.gov (United States)

    Fertig, M; Brenner, K-H

    2010-04-01

    In this paper, we extend the scalar wave propagation method (WPM) to vector fields. The WPM [Appl. Opt.32, 4984 (1993)] was introduced in order to overcome the major limitations of the beam propagation method (BPM). With the WPM, the range of application can be extended from the simulation of waveguides to simulation of other optical elements like lenses, prisms and gratings. In that reference it was demonstrated that the wave propagation scheme provides valid results for propagation angles up to 85 degrees and that it is not limited to small index variations in the axis of propagation. Here, we extend the WPM to three-dimensional vectorial fields (VWPMs) by considering the polarization dependent Fresnel coefficients for transmission in each propagation step. The continuity of the electric field is maintained in all three dimensions by an enhanced propagation vector and the transfer matrix. We verify the validity of the method by transmission through a prism and by comparison with the focal distribution from vectorial Debye theory. Furthermore, a two-dimensional grating is simulated and compared with the results from three-dimensional RCWA. Especially for 3D problems, the runtime of the VWPM exhibits special advantage over the RCWA.

  8. Hybrid viral vectors for vaccine and antibody production in plants.

    Science.gov (United States)

    Yusibov, Vidadi; Streatfield, Stephen J; Kushnir, Natasha; Roy, Gourgopal; Padmanaban, Annamalai

    2013-01-01

    Plants have a demonstrated potential for large-scale, rapid production of recombinant proteins for diverse product applications, including subunit vaccines and monoclonal antibodies. In this field, the accent has recently shifted from the engineering of "edible" vaccines based on stable expression of target protein in transgenic or transplastomic plants to the development of purified formulated vaccines that are delivered via injection. The injectable vaccines are commonly produced using transient expression of target gene delivered into genetically unmodified plant host via viral or bacterial vectors. Most viral vectors are based on plant RNA viruses, where nonessential sequences are replaced with the gene of interest. Utilization of viral hybrids that consist of genes and regulatory elements of different virus species, or transcomplementation systems (vector/transgene) had a substantial impact on the level of target protein expression. Development and introduction of agroviral hybrid vectors that combine genetic elements of bacterial binary plasmids and plant viral vectors, and agroinfiltration as a tool of the vector delivery have resulted in significant progress in large-scale production of recombinant vaccines and monoclonal antibodies in plants. This article presents an overview of plant hybrid viral vector expression systems developed so far.

  9. Highly evolvable malaria vectors : The genomes of 16 Anopheles mosquitoes

    NARCIS (Netherlands)

    Neafsey, D. E.; Waterhouse, R. M.; Abai, M. R.; Aganezov, S. S.; Alekseyev, M. A.; Allen, J. E.; Amon, J.; Arca, B.; Arensburger, P.; Artemov, G.; Assour, L. A.; Basseri, H.; Berlin, A.; Birren, B. W.; Blandin, S. A.; Brockman, A. I.; Burkot, T. R.; Burt, A.; Chan, C. S.; Chauve, C.; Chiu, J. C.; Christensen, M.; Costantini, C.; Davidson, V. L. M.; Deligianni, E.; Dottorini, T.; Dritsou, V.; Gabriel, S. B.; Guelbeogo, W. M.; Hall, A. B.; Han, M. V.; Hlaing, T.; Hughes, D. S. T.; Jenkins, A. M.; Jiang, X.; Jungreis, I.; Kakani, E. G.; Kamali, M.; Kemppainen, P.; Kennedy, R. C.; Kirmitzoglou, I. K.; Koekemoer, L. L.; Laban, N.; Langridge, N.; Lawniczak, M. K. N.; Lirakis, M.; Lobo, N. F.; Lowy, E.; Maccallum, R. M.; Mao, C.; Maslen, G.; Mbogo, C.; Mccarthy, J.; Michel, K.; Mitchell, S. N.; Moore, W.; Murphy, K. A.; Naumenko, A. N.; Nolan, T.; Novoa, E. M.; O'loughlin, S.; Oringanje, C.; Oshaghi, M. A.; Pakpour, N.; Papathanos, P. A.; Peery, A. N.; Povelones, M.; Prakash, A.; Price, D. P.; Rajaraman, A.; Reimer, L. J.; Rinker, D. C.; Rokas, A.; Russell, T. L.; Sagnon, N.; Sharakhova, M. V.; Shea, T.; Simao, F. A.; Simard, F.; Slotman, M. A.; Somboon, P.; Stegniy, V.; Struchiner, C. J.; Thomas, G. W. C.; Tojo, M.; Topalis, P.; Tubio, J. M. C.; Unger, M. F.; Vontas, J.; Walton, C.; Wilding, C. S.; Willis, J. H.; Wu, Y.-c.; Yan, G.; Zdobnov, E. M.; Zhou, X.; Catteruccia, F.; Christophides, G. K.; Collins, F. H.; Cornman, R. S.; Crisanti, A.; Donnelly, M. J.; Emrich, S. J.; Fontaine, M. C.; Gelbart, W.; Hahn, M. W.; Hansen, I. A.; Howell, P. I.; Kafatos, F. C.; Kellis, M.; Lawson, D.; Louis, C.; Luckhart, S.; Muskavitch, M. A. T.; Ribeiro, J. M.; Riehle, M. A.; Sharakhov, I. V.; Tu, Z.; Zwiebel, L. J.; Besansky, N. J.

    2015-01-01

    Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16

  10. Construction of lentiviral shRNA expression vector targeting ...

    African Journals Online (AJOL)

    The optimal interfering target was then selected, while the titer of lentiviral packing PLD2-shRNA was 3.47 × 104 TU/ml and the virus was successfully packaged. PCR and sequencing analyses revealed that lentiviral shRNA vectors of three targeting PLD2 gene were successfully constructed. Key words: RNA interference ...

  11. Adenoviral vectors as genome editing tools : repairing defective DMD alleles

    NARCIS (Netherlands)

    Maggio, Ignazio

    2016-01-01

    Adenoviral vectors (AdVs) constitute powerful gene delivery vehicles. However, so far, their potential for genome editing has not been extensively investigated. By tailoring AdVs as carriers of designer nucleases and donor DNA sequences, the research presented in this thesis expands the utility of

  12. "Analytical" vector-functions I

    Science.gov (United States)

    Todorov, Vladimir Todorov

    2017-12-01

    In this note we try to give a new (or different) approach to the investigation of analytical vector functions. More precisely a notion of a power xn; n ∈ ℕ+ of a vector x ∈ ℝ3 is introduced which allows to define an "analytical" function f : ℝ3 → ℝ3. Let furthermore f (ξ )= ∑n =0 ∞ anξn be an analytical function of the real variable ξ. Here we replace the power ξn of the number ξ with the power of a vector x ∈ ℝ3 to obtain a vector "power series" f (x )= ∑n =0 ∞ anxn . We research some properties of the vector series as well as some applications of this idea. Note that an "analytical" vector function does not depend of any basis, which may be used in research into some problems in physics.

  13. RNAi in Arthropods: Insight into the Machinery and Applications for Understanding the Pathogen-Vector Interface

    Directory of Open Access Journals (Sweden)

    Christian Stutzer

    2012-11-01

    Full Text Available The availability of genome sequencing data in combination with knowledge of expressed genes via transcriptome and proteome data has greatly advanced our understanding of arthropod vectors of disease. Not only have we gained insight into vector biology, but also into their respective vector-pathogen interactions. By combining the strengths of postgenomic databases and reverse genetic approaches such as RNAi, the numbers of available drug and vaccine targets, as well as number of transgenes for subsequent transgenic or paratransgenic approaches, have expanded. These are now paving the way for in-field control strategies of vectors and their pathogens. Basic scientific questions, such as understanding the basic components of the vector RNAi machinery, is vital, as this allows for the transfer of basic RNAi machinery components into RNAi-deficient vectors, thereby expanding the genetic toolbox of these RNAi-deficient vectors and pathogens. In this review, we focus on the current knowledge of arthropod vector RNAi machinery and the impact of RNAi on understanding vector biology and vector-pathogen interactions for which vector genomic data is available on VectorBase.

  14. A Versatile System for USER Cloning-Based Assembly of Expression Vectors for Mammalian Cell Engineering

    DEFF Research Database (Denmark)

    Lund, Anne Mathilde; Kildegaard, Helene Faustrup; Petersen, Maja Borup Kjær

    2014-01-01

    A new versatile mammalian vector system for protein production, cell biology analyses, and cell factory engineering was developed. The vector system applies the ligation-free uracil-excision based technique – USER cloning – to rapidly construct mammalian expression vectors of multiple DNA fragments...... efficiency above 90%. The functionality of basic vectors for FAST assembly was tested and validated by transient expression of fluorescent model proteins in CHO, U-2-OS and HEK293 cell lines. In this test, we included many of the most common vector elements for heterologous gene expression in mammalian cells......, in addition the system is fully extendable by other users. The vector system is designed to facilitate high-throughput genome-scale studies of mammalian cells, such as the newly sequenced CHO cell lines, through the ability to rapidly generate high-fidelity assembly of customizable gene expression vectors....

  15. Status and prospects of plant virus control through interference with vector transmission.

    Science.gov (United States)

    Bragard, C; Caciagli, P; Lemaire, O; Lopez-Moya, J J; MacFarlane, S; Peters, D; Susi, P; Torrance, L

    2013-01-01

    Most plant viruses rely on vector organisms for their plant-to-plant spread. Although there are many different natural vectors, few plant virus-vector systems have been well studied. This review describes our current understanding of virus transmission by aphids, thrips, whiteflies, leafhoppers, planthoppers, treehoppers, mites, nematodes, and zoosporic endoparasites. Strategies for control of vectors by host resistance, chemicals, and integrated pest management are reviewed. Many gaps in the knowledge of the transmission mechanisms and a lack of available host resistance to vectors are evident. Advances in genome sequencing and molecular technologies will help to address these problems and will allow innovative control methods through interference with vector transmission. Improved knowledge of factors affecting pest and disease spread in different ecosystems for predictive modeling is also needed. Innovative control measures are urgently required because of the increased risks from vector-borne infections that arise from environmental change.

  16. Optimality Conditions in Vector Optimization

    CERN Document Server

    Jiménez, Manuel Arana; Lizana, Antonio Rufián

    2011-01-01

    Vector optimization is continuously needed in several science fields, particularly in economy, business, engineering, physics and mathematics. The evolution of these fields depends, in part, on the improvements in vector optimization in mathematical programming. The aim of this Ebook is to present the latest developments in vector optimization. The contributions have been written by some of the most eminent researchers in this field of mathematical programming. The Ebook is considered essential for researchers and students in this field.

  17. Insect cell transformation vectors that support high level expression and promoter assessment in insect cell culture

    Science.gov (United States)

    A somatic transformation vector, pDP9, was constructed that provides a simplified means of producing permanently transformed cultured insect cells that support high levels of protein expression of foreign genes. The pDP9 plasmid vector incorporates DNA sequences from the Junonia coenia densovirus th...

  18. Volumetric 3-D Vector Flow Measurements using a 62+62 Row-Column Addressed Array

    DEFF Research Database (Denmark)

    Holbek, Simon; Stuart, Matthias Bo; Jensen, Jørgen Arendt

    2017-01-01

    Experimental results from volumetric 3-D vector flow measurements using a 62+62 row-column addressed (RCA) array are presented. A plane-by-plane steered transmit sequence and its post processing steps are described for obtaining 3-D vector flow in a volume. A modified version of the transverse...

  19. Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi

    National Research Council Canada - National Science Library

    Frandsen, Rasmus J N; Andersson, Jens A; Kristensen, Matilde B; Giese, Henriette

    2008-01-01

    ... markers such as GFP are essential for this process. Construction of vectors for these experiments depends on the directional cloning of two homologous recombination sequences on each side of a selection marker gene...

  20. Estimation of vector velocity

    DEFF Research Database (Denmark)

    2000-01-01

    Using a pulsed ultrasound field, the two-dimensional velocity vector can be determined with the invention. The method uses a transversally modulated ultrasound field for probing the moving medium under investigation. A modified autocorrelation approach is used in the velocity estimation. The new...... estimator automatically compensates for the axial velocity, when determining the transverse velocity by using fourth order moments rather than second order moments. The estimation is optimized by using a lag different from one in the estimation process, and noise artifacts are reduced by using averaging...... of RF samples. Further, compensation for the axial velocity can be introduced, and the velocity estimation is done at a fixed depth in tissue to reduce spatial velocity dispersion....

  1. Multistage vector (MSV) therapeutics

    Science.gov (United States)

    Wolfram, Joy; Shen, Haifa; Ferrari, Mauro

    2015-01-01

    One of the greatest challenges in the field of medicine is obtaining controlled distribution of systemically administered therapeutic agents within the body. Indeed, biological barriers such as physical compartmentalization, pressure gradients, and excretion pathways adversely affect localized delivery of drugs to pathological tissue. The diverse nature of these barriers requires the use of multifunctional drug delivery vehicles that can overcome a wide range of sequential obstacles. In this review, we explore the role of multifunctionality in nanomedicine by primarily focusing on multistage vectors (MSVs). The MSV is an example of a promising therapeutic platform that incorporates several components, including a microparticle, nanoparticles, and small molecules. In particular, these components are activated in a sequential manner in order to successively address transport barriers. PMID:26264836

  2. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...... and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  3. Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi

    Directory of Open Access Journals (Sweden)

    Kristensen Matilde B

    2008-08-01

    Full Text Available Abstract Background The rapid increase in whole genome fungal sequence information allows large scale functional analyses of target genes. Efficient transformation methods to obtain site-directed gene replacement, targeted over-expression by promoter replacement, in-frame epitope tagging or fusion of coding sequences with fluorescent markers such as GFP are essential for this process. Construction of vectors for these experiments depends on the directional cloning of two homologous recombination sequences on each side of a selection marker gene. Results Here, we present a USER Friendly cloning based technique that allows single step cloning of the two required homologous recombination sequences into different sites of a recipient vector. The advantages are: A simple experimental design, free choice of target sequence, few procedures and user convenience. The vectors are intented for Agrobacterium tumefaciens and protoplast based transformation technologies. The system has been tested by the construction of vectors for targeted replacement of 17 genes and overexpression of 12 genes in Fusarium graminearum. The results show that four fragment vectors can be constructed in a single cloning step with an average efficiency of 84% for gene replacement and 80% for targeted overexpression. Conclusion The new vectors designed for USER Friendly cloning provided a fast reliable method to construct vectors for targeted gene manipulations in fungi.

  4. Vector-Tensor and Vector-Vector Decay Amplitude Analysis of B0->phi K*0

    CERN Document Server

    Aubert, B; Abrams, G S; Adye, T; Ahmed, S; Alam, M S; Albert, J; Aleksan, R; Allen, M T; Allison, J; Altenburg, D D; Andreotti, M; Angelini, C; Anulli, F; Arnaud, N; Asgeirsson, D J; Aston, D; Azzolini, V; Baak, M A; Back, J J; Baldini-Ferroli, R; Band, H R; Banerjee, Sw; Bard, D J; Barlow, N R; Barlow, R J; Barrett, M; Bartoldus, R; Batignani, G; Battaglia, M; Bauer, J M; Bechtle, P; Beck, T W; Behera, P K; Bellini, F; Benayoun, M; Benelli, G; Berger, N; Bernard, D; Berryhill, J W; Best, D S; Bettarini, S; Bettoni, D; Bevan, A J; Bhimji, W; Bhuyan, B; Bianchi, F; Biasini, M; Biesiada, J; Blanc, F; Blaylock, G; Blinov, V E; Bloom, P C; Blount, N L; Bomben, M; Bondioli, M; Bonneaud, G R; Bosisio, L; Boutigny, D; Bowerman, D A; Boyd, J T; Bozzi, C; Brandenburg, G; Brandt, T; Brau, J E; Briand, H; Brown, C M; Brown, D N; Bruinsma, M; Brunet, S; Bucci, F; Buchanan, C; Bugg, W; Bukin, A D; Bula, R; Burchat, P R; Burke, J P; Button-Shafer, J; Buzzo, A; Bóna, M; Cahn, R N; Calabrese, R; Calcaterra, A; Calderini, G; Campagnari, C; Carpinelli, M; Cartaro, C; Cavallo, N; Cavoto, G; Cenci, R; Chai, X; Chaisanguanthum, K S; Chao, M; Charles, E; Charles, M J; Chauveau, J; Chavez, C A; Chen, A; Chen, C; Chen, E; Chen, J C; Chen, S; Chen, X; Chen, X R; Cheng, B; Cheng, C H; Chia, Y M; Cibinetto, G; Clark, P J; Clarke, C K; Claus, R; Cochran, J; Coleman, J P; Contri, R; Convery, M R; Corwin, L A; Cossutti, F; Cottingham, W N; Couderc, F; Covarelli, R; Cowan, G; Cowan, R; Crawley, H B; Cremaldi, L; Cunha, A; Curry, S; Côté, D; D'Orazio, A; Dahmes, B; Dallapiccola, C; Danielson, N; Dasu, S; Datta, M; Dauncey, P D; David, P; Davier, M; Davis, C L; De Nardo, Gallieno; De Sangro, R; Del Amo-Sánchez, P; Del Buono, L; Del Re, D; Della Ricca, G; Denig, A G; Di Lodovico, F; Di Marco, E; Dingfelder, J C; Dittongo, S; Dong, L; Dorfan, J; Druzhinin, V P; Dubitzky, R S; Dubois-Felsmann, G P; Dujmic, D; Dunwoodie, W M; Dvoretskii, A; Ebert, M; Eckhart, E A; Eckmann, R; Edgar, C L; Edwards, A J; Egede, U; Eigen, G; Eisner, A M; Elmer, P; Emery, S; Ernst, J A; Eschenburg, V; Eschrich, I; Eyges, V; Fabozzi, F; Faccini, R; Fang, F; Feltresi, E; Ferrarotto, F; Ferroni, F; Field, R C; Finocchiaro, G; Flacco, C J; Flack, R L; Flächer, H U; Flood, K T; Ford, K E; Ford, W T; Forster, I J; Forti, F; Fortin, D; Foulkes, S D; Franek, B; Frey, R; Fritsch, M; Fry, J R; Fulsom, B G; Gabathuler, E; Gaidot, A; Gallo, F; Gamba, D; Gamet, R; Gan, K K; Ganzhur, S F; Gao, Y; Gary, J W; Gaspero, M; Gatto, C; Gaz, A; George, K A; Gill, M S; Giorgi, M A; Gladney, L; Glanzman, T; Godang, R; Golubev, V B; Gowdy, S J; Gradl, W; Graham, M T; Graugès-Pous, E; Grenier, P; Gritsan, A V; Grosdidier, G; Groysman, Y; Guo, Z J; Hadavand, H K; Haire, M; Halyo, V; Hamano, K; Hamel de Monchenault, G; Hamon, O; Harrison, P F; Harrison, T J; Hart, A J; Hartfiel, B L; Hast, C; Hauke, A; Hawkes, C M; Hearty, C; Held, T; Hertzbach, S S; Heusch, C A; Hill, E J; Hirschauer, J F; Hitlin, D G; Hollar, J J; Hong, T M; Honscheid, K; Hopkins, D A; Hrynóva, T; Hufnagel, D; Hulsbergen, W D; Hutchcroft, D E; Höcker, A; Igonkina, O; Innes, W R; Izen, J M; Jackson, P D; Jackson, P S; Jacobsen, R G; Jain, V; Jasper, H; Jawahery, A; Jessop, C P; Judd, D; Kadyk, J A; Kagan, H; Karyotakis, Yu; Kass, R; Kelsey, M H; Kerth, L T; Khan, A; Kim, H; Kim, P; Kirkby, D; Klose, V; Knecht, N S; Koch, H; Kolb, J A; Kolomensky, Yu G; Kovalskyi, D; Kowalewski, R V; Kozanecki, Witold; Kreisel, A; Krishnamurthy, M; Kroeger, R; Kroseberg, J; Kukartsev, G; Kutter, P E; Kyberd, P; La Vaissière, C de; Lacker, H M; Lae, C K; Lafferty, G D; Lanceri, L; Lange, D J; Lankford, A J; Latham, T E; Latour, E; Lau, Y P; Lazzaro, A; Le Diberder, F R; Lee, C L; Lees, J P; Legendre, M; Leith, D W G S; Lepeltier, V; Leruste, P; Lewandowski, B; Li Gioi, L; Li, S; Li, X; Lista, L; Liu, H; Lo Vetere, M; LoSecco, J M; Lockman, W S; Lombardo, V; Long, O; Lopes-Pegna, D; Lopez-March, N; Lou, X C; Lu, M; Luitz, S; Lund, P; Luppi, E; Lusiani, A; Lutz, A M; Lynch, G; Lynch, H L; Lü, C; Lüth, V; MacFarlane, D B; Macri, M M; Mader, W F; Majewski, S A; Malcles, J; Mallik, U; Mancinelli, G; Mandelkern, M A; Marchiori, G; Margoni, M; Marks, J; Marsiske, H; Martínez-Vidal, F; Mattison, T S; Mazur, M A; Mazzoni, M A; McKenna, J A; McMahon, T R; Mclachlin, S E; Meadows, B T; Mellado, B; Menges, W; Merkel, J; Messner, R; Meyer, N T; Meyer, W T; Mihályi, A; Mir, L M; Mishra, K; Mohanty, G B; Monge, M R; Monorchio, D; Moore, T B; Morandin, M; Morganti, M; Morganti, S; Morii, M; Muheim, F; Müller, D R; Nagel, M; Naisbit, M T; Narsky, I; Nash, J A; Nauenberg, U; Neal, H; Negrini, M; Neri, N; Nesom, G; Nicholson, H; Nikolich, M B; Nogowski, R; Nugent, I M; O'Grady, C P; Ocariz, J; Ofte, I; Olaiya, E O; Olivas, A; Olsen, J; Onuchin, A P; Orimoto, T J; Oyanguren, A; Ozcan, V E; Paar, H P; Pacetti, S; Palano, A; Palombo, F; Pan, B; Pan, Y; Panduro, W; Paoloni, E; Paolucci, P; Pappagallo, M; Park, W; Passaggio, S; Patel, P M; Patrignani, C; Patteri, P; Payne, D J; Pelizaeus, M; Perazzo, A; Perl, M; Peruzzi, I M; Peters, K; Petersen, B A; Petrella, A; Petzold, A; Piatenko, T; Piccolo, D; Piccolo, M; Piemontese, L; Pierini, M; Piredda, G; Playfer, S; Poireau, V; Polci, F; Pompili, A; Porter, F C; Posocco, M; Potter, C T; Prell, S; Prencipe, E; Prepost, R; Pripstein, M; Pruvot, S; Pulliam, T; Purohit, M V; Qi, N D; Rahatlou, S; Rahimi, A M; Rahmat, R; Rama, M; Ratcliff, B N; Raven, G; Regensburger, J J; Ricciardi, S; Richman, J D; Ritchie, J L; Rizzo, G; Roberts, D A; Robertson, A I; Robertson, S H; Robutti, E; Rodier, S; Roe, N A; Ronan, M T; Roney, J M; Rong, G; Roodman, A; Roos, L; Rosenberg, E I; Rotondo, M; Roudeau, P; Rubin, A E; Ruddick, W O; Röthel, W; Sacco, R; Saeed, M A; Safai-Tehrani, F; Saleem, M; Salnikov, A A; Salvatore, F; Sanders, D A; Santroni, A; Saremi, S; Satpathy, A; Schalk, T; Schenk, S; Schilling, C J; Schindler, R H; Schofield, K C; Schott, G; Schröder, T; Schröder, H; Schubert, J; Schubert, K R; Schumm, B A; Schune, M H; Schwiening, J; Schwierz, R; Schwitters, R F; Sciacca, C; Sciolla, G; Seiden, A; Sekula, S J; Serednyakov, S I; Serrano, J; Sharma, V; Shen, B C; Sherwood, D J; Simard, M; Simi, G; Simonetto, F; Sinev, N B; Skovpen, Yu I; Smith, A J S; Smith, J G; Snoek, H L; Snyder, A; Sobie, R J; Soffer, A; Sokoloff, M D; Solodov, E P; Spaan, B; Spanier, S M; Spitznagel, M; Spradlin, P; Steinke, M; Stelzer, J; Stocchi, A; Stoker, D P; Stroili, R; Strom, D; Strube, J; Stugu, B; Stängle, H; Su, D; Sullivan, M K; Summers, D J; Sundermann, J E; Suzuki, K; Swain, S K; Taras, P; Taylor, F; Telnov, A V; Teodorescu, L; Ter-Antonian, R; Therin, G; Thiebaux, C; Thompson, J M; Tisserand, V; Todyshev, Y K; Toki, W H; Torrence, E; Tosi, S; Touramanis, C; Ulmer, K A; Uwer, U; Van Bakel, N; Vasseur, G; Vavra, J; Vazquez, A; Verderi, M; Viaud, F B; Vitale, L; Voci, C; Voena, C; Volk, A; Wagner, A P; Wagner, S R; Wagoner, D E; Waldi, R; Walker, D; Walsh, J J; Wang, K; Wang, P; Wang, W F; Wappler, F R; Watson, A T; Weaver, M; Weinstein, A J R; Wenzel, W A; Wilden, L; Williams, D C; Williams, J C; Wilson, F F; Wilson, J R; Wilson, M G; Wilson, R J; Winklmeier, F; Wisniewski, W J; Wittgen, M; Wong, Q K; Wormser, G; Wren, A C; Wright, D H; Wright, D M; Wu, J; Wu, S L; Wulsin, H W; Xie, Y; Yamamoto, R K; Yarritu, A K; Ye, S; Yi, J I; Yi, K; Young, C C; Yu, Z; Yéche, C; Zain, S B; Zallo, A; Zeng, Q; Zghiche, A; Zhang, J; Zhang, L; Zhao, H W; Zhu, Y S; Ziegler, V; Zito, M; Çuhadar-Dönszelmann, T; al, et

    2007-01-01

    We perform an amplitude analysis of the decays B0->phi K^*_2(1430)0, phi K^*(892)0, and phi(K pi)^0_S-wave with a sample of about 384 million BBbar pairs recorded with the BABAR detector. The fractions of longitudinal polarization f_L of the vector-tensor and vector-vector decay modes are measured to be 0.853 +0.061-0.069 +-0.036 and 0.506 +-0.040 +-0.015, respectively. Overall, twelve parameters are measured for the vector-vector decay and seven parameters for the vector-tensor decay, including the branching fractions and parameters sensitive to CP-violation.

  5. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  6. Design of 2D Time-Varying Vector Fields

    KAUST Repository

    Chen, Guoning

    2012-10-01

    Design of time-varying vector fields, i.e., vector fields that can change over time, has a wide variety of important applications in computer graphics. Existing vector field design techniques do not address time-varying vector fields. In this paper, we present a framework for the design of time-varying vector fields, both for planar domains as well as manifold surfaces. Our system supports the creation and modification of various time-varying vector fields with desired spatial and temporal characteristics through several design metaphors, including streamlines, pathlines, singularity paths, and bifurcations. These design metaphors are integrated into an element-based design to generate the time-varying vector fields via a sequence of basis field summations or spatial constrained optimizations at the sampled times. The key-frame design and field deformation are also introduced to support other user design scenarios. Accordingly, a spatial-temporal constrained optimization and the time-varying transformation are employed to generate the desired fields for these two design scenarios, respectively. We apply the time-varying vector fields generated using our design system to a number of important computer graphics applications that require controllable dynamic effects, such as evolving surface appearance, dynamic scene design, steerable crowd movement, and painterly animation. Many of these are difficult or impossible to achieve via prior simulation-based methods. In these applications, the time-varying vector fields have been applied as either orientation fields or advection fields to control the instantaneous appearance or evolving trajectories of the dynamic effects. © 1995-2012 IEEE.

  7. Viral Vectors for Plant Genome Engineering.

    Science.gov (United States)

    Zaidi, Syed Shan-E-Ali; Mansoor, Shahid

    2017-01-01

    Recent advances in genome engineering (GE) has made it possible to precisely alter DNA sequences in plant cells, providing specifically engineered plants with traits of interest. Gene targeting efficiency depends on the delivery-method of both sequence-specific nucleases and repair templates, to plant cells. Typically, this is achieved using Agrobacterium mediated transformation or particle bombardment, both of which transform only a subset of cells in treated tissues. The alternate in planta approaches, stably integrating nuclease-encoding cassettes and repair templates into the plant genome, are time consuming, expensive and require extra regulations. More efficient GE reagents delivery methods are clearly needed if GE is to become routine, especially in economically important crops that are difficult to transform. Recently, autonomously replicating virus-based vectors have been demonstrated as efficient means of delivering GE reagents in plants. Both DNA viruses (Bean yellow dwarf virus, Wheat dwarf virus and Cabbage leaf curl virus) and RNA virus (Tobacco rattle virus) have demonstrated efficient gene targeting frequencies in model plants (Nicotiana benthamiana) and crops (potato, tomato, rice, and wheat). Here we discuss the recent advances using viral vectors for plant genome engineering, the current limitations and future directions.

  8. Transcriptional Silencing of Retroviral Vectors

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M.; Pedersen, F.S.

    1996-01-01

    Although retroviral vector systems have been found to efficiently transduce a variety of cell types in vitro, the use of vectors based on murine leukemia virus in preclinical models of somatic gene therapy has led to the identification of transcriptional silencing in vivo as an important problem...

  9. On the Witt vector Frobenius

    DEFF Research Database (Denmark)

    Davis, Christopher James; Kedlaya, Kiran

    2014-01-01

    We study the kernel and cokernel of the Frobenius map on the p-typical Witt vectors of a commutative ring, not necessarily of characteristic p. We give many equivalent conditions to surjectivity of the Frobenius map on both finite and infinite length Witt vectors. In particular, surjectivity on f...

  10. Vectors on the Basketball Court

    Science.gov (United States)

    Bergman, Daniel

    2010-01-01

    An Idea Bank published in the April/May 2009 issue of "The Science Teacher" describes an experiential physics lesson on vectors and vector addition (Brown 2009). Like its football predecessor, the basketball-based investigation presented in this Idea Bank addresses National Science Education Standards Content B, Physical Science, 9-12 (NRC 1996)…

  11. The Neural Support Vector Machine

    NARCIS (Netherlands)

    Wiering, Marco; van der Ree, Michiel; Embrechts, Mark; Stollenga, Marijn; Meijster, Arnold; Nolte, A; Schomaker, Lambertus

    2013-01-01

    This paper describes a new machine learning algorithm for regression and dimensionality reduction tasks. The Neural Support Vector Machine (NSVM) is a hybrid learning algorithm consisting of neural networks and support vector machines (SVMs). The output of the NSVM is given by SVMs that take a

  12. GPU Accelerated Vector Median Filter

    Science.gov (United States)

    Aras, Rifat; Shen, Yuzhong

    2011-01-01

    Noise reduction is an important step for most image processing tasks. For three channel color images, a widely used technique is vector median filter in which color values of pixels are treated as 3-component vectors. Vector median filters are computationally expensive; for a window size of n x n, each of the n(sup 2) vectors has to be compared with other n(sup 2) - 1 vectors in distances. General purpose computation on graphics processing units (GPUs) is the paradigm of utilizing high-performance many-core GPU architectures for computation tasks that are normally handled by CPUs. In this work. NVIDIA's Compute Unified Device Architecture (CUDA) paradigm is used to accelerate vector median filtering. which has to the best of our knowledge never been done before. The performance of GPU accelerated vector median filter is compared to that of the CPU and MPI-based versions for different image and window sizes, Initial findings of the study showed 100x improvement of performance of vector median filter implementation on GPUs over CPU implementations and further speed-up is expected after more extensive optimizations of the GPU algorithm .

  13. Emerging vector borne diseases – incidence through vectors

    Directory of Open Access Journals (Sweden)

    Sara eSavic

    2014-12-01

    Full Text Available Vector borne diseases use to be a major public health concern only in tropical and subtropical areas, but today they are an emerging threat for the continental and developed countries also. Nowdays, in intercontinetal countries, there is a struggle with emerging diseases which have found their way to appear through vectors. Vector borne zoonotic diseases occur when vectors, animal hosts, climate conditions, pathogens and susceptible human population exist at the same time, at the same place. Global climate change is predicted to lead to an increase in vector borne infectious diseases and disease outbreaks. It could affect the range and popultion of pathogens, host and vectors, transmission season, etc. Reliable surveilance for diseases that are most likely to emerge is required. Canine vector borne diseases represent a complex group of diseases including anaplasmosis, babesiosis, bartonellosis, borreliosis, dirofilariosis, erlichiosis, leishmaniosis. Some of these diseases cause serious clinical symptoms in dogs and some of them have a zoonotic potential with an effect to public health. It is expected from veterinarians in coordination with medical doctors to play a fudamental role at primeraly prevention and then treatment of vector borne diseases in dogs. The One Health concept has to be integrated into the struggle against emerging diseases.During a four year period, from 2009-2013, a total number of 551 dog samples were analysed for vector borne diseases (borreliosis, babesiosis, erlichiosis, anaplasmosis, dirofilariosis and leishmaniasis in routine laboratory work. The analysis were done by serological tests – ELISA for borreliosis, dirofilariosis and leishmaniasis, modified Knott test for dirofilariosis and blood smear for babesiosis, erlichiosis and anaplasmosis. This number of samples represented 75% of total number of samples that were sent for analysis for different diseases in dogs. Annually, on avarege more then half of the samples

  14. Identification and Characterization of Enhancer-Blocking Insulators to Reduce Retroviral Vector Genotoxicity

    Science.gov (United States)

    Wang, Hao; Lovelett, Emilie; Emery, David W.

    2013-01-01

    The chromatin insulator cHS4 can reduce silencing chromosomal position effects and genotoxicity associated with integrating viral vectors. However, the fully active version of this element can also reduce vector titers and is only partially effective. In order to identify alternatives to cHS4, we developed a functional lentiviral vector-based reporter screen for enhancer-blocking insulators. Using this system, we screened candidate sequences that were initially identified by chromatin profiling for binding by CTCF and for DNase hypersensitivity. All 12 analyzed candidates blocked enhancer-promoter activity. The enhancer-blocking activity of the top two candidates was confirmed in two complementary plasmid-based assays. Studies in a gammaretroviral reporter vector indicated these two candidates have little to no effect on vector titers, and do not diminish vector expression in primary mouse bone marrow cultures. Subsequent assessment in a mouse in vivo tumor formation model demonstrated that both candidates reduced the rate of gammaretroviral vector-mediated genotoxicity as effectively as the cHS4 insulator. In summary, we have developed a novel lentiviral vector-based method of screening candidate elements for insulator activity, and have used this method to identify two new insulator elements capable of improving the safety of retroviral vectors without diminishing vector titers or expression. These findings expand the limited arsenal of insulators functionally validated to reduce the rate of retroviral vector-mediated genotoxicity. PMID:24098520

  15. Identification and characterization of enhancer-blocking insulators to reduce retroviral vector genotoxicity.

    Directory of Open Access Journals (Sweden)

    Amy C Groth

    Full Text Available The chromatin insulator cHS4 can reduce silencing chromosomal position effects and genotoxicity associated with integrating viral vectors. However, the fully active version of this element can also reduce vector titers and is only partially effective. In order to identify alternatives to cHS4, we developed a functional lentiviral vector-based reporter screen for enhancer-blocking insulators. Using this system, we screened candidate sequences that were initially identified by chromatin profiling for binding by CTCF and for DNase hypersensitivity. All 12 analyzed candidates blocked enhancer-promoter activity. The enhancer-blocking activity of the top two candidates was confirmed in two complementary plasmid-based assays. Studies in a gammaretroviral reporter vector indicated these two candidates have little to no effect on vector titers, and do not diminish vector expression in primary mouse bone marrow cultures. Subsequent assessment in a mouse in vivo tumor formation model demonstrated that both candidates reduced the rate of gammaretroviral vector-mediated genotoxicity as effectively as the cHS4 insulator. In summary, we have developed a novel lentiviral vector-based method of screening candidate elements for insulator activity, and have used this method to identify two new insulator elements capable of improving the safety of retroviral vectors without diminishing vector titers or expression. These findings expand the limited arsenal of insulators functionally validated to reduce the rate of retroviral vector-mediated genotoxicity.

  16. Source-specific Informative Prior for i-Vector Extraction

    DEFF Research Database (Denmark)

    Shepstone, Sven Ewan; Lee, Kong Aik; Li, Haizhou

    2015-01-01

    An i-vector is a low-dimensional fixed-length representation of a variable-length speech utterance, and is defined as the posterior mean of a latent variable conditioned on the observed feature sequence of an utterance. The assumption is that the prior for the latent variable is non-informative......, since for homogeneous datasets there is no gain in generality in using an informative prior. This work shows that extracting i-vectors for a heterogeneous dataset, containing speech samples recorded from multiple sources, using informative priors instead is applicable, and leads to favorable results...

  17. Stable piecewise polynomial vector fields

    Directory of Open Access Journals (Sweden)

    Claudio Pessoa

    2012-09-01

    Full Text Available Let $N={y>0}$ and $S={y<0}$ be the semi-planes of $mathbb{R}^2$ having as common boundary the line $D={y=0}$. Let $X$ and $Y$ be polynomial vector fields defined in $N$ and $S$, respectively, leading to a discontinuous piecewise polynomial vector field $Z=(X,Y$. This work pursues the stability and the transition analysis of solutions of $Z$ between $N$ and $S$, started by Filippov (1988 and Kozlova (1984 and reformulated by Sotomayor-Teixeira (1995 in terms of the regularization method. This method consists in analyzing a one parameter family of continuous vector fields $Z_{epsilon}$, defined by averaging $X$ and $Y$. This family approaches $Z$ when the parameter goes to zero. The results of Sotomayor-Teixeira and Sotomayor-Machado (2002 providing conditions on $(X,Y$ for the regularized vector fields to be structurally stable on planar compact connected regions are extended to discontinuous piecewise polynomial vector fields on $mathbb{R}^2$. Pertinent genericity results for vector fields satisfying the above stability conditions are also extended to the present case. A procedure for the study of discontinuous piecewise vector fields at infinity through a compactification is proposed here.

  18. Chikungunya Virus–Vector Interactions

    Directory of Open Access Journals (Sweden)

    Lark L. Coffey

    2014-11-01

    Full Text Available Chikungunya virus (CHIKV is a mosquito-borne alphavirus that causes chikungunya fever, a severe, debilitating disease that often produces chronic arthralgia. Since 2004, CHIKV has emerged in Africa, Indian Ocean islands, Asia, Europe, and the Americas, causing millions of human infections. Central to understanding CHIKV emergence is knowledge of the natural ecology of transmission and vector infection dynamics. This review presents current understanding of CHIKV infection dynamics in mosquito vectors and its relationship to human disease emergence. The following topics are reviewed: CHIKV infection and vector life history traits including transmission cycles, genetic origins, distribution, emergence and spread, dispersal, vector competence, vector immunity and microbial interactions, and co-infection by CHIKV and other arboviruses. The genetics of vector susceptibility and host range changes, population heterogeneity and selection for the fittest viral genomes, dual host cycling and its impact on CHIKV adaptation, viral bottlenecks and intrahost diversity, and adaptive constraints on CHIKV evolution are also discussed. The potential for CHIKV re-emergence and expansion into new areas and prospects for prevention via vector control are also briefly reviewed.

  19. Chikungunya Virus–Vector Interactions

    Science.gov (United States)

    Coffey, Lark L.; Failloux, Anna-Bella; Weaver, Scott C.

    2014-01-01

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes chikungunya fever, a severe, debilitating disease that often produces chronic arthralgia. Since 2004, CHIKV has emerged in Africa, Indian Ocean islands, Asia, Europe, and the Americas, causing millions of human infections. Central to understanding CHIKV emergence is knowledge of the natural ecology of transmission and vector infection dynamics. This review presents current understanding of CHIKV infection dynamics in mosquito vectors and its relationship to human disease emergence. The following topics are reviewed: CHIKV infection and vector life history traits including transmission cycles, genetic origins, distribution, emergence and spread, dispersal, vector competence, vector immunity and microbial interactions, and co-infection by CHIKV and other arboviruses. The genetics of vector susceptibility and host range changes, population heterogeneity and selection for the fittest viral genomes, dual host cycling and its impact on CHIKV adaptation, viral bottlenecks and intrahost diversity, and adaptive constraints on CHIKV evolution are also discussed. The potential for CHIKV re-emergence and expansion into new areas and prospects for prevention via vector control are also briefly reviewed. PMID:25421891

  20. Construction of RNAi lentiviral vector targeting mouse Islet-1 gene

    Directory of Open Access Journals (Sweden)

    Shen-shen ZHI

    2011-02-01

    Full Text Available Objective To construct and select RNAi lentiviral vectors that can silence mouse Islet-1 gene effectively.Methods Three groups of RNAi-target of mouse Islet-1 gene were designed,and corresponding shRNA oligo(sh1,sh2 and sh3 were synthesized,and then they were respectively inserted to the PLVTHM vector that had been digested by endonuclease.Agarose gel electrophoresis and sequencing were used to select and indentify the positive clones.The positive clones were extracted and then mixed with E.coli to amplify positive clones.The amplified clones were then infected into 293T along with the other 3 helper plasmids to produce lentiviral vector.After the construction of the lentiviral vector,plaque formation test was performed to determine the titer of lentiviral vector.The lentiviral vectors were then infected into C3H10T1/2 cells.The transfect efficiency of the lentiviral vectors was determined with flow cytometry with detection of green fluorescent protein(GFP.Q-PCR was employed to detect the RNAi efficiency of the lentiviral vectors.Results Agarose gel electrophoresis analysis showed that the clones with right gene at the target size were successfully established;gene sequencing showed that the right DNA fragments had been inserted;plaque formation test showed that the titer of the virus solution was 3.87×108TU/ml;the transfect efficiency of the lentiviral vector infected into C3H10T1/2 cells was 90.36%.All the 3 groups of shRNA targets(sh1,sh2 and sh3 showed an inhibitory effect on Islet-1 gene,and the sh1 showed the highest inhibitory effect(76.8%,as compared with that of normal cells(P < 0.05.Conclusion The RNAi lentiviral vector that can effectively silence the mouse Islet-1 gene has been constructed successfully,which may lay a foundation for further investigation of Islet-1 gene.

  1. Insecticide resistance status of malaria vectors in Lao PDR.

    Science.gov (United States)

    Marcombe, Sébastien; Bobichon, Julie; Somphong, Boutsady; Phommavan, Nothasin; Maithaviphet, Santi; Nambanya, Simone; Corbel, Vincent; Brey, Paul T

    2017-01-01

    Knowledge on insecticide resistance in Anopheles species is a basic requirement to guide malaria vector control programs. In Lao PDR, vector control relies on insecticide residual spraying (IRS) and impregnated bed-nets (ITNs) with the use of pyrethroids. Here, the susceptibility of Anopheles species, including several malaria vectors (An. maculatus and An. minimus), to various insecticides was investigated in ten provinces of Lao PDR through a north-south transect. Bioassays were performed on field caught female mosquitoes using the standard WHO susceptibility tests with DDT (4%), deltamethrin (0.05%) and permethrin (0.75%). In addition, the DIIS6 region of the para-type sodium channel gene was amplified and sequenced to identify knockdown resistance mutations (kdr). Resistance to DDT and permethrin was detected in suspected malaria vectors, such as An. nivipes and An. philippinensis in Lao PDR. Resistance to the formerly used DDT was found in a population of An. maculatus s.l. from Luang Prabang province. No resistance to pyrethroids was found in primary vectors, indicating that these insecticides are still adequate for malaria vector control. However, high resistance levels to pyrethroids was found in-vector species and reduced susceptibility to permethrin in An. minimus and An. maculatus was reported in specific localities which raises concerns for pyrethroid-based control in the future. No kdr mutation was found in any of the resistant populations tested hence suggesting a probable role detoxification enzymes in resistance. This study highlights the necessity to continue the monitoring of insecticide susceptibility to early detect potential occurrence and/or migration of insecticide resistance in malaria vectors in Lao PDR.

  2. Insecticide resistance status of malaria vectors in Lao PDR.

    Directory of Open Access Journals (Sweden)

    Sébastien Marcombe

    Full Text Available Knowledge on insecticide resistance in Anopheles species is a basic requirement to guide malaria vector control programs. In Lao PDR, vector control relies on insecticide residual spraying (IRS and impregnated bed-nets (ITNs with the use of pyrethroids. Here, the susceptibility of Anopheles species, including several malaria vectors (An. maculatus and An. minimus, to various insecticides was investigated in ten provinces of Lao PDR through a north-south transect. Bioassays were performed on field caught female mosquitoes using the standard WHO susceptibility tests with DDT (4%, deltamethrin (0.05% and permethrin (0.75%. In addition, the DIIS6 region of the para-type sodium channel gene was amplified and sequenced to identify knockdown resistance mutations (kdr. Resistance to DDT and permethrin was detected in suspected malaria vectors, such as An. nivipes and An. philippinensis in Lao PDR. Resistance to the formerly used DDT was found in a population of An. maculatus s.l. from Luang Prabang province. No resistance to pyrethroids was found in primary vectors, indicating that these insecticides are still adequate for malaria vector control. However, high resistance levels to pyrethroids was found in-vector species and reduced susceptibility to permethrin in An. minimus and An. maculatus was reported in specific localities which raises concerns for pyrethroid-based control in the future. No kdr mutation was found in any of the resistant populations tested hence suggesting a probable role detoxification enzymes in resistance. This study highlights the necessity to continue the monitoring of insecticide susceptibility to early detect potential occurrence and/or migration of insecticide resistance in malaria vectors in Lao PDR.

  3. Malaria vectors of Timor-Leste.

    Science.gov (United States)

    Cooper, Robert D; Edstein, Michael D; Frances, Stephen P; Beebe, Nigel W

    2010-02-02

    The island of Timor lies at the south-eastern edge of Indonesia on the boundary of the Oriental and Australian faunal regions. The country of Timor-Leste, which occupies the eastern part of the island, is malarious, but anopheline faunal surveys and malaria vector incrimination date back to the 1960 s. Over the last decade the malaria vectors of south-east Asia and the south-west Pacific have been intensely studied using molecular techniques that can confirm identification within complexes of isomorphic species. The aim of this study is to accurately identify the Anopheles fauna of Timor-Leste using these techniques. The survey was carried out over the period February to June 2001. Standard entomological techniques--human landing collections, larval collections and CO2 baited light traps--were used to collect anophelines from the main geographical regions: coastal plains, inland plains, and highlands. Specimens were processed for identification by morphology and genotyped for the ribosomal DNA ITS2 by restriction analysis and/or DNA sequencing. Phylogenetic relationship of Anopheles sundaicus and Anopheles subpictus individuals was also assessed using DNA sequences from the ITS2 and mitochondrial cytochrome-b. All specimens, other than those from larval surveys, were processed to detect the presence of the Plasmodium parasite circumsporozoite protein by ELISA for vector incrimination. Of 2,030 specimens collected, seven species were identified by morphology: Anopheles barbirostris, Anopheles aconitus, Anopheles annularis, Anopheles maculatus, Anopheles peditaeniatus, An. sundaicus and Anopheles vagus. These were confirmed by molecular analysis with the addition of Anopheles flavirostris and an unidentified species designated here as An. vagus genotype B. This latter species was morphologically similar to An. vagus and An. subpictus and is likely to be the An. subpictus described by other workers for Timor. However, genetically this species showed strong affinities

  4. Malaria vectors of Timor-Leste

    Directory of Open Access Journals (Sweden)

    Frances Stephen P

    2010-02-01

    Full Text Available Abstract Background The island of Timor lies at the south-eastern edge of Indonesia on the boundary of the Oriental and Australian faunal regions. The country of Timor-Leste, which occupies the eastern part of the island, is malarious but anopheline faunal surveys and malaria vector incrimination date back to the 1960 s. Over the last decade the malaria vectors of south-east Asia and the south-west Pacific have been intensely studied using molecular techniques that can confirm identification within complexes of isomorphic species. The aim of this study is to accurately identify the Anopheles fauna of Timor-Leste using these techniques. Methods The survey was carried out over the period February to June 2001. Standard entomological techniques - human landing collections, larval collections and CO2 baited light traps - were used to collect anophelines from the main geographical regions: coastal plains, inland plains, and highlands. Specimens were processed for identification by morphology and genotyped for the ribosomal DNA ITS2 by restriction analysis and/or DNA sequencing. Phylogenetic relationship of Anopheles sundaicus and Anopheles subpictus individuals was also assessed using DNA sequences from the ITS2 and mitochondrial cytochrome-b. All specimens, other than those from larval surveys, were processed to detect the presence of the Plasmodium parasite circumsporozoite protein by ELISA for vector incrimination. Results Of 2,030 specimens collected, seven species were identified by morphology: Anopheles barbirostris, Anopheles aconitus, Anopheles annularis, Anopheles maculatus, Anopheles peditaeniatus, An. sundaicus and Anopheles vagus. These were confirmed by molecular analysis with the addition of Anopheles flavirostris and an unidentified species designated here as An. vagus genotype B. This latter species was morphologically similar to An. vagus and An. subpictus and is likely to be the An. subpictus described by other workers for Timor

  5. Emerging Vector-Borne Diseases - Incidence through Vectors.

    Science.gov (United States)

    Savić, Sara; Vidić, Branka; Grgić, Zivoslav; Potkonjak, Aleksandar; Spasojevic, Ljubica

    2014-01-01

    Vector-borne diseases use to be a major public health concern only in tropical and subtropical areas, but today they are an emerging threat for the continental and developed countries also. Nowadays, in intercontinental countries, there is a struggle with emerging diseases, which have found their way to appear through vectors. Vector-borne zoonotic diseases occur when vectors, animal hosts, climate conditions, pathogens, and susceptible human population exist at the same time, at the same place. Global climate change is predicted to lead to an increase in vector-borne infectious diseases and disease outbreaks. It could affect the range and population of pathogens, host and vectors, transmission season, etc. Reliable surveillance for diseases that are most likely to emerge is required. Canine vector-borne diseases represent a complex group of diseases including anaplasmosis, babesiosis, bartonellosis, borreliosis, dirofilariosis, ehrlichiosis, and leishmaniosis. Some of these diseases cause serious clinical symptoms in dogs and some of them have a zoonotic potential with an effect to public health. It is expected from veterinarians in coordination with medical doctors to play a fundamental role at primarily prevention and then treatment of vector-borne diseases in dogs. The One Health concept has to be integrated into the struggle against emerging diseases. During a 4-year period, from 2009 to 2013, a total number of 551 dog samples were analyzed for vector-borne diseases (borreliosis, babesiosis, ehrlichiosis, anaplasmosis, dirofilariosis, and leishmaniasis) in routine laboratory work. The analysis was done by serological tests - ELISA for borreliosis, dirofilariosis, and leishmaniasis, modified Knott test for dirofilariosis, and blood smear for babesiosis, ehrlichiosis, and anaplasmosis. This number of samples represented 75% of total number of samples that were sent for analysis for different diseases in dogs. Annually, on average more then half of the samples

  6. Vector control of induction machines

    CERN Document Server

    Robyns, Benoit

    2012-01-01

    After a brief introduction to the main law of physics and fundamental concepts inherent in electromechanical conversion, ""Vector Control of Induction Machines"" introduces the standard mathematical models for induction machines - whichever rotor technology is used - as well as several squirrel-cage induction machine vector-control strategies. The use of causal ordering graphs allows systematization of the design stage, as well as standardization of the structure of control devices. ""Vector Control of Induction Machines"" suggests a unique approach aimed at reducing parameter sensitivity for

  7. Vector boson scattering at CLIC

    Energy Technology Data Exchange (ETDEWEB)

    Kilian, Wolfgang; Fleper, Christian [Department Physik, Universitaet Siegen, 57068 Siegen (Germany); Reuter, Juergen [DESY Theory Group, 22603 Hamburg (Germany); Sekulla, Marco [Institut fuer Theoretische Physik, Karlsruher Institut fuer Technologie, 76131 Karlsruhe (Germany)

    2016-07-01

    Linear colliders operating in a range of multiple TeV are able to investigate the details of vector boson scattering and electroweak symmetry breaking. We calculate cross sections with the Monte Carlo generator WHIZARD for vector boson scattering processes at the future linear e{sup +} e{sup -} collider CLIC. By finding suitable cuts, the vector boson scattering signal processes are isolated from the background. Finally, we are able to determine exclusion sensitivities on the non-Standard Model parameters of the relevant dimension eight operators.

  8. Vector independent transmission of the vector-borne bluetongue virus.

    Science.gov (United States)

    van der Sluijs, Mirjam Tineke Willemijn; de Smit, Abraham J; Moormann, Rob J M

    2016-01-01

    Bluetongue is an economically important disease of ruminants. The causative agent, Bluetongue virus (BTV), is mainly transmitted by insect vectors. This review focuses on vector-free BTV transmission, and its epizootic and economic consequences. Vector-free transmission can either be vertical, from dam to fetus, or horizontal via direct contract. For several BTV-serotypes, vertical (transplacental) transmission has been described, resulting in severe congenital malformations. Transplacental transmission had been mainly associated with live vaccine strains. Yet, the European BTV-8 strain demonstrated a high incidence of transplacental transmission in natural circumstances. The relevance of transplacental transmission for the epizootiology is considered limited, especially in enzootic areas. However, transplacental transmission can have a substantial economic impact due to the loss of progeny. Inactivated vaccines have demonstrated to prevent transplacental transmission. Vector-free horizontal transmission has also been demonstrated. Since direct horizontal transmission requires close contact of animals, it is considered only relevant for within-farm spreading of BTV. The genetic determinants which enable vector-free transmission are present in virus strains circulating in the field. More research into the genetic changes which enable vector-free transmission is essential to better evaluate the risks associated with outbreaks of new BTV serotypes and to design more appropriate control measures.

  9. A 5' Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo.

    Science.gov (United States)

    Lu, Jiamiao; Williams, James A; Luke, Jeremy; Zhang, Feijie; Chu, Kirk; Kay, Mark A

    2017-01-01

    We previously developed a mini-intronic plasmid (MIP) expression system in which the essential bacterial elements for plasmid replication and selection are placed within an engineered intron contained within a universal 5' UTR noncoding exon. Like minicircle DNA plasmids (devoid of bacterial backbone sequences), MIP plasmids overcome transcriptional silencing of the transgene. However, in addition MIP plasmids increase transgene expression by 2 and often >10 times higher than minicircle vectors in vivo and in vitro. Based on these findings, we examined the effects of the MIP intronic sequences in a recombinant adeno-associated virus (AAV) vector system. Recombinant AAV vectors containing an intron with a bacterial replication origin and bacterial selectable marker increased transgene expression by 40 to 100 times in vivo when compared with conventional AAV vectors. Therefore, inclusion of this noncoding exon/intron sequence upstream of the coding region can substantially enhance AAV-mediated gene expression in vivo.

  10. [Construction of Trim6 eukaryotic expression vector and its expression in HEK293 cells].

    Science.gov (United States)

    Sun, Da-Kang; An, Xin-Ye; Hu, Feng-Ai; Li, Cai-Yu; Zheng, Jing

    2011-09-01

    To construct the recombinant eukaryotic expression vector pcDNA3.1 (+)-Trim6, and observe its expression in HEK293T cells in vitro. The total RNA was isolated from HeLa cells. After amplification with reverse transcription polymerase chain reaction (RT-PCR), the target sequences were cloned into the pcDNA3.1(+). The recombinant vector was confirmed by restriction enzyme digestion, PCR and sequencing. Then it was transfected into HEK293T cells.After 24 hours, the Trim6 expression was detected by Western blot. The results of the restriction enzyme digestion, PCR and sequencing confirmed the vector was constructed successfully, and it can express Trim6 protein in HEK293T cells. The vector is constructed successfully, which establishes the foundation for future research on the effect of Trim6.

  11. Predicting the host of influenza viruses based on the word vector

    Directory of Open Access Journals (Sweden)

    Beibei Xu

    2017-07-01

    Full Text Available Newly emerging influenza viruses continue to threaten public health. A rapid determination of the host range of newly discovered influenza viruses would assist in early assessment of their risk. Here, we attempted to predict the host of influenza viruses using the Support Vector Machine (SVM classifier based on the word vector, a new representation and feature extraction method for biological sequences. The results show that the length of the word within the word vector, the sequence type (DNA or protein and the species from which the sequences were derived for generating the word vector all influence the performance of models in predicting the host of influenza viruses. In nearly all cases, the models built on the surface proteins hemagglutinin (HA and neuraminidase (NA (or their genes produced better results than internal influenza proteins (or their genes. The best performance was achieved when the model was built on the HA gene based on word vectors (words of three-letters long generated from DNA sequences of the influenza virus. This results in accuracies of 99.7% for avian, 96.9% for human and 90.6% for swine influenza viruses. Compared to the method of sequence homology best-hit searches using the Basic Local Alignment Search Tool (BLAST, the word vector-based models still need further improvements in predicting the host of influenza A viruses.

  12. Challenges and Prospects for Helper-Dependent Adenoviral Vector-Mediated Gene Therapy

    Directory of Open Access Journals (Sweden)

    Pasquale Piccolo

    2014-04-01

    Full Text Available Helper-dependent adenoviral (HDAd vectors that are devoid of all viral coding sequences are promising non-integrating vectors for gene therapy because they efficiently transduce a variety of cell types in vivo, have a large cloning capacity, and drive long-term transgene expression without chronic toxicity. The main obstacle preventing clinical applications of HDAd vectors is the host innate inflammatory response against the vector capsid proteins that occurs shortly after intravascular vector administration and result in acute toxicity, the severity of which is dose dependent. Intense efforts have been focused on elucidating adenoviral vector–host interactions and the factors involved in the acute toxicity. This review focuses on the recent acquisition of data on such interactions and on strategies investigated to improve the therapeutic index of HDAd vectors.

  13. Introduction to matrices and vectors

    CERN Document Server

    Schwartz, Jacob T

    2001-01-01

    In this concise undergraduate text, the first three chapters present the basics of matrices - in later chapters the author shows how to use vectors and matrices to solve systems of linear equations. 1961 edition.

  14. All optical vector magnetometer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Phase I research project will investigate a novel method of operating an atomic magnetometer to simultaneously measure total magnetic fields and vector magnetic...

  15. GRE Enzymes for Vector Analysis

    Data.gov (United States)

    U.S. Environmental Protection Agency — Microbial enzyme data that were collected during the 2004-2006 EMAP-GRE program. These data were then used by Moorhead et al (2016) in their ecoenzyme vector...

  16. Single-dose protection against Plasmodium berghei by a simian adenovirus vector using a human cytomegalovirus promoter containing intron A.

    Science.gov (United States)

    Sridhar, S; Reyes-Sandoval, A; Draper, S J; Moore, A C; Gilbert, S C; Gao, G P; Wilson, J M; Hill, A V S

    2008-04-01

    Human adenovirus serotype 5 (AdH5) vector vaccines elicit strong immune responses to the encoded antigen and have been used in various disease models. We designed AdH5 vectors expressing antigen under the control of a human cytomegalovirus (HCMV) immediate-early promoter containing its intron A sequence. The transcriptional levels of antigen and immune responses to antigen for vectors with the HCMV promoter with the intron A sequence (LP) were greater than those for AdH5 vectors using the HCMV promoter sequence without intron A (SP). We compared an E1E3-deleted AdH5 adenoviral vector, which affords more space for insertion of foreign sequences, and showed it to be as immunogenic as an E1-deleted AdH5 vector. Neutralizing antibodies to AdH5 limit the efficacy of vaccines based on the AdH5 serotype, and simian adenoviral vectors offer an attractive option to overcome this problem. We constructed E1E3-deleted human and simian adenoviral vectors encoding the pre-erythrocytic-stage malarial antigen Plasmodium berghei circumsporozoite protein. We compared the immunogenicity and efficacy of AdC6, a recombinant simian adenovirus serotype 6 vector, in a murine malaria model to those of AdH5 and the poxviral vectors MVA and FP9. AdC6 induced sterile protection from a single dose in 90% of mice, in contrast to AdH5 (25%) and poxviral vectors MVA and FP9 (0%). Adenoviral vectors maintained potent CD8(+) T-cell responses for a longer period after immunization than did poxviral vectors and mainly induced an effector memory phenotype of cells. Significantly, AdC6 was able to maintain protection in the presence of preexisting immunity to AdH5.

  17. A Note on Vector Bimeasures.

    Science.gov (United States)

    1987-11-01

    Phrases: N/A ] 19 RCT lontilue on revrm if necozsary and identify by block number) •"SA Fubini type theorem is obtained for vector bimasure integrals...Abstract A Fubini type theorem is obtained for vector bimeasure integrals. AMS (1980) subject classification: Primary 28B05; Secondary 60G12...Ylinen [11]. In the works mentioned above the authors consistently impose, in their definition of integrability. a Fubini type condition which cannot

  18. The Evolutionary Origin of Diversity in Chagas Disease Vectors.

    Science.gov (United States)

    Justi, Silvia A; Galvão, Cleber

    2017-01-01

    Chagas disease is amongst the ten most important neglected tropical diseases but knowledge on the diversification of its vectors, Triatominae (Hemiptera: Reduviidae), is very scarce. Most Triatominae species occur in the Americas, and are all considered potential vectors. Despite its amazing ecological vignette, there are remarkably few evolutionary studies of the whole subfamily, and only one genome sequence has been published. The young age of the subfamily, coupled with the high number of independent lineages, are intriguing, yet the lack of genome-wide data makes it a challenge to infer the phylogenetic relationships within Triatominae. Here we synthesize what is known, and suggest the next steps towards a better understanding of how this important group of disease vectors came to be. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. In Vivo 3-D Vector Velocity Estimation with Continuous Data

    DEFF Research Database (Denmark)

    Holbek, Simon; Pihl, Michael Johannes; Ewertsen, Caroline

    2015-01-01

    In this study, a method for estimating 3-D vector velocities at very high frame rate using continuous data acquisition is presented. An emission sequence was designed to acquire real-time continuous data in one plane. The transverse oscillation (TO) method was used to estimate 3-D vector flow...... measurements, three heart cycles acquired at 2.1 kHz showed peak out-of-plane velocities of 83 cm/s, 87 cm/s and 90 cm/s in agreement with the 92 cm/s found with spectral Doppler. Mean flow rate was estimated to 257 ml/min. The results demonstrate that accurate real-time 3- D vector velocities can be obtained...

  20. In Vivo High Frame Rate Vector Flow Imaging Using Plane Waves and Directional Beamforming

    DEFF Research Database (Denmark)

    Jensen, Jonas; Villagómez Hoyos, Carlos Armando; Stuart, Matthias Bo

    2016-01-01

    oscillation (TO) estimators and only 3 directional beamformed lines. The suggested DB vector flow estimator is employed with steered plane wave transmissions for high frame rate imaging.Two distinct plane wave sequences are used: a short sequence(3 angles) for fast flow and an interleaved long sequence (21....... The long sequence has a higher sensitivity, and when used forestimation of slow flow with a peak velocity of 0.04 m/s, the SDis 2.5 % and bias is 0.1 %. This is a factor of 4 better than ifthe short sequence is used. The carotid bifurcation was scanned on a healthy volunteer, and the short sequence...

  1. Predicting Solar Flares Using SDO/HMI Vector Magnetic Data Products and the Random Forest Algorithm

    Science.gov (United States)

    Liu, Chang; Deng, Na; Wang, Jason T. L.; Wang, Haimin

    2017-07-01

    Adverse space-weather effects can often be traced to solar flares, the prediction of which has drawn significant research interests. The Helioseismic and Magnetic Imager (HMI) produces full-disk vector magnetograms with continuous high cadence, while flare prediction efforts utilizing this unprecedented data source are still limited. Here we report results of flare prediction using physical parameters provided by the Space-weather HMI Active Region Patches (SHARP) and related data products. We survey X-ray flares that occurred from 2010 May to 2016 December and categorize their source regions into four classes (B, C, M, and X) according to the maximum GOES magnitude of flares they generated. We then retrieve SHARP-related parameters for each selected region at the beginning of its flare date to build a database. Finally, we train a machine-learning algorithm, called random forest (RF), to predict the occurrence of a certain class of flares in a given active region within 24 hr, evaluate the classifier performance using the 10-fold cross-validation scheme, and characterize the results using standard performance metrics. Compared to previous works, our experiments indicate that using the HMI parameters and RF is a valid method for flare forecasting with fairly reasonable prediction performance. To our knowledge, this is the first time that RF has been used to make multiclass predictions of solar flares. We also find that the total unsigned quantities of vertical current, current helicity, and flux near the polarity inversion line are among the most important parameters for classifying flaring regions into different classes.

  2. VectorBase: a home for invertebrate vectors of human pathogens

    Science.gov (United States)

    Lawson, Daniel; Arensburger, Peter; Atkinson, Peter; Besansky, Nora J.; Bruggner, Robert V.; Butler, Ryan; Campbell, Kathryn S.; Christophides, George K.; Christley, Scott; Dialynas, Emmanuel; Emmert, David; Hammond, Martin; Hill, Catherine A.; Kennedy, Ryan C.; Lobo, Neil F.; MacCallum, M. Robert; Madey, Greg; Megy, Karine; Redmond, Seth; Russo, Susan; Severson, David W.; Stinson, Eric O.; Topalis, Pantelis; Zdobnov, Evgeny M.; Birney, Ewan; Gelbart, William M.; Kafatos, Fotis C.; Louis, Christos; Collins, Frank H.

    2007-01-01

    VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. PMID:17145709

  3. Decays of the vector glueball

    Science.gov (United States)

    Giacosa, Francesco; Sammet, Julia; Janowski, Stanislaus

    2017-06-01

    We calculate two- and three-body decays of the (lightest) vector glueball into (pseudo)scalar, (axial-)vector, as well as pseudovector and excited vector mesons in the framework of a model of QCD. While absolute values of widths cannot be predicted because the corresponding coupling constants are unknown, some interesting branching ratios can be evaluated by setting the mass of the yet hypothetical vector glueball to 3.8 GeV as predicted by quenched lattice QCD. We find that the decay mode ω π π should be one of the largest (both through the decay chain O →b1π →ω π π and through the direct coupling O →ω π π ). Similarly, the (direct and indirect) decay into π K K*(892 ) is sizable. Moreover, the decays into ρ π and K*(892 )K are, although subleading, possible and could play a role in explaining the ρ π puzzle of the charmonium state ψ (2 S ) thanks to a (small) mixing with the vector glueball. The vector glueball can be directly formed at the ongoing BESIII experiment as well as at the future PANDA experiment at the FAIR facility. If the width is sufficiently small (≲100 MeV ) it should not escape future detection. It should be stressed that the employed model is based on some inputs and simplifying assumptions: the value of glueball mass (at present, the quenched lattice value is used), the lack of mixing of the glueball with other quarkonium states, and the use of few interaction terms. It then represents a first step toward the identification of the main decay channels of the vector glueball, but shall be improved when corresponding experimental candidates and/or new lattice results will be available.

  4. The biological control of disease vectors.

    Science.gov (United States)

    Okamoto, Kenichi W; Amarasekare, Priyanga

    2012-09-21

    Vector-borne diseases are common in nature and can have a large impact on humans, livestock and crops. Biological control of vectors using natural enemies or competitors can reduce vector density and hence disease transmission. However, the indirect interactions inherent in host-vector disease systems make it difficult to use traditional pest control theory to guide biological control of disease vectors. This necessitates a conceptual framework that explicitly considers a range of indirect interactions between the host-vector disease system and the vector's biological control agent. Here we conduct a comparative analysis of the efficacy of different types of biological control agents in controlling vector-borne diseases. We report three key findings. First, highly efficient predators and parasitoids of the vector prove to be effective biological control agents, but highly virulent pathogens of the vector also require a high transmission rate to be effective. Second, biocontrol agents can successfully reduce long-term host disease incidence even though they may fail to reduce long-term vector densities. Third, inundating a host-vector disease system with a natural enemy of the vector has little or no effect on reducing disease incidence, but inundating the system with a competitor of the vector has a large effect on reducing disease incidence. The comparative framework yields predictions that are useful in developing biological control strategies for vector-borne diseases. We discuss how these predictions can inform ongoing biological control efforts for host-vector disease systems. Copyright © 2012. Published by Elsevier Ltd.

  5. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    Full Text Available Abstract Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on

  6. Main: Sequences [KOME

    Lifescience Database Archive (English)

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

  7. Zika Virus Mosquito Vectors: Competence, Biology, and Vector Control.

    Science.gov (United States)

    Kauffman, Elizabeth B; Kramer, Laura D

    2017-12-16

    Zika virus (ZIKV) (Flaviviridae, Flavivirus) has become one of the most medically important mosquito-borne viruses because of its ability to cause microcephaly in utero and Guillain-Barré syndrome in adults. This virus emerged from its sylvatic cycle in Africa to cause an outbreak in Yap, Federated States of Micronesia in 2007, French Polynesia in 2014, and most recently South America in 2015. The rapid expansion of ZIKV in the Americas largely has been due to the biology and behavior of its vector, Aedes aegypti. Other arboviruses transmitted by Ae. aegypti include the 2 flaviviruses dengue virus and yellow fever virus and the alphavirus chikungunya virus, which are also (re)emerging viruses in the Americas. This mosquito vector is highly domesticated, living in close association with humans in urban households. Its eggs are desiccation resistant, and the larvae develop rapidly in subtropical and tropical environments. Climate warming is facilitating range expansion of Ae. aegypti, adding to the threat this mosquito poses to human health, especially in light of the difficulty controlling it. Aedes albopictus, another highly invasive arbovirus vector that has only been implicated in one country (Gabon), is an important vector of ZIKV, but because of its wide geographic distribution may become a more important vector in the future. This article discusses the historical background of ZIKV and the biology and ecology of these 2 vectors. © The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  8. Transposon-containing DNA cloning vector and uses thereof

    Science.gov (United States)

    Berg, Claire M.; Berg, Douglas E.; Wang, Gan

    1997-01-01

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed.

  9. Vector sequences - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available //) != -1 ) { url = url.replace(/contents/,/contents-en/); document.getElementById(lang).innerHTML=[ Japanes...e(/contents-en/,/contents/); document.getElementById(lang).innerHTML=[ Japanese | English ]; } else if( url....search(/contents-en/) != -1 || url.search(/index-e.html/) != -1 ) { document.getElementById(lang).innerHTML=...h)-e.html/) != -1 ) { url = url.replace(-e.html,.html); document.getElementById(lang).innerHTML=[ Japanese |... English ]; } else { document.getElementById(lang).innerHTML= '[ Japanese | English ]'; } } window.onload =

  10. Generalized Selection Weighted Vector Filters

    Directory of Open Access Journals (Sweden)

    Rastislav Lukac

    2004-09-01

    Full Text Available This paper introduces a class of nonlinear multichannel filters capable of removing impulsive noise in color images. The here-proposed generalized selection weighted vector filter class constitutes a powerful filtering framework for multichannel signal processing. Previously defined multichannel filters such as vector median filter, basic vector directional filter, directional-distance filter, weighted vector median filters, and weighted vector directional filters are treated from a global viewpoint using the proposed framework. Robust order-statistic concepts and increased degree of freedom in filter design make the proposed method attractive for a variety of applications. Introduced multichannel sigmoidal adaptation of the filter parameters and its modifications allow to accommodate the filter parameters to varying signal and noise statistics. Simulation studies reported in this paper indicate that the proposed filter class is computationally attractive, yields excellent performance, and is able to preserve fine details and color information while efficiently suppressing impulsive noise. This paper is an extended version of the paper by Lukac et al. presented at the 2003 IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP '03 in Grado, Italy.

  11. A generalized nonlocal vector calculus

    Science.gov (United States)

    Alali, Bacim; Liu, Kuo; Gunzburger, Max

    2015-10-01

    A nonlocal vector calculus was introduced in Du et al. (Math Model Meth Appl Sci 23:493-540, 2013) that has proved useful for the analysis of the peridynamics model of nonlocal mechanics and nonlocal diffusion models. A formulation is developed that provides a more general setting for the nonlocal vector calculus that is independent of particular nonlocal models. It is shown that general nonlocal calculus operators are integral operators with specific integral kernels. General nonlocal calculus properties are developed, including nonlocal integration by parts formula and Green's identities. The nonlocal vector calculus introduced in Du et al. (Math Model Meth Appl Sci 23:493-540, 2013) is shown to be recoverable from the general formulation as a special example. This special nonlocal vector calculus is used to reformulate the peridynamics equation of motion in terms of the nonlocal gradient operator and its adjoint. A new example of nonlocal vector calculus operators is introduced, which shows the potential use of the general formulation for general nonlocal models.

  12. Engineering support vector machine kernels that recognize translation initiation sites.

    Science.gov (United States)

    Zien, A; Rätsch, G; Mika, S; Schölkopf, B; Lengauer, T; Müller, K R

    2000-09-01

    In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

  13. An ImprovedBrome mosaic virusSilencing Vector: Greater Insert Stability and More Extensive VIGS.

    Science.gov (United States)

    Ding, Xin Shun; Mannas, Stephen W; Bishop, Bethany A; Rao, Xiaolan; Lecoultre, Mitchell; Kwon, Soonil; Nelson, Richard S

    2018-01-01

    Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus-silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient phenotypes is the instability of the foreign gene fragment (insert) in the vector during VIGS. Here, we report the development of a Brome mosaic virus (BMV)-based vector that better maintains inserts through modification of the original BMV vector RNA sequence. Modification of the BMV RNA3 sequence yielded a vector, BMVCP5, that better maintained phytoene desaturase and heat shock protein70-1 ( HSP70-1 ) inserts in Nicotiana benthamiana and maize ( Zea mays ). Longer maintenance of inserts was correlated with greater target gene silencing and more extensive visible silencing phenotypes displaying greater tissue penetration and involving more leaves. The modified vector accumulated similarly to the original vector in N. benthamiana after agroinfiltration, thus maintaining a high titer of virus in this intermediate host used to produce virus inoculum for grass hosts. For HSP70 , silencing one family member led to a large increase in the expression of another family member, an increase likely related to the target gene knockdown and not a general effect of virus infection. The cause of the increased insert stability in the modified vector is discussed in relationship to its recombination and accumulation potential. The modified vector will improve functional genomic studies in grasses, and the conceptual methods used to improve the vector may be applied to other VIGS vectors. © 2018 American Society of Plant Biologists. All Rights Reserved.

  14. Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries

    Directory of Open Access Journals (Sweden)

    Gray Elizabeth C

    2009-11-01

    Full Text Available Abstract Background In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. Results It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. Conclusion These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The

  15. Synthetic Aperture Vector Flow Imaging

    DEFF Research Database (Denmark)

    Oddershede, Niels

    2008-01-01

    Current ultrasonic blood flow velocity measurement systems are subject to a number of limitations, including limited frame rate, aliasing artifacts, and that only the velocity component along the ultrasound beam is estimated. This dissertation aims at solving some of these problems. The main part...... of the thesis considers a method for estimating the two-dimensional velocity vector within the image plane. This method, called synthetic aperture vector flow imaging, is first shortly reviewed. The main contribution of this work is partly an analysis of the method with respect to focusing effects, motion...... estimation. The method can be used for increasing the frame rate of color flow maps or alternatively for a new imaging modality entitled quadroplex imaging, featuring a color flow map and two independent spectrograms at a high frame rate. The second is an alternative method for ultrasonic vector velocity...

  16. Gauge Theories of Vector Particles

    Science.gov (United States)

    Glashow, S. L.; Gell-Mann, M.

    1961-04-24

    The possibility of generalizing the Yang-Mills trick is examined. Thus we seek theories of vector bosons invariant under continuous groups of coordinate-dependent linear transformations. All such theories may be expressed as superpositions of certain "simple" theories; we show that each "simple theory is associated with a simple Lie algebra. We may introduce mass terms for the vector bosons at the price of destroying the gauge-invariance for coordinate-dependent gauge functions. The theories corresponding to three particular simple Lie algebras - those which admit precisely two commuting quantum numbers - are examined in some detail as examples. One of them might play a role in the physics of the strong interactions if there is an underlying super-symmetry, transcending charge independence, that is badly broken. The intermediate vector boson theory of weak interactions is discussed also. The so-called "schizon" model cannot be made to conform to the requirements of partial gauge-invariance.

  17. 3-D Vector Flow Imaging

    DEFF Research Database (Denmark)

    Holbek, Simon

    ultrasonic vector flow estimation and bring it a step closer to a clinical application. A method for high frame rate 3-D vector flow estimation in a plane using the transverse oscillation method combined with a 1024 channel 2-D matrix array is presented. The proposed method is validated both through phantom......For the last decade, the field of ultrasonic vector flow imaging has gotten an increasingly attention, as the technique offers a variety of new applications for screening and diagnostics of cardiovascular pathologies. The main purpose of this PhD project was therefore to advance the field of 3-D...... hampers the task of real-time processing. In a second study, some of the issue with the 2-D matrix array are solved by introducing a 2-D row-column (RC) addressing array with only 62 + 62 elements. It is investigated both through simulations and via experimental setups in various flow conditions...

  18. Toward lattice fractional vector calculus

    Science.gov (United States)

    Tarasov, Vasily E.

    2014-09-01

    An analog of fractional vector calculus for physical lattice models is suggested. We use an approach based on the models of three-dimensional lattices with long-range inter-particle interactions. The lattice analogs of fractional partial derivatives are represented by kernels of lattice long-range interactions, where the Fourier series transformations of these kernels have a power-law form with respect to wave vector components. In the continuum limit, these lattice partial derivatives give derivatives of non-integer order with respect to coordinates. In the three-dimensional description of the non-local continuum, the fractional differential operators have the form of fractional partial derivatives of the Riesz type. As examples of the applications of the suggested lattice fractional vector calculus, we give lattice models with long-range interactions for the fractional Maxwell equations of non-local continuous media and for the fractional generalization of the Mindlin and Aifantis continuum models of gradient elasticity.

  19. Learning with Support Vector Machines

    CERN Document Server

    Campbell, Colin

    2010-01-01

    Support Vectors Machines have become a well established tool within machine learning. They work well in practice and have now been used across a wide range of applications from recognizing hand-written digits, to face identification, text categorisation, bioinformatics, and database marketing. In this book we give an introductory overview of this subject. We start with a simple Support Vector Machine for performing binary classification before considering multi-class classification and learning in the presence of noise. We show that this framework can be extended to many other scenarios such a

  20. Topological vector spaces and distributions

    CERN Document Server

    Horvath, John

    2012-01-01

    ""The most readable introduction to the theory of vector spaces available in English and possibly any other language.""-J. L. B. Cooper, MathSciNet ReviewMathematically rigorous but user-friendly, this classic treatise discusses major modern contributions to the field of topological vector spaces. The self-contained treatment includes complete proofs for all necessary results from algebra and topology. Suitable for undergraduate mathematics majors with a background in advanced calculus, this volume will also assist professional mathematicians, physicists, and engineers.The precise exposition o

  1. VECTOR MAPS IN MOBILE ROBOTICS

    Directory of Open Access Journals (Sweden)

    Ales Jelinek

    2015-12-01

    Full Text Available The aim of this paper is to provide a brief overview of vector map techniques used in mobile robotics and to present current state of the research in this field at the Brno University of Technology. Vector maps are described as a part of the simultaneous localization and mapping (SLAM problem in the environment without artificial landmarks or global navigation system. The paper describes algorithms from data acquisition to map building but particular emphasis is put on segmentation, line extraction and scan matching algorithms. All significant algorithms are illustrated with experimental results.

  2. Plasmodium prevalence across avian host species is positively associated with exposure to mosquito vectors.

    Science.gov (United States)

    Medeiros, Matthew C I; Ricklefs, Robert E; Brawn, Jeffrey D; Hamer, Gabriel L

    2015-11-01

    The prevalence of vector-borne parasites varies greatly across host species, and this heterogeneity has been used to relate infectious disease susceptibility to host species traits. However, a few empirical studies have directly associated vector-borne parasite prevalence with exposure to vectors across hosts. Here, we use DNA sequencing of blood meals to estimate utilization of different avian host species by Culex mosquitoes, and relate utilization by these malaria vectors to avian Plasmodium prevalence. We found that avian host species that are highly utilized as hosts by avian malaria vectors are significantly more likely to have Plasmodium infections. However, the effect was not consistent among individual Plasmodium taxa. Exposure to vector bites may therefore influence the relative number of all avian Plasmodium infections among host species, while other processes, such as parasite competition and host-parasite coevolution, delimit the host distributions of individual Plasmodium species. We demonstrate that links between avian malaria susceptibility and host traits can be conditioned by patterns of exposure to vectors. Linking vector utilization rates to host traits may be a key area of future research to understand mechanisms that produce variation in the prevalence of vector-borne pathogens among host species.

  3. Mining olive genome through library sequencing and bioinformatics ...

    African Journals Online (AJOL)

    As one of the initial steps of olive (Olea europaea L.) genome analysis, a small insert genomic DNA library was constructed (digesting olive genomic DNA with SmaI and cloning the digestion products into pUC19 vector) and randomly picked 83 colonies were sequenced. Analysis of the insert sequences revealed 12 clones ...

  4. p lambda Zd39: a new type of cDNA expression vector for low background, high efficiency directional cloning.

    OpenAIRE

    Murphy, A J; Schimke, R T

    1991-01-01

    We have developed a new type of bacteriophage lambda vector which provides a strong biological selection against non-recombinants that is independent of the sequences immediately surrounding the cloning site. This system, which we call 'selective substitution', is ideally suited for cDNA expression vectors where it is necessary to flank the cDNA insert with sequence elements (promoters etc.) required to produce a biologically active mRNA in vivo. Selective substitution is a general method, wh...

  5. SCALAR AND VECTOR IN COMPULATION

    Directory of Open Access Journals (Sweden)

    Valery F. Ochkov

    2013-01-01

    Full Text Available The article deals with two fundamental data types – scalar and vector (array, without the ability of working with them one cannot solve using computer school or university tasks in mathematics, physics, chemistry and other technical training courses. Some fundamentals of teaching computer science at school and university are covered as well. 

  6. Disease Vector Ecology Profile: Ecuador

    Science.gov (United States)

    1998-12-01

    species) only during the pupal and adult stages. Formulations of Bacillus thuringiensis israelensis are economical, operationally feasible, and...12. Bees , Wasps and Hornets ..................................................................................31 B. Snakes...epidemic proportions. Transmission of the plague bacillus by fleas is species- specific. Not all fleas are competent vectors. Xenopsylla cheopis is the

  7. Parallel Sparse Matrix - Vector Product

    DEFF Research Database (Denmark)

    Alexandersen, Joe; Lazarov, Boyan Stefanov; Dammann, Bernd

    This technical report contains a case study of a sparse matrix-vector product routine, implemented for parallel execution on a compute cluster with both pure MPI and hybrid MPI-OpenMP solutions. C++ classes for sparse data types were developed and the report shows how these class can be used...

  8. Synthetic Aperture Vector Flow Imaging

    DEFF Research Database (Denmark)

    Villagómez Hoyos, Carlos Armando

    The main objective of this project was to continue the development of a synthetic aperture vector flow estimator. This type of estimator is capable of overcoming two of the major limitations in conventional ultrasound systems: 1) the inability to scan large region of interest with high temporal r...

  9. The consequences of poor vectorization

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    This talk briefly discusses the vectorization problem and how it impacts scientific and engineering systems. A simple cost model of designing such system in context of different phases of software lifetime is considered. Finally a concept for scalable solution is presented.

  10. Constraints in vector meson photoproduction

    Energy Technology Data Exchange (ETDEWEB)

    Kloet, W. M.; Tabakin, F

    2000-01-31

    Constraints are discussed for spin observables extracted from photoproduction of vector mesons. These constraints originate from positivity of the spin density matrix and should be part of any future analysis of experimental data. Spin observables need to be defined in the photon-nucleon c.m. frame.

  11. Constraints in Vector Meson Photoproduction

    Science.gov (United States)

    Kloet, W. M.; Tabakin, F.

    2000-01-01

    Constraints are discussed for spin observables extracted from photoproduction of vector mesons. These constraints originate from positivity of the spin density matrix and should be part of any future analysis of experimental data. Spin observables need to be defined in the photon-nucleon c.m. frame.

  12. On Weighted Support Vector Regression

    DEFF Research Database (Denmark)

    Han, Xixuan; Clemmensen, Line Katrine Harder

    2014-01-01

    We propose a new type of weighted support vector regression (SVR), motivated by modeling local dependencies in time and space in prediction of house prices. The classic weights of the weighted SVR are added to the slack variables in the objective function (OF‐weights). This procedure directly...

  13. Portfolio Analysis for Vector Calculus

    Science.gov (United States)

    Kaplan, Samuel R.

    2015-01-01

    Classic stock portfolio analysis provides an applied context for Lagrange multipliers that undergraduate students appreciate. Although modern methods of portfolio analysis are beyond the scope of vector calculus, classic methods reinforce the utility of this material. This paper discusses how to introduce classic stock portfolio analysis in a…

  14. Large N Expansion. Vector Models

    OpenAIRE

    Nissimov, Emil; Pacheva, Svetlana

    2006-01-01

    Preliminary version of a contribution to the "Quantum Field Theory. Non-Perturbative QFT" topical area of "Modern Encyclopedia of Mathematical Physics" (SELECTA), eds. Aref'eva I, and Sternheimer D, Springer (2007). Consists of two parts - "main article" (Large N Expansion. Vector Models) and a "brief article" (BPHZL Renormalization).

  15. Vector-meson dominance revisited

    Directory of Open Access Journals (Sweden)

    Terschlüsen Carla

    2012-12-01

    Full Text Available The interaction of mesons with electromagnetism is often well described by the concept of vector-meson dominance (VMD. However, there are also examples where VMD fails. A simple chiral Lagrangian for pions, rho and omega mesons is presented which can account for the respective agreement and disagreement between VMD and phenomenology in the sector of light mesons.

  16. Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi

    DEFF Research Database (Denmark)

    Frandsen, Rasmus John Normand; Andersson, Jens A.; Kristensen, Matilde Bylov

    2008-01-01

    Background: The rapid increase in whole genome fungal sequence information allows large scale functional analyses of target genes. Efficient transformation methods to obtain site-directed gene replacement, targeted over-expression by promoter replacement, in-frame epitope tagging or fusion of cod...... with an average efficiency of 84% for gene replacement and 80% for targeted overexpression. Conclusion: The new vectors designed for USER Friendly cloning provided a fast reliable method to construct vectors for targeted gene manipulations in fungi....

  17. Sum rule analysis of vector and axial-vector spectral functions with excited states in vacuum

    OpenAIRE

    Hohler, Paul M.; Rapp, Ralf

    2012-01-01

    We simultaneously analyze vector and axial-vector spectral functions in vacuum using hadronic models constrained by experimental data and the requirement that Weinberg-type sum rules are satisfied. Upon explicit inclusion of an excited vector state, viz. rho', and the requirement that the perturbative continua are degenerate in vector and axial-vector channels, we deduce the existence of an excited axial-vector resonance state, a1', in order that the Weinberg sum rules are satisfied. The resu...

  18. Adeno-Associated Virus Vector-Mediated Transgene Integration into Neurons and Other Nondividing Cell Targets

    OpenAIRE

    WU, Ping; Phillips, M. Ian; Bui, John; Terwilliger, Ernest F.

    1998-01-01

    The site-specific integration of wild-type adeno-associated virus (wtAAV) into the human genome is a very attractive feature for the development of AAV-based gene therapy vectors. However, knowledge about integration of wtAAV, as well as currently configured recombinant AAV (rAAV) vectors, is limited. By using a modified Alu-PCR technique to amplify and sequence the vector-cellular junctions, we provide the first direct evidence both in vitro and in vivo of rAAV-mediated transgene integration...

  19. Complex blood flow quantification using real-time in vivo vector flow ultrasound

    DEFF Research Database (Denmark)

    Pedersen, Mads Møller; Pihl, Michael Johannes; Per, Haugaard

    A new method to define and quantify complex blood flow is presented. The standard deviations of real-time in vivo vector flow angle estimates are used. Using vector flow ultrasound imaging both carotid bifurcations of two healthy volunteers were scanned. Scanning was performed with a 7.6 MHz linear...... transducer (8670, B-K Medical, Denmark) and a commercial vector flow ultrasound scanner (ProFocus 2202, B-K Medical). Eight video sequences of one cardiac cycle were obtained. In every frame boxes were placed to define the common carotid artery(box1) and the carotid bulb(box2). The standard deviation...

  20. Vector variational inequalities and their relations with vector optimization

    Directory of Open Access Journals (Sweden)

    Surjeet Kaur Suneja

    2014-01-01

    Full Text Available In this paper, K- quasiconvex, K- pseudoconvex and other related functions have been introduced in terms of their Clarke subdifferentials, where is an arbitrary closed convex, pointed cone with nonempty interior. The (strict, weakly -pseudomonotonicity, (strict K- naturally quasimonotonicity and K- quasimonotonicity of Clarke subdifferential maps have also been defined. Further, we introduce Minty weak (MVVIP and Stampacchia weak (SVVIP vector variational inequalities over arbitrary cones. Under regularity assumption, we have proved that a weak minimum solution of vector optimization problem (VOP is a solution of (SVVIP and under the condition of K- pseudoconvexity we have obtained the converse for MVVIP (SVVIP. In the end we study the interrelations between these with the help of strict K-naturally quasimonotonicity of Clarke subdifferential map.

  1. Construction and application of epitope- and green fluorescent protein-tagging integration vectors for Bacillus subtilis.

    Science.gov (United States)

    Kaltwasser, Marcus; Wiegert, Thomas; Schumann, Wolfgang

    2002-05-01

    Here we describe the construction and application of six new tagging vectors allowing the fusion of two different types of tagging sequences, epitope and localization tags, to any Bacillus subtilis protein. These vectors are based on the backbone of pMUTIN2 and replace the lacZ gene with tagging sequences. Fusion of the tagging sequences occurs by PCR amplification of the 3' terminal part of the gene of interest (about 300 bp), insertion into the tagging vector in such a way that a fusion protein will be synthesized upon integration of the whole vector via homologous recombination with the chromosomal gene. Three of these tagging sequences (FLAG, hemagglutinin, and c-Myc) allow the covalent addition of a short epitope tag and thereby detection of the fusion proteins in immunoblots, while three other tags (green fluorescent protein(+), yellow fluorescent protein, and cyan fluorescent protein) are helpful in assigning proteins within one of the compartments of the cell. The versatility of these vectors was demonstrated by fusing these tags to the cytoplasmically located HtpG and the inner membrane protein FtsH.

  2. DNA transformations of Candida tropicalis with replicating and integrative vectors.

    Science.gov (United States)

    Sanglard, D; Fiechter, A

    1992-12-01

    The alkane-assimilating yeast Candida tropicalis was used as a host for DNA transformations. A stable ade2 mutant (Ha900) obtained by UV-mutagenesis was used as a recipient for different vectors carrying selectable markers. A first vector, pMK16, that was developed for the transformation of C. albicans and carries an ADE2 gene marker and a Candida autonomously replicating sequence (CARS) element promoting autonomous replication, was compatible for transforming Ha900. Two transformant types were observed: (i) pink transformants which easily lose pMK16 under non-selective growth conditions; (ii) white transformants, in which the same plasmid exhibited a higher mitotic stability. In both cases pMK16 could be rescued from these cells in Escherichia coli. A second vector, pADE2, containing the isolated C. tropicalis ADE2, gene, was used to transform Ha900. This vector integrated in the yeast genome at homologous sites of the ade2 locus. Different integration types were observed at one or both ade2 alleles in single or in tandem repeats.

  3. Vectors expressing chimeric Japanese encephalitis dengue 2 viruses.

    Science.gov (United States)

    Wei, Y; Wang, S; Wang, X

    2014-01-01

    Vectors based on self-replicating RNAs (replicons) of flaviviruses are becoming powerful tool for expression of heterologous genes in mammalian cells and development of novel antiviral and anticancer vaccines. We constructed two vectors expressing chimeric viruses consisting of attenuated SA14-14-2 strain of Japanese encephalitis virus (JEV) in which the PrM/M-E genes were replaced fully or partially with those of dengue 2 virus (DENV-2). These vectors, named pJED2 and pJED2-1770 were transfected to BHK-21 cells and produced chimeric viruses JED2V and JED2-1770V, respectively. The chimeric viruses could be passaged in C6/36 but not BHK-21 cells. The chimeric viruses produced in C6/36 cells CPE 4-5 days after infection and RT-PCR, sequencing, immunofluorescence assay (IFA) and Western blot analysis confirmed the chimeric nature of produced viruses. The immunogenicity of chimeric viruses in mice was proved by detecting DENV-2 E protein-specific serum IgG antibodies with neutralization titer of 10. Successful preparation of infectious clones of chimeric JEV-DENV-2 viruses showed that JEV-based expression vectors are fully functional.

  4. Vector Disparity Sensor with Vergence Control for Active Vision Systems

    Directory of Open Access Journals (Sweden)

    Eduardo Ros

    2012-02-01

    Full Text Available This paper presents an architecture for computing vector disparity for active vision systems as used on robotics applications. The control of the vergence angle of a binocular system allows us to efficiently explore dynamic environments, but requires a generalization of the disparity computation with respect to a static camera setup, where the disparity is strictly 1-D after the image rectification. The interaction between vision and motor control allows us to develop an active sensor that achieves high accuracy of the disparity computation around the fixation point, and fast reaction time for the vergence control. In this contribution, we address the development of a real-time architecture for vector disparity computation using an FPGA device. We implement the disparity unit and the control module for vergence, version, and tilt to determine the fixation point. In addition, two on-chip different alternatives for the vector disparity engines are discussed based on the luminance (gradient-based and phase information of the binocular images. The multiscale versions of these engines are able to estimate the vector disparity up to 32 fps on VGA resolution images with very good accuracy as shown using benchmark sequences with known ground-truth. The performances in terms of frame-rate, resource utilization, and accuracy of the presented approaches are discussed. On the basis of these results, our study indicates that the gradient-based approach leads to the best trade-off choice for the integration with the active vision system.

  5. The Role of Chromatin in Adenoviral Vector Function

    Directory of Open Access Journals (Sweden)

    Carmen M. Wong

    2013-06-01

    Full Text Available Vectors based on adenovirus (Ad are one of the most commonly utilized platforms for gene delivery to cells in molecular biology studies and in gene therapy applications. Ad is also the most popular vector system in human clinical gene therapy trials, largely due to its advantageous characteristics such as high cloning capacity (up to 36 kb, ability to infect a wide variety of cell types and tissues, and relative safety due to it remaining episomal in transduced cells. The latest generation of Ad vectors, helper‑dependent Ad (hdAd, which are devoid of all viral protein coding sequences, can mediate high-level expression of a transgene for years in a variety of species ranging from rodents to non-human primates. Given the importance of histones and chromatin in modulating gene expression within the host cell, it is not surprising that Ad, a nuclear virus, also utilizes these proteins to protect the genome and modulate virus- or vector‑encoded genes. In this review, we will discuss our current understanding of the contribution of chromatin to Ad vector function.

  6. Word Vectorization Using Relations among Words for Neural Network

    Science.gov (United States)

    Hotta, Hajime; Kittaka, Masanobu; Hagiwara, Masafumi

    In this paper, we propose a new vectorization method for a new generation of computational intelligence including neural networks and natural language processing. In recent years, various techniques of word vectorization have been proposed, many of which rely on the preparation of dictionaries. However, these techniques don't consider the symbol grounding problem for unknown types of data, which is one of the most fundamental issues on artificial intelligence. In order to avoid the symbol-grounding problem, pattern processing based methods, such as neural networks, are often used in various studies on self-directive systems and algorithms, and the merit of neural network is not exception in the natural language processing. The proposed method is a converter from one word input to one real-valued vector, whose algorithm is inspired by neural network architecture. The merits of the method are as follows: (1) the method requires no specific knowledge of linguistics e.g. word classes or grammatical one; (2) the method is a sequence learning technique and it can learn additional knowledge. The experiment showed the efficiency of word vectorization in terms of similarity measurement.

  7. Sequence elements in the Escherichia coli araFGH promoter.

    OpenAIRE

    Hendrickson, W; Flaherty, C.; Molz, L

    1992-01-01

    The Escherichia coli araFGH operon codes for proteins involved in the L-arabinose high-affinity transport system. Transcriptional regulation of the operon was studied by creating point mutations and deletions in the control region cloned into a GalK expression vector. The transcription start site was confirmed by RNA sequencing of transcripts. The sequences essential for polymerase function were localized by deletions and point mutations. Surprisingly, only a weak -10 consensus sequence, and ...

  8. The Genome of Anopheles darlingi, the main neotropical malaria vector

    Science.gov (United States)

    Marinotti, Osvaldo; Cerqueira, Gustavo C.; de Almeida, Luiz Gonzaga Paula; Ferro, Maria Inês Tiraboschi; Loreto, Elgion Lucio da Silva; Zaha, Arnaldo; Teixeira, Santuza M. R.; Wespiser, Adam R.; Almeida e Silva, Alexandre; Schlindwein, Aline Daiane; Pacheco, Ana Carolina Landim; da Silva, Artur Luiz da Costa; Graveley, Brenton R.; Walenz, Brian P.; Lima, Bruna de Araujo; Ribeiro, Carlos Alexandre Gomes; Nunes-Silva, Carlos Gustavo; de Carvalho, Carlos Roberto; Soares, Célia Maria de Almeida; de Menezes, Claudia Beatriz Afonso; Matiolli, Cleverson; Caffrey, Daniel; Araújo, Demetrius Antonio M.; de Oliveira, Diana Magalhães; Golenbock, Douglas; Grisard, Edmundo Carlos; Fantinatti-Garboggini, Fabiana; de Carvalho, Fabíola Marques; Barcellos, Fernando Gomes; Prosdocimi, Francisco; May, Gemma; de Azevedo Junior, Gilson Martins; Guimarães, Giselle Moura; Goldman, Gustavo Henrique; Padilha, Itácio Q. M.; Batista, Jacqueline da Silva; Ferro, Jesus Aparecido; Ribeiro, José M. C.; Fietto, Juliana Lopes Rangel; Dabbas, Karina Maia; Cerdeira, Louise; Agnez-Lima, Lucymara Fassarella; Brocchi, Marcelo; de Carvalho, Marcos Oliveira; Teixeira, Marcus de Melo; Diniz Maia, Maria de Mascena; Goldman, Maria Helena S.; Cruz Schneider, Maria Paula; Felipe, Maria Sueli Soares; Hungria, Mariangela; Nicolás, Marisa Fabiana; Pereira, Maristela; Montes, Martín Alejandro; Cantão, Maurício E.; Vincentz, Michel; Rafael, Miriam Silva; Silverman, Neal; Stoco, Patrícia Hermes; Souza, Rangel Celso; Vicentini, Renato; Gazzinelli, Ricardo Tostes; Neves, Rogério de Oliveira; Silva, Rosane; Astolfi-Filho, Spartaco; Maciel, Talles Eduardo Ferreira; Ürményi, Turán P.; Tadei, Wanderli Pedro; Camargo, Erney Plessmann; de Vasconcelos, Ana Tereza Ribeiro

    2013-01-01

    Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi. PMID:23761445

  9. Characteristic element of matrix attachment region mediates vector attachment and enhances nerve growth factor expression in Chinese hamster ovary cells.

    Science.gov (United States)

    Wang, X Y; Zhang, J H; Sun, Q L; Yao, Z Y; Deng, B G; Guo, W Y; Wang, L; Dong, W H; Wang, F; Zhao, C P; Wang, T Y

    2015-08-07

    Preliminary studies have suggested that a characteristic element of the matrix attachment region (MAR) in human interferon-β mediates the adhesion of vectors to Chinese hamster ovary (CHO) cells. In this study, we investigated if vector adhesion increased nerve growth factor (NGF) expression in CHO cells. The MAR characteristic element sequence of human interferon-β was inserted into the multiple-cloning site of the pEGFP-C1 vector. The target NGF gene was inserted upstream of the MAR characteristic element sequence to construct the MAR/NGF expression vector. The recombinant plasmid was transfected into CHO cells and stable monoclonal cells were selected using G418. NGF mRNA and protein expression was detected by reverse transcriptase-polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. Plasmid reduction experiments were used to determine the state of transfected plasmid in mammalian cells. The insertion of MAR into the vector increased NGF expression levels in CHO cells (1.93- fold) compared to the control. The recombinant plasmid expressing the MAR sequence was digested into a linear space vector. The inserted MAR and NGF sequences were consistent with those inserted into the plasmid before recombination. Therefore, we concluded that the MAR characteristic element mediates vector adhesion to CHO cells and enhances the stability and efficiency of the target gene expression.

  10. Introduction to vector velocity imaging

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Udesen, Jesper; Hansen, Kristoffer Lindskov

    over the full region of interest and a real time image at a frame rate of 20 Hz can be displayed. Real time videos have been obtained from both our research systems and from commercial BK Medical scanners. The vector velocity images reveal the full complexity of the human blood flow. It is easy to see...... direction and the correct velocity magnitude for any orientation of the vessels. At complex geometries like bifurcations, branching and for valves the approach reveals how the velocity changes magnitude and direction over the cardiac cycle. Vector velocity reveals a wealth of new information that now...... is accessible to the ultrasound community. The displaying and studying of this information is challenging as complex flow changes rapidly over the cardiac cycle....

  11. Vector Galileon and inflationary magnetogenesis

    Science.gov (United States)

    Nandi, Debottam; Shankaranarayanan, S.

    2018-01-01

    Cosmological inflation provides the initial conditions for the structure formation. However, the origin of large-scale magnetic fields can not be addressed in this framework. The key issue for this long-standing problem is the conformal invariance of the electromagnetic (EM) field in 4-D. While many approaches have been proposed in the literature for breaking conformal invariance of the EM action, here, we provide a completely new way of looking at the modifications to the EM action and generation of primordial magnetic fields during inflation. We explicitly construct a higher derivative EM action that breaks conformal invariance by demanding three conditions—theory be described by vector potential Aμ and its derivatives, Gauge invariance be satisfied, and equations of motion be linear in second derivatives of vector potential. The unique feature of our model is that appreciable magnetic fields are generated at small wavelengths while tiny magnetic fields are generated at large wavelengths that are consistent with current observations.

  12. Clinical applications of power vectors.

    Science.gov (United States)

    Miller, Joseph M

    2009-06-01

    The study of infant vision is closely coupled to the study of the refraction, change in refraction over time, and the effect of spectacle correction on visual development. Frequently, reports are limited to descriptions of spherical equivalent or cylinder power without regard to axis, as data are frequently collected in the clinical format of sphere, cylinder, and axis (S, C, A). Conversion from clinical notation to a power vector representation of refraction allows unambiguous description of how refractions change over time and differ between repeated measurements. This article presents a series of examples of Microsoft Excel spreadsheet formulas that make the conversion from clinical notation to power vector format, and provides examples of useful applications of these methods.

  13. Active set support vector regression.

    Science.gov (United States)

    Musicant, David R; Feinberg, Alexander

    2004-03-01

    This paper presents active set support vector regression (ASVR), a new active set strategy to solve a straightforward reformulation of the standard support vector regression problem. This new algorithm is based on the successful ASVM algorithm for classification problems, and consists of solving a finite number of linear equations with a typically large dimensionality equal to the number of points to be approximated. However, by making use of the Sherman-Morrison-Woodbury formula, a much smaller matrix of the order of the original input space is inverted at each step. The algorithm requires no specialized quadratic or linear programming code, but merely a linear equation solver which is publicly available. ASVR is extremely fast, produces comparable generalization error to other popular algorithms, and is available on the web for download.

  14. Lentiviral vectors in cancer immunotherapy.

    Science.gov (United States)

    Oldham, Robyn Aa; Berinstein, Elliot M; Medin, Jeffrey A

    2015-01-01

    Basic science advances in cancer immunotherapy have resulted in various treatments that have recently shown success in the clinic. Many of these therapies require the insertion of genes into cells to directly kill them or to redirect the host's cells to induce potent immune responses. Other analogous therapies work by modifying effector cells for improved targeting and enhanced killing of tumor cells. Initial studies done using γ-retroviruses were promising, but safety concerns centered on the potential for insertional mutagenesis have highlighted the desire to develop other options for gene delivery. Lentiviral vectors (LVs) have been identified as potentially more effective and safer alternative delivery vehicles. LVs are now in use in clinical trials for many different types of inherited and acquired disorders, including cancer. This review will discuss current knowledge of LVs and the applications of this viral vector-based delivery vehicle to cancer immunotherapy.

  15. Vector fields on singular varieties

    CERN Document Server

    Brasselet, Jean-Paul; Suwa, Tatsuo

    2009-01-01

    Vector fields on manifolds play a major role in mathematics and other sciences. In particular, the Poincaré-Hopf index theorem gives rise to the theory of Chern classes, key manifold-invariants in geometry and topology. It is natural to ask what is the ‘good’ notion of the index of a vector field, and of Chern classes, if the underlying space becomes singular. The question has been explored by several authors resulting in various answers, starting with the pioneering work of M.-H. Schwartz and R. MacPherson. We present these notions in the framework of the obstruction theory and the Chern-Weil theory. The interplay between these two methods is one of the main features of the monograph.

  16. Improvement of lentiviral transfer vectors using cis-acting regulatory elements for increased gene expression.

    Science.gov (United States)

    Real, Gonçalo; Monteiro, Francisca; Burger, Christa; Alves, Paula M

    2011-09-01

    Lentiviral vectors are an important tool for gene delivery in vivo and in vitro. The success of gene transfer approaches relies on high and stable levels of gene expression. To this end, several molecular strategies have been employed to manipulate these vectors towards improving gene expression in the targeted animal cells. Low gene expression can be accepted due to the weak transcription from the majority of available mammalian promoters; however, this obstacle can be in part overcome by the insertion of cis-acting elements that enhance gene expression in various expression contexts. In this work, we created different lentiviral vectors in which several posttranscriptional regulatory elements, namely the Woodchuck hepatitis posttranscriptional regulatory element (WPRE) and different specialized poly(A) termination sequences (BGH and SV40) were used to develop vectors leading to improved transgene expression. These vectors combine the advantages of restriction enzyme/ligation-independent cloning eliminating the instability and recombinogenic problems occurring from traditional cloning methods in lentiviral expression vectors and were tested by expressing GFP and the firefly Luciferase reporter gene from different cellular promoters in different cell lines. We show that the promoter activity varies between cell lines and is affected by the lentiviral genomic context. Moreover, we show that the combination of the WPRE element with the BGH poly(A) signal significantly enhances transgene expression. The vectors herein created can be easily modified and adapted without the need for extensive recloning making them a valuable tool for viral vector development.

  17. Host Life History Strategy, Species Diversity, and Habitat Influence Trypanosoma cruzi Vector Infection in Changing Landscapes

    Science.gov (United States)

    Gottdenker, Nicole L.; Chaves, Luis Fernando; Calzada, José E.; Saldaña, Azael; Carroll, C. Ronald

    2012-01-01

    Background Anthropogenic land use may influence transmission of multi-host vector-borne pathogens by changing diversity, relative abundance, and community composition of reservoir hosts. These reservoir hosts may have varying competence for vector-borne pathogens depending on species-specific characteristics, such as life history strategy. The objective of this study is to evaluate how anthropogenic land use change influences blood meal species composition and the effects of changing blood meal species composition on the parasite infection rate of the Chagas disease vector Rhodnius pallescens in Panama. Methodology/Principal Findings R. pallescens vectors (N = 643) were collected in different habitat types across a gradient of anthropogenic disturbance. Blood meal species in DNA extracted from these vectors was identified in 243 (40.3%) vectors by amplification and sequencing of a vertebrate-specific fragment of the 12SrRNA gene, and T. cruzi vector infection was determined by pcr. Vector infection rate was significantly greater in deforested habitats as compared to contiguous forests. Forty-two different species of blood meal were identified in R. pallescens, and species composition of blood meals varied across habitat types. Mammals (88.3%) dominated R. pallescens blood meals. Xenarthrans (sloths and tamanduas) were the most frequently identified species in blood meals across all habitat types. A regression tree analysis indicated that blood meal species diversity, host life history strategy (measured as rmax, the maximum intrinsic rate of population increase), and habitat type (forest fragments and peridomiciliary sites) were important determinants of vector infection with T. cruzi. The mean intrinsic rate of increase and the skewness and variability of rmax were positively associated with higher vector infection rate at a site. Conclusions/Significance In this study, anthropogenic landscape disturbance increased vector infection with T. cruzi, potentially

  18. Host life history strategy, species diversity, and habitat influence Trypanosoma cruzi vector infection in Changing landscapes.

    Directory of Open Access Journals (Sweden)

    Nicole L Gottdenker

    Full Text Available Anthropogenic land use may influence transmission of multi-host vector-borne pathogens by changing diversity, relative abundance, and community composition of reservoir hosts. These reservoir hosts may have varying competence for vector-borne pathogens depending on species-specific characteristics, such as life history strategy. The objective of this study is to evaluate how anthropogenic land use change influences blood meal species composition and the effects of changing blood meal species composition on the parasite infection rate of the Chagas disease vector Rhodnius pallescens in Panama.R. pallescens vectors (N = 643 were collected in different habitat types across a gradient of anthropogenic disturbance. Blood meal species in DNA extracted from these vectors was identified in 243 (40.3% vectors by amplification and sequencing of a vertebrate-specific fragment of the 12SrRNA gene, and T. cruzi vector infection was determined by pcr. Vector infection rate was significantly greater in deforested habitats as compared to contiguous forests. Forty-two different species of blood meal were identified in R. pallescens, and species composition of blood meals varied across habitat types. Mammals (88.3% dominated R. pallescens blood meals. Xenarthrans (sloths and tamanduas were the most frequently identified species in blood meals across all habitat types. A regression tree analysis indicated that blood meal species diversity, host life history strategy (measured as r(max, the maximum intrinsic rate of population increase, and habitat type (forest fragments and peridomiciliary sites were important determinants of vector infection with T. cruzi. The mean intrinsic rate of increase and the skewness and variability of r(max were positively associated with higher vector infection rate at a site.In this study, anthropogenic landscape disturbance increased vector infection with T. cruzi, potentially by changing host community structure to favor hosts

  19. Altering the selection capabilities of common cloning vectors via restriction enzyme mediated gene disruption

    Science.gov (United States)

    2013-01-01

    Background The cloning of gene sequences forms the basis for many molecular biological studies. One important step in the cloning process is the isolation of bacterial transformants carrying vector DNA. This involves a vector-encoded selectable marker gene, which in most cases, confers resistance to an antibiotic. However, there are a number of circumstances in which a different selectable marker is required or may be preferable. Such situations can include restrictions to host strain choice, two phase cloning experiments and mutagenesis experiments, issues that result in additional unnecessary cloning steps, in which the DNA needs to be subcloned into a vector with a suitable selectable marker. Results We have used restriction enzyme mediated gene disruption to modify the selectable marker gene of a given vector by cloning a different selectable marker gene into the original marker present in that vector. Cloning a new selectable marker into a pre-existing marker was found to change the selection phenotype conferred by that vector, which we were able to demonstrate using multiple commonly used vectors and multiple resistance markers. This methodology was also successfully applied not only to cloning vectors, but also to expression vectors while keeping the expression characteristics of the vector unaltered. Conclusions Changing the selectable marker of a given vector has a number of advantages and applications. This rapid and efficient method could be used for co-expression of recombinant proteins, optimisation of two phase cloning procedures, as well as multiple genetic manipulations within the same host strain without the need to remove a pre-existing selectable marker in a previously genetically modified strain. PMID:23497512

  20. Angles in Complex Vector Spaces

    OpenAIRE

    Scharnhorst, K.

    1999-01-01

    The article reviews some of the (fairly scattered) information available in the mathematical literature on the subject of angles in complex vector spaces. The following angles and their relations are considered: Euclidean, complex, and Hermitian angles, (Kasner's) pseudo-angle, the Kaehler angle (synonyms for the latter used in the literature are: angle of inclination, characteristic deviation, holomorphic deviation, holomorphy angle, Wirtinger angle, slant angle).

  1. GAPS IN SUPPORT VECTOR OPTIMIZATION

    Energy Technology Data Exchange (ETDEWEB)

    STEINWART, INGO [Los Alamos National Laboratory; HUSH, DON [Los Alamos National Laboratory; SCOVEL, CLINT [Los Alamos National Laboratory; LIST, NICOLAS [Los Alamos National Laboratory

    2007-01-29

    We show that the stopping criteria used in many support vector machine (SVM) algorithms working on the dual can be interpreted as primal optimality bounds which in turn are known to be important for the statistical analysis of SVMs. To this end we revisit the duality theory underlying the derivation of the dual and show that in many interesting cases primal optimality bounds are the same as known dual optimality bounds.

  2. Ultrasonic Dynamic Vector Stress Sensor

    Science.gov (United States)

    Heyman, Joseph S.; Froggatt, Mark

    1992-01-01

    Stress inferred from measurements in specimens rather than in bonded gauges. Ultrasonic dynamic vector stress sensor (UDVSS) measures changes in dynamic directional stress occurring in material or structure at location touched by device when material or structure put under cyclic load. Includes phase-locked loop, synchronous amplifier, and contact probe. Useful among manufacturers of aerospace and automotive structures for stress testing and evaluation of designs.

  3. A ocean bottom vector magnetometer

    Science.gov (United States)

    Wang, Xiaomei; Teng, Yuntian; Wang, Chen; Ma, Jiemei

    2017-04-01

    The new development instrument with a compact spherical coil system and Overhauser magnetometer for measuring the total strength of the magnetic field and the vectors of strength, Delta inclination - Delta declination, meanwhile we also use a triaxial fluxgate instrument of the traditional instrument for geomagnetic vector filed measurement. The advantages of this method are be calibrated by each other and get good performances with automatic operation, good stability and high resolution. Firstly, a brief description of the instrument measurement principles and the key technologies are given. The instrument used a spherical coil system with 34 coils to product the homogeneous volume inside the coils which is large enough to accommodate the sensor of Overhauser total field sensor; the rest of the footlocker-sized ocean-bottom vector magnetometer consists of equipment to run the sensors and records its data (batteries and a data logger), weight to sink it to the sea floor, a remote-controlled acoustic release and flotation to bring the instrument back to the surface. Finally, the accuracy of the instrument was tested in the Geomagnetic station, and the measurement accuracies of total strength and components were better than 0.2nT and 1nT respectively. The figure 1 shows the development instrument structure. it includes six thick glass spheres which protect the sensor, data logger and batteries from the pressures of the deep sea, meanwhile they also provide recycling positive buoyancy; To cushion the glass, the spheres then go inside yellow plastic "hardhats". The triaxial fluxgate is inside No.1 glass spheres, data logger and batteries are inside No.2 glass spheres, the new vector sensor is inside No.3 glass spheres, acoustic communication unit is inside No.4 glass spheres, No.5 and No.6 glass spheres are empty which only provide recycling positive buoyancy. The figure 2 shows the development instrument Physical photo.

  4. Olfaction in vector-host interactions

    NARCIS (Netherlands)

    Takken, W.; Knols, B.G.J.

    2010-01-01

    This book addresses the topic how blood-feeding arthropods interact with their vertebrate hosts. As the transmission of infectious vector-borne pathogens is much dependent on the contact between vector and host, the efficacy of host location is of profound importance. Interruption of vector-host

  5. Herbivore arthropods benefit from vectoring plant viruses

    NARCIS (Netherlands)

    Belliure, B.; Janssen, A.; Maris, P.C.; Peters, D.; Sabelis, M.W.

    2005-01-01

    Plants infected with pathogens often attract the pathogens' vectors, but it is not clear if this is advantageous to the vectors. We therefore quantified the direct and indirect (through the host plant) effects of a pathogen on its vector. A positive direct effect of the plant-pathogenic Tomato

  6. Vector and tensor analysis with applications

    CERN Document Server

    Borisenko, A I; Silverman, Richard A

    1979-01-01

    Concise and readable, this text ranges from definition of vectors and discussion of algebraic operations on vectors to the concept of tensor and algebraic operations on tensors. It also includes a systematic study of the differential and integral calculus of vector and tensor functions of space and time. Worked-out problems and solutions. 1968 edition.

  7. Vectorizing and machine-spanning techniques

    Energy Technology Data Exchange (ETDEWEB)

    Giroux, E D

    1983-09-22

    Techniques for vectorizing complex logic are shown using a decoupled sliding-surface calculation that is part of a two-dimensional Lagrangian simulation model. The same source coding can be run on many vector, parallel, and multiprocessor computers with very little or no alteration. The vectorizing techniques have been used for a wide range of problems.

  8. Fubini's Theorem for Vector-Valued Measures

    Science.gov (United States)

    Uglanov, A. V.

    1991-02-01

    The situation is considered when either the transitional or initial measure is vector-valued (the other is, respectively, scalar-valued; thus the product measure is also vector-valued). The integrable function is vector-valued. In this situation two theorems of Fubini type are proved.

  9. On the Distribution of Norm of Vector Projection and Rejection of Two Complex Normal Random Vectors

    Directory of Open Access Journals (Sweden)

    Mehdi Maleki

    2015-01-01

    Full Text Available Vector projection and vector rejection are highly common and useful operations in mathematics, information theory, and signal processing. In this paper, we find the distribution of the norm of projection and rejection vectors when the original vectors are standard complex normally distributed.

  10. New yeast/E. coli/Drosophila triple shuttle vectors for efficient generation of Drosophila P element transformation constructs.

    Science.gov (United States)

    Paululat, Achim; Heinisch, Jürgen J

    2012-12-15

    We have generated a set of novel triple shuttle vectors that facilitate the construction of Drosophila-P-element transformations vectors. These YED-vectors allow the insertion of any kind of sequence at any chosen position due to the presence of a yeast casette which ensures replication and allows for homologous recombination in Saccharomyces cerevisiae. As a proof of principle we generated several reporter constructs and tested them in transgenic flies for expression and correct subcellular localization. YED-vectors can be used for many purposes including promoter analysis or the expression of tagged or truncated proteins. Thus, time-consuming conventional restriction site based multi-step cloning procedures can be circumvented by using the new YED-vectors. The new set of triple shuttle vectors will be highly beneficial for the rapid construction of complex Drosophila transformation plasmids. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Gaussian statistics for palaeomagnetic vectors

    Science.gov (United States)

    Love, J.J.; Constable, C.G.

    2003-01-01

    With the aim of treating the statistics of palaeomagnetic directions and intensities jointly and consistently, we represent the mean and the variance of palaeomagnetic vectors, at a particular site and of a particular polarity, by a probability density function in a Cartesian three-space of orthogonal magnetic-field components consisting of a single (unimoda) non-zero mean, spherically-symmetrical (isotropic) Gaussian function. For palaeomagnetic data of mixed polarities, we consider a bimodal distribution consisting of a pair of such symmetrical Gaussian functions, with equal, but opposite, means and equal variances. For both the Gaussian and bi-Gaussian distributions, and in the spherical three-space of intensity, inclination, and declination, we obtain analytical expressions for the marginal density functions, the cumulative distributions, and the expected values and variances for each spherical coordinate (including the angle with respect to the axis of symmetry of the distributions). The mathematical expressions for the intensity and off-axis angle are closed-form and especially manageable, with the intensity distribution being Rayleigh-Rician. In the limit of small relative vectorial dispersion, the Gaussian (bi-Gaussian) directional distribution approaches a Fisher (Bingham) distribution and the intensity distribution approaches a normal distribution. In the opposite limit of large relative vectorial dispersion, the directional distributions approach a spherically-uniform distribution and the intensity distribution approaches a Maxwell distribution. We quantify biases in estimating the properties of the vector field resulting from the use of simple arithmetic averages, such as estimates of the intensity or the inclination of the mean vector, or the variances of these quantities. With the statistical framework developed here and using the maximum-likelihood method, which gives unbiased estimates in the limit of large data numbers, we demonstrate how to

  12. The Standard European Vector Architecture (SEVA) plasmid toolkit.

    Science.gov (United States)

    Durante-Rodríguez, Gonzalo; de Lorenzo, Víctor; Martínez-García, Esteban

    2014-01-01

    The Standard European Vector Architecture (SEVA) toolkit is a simple and powerful resource for constructing optimal plasmid vectors based on a backbone and three interchangeable modules flanked by uncommon restriction sites. Functional modules encode several origins of replication, diverse antibiotic selection markers, and a variety of cargoes with different applications. The backbone and DNA modules have been minimized and edited for flaws in their sequence and/or functionality. A protocol for the utilization of the SEVA platform to construct transcriptional and translational fusions between a promoter under study (the arsenic-responsive Pars of Pseudomonas putida KT2440) and the reporter lacZ gene is described. The resulting plasmid collection was instrumental to measure and compare the β-galactosidase activity that report gene expression (i.e., transcription and translation) in different genetic backgrounds.

  13. A family of E. coli expression vectors for laboratory scale and high throughput soluble protein production

    Directory of Open Access Journals (Sweden)

    Bottomley Stephen P

    2006-03-01

    Full Text Available Abstract Background In the past few years, both automated and manual high-throughput protein expression and purification has become an accessible means to rapidly screen and produce soluble proteins for structural and functional studies. However, many of the commercial vectors encoding different solubility tags require different cloning and purification steps for each vector, considerably slowing down expression screening. We have developed a set of E. coli expression vectors with different solubility tags that allow for parallel cloning from a single PCR product and can be purified using the same protocol. Results The set of E. coli expression vectors, encode for either a hexa-histidine tag or the three most commonly used solubility tags (GST, MBP, NusA and all with an N-terminal hexa-histidine sequence. The result is two-fold: the His-tag facilitates purification by immobilised metal affinity chromatography, whilst the fusion domains act primarily as solubility aids during expression, in addition to providing an optional purification step. We have also incorporated a TEV recognition sequence following the solubility tag domain, which allows for highly specific cleavage (using TEV protease of the fusion protein to yield native protein. These vectors are also designed for ligation-independent cloning and they possess a high-level expressing T7 promoter, which is suitable for auto-induction. To validate our vector system, we have cloned four different genes and also one gene into all four vectors and used small-scale expression and purification techniques. We demonstrate that the vectors are capable of high levels of expression and that efficient screening of new proteins can be readily achieved at the laboratory level. Conclusion The result is a set of four rationally designed vectors, which can be used for streamlined cloning, expression and purification of target proteins in the laboratory and have the potential for being adaptable to a high

  14. Problems and worked solutions in vector analysis

    CERN Document Server

    Shorter, LR

    2014-01-01

    ""A handy book like this,"" noted The Mathematical Gazette, ""will fill a great want."" Devoted to fully worked out examples, this unique text constitutes a self-contained introductory course in vector analysis for undergraduate and graduate students of applied mathematics.Opening chapters define vector addition and subtraction, show how to resolve and determine the direction of two or more vectors, and explain systems of coordinates, vector equations of a plane and straight line, relative velocity and acceleration, and infinitely small vectors. The following chapters deal with scalar and vect

  15. Integration of vector-valued functions with respect to vector measures defined on δ-rings

    OpenAIRE

    Chakraborty, N. D.; Basu, Santwana

    2011-01-01

    This paper extends the theory of scalar-valued integrable functions with respect to vector measures defined on δ-rings to the case of vector-valued tensor integrable functions with respect to vector measures defined on δ-rings. This paper also generalizes some results of G. F. Stefánsson for tensor integration theory of vector-valued functions with respect to vector measures defined on σ-algebras.

  16. Multiscale vector fields for image pattern recognition

    Science.gov (United States)

    Low, Kah-Chan; Coggins, James M.

    1990-01-01

    A uniform processing framework for low-level vision computing in which a bank of spatial filters maps the image intensity structure at each pixel into an abstract feature space is proposed. Some properties of the filters and the feature space are described. Local orientation is measured by a vector sum in the feature space as follows: each filter's preferred orientation along with the strength of the filter's output determine the orientation and the length of a vector in the feature space; the vectors for all filters are summed to yield a resultant vector for a particular pixel and scale. The orientation of the resultant vector indicates the local orientation, and the magnitude of the vector indicates the strength of the local orientation preference. Limitations of the vector sum method are discussed. Investigations show that the processing framework provides a useful, redundant representation of image structure across orientation and scale.

  17. Rotations with Rodrigues' vector

    Energy Technology Data Exchange (ETDEWEB)

    Pina, E, E-mail: pge@xanum.uam.mx [Prof. Eugenio Mendez Docurro de la, Escuela Superior de Fisica y Matematicas del IPN, Zacatenco 07738, Mexico DF (Mexico)

    2011-09-15

    The rotational dynamics was studied from the point of view of Rodrigues' vector. This vector is defined here by its connection with other forms of parametrization of the rotation matrix. The rotation matrix was expressed in terms of this vector. The angular velocity was computed using the components of Rodrigues' vector as coordinates. It appears to be a fundamental matrix that is used to express the components of the angular velocity, the rotation matrix and the angular momentum vector. The Hamiltonian formalism of rotational dynamics in terms of this vector uses the same matrix. The quantization of the rotational dynamics is performed with simple rules if one uses Rodrigues' vector and similar formal expressions for the quantum operators that mimic the Hamiltonian classical dynamics.

  18. Transversals of Complex Polynomial Vector Fields

    DEFF Research Database (Denmark)

    Dias, Kealey

    Vector fields in the complex plane are defined by assigning the vector determined by the value P(z) to each point z in the complex plane, where P is a polynomial of one complex variable. We consider special families of so-called rotated vector fields that are determined by a polynomial multiplied...... by rotational constants. Transversals are a certain class of curves for such a family of vector fields that represent the bifurcation states for this family of vector fields. More specifically, transversals are curves that coincide with a homoclinic separatrix for some rotation of the vector field. Given...... examples of rotated families to argue this. There will be discussed several open questions concerning the number of transversals that can appear for a certain degree d of a polynomial vector field, and furthermore how transversals are analyzed with respect to bifurcations around multiple equilibrium points....

  19. Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy.

    Science.gov (United States)

    Carpi, Giovanna; Kitchen, Andrew; Kim, Hie Lim; Ratan, Aakrosh; Drautz-Moses, Daniela I; McGraw, John J; Kazimirova, Maria; Rizzoli, Annapaola; Schuster, Stephan C

    2016-08-01

    In Europe, the Ixodes ricinus tick is the most important vector of the etiological agents of Lyme borreliosis and several other emerging tick-borne diseases. Because tick-borne pathogens are dependent on their vectors for transmission, understanding the vector population structure is crucial to inform public health research of pathogen dynamics and spread. However, the population structure and dynamics of this important vector species are not well understood as most genetic studies utilize short mitochondrial and nuclear sequences with little diversity. Herein we obtained and analyzed complete mitochondrial genome (hereafter "mitogenome") sequences to better understand the genetic diversity and the population structure of I. ricinus from two long-standing tick-borne disease foci in northern Italy. Complete mitogenomes of 23 I. ricinus ticks were sequenced at high coverage. Out of 23 mitogenome sequences we identified 17 unique haplotypes composed of 244 segregating sites. Phylogenetic reconstruction using 18 complete mitogenome sequences revealed the coexistence of four highly divergent I. ricinus maternal lineages despite the narrow spatial scale over which these samples were obtained (100km). Notably, the estimated coalescence time of the 18 mitogenome haplotypes is ∼427 thousand years ago (95% HPD 330, 540). This divergence between I. ricinus lineages is consistent with the mitochondrial diversity of other arthropod vector species and indicates that long-term I. ricinus populations may have been less structured and larger than previously thought. Thus, this study suggests that a rapid and accurate retrieval of full mitochondrial genomes from this disease vector enables fine-resolution studies of tick intraspecies genetic relationships, population differentiation, and demographic history. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Error compensation in random vector double step saccades with and without global adaptation.

    Science.gov (United States)

    Zerr, Paul; Thakkar, Katharine N; Uzunbajakau, Siarhei; Van der Stigchel, Stefan

    2016-10-01

    In saccade sequences without visual feedback endpoint errors pose a problem for subsequent saccades. Accurate error compensation has previously been demonstrated in double step saccades (DSS) and is thought to rely on a copy of the saccade motor vector. However, these studies typically use fixed target vectors on each trial, calling into question the generalizability of the findings due to the high stimulus predictability. We present a random walk DSS paradigm (random target vector amplitudes and directions) to provide a more complete, realistic and generalizable description of error compensation in saccade sequences. We regressed the vector between the endpoint of the second saccade and the endpoint of a hypothetical second saccade that does not take first saccade error into account on the ideal compensation vector. This provides a direct and complete estimation of error compensation in DSS. We observed error compensation with varying stimulus displays that was comparable to previous findings. We also employed this paradigm to extend experiments that showed accurate compensation for systematic undershoots after specific-vector saccade adaptation. Utilizing the random walk paradigm for saccade adaptation by Rolfs et al. (2010) together with our random walk DSS paradigm we now also demonstrate transfer of adaptation from reactive to memory guided saccades for global saccade adaptation. We developed a new, generalizable DSS paradigm with unpredictable stimuli and successfully employed it to verify, replicate and extend previous findings, demonstrating that endpoint errors are compensated for saccades in all directions and variable amplitudes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Deciphering Babesia-Vector Interactions

    Directory of Open Access Journals (Sweden)

    Sandra Antunes

    2017-09-01

    Full Text Available Understanding host-pathogen-tick interactions remains a vitally important issue that might be better understood by basic research focused on each of the dyad interplays. Pathogens gain access to either the vector or host during tick feeding when ticks are confronted with strong hemostatic, inflammatory and immune responses. A prominent example of this is the Babesia spp.—tick—vertebrate host relationship. Babesia spp. are intraerythrocytic apicomplexan organisms spread worldwide, with a complex life cycle. The presence of transovarial transmission in almost all the Babesia species is the main difference between their life cycle and that of other piroplasmida. With more than 100 species described so far, Babesia are the second most commonly found blood parasite of mammals after trypanosomes. The prevalence of Babesia spp. infection is increasing worldwide and is currently classified as an emerging zoonosis. Babesia microti and Babesia divergens are the most frequent etiological agents associated with human babesiosis in North America and Europe, respectively. Although the Babesia-tick system has been extensively researched, the currently available prophylactic and control methods are not efficient, and chemotherapeutic treatment is limited. Studying the molecular changes induced by the presence of Babesia in the vector will not only elucidate the strategies used by the protozoa to overcome mechanical and immune barriers, but will also contribute toward the discovery of important tick molecules that have a role in vector capacity. This review provides an overview of the identified molecules involved in Babesia-tick interactions, with an emphasis on the fundamentally important ones for pathogen acquisition and transmission.

  2. Bridging the Vector Calculus Gap

    Science.gov (United States)

    Dray, Tevian; Manogue, Corinne

    2003-05-01

    As with Britain and America, mathematicians and physicists are separated from each other by a common language. In a nutshell, mathematics is about functions, but physics is about things. For the last several years, we have led an NSF-supported effort to "bridge the vector calculus gap" between mathematics and physics. The unifying theme we have discovered is to emphasize geometric reasoning, not (just) algebraic computation. In this talk, we will illustrate the language differences between mathematicians and physicists, and how we are trying reconcile them in the classroom. For further information about the project go to: http://www.physics.orst.edu/bridge

  3. Amino acid "little Big Bang": representing amino acid substitution matrices as dot products of Euclidian vectors.

    Science.gov (United States)

    Zimmermann, Karel; Gibrat, Jean-François

    2010-01-04

    Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.

  4. Development of hybrid baculovirus vectors for artificial MicroRNA delivery and prolonged gene suppression.

    Science.gov (United States)

    Chen, Chiu-Ling; Luo, Wen-Yi; Lo, Wen-Hsin; Lin, Kun-Ju; Sung, Li-Yu; Shih, Yung-Shen; Chang, Yu-Han; Hu, Yu-Chen

    2011-12-01

    MicroRNA (miRNA) plays essential roles in regulating gene expression, but miRNA delivery remains a hurdle, thus entailing a vector system for efficient transfer. Baculovirus emerges as a promising gene delivery vector but its inherent transient expression restricts its applications in some scenarios. Therefore, this study primarily aimed to develop baculovirus as a miRNA expression vector for prolonged gene suppression. We constructed recombinant baculoviruses carrying artificial egfp-targeting miRNA sequences within the miR155 backbone, which after expression by the cytomegalovirus promoter could knockdown the enhanced green fluorescent protein (EGFP) expression in a sequence- and dose-dependent manner. By swapping the mature miRNA sequences, the baculovirus miRNA shuttle effectively repressed the overexpression of endogenous TNF-α in arthritic synoviocytes without inducing apoptosis. To prolong the baculovirus-mediated expression, we further developed a hybrid baculovirus vector that exploited the Sleeping Beauty (SB) transposon for gene integration and sustained miRNA expression. The hybrid baculovirus vector that combined the miR155 scaffold and SB transposon effectively repressed the transgene expression for a prolonged period of time, hence diversifying the applications of baculovirus to indications necessitating prolonged gene regulation such as arthritis. Copyright © 2011 Wiley Periodicals, Inc.

  5. Transgenesis of Tol2-mediated seamlessly constructed BAC mammary gland expression vectors in Mus musculus.

    Science.gov (United States)

    Yang, Yaohui; Wang, Wenyuan; Huang, Tian; Ruan, Weimin; Cao, Gengsheng

    2016-01-20

    Bacterial artificial chromosomes (BACs) are vectors that are capable of carrying gene fragments of up to 300 kb in size, and in theory, harbor cis-regulatory elements that are necessary for the expression of specific genes. Therefore, BACs can effectively alleviate or even eliminate the position effect induced by gene-integration, rendering these as ideal expression vectors of exogenous genes. However, the number of relevant studies involving BACs as vectors of exogenous genes are limited. In the present study, we converted the BAC regulatory region of the Mus musculus Wap gene into a mammary gland-specific expression vector. Using the galK-based positive-negative selection method, we seamlessly replaced the Wap gene in a BAC with Homo sapiens GPX3, MT2, and Luc genes while keeping the original mammary gland-specific regulatory sequence intact, without introducing any extra sequences (Loxp/Frt). To improve the efficiency of creating BAC transgenic mice, we used a Tol2 transposon system optimized for mammalian codons and eliminated 100 kb of sequence from the BAC 5' end (173 kb), which resulted in an 8.5% rate of successful gene transmission via pronuclear injection. The results of the present study indicate that seamlessly constructed BAC expression vectors can be used for the transmission of the GPX3 gene. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors

    Directory of Open Access Journals (Sweden)

    Zimmermann Karel

    2010-01-01

    Full Text Available Abstract Background Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. Results We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. Conclusions This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.

  7. Infectious Clones and Vectors Derived from Adeno-Associated Virus (AAV) Serotypes Other Than AAV Type 2

    OpenAIRE

    Rutledge, Elizabeth A.; Halbert, Christine L.; Russell, David W.

    1998-01-01

    Adeno-associated viruses (AAVs) are single-stranded dependent parvoviruses being developed as transducing vectors. Although at least five serotypes exist (AAV types 1 to 5 [AAV1 to -5]), only AAV2, AAV3, and AAV4 have been sequenced, and the vectors in use were almost all derived from AAV2. Here we report the cloning and sequencing of a second AAV3 genome and a new AAV serotype designated AAV6 that is related to AAV1. AAV2, AAV3, and AAV6 were 82% identical at the nucleotide sequence level, a...

  8. MATRIX-VECTOR ALGORITHMS FOR NORMALIZING FACTORS IN ALGEBRAIC BAYESIAN NETWORKS LOCAL POSTERIORI INFERENCE

    Directory of Open Access Journals (Sweden)

    A. A. Zolotin

    2015-01-01

    Full Text Available We consider a task of local posteriori inference description by means of matrix-vector equations in algebraical Bayesian networks that represent a class of probabilistic graphical models. Such equations were generally presented in previous publications, however containing normalizing factors that were provided with algorithmic descriptions of their calculations instead of the desired matrix-vector interpretation. To eliminate this gap, the normalized factors were firstly represented as scalar products. Then, it was successfully shown that one of the components in each scalar product can be expressed as a Kronecker degree of a constant two-dimensional vector. Later on, non-normalized posteriori inference matrixoperator transplantation and further transfer within each scalar product yielded a representation of one of the scalar product components as a sequence of tensor products of two-dimensional vectors. The latter vectors have only two possible values in one case and three values in the other. The choice among those values is determined by the structure of input evidence. The second component of each scalar products is the vector with original data. The calculations performed gave the possibility for constructing corresponding vectors; the paper contains a table with proper examples for some of them. Local posteriori inference representation for matrix-vector equations simplify the development of local posteriori inference algorithms, their verification and further implementation based on available libraries. These equations also give the possibility for application of classical mathematical techniques to the obtained results analysis. Finally, the results obtained make it possible to apply the method of postponed calculations. This method helps avoiding construction of big-size vectors; instead, the vectors components can be calculated just in time they are needed by means of bitwise operations.

  9. Dengue Vectors and their Spatial Distribution.

    Science.gov (United States)

    Higa, Yukiko

    2011-12-01

    The distribution of dengue vectors, Ae. aegypti and Ae. albopictus, is affected by climatic factors. In addition, since their life cycles are well adapted to the human environment, environmental changes resulting from human activity such as urbanization exert a great impact on vector distribution. The different responses of Ae. aegypti and Ae albopictus to various environments result in a difference in spatial distribution along north-south and urban-rural gradients, and between the indoors and outdoors. In the north-south gradient, climate associated with survival is an important factor in spatial distribution. In the urban-rural gradient, different distribution reflects a difference in adult niches and is modified by geographic and human factors. The direct response of the two species to the environment around houses is related to different spatial distribution indoors and outdoors. Dengue viruses circulate mainly between human and vector mosquitoes, and the vector presence is a limiting factor of transmission. Therefore, spatial distribution of dengue vectors is a significant concern in the epidemiology of the disease.Current technologies such as GIS, satellite imagery and statistical models allow researchers to predict the spatial distribution of vectors in the changing environment. Although it is difficult to confirm the actual effect of environmental and climate changes on vector abundance and vector-borne diseases, environmental changes caused by humans and human behavioral changes due to climate change can be expected to exert an impact on dengue vectors. Longitudinal monitoring of dengue vectors and viruses is therefore necessary.

  10. Predicting post-translational lysine acetylation using support vector machines

    DEFF Research Database (Denmark)

    Gnad, Florian; Ren, Shubin; Choudhary, Chunaram

    2010-01-01

    Lysine acetylation is a post-translational protein modification and a primary regulatory mechanism that controls many cell signaling processes. Lysine acetylation sites are recognized by acetyltransferases and deacetylases through sequence patterns (motifs). Recently, we used high-resolution mass...... spectrometry to identify 3600 lysine acetylation sites on 1750 human proteins covering most of the previously annotated sites and providing the most comprehensive acetylome so far. This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico...

  11. A New Conic Approach to Semisupervised Support Vector Machines

    Directory of Open Access Journals (Sweden)

    Ye Tian

    2016-01-01

    Full Text Available We propose a completely positive programming reformulation of the 2-norm soft margin S3VM model. Then, we construct a sequence of computable cones of nonnegative quadratic forms over a union of second-order cones to approximate the underlying completely positive cone. An ϵ-optimal solution can be found in finite iterations using semidefinite programming techniques by our method. Moreover, in order to obtain a good lower bound efficiently, an adaptive scheme is adopted in our approximation algorithm. The numerical results show that the proposed algorithm can achieve more accurate classifications than other well-known conic relaxations of semisupervised support vector machine models in the literature.

  12. Capsid Engineering of Adenovirus Vectors: Overcoming Early Vector-Host Interactions for Therapy.

    Science.gov (United States)

    Hagedorn, Claudia; Kreppel, Florian

    2017-10-01

    Adenovirus-based vectors comprise the most frequently used vector type in clinical studies to date. Both intense lab research and insights from the clinical trials reveal the importance of a comprehensive understanding of vector-host interactions. Especially for systemic intravenous adenovirus vector delivery, it is paramount to develop safe and efficacious vectors. Very early vector-host interactions that take place in blood long before the first cell is being transduced are phenomena triggered by the surface, shape, and size of the adenovirus vector particles. Not surprisingly, a multitude of different technologies ranging from genetics to chemistry has been developed to alter the adenovirus vector surface. In this review, we discuss the most important technologies and evaluate them for their suitability to overcome hurdles imposed by early vector-host interactions.

  13. Stability and Safety of an AAV Vector for Treating RPGR-ORF15 X-Linked Retinitis Pigmentosa.

    Science.gov (United States)

    Deng, Wen-Tao; Dyka, Frank M; Dinculescu, Astra; Li, Jie; Zhu, Ping; Chiodo, Vince A; Boye, Sanford L; Conlon, Thomas J; Erger, Kirsten; Cossette, Travis; Hauswirth, William W

    2015-09-01

    Our collaborative successful gene replacement therapy using AAV vectors expressing a variant of human RPGR-ORF15 in two canine models provided therapeutic proof of concept for translation into human treatment. The ORF15 sequence contained within this AAV vector, however, has ORF15 DNA sequence variations compared to the published sequence that are likely due to its unusual composition of repetitive purine nucleotides. This mutability is a concern for AAV vector production and safety when contemplating a human trial. In this study, we establish the safety profile of AAV-hIRBP-hRPGR and AAV-hGRK1-hRPGR vectors used in the initial canine proof-of-principle experiments by demonstrating hRPGR-ORF15 sequence stability during all phases of manipulation, from plasmid propagation to vector production to its stability in vivo after subretinal administration to animals. We also evaluate potential toxicity in vivo by investigating protein expression, retinal structure and function, and vector biodistribution. Expression of hRPGR is detected in the inner segments and synaptic terminals of photoreceptors and is restricted to the connecting cilium when the vector is further diluted. Treated eyes exhibit no toxicity as assessed by retinal histopathology, immunocytochemistry, optical coherence tomography, fundoscopy, electroretinogram, and vector biodistribution. Therefore, the hRPGR-ORF15 variant in our AAV vectors appears to be a more stable form than the endogenous hRPGR cDNA when propagated in vitro. Its safety profile presented here in combination with its proven efficacy supports future gene therapy clinical trials.

  14. Holistic quaternion vector convolution filter for RGB-depth video contour detection

    Science.gov (United States)

    Ti, Chunli; Xu, Guodong; Guan, Yudong; Teng, Yidan; Zhang, Ye

    2017-05-01

    A quaternion vector gradient filter is proposed for RGB-depth (RGB-D) video contour detection. First, a holistic quaternion vector system is introduced to synthetically express the color and depth information, by adding the depth to its scalar part. Then, a convolution differential operator for quaternion vector is proposed to highlight edges with both depth and chromatic variations but restrain the gradient of intensity term. In addition, the quaternion vector gradients are adaptively weighted utilizing depth confidence measure and the quadtree decomposition of the coding tree units in the video streaming. Results on the 3-D high-efficiency video coding test sequences and quantitative simulated experiments on Berkeley segmentation datasets both indicate the availability of the proposed gradient-based method on detecting the semantic contour of the RGB-D videos.

  15. Gene Therapy with Helper-Dependent Adenoviral Vectors: Current Advances and Future Perspectives

    Directory of Open Access Journals (Sweden)

    Philip Ng

    2010-09-01

    Full Text Available Recombinant Adenoviral vectors represent one of the best gene transfer platforms due to their ability to efficiently transduce a wide range of quiescent and proliferating cell types from various tissues and species. The activation of an adaptive immune response against the transduced cells is one of the major drawbacks of first generation Adenovirus vectors and has been overcome by the latest generation of recombinant Adenovirus, the Helper-Dependent Adenoviral (HDAd vectors. HDAds have innovative features including the complete absence of viral coding sequences and the ability to mediate high level transgene expression with negligible chronic toxicity. This review summarizes the many aspects of HDAd biology and structure with a major focus on in vivo gene therapy application and with an emphasis on the unsolved issues that these vectors still presents toward clinical application.

  16. Adeno-associated virus vector-mediated transgene integration into neurons and other nondividing cell targets.

    Science.gov (United States)

    Wu, P; Phillips, M I; Bui, J; Terwilliger, E F

    1998-07-01

    The site-specific integration of wild-type adeno-associated virus (wtAAV) into the human genome is a very attractive feature for the development of AAV-based gene therapy vectors. However, knowledge about integration of wtAAV, as well as currently configured recombinant AAV (rAAV) vectors, is limited. By using a modified Alu-PCR technique to amplify and sequence the vector-cellular junctions, we provide the first direct evidence both in vitro and in vivo of rAAV-mediated transgene integration in several types of nondividing cells, including neurons. This novel technique will be highly useful for further delineating the mechanisms underlying AAV-mediated integration, including issues of frequency, site preference, and DNA rearrangement in human as well as animal cells. Results from these studies should be beneficial for the development of the next generation of gene delivery vectors.

  17. A cryptic promoter in potato virus X vector interrupted plasmid construction

    Directory of Open Access Journals (Sweden)

    Schultz Ronald D

    2007-03-01

    Full Text Available Abstract Background Potato virus X has been developed into an expression vector for plants. It is widely used to express foreign genes. In molecular manipulation, the foreign genes need to be sub-cloned into the vector. The constructed plasmid needs to be amplified. Usually, during amplification stage, the foreign genes are not expressed. However, if the foreign gene is expressed, the construction work could be interrupted. Two different viral genes were sub-cloned into the vector, but only one foreign gene was successfully sub-cloned. The other foreign gene, canine parvovirus type 2 (CPV-2 VP1 could not be sub-cloned into the vector and amplified without mutation (frame shift mutation. Results A cryptic promoter in the PVX vector was discovered with RT-PCR. The promoter activity was studied with Northern blots and Real-time RT-PCR. Conclusion It is important to recognize the homologous promoter sequences in the vector when a virus is developed as an expression vector. During the plasmid amplification stage, an unexpected expression of the CPV-2 VP1 gene (not in the target plants, but in E. coli can interrupt the downstream work.

  18. Radioiodinated Capsids Facilitate In Vivo Non-Invasive Tracking of Adeno-Associated Gene Transfer Vectors.

    Science.gov (United States)

    Kothari, P; De, B P; He, B; Chen, A; Chiuchiolo, M J; Kim, D; Nikolopoulou, A; Amor-Coarasa, A; Dyke, J P; Voss, H U; Kaminsky, S M; Foley, C P; Vallabhajosula, S; Hu, B; DiMagno, S G; Sondhi, D; Crystal, R G; Babich, J W; Ballon, D

    2017-01-06

    Viral vector mediated gene therapy has become commonplace in clinical trials for a wide range of inherited disorders. Successful gene transfer depends on a number of factors, of which tissue tropism is among the most important. To date, definitive mapping of the spatial and temporal distribution of viral vectors in vivo has generally required postmortem examination of tissue. Here we present two methods for radiolabeling adeno-associated virus (AAV), one of the most commonly used viral vectors for gene therapy trials, and demonstrate their potential usefulness in the development of surrogate markers for vector delivery during the first week after administration. Specifically, we labeled adeno-associated virus serotype 10 expressing the coding sequences for the CLN2 gene implicated in late infantile neuronal ceroid lipofuscinosis with iodine-124. Using direct (Iodogen) and indirect (modified Bolton-Hunter) methods, we observed the vector in the murine brain for up to one week using positron emission tomography. Capsid radioiodination of viral vectors enables non-invasive, whole body, in vivo evaluation of spatial and temporal vector distribution that should inform methods for efficacious gene therapy over a broad range of applications.

  19. Recent advances in genetic modification of adenovirus vectors for cancer treatment.

    Science.gov (United States)

    Yamamoto, Yuki; Nagasato, Masaki; Yoshida, Teruhiko; Aoki, Kazunori

    2017-05-01

    Adenoviruses are widely used to deliver genes to a variety of cell types and have been used in a number of clinical trials for gene therapy and oncolytic virotherapy. However, several concerns must be addressed for the clinical use of adenovirus vectors. Selective delivery of a therapeutic gene by adenovirus vectors to target cancer is precluded by the widespread distribution of the primary cellular receptors. The systemic administration of adenoviruses results in hepatic tropism independent of the primary receptors. Adenoviruses induce strong innate and acquired immunity in vivo. Furthermore, several modifications to these vectors are necessary to enhance their oncolytic activity and ensure patient safety. As such, the adenovirus genome has been engineered to overcome these problems. The first part of the present review outlines recent progress in the genetic modification of adenovirus vectors for cancer treatment. In addition, several groups have recently developed cancer-targeting adenovirus vectors by using libraries that display random peptides on a fiber knob. Pancreatic cancer-targeting sequences have been isolated, and these oncolytic vectors have been shown by our group to be associated with a higher gene transduction efficiency and more potent oncolytic activity in cell lines, murine models, and surgical specimens of pancreatic cancer. In the second part of this review, we explain that combining cancer-targeting strategies can be a promising approach to increase the clinical usefulness of oncolytic adenovirus vectors. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  20. Genetic manipulation of specific neural circuits by use of a viral vector system.

    Science.gov (United States)

    Kobayashi, Kenta; Kato, Shigeki; Kobayashi, Kazuto

    2017-01-05

    To understand the mechanisms underlying higher brain functions, we need to analyze the roles of specific neuronal pathways or cell types forming the complex neural networks. In the neuroscience field, the transgenic approach has provided a useful gene engineering tool for experimental studies of neural functions. The conventional transgenic technique requires the appropriate promoter regions that drive a neuronal type-specific gene expression, but the promoter sequences specifically functioning in each neuronal type are limited. Previously, we developed novel types of lentiviral vectors showing high efficiency of retrograde gene transfer in the central nervous system, termed highly efficient retrograde gene transfer (HiRet) vector and neuron-specific retrograde gene transfer (NeuRet) vector. The HiRet and NeuRet vectors enable genetical manipulation of specific neural pathways in diverse model animals in combination with conditional cell targeting, synaptic transmission silencing, and gene expression systems. These newly developed vectors provide powerful experimental strategies to investigate, more precisely, the machineries exerting various neural functions. In this review, we give an outline of the HiRet and NeuRet vectors and describe recent representative applications of these viral vectors for studies on neural circuits.

  1. VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

    Directory of Open Access Journals (Sweden)

    Yiqing Xu

    2016-01-01

    Full Text Available Background. In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output. Implementation. To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG and vector graphic (SVG, EPS, and PDF. Result. Users can upload sequence alignments from blast and collinearity relationship from the synteny analysis tools. The website can generate the vector or raster graphical results automatically. We also provide a java-based bytecode binary to enable the command-line execution.

  2. Ectopic expression of the erythrocyte band 3 anion exchange protein, using a new avian retrovirus vector

    DEFF Research Database (Denmark)

    Fuerstenberg, S; Beug, H; Introna, M

    1990-01-01

    into protein. Using the Escherichia coli beta-galactosidase gene cloned into the vector as a test construct, expression of enzyme activity could be detected in 90 to 95% of transfected target cells and in 80 to 85% of subsequently infected cells. In addition, a cDNA encoding the avian erythrocyte band 3 anion......A retrovirus vector was constructed from the genome of avian erythroblastosis virus ES4. The v-erbA sequences of avian erythroblastosis virus were replaced by those coding for neomycin phosphotransferase, creating a gag-neo fusion protein which provides G418 resistance as a selectable marker. The v......-erbB sequences following the splice acceptor were replaced by a cloning linker allowing insertion of foreign genes. The vector has been tested in conjunction with several helper viruses for the transmission of G418 resistance, titer, stability, transcription, and the transduction and expression of foreign genes...

  3. Detection of distorted frames in retinal video-sequences via machine learning

    Science.gov (United States)

    Kolar, Radim; Liberdova, Ivana; Odstrcilik, Jan; Hracho, Michal; Tornow, Ralf P.

    2017-07-01

    This paper describes detection of distorted frames in retinal sequences based on set of global features extracted from each frame. The feature vector is consequently used in classification step, in which three types of classifiers are tested. The best classification accuracy 96% has been achieved with support vector machine approach.

  4. Engineered XcmI cassette-containing vector for PCR-based ...

    Indian Academy of Sciences (India)

    T-vector; direct cloning; XcmI cassette; sequencing; PCR; marine population genetics. Author Affiliations. Futoshi Aranishi1 2 Takane Okimoto1 3. Molecular Biology Division, National Institute of Fisheries Science, Yokohama 236-8648, Japan; Department of Biological and Environmental Sciences, Mirjazaki University, ...

  5. Methods of treating Parkinson's disease using viral vectors

    Energy Technology Data Exchange (ETDEWEB)

    Bankiewicz, Krystof; Cunningham, Janet

    2016-11-15

    Methods of delivering viral vectors, particularly recombinant adeno-associated virus (rAAV) virions, to the central nervous system (CNS) using convection enhanced delivery (CED) are provided. The rAAV virions include a nucleic acid sequence encoding a therapeutic polypeptide. The methods can be used for treating CNS disorders such as for treating Parkinson's Disease.

  6. Factors Affecting Learning of Vector Math from Computer-Based Practice: Feedback Complexity and Prior Knowledge

    Science.gov (United States)

    Heckler, Andrew F.; Mikula, Brendon D.

    2016-01-01

    In experiments including over 450 university-level students, we studied the effectiveness and time efficiency of several levels of feedback complexity in simple, computer-based training utilizing static question sequences. The learning domain was simple vector math, an essential skill in introductory physics. In a unique full factorial design, we…

  7. Constrained set-up of the tGAP structure for progressive vector data transfer

    NARCIS (Netherlands)

    Haunert, Jan-Henrik; Yang, B.; Weibel, R.; Dilo, Arta; van Oosterom, Peter

    A promising approach to submit a vector map from a server to a mobile client is to send a coarse representation first, which then is incrementally refined. We consider the problem of defining a sequence of such increments for areas of different land-cover classes in a planar partition. In order to

  8. Introduction of the Anopheles bancroftii Mosquito, a Malaria Vector, into New Caledonia.

    Science.gov (United States)

    Pol, Morgane; Kilama, Sosiasi; Duperier, Sandy; Soupé-Gilbert, Marie-Estelle; Calvez, Elodie; Pocquet, Nicolas

    2018-03-01

    In June 2017, an Anopheles mosquito species was detected in New Caledonia. Morphologic identification and genomic sequencing revealed that the specimens tested belong to An. bancroftii genotype A1. This introduction underscores the risk for local malaria transmission and the vulnerability of New Caledonia to vector introduction.

  9. Supporting medical decisions with vector decision trees.

    Science.gov (United States)

    Sprogar, M; Kokol, P; Zorman, M; Podgorelec, V; Yamamoto, R; Masuda, G; Sakamoto, N

    2001-01-01

    The article presents the extension of a common decision tree concept to a multidimensional - vector - decision tree constructed with the help of evolutionary techniques. In contrary to the common decision tree the vector decision tree can make more than just one suggestion per input sample. It has the functionality of many separate decision trees acting on a same set of training data and answering different questions. Vector decision tree is therefore simple in its form, is easy to use and analyse and can express some relationships between decisions not visible before. To explore and test the possibilities of this concept we developed a software tool--DecRain--for building vector decision trees using the ideas of evolutionary computing. Generated vector decision trees showed good results in comparison to classical decision trees. The concept of vector decision trees can be safely and effectively used in any decision making process.

  10. Vector assembly of colloids on monolayer substrates

    Science.gov (United States)

    Jiang, Lingxiang; Yang, Shenyu; Tsang, Boyce; Tu, Mei; Granick, Steve

    2017-06-01

    The key to spontaneous and directed assembly is to encode the desired assembly information to building blocks in a programmable and efficient way. In computer graphics, raster graphics encodes images on a single-pixel level, conferring fine details at the expense of large file sizes, whereas vector graphics encrypts shape information into vectors that allow small file sizes and operational transformations. Here, we adapt this raster/vector concept to a 2D colloidal system and realize `vector assembly' by manipulating particles on a colloidal monolayer substrate with optical tweezers. In contrast to raster assembly that assigns optical tweezers to each particle, vector assembly requires a minimal number of optical tweezers that allow operations like chain elongation and shortening. This vector approach enables simple uniform particles to form a vast collection of colloidal arenes and colloidenes, the spontaneous dissociation of which is achieved with precision and stage-by-stage complexity by simply removing the optical tweezers.

  11. Functional characterization of a monoclonal antibody epitope using a lambda phage display-deep sequencing platform

    National Research Council Canada - National Science Library

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; Venza, Mario; Venza, Isabella; Borgogni, Erica; Castellino, Flora; Midiri, Angelina; Galbo, Roberta; Romeo, Letizia; Biondo, Carmelo; Masignani, Vega; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2016-01-01

    ...), which is recognized by mAb 12C1. An fHbp library, engineered on a lambda phage vector enabling surface expression of polypeptides of widely different length, was subjected to massive parallel sequencing of the phage inserts...

  12. [Spatial vector electrocardiography: technique, perspectives of use].

    Science.gov (United States)

    Bakutskiĭ, V N; Volobuev, A N; Kriukov, N N; Romanchuk, P I

    2003-01-01

    Potentials of the use of computer synthesis of integral electrical vector of the heart D0 are described. Calculation of spatial angular vector velocity and linear velocity of its movement along trajectory can be carried out in a framework of biophysical dipole model. Spatial presentation of vector is realized and its behavior in accordance with established pathologies discussed. Possible diagnostic value of obtained results and utility of their introduction into clinical practice are stressed.

  13. A novel hierarchical clustering algorithm for gene sequences

    Directory of Open Access Journals (Sweden)

    Wei Dan

    2012-07-01

    Full Text Available Abstract Background Clustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. This method transforms DNA sequences into the feature vectors which contain the occurrence, location and order relation of k-tuples in DNA sequence. Afterwards, a hierarchical procedure is applied to clustering DNA sequences based on the feature vectors. Results The proposed distance measure and clustering method are evaluated by clustering functionally related genes and by phylogenetic analysis. This method is also compared with BlastClust, CD-HIT-EST and some others. The experimental results show our method is effective in classifying DNA sequences with similar biological characteristics and in discovering the underlying relationship among the sequences. Conclusions We introduced a novel clustering algorithm which is based on a new sequence similarity measure. It is effective in classifying DNA sequences with similar biological characteristics and in discovering the relationship among the sequences.

  14. Genetic manipulation of endosymbionts to control vector and vector borne diseases

    Directory of Open Access Journals (Sweden)

    Jay Prakash Gupta

    Full Text Available Vector borne diseases (VBD are on the rise because of failure of the existing methods of control of vector and vector borne diseases and the climate change. A steep rise of VBDs are due to several factors like selection of insecticide resistant vector population, drug resistant parasite population and lack of effective vaccines against the VBDs. Environmental pollution, public health hazard and insecticide resistant vector population indicate that the insecticides are no longer a sustainable control method of vector and vector-borne diseases. Amongst the various alternative control strategies, symbiont based approach utilizing endosymbionts of arthropod vectors could be explored to control the vector and vector borne diseases. The endosymbiont population of arthropod vectors could be exploited in different ways viz., as a chemotherapeutic target, vaccine target for the control of vectors. Expression of molecules with antiparasitic activity by genetically transformed symbiotic bacteria of disease-transmitting arthropods may serve as a powerful approach to control certain arthropod-borne diseases. Genetic transformation of symbiotic bacteria of the arthropod vector to alter the vector’s ability to transmit pathogen is an alternative means of blocking the transmission of VBDs. In Indian scenario, where dengue, chikungunya, malaria and filariosis are prevalent, paratransgenic based approach can be used effectively. [Vet World 2012; 5(9.000: 571-576

  15. Scalar Calibration of Vector Magnetometers

    DEFF Research Database (Denmark)

    Merayo, José M.G.; Brauer, Peter; Primdahl, Fritz

    2000-01-01

    The calibration parameters of a vector magnetometer are estimated only by the use of a scalar reference magnetometer. The method presented in this paper differs from those previously reported in its linearized parametrization. This allows the determination of three offsets or signals in the absence...... of a magnetic field, three scale factors for normalization of the axes and three non-orthogonality angles which build up an orthogonal system intrinsically in the sensor. The advantage of this method compared with others lies in its linear least squares estimator, which finds independently and uniquely...... the parameters for a given data set. Therefore, a magnetometer may be characterized inexpensively in the Earth's magnetic-field environment. This procedure has been used successfully in the pre-flight calibration of the state-of-the-art magnetometers on board the magnetic mapping satellites Orsted, Astrid-2...

  16. 3D vector flow imaging

    DEFF Research Database (Denmark)

    Pihl, Michael Johannes

    The main purpose of this PhD project is to develop an ultrasonic method for 3D vector flow imaging. The motivation is to advance the field of velocity estimation in ultrasound, which plays an important role in the clinic. The velocity of blood has components in all three spatial dimensions, yet...... Oscillation (TO) method, which estimates both the axial and the lateral velocity components. The first part of the scientific contribution demonstrates that a commercial implementation of the TO method is feasible. Afterwards, the method is expanded to a phased array geometry, and performance metrics based......:1 parallel receive beamforming. Simulation results demonstrate the feasibility of the method. In the final part, an experimental investigation of the 3D TO method is presented. Velocity measurements of steady flow were conducted in a flow-rig system, and the data were acquired using an experimental...

  17. An elusive vector dark matter

    Directory of Open Access Journals (Sweden)

    Chuan-Ren Chen

    2015-02-01

    Full Text Available Even though the sensitivity of direct dark matter search experiments reaches the level of about 10−45 cm2, no confident signal of dark matter has been observed. We point out that, if dark matter is a vector boson, the null result in direct dark matter search experiments may be due to the destructive effects in dark-matter–nucleon elastic scattering. We illustrate the scenario using a modified Higgs portal model that includes exotic quarks. The significant cancellation can occur for a certain mass gap between new heavy quark and dark matter. As a result, the spin-independent dark-matter–nucleon elastic scattering is so suppressed that the future direct search experiments will hardly observe the signal of dark matter.

  18. New high-cloning-efficiency vectors for complementation studies and recombinant protein overproduction in Escherichia coli and Salmonella enterica.

    Science.gov (United States)

    VanDrisse, C M; Escalante-Semerena, J C

    2016-07-01

    Galloway et al. recently described a method to alter vectors to include Type IIS restriction enzymes for high efficiency cloning. Utilizing this method, the multiple cloning sites of complementation and overexpression vectors commonly used in our laboratory were altered to contain recognition sequences of the Type IIS restriction enzyme, BspQI. Use of this enzyme increased the rate of cloning success to >97% efficiency. L(+)-Arabinose-inducible complementation vectors and overexpression vectors encoding N-terminal recombinant tobacco etch virus protease (rTEV)-cleavable H6-tags were altered to contain BspQI sites that allowed for cloning into all vectors using identical primer overhangs. Additionally, a vector used for directing the synthesis of proteins with a C-terminal, rTEV-cleavable H6-tag was engineered to contain BspQI sites, albeit with different overhangs from that of the previously mentioned vectors. Here we apply a method used to engineer cloning vectors to contain BspQI sites and the use of each vector in either in vivo complementation studies or in vitro protein purifications. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Main: Sequences [KOME

    Lifescience Database Archive (English)

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

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

    Science.gov (United States)

    Heather, James M.; Chain, Benjamin

    2016-01-01

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

  1. Vector optimization set-valued and variational analysis

    CERN Document Server

    Chen, Guang-ya; Yang, Xiaogi

    2005-01-01

    This book is devoted to vector or multiple criteria approaches in optimization. Topics covered include: vector optimization, vector variational inequalities, vector variational principles, vector minmax inequalities and vector equilibrium problems. In particular, problems with variable ordering relations and set-valued mappings are treated. The nonlinear scalarization method is extensively used throughout the book to deal with various vector-related problems. The results presented are original and should be interesting to researchers and graduates in applied mathematics and operations research

  2. Zinc finger nuclease and homing endonuclease-mediated assembly of multigene plant transformation vectors.

    Science.gov (United States)

    Zeevi, Vardit; Liang, Zhuobin; Arieli, Uri; Tzfira, Tzvi

    2012-01-01

    Binary vectors are an indispensable component of modern Agrobacterium tumefaciens-mediated plant genetic transformation systems. A remarkable variety of binary plasmids have been developed to support the cloning and transfer of foreign genes into plant cells. The majority of these systems, however, are limited to the cloning and transfer of just a single gene of interest. Thus, plant biologists and biotechnologists face a major obstacle when planning the introduction of multigene traits into transgenic plants. Here, we describe the assembly of multitransgene binary vectors by using a combination of engineered zinc finger nucleases (ZFNs) and homing endonucleases. Our system is composed of a modified binary vector that has been engineered to carry an array of unique recognition sites for ZFNs and homing endonucleases and a family of modular satellite vectors. By combining the use of designed ZFNs and commercial restriction enzymes, multiple plant expression cassettes were sequentially cloned into the acceptor binary vector. Using this system, we produced binary vectors that carried up to nine genes. Arabidopsis (Arabidopsis thaliana) protoplasts and plants were transiently and stably transformed, respectively, by several multigene constructs, and the expression of the transformed genes was monitored across several generations. Because ZFNs can potentially be engineered to digest a wide variety of target sequences, our system allows overcoming the problem of the very limited number of commercial homing endonucleases. Thus, users of our system can enjoy a rich resource of plasmids that can be easily adapted to their various needs, and since our cloning system is based on ZFN and homing endonucleases, it may be possible to reconstruct other types of binary vectors and adapt our vectors for cloning on multigene vector systems in various binary plasmids.

  3. Whole Genome Sequencing

    Science.gov (United States)

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

  4. Sequence Read Archive (SRA)

    Data.gov (United States)

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

  5. Single-Step Conversion of Cells to Retrovirus Vector Producers with Herpes Simplex Virus–Epstein-Barr Virus Hybrid Amplicons

    Science.gov (United States)

    Sena-Esteves, Miguel; Saeki, Yoshinaga; Camp, Sara M.; Chiocca, E. Antonio; Breakefield, Xandra O.

    1999-01-01

    We report here on the development and characterization of a novel herpes simplex virus type 1 (HSV-1) amplicon-based vector system which takes advantage of the host range and retention properties of HSV–Epstein-Barr virus (EBV) hybrid amplicons to efficiently convert cells to retrovirus vector producer cells after single-step transduction. The retrovirus genes gag-pol and env (GPE) and retroviral vector sequences were modified to minimize sequence overlap and cloned into an HSV-EBV hybrid amplicon. Retrovirus expression cassettes were used to generate the HSV-EBV-retrovirus hybrid vectors, HERE and HERA, which code for the ecotropic and the amphotropic envelopes, respectively. Retrovirus vector sequences encoding lacZ were cloned downstream from the GPE expression unit. Transfection of 293T/17 cells with amplicon plasmids yielded retrovirus titers between 106 and 107 transducing units/ml, while infection of the same cells with amplicon vectors generated maximum titers 1 order of magnitude lower. Retrovirus titers were dependent on the extent of transduction by amplicon vectors for the same cell line, but different cell lines displayed varying capacities to produce retrovirus vectors even at the same transduction efficiencies. Infection of human and dog primary gliomas with this system resulted in the production of retrovirus vectors for more than 1 week and the long-term retention and increase in transgene activity over time in these cell populations. Although the efficiency of this system still has to be determined in vivo, many applications are foreseeable for this approach to gene delivery. PMID:10559361

  6. 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.

    OpenAIRE

    Hernandez Castro, Luis E.; Paterno, Marta; Villacís, Anita G.; Andersson, Björn; Costales, Jaime A.; De Noia, Michele; Ocaña-Mayorga, Sofía; Cesar A Yumiseva; Grijalva, Mario J.; Llewellyn, Martin S.

    2017-01-01

    Background:\\ud \\ud Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide ...

  7. Human papillomavirus gene sequences in washed human sperm deoxyribonucleic acid.

    Science.gov (United States)

    Chan, P J; Su, B C; Kalugdan, T; Seraj, I M; Tredway, D R; King, A

    1994-05-01

    The present study demonstrated the presence of HPV gene sequences in Percoll-washed sperm cells using polymerase chain reaction primers targeting smaller gene regions. Up to 64% of the sperm specimens were shown to contain gene sequences indicative of the presence of HPV. Human papillomavirus type 16 was detected about twice as often as HPV type 18. The results suggest the possible role of sperm as a vector for HPV.

  8. Extremal vectors and rectifiability | Enflo | Quaestiones Mathematicae

    African Journals Online (AJOL)

    The concept of extremal vectors of a linear operator with a dense range but not onto on a Hilbert space was introduced by P. Enflo in 1996 as a new approach to study invariant subspaces. Following this, there were several studies on analytic and geometric properties of backward minimal vectors and their applications to ...

  9. Nonlinear dynamics of a vectored thrust aircraft

    DEFF Research Database (Denmark)

    Sørensen, C.B; Mosekilde, Erik

    1996-01-01

    With realistic relations for the aerodynamic coefficients, numerical simulations are applied to study the longitudional dynamics of a thrust vectored aircraft. As function of the thrust magnitude and the thrust vectoring angle the equilibrium state exhibits two saddle-node bifurcations and three...

  10. Clustering Categories in Support Vector Machines

    DEFF Research Database (Denmark)

    Carrizosa, Emilio; Nogales-Gómez, Amaya; Morales, Dolores Romero

    2017-01-01

    The support vector machine (SVM) is a state-of-the-art method in supervised classification. In this paper the Cluster Support Vector Machine (CLSVM) methodology is proposed with the aim to increase the sparsity of the SVM classifier in the presence of categorical features, leading to a gain in in...

  11. Semantic Vector Space Model: Implementation and Evaluation.

    Science.gov (United States)

    Liu, Geoffrey Z.

    1997-01-01

    Presents the Semantic Vector Space Model, a text representation and searching technique based on the combination of Vector Space Model with heuristic syntax parsing and distributed representation of semantic case structures. In this model, both documents and queries are represented as semantic matrices, and retrieval is achieved by computing…

  12. Construction of expression vectors carrying mouse peroxisomal ...

    African Journals Online (AJOL)

    pUcD3 eukaryotic expression vector to express tagged-PEP protein for transient transfection analysis and identifying intracellular localization of PEP protein in future experiments. PEP-cDNA was amplified in different PCR reactions using pEGFP-PEP vector and 2 sets of primers introducing specific restriction sites at the ...

  13. Radiative corrections to vector boson masses

    NARCIS (Netherlands)

    Veltman, M.J.G.

    1980-01-01

    Weak and e.m. radiative corrections to vector boson masses are computed. Including corrections due to the presently known leptons and quarks, mass shifts of+3080 and +3310 MeV are obtained for the masses of the charged and neutral vector boson.

  14. Deep Support Vector Machines for Regression Problems

    NARCIS (Netherlands)

    Wiering, Marco; Schutten, Marten; Millea, Adrian; Meijster, Arnold; Schomaker, Lambertus

    2013-01-01

    In this paper we describe a novel extension of the support vector machine, called the deep support vector machine (DSVM). The original SVM has a single layer with kernel functions and is therefore a shallow model. The DSVM can use an arbitrary number of layers, in which lower-level layers contain

  15. Painleve-Kuratowski Convergences for the Solution Sets of Set-Valued Weak Vector Variational Inequalities

    Directory of Open Access Journals (Sweden)

    Teo KL

    2008-01-01

    Full Text Available Painleve-Kuratowski convergence of the solution sets is investigated for the perturbed set-valued weak vector variational inequalities with a sequence of mappings converging continuously. The closedness and Painleve-Kuratowski upper convergence of the solution sets are obtained. We also obtain Painleve-Kuratowski upper convergence when the sequence of mappings converges graphically. By virtue of a sequence of gap functions and a key assumption, Painleve-Kuratowski lower convergence of the solution sets is established. Some examples are given for the illustration of our results.

  16. Cloning of Soluble Human Stem Cell Factor in pET-26b(+ Vector

    Directory of Open Access Journals (Sweden)

    Salman Asghari

    2014-03-01

    Full Text Available Purpose: Stem cell factor (SCF plays an important role in the survival, proliferation and differentiation of hematopoietic stem cells and progenitor cells. Potential therapeutic applications of SCF include hematopoietic stem cell mobilization, exvivo stem/progenitor cell expansion, gene therapy, and immunotherapy. Considering the cost and problem in accessibility of this product in Iran, clears the importance of indigenizing production of rhSCF. In the present work, we describe the construction of the soluble rhSCF expression vector in pET-26b (+ with periplasmic localization potential. Methods: Following PCR amplification of human SCF ORF, it is cloned in pET-26b (+ vector in NcoI and XhoI sites. The recombinant construct was transformed into BL21 (DE3 Ecoli strains. Results: The construction of recombinant vector was verified by colony PCR and sequence analysis of pET26b-hSCF vector. Sequence analyses proved that human SCF ORF has been inserted into NcoI and XhoI site with correct orientation downstream of strong T7 promotor and showed no nucleotide errors. Conclusion: The SCF ORF was successfully cloned in pET-26b (+ expression vector and is ready for future production of SCF protein.

  17. A Narcissus mosaic viral vector system for protein expression and flavonoid production

    Science.gov (United States)

    2013-01-01

    Background With the explosive numbers of sequences generated by next generation sequencing, the demand for high throughput screening to understand gene function has grown. Plant viral vectors have been widely used as tools in down-regulating plant gene expression. However, plant viral vectors can also express proteins in a very efficient manner and, therefore, can also serve as a valuable tool for characterizing proteins and their functions in metabolic pathways in planta. Results In this study, we have developed a Gateway®-based high throughput viral vector cloning system from Narcissus Mosaic Virus (NMV). Using the reporter genes of GFP and GUS, and the plant genes PAP1 (an R2R3 MYB which activates the anthocyanin pathway) and selenium-binding protein 1 (SeBP), we show that NMV vectors and the model plant Nicotiana benthamiana can be used for efficient protein expression, protein subcellular localization and secondary metabolite production. Conclusions Our results suggest that not only can the plant viral vector system be employed for protein work but also can potentially be amenable to producing valuable secondary metabolites on a large scale, as the system does not require plant regeneration from seed or calli, which are stages where certain secondary metabolites can interfere with development. PMID:23849589

  18. On Banach spaces of sequences and free linear logic exponential modality

    OpenAIRE

    Slavnov, Sergey

    2015-01-01

    We introduce a category of vector spaces modelling full propositional linear logic, similar to probabilistic coherence spaces and to Koethe sequences spaces. Its objects are {\\it rigged sequences spaces}, Banach spaces of sequences, with norms defined from pairing with finite sequences, and morphisms are bounded linear maps, continuous in a suitable topology. The main interest of the work is that our model gives a realization of the free linear logic exponentials construction.

  19. Malaria vector control: from past to future.

    Science.gov (United States)

    Raghavendra, Kamaraju; Barik, Tapan K; Reddy, B P Niranjan; Sharma, Poonam; Dash, Aditya P

    2011-04-01

    Malaria is one of the most common vector-borne diseases widespread in the tropical and subtropical regions. Despite considerable success of malaria control programs in the past, malaria still continues as a major public health problem in several countries. Vector control is an essential part for reducing malaria transmission and became less effective in recent years, due to many technical and administrative reasons, including poor or no adoption of alternative tools. Of the different strategies available for vector control, the most successful are indoor residual spraying and insecticide-treated nets (ITNs), including long-lasting ITNs and materials. Earlier DDT spray has shown spectacular success in decimating disease vectors but resulted in development of insecticide resistance, and to control the resistant mosquitoes, organophosphates, carbamates, and synthetic pyrethroids were introduced in indoor residual spraying with needed success but subsequently resulted in the development of widespread multiple insecticide resistance in vectors. Vector control in many countries still use insecticides in the absence of viable alternatives. Few developments for vector control, using ovitraps, space spray, biological control agents, etc., were encouraging when used in limited scale. Likewise, recent introduction of safer vector control agents, such as insect growth regulators, biocontrol agents, and natural plant products have yet to gain the needed scale of utility for vector control. Bacterial pesticides are promising and are effective in many countries. Environmental management has shown sufficient promise for vector control and disease management but still needs advocacy for inter-sectoral coordination and sometimes are very work-intensive. The more recent genetic manipulation and sterile insect techniques are under development and consideration for use in routine vector control and for these, standardized procedures and methods are available but need thorough

  20. Axial vector Z‧ and anomaly cancellation

    Science.gov (United States)

    Ismail, Ahmed; Keung, Wai-Yee; Tsao, Kuo-Hsing; Unwin, James

    2017-05-01

    Whilst the prospect of new Z‧ gauge bosons with only axial couplings to the Standard Model (SM) fermions is widely discussed, examples of anomaly-free renormalisable models are lacking in the literature. We look to remedy this by constructing several motivated examples. Specifically, we consider axial vectors which couple universally to all SM fermions, as well as those which are generation-specific, leptophilic, and leptophobic. Anomaly cancellation typically requires the presence of new coloured and charged chiral fermions, and we argue that in a large class of models masses of these new states are expected to be comparable to that of the axial vector. Finally, an axial vector mediator could provide a portal between SM and hidden sector states, and we also consider the possibility that the axial vector couples to dark matter. If the dark matter relic density is set due to freeze-out via the axial vector, this strongly constrains the parameter space.

  1. Cascade Support Vector Machines with Dimensionality Reduction

    Directory of Open Access Journals (Sweden)

    Oliver Kramer

    2015-01-01

    Full Text Available Cascade support vector machines have been introduced as extension of classic support vector machines that allow a fast training on large data sets. In this work, we combine cascade support vector machines with dimensionality reduction based preprocessing. The cascade principle allows fast learning based on the division of the training set into subsets and the union of cascade learning results based on support vectors in each cascade level. The combination with dimensionality reduction as preprocessing results in a significant speedup, often without loss of classifier accuracies, while considering the high-dimensional pendants of the low-dimensional support vectors in each new cascade level. We analyze and compare various instantiations of dimensionality reduction preprocessing and cascade SVMs with principal component analysis, locally linear embedding, and isometric mapping. The experimental analysis on various artificial and real-world benchmark problems includes various cascade specific parameters like intermediate training set sizes and dimensionalities.

  2. Geoacoustic inversion using the vector field

    Science.gov (United States)

    Crocker, Steven E.

    The main goal of this project was to study the use of the acoustic vector field, separately or in combination with the scalar field, to estimate the depth dependent geoacoustic properties of the seafloor via non-linear inversion. The study was performed in the context of the Sediment Acoustics Experiment 2004 (SAX04) conducted in the Northern Gulf of Mexico (GOM) where a small number of acoustic vector sensors were deployed in close proximity to the seafloor. A variety of acoustic waveforms were transmitted into the seafloor at normal incidence. The acoustic vector sensors were located both above and beneath the seafloor interface where they measured the acoustic pressure and the acoustic particle acceleration. Motion data provided by the buried vector sensors were affected by a suspension response that was sensitive to the mass properties of the sensor, the sediment density and sediment elasticity (e.g., shear wave speed). The suspension response for the buried vector sensors included a resonance within the analysis band of 0.4 to 2.0 kHz. The suspension resonance represented an unknown complex transfer function between the acoustic vector field in the seabed and data representing that field. Therefore, inverse methods developed for this study were required to 1) estimate dynamic properties of the sensor suspension resonance and 2) account for the associated corruption of vector field data. A method to account for the vector sensor suspense response function was integrated directly into the inversion methods such that vector channel data corruption was reduced and an estimate of the shear wave speed in the sediment was returned. Inversions of real and synthetic data sets indicated that information about sediment shear wave speed was carried by the suspension response of the buried sensors, as opposed to being contained inherently within the acoustic vector field.

  3. Infectious bursal disease virus as a replication-incompetent viral vector expressing green fluorescent protein.

    Science.gov (United States)

    Mosley, Yung-Yi C; Wu, Ching Ching; Lin, Tsang Long

    2017-01-01

    Infectious bursal disease virus (IBDV) has been established as a replication-competent viral vector capable of carrying an epitope at multiple loci in the genome. To enhance the safety and increase the insertion capacity of IBDV as a vector, a replication-incompetent IBDV vector was developed in the present study. The feasibility of replacing one of the viral gene loci, including pvp2, vp3, vp1, or the polyprotein vp243, with the sequence of green fluorescent protein (GFP) was explored. A method combining TCID50 and immunoperoxidase monolayer assay (IPMA) determined the most feasible locus for gene replacement to be pvp2. The genomic segment containing gfp at the pvp2 locus was able to be encapsidated into IBDV particles. Furthermore, the expression of GFP in GFP-IBDV infected cells was confirmed by Western blotting and GFP-IBDV particles showed similar morphology and size to that of wildtype IBDV by electron microscopy. By providing the deleted protein in trans in a packaging cell line (pVP2-DF1), replication-incompetent GFP-IBDV particles were successfully plaque-quantified. The gfp sequence from the plaque-forming GFP-IBDV in pVP2-DF1 was confirmed by RT-PCR and sequencing. To our knowledge, GFP-IBDV developed in the present study is the first replication-incompetent IBDV vector which expresses a foreign protein in infected cells without the capability to produce viral progeny. Additionally, such replication-incompetent IBDV vectors could serve as bivalent vaccine vectors for conferring protection against infections with IBDV and other economically important, or zoonotic, avian pathogens.

  4. Comparative genomic analysis of Drosophila melanogaster and vector mosquito developmental genes.

    Directory of Open Access Journals (Sweden)

    Susanta K Behura

    Full Text Available Genome sequencing projects have presented the opportunity for analysis of developmental genes in three vector mosquito species: Aedes aegypti, Culex quinquefasciatus, and Anopheles gambiae. A comparative genomic analysis of developmental genes in Drosophila melanogaster and these three important vectors of human disease was performed in this investigation. While the study was comprehensive, special emphasis centered on genes that 1 are components of developmental signaling pathways, 2 regulate fundamental developmental processes, 3 are critical for the development of tissues of vector importance, 4 function in developmental processes known to have diverged within insects, and 5 encode microRNAs (miRNAs that regulate developmental transcripts in Drosophila. While most fruit fly developmental genes are conserved in the three vector mosquito species, several genes known to be critical for Drosophila development were not identified in one or more mosquito genomes. In other cases, mosquito lineage-specific gene gains with respect to D. melanogaster were noted. Sequence analyses also revealed that numerous repetitive sequences are a common structural feature of Drosophila and mosquito developmental genes. Finally, analysis of predicted miRNA binding sites in fruit fly and mosquito developmental genes suggests that the repertoire of developmental genes targeted by miRNAs is species-specific. The results of this study provide insight into the evolution of developmental genes and processes in dipterans and other arthropods, serve as a resource for those pursuing analysis of mosquito development, and will promote the design and refinement of functional analysis experiments.

  5. Quaternion representation of RNA sequences and tertiary structures.

    Science.gov (United States)

    Magarshak, Y

    1993-01-01

    A quaternion representation of nucleotides is proposed, with representation of RNA sequences by vectors whose elements are quaternions. Structure and transition matrices in quaternion representation are defined. Correspondence between diagrammatic technique in complex-number and quaternion representation of nucleotides is delineated.

  6. On sequences not enjoying Schur’s property

    Directory of Open Access Journals (Sweden)

    Jiménez-Rodríguez Pablo

    2017-04-01

    Full Text Available Here we proved the existence of a closed vector space of sequences - any nonzero element of which does not comply with Schur’s property, that is, it is weakly convergent but not norm convergent. This allows us to find similar algebraic structures in some subsets of functions.

  7. 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 ...

  8. APPLICATION OF BIOTECHNOLOGY TO THE STUDY OF FILARIAL PARASITES AND THEIR VECTORS

    Directory of Open Access Journals (Sweden)

    A. C. Vickery

    2012-09-01

    Full Text Available Over 200 species of filarial parasites have been described, although the life cycle and nature of their obligate intermediate arthropod vectors have been identified for only about a quarter of them. Traditional methods of studying phylogenetic relationships between closely related parasite species have utilized morphologic, biochemical and biologic characteristics, usually of the microfilarial stage. Identification of competent vectors from among complexes of sibling species, has employed similar techniques, despite the fact that differences between geographical isolates may reflect environmental rather than genetically controlled factors. Studies of the prevalence and transmission of animal, human and zoonotic filarids, so important for vector identification and control, has lead to the examination of filarial parasites at the genetic level. Genomic DNA libraries are being constructed and screened for clones which are species specific. From this work, DNA probes which can accurately enumerate larval stages in vector squash preparations, and monoclonal antibodies specific for defined filarial antigens, are being prepared. The nucleotide sequences of rRNA are also being defined. The application of these technologies to the study of filarial parasites and their vectors, promises to not only allow the construction of accurate phylogenetic trees, but also to provide the data necessary for the identification and control of the vectors of filarial pathogens of animals and man.

  9. A novel chloroplast transformation vector compatible with the Gateway(®) recombination cloning technology.

    Science.gov (United States)

    Gottschamel, Johanna; Waheed, Mohammad Tahir; Clarke, Jihong L; Lössl, Andreas G

    2013-12-01

    To analyze the suitability of Gateway(®) vectors for transformation of chloroplasts, we converted a standard plastid transformation vector into a Gateway(®) destination vector containing the necessary recombination sites attR1 and attR2. Insertion of the green fluorescent protein (GFP) coding sequence with associated T7g10 ribosome binding site into this destination vector created the expression vector for transformation of tobacco chloroplasts with the biolistic method. Correct integration of the transgene into the plastid genome was verified by PCR and the homoplasmic nature of the transformed plants was confirmed by Southern Blot analysis. Expression of the GFP reporter protein was monitored by confocal laser scanning microscopy (CLSM) and quantification by western blot analysis showed a GFP accumulation level of 3% total soluble protein (TSP). The presented results clearly demonstrate that the Gateway(®) recombination sites are compatible with all steps of plastid transformation, from generation of transplastomic plants to expression of GFP. This is the first report of a plastid transformation vector made by the Gateway(®) recombinant cloning technology, which proves the suitability of this system for use in chloroplasts.

  10. Vector 33: A reduce program for vector algebra and calculus in orthogonal curvilinear coordinates

    Science.gov (United States)

    Harper, David

    1989-06-01

    This paper describes a package with enables REDUCE 3.3 to perform algebra and calculus operations upon vectors. Basic algebraic operations between vectors and between scalars and vectors are provided, including scalar (dot) product and vector (cross) product. The vector differential operators curl, divergence, gradient and Laplacian are also defined, and are valid in any orthogonal curvilinear coordinate system. The package is written in RLISP to allow algebra and calculus to be performed using notation identical to that for operations. Scalars and vectors can be mixed quite freely in the same expression. The package will be of interest to mathematicians, engineers and scientists who need to perform vector calculations in orthogonal curvilinear coordinates.

  11. GRASS GIS Vector Processing: Towards GRASS 7

    Science.gov (United States)

    Metz, Markus; Landa, Martin; Petrasova, Anna; Petras, Vaclav; Chemin, Yann; Neteler, Markus

    2014-05-01

    The upcoming GRASS GIS 7 release improves not only raster processing and general design but the vector processing in the first place. GRASS GIS, as a topological GIS, recognizes that the topology plays the key role in the vector processing and analysis. Topology ensures that adjacent geographic components in a single vector map are related. In contrast to non-topological GIS, a border common to two areas exists only once and is shared between the two areas. Topological representation of vector data helps to produce and maintain vector maps with clean geometry as well as enables the user to perform certain analyses that can not be conducted with non-topological or spaghetti data. Non-topological vector data are automatically converted to a topological representation upon import. Further more, various cleaning tools exist to remove non-trivial topological errors. In the upcoming GRASS GIS 7 release the vector library was particularly improved to make it faster and more efficient with an improved internal vector file format. This new topological format reduces memory and disk space requirements, leading to a generally faster processing. Opening an existing vector requires less memory providing additionally support for large files. The new spatial index performs queries faster (compared to GRASS GIS 6 more than 10 times for large vectors). As a new option the user can select a file-based version of the spatial index for large vector data. All topological cleaning tools have been optimized with regard to processing speed, robustness, and system requirements. The topological engine comes with a new prototype for direct read/write support of Simple Features API/OGR. Additionally vector data can be directly exchanged with topological PostGIS 2 databases. Considering the wide spread usage of ESRI Shapefile, a non-topological format for vector data exchange, it is particularly advantageous that GRASS GIS 7 offers advanced cleaning tools. For power users and programmers, the

  12. Long term expression of bicistronic vector driven by the FGF-1 IRES in mouse muscle

    Directory of Open Access Journals (Sweden)

    Van den Berghe Loïc

    2007-10-01

    FGF-1 IRES. The use of a cellular IRES over one of viral origin is of particular interest in the goal of eliminating viral sequences from transgenic vectors. In addition, the FGF-1 IRES, compared to the EMCV IRES, has a more stable activity, is shorter in length and more flexible in terms of downstream cloning of second cistrons. Finally, the FGF-1 IRES is very attractive to develop multicistronic expression cassettes for gene transfer in mouse muscle.

  13. Long term expression of bicistronic vector driven by the FGF-1 IRES in mouse muscle.

    Science.gov (United States)

    Allera-Moreau, Camille; Delluc-Clavières, Aurélie; Castano, Caroline; Van den Berghe, Loïc; Golzio, Muriel; Moreau, Marc; Teissié, Justin; Arnal, Jean-François; Prats, Anne-Catherine

    2007-10-28

    origin is of particular interest in the goal of eliminating viral sequences from transgenic vectors. In addition, the FGF-1 IRES, compared to the EMCV IRES, has a more stable activity, is shorter in length and more flexible in terms of downstream cloning of second cistrons. Finally, the FGF-1 IRES is very attractive to develop multicistronic expression cassettes for gene transfer in mouse muscle.

  14. In-vivo Examples of Flow Patterns With The Fast Vector Velocity Ultrasound Method

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Lindskov; Udesen, Jesper; Gran, Fredrik

    2009-01-01

    and using a 100 CPU linux cluster for post processing, PWE can achieve a frame of 100 Hz where one vector velocity sequence of approximately 3 sec, takes 10 h to store and 48 h to process. In this paper a case study is presented of in-vivo vector velocity estimates in different complex vessel geometries....... Results: The flow patterns of six bifurcations and two veins were investigated. It was shown: 1. that a stable vortex in the carotid bulb was present opposed to other examined bifurcations, 2. that retrograde flow was present in the superficial branch of the femoral artery during diastole, 3...

  15. High frame-rate blood vector velocity imaging using plane waves: simulations and preliminary experiments

    DEFF Research Database (Denmark)

    Udesen, J.; Gran, F.; Hansen, K.L.

    2008-01-01

    Conventional ultrasound methods for acquiring color images of blood velocity are limited by a relatively low frame-rate and are restricted to give velocity estimates along the ultrasound beam direction only. To circumvent these limitations, the method presented in this paper uses 3 techniques: 1...... carotid artery of a healthy male was scanned with a scan sequence that satisfies the limits set by the Food and Drug Administration. Vector velocity images were obtained with a frame-rate of 100 Hz where 40 speckle images are used for each vector velocity image. It was found that the blood flow...

  16. High Frame-Rate Blood Vector Velocity Imaging Using Plane Waves: Simulations and Preliminary Experiments

    DEFF Research Database (Denmark)

    Udesen, Jesper; Gran, Fredrik; Hansen, Kristoffer Lindskov

    2008-01-01

    Conventional ultrasound methods for acquiring color images of blood velocity are limited by a relatively low frame-rate and are restricted to give velocity estimates along the ultrasound beam direction only. To circumvent these limitations, the method presented in this paper uses 3 techniques: 1...... carotid artery of a healthy male was scanned with a scan sequence that satisfies the limits set by the Food and Drug Administration. Vector velocity images were obtained with a frame-rate of 100 Hz where 40 speckle images are used for each vector velocity image. It was found that the blood flow...

  17. Correlated Topic Vector for Scene Classification.

    Science.gov (United States)

    Wei, Pengxu; Qin, Fei; Wan, Fang; Zhu, Yi; Jiao, Jianbin; Ye, Qixiang

    2017-07-01

    Scene images usually involve semantic correlations, particularly when considering large-scale image data sets. This paper proposes a novel generative image representation, correlated topic vector, to model such semantic correlations. Oriented from the correlated topic model, correlated topic vector intends to naturally utilize the correlations among topics, which are seldom considered in the conventional feature encoding, e.g., Fisher vector, but do exist in scene images. It is expected that the involvement of correlations can increase the discriminative capability of the learned generative model and consequently improve the recognition accuracy. Incorporated with the Fisher kernel method, correlated topic vector inherits the advantages of Fisher vector. The contributions to the topics of visual words have been further employed by incorporating the Fisher kernel framework to indicate the differences among scenes. Combined with the deep convolutional neural network (CNN) features and Gibbs sampling solution, correlated topic vector shows great potential when processing large-scale and complex scene image data sets. Experiments on two scene image data sets demonstrate that correlated topic vector improves significantly the deep CNN features, and outperforms existing Fisher kernel-based features.

  18. HVJ liposomes and HVJ envelope vectors.

    Science.gov (United States)

    Kaneda, Yasufumi

    2011-10-01

    This protocol describes techniques for construction of fusion-mediated vectors based on inactivated HVJ (hemagglutinating virus of Japan; Sendai virus). HVJ liposomes are constructed by fusing liposomes containing DNA with inactivated HVJ. The HVJ envelope vector, a more simplified vector, incorporates DNA into inactivated HVJ particles without liposomes. Both vectors have many advantages. They can be used to introduce proteins, peptides, oligonucleotides (including antisense oligonucleotides, decoy oligonucleotides, and ribozymes), and short interfering RNA (siRNA), as well as plasmid DNA, into cultured cells in vitro and into organs in vivo. Fusion-mediated delivery avoids the degradation of therapeutic molecules before reaching the cytoplasm. Finally, repeated injection of the vector in vivo is not inhibited and even enhances the effects of the delivered molecules. These vectors have been used in many gene therapy experiments in animal models to address problems such as liver cirrhosis, hearing impairment, ischemic brain damage, peripheral arterial diseases, and cancers. This protocol describes methods for the preparation of HVJ liposomes and of HVJ envelope vectors and their use in delivery of plasmid DNA into various cells and tissues.

  19. Malaria vector control and personal protection.

    Science.gov (United States)

    2006-01-01

    Malaria transmission rates and risks can be greatly reduced by vector control, mitigating high malaria incidence and prevalence rates. Methods and strategies for malaria vector control (MVC) have been well documented by WHO, although its implementation varies widely. Technical guidelines for MVC strategies and materials are readily available, but the status and role of MVC have not been reviewed and redefined in terms of programme management and resource allocation. There are huge changes since November 1993 when the last WHO Study Group reviewed vector control for malaria and other mosquito-borne diseases, following the 1992 adoption of the Global Malaria Control Strategy. Operationally, with reform of the health sector in many countries, the centrally managed and vertically structured malaria control programme (MCP) has been superseded by a community-based and decentralized one. This poses challenges for effective implementation of MVC strategies. Therefore it became evident that the role of vector control in malaria control needs to be reconsidered to develop a strategic framework for MVC implementation by national malaria control programmes and other partners. This report of a WHO Study Group on Malaria Vector Control and Personal Protection reviewed the current vector control strategies and their effectiveness in various operational and eco-epidemiological settings, and identified challenges for implementation in different health systems. An outline strategic framework for strengthening malaria vector control implementation was developed. The process of deciding about which mosquito control method is appropriate in a given situation should be guided by an analysis of the level of malaria endemicity and vector bionomics, the eco-epidemiological setting, the health management system and an estimate of the programme sustainability. This report also provides a basis for the development of a strategic framework for strengthening malaria vector control

  20. Diversity of Thrips Species and Vectors of Tomato Spotted Wilt Virus in Tomato Production Systems in Kenya.

    Science.gov (United States)

    Macharia, Isaac; Backhouse, David; Skilton, Rob; Ateka, Elijah; Wu, Shu-Biao; Njahira, Moses; Maina, Solomon; Harvey, Jagger

    2015-02-01

    Thrips have been recognized as primary vectors of tomato spotted wilt virus (TSWV) with Frankliniella occidentalis (Pergande) reported as the most important and efficient vector, while other species such as Thrips tabaci Lindeman also include populations that can vector the virus. A study was undertaken to establish the diversity of thrips and presence of vectors for TSWV in four major tomato production areas in Kenya. The cytochrome oxidase 1 (CO1) gene was used to generate sequences from thrips samples collected from tomatoes and weeds, and phylogenetic analysis done to establish the variation within potential vector populations. Ceratothripoides brunneus Bagnall was the predominant species of thrips in all areas. F. occidentalis and T. tabaci were abundant in Nakuru, Kirinyaga, and Loitokitok but not detected at Bungoma. Other vectors of tospoviruses identified in low numbers were Frankliniella schultzei (Trybom) and Scirtothrips dorsalis Hood. Variation was observed in T. tabaci, F. occidentalis, and F. schultzei. Kenyan specimens of T. tabaci from tomato belonged to the arrhenotokous group, while those of F. occidentalis clustered with the Western flower thrips G group. The detection of RNA of TSWV in both of these species of thrips supported the role they play as vectors. The study has demonstrated the high diversity of thrips species in tomato production and the occurrence of important vectors of TSWV and other tospoviruses. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Bloodmeal analysis reveals avian Plasmodium infections and broad host preferences of Culicoides (Diptera: Ceratopogonidae vectors.

    Directory of Open Access Journals (Sweden)

    Diego Santiago-Alarcon

    Full Text Available Changing environmental conditions and human encroachment on natural habitats bring human populations closer to novel sources of parasites, which might then develop into new emerging diseases. Diseases transmitted by host generalist vectors are of special interest due to their capacity to move pathogens into novel hosts. We hypothesize that humans using forests for recreation are exposed to a broad range of parasites from wild animals and their vectors. A corollary of this is that new vector-host, parasite-host, and vector-parasite associations could eventually develop. Thus, we expect to observe atypical vector-host associations. Using molecular bloodmeal analysis via amplification of the mtDNA COI gene we identified the vertebrate hosts of Culicoides (Diptera: Ceratopogonidae species in a sub-urban forest of Southwestern Germany. Bloodmeals were also checked for haemosporidian infections by amplifying a fragment of the mtDNA cyt b gene. We identified a total of 20 Culicoides species, thirteen of which fed on humans. From 105 screened bloodmeals we obtained high quality sequences for 77 samples, 73 (94.8% originated from humans, two from livestock (Bos taurus and Equus caballus, and two from wild birds (Sylvia atricapilla and Turdus merula. We found that four Culicoides species previously assumed to feed exclusively on either birds (C. kibunensis or domestic mammals (C. chiopterus, C. deltus, C. scoticus fed also on humans. A total of six Culicoides abdomens were infected with avian haemosporidian parasites (Plasmodium or Haemoproteus, four of those abdomens contained blood derived from humans. Our results suggest that parasites of wild animals may be transferred to humans through infectious bites of Culicoides vectors. Further, we show that Culicoides vectors believed to be a specialist on specific vertebrate groups can have plastic feeding preferences, and that Culicoides are susceptible to infection by Plasmodium parasites, though vector

  2. pEPito: a significantly improved non-viral episomal expression vector for mammalian cells

    Directory of Open Access Journals (Sweden)

    Ogris Manfred

    2010-03-01

    Full Text Available Abstract Background The episomal replication of the prototype vector pEPI-1 depends on a transcription unit starting from the constitutively expressed Cytomegalovirus immediate early promoter (CMV-IEP and directed into a 2000 bp long matrix attachment region sequence (MARS derived from the human β-interferon gene. The original pEPI-1 vector contains two mammalian transcription units and a total of 305 CpG islands, which are located predominantly within the vector elements necessary for bacterial propagation and known to be counterproductive for persistent long-term transgene expression. Results Here, we report the development of a novel vector pEPito, which is derived from the pEPI-1 plasmid replicon but has considerably improved efficacy both in vitro and in vivo. The pEPito vector is significantly reduced in size, contains only one transcription unit and 60% less CpG motives in comparison to pEPI-1. It exhibits major advantages compared to the original pEPI-1 plasmid, including higher transgene expression levels and increased colony-forming efficiencies in vitro, as well as more persistent transgene expression profiles in vivo. The performance of pEPito-based vectors was further improved by replacing the CMV-IEP with the human CMV enhancer/human elongation factor 1 alpha promoter (hCMV/EF1P element that is known to be less affected by epigenetic silencing events. Conclusions The novel vector pEPito can be considered suitable as an improved vector for biotechnological applications in vitro and for non-viral gene delivery in vivo.

  3. Aberrant cryptic responsiveness of the pCAT 3- and pGL3-promoter reporter vectors.

    Science.gov (United States)

    Giannakis, G; Edmondson, S R; Favaloro, J M; Zajac, J D; Greenland, K J

    2003-08-01

    Transfection analyses are an informative method to assess the activity of specific promoter or enhancer elements in mammalian cells. Commercially available reporter vectors can be extremely useful investigative tools for such studies. This study reports that the pCAT 3- and pGL3-promoter vectors display cryptic responsiveness to androgens when they contain a DNA insert, while the empty vector, a commonly used negative control, is nonresponsive. Our studies initially aimed to characterize novel androgen-responsive DNA sequences in human genomic DNA through transactivational analyses. An isolated DNA fragment, designated ARC-3, contained three putative androgen response element "half-sites" and was androgen-responsive when cloned into the pCAT3-promoter vector. While we originally believed this to be a novel enhancer element, subsequent analyses of this clone revealed that this vector displays cryptic activity in the presence of an androgen. This was confirmed by cloning several unrelated DNA fragments that did not contain any known classic response elements into the pCAT3-promoter vector, all of which were found to be responsive. The empty vector (negative control) was again nonresponsive. The ARC-3 DNA fragment was also weakly responsive to stimulation when cloned into the pGL3-promotor vector, which is identical to the pCAT3-promoter vector, with the exception of an intron located 5' of the chloramphenicol acetyltransferase gene, and the reporter genes. This work demonstrates that both the pCAT3- and pGL3-promoter vectors are inappropriate to assess androgen-responsive enhancers and emphasizes the importance of the careful selection of reporter vectors and controls when conducting transactivational analysis.

  4. Meromorphic Vector Fields and Circle Packings

    DEFF Research Database (Denmark)

    Dias, Kealey

    of dynamical systems, continuous and discrete, correspond to the study of differential equations (vector fields) and iteration of mappings respectively. In holomorphic dynamics, the systems studied are restricted to those described by holomorphic (complex analytic) functions or meromorphic (allowing poles...... problems. Since the class of complex polynomial vector fields in the plane is natural to consider, it is remarkable that its study has only begun very recently. There are numerous fundamental questions that are still open, both in the general classification of these vector fields, the decomposition...

  5. Vector analysis for mathematicians, scientists and engineers

    CERN Document Server

    Simons, S

    1970-01-01

    Vector Analysis for Mathematicians, Scientists and Engineers, Second Edition, provides an understanding of the methods of vector algebra and calculus to the extent that the student will readily follow those works which make use of them, and further, will be able to employ them himself in his own branch of science. New concepts and methods introduced are illustrated by examples drawn from fields with which the student is familiar, and a large number of both worked and unworked exercises are provided. The book begins with an introduction to vectors, covering their representation, addition, geome

  6. Interior point decoding for linear vector channels

    Energy Technology Data Exchange (ETDEWEB)

    Wadayama, T [Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, Aichi, 466-8555 (Japan)], E-mail: wadayama@nitech.ac.jp

    2008-01-15

    In this paper, a novel decoding algorithm for low-density parity-check (LDPC) codes based on convex optimization is presented. The decoding algorithm, called interior point decoding, is designed for linear vector channels. The linear vector channels include many practically important channels such as inter-symbol interference channels and partial response channels. It is shown that the maximum likelihood decoding (MLD) rule for a linear vector channel can be relaxed to a convex optimization problem, which is called a relaxed MLD problem.

  7. Some remarks on a generalized vector product

    OpenAIRE

    Primitivo Acosta-Humánez; Moisés Aranda; Reinaldo Núñez

    2011-01-01

    In this paper we use a generalized vector product to construct an exterior form ∧ : (Rn) k → R( n k), where n k = n! (n−k)!k! , k ≤ n. Finally, for n = k − 1 we introduce the reversing operation to study this generalized vector product over palindromic and antipalindromic vectors Resumen. En este artículo usamos un producto vectorial generalizado para construir una forma exterior ∧ : (Rn) k → R( n k), en donde como es natural, n k = n! ...

  8. Gene therapy using retrovirus vectors: vector development and biosafety at clinical trials.

    Science.gov (United States)

    Doi, Knayo; Takeuchi, Yasuhiro

    2015-01-01

    Retrovirus vectors (gammaretroviral and lentiviral vectors) have been considered as promising tools to transfer therapeutic genes into patient cells because they can permanently integrate into host cellular genome. To treat monogenic, inherited diseases, retroviral vectors have been used to add correct genes into patient cells. Conventional gammaretroviral vectors achieved successful results in clinical trials: treated patients had therapeutic gene expression in target cells and had improved symptoms of diseases. However, serious side-effects of leukemia occurred, caused by retroviral insertional mutagenesis (IM). These incidences stressed the importance of monitoring vector integration sites in patient cells as well as of re-consideration on safer vectors. More recently lentiviral vectors which can deliver genes into non-dividing cells started to be used in clinical trials including neurological disorders, showing their efficacy. Vector integration site analysis revealed that lentiviruses integrate less likely to near promoter regions of oncogenes than gammaretroviruses and no adverse events have been reported in lentiviral vector-mediated gene therapy clinical trials. Therefore lentiviral vectors have promises to be applied to a wide range of common diseases in near future. For example, T cells from cancer patients were transduced to express chimeric T cell receptors recognizing their tumour cells enhancing patients' anti-cancer immunity.

  9. Adenovirus Vectors for Gene Therapy, Vaccination and Cancer Gene Therapy

    OpenAIRE

    Wold, William S. M.; Toth, Karoly

    2013-01-01

    Adenovirus vectors are the most commonly employed vector for cancer gene therapy. They are also used for gene therapy and as vaccines to express foreign antigens. Adenovirus vectors can be replication-defective; certain essential viral genes are deleted and replaced by a cassette that expresses a foreign therapeutic gene. Such vectors are used for gene therapy, as vaccines, and for cancer therapy. Replication-competent (oncolytic) vectors are employed for cancer gene therapy. Oncolytic vector...

  10. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki

    2015-09-01

    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  11. Taxonomy and Biology of Phlebotomine Vectors of Human Disease.

    Science.gov (United States)

    DIPTERA, *DISEASE VECTORS, *TAXONOMY, *VECTOR ANALYSIS , ANTIBODIES, BIOLOGY , BRAIN, CHROMOSOMES, COLOMBIA, COLONIES( BIOLOGY ), DISEASES, FEMALES... HUMANS , INFECTIOUS DISEASES, LABORATORIES, LEISHMANIA, LEISHMANIASIS, NEUTRALIZATION, PATIENTS, SEROLOGY, STRAINS( BIOLOGY ).

  12. Dengue Vectors and their Spatial Distribution

    National Research Council Canada - National Science Library

    Higa, Yukiko

    2011-01-01

    .... In addition, since their life cycles are well adapted to the human environment, environmental changes resulting from human activity such as urbanization exert a great impact on vector distribution...

  13. Regional Disease Vector Ecology Profile: The Koreas

    Science.gov (United States)

    2015-01-01

    Similarly, the civilian population may experience displacement, homelessness , reduced sanitation, increased exposure to vectors and disease, and...visit either of the following websites: 1. The WHO Searchable Snake/Antivenin Database 2. The Toxinology website ( Australia based) 69 REFERENCES

  14. Viruses vector control proposal: genus Aedes emphasis

    Directory of Open Access Journals (Sweden)

    Nelson Nogueira Reis

    Full Text Available Abstract The dengue fever is a major public health problem in the world. In Brazil, in 2015, there were 1,534,932 cases, being 20,320 cases of severe form, and 811 deaths related to this disease. The distribution of Aedes aegypti, the vector, is extensive. Recently, Zika and Chikungunya viruses had arisen, sharing the same vector as dengue and became a huge public health issue. Without specific treatment, it is urgently required as an effective vector control. This article is focused on reviewing vector control strategies, their effectiveness, viability and economical impact. Among all, the Sterile Insect Technique is highlighted as the best option to be adopted in Brazil, once it is largely effectively used in the USA and Mexico for plagues related to agribusiness.

  15. Viral vector-based influenza vaccines

    Science.gov (United States)

    de Vries, Rory D.; Rimmelzwaan, Guus F.

    2016-01-01

    ABSTRACT Antigenic drift of seasonal influenza viruses and the occasional introduction of influenza viruses of novel subtypes into the human population complicate the timely production of effective vaccines that antigenically match the virus strains that cause epidemic or pandemic outbreaks. The development of game-changing vaccines that induce broadly protective immunity against a wide variety of influenza viruses is an unmet need, in which recombinant viral vectors may provide. Use of viral vectors allows the delivery of any influenza virus antigen, or derivative thereof, to the immune system, resulting in the optimal induction of virus-specific B- and T-cell responses against this antigen of choice. This systematic review discusses results obtained with vectored influenza virus vaccines and advantages and disadvantages of the currently available viral vectors. PMID:27455345

  16. Viruses vector control proposal: genus Aedes emphasis

    Directory of Open Access Journals (Sweden)

    Nelson Nogueira Reis

    2017-07-01

    Full Text Available The dengue fever is a major public health problem in the world. In Brazil, in 2015, there were 1,534,932 cases, being 20,320 cases of severe form, and 811 deaths related to this disease. The distribution of Aedes aegypti, the vector, is extensive. Recently, Zika and Chikungunya viruses had arisen, sharing the same vector as dengue and became a huge public health issue. Without specific treatment, it is urgently required as an effective vector control. This article is focused on reviewing vector control strategies, their effectiveness, viability and economical impact. Among all, the Sterile Insect Technique is highlighted as the best option to be adopted in Brazil, once it is largely effectively used in the USA and Mexico for plagues related to agribusiness.

  17. Low Power, Self Calibrated Vector Magnetometer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Phase I SBIR project investigates a novel approach to vector magnetometry based on high precision measurements of the total magnetic field. The calibration is...

  18. Inflight parity vector compensation for FDI

    Science.gov (United States)

    Hall, S. R.; Motyka, P.; Gai, E.; Deyst, J. J., Jr.

    The performance of a failure detection and isolation (FDI) algorithm applied to a redundant strapdown inertial measurement unit (IMU) is limited by sensor errors such as input axis misalignment, scale factor errors, and biases. This paper presents a technique for improving the performance of FDI algorithms applied to redundant strapdown IMUs. A Kalman filter provides estimates of those linear combinations of sensor errors that affect the parity vector. These estimates are used to form a compensated parity vector which does not include the effects of sensor errors. The compensated parity vector is then used in place of the uncompensated parity vector to make FDI decisions. Simulation results are presented in which the algorithm is tested in a realistic flight environment that includes vehicle maneuvers, the effects of turbulence, and sensor failures. The results show that the algorithm can significantly improve FDI performance, especially during vehicle maneuvers.

  19. Vector optimization theory, applications, and extensions

    CERN Document Server

    Jahn, Johannes

    2011-01-01

    This new edition of a key monograph has fresh sections on the work of Edgeworth and Pareto in its presentation in a general setting of the fundamentals and important results of vector optimization. It examines background material, applications and theories.

  20. Sensorless vector and direct torque control

    CERN Document Server

    Vas, Peter

    1998-01-01

    This is the first comprehensive book on sensorless high performance a.c. drives. It is essential reading for anyone interested in acquiring a solid background on sensorless torque-controlled drives. It presents a detailed and unified treatment of sensorless vector-controlled and direct-torque controlled drive systems. It also discusses the applications of artificial intelligence to drives. Where possible, space vector theory is used and emphasis is laid on detailed mathematical and physical analysis. Sensorless drive schemes for different types of permanent magnet synchronous motors, synchronous reluctance motors, and induction motors are also presented. These include more than twenty vector drives e.g. five types of MRAS-based vector drives, and eleven types of direct-torque-controlled (DTC) drives, e.g. the ABB DTC drive. However, torque-controlled switched reluctance motor drives are also discussed due to their emerging importance. The book also covers various drive applications using artificial intellige...

  1. Weaving Knotted Vector Fields with Tunable Helicity

    Science.gov (United States)

    Kedia, Hridesh; Foster, David; Dennis, Mark R.; Irvine, William T. M.

    2016-12-01

    We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot, and its generalizations. As finite-energy physical fields, they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly, we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.

  2. Insects as vectors: systematics and biology.

    Science.gov (United States)

    Rodhain, F

    2015-04-01

    Among the many complex relationships between insects and microorganisms such as viruses, bacteria and parasites, some have resulted in the establishment of biological systems within which the insects act as a biological vector for infectious agents. It is therefore advisable to understand the identity and biology of these vectors in depth, in order to define procedures for epidemiological surveillance and anti-vector control. The following are successively reviewed in this article: Anoplura (lice), Siphonaptera (fleas), Heteroptera (bugs: Cimicidae, Triatoma, Belostomatidae), Psychodidae (sandflies), Simuliidae (black flies), Ceratopogonidae (biting midges), Culicidae (mosquitoes), Tabanidae (horseflies) and Muscidae (tsetse flies, stable flies and pupipara). The authors provide a rapid overview of the morphology, systematics, development cycle and bio-ecology of each of these groups of vectors. Finally, their medical and veterinary importance is briefly reviewed.

  3. Some remarks on a generalized vector product

    Directory of Open Access Journals (Sweden)

    Primitivo Acosta-Humánez

    2011-12-01

    Full Text Available In this paper we use a generalized vector product to construct an exterior form ∧ : (Rn k → R( n k, where n k = n! (n−k!k! , k ≤ n. Finally, for n = k − 1 we introduce the reversing operation to study this generalized vector product over palindromic and antipalindromic vectors Resumen. En este artículo usamos un producto vectorial generalizado para construir una forma exterior ∧ : (Rn k → R( n k, en donde como es natural, n k = n! (n−k!k! , k ≤ n. Finalmente, para n = k − 1 introducimos la operación reversar para estudiar este producto vectorial generalizado sobre vectores palindrómicos y antipalindrómicos.

  4. Weaving Knotted Vector Fields with Tunable Helicity.

    Science.gov (United States)

    Kedia, Hridesh; Foster, David; Dennis, Mark R; Irvine, William T M

    2016-12-30

    We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot, and its generalizations. As finite-energy physical fields, they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly, we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.

  5. MAGELLAN SURFACE CHARACTERISTICS VECTOR DATA RECORD

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set contains the Magellan Surface Characteristics Vector Data Record (SCVDR) which is an orbit-by-orbit reduction of Magellan scattering and emission...

  6. VEST: Abstract vector calculus simplification in Mathematica

    Science.gov (United States)

    Squire, J.; Burby, J.; Qin, H.

    2014-01-01

    We present a new package, VEST (Vector Einstein Summation Tools), that performs abstract vector calculus computations in Mathematica. Through the use of index notation, VEST is able to reduce three-dimensional scalar and vector expressions of a very general type to a well defined standard form. In addition, utilizing properties of the Levi-Civita symbol, the program can derive types of multi-term vector identities that are not recognized by reduction, subsequently applying these to simplify large expressions. In a companion paper Burby et al. (2013) [12], we employ VEST in the automation of the calculation of high-order Lagrangians for the single particle guiding center system in plasma physics, a computation which illustrates its ability to handle very large expressions. VEST has been designed to be simple and intuitive to use, both for basic checking of work and more involved computations.

  7. Application of Vector Triggering Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

    1997-01-01

    result is a Random Decrement function from each measurement. In traditional Random Decrement estimation the triggering condition is a scalar condition, which should only be fulfilled in a single measurement. In vector triggering Random Decrement the triggering condition is a vector condition....... The advantage of this new approach should be a reduction in estimation time without a significant loss of accuracy, since the vector triggering conditions ensure cross information between the measurements in the Random Decrement functions. The different problems with this technique is highlighted in two......This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented...

  8. Application of Vector Triggering Random Decrement

    DEFF Research Database (Denmark)

    Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

    result is a Random Decrement function from each measurement. In traditional Random Decrement estimation the triggering condition is a scalar condition, which should only be fulfilled in a single measurement. In vector triggering Random Decrement the triggering condition is a vector condition....... The advantage of this new approach should be a reduction in estimation time without a significant loss of accuracy, since the vector triggering conditions ensure cross information between the measurements in the Random Decrement functions. The different problems with this technique is highlighted in two......This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented...

  9. Free divisors in prehomogeneous vector spaces

    OpenAIRE

    Granger, Michel; Mond, David; Schulze, Mathias

    2009-01-01

    We study linear free divisors, that is, free divisors arising as discriminants in prehomogeneous vector spaces, and in particular in quiver representation spaces. We give a characterization of the prehomogeneous vector spaces containing such linear free divisors. For reductive linear free divisors, we prove that the numbers of geometric and representation theoretic irreducible components coincide. As a consequence, we find that a quiver can only give rise to a linear free divisor if it has no...

  10. Acoustical vector solitons in anisotropic media

    Science.gov (United States)

    Adamashvili, G. T.; Peikrishvili, M. D.; Koplatadze, R. R.

    2017-04-01

    A theory of acoustical vector solitons of self-induced transparency in anisotropic media is developed. It is shown that, in these systems, a two-component vector soliton oscillating with the difference and sum of the frequencies in the vicinity of the frequency of a carrying acoustic wave may arise. Explicit analytical expressions for the form and parameters of a nonlinear wave depending on the direction of pulse propagation are given.

  11. Trichophoromyia auraensis is a putative vector

    Directory of Open Access Journals (Sweden)

    Carolina Bioni Garcia Teles

    Full Text Available The sandfly Trichophoromyia auraensis has recently evolved as a proven vector of Leishmania (Viannia endemic to state of Acre in the north of Brazil. This note is intended to propose a correction in the report of the first occurrence of natural infection of Leishmania (Viannia in this species. We and the other scientific groups reinforced that Tr. auraensis is a possible vector involved in the transmission of American cutaneous leishmaniasis in Acre, Brazil.

  12. Engineering HSV-1 vectors for gene therapy.

    Science.gov (United States)

    Goins, William F; Huang, Shaohua; Cohen, Justus B; Glorioso, Joseph C

    2014-01-01

    Virus vectors have been employed as gene transfer vehicles for various preclinical and clinical gene therapy applications, and with the approval of Glybera (alipogene tiparvovec) as the first gene therapy product as a standard medical treatment (Yla-Herttuala, Mol Ther 20: 1831-1832, 2013), gene therapy has reached the status of being a part of standard patient care. Replication-competent herpes simplex virus (HSV) vectors that replicate specifically in actively dividing tumor cells have been used in Phase I-III human trials in patients with glioblastoma multiforme, a fatal form of brain cancer, and in malignant melanoma. In fact, T-VEC (talimogene laherparepvec, formerly known as OncoVex GM-CSF) displayed efficacy in a recent Phase III trial when compared to standard GM-CSF treatment alone (Andtbacka et al. J Clin Oncol 31: sLBA9008, 2013) and may soon become the second FDA-approved gene therapy product used in standard patient care. In addition to the replication-competent oncolytic HSV vectors like T-VEC, replication-defective HSV vectors have been employed in Phase I-II human trials and have been explored as delivery vehicles for disorders such as pain, neuropathy, and other neurodegenerative conditions. Research during the last decade on the development of HSV vectors has resulted in the engineering of recombinant vectors that are totally replication defective, nontoxic, and capable of long-term transgene expression in neurons. This chapter describes methods for the construction of recombinant genomic HSV vectors based on the HSV-1 replication-defective vector backbones, steps in their purification, and their small-scale production for use in cell culture experiments as well as preclinical animal studies.

  13. Effect of pathogen-resistant vectors on the transmission dynamics of a vector-borne disease.

    Science.gov (United States)

    Arino, Julien; Bowman, Chris; Gumel, Abba; Portet, Stéphanie

    2007-10-01

    A model is introduced for the transmission dynamics of a vector-borne disease with two vector strains, one wild and one pathogen-resistant; resistance comes at the cost of reduced reproductive fitness. The model, which assumes that vector reproduction can lead to the transmission or loss of resistance (reversion), is analyzed in a particular case with specified forms for the birth and force of infection functions. The vector component can have, in the absence of disease, a coexistence equilibrium where both strains survive. In the case where reversion is possible, this coexistence equilibrium is globally asymptotically stable when it exists. This equilibrium is still present in the full vector-host system, leading to a reduction of the associated reproduction number, thereby making elimination of the disease more feasible. When reversion is not possible, there can exist an additional equilibrium with only resistant vectors.

  14. Effects of Climate and Climate Change on Vectors and Vector-Borne Diseases: Ticks Are Different.

    Science.gov (United States)

    Ogden, Nick H; Lindsay, L Robbin

    2016-08-01

    There has been considerable debate as to whether global risk from vector-borne diseases will be impacted by climate change. This has focussed on important mosquito-borne diseases that are transmitted by the vectors from infected to uninfected humans. However, this debate has mostly ignored the biological diversity of vectors and vector-borne diseases. Here, we review how climate and climate change may impact those most divergent of arthropod disease vector groups: multivoltine insects and hard-bodied (ixodid) ticks. We contrast features of the life cycles and behaviour of these arthropods, and how weather, climate, and climate change may have very different impacts on the spatiotemporal occurrence and abundance of vectors, and the pathogens they transmit. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

  15. A comparative analysis of reproductive biology of insect vectors of human disease.

    Science.gov (United States)

    Shaw, W Robert; Attardo, Geoffrey M; Aksoy, Serap; Catteruccia, Flaminia

    2015-08-01

    Studying the reproductive strategies of insect species that transmit diseases to humans can identify new exploitable targets for the development of vector control methods. Here we describe shared characteristics and individual features of the reproductive biology of three major disease vectors: Anopheles gambiae, Aedes aegypti and Glossina morsitans. Current studies are identifying i) species-specific molecular cascades that determine female monandrous behavior, ii) core aspects of egg development that could be disrupted for controlling natural populations, and iii) the increasingly apparent role of resident microbiota in shaping reproductive success and disease transmission potential. The recent completion of multiple genome sequencing projects is allowing comparative genomics studies that not only increase our knowledge of reproductive processes but also facilitate the identification of novel targets for vector control.

  16. Identification of unique reciprocal and non reciprocal cross packaging relationships between HIV-1, HIV-2 and SIV reveals an efficient SIV/HIV-2 lentiviral vector system with highly favourable features for in vivo testing and clinical usage

    Directory of Open Access Journals (Sweden)

    Caldwell Maeve

    2005-09-01

    Full Text Available Abstract Background Lentiviral vectors have shown immense promise as vehicles for gene delivery to non-dividing cells particularly to cells of the central nervous system (CNS. Improvements in the biosafety of viral vectors are paramount as lentiviral vectors move into human clinical trials. This study investigates the packaging relationship between gene transfer (vector and Gag-Pol expression constructs of HIV-1, HIV-2 and SIV. Cross-packaged vectors expressing GFP were assessed for RNA packaging, viral vector titre and their ability to transduce rat primary glial cell cultures and human neural stem cells. Results HIV-1 Gag-Pol demonstrated the ability to cross package both HIV-2 and SIV gene transfer vectors. However both HIV-2 and SIV Gag-Pol showed a reduced ability to package HIV-1 vector RNA with no significant gene transfer to target cells. An unexpected packaging relationship was found to exist between HIV-2 and SIV with SIV Gag-Pol able to package HIV-2 vector RNA and transduce dividing SV2T cells and CNS cell cultures with an efficiency equivalent to the homologous HIV-1 vector however HIV-2 was unable to deliver SIV based vectors. Conclusion This new non-reciprocal cross packaging relationship between SIV and HIV-2 provides a novel way of significantly increasing bio-safety with a reduced sequence homology between the HIV-2 gene transfer vector and the SIV Gag-Pol construct thus ensuring that vector RNA packaging is unidirectional.

  17. Blocking transmission of vector-borne diseases.

    Science.gov (United States)

    Schorderet-Weber, Sandra; Noack, Sandra; Selzer, Paul M; Kaminsky, Ronald

    2017-04-01

    Vector-borne diseases are responsible for significant health problems in humans, as well as in companion and farm animals. Killing the vectors with ectoparasitic drugs before they have the opportunity to pass on their pathogens could be the ideal way to prevent vector borne diseases. Blocking of transmission might work when transmission is delayed during blood meal, as often happens in ticks. The recently described systemic isoxazolines have been shown to successfully prevent disease transmission under conditions of delayed pathogen transfer. However, if the pathogen is transmitted immediately at bite as it is the case with most insects, blocking transmission becomes only possible if ectoparasiticides prevent the vector from landing on or, at least, from biting the host. Chemical entities exhibiting repellent activity in addition to fast killing, like pyrethroids, could prevent pathogen transmission even in cases of immediate transfer. Successful blocking depends on effective action in the context of the extremely diverse life-cycles of vectors and vector-borne pathogens of medical and veterinary importance which are summarized in this review. This complexity leads to important parameters to consider for ectoparasiticide research and when considering the ideal drug profile for preventing disease transmission. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Feature Vector Construction Method for IRIS Recognition

    Science.gov (United States)

    Odinokikh, G.; Fartukov, A.; Korobkin, M.; Yoo, J.

    2017-05-01

    One of the basic stages of iris recognition pipeline is iris feature vector construction procedure. The procedure represents the extraction of iris texture information relevant to its subsequent comparison. Thorough investigation of feature vectors obtained from iris showed that not all the vector elements are equally relevant. There are two characteristics which determine the vector element utility: fragility and discriminability. Conventional iris feature extraction methods consider the concept of fragility as the feature vector instability without respect to the nature of such instability appearance. This work separates sources of the instability into natural and encodinginduced which helps deeply investigate each source of instability independently. According to the separation concept, a novel approach of iris feature vector construction is proposed. The approach consists of two steps: iris feature extraction using Gabor filtering with optimal parameters and quantization with separated preliminary optimized fragility thresholds. The proposed method has been tested on two different datasets of iris images captured under changing environmental conditions. The testing results show that the proposed method surpasses all the methods considered as a prior art by recognition accuracy on both datasets.

  19. Black holes in vector-tensor theories

    Science.gov (United States)

    Heisenberg, Lavinia; Kase, Ryotaro; Minamitsuji, Masato; Tsujikawa, Shinji

    2017-08-01

    We study static and spherically symmetric black hole (BH) solutions in second-order generalized Proca theories with nonminimal vector field derivative couplings to the Ricci scalar, the Einstein tensor, and the double dual Riemann tensor. We find concrete Lagrangians which give rise to exact BH solutions by imposing two conditions of the two identical metric components and the constant norm of the vector field. These exact solutions are described by either Reissner-Nordström (RN), stealth Schwarzschild, or extremal RN solutions with a non-trivial longitudinal mode of the vector field. We then numerically construct BH solutions without imposing these conditions. For cubic and quartic Lagrangians with power-law couplings which encompass vector Galileons as the specific cases, we show the existence of BH solutions with the difference between two non-trivial metric components. The quintic-order power-law couplings do not give rise to non-trivial BH solutions regular throughout the horizon exterior. The sixth-order and intrinsic vector-mode couplings can lead to BH solutions with a secondary hair. For all the solutions, the vector field is regular at least at the future or past horizon. The deviation from General Relativity induced by the Proca hair can be potentially tested by future measurements of gravitational waves in the nonlinear regime of gravity.

  20. Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential.

    Science.gov (United States)

    Goodman, Michael Aaron; Arumugam, Paritha; Pillis, Devin Marie; Loberg, Anastacia; Nasimuzzaman, Mohammed; Lynn, Danielle; van der Loo, Johannes Christiaan Maria; Dexheimer, Phillip Joseph; Keddache, Mehdi; Bauer, Thomas Roy; Hickstein, Dennis Durand; Russell, David William; Malik, Punam

    2018-01-01

    Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in "enhancerless" self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that strong viral enhancers/promoters placed in foamy viral vectors caused extremely low immortalization of primary mouse hematopoietic stem/progenitor cells compared to analogous gammaretrovirus/lentivirus vectors carrying the same enhancers/promoters, an effect not explained solely by foamy virus' modest insertional site preference for nongenic regions compared to gammaretrovirus/lentivirus vectors. Using CRISPR/Cas9-mediated targeted insertion of analogous proviral sequences into the LMO2 gene and then measuring LMO2 expression, we demonstrate a sequence-specific effect of foamy virus, independent of insertional bias, contributing to reduced genotoxicity. We show that this effect is mediated by a 36-bp insulator located in the foamy virus long terminal repeat (LTR) that has high-affinity binding to the CCCTC-binding factor. Using our LMO2 activation assay, LMO2 expression was significantly increased when this insulator was removed from foamy virus and significantly reduced when the insulator was inserted into the lentiviral LTR. Our results elucidate a mechanism underlying the low genotoxicity of foamy virus, identify a novel insulator, and support the use of foamy virus as a vector for gene therapy, especially when strong enhancers/promoters are required.IMPORTANCE Understanding the genotoxic potential of viral vectors is important in designing safe and efficacious vectors for gene

  1. Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors.

    Science.gov (United States)

    Oppenheim, Sara J; Rosenfeld, Jeffrey A; DeSalle, Rob

    2017-02-27

    The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they

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

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

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

  3. Criteria for effective design, construction, and gene knockdown by shRNA vectors

    Directory of Open Access Journals (Sweden)

    Lich John D

    2006-01-01

    Full Text Available Abstract Background RNA interference (RNAi technology is a powerful methodology recently developed for the specific knockdown of targeted genes. RNAi is most commonly achieved either transiently by transfection of small interfering (si RNA oligonucleotides, or stably using short hairpin (sh RNA expressed from a DNA vector or virus. Much controversy has surrounded the development of rules for the design of effective siRNA oligonucleotides; and whether these rules apply to shRNA is not well characterized. Results To determine whether published algorithms for siRNA oligonucleotide design apply to shRNA, we constructed 27 shRNAs from 11 human genes expressed stably using retroviral vectors. We demonstrate an efficient method for preparing wild-type and mutant control shRNA vectors simultaneously using oligonucleotide hybrids. We show that sequencing through shRNA vectors can be problematic due to the intrinsic secondary structure of the hairpin, and we determine a strategy for effective sequencing by using a combination of modified BigDye chemistries and DNA relaxing agents. The efficacy of knockdown for the 27 shRNA vectors was evaluated against six published algorithms for siRNA oligonucleotide design. Our results show that none of the scoring algorithms can explain a significant percentage of variance in shRNA knockdown efficacy as assessed by linear regression analysis or ROC curve analysis. Application of a modification based on the stability of the 6 central bases of each shRNA provides fair-to-good predictions of knockdown efficacy for three of the algorithms. Analysis of an independent set of data from 38 shRNAs pooled from previous publications confirms these findings. Conclusion The use of mixed oligonucleotide pairs provides a time and cost efficient method of producing wild type and mutant control shRNA vectors. The addition to sequencing reactions of a combination of mixed dITP/dGTP chemistries and DNA relaxing agents enables read

  4. Comparison of metagenomic samples using sequence signatures

    Directory of Open Access Journals (Sweden)

    Jiang Bai

    2012-12-01

    Full Text Available Abstract Background Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams, have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. Results We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao used in CVTree developed from Hao’s group (Qi et al., 2004, measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009, as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples

  5. Auto-tuning Dense Vector and Matrix-vector Operations for Fermi GPUs

    DEFF Research Database (Denmark)

    Sørensen, Hans Henrik Brandenborg

    2012-01-01

    In this paper, we consider the automatic performance tuning of dense vector and matrix-vector operations on GPUs. Such operations form the backbone of level 1 and level 2 routines in the Basic Linear Algebra Subroutines (BLAS) library and are therefore of great importance in many scientific...... for dense vector and matrix-vector operations by appropriately utilizing the fine-grained parallelism of the GPU. Our tuned kernels display between 25-100% better performance than the current CUBLAS 3.2 library....

  6. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-04-25

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

  7. Learning to predict expression efficacy of vectors in recombinant protein production.

    Science.gov (United States)

    Chan, Wen-Ching; Liang, Po-Huang; Shih, Yan-Ping; Yang, Ueng-Cheng; Lin, Wen-chang; Hsu, Chun-Nan

    2010-01-18

    Recombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vectors in Escherichia coli (E. coli). However, the production efficacy of different vectors varies for different target proteins. Trial-and-error is still the common practice to find out the efficacy of a vector for a given target protein. Previous studies are limited in that they assumed that proteins would be over-expressed and focused only on the solubility of expressed proteins. In fact, many pairings of vectors and proteins result in no expression. In this study, we applied machine learning to train prediction models to predict whether a pairing of vector-protein will express or not express in E. coli. For expressed cases, the models further predict whether the expressed proteins would be soluble. We collected a set of real cases from the clients of our recombinant protein production core facility, where six different vectors were designed and studied. This set of cases is used in both training and evaluation of our models. We evaluate three different models based on the support vector machines (SVM) and their ensembles. Unlike many previous works, these models consider the sequence of the target protein as well as the sequence of the whole fusion vector as the features. We show that a model that classifies a case into one of the three classes (no expression, inclusion body and soluble) outperforms a model that considers the nested structure of the three classes, while a model that can take advantage of the hierarchical structure of the three classes performs slight worse but comparably to the best model. Meanwhile, compared to previous works, we show that the prediction accuracy of our best method still performs the best. Lastly, we briefly present two methods to use the trained model in the design of the recombinant protein production systems to improve

  8. Targeting photoreceptors via intravitreal delivery using novel, capsid-mutated AAV vectors.

    Directory of Open Access Journals (Sweden)

    Christine N Kay

    Full Text Available Development of viral vectors capable of transducing photoreceptors by less invasive methods than subretinal injection would provide a major advancement in retinal gene therapy. We sought to develop novel AAV vectors optimized for photoreceptor transduction following intravitreal delivery and to develop methodology for quantifying this transduction in vivo. Surface exposed tyrosine (Y and threonine (T residues on the capsids of AAV2, AAV5 and AAV8 were changed to phenylalanine (F and valine (V, respectively. Transduction efficiencies of self-complimentary, capsid-mutant and unmodified AAV vectors containing the smCBA promoter and mCherry cDNA were initially scored in vitro using a cone photoreceptor cell line. Capsid mutants exhibiting the highest transduction efficiencies relative to unmodified vectors were then injected intravitreally into transgenic mice constitutively expressing a Rhodopsin-GFP fusion protein in rod photoreceptors (Rho-GFP mice. Photoreceptor transduction was quantified by fluorescent activated cell sorting (FACS by counting cells positive for both GFP and mCherry. To explore the utility of the capsid mutants, standard, (non-self-complementary AAV vectors containing the human rhodopsin kinase promoter (hGRK1 were made. Vectors were intravitreally injected in wildtype mice to assess whether efficient expression exclusive to photoreceptors was achievable. To restrict off-target expression in cells of the inner and middle retina, subsequent vectors incorporated multiple target sequences for miR181, an miRNA endogenously expressed in the inner and middle retina. Results showed that AAV2 containing four Y to F mutations combined with a single T to V mutation (quadY-F+T-V transduced photoreceptors most efficiently. Robust photoreceptor expression was mediated by AAV2(quadY-F+T-V -hGRK1-GFP. Observed off-target expression was reduced by incorporating target sequence for a miRNA highly expressed in inner/middle retina, miR181c. Thus

  9. Targeting photoreceptors via intravitreal delivery using novel, capsid-mutated AAV vectors.

    Science.gov (United States)

    Kay, Christine N; Ryals, Renee C; Aslanidi, George V; Min, Seok Hong; Ruan, Qing; Sun, Jingfen; Dyka, Frank M; Kasuga, Daniel; Ayala, Andrea E; Van Vliet, Kim; Agbandje-McKenna, Mavis; Hauswirth, William W; Boye, Sanford L; Boye, Shannon E

    2013-01-01

    Development of viral vectors capable of transducing photoreceptors by less invasive methods than subretinal injection would provide a major advancement in retinal gene therapy. We sought to develop novel AAV vectors optimized for photoreceptor transduction following intravitreal delivery and to develop methodology for quantifying this transduction in vivo. Surface exposed tyrosine (Y) and threonine (T) residues on the capsids of AAV2, AAV5 and AAV8 were changed to phenylalanine (F) and valine (V), respectively. Transduction efficiencies of self-complimentary, capsid-mutant and unmodified AAV vectors containing the smCBA promoter and mCherry cDNA were initially scored in vitro using a cone photoreceptor cell line. Capsid mutants exhibiting the highest transduction efficiencies relative to unmodified vectors were then injected intravitreally into transgenic mice constitutively expressing a Rhodopsin-GFP fusion protein in rod photoreceptors (Rho-GFP mice). Photoreceptor transduction was quantified by fluorescent activated cell sorting (FACS) by counting cells positive for both GFP and mCherry. To explore the utility of the capsid mutants, standard, (non-self-complementary) AAV vectors containing the human rhodopsin kinase promoter (hGRK1) were made. Vectors were intravitreally injected in wildtype mice to assess whether efficient expression exclusive to photoreceptors was achievable. To restrict off-target expression in cells of the inner and middle retina, subsequent vectors incorporated multiple target sequences for miR181, an miRNA endogenously expressed in the inner and middle retina. Results showed that AAV2 containing four Y to F mutations combined with a single T to V mutation (quadY-F+T-V) transduced photoreceptors most efficiently. Robust photoreceptor expression was mediated by AAV2(quadY-F+T-V) -hGRK1-GFP. Observed off-target expression was reduced by incorporating target sequence for a miRNA highly expressed in inner/middle retina, miR181c. Thus we have

  10. Viral Vectors for in Vivo Gene Transfer

    Science.gov (United States)

    Thévenot, E.; Dufour, N.; Déglon, N.

    The transfer of DNA into the nucleus of a eukaryotic cell (gene transfer) is a central theme of modern biology. The transfer is said to be somatic when it refers to non-germline organs of a developed individual, and germline when it concerns gametes or the fertilised egg of an animal, with the aim of transmitting the relevant genetic modification to its descendents [1]. The efficient introduction of genetic material into a somatic or germline cell and the control of its expression over time have led to major advances in understanding how genes work in vivo, i.e., in living organisms (functional genomics), but also to the development of innovative therapeutic methods (gene therapy). The efficiency of gene transfer is conditioned by the vehicle used, called the vector. Desirable features for a vector are as follows: Easy to produce high titer stocks of the vector in a reproducible way. Absence of toxicity related to transduction (transfer of genetic material into the target cell, and its expression there) and no immune reaction of the organism against the vector and/or therapeutic protein. Stability in the expression of the relevant gene over time, and the possibility of regulation, e.g., to control expression of the therapeutic protein on the physiological level, or to end expression at the end of treatment. Transduction of quiescent cells should be as efficient as transduction of dividing cells. Vectors currently used fall into two categories: non-viral and viral vectors. In non-viral vectors, the DNA is complexed with polymers, lipids, or cationic detergents (described in Chap. 3). These vectors have a low risk of toxicity and immune reaction. However, they are less efficient in vivo than viral vectors when it comes to the number of cells transduced and long-term transgene expression. (Naked DNA transfer or electroporation is rather inefficient in the organism. This type of gene transfer will not be discussed here, and the interested reader is referred to the

  11. Immune Activities of Polycationic Vectors for Gene Delivery

    Directory of Open Access Journals (Sweden)

    Xiaotian Zhao

    2017-08-01

    Full Text Available Polycationic vectors are used widely in the field of gene delivery, while currently their immune activities in vivo are poorly understood. In this comprehensive review, we aim to present an overview of existing mechanisms of adverse immune responses induced by the polycation/gene complexes, which includes the polycations themselves, the gene sequences and the ROS produced by them. These causes can induce pro-inflammatory cytokines, hypersensitivity as well as the activation of toll-like receptors, and finally the immunostimulation occur. In addition, we introduce some different opinions and research results on the immunogenicity of classical polycations such as polylysine (PLL, polyethyleneimine (PEI, polyamidoamine dendrimers (PAMAM, chitosan and gelatin, most of which have immunogenicity and can induce immunoreactions in vivo. The methods now used to adjust their immunogenicity are shown in the final part of this review. Nowadays, there is still no accurate conclusion on immunogenicity of polycations, which confuses researchers seriously in in vivo test. We conclude that further research is needed in order to skillfully utilize or inhibit the immunogenicity of these polycationic vectors.

  12. The LHC Sequencer

    CERN Document Server

    Alemany-Fernandez, Reyes; Gorbonosov, Roman; Khasbulatov, Denis; Lamont, Mike; Le Roux, Pascal; Roderick, Chris

    2011-01-01

    The Large Hadron Collider (LHC) at CERN is a highly complex system made of many different sub-systems whose operation implies the execution of many tasks with stringent constraints on the order and duration of the execution. To be able to operate such a system in the most efficient and reliable way, the operators in the CERN control room use a high level control system: the LHC Sequencer. The LHC Sequencer system is composed of several components, including an Oracle database where operational sequences are configured, a core server that orchestrates the execution of the sequences, and two graphical user interfaces: one for sequence edition, and another for sequence execution. This paper describes the architecture of the LHC Sequencer system, and how the sequences are prepared and used for LHC operation.

  13. Anomaly Detection in Sequences

    Data.gov (United States)

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

  14. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  15. sequenceMiner algorithm

    Data.gov (United States)

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

  16. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  17. Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes.

    Science.gov (United States)

    Brown, J K

    2000-11-01

    Recent unprecedented upsurges in populations of the whitefly Bemisia tabaci (Genn.) have drawn much attention to its worldwide importance as an insect pest and as the vector of emergent begomoviruses (Family: Geminiviridae; Genus: Begomovirus). Several begomoviruses that are considered 'new' and others previously regarded as minor pathogens have been linked to recent epidemics. Recent studies have revealed much variation in begomoviruses, despite the view that DNA-containing viruses do not rapidly accumulate mutations. Also, certain B. tabaci 'variants' are known that more effectively or selectively transmit certain begomoviruses and exhibit biotic differences that may influence their spread. Patterns of distribution and dissemination of begomoviruses transmitted by B. tabaci are poorly understood because standardized molecular-based tracking methods have not been available. Understanding virus/whitefly vector/host plant interrelationships in the context of emerging problems can be achieved only by linking predicted evolutionary histories with epidemiology using molecular phylogenetic approaches. Identification and validation of informative molecular sequences are essential initial steps in this process. Genus-wide degenerate polymerase chain reaction (PCR) primers have been developed to amplify and sequence the 'core' region of the coat protein open reading frame (ORF) (V1), permitting 'universal' detection and provisional virus identification by comparisons with described viral genotypes. In subsequent studies reported here, several potentially informative viral ORFs and a non-coding region are explored. Of particular use for expanding diversity studies are group- or virus-specific sequences that can be targeted by utilizing newly available core CP sequences, or additional conserved regions around which broad spectrum primers can be designed to target variable sequences in key ORFs or non-coding regions. Prospective markers under exploration were selected with a

  18. Complex-Vector Time-Delay Control of Power Converters

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Loh, P. C.; Tang, Y.

    2008-01-01

    to develop dynamically fast and accurate current controllers is even more intensive with more features expected to be embedded within a single control module. Believing in its continual importance, this paper contributes by proposing a complex-vector time-delay control scheme that can achieve high tracking......Precise controlling of current produced by power converters is an important topic that has attracted interests over the last few decades. With the recent proliferation of grid-tied converters where the control of power flow is indirectly governed by the accuracy of current tracking, motivation...... a set of load-matching control characteristics that are less sensitive to external noise interferences. These added features, complementing the basic requirement of fast and accurate fundamental positive-sequence tracking, render the proposed scheme as an attractive alternative for high-end converter...

  19. Transverse oscillation vector flow imaging for transthoracic echocardiography

    DEFF Research Database (Denmark)

    Bradway, David; Lindskov Hansen, Kristoffer; Nielsen, Michael Bachmann

    2015-01-01

    This work presents the development and first results of in vivo transthoracic cardiac imaging using an implementation of Vector Flow Imaging (VFI) via the Transverse Oscillation (TO) method on a phased-array transducer. Optimal selection of the lateral wavelength of the transversely...... velocity flow images. A flow pump was programmed for constant flow for in vitro acquisitions at varying depths in a tissue-mimicking fluid. Additionally, mitral, aortic,and tricuspid valves of two healthy volunteers were scanned from intercostal acoustic windows. The acquired RF data were beamformed via...... the TO method, and fourth-order estimators were employed for the velocity estimation. The resulting images were compared with those from conventional spectral Doppler and color flow mapping sequences. VFI is shown to be a clinically-feasible tool, which enables new exibility for choosing acoustic windows...

  20. Balanced metrics for vector bundles and polarised manifolds

    DEFF Research Database (Denmark)

    Garcia Fernandez, Mario; Ross, Julius

    2012-01-01

    We consider a notion of balanced metrics for triples (X, L, E) which depend on a parameter α, where X is smooth complex manifold with an ample line bundle L and E is a holomorphic vector bundle over X. For generic choice of α, we prove that the limit of a convergent sequence of balanced metrics...... leads to a Hermitian-Einstein metric on E and a constant scalar curvature Kähler metric in c_1(L). For special values of α, limits of balanced metrics are solutions of a system of coupled equations relating a Hermitian-Einstein metric on E and a Kähler metric in c1(L). For this, we compute the top two...

  1. On the density of the sum of two independent Student t-random vectors

    DEFF Research Database (Denmark)

    Berg, Christian; Vignat, Christophe

    2010-01-01

    In this paper, we find an expression for the density of the sum of two independent d-dimensional Student t-random vectors X and Y with arbitrary degrees of freedom. As a byproduct we also obtain an expression for the density of the sum N+X, where N is normal and X is an independent Student t......-vector. In both cases the density is given as an infinite series $\\sum_{n=0}^\\infty c_nf_n$ where f_n is a sequence of probability densities on R^d and c_n is a sequence of positive numbers of sum 1, i.e. the distribution of a non-negative integer-valued random variable C, which turns out to be infinitely...

  2. Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells.

    Science.gov (United States)

    Yu, Jian; Ciaudo, Constance

    2017-03-17

    Forward genetic screens using retroviral (or transposon) gene-trap vectors in a haploid genome revolutionized the investigation of molecular networks in mammals. However, the sequencing data generated by Phenotypic interrogation followed by Tag sequencing (PhiT-seq) were not well characterized. The analysis of human and mouse haploid screens allowed us to describe PhiT-seq data and to define quality control steps. Moreover, we identified several blind spots in both haploid genomes where gene-trap vectors can hardly integrate. Integration of transcriptomic data improved the performance of candidate gene identification. Furthermore, we experimented with various statistical tests to account for biological replicates in PhiT-seq and investigated the effect of normalization methods and other parameters on the performance. Finally, we developed: VISITs, a dedicated pipeline for analyzing PhiT-seq data (https://sourceforge.net/projects/visits/).

  3. A Simple and High Performing Rate Control Initialization Method for H.264 AVC Coding Based on Motion Vector Map and Spatial Complexity at Low Bitrate

    Directory of Open Access Journals (Sweden)

    Yalin Wu

    2014-01-01

    Full Text Available The temporal complexity of video sequences can be characterized by motion vector map which consists of motion vectors of each macroblock (MB. In order to obtain the optimal initial QP (quantization parameter for the various video sequences which have different spatial and temporal complexities, this paper proposes a simple and high performance initial QP determining method based on motion vector map and temporal complexity to decide an initial QP in given target bit rate. The proposed algorithm produces the reconstructed video sequences with outstanding and stable quality. For any video sequences, the initial QP can be easily determined from matrices by target bit rate and mapped spatial complexity using proposed mapping method. Experimental results show that the proposed algorithm can show more outstanding objective and subjective performance than other conventional determining methods.

  4. A preferred region for recombinational patch repair in the 5' untranslated region of primer binding site-impaired murine leukemia virus vectors

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Kristensen, K D

    1996-01-01

    Transduction of primer binding site-impaired Akv murine leukemia virus-based retroviral vectors from the murine packaging cell lines psi-2 and omega E was studied. The efficiency of transduction of the neo marker of all mutated constructs was found to decrease by 5 to 6 orders of magnitude compared...... with that of the wild-type vector. Thirty-two of 60 transduced proviruses analyzed harbored a primer binding site sequence matching a glutamine tRNA primer. Sequence analysis of the regions flanking the glutamine tRNA primer binding site revealed a distinct pattern of nucleotide differences from the Akv-based vector......, suggesting the involvement of a specific endogenous virus-like sequence in patch repair rescue of the primer binding site mutants. The putative recombination partner RNA was found in virions from psi-2 cells as detected by analysis of glutamine tRNA-initiated cDNA and by sequence analysis of regions...

  5. Analysis of Human Papillomavirus Using Datamining - Apriori, Decision Tree, and Support Vector Machine (SVM) and its Application Field

    OpenAIRE

    Cho Younghoon; Burm Seungwon; Choi Nayoung; Yoon Taeseon

    2016-01-01

    Human Papillomavirus(HPV) has various types (compared to other viruses) and plays a key role in evoking diverse diseases, especially cervical cancer. In this study, we aim to distinguish the features of HPV of different degree of fatality by analyzing their DNA sequences. We used Decision Tree Algorithm, Apriori Algorithm, and Support Vector Machine in our experiment. By analyzing their DNA sequences, we discovered some relationships between certain types of HPV, especially on the most fatal ...

  6. Boundaries of the origin of replication: creation of a pET-28a-derived vector with p15A copy control allowing compatible coexistence with pET vectors.

    Directory of Open Access Journals (Sweden)

    Sarmitha Sathiamoorthy

    Full Text Available During our studies involving protein-DNA interactions, we constructed plasmid pSAM to fulfill two requirements: 1 to facilitate transfer of cloned sequences from widely used expression vector pET-28a(+, and 2 to provide a vector compatible with pBR322-derived plasmids for use in cells harboring two different plasmids. Vector pSAM is a pET-28a(+-derived plasmid with the p15A origin of replication (ori; pET-28a(+ contains the pBR322 replicon that is incompatible with other pBR322-derived plasmids. By replacing the original pET-28a(+ replicon-comprising the ori, RNAI, RNAII, and Rom-with the p15A replicon, we generated pSAM, which contains the pET-28a(+ multiple cloning site and is now compatible with pBR322-derived vectors. Plasmid copy number was assessed using quantitative PCR: pSAM copy number was maintained at 18±4 copies per cell, consistent with that of other p15A-type vectors. Compatibility with pBR322-derived vectors was tested with pGEX-6p-1 and pSAM, which maintained their copy numbers of 49±10 and 14±4, respectively, when both were present within the same cell. Swapping of the ori is a common practice; however, it is vital that all regions of the original replicon be removed. Additional vector pSAMRNAI illustrated that incompatibility remains when portions of the replicon, such as RNAI and/or Rom, are retained; pSAMRNAI, which contains the intact RNAI but not ROM, lowered the copy number of pGEX-6p-1 to 18±2 in doubly transformed cells due to retention of the pET-28a(+-derived RNAI. Thus, pSAMRNAI is incompatible with vectors controlled by the pBR322 replicon and further demonstrates the need to remove all portions of the original replicon and to quantitatively assess copy number, both individually and in combination, to ensure vector compatibility. To our knowledge, this is the first instance where the nascent vector has been quantitatively assessed for both plasmid copy number and compatibility. New vector pSAM provides ease of

  7. A microRNA embedded AAV α-synuclein gene silencing vector for dopaminergic neurons.

    Science.gov (United States)

    Han, Ye; Khodr, Christina E; Sapru, Mohan K; Pedapati, Jyothi; Bohn, Martha C

    2011-04-22

    Alpha-synuclein (SNCA), an abundantly expressed presynaptic protein, is implicated in Parkinson's disease (PD). Since over-expression of human SNCA (hSNCA) leads to death of dopaminergic (DA) neurons in human, rodent and fly brain, hSNCA gene silencing may reduce levels of toxic forms of SNCA and ameliorate degeneration of DA neurons in PD. To begin to develop a gene therapy for PD based on hSNCA gene silencing, two AAV gene silencing vectors were designed, and tested for efficiency and specificity of silencing, as well as toxicity in vitro. The same hSNCA silencing sequence (shRNA) was used in both vectors, but in one vector, the shRNA was embedded in a microRNA backbone and driven by a pol II promoter, and in the other the shRNA was not embedded in a microRNA and was driven by a pol III promoter. Both vectors silenced hSNCA to the same extent in 293T cells transfected with hSNCA. In DA PC12 cells, neither vector decreased expression of rat SNCA, tyrosine hydroxylase (TH), dopamine transporter (DAT) or the vesicular monoamine transporter (VMAT). However, the mir30 embedded vector was significantly less toxic to both PC12 and SH-SY5Y cells. Our in vitro data suggest that this miRNA-embedded silencing vector may be ideal for chronic in vivo SNCA gene silencing in DA neurons. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. Modular broad-host-range expression vectors for single-protein and protein complex purification.

    Science.gov (United States)

    Fodor, Barna D; Kovács, Akos T; Csáki, Róbert; Hunyadi-Gulyás, Eva; Klement, Eva; Maróti, Gergely; Mészáros, Lívia S; Medzihradszky, Katalin F; Rákhely, Gábor; Kovács, Kornél L

    2004-02-01

    A set of modular broad-host-range expression vectors with various affinity tags (six-His-tag, FLAG-tag, Strep-tag II, T7-tag) was created. The complete nucleotide sequences of the vectors are known, and these small vectors can be mobilized by conjugation. They are useful in the purification of proteins and protein complexes from gram-negative bacterial species. The plasmids were easily customized for Thiocapsa roseopersicina, Rhodobacter capsulatus, and Methylococcus capsulatus by inserting an appropriate promoter. These examples demonstrate the versatility and flexibility of the vectors. The constructs harbor the T7 promoter for easy overproduction of the desired protein in an appropriate Escherichia coli host. The vectors were useful in purifying different proteins from T. roseopersicina. The FLAG-tag-Strep-tag II combination was utilized for isolation of the HynL-HypC2 protein complex involved in hydrogenase maturation. These tools should be useful for protein purification and for studying protein-protein interactions in a range of bacterial species.

  9. Epitope-tagging vectors for the expression and detection of recombinant proteins in mycobacteria.

    Science.gov (United States)

    Spratt, Joanne M; Ryan, Anthony A; Britton, Warwick J; Triccas, James A

    2005-05-01

    New tools are required to study the growing number of uncharacterised genes derived from genome sequence projects that are specific to bacterial pathogens such as Mycobacterium tuberculosis. We have developed a series of vectors that permit the specific detection of recombinant proteins expressed in mycobacterial species. Gene expression in these vectors is driven by the strong hsp60 promoter of Mycobacterium bovis BCG and detection of expressed products is facilitated by C-terminal fusion of residues 409-419 of the human c-myc proto-oncogene. Using the M. tuberculosis Ag85B as a reporter of gene expression, we demonstrate that the vectors permit the specific detection of recombinant products expressed in the host species M. bovis BCG. BCG over-expressing Ag85B was a potent inducer of Ag85B-specific T cells in immunised mice, indicating that the C-terminal c-myc tag did not alter the characteristics of the recombinant protein. The versatility of the epitope-tagging vectors was demonstrated by the efficient secretion and detection of recombinant products in BCG. The vectors described in this study will facilitate the expression of foreign proteins in mycobacterial host systems.

  10. Update on the proteomics of major arthropod vectors of human and animal pathogens.

    Science.gov (United States)

    Patramool, Sirilaksana; Choumet, Valérie; Surasombatpattana, Pornapat; Sabatier, Laurence; Thomas, Frédéric; Thongrungkiat, Supatra; Rabilloud, Thierry; Boulanger, Nathalie; Biron, David G; Missé, Dorothée

    2012-12-01

    Vector-borne diseases (VBDs) are defined as infectious diseases of humans and animals caused by pathogenic agents such as viruses, protists, bacteria, and helminths transmitted by the bite of blood-feeding arthropod (BFA) vectors. VBDs represent a major public health threat in endemic areas, generally subtropical zones, and many are considered to be neglected diseases. Genome sequencing of some arthropod vectors as well as modern proteomic and genomic technologies are expanding our knowledge of arthropod-pathogen interactions. This review describes the proteomic approaches that have been used to investigate diverse biological questions about arthropod vectors, including the interplay between vectors and pathogens. Proteomic studies have identified proteins and biochemical pathways that may be involved in molecular crosstalk in BFA-pathogen associations. Future work can build upon this promising start and functional analyses coupled with interactome bioassays will be carried out to investigate the role of candidate peptides and proteins in BFA-human pathogen associations. Dissection of the host-pathogen interactome will be key to understanding the strategies and biochemical pathways used by BFAs to cope with pathogens. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Measurement of lentiviral vector titre and copy number by cross-species duplex quantitative PCR.

    Science.gov (United States)

    Christodoulou, I; Patsali, P; Stephanou, C; Antoniou, M; Kleanthous, M; Lederer, C W

    2016-01-01

    Lentiviruses are the vectors of choice for many preclinical studies and clinical applications of gene therapy. Accurate measurement of biological vector titre before treatment is a prerequisite for vector dosing, and the calculation of vector integration sites per cell after treatment is as critical to the characterisation of modified cell products as it is to long-term follow-up and the assessment of risk and therapeutic efficiency in patients. These analyses are typically based on quantitative real-time PCR (qPCR), but as yet compromise accuracy and comparability between laboratories and experimental systems, the former by using separate simplex reactions for the detection of endogene and lentiviral sequences and the latter by designing different PCR assays for analyses in human cells and animal disease models. In this study, we validate in human and murine cells a qPCR system for the single-tube assessment of lentiviral vector copy numbers that is suitable for analyses in at least 33 different mammalian species, including human and other primates, mouse, pig, cat and domestic ruminants. The established assay combines the accuracy of single-tube quantitation by duplex qPCR with the convenience of one-off assay optimisation for cross-species analyses and with the direct comparability of lentiviral transduction efficiencies in different species.

  12. A novel chimeric ribozyme vector produces potent inhibition of ICAM-1 expression on ischemic vascular endothelium.

    Science.gov (United States)

    Sonnenday, Christopher J; Warren, Daniel S; Cooke, Sara K; Dietz, Harry C; Montgomery, Robert A

    2004-12-01

    Inhibition of intercellular adhesion molecule-1 (ICAM-1) expression can ameliorate the inflammation induced by ischemia-reperfusion injury (IRI) in animal models. However, current strategies to reduce ICAM-1 expression have been limited by the lack of stability, poor specificity, and the transient nature of synthesized regulatory molecules (antisense/ribozyme). A chimeric expression vector was generated by fusing a ribozyme targeting sequence against ICAM-1 to stabilizing stem-loop structures and nuclear localization signals that are components of endogenous U1 small nuclear RNA. Oligonucleotide scanning was used to predict accessible sites for targeting within the rat ICAM-1 transcript. Efficacy of the chimeric ribozyme vector was tested by transfection of rat aortic endothelial (RAE) cells (in vitro) and intraportal delivery in a rat hepatic IRI model (in vivo). Transfection of RAE cells with the chimeric ribozyme vector produced potent and specific inhibition of ICAM-1 mRNA and protein levels by >65%. This reduction in ICAM-1 expression was accompanied by a proportional decrease in neutrophil adhesion to RAE cells. In vivo intraportal delivery of the chimeric targeting vector to rats sustaining hepatic IRI produced a marked reduction in ICAM-1 expression on liver endothelium after reperfusion. A chimeric ribozyme vector effectively inhibited ICAM-1 expression in vascular endothelial cells and in rat liver following IRI, demonstrating a novel gene targeting technique that may be ideally suited to clinical applications aimed at ameliorating IRI. Copyright 2004 John Wiley & Sons, Ltd.

  13. Construction of adenovirus vectors encoding the lumican gene by gateway recombinant cloning technology.

    Science.gov (United States)

    Wang, Gui-Fang; Qi, Bing; Tu, Lei-Lei; Liu, Lian; Yu, Guo-Cheng; Zhong, Jing-Xiang

    2016-01-01

    To construct adenovirus vectors of lumican gene by gateway recombinant cloning technology to further understand the role of lumican gene in myopia. Gateway recombinant cloning technology was used to construct adenovirus vectors. The wild-type (wt) and mutant (mut) forms of the lumican gene were synthesized and amplified by polymerase chain reaction (PCR). The lumican cDNA fragments were purified and ligated into the adenovirus shuttle vector pDown-multiple cloning site (MCS)-/internal ribozyme entry site (IRES)/enhanced green fluorescent protein (EGFP). Then the desired DNA fragments were integrated into the destination vector pAV.Des1d yielding the final expression constructs pAV.Ex1d-cytomegalovirus (CMV)>wt-lumican/IRES/EGFP and pAV.Ex1d-CMV>mut-lumican/IRES /EGFP, respectively. The adenovirus plasmids pAV.Ex1d-CMV>wt-lumican/IRES/EGFP and pAV.Ex1d-CMV>mut-lumican/IRES/EGFP were successfully constructed by gateway recombinant cloning technology. Positive clones identified by PCR and sequencing were selected and packaged into recombinant adenovirus in HEK293 cells. We construct adenovirus vectors containing the lumican gene by gateway recombinant cloning technology, which provides a basis for investigating the role of lumican gene in the pathogenesis of high myopia.

  14. [Preparation of a novel AAV-ITR gene expression mini vector in Sf9 insect cells via baculovirus].

    Science.gov (United States)

    Li, Taiming; Pan, Junjie; Qi, Jing; Zhang, Chun

    2015-08-01

    AAV-ITR gene expression mini vector is a double-strand or single-strand DNA that only contains inverted terminal repeats of adeno-associated virus, cis-elements and gene of interest and does not contain any other foreign DNA sequences. We prepared Bac-ITR-EGFP and Bac-inrep. Spodoptera frugiperda cells were infected with Bac-ITR-EGFP (P3) and Bac-inrep (P3). Up to 100 μg of AAV-ITR-EGFP gene expression mini vectors were extracted from 2 x 10(7) cells of Sf9 72 h after infection. The gel electrophoresis analysis shows that most forms of AAV-ITR-EGFP gene expression mini vector were monomer and dimer. The mini vector expression efficacy was examined in vitro with HEK 293T cells. The EGFP expression was observed at 24 h after transfection, and the positive ratio reached 65% at 48 h after transfection.

  15. Is the Sequence of SuperAlarm Triggers More Predictive Than Sequence of the Currently Utilized Patient Monitor Alarms?

    Science.gov (United States)

    Bai, Yong; Do, Duc; Ding, Quan; Palacios, Jorge Arroyo; Shahriari, Yalda; Pelter, Michele M; Boyle, Noel; Fidler, Richard; Hu, Xiao

    2017-05-01

    Our previous studies have shown that "code blue" events can be predicted by SuperAlarm patterns that are multivariate combinations of monitor alarms and laboratory test results cooccurring frequently preceding the events but rarely among control patients. Deploying these patterns to the monitor data streams can generate SuperAlarm sequences. The objective of this study is to test the hypothesis that SuperAlarm sequences may contain more predictive sequential patterns than monitor alarms sequences. Monitor alarms and laboratory test results are extracted from a total of 254 adult coded and 2213 control patients. The training dataset is composed of subsequences that are sampled from complete sequences and then further represented as fixed-dimensional vectors by the term frequency inverse document frequency method. The information gain technique and weighted support vector machine are adopted to select the most relevant features and train a classifier to differentiate sequences between coded patients and control patients. Performances are assessed based on an independent dataset using three metrics: sensitivity of lead time (Sen L @T), alarm frequency reduction rate (AFRR), and work-up to detection ratio (WDR). The performance of 12-h-long sequences of SuperAlarm can yield a Sen L@2 of 93.33%, an AFRR of 87.28%, and a WDR of 3.01. At an AFRR = 87.28%, Sen L@2 for raw alarm sequences and discretized alarm sequences are 73.33% and 70.19%, respectively. At a WDR = 3.01, Sen L@2 are 49.88% and 43.33%. The results demonstrate that SuperAlarm sequences indeed outperform monitor alarm sequences and suggest that one can focus on sequential patterns from SuperAlarm sequences to develop more precise patient monitoring solutions.

  16. New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae.

    Science.gov (United States)

    Laughery, Marian F; Hunter, Tierra; Brown, Alexander; Hoopes, James; Ostbye, Travis; Shumaker, Taven; Wyrick, John J

    2015-12-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is an important tool for genome editing because the Cas9 endonuclease can induce targeted DNA double-strand breaks. Targeting of the DNA break is typically controlled by a single-guide RNA (sgRNA), a chimeric RNA containing a structural segment important for Cas9 binding and a 20mer guide sequence that hybridizes to the genomic DNA target. Previous studies have demonstrated that CRISPR-Cas9 technology can be used for efficient, marker-free genome editing in Saccharomyces cerevisiae. However, introducing the 20mer guide sequence into yeast sgRNA expression vectors often requires cloning procedures that are complex, time-consuming and/or expensive. To simplify this process, we have developed a new sgRNA expression cassette with internal restriction enzyme sites that permit rapid, directional cloning of 20mer guide sequences. Here we describe a flexible set of vectors based on this design for cloning and expressing sgRNAs (and Cas9) in yeast using different selectable markers. We anticipate that the Cas9-sgRNA expression vector with the URA3 selectable marker (pML104) will be particularly useful for genome editing in yeast, since the Cas9 machinery can be easily removed by counter-selection using 5-fluoro-orotic acid (5-FOA) following successful genome editing. The availability of new vectors that simplify and streamline the technical steps required for guide sequence cloning should help accelerate the use of CRISPR-Cas9 technology in yeast genome editing. Copyright © 2015 John Wiley & Sons, Ltd.

  17. Recombinant rubella vectors elicit SIV Gag-specific T cell responses with cytotoxic potential in rhesus macaques.

    Science.gov (United States)

    Rosati, Margherita; Alicea, Candido; Kulkarni, Viraj; Virnik, Konstantin; Hockenbury, Max; Sardesai, Niranjan Y; Pavlakis, George N; Valentin, Antonio; Berkower, Ira; Felber, Barbara K

    2015-04-27

    Live-attenuated rubella vaccine strain RA27/3 has been demonstrated to be safe and immunogenic in millions of children. The vaccine strain was used to insert SIV gag sequences and the resulting rubella vectors were tested in rhesus macaques alone and together with SIV gag DNA in different vaccine prime-boost combinations. We previously reported that such rubella vectors induce robust and durable SIV-specific humoral immune responses in macaques. Here, we report that recombinant rubella vectors elicit robust de novo SIV-specific cellular immune responses detectable for >10 months even after a single vaccination. The antigen-specific responses induced by the rubella vector include central and effector memory CD4(+) and CD8(+) T cells with cytotoxic potential. Rubella vectors can be administered repeatedly even after vaccination with the rubella vaccine strain RA27/3. Vaccine regimens including rubella vector and SIV gag DNA in different prime-boost combinations resulted in robust long-lasting cellular responses with significant increase of cellular responses upon boost. Rubella vectors provide a potent platform for inducing HIV-specific immunity that can be combined with DNA in a prime-boost regimen to elicit durable cellular immunity. Published by Elsevier Ltd.

  18. Opportunities for Improved Chagas Disease Vector Control Based on Knowledge, Attitudes and Practices of Communities in the Yucatan Peninsula, Mexico

    Science.gov (United States)

    Rosecrans, Kathryn; Cruz-Martin, Gabriela; King, Ashley; Dumonteil, Eric

    2014-01-01

    Background Chagas disease is a vector-borne parasitic disease of major public health importance. Current prevention efforts are based on triatomine vector control to reduce transmission to humans. Success of vector control interventions depends on their acceptability and value to affected communities. We aimed to identify opportunities for and barriers to improved vector control strategies in the Yucatan peninsula, Mexico. Methodology/principal findings We employed a sequence of qualitative and quantitative research methods to investigate knowledge, attitudes and practices surrounding Chagas disease, triatomines and vector control in three rural communities. Our combined data show that community members are well aware of triatomines and are knowledgeable about their habits. However, most have a limited understanding of the transmission dynamics and clinical manifestations of Chagas disease. While triatomine control is not a priority for community members, they frequently use domestic insecticide products including insecticide spray, mosquito coils and plug-in repellents. Families spend about $32 US per year on these products. Alternative methods such as yard cleaning and window screens are perceived as desirable and potentially more effective. Screens are nonetheless described as unaffordable, in spite of a cost comparable to the average annual spending on insecticide products. Conclusion/Significance Further education campaigns and possibly financing schemes may lead families to redirect their current vector control spending from insecticide products to window screens. Also, synergism with mosquito control efforts should be further explored to motivate community involvement and ensure sustainability of Chagas disease vector control. PMID:24676038

  19. The Sea Urchin sns5 Chromatin Insulator Shapes the Chromatin Architecture of a Lentivirus Vector Integrated in the Mammalian Genome.

    Science.gov (United States)

    Baiamonte, Elena; Spinelli, Giovanni; Maggio, Aurelio; Acuto, Santina; Cavalieri, Vincenzo

    2016-10-01

    Lentivirus vectors are presently the favorite vehicles for therapeutic gene transfer in hematopoietic cells. Nonetheless, these vectors integrate randomly throughout the genome, exhibiting variegation of transgene expression due to the spreading of heterochromatin into the vector sequences. Moreover, the cis-regulatory elements harbored by the vector could disturb the proper transcription of resident genes neighboring the integration site. The incorporation of chromatin insulators in flanking position to the transferred unit can alleviate both the above-mentioned dangerous effects, due to the insulator-specific barrier and enhancer-blocking activities. In this study, we report the valuable properties of the sea urchin-derived sns5 insulator in improving the expression efficiency of a lentivirus vector integrated in the mammalian erythroid genome. We show that these results neither reflect an intrinsic sns5 enhancer activity nor rely on the recruitment of the erythroid-specific GATA-1 factor to sns5. Furthermore, by using the Chromosome Conformation Capture technology, we report that a single copy of the sns5-insulated vector is specifically organized into an independent chromatin loop at the provirus locus. Our results not only provide new clues concerning the molecular mechanism of sns5 function in the erythroid genome but also reassure the use of sns5 to improve the performance of gene therapy vectors.

  20. Vectorization, parallelization and porting of nuclear codes. Vectorization and parallelization. Progress report fiscal 1999

    Energy Technology Data Exchange (ETDEWEB)

    Adachi, Masaaki; Ogasawara, Shinobu; Kume, Etsuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Ishizuki, Shigeru; Nemoto, Toshiyuki; Kawasaki, Nobuo; Kawai, Wataru [Fujitsu Ltd., Tokyo (Japan); Yatake, Yo-ichi [Hitachi Ltd., Tokyo (Japan)

    2001-02-01

    Several computer codes in the nuclear field have been vectorized, parallelized and trans-ported on the FUJITSU VPP500 system, the AP3000 system, the SX-4 system and the Paragon system at Center for Promotion of Computational Science and Engineering in Japan Atomic Energy Research Institute. We dealt with 18 codes in fiscal 1999. These results are reported in 3 parts, i.e., the vectorization and the parallelization part on vector processors, the parallelization part on scalar processors and the porting part. In this report, we describe the vectorization and parallelization on vector processors. In this vectorization and parallelization on vector processors part, the vectorization of Relativistic Molecular Orbital Calculation code RSCAT, a microscopic transport code for high energy nuclear collisions code JAM, three-dimensional non-steady thermal-fluid analysis code STREAM, Relativistic Density Functional Theory code RDFT and High Speed Three-Dimensional Nodal Diffusion code MOSRA-Light on the VPP500 system and the SX-4 system are described. (author)

  1. Improved Coinfection with Amphotropic Pseudotyped Retroviral Vectors

    Directory of Open Access Journals (Sweden)

    Yuehong Wu

    2009-01-01

    Full Text Available Amphotropic pseudotyped retroviral vectors have typically been used to infect target cells without prior concentration. Although this can yield high rates of infection, higher rates may be needed where highly efficient coinfection of two or more vectors is needed. In this investigation we used amphotropic retroviral vectors produced by the Plat-A cell line and studied coinfection rates using green and red fluorescent proteins (EGFP and dsRed2. Target cells were primary human fibroblasts (PHF and 3T3 cells. Unconcentrated vector preparations produced a coinfection rate of ∼4% (defined as cells that are both red and green as a percentage of all cells infected. Optimized spinoculation, comprising centrifugation at 1200 g for 2 hours at 15∘C, increased the coinfection rate to ∼10%. Concentration by centrifugation at 10,000 g or by flocculation using Polybrene increased the coinfection rate to ∼25%. Combining the two processes, concentration by Polybrene flocculation and optimized spinoculation, increased the coinfection rate to 35% (3T3 or >50% (PHF. Improved coinfection should be valuable in protocols that require high transduction by combinations of two or more retroviral vectors.

  2. Could dark energy be vector-like?

    Science.gov (United States)

    Armendáriz-Picón, C.

    2004-07-01

    In this paper I explore whether a vector field can be the origin of the present stage of cosmic acceleration. In order to avoid violations of isotropy, the vector has be part of a 'cosmic triad', that is, a set of three identical vectors pointing in mutually orthogonal spatial directions. A triad is indeed able to drive a stage of late accelerated expansion in the universe, and there exist tracking attractors that render cosmic evolution insensitive to initial conditions. However, as in most other models, the onset of cosmic acceleration is determined by a parameter that has to be tuned to reproduce current observations. The triad equation of state can be sufficiently close to minus one today, and for tachyonic models it might be even less than that. I briefly analyse linear cosmological perturbation theory in the presence of a triad. It turns out that the existence of non-vanishing spatial vectors invalidates the decomposition theorem, i.e. scalar, vector and tensor perturbations do not decouple from each other. In a simplified case it is possible to analytically study the stability of the triad along the different cosmological attractors. The triad is classically stable during inflation, radiation and matter domination, but it is unstable during (late time) cosmic acceleration. I argue that this instability is not likely to have a significant impact at present.

  3. Retroviral hybrid LTR vector strategy: functional analysis of LTR elements and generation of endothelial cell specificity.

    Science.gov (United States)

    Richardson, T B; Kaspers, J; Porter, C D

    2004-05-01

    Transcriptional targeting is an important aspect of developing gene therapy vectors in order to restrict transgene expression to selected target cells. One approach, when using retroviral vectors, is to replace viral transcriptional control elements within the long terminal repeat (LTR) with sequences imparting the desired specificity. We have developed such hybrid LTR retroviruses, incorporating sequences from each of the human promoters for flt-1, ICAM-2 and KDR, as part of our antivascular cancer gene therapy strategy targeting tumour endothelial cells. The chosen fragments were used to replace the enhancer or combined enhancer and proximal promoter regions of the viral LTR. All showed activity in primary human breast microvascular endothelial cells, with viruses incorporating ICAM-2 sequences exhibiting the greatest specificity versus nonendothelial cells in vitro and a marked alteration of specificity towards endothelial cells in a subcutaneous xenograft model in vivo. Moreover, our study documents the effect of enhancer and/or proximal promoter deletion on LTR activity and reports that differential dependence in different cell lines can give the false impression of specificity if experiments are not adequately controlled. This finding also has implications for other retroviral vector designs seeking to provide transcriptional specificity and for their safety with respect to prevention of gene activation at sites of proviral integration.

  4. Design and cloning strategies for constructing shRNA expression vectors

    Directory of Open Access Journals (Sweden)

    McIntyre Glen J

    2006-01-01

    Full Text Available Abstract Background Short hairpin RNA (shRNA encoded within an expression vector has proven an effective means of harnessing the RNA interference (RNAi pathway in mammalian cells. A survey of the literature revealed that shRNA vector construction can be hindered by high mutation rates and the ensuing sequencing is often problematic. Current options for constructing shRNA vectors include the use of annealed complementary oligonucleotides (74 % of surveyed studies, a PCR approach using hairpin containing primers (22 % and primer extension of hairpin templates (4 %. Results We considered primer extension the most attractive method in terms of cost. However, in initial experiments we encountered a mutation frequency of 50 % compared to a reported 20 – 40 % for other strategies. By modifying the technique to be an isothermal reaction using the DNA polymerase Phi29, we reduced the error rate to 10 %, making primer extension the most efficient and cost-effective approach tested. We also found that inclusion of a restriction site in the loop could be exploited for confirming construct integrity by automated sequencing, while maintaining intended gene suppression. Conclusion In this study we detail simple improvements for constructing and sequencing shRNA that overcome current limitations. We also compare the advantages of our solutions against proposed alternatives. Our technical modifications will be of tangible benefit to researchers looking for a more efficient and reliable shRNA construction process.

  5. Development of a novel plasmid as a shuttle vector for heterologous gene expression in Mycoplasma yeatsii.

    Science.gov (United States)

    Kent, Bethany N; Foecking, Mark F; Calcutt, Michael J

    2012-10-01

    A circular plasmid, pMyBK1, was detected in Mycoplasma yeatsii strain GIH(T). Analysis of the sequence of the 3432-bp replicon identified two predicted open reading frames (ORFs), one with sequence similarity to multiple plasmid mobilization proteins and one that matches only to hypothetical ORFs encoded by integrated chromosomal elements in the sequenced genomes of two Mycoplasma species. Shuttle vectors were constructed in Escherichia coli which could be introduced into M. yeatsii at high efficiency (10(4)-10(5) per μg DNA) by electroporation. Independent deletion analysis of the two ORFs disclosed that whereas mob was dispensable, orf2 was necessary for plasmid replication or maintenance. The absence of plasmid-encoded database matches for ORF2 indicates that pMyBK1 represents a novel plasmid family. One shuttle vector was used to demonstrate heterologous expression of the Mycoplasma fermentans malp gene and was stable during multiple passages. The host-plasmid system described has potential application for genetic manipulation in a genus for which few replicative vectors are available. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Emergence and Prevalence of Human Vector-Borne Diseases in Sink Vector Populations

    Science.gov (United States)

    Rascalou, Guilhem; Pontier, Dominique; Menu, Frédéric; Gourbière, Sébastien

    2012-01-01

    Vector-borne diseases represent a major public health concern in most tropical and subtropical areas, and an emerging threat for more developed countries. Our understanding of the ecology, evolution and control of these diseases relies predominantly on theory and data on pathogen transmission in large self-sustaining ‘source’ populations of vectors representative of highly endemic areas. However, there are numerous places where environmental conditions are less favourable to vector populations, but where immigration allows them to persist. We built an epidemiological model to investigate the dynamics of six major human vector borne-diseases in such non self-sustaining ‘sink’ vector populations. The model was parameterized through a review of the literature, and we performed extensive sensitivity analysis to look at the emergence and prevalence of the pathogen that could be encountered in these populations. Despite the low vector abundance in typical sink populations, all six human diseases were able to spread in 15–55% of cases after accidental introduction. The rate of spread was much more strongly influenced by vector longevity, immigration and feeding rates, than by transmission and virulence of the pathogen. Prevalence in humans remained lower than 5% for dengue, leishmaniasis and Japanese encephalitis, but substantially higher for diseases with longer duration of infection; malaria and the American and African trypanosomiasis. Vector-related parameters were again the key factors, although their influence was lower than on pathogen emergence. Our results emphasize the need for ecology and evolution to be thought in the context of metapopulations made of a mosaic of sink and source habitats, and to design vector control program not only targeting areas of high vector density, but working at a larger spatial scale. PMID:22629337

  7. Reducing the risk of adeno-associated virus (AAV) vector mobilization with AAV type 5 vectors.

    Science.gov (United States)

    Hewitt, F Curtis; Li, Chengwen; Gray, Steven J; Cockrell, Shelley; Washburn, Michael; Samulski, R Jude

    2009-04-01

    Current adeno-associated virus (AAV) gene therapy vectors package a transgene flanked by the terminal repeats (TRs) of AAV type 2 (AAV2). Although these vectors are replication deficient, wild-type (wt) AAV2 prevalent in the human population could lead to replication and packaging of a type 2 TR (TR2)-flanked transgene in trans during superinfection by a helper virus, leading to "mobilization" of the vector genome from treated cells. More importantly, it appears likely that the majority of currently characterized AAV serotypes as well as the majority of new novel isolates are capable of rescuing and replicating AAV2 vector templates. To investigate this possibility, we flanked a green fluorescent protein transgene with type 2 and, the most divergent AAV serotype, type 5 TRs (TR2 or TR5). Consistent with AAV clades, AAV5 specifically replicated TR5 vectors, while AAV2 and AAV6 replicated TR2-flanked vectors. To exploit this specificity, we created a TR5 vector production system for Cap1 to Cap5. Next, we showed that persisting recombinant AAV genomes flanked by TR2s or TR5s were mobilized in vitro after addition of the cognate AAV Rep (as well as Rep6 for TR2) and adenoviral helper. Finally, we showed that a cell line containing a stably integrated wt AAV2 genome resulted in mobilization of a TR2-flanked vector but not a TR5-flanked vector upon adenoviral superinfection. Based on these data and the relative prevalence of wt AAV serotypes in the population, we propose that TR5 vectors have a significantly lower risk of mobilization and should be considered for clinical use.

  8. Emergence and prevalence of human vector-borne diseases in sink vector populations.

    Science.gov (United States)

    Rascalou, Guilhem; Pontier, Dominique; Menu, Frédéric; Gourbière, Sébastien

    2012-01-01

    Vector-borne diseases represent a major public health concern in most tropical and subtropical areas, and an emerging threat for more developed countries. Our understanding of the ecology, evolution and control of these diseases relies predominantly on theory and data on pathogen transmission in large self-sustaining 'source' populations of vectors representative of highly endemic areas. However, there are numerous places where environmental conditions are less favourable to vector populations, but where immigration allows them to persist. We built an epidemiological model to investigate the dynamics of six major human vector borne-diseases in such non self-sustaining 'sink' vector populations. The model was parameterized through a review of the literature, and we performed extensive sensitivity analysis to look at the emergence and prevalence of the pathogen that could be encountered in these populations. Despite the low vector abundance in typical sink populations, all six human diseases were able to spread in 15-55% of cases after accidental introduction. The rate of spread was much more strongly influenced by vector longevity, immigration and feeding rates, than by transmission and virulence of the pathogen. Prevalence in humans remained lower than 5% for dengue, leishmaniasis and Japanese encephalitis, but substantially higher for diseases with longer duration of infection; malaria and the American and African trypanosomiasis. Vector-related parameters were again the key factors, although their influence was lower than on pathogen emergence. Our results emphasize the need for ecology and evolution to be thought in the context of metapopulations made of a mosaic of sink and source habitats, and to design vector control program not only targeting areas of high vector density, but working at a larger spatial scale.

  9. Emergence and prevalence of human vector-borne diseases in sink vector populations.

    Directory of Open Access Journals (Sweden)

    Guilhem Rascalou

    Full Text Available Vector-borne diseases represent a major public health concern in most tropical and subtropical areas, and an emerging threat for more developed countries. Our understanding of the ecology, evolution and control of these diseases relies predominantly on theory and data on pathogen transmission in large self-sustaining 'source' populations of vectors representative of highly endemic areas. However, there are numerous places where environmental conditions are less favourable to vector populations, but where immigration allows them to persist. We built an epidemiological model to investigate the dynamics of six major human vector borne-diseases in such non self-sustaining 'sink' vector populations. The model was parameterized through a review of the literature, and we performed extensive sensitivity analysis to look at the emergence and prevalence of the pathogen that could be encountered in these populations. Despite the low vector abundance in typical sink populations, all six human diseases were able to spread in 15-55% of cases after accidental introduction. The rate of spread was much more strongly influenced by vector longevity, immigration and feeding rates, than by transmission and virulence of the pathogen. Prevalence in humans remained lower than 5% for dengue, leishmaniasis and Japanese encephalitis, but substantially higher for diseases with longer duration of infection; malaria and the American and African trypanosomiasis. Vector-related parameters were again the key factors, although their influence was lower than on pathogen emergence. Our results emphasize the need for ecology and evolution to be thought in the context of metapopulations made of a mosaic of sink and source habitats, and to design vector control program not only targeting areas of high vector density, but working at a larger spatial scale.

  10. Resonance vector soliton of the Rayleigh wave.

    Science.gov (United States)

    Adamashvili, G T

    2016-02-01

    A theory of acoustic vector solitons of self-induced transparency of the Rayleigh wave is constructed. A thin resonance transition layer on an elastic surface is considered using a model of a two-dimensional gas of impurity paramagnetic atoms or quantum dots. Explicit analytical expressions for the profile and parameters of the Rayleigh vector soliton with two different oscillation frequencies is obtained, as well as simulations of this nonlinear surface acoustic wave with realistic parameters, which can be used in acoustic experiments. It is shown that the properties of a surface vector soliton of the Rayleigh wave depend on the parameters of the resonance layer, the elastic medium, and the transverse structure of the surface acoustic wave.

  11. Phase interaction of short vector solitons

    Energy Technology Data Exchange (ETDEWEB)

    Aseeva, N.V., E-mail: naseeva@hse.ru [Higher School of Economics, Faculty of Business Informatics and Applied Mathematics, State University, Bolshaya Pecherskaya 25/12, 603155 Nizhny Novgorod (Russian Federation); Gromov, E.M.; Tyutin, V.V. [Higher School of Economics, Faculty of Business Informatics and Applied Mathematics, State University, Bolshaya Pecherskaya 25/12, 603155 Nizhny Novgorod (Russian Federation)

    2012-01-16

    An interaction of vector solitons in the frame of coupled third-order nonlinear Schrödinger equations taking into account third-order linear dispersion, nonlinear dispersion, and cross-phase modulation terms is considered. Phase nature of the solitons' interaction is shown. In particular, dependence of solitons' trajectories on initial distance between solitons is shown. Conditions of reflection and propagation of solitons through each other are obtained. -- Highlights: ► Short vector soliton's interaction in the frame of CTNSE without SRS is studied. ► Analytical and numerical approaches are considered. ► Phase effects lead to short vector soliton's interaction character change.

  12. On-demand tailored vector beams.

    Science.gov (United States)

    Perez-Garcia, Benjamin; López-Mariscal, Carlos; Hernandez-Aranda, Raul I; Gutiérrez-Vega, Julio C

    2017-08-20

    We introduce an effective optical system to produce optical beams with arbitrary, inhomogeneous polarization states. Using our system, we are capable of generating vector beams with discretionarily chosen transverse complex fields in a straightforward way. We generate several different instances of well-known vector beams and the less common spirally polarized vector beams, as well as a full Poincaré beam. We visually show the continual transition between azimuthally and radially polarized beams via a collection of spirally polarized beams. We experimentally determine the polarization states of the generated beams and quantitatively assess the performance of our system. We find that the measured polarization distributions accurately coincide with the intended input polarization distributions.

  13. Risk based surveillance for vector borne diseases

    DEFF Research Database (Denmark)

    Bødker, Rene

    an increasing trend in transmission potential over the last 25 years. However the model suggested that the climate in the Baltic See Region has always permitted transmission of these diseases. The model therefore suggests that a presently unknown factor until recently prevented introduction and spread......Increased temperatures and changes in rainfall pattern are likely to facilitate the spread and establishment of new vector borne diseases in the Baltic See Region. There are a large number of potential vector borne threats to the area. Existing endemic vector borne diseases are likely to increase...... and new exotic diseases like Usutu and West Nile Virus may lead to outbreaks in the region. In the worst case the combined effect of climate change and globalization may potentially lead to European outbreaks of important zoonotic mosquito borne infections like Rift Valley Fever in cattle and Japanese...

  14. Generating Series for Nested Bethe Vectors

    Directory of Open Access Journals (Sweden)

    Sergey Khoroshkin

    2008-11-01

    Full Text Available We reformulate nested relations between off-shell U_q(^gl_N Bethe vectors as a certain equation on generating series of strings of the composed U_q(^gl_N currents. Using inversion of the generating series we find a new type of hierarchical relations between universal off-shell Bethe vectors, useful for a derivation of Bethe equation. As an example of application, we use these relations for a derivation of analytical Bethe ansatz equations [Arnaudon D. et al., Ann. Henri Poincaré 7 (2006, 1217-1268, math-ph/0512037] for the parameters of universal Bethe vectors of the algebra U_q(^gl_2.

  15. Interactions between parasites and insects vectors

    Directory of Open Access Journals (Sweden)

    Hilary Hurd

    1994-01-01

    Full Text Available This review stresses the importance of studies that will provide a basic understanding of the pathology of parasite-infected vector insects. This knowledge should be a vital component of the very focussed initiatives currently being funded in the areas of vector control. Vector fecundity reduction is discussed as an example of such pathology. Underlying mechanisms are being investigated in a model system, Hymenolepis diminuta-infected Tenebrio molitor and in Onchocerca-infected blackflies and Plasmodium-infected Anopheles stephensi. In all cases, host vitellogenesis is disrupted by the parasite and, in the tapeworm/beetle model, interaction between the parasite and the endocrine control of the insect's reproductive physiology has been demonstrated.

  16. Black hole superradiance signatures of ultralight vectors

    Science.gov (United States)

    Baryakhtar, Masha; Lasenby, Robert; Teo, Mae

    2017-08-01

    The process of superradiance can extract angular momentum and energy from astrophysical black holes (BHs) to populate gravitationally bound states with an exponentially large number of light bosons. We analytically calculate superradiant growth rates for vectors around rotating BHs in the regime where the vector Compton wavelength is much larger than the BH size. Spin-1 bound states have superradiance times as short as a second around stellar BHs, growing up to a thousand times faster than their spin-0 counterparts. The fast rates allow us to use measurements of rapidly spinning BHs in x-ray binaries to exclude a wide range of masses for weakly coupled spin-1 particles, 5 ×10-14-2 ×10-11 eV ; lighter masses in the range 6 ×10-20-2 ×10-17 eV start to be constrained by supermassive BH spin measurements at a lower level of confidence. We also explore routes to detection of new vector particles possible with the advent of gravitational wave (GW) astronomy. The LIGO-Virgo Collaboration could discover hints of a new light vector particle in statistical analyses of masses and spins of merging BHs. Vector annihilations source continuous monochromatic gravitational radiation which could be observed by current GW observatories. At design sensitivity, Advanced LIGO may measure up to thousands of annihilation signals from within the Milky Way, while hundreds of BHs born in binary mergers across the observable Universe may superradiate vector bound states and become new beacons of monochromatic gravitational waves.

  17. Application of Bred Vectors To Data Assimilation

    Science.gov (United States)

    Corazza, M.; Kalnay, E.; Patil, Dj

    We introduced a statistic, the BV-dimension, to measure the effective local finite-time dimensionality of the atmosphere. We show that this dimension is often quite low, and suggest that this finding has important implications for data assimilation and the accuracy of weather forecasting (Patil et al, 2001). The original database for this study was the forecasts of the NCEP global ensemble forecasting system. The initial differences between the control forecast and the per- turbed forecasts are called bred vectors. The control and perturbed initial conditions valid at time t=n(t are evolved using the forecast model until time t=(n+1) (t. The differences between the perturbed and the control forecasts are scaled down to their initial amplitude, and constitute the bred vectors valid at (n+1) (t. Their growth rate is typically about 1.5/day. The bred vectors are similar by construction to leading Lya- punov vectors except that they have small but finite amplitude, and they are valid at finite times. The original NCEP ensemble data set has 5 independent bred vectors. We define a local bred vector at each grid point by choosing the 5 by 5 grid points centered at the grid point (a region of about 1100km by 1100km), and using the north-south and east- west velocity components at 500mb pressure level to form a 50 dimensional column vector. Since we have k=5 global bred vectors, we also have k local bred vectors at each grid point. We estimate the effective dimensionality of the subspace spanned by the local bred vectors by performing a singular value decomposition (EOF analysis). The k local bred vector columns form a 50xk matrix M. The singular values s(i) of M measure the extent to which the k column unit vectors making up the matrix M point in the direction of v(i). We define the bred vector dimension as BVDIM={Sum[s(i)]}^2/{Sum[s(i)]^2} For example, if 4 out of the 5 vectors lie along v, and one lies along v, the BV- dimension would be BVDIM[sqrt(4), 1, 0

  18. A single copy integration vector that integrates at an engineered site on the Staphylococcus aureus chromosome

    Directory of Open Access Journals (Sweden)

    Lei Mei G

    2012-01-01

    Full Text Available Abstract Background Single-copy integration vectors based upon the site-specific recombination systems of bacteriophage are invaluable tools in the study of bacterial pathogenesis. The utility of such vectors is often limited, however, by the fact that integration often results in the inactivation of bacterial genes or has undesirable effects on gene transcription. The aim of this study is to develop an integration vector that does not have a detectable effect on gene transcription upon integration. Findings We have developed a single-copy integration system that enables the cloning vector to integrate at a specific engineered site, within an untranscribed intergenic region, in the chromosome of Staphylococcus aureus. This system is based on the lysogenic phage L54a site-specific recombination system in which the L54a phage (attP and chromosome (attB attachment sites, which share an 18-bp identical core sequence, were modified with identical mutations. The integration vector, pLL102, was constructed to contain the modified L54a attP site (attP2 that was altered at 5 nucleotide positions within the core sequence. In the recipient strain, the similarly modified attB site (attB2 was inserted in an intergenic region devoid of detectable transcription read-through. Integration of the vector, which is unable to replicate in S. aureus extrachromosomally, was achieved by providing the L54a integrase gene in a plasmid in the recipient. We showed that pLL102 integrated specifically at the engineered site rather than at the native L54a attB site and that integration did not have a significant effect on transcription of genes immediately upstream or downstream of the integration site. Conclusions In this work, we describe an E. coli-S. aureus shuttle vector that can be used to introduce any cloned gene into the S. aureus chromosome at a select site without affecting gene expression. The vector should be useful for genetic manipulation of S. aureus and for

  19. Delivering Transgenic DNA Exceeding the Carrying Capacity of AAV Vectors.

    Science.gov (United States)

    Hirsch, Matthew L; Wolf, Sonya J; Samulski, R J

    2016-01-01

    Gene delivery using recombinant adeno-associated virus (rAAV) has emerged to the forefront demonstrating safe and effective phenotypic correction of diverse diseases including hemophilia B and Leber's congenital amaurosis. In addition to rAAV's high efficiency of transduction and the capacity for long-term transgene expression, the safety profile of rAAV remains unsoiled in humans with no deleterious vector-related consequences observed thus far. Despite these favorable attributes, rAAV vectors have a major disadvantage preventing widespread therapeutic applications; as the AAV capsid is the smallest described to date, it cannot package "large" genomes. Currently, the packaging capacity of rAAV has yet to be definitively defined but is approximately 5 kb, which has served as a limitation for large gene transfer. There are two main approaches that have been developed to overcome this limitation, split AAV vectors, and fragment AAV (fAAV) genome reassembly (Hirsch et al., Mol Ther 18(1):6-8, 2010). Split rAAV vector applications were developed based upon the finding that rAAV genomes naturally concatemerize in the cell post-transduction and are substrates for enhanced homologous recombination (HR) (Hirsch et al., Mol Ther 18(1):6-8, 2010; Duan et al., J Virol 73(1):161-169, 1999; Duan et al., J Virol 72(11):8568-8577, 1998; Duan et al., Mol Ther 4(4):383-391, 2001; Halbert et al., Nat Biotechnol 20(7):697-701, 2002). This method involves "splitting" the large transgene into two separate vectors and upon co-transduction, intracellular large gene reconstruction via vector genome concatemerization occurs via HR or nonhomologous end joining (NHEJ). Within the split rAAV approaches there currently exist three strategies: overlapping, trans-splicing, and hybrid trans-splicing (Duan et al., Mol Ther 4(4):383-391, 2001; Halbert et al., Nat Biotechnol 20(7):697-701, 2002; Ghosh et al., Mol Ther 16(1):124-130, 2008; Ghosh et al., Mol Ther 15(4):750-755, 2007). The other major

  20. Wiggle-predicting functionally flexible regions from primary sequence.

    Directory of Open Access Journals (Sweden)

    Jenny Gu

    2006-07-01

    Full Text Available The Wiggle series are support vector machine-based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship between protein sequence and flexibility. A coarse-grained protein dynamic modeling approach was used to generate the dataset required for support vector machine training. We define our regions of interest based on the participation of residues in correlated large-scale fluctuations. Even with this structure-based approach to computationally define regions of functional flexibility, predictors successfully extract sequence-flexibility relationships that have been experimentally confirmed to be functionally important. Thus, a sequence-based tool to identify flexible regions important for protein function has been created. The ability to identify functional flexibility using a sequence based approach complements structure-based definitions and will be especially useful for the large majority of proteins with unknown structures. The methodology offers promise to identify structural genomics targets amenable to crystallization and the possibility to engineer more flexible or rigid regions within proteins to modify their bioactivity.

  1. [Down-regulation of human intercellular adhesion molecule-1 expression in MCF-7 cells infected by lentiviral short hairpin RNA interference vectors].

    Science.gov (United States)

    Di, Dalin; Chen, Lei; Wang, Lina; Wang, Chengdong; Ju, Jiyu

    2015-08-01

    To construct lentiviral interference vectors of human intercellular adhesion molecule-1 (ICAM-1), then infect human breast cancer MCF-7 cells and identify the interference effects. Three short hairpin RNA (shRNA) interference sequences targeting human ICAM-1 gene (ICAM-1 shRNA1, ICAM-1 shRNA2 and ICAM-1 shRNA3) and a negative control sequence (NS) were designed, synthesized and cloned into the pLKO.1-SP6-PGK-GFP vector. After DNA sequencing, three plasmid-based lentiviral packaging system (vector plasmid-psPAX2-pMD2.G) was used to transfect HEK293T cells to package lentiviruses. The supernatants containing viruses were harvested to detect the viral titer. Human MCF-7 breast cancer cells were infected with the lentiviruses and the interference efficiency was detected by real-time quantitative PCR (qRT-PCR) and Western blotting. PCR showed that the designed sequences were successfully inserted into the pLKO.1-SP6-PGK-GFP vector and DNA sequencing results were correct. The qRT-PCR and Western blotting showed that the mRNA and protein expression levels of ICAM-1 in the infected MCF-7 cells decreased significantly in the ICAM-1 shRNA3 group. Lentiviral interference vectors of human ICAM-1 were constructed successfully and the expression of ICAM-1 in MCF-7 cells was down-regulated by ICAM-1 shRNA.

  2. Integrated vector management for malaria control

    Directory of Open Access Journals (Sweden)

    Impoinvil Daniel E

    2008-12-01

    Full Text Available Abstract Integrated vector management (IVM is defined as "a rational decision-making process for the optimal use of resources for vector control" and includes five key elements: 1 evidence-based decision-making, 2 integrated approaches 3, collaboration within the health sector and with other sectors, 4 advocacy, social mobilization, and legislation, and 5 capacity-building. In 2004, the WHO adopted IVM globally for the control of all vector-borne diseases. Important recent progress has been made in developing and promoting IVM for national malaria control programmes in Africa at a time when successful malaria control programmes are scaling-up with insecticide-treated nets (ITN and/or indoor residual spraying (IRS coverage. While interventions using only ITNs and/or IRS successfully reduce transmission intensity and the burden of malaria in many situations, it is not clear if these interventions alone will achieve those critical low levels that result in malaria elimination. Despite the successful employment of comprehensive integrated malaria control programmes, further strengthening of vector control components through IVM is relevant, especially during the "end-game" where control is successful and further efforts are required to go from low transmission situations to sustained local and country-wide malaria elimination. To meet this need and to ensure sustainability of control efforts, malaria control programmes should strengthen their capacity to use data for decision-making with respect to evaluation of current vector control programmes, employment of additional vector control tools in conjunction with ITN/IRS tactics, case-detection and treatment strategies, and determine how much and what types of vector control and interdisciplinary input are required to achieve malaria elimination. Similarly, on a global scale, there is a need for continued research to identify and evaluate new tools for vector control that can be integrated with

  3. Vector domain decomposition schemes for parabolic equations

    Science.gov (United States)

    Vabishchevich, P. N.

    2017-09-01

    A new class of domain decomposition schemes for finding approximate solutions of timedependent problems for partial differential equations is proposed and studied. A boundary value problem for a second-order parabolic equation is used as a model problem. The general approach to the construction of domain decomposition schemes is based on partition of unity. Specifically, a vector problem is set up for solving problems in individual subdomains. Stability conditions for vector regionally additive schemes of first- and second-order accuracy are obtained.

  4. [Conflicts and vector-borne diseases].

    Science.gov (United States)

    Bygbjerg, Ib Christian

    2010-01-11

    Based on literature and personal experiences, vector-borne diseases and conflicts are reviewed. Simple rapid diagnostic tests for three important parasitoses are available. Resort is often made to case definitions and to presumptive treatment. Resistance is an emerging problem. Vaccines are still not available for most diseases. Promising preventive methods, including long-lasting impregnated bed-nets and tents, are available. War has been an impetus for disclosing life-cycles of vector-borne diseases and for control methods; peace, reconciliation and poverty reduction are required to achieve lasting control.

  5. Vectorized algorithms for spiking neural network simulation.

    Science.gov (United States)

    Brette, Romain; Goodman, Dan F M

    2011-06-01

    High-level languages (Matlab, Python) are popular in neuroscience because they are flexible and accelerate development. However, for simulating spiking neural networks, the cost of interpretation is a bottleneck. We describe a set of algorithms to simulate large spiking neural networks efficiently with high-level languages using vector-based operations. These algorithms constitute the core of Brian, a spiking neural network simulator written in the Python language. Vectorized simulation makes it possible to combine the flexibility of high-level languages with the computational efficiency usually associated with compiled languages.

  6. Variable ordering structures in vector optimization

    CERN Document Server

    Eichfelder, Gabriele

    2014-01-01

    This book provides an introduction to vector optimization with variable ordering structures, i.e., to optimization problems with a vector-valued objective function where the elements in the objective space are compared based on a variable ordering structure: instead of a partial ordering defined by a convex cone, we see a whole family of convex cones, one attached to each element of the objective space. The book starts by presenting several applications that have recently sparked new interest in these optimization problems, and goes on to discuss fundamentals and important results on a wide ra

  7. Vector Fields European user group meeting

    CERN Multimedia

    2007-01-01

    The "Vector Fields European user group meeting" will take place at CERN on 26 and 27 September 2007. Within this framework two workshops are organized at the CERN Training Centre: 24 September 2007
 Modelling Magnets with Opera 25 September 2007
Modelling of Charged Particle Beam Devices with Opera If you are interested in attending the workshop or the user group meeting please contact Julie Shepherd (Vector Fields) or Pierre Baehler (CERN) directly at: Julie.Shepherd@vectorfields.co.uk, +44 (0) 1865 854933 or +44 (0) 1865 370151 Pierre.Baehler@cern.ch, 75016 / 160156.

  8. Learning and Memory in Disease Vector Insects.

    Science.gov (United States)

    Vinauger, Clément; Lahondère, Chloé; Cohuet, Anna; Lazzari, Claudio R; Riffell, Jeffrey A

    2016-10-01

    Learning and memory plays an important role in host preference and parasite transmission by disease vector insects. Historically there has been a dearth of standardized protocols that permit testing their learning abilities, thus limiting discussion on the potential epidemiological consequences of learning and memory to a largely speculative extent. However, with increasing evidence that individual experience and associative learning can affect processes such as oviposition site selection and host preference, it is timely to review the recently acquired knowledge, identify research gaps and discuss the implication of learning in disease vector insects in perspective with control strategies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Constraints on vector meson photoproduction spin observables

    Science.gov (United States)

    Kloet, W. M.; Tabakin, Frank

    2000-01-01

    Extraction of spin observables from vector meson photoproduction on a nucleon target is described. Starting from density matrix elements in the vector meson's rest frame, we transform to spin observables in the photon-nucleon c.m. frame. Several constraints on the transformed density matrix and on the spin observables follow from requiring that the angular distribution and the density matrix be positive definite. A set of constraints that are required in order to extract meaningful spin observables from forthcoming data are enunciated.

  10. Vector coherent states for nanoparticle systems

    Energy Technology Data Exchange (ETDEWEB)

    Aremua, Isiaka [Institut de Mathematiques et de Sciences Physiques (IMSP), University of Abomey-Calavi, 01 BP 613 Porto-Novo (Benin); Hounkonnou, Mahouton Norbert, E-mail: iaremua@imsp-uac.org, E-mail: norbert.hounkonnou@cipma.uac.bj [International Chair of Mathematical Physics and Applications (ICMPA-UNESCO Chair), University of Abomey-Calavi, 072 BP 50 Cotonou (Benin)

    2011-11-18

    The first part of this work deals with a formalism of vector coherent states construction for a system of M Fermi-type modes associated with N bosonic modes. Then follows a generalization to a Hamiltonian describing the translational motion of the center of mass of a nanoparticle. The latter gives rise to a new mechanism for the electronic energy relaxation in nanocrystals, intensively studied today in condensed matter physics. Finite degeneracies of the involved Hamiltonian systems are also investigated. The defined vector coherent states satisfy relevant mathematical properties of continuity, resolution of identity, temporal stability and action identity. (paper)

  11. Vector Fields and Flows on Differentiable Stacks

    DEFF Research Database (Denmark)

    A. Hepworth, Richard

    2009-01-01

    and uniqueness of flows on a manifold as well as the author's existing results for orbifolds. It sets the scene for a discussion of Morse Theory on a general proper stack and also paves the way for the categorification of other key aspects of differential geometry such as the tangent bundle and the Lie algebra......This paper introduces the notions of vector field and flow on a general differentiable stack. Our main theorem states that the flow of a vector field on a compact proper differentiable stack exists and is unique up to a uniquely determined 2-cell. This extends the usual result on the existence...

  12. The Cross Product of Two Vectors Is Not Just Another Vector--A Major Misconception Being Perpetuated in Calculus and Vector Analysis Textbooks.

    Science.gov (United States)

    Elk, Seymour B.

    1997-01-01

    Suggests that the cross product of two vectors can be more easily and accurately explained by starting from the perspective of dyadics because then the concept of vector multiplication has a simple geometrical picture that encompasses both the dot and cross products in any number of dimensions in terms of orthogonal unit vector components. (AIM)

  13. Identifying translation initiation sites in prokaryotes using support vector machine.

    Science.gov (United States)

    Gao, Tingting; Yang, Zhixia; Wang, Yong; Jing, Ling

    2010-02-21

    Gene identification in genomes has been a fundamental and long-standing task in bioinformatics and computational biology. Many computational methods have been developed to predict genes in prokaryote genomes by identifying translation initiation site (TIS) in transcript data. However, the pseudo-TISs at the genome level make these methods suffer from a high number of false positive predictions. In addition, most of the existing tools use an unsupervised learning framework, whose predictive accuracy may depend on the choice of specific organism. In this paper, we present a supervised learning method, support vector machine (SVM), to identify translation initiation site at the genome level. The features are extracted from the sequence data by modeling the sequence segment around predicted TISs as a position specific weight matrix (PSWM). We train the parameters of our SVM through well constructed positive and negative TIS datasets. Then we apply the method to recognize translation initiation sites in E. coli, B. subtilis, and validate our method on two GC-rich bacteria genomes: Pseudomonas aeruginosa and Burkholderia pseudomallei K96243. We show that translation initiation sites can be recognized accurately at the genome level by our method, irrespective of their GC content. Furthermore, we compare our method with four existing methods and demonstrate that our method outperform these methods by obtaining better performance in all the four organisms. (c) 2009. Published by Elsevier Ltd.

  14. Double sequence core theorems

    Directory of Open Access Journals (Sweden)

    Richard F. Patterson

    1999-01-01

    Full Text Available In 1900, Pringsheim gave a definition of the convergence of double sequences. In this paper, that notion is extended by presenting definitions for the limit inferior and limit superior of double sequences. Also the core of a double sequence is defined. By using these definitions and the notion of regularity for 4-dimensional matrices, extensions, and variations of the Knopp Core theorem are proved.

  15. Efficient probability sequence

    OpenAIRE

    Regnier, Eva

    2014-01-01

    A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficient forecasting systems, including memorylessness and increasing discrimination. These results suggest tests for efficiency and ...

  16. Efficient probability sequences

    OpenAIRE

    Regnier, Eva

    2014-01-01

    DRMI working paper A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficiency forecasting systems, including memorylessness and increasing discrimination. These res...

  17. Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases.

    Science.gov (United States)

    Okamoto, Kenichi W; Gould, Fred; Lloyd, Alun L

    2016-03-01

    Many vector-borne diseases lack effective vaccines and medications, and the limitations of traditional vector control have inspired novel approaches based on using genetic engineering to manipulate vector populations and thereby reduce transmission. Yet both the short- and long-term epidemiological effects of these transgenic strategies are highly uncertain. If neither vaccines, medications, nor transgenic strategies can by themselves suffice for managing vector-borne diseases, integrating these approaches becomes key. Here we develop a framework to evaluate how clinical interventions (i.e., vaccination and medication) can be integrated with transgenic vector manipulation strategies to prevent disease invasion and reduce disease incidence. We show that the ability of clinical interventions to accelerate disease suppression can depend on the nature of the transgenic manipulation deployed (e.g., whether vector population reduction or replacement is attempted). We find that making a specific, individual strategy highly effective may not be necessary for attaining public-health objectives, provided suitable combinations can be adopted. However, we show how combining only partially effective antimicrobial drugs or vaccination with transgenic vector manipulations that merely temporarily lower vector competence can amplify disease resurgence following transient suppression. Thus, transgenic vector manipulation that cannot be sustained can have adverse consequences-consequences which ineffective clinical interventions can at best only mitigate, and at worst temporarily exacerbate. This result, which arises from differences between the time scale on which the interventions affect disease dynamics and the time scale of host population dynamics, highlights the importance of accounting for the potential delay in the effects of deploying public health strategies on long-term disease incidence. We find that for systems at the disease-endemic equilibrium, even modest

  18. Broad patterns in domestic vector-borne Trypanosoma cruzi transmission dynamics: synanthropic animals and vector control.

    Science.gov (United States)

    Peterson, Jennifer K; Bartsch, Sarah M; Lee, Bruce Y; Dobson, Andrew P

    2015-10-22

    Chagas disease (caused by Trypanosoma cruzi) is the most important neglected tropical disease (NTD) in Latin America, infecting an estimated 5.7 million people in the 21 countries where it is endemic. It is one of the NTDs targeted for control and elimination by the 2020 London Declaration goals, with the first goal being to interrupt intra-domiciliary vector-borne T. cruzi transmission. A key question in domestic T. cruzi transmission is the role that synanthropic animals play in T. cruzi transmission to humans. Here, we ask, (1) do synanthropic animals need to be targeted in Chagas disease prevention policies?, and (2) how does the presence of animals affect the efficacy of vector control? We developed a simple mathematical model to simulate domestic vector-borne T. cruzi transmission and to specifically examine the interaction between the presence of synanthropic animals and effects of vector control. We used the model to explore how the interactions between triatomine bugs, humans and animals impact the number and proportion of T. cruzi-infected bugs and humans. We then examined how T. cruzi dynamics change when control measures targeting vector abundance are introduced into the system. We found that the presence of synanthropic animals slows the speed of T. cruzi transmission to humans, and increases the sensitivity of T. cruzi transmission dynamics to vector control measures at comparable triatomine carrying capacities. However, T. cruzi transmission is amplified when triatomine carrying capacity increases with the abundance of syntathoropic hosts. Our results suggest that in domestic T. cruzi transmission scenarios where no vector control measures are in place, a reduction in synanthropic animals may slow T. cruzi transmission to humans, but it would not completely eliminate transmission. To reach the 2020 goal of interrupting intra-domiciliary T. cruzi transmission, it is critical to target vector populations. Additionally, where vector control measures

  19. New Constraints on Light Vectors Coupled to Anomalous Currents

    Science.gov (United States)

    Dror, Jeff A.; Lasenby, Robert; Pospelov, Maxim

    2017-10-01

    We derive new constraints on light vectors coupled to standard model (SM) fermions, when the corresponding SM current is broken by the chiral anomaly. The cancellation of the anomaly by heavy fermions results, in the low-energy theory, in Wess-Zumino-type interactions between the new vector and the SM gauge bosons. These interactions are determined by the requirement that the heavy sector preserves the SM gauge groups and lead to (energy /vector mass )2 enhanced rates for processes involving the longitudinal mode of the new vector. Taking the example of a vector coupled to a vector coupled to SM baryon number, Z decays and flavor-changing neutral current meson decays via the new vector can occur with (weak scale /vector mass )2 enhanced rates. These processes place significantly stronger coupling bounds than others considered in the literature, over a wide range of vector masses.

  20. Tumor-specific suicide gene therapy for hepatocellular carcinoma by transcriptionally targeted retroviral replicating vectors.

    Science.gov (United States)

    Lai, Y-H; Lin, C-C; Chen, S-H; Tai, C-K

    2015-02-01

    Replicating virus vectors are attractive tools for anticancer gene therapy, but the potential for adverse events due to uncontrolled spread of the vectors has been a major concern. To design a tumor-specific retroviral replicating vector (RRV), we replaced the U3 region of the RRV ACE-GFP with a regulatory sequence consisting of the hepatitis B virus enhancer II (EII) and human α-fetoprotein (AFP) core promoter to produce ACE-GFP-EIIAFP, a hepatocellular carcinoma (HCC)-targeting RRV. Similar to ACE-GFP, ACE-GFP-EIIAFP exhibited robust green fluorescent protein (GFP) expression in HCC cells and, most importantly, it exhibited HCC-specific replication and did not replicate in non-HCC tumor cells or normal liver cells. We sequenced the promoter region of ACE-GFP-EIIAFP collected from serial infection cycles to examine the genomic stability of the vector during its replicative spread, and found that the vector could retain the hybrid promoter in the genome for at least six infection cycles. In vitro studies revealed that ACE-CD-EIIAFP and ACE-PNP-EIIAFP, which express the yeast cytosine deaminase and Escherichia coli purine nucleoside phosphorylase, respectively, exert a highly potent cytotoxic effect on HCC cells in the presence of their respective prodrugs. In vivo, ACE-CD-EIIAFP-mediated suicide gene therapy efficiently suppressed HCC tumor growth and no detectable RRV signal was observed in extratumoral tissues. These results suggest that the tumor-specific, suicide-gene-encoding RRV may fulfill the promise of retroviral gene therapy for cancer.

  1. Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

    Directory of Open Access Journals (Sweden)

    Liao Li

    2010-10-01

    Full Text Available Abstract Background Protein-protein interaction (PPI plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs, based on domains represented as interaction profile hidden Markov models (ipHMM where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB. Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD. Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure, an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on

  2. Effect of genome size on AAV vector packaging.

    Science.gov (United States)

    Wu, Zhijian; Yang, Hongyan; Colosi, Peter

    2010-01-01

    Adeno-associated virus (AAV) vector genomes have been limited to 5 kilobases (kb) in length because their packaging limit was thought to be similar to the size of the parent AAV genome. Recent reports claim that significantly larger vector genomes can be packaged intact. We examined the packaged vector genomes from plasmid-encoded AAV vectors that ranged from 4.7 to 8.7 kb in length, using AAV types 2, 5, and 8 capsids. Southern blot analysis indicated that packaged AAV vector genomes never exceeded 5.2 kb in length irrespective of the size of the plasmid-encoded vector or the capsid type. This result was confirmed by vector genome probing with strand-specific oligonucleotides. The packaged vector genomes derived from plasmid-encoded vectors exceeding 5 kb were heterogeneous in length and truncated on the 5' end. Despite their truncated genomes, vector preparations produced from plasmid-encoded vectors exceeding 5.2 kb mediated reporter gene expression in vitro at high multiplicity of infection (MOI). The efficiency of expression was substantially lower than that of reporter vectors with genomes <5 kb in length. We propose that transcriptionally functional, intact vector genomes are generated in cells transduced at high MOI from the fragmentary genomes of these larger vectors, probably by recombination.

  3. New Aspects of a Lid-Removal Mechanism in the Onset of a SEP-Producing Eruption Sequence

    Science.gov (United States)

    Sterling, Alphonse C.; Moore, Ronald L.; Falconer, David A.; Knox, Javon M.

    2014-01-01

    We examine a sequence of two ejective eruptions from a single active region on 2012 January 23, using magnetograms and EUV images from SDO/HMI and SDO/AIA, and EUV images from STEREO. Cheng et al. (2013) showed that the first eruption's ("Eruption 1'') flux rope was apparent only in "hotter'' AIA channels, and that it removed overlying field that allowed the second eruption (``Eruption 2'') to begin via ideal MHD instability; here we say Eruption 2 began via a ``lid removal'' mechanism. We show that during Eruption-1's onset, its flux rope underwent ``tether weakening'' (TW) reconnection with the field of an adjacent active region. Standard flare loops from Eruption 1 developed over Eruption-2's flux rope and enclosed filament, but these overarching new loops were unable to confine that flux rope/filament. Eruption-1's flare loops, from both TW reconnection and standard-flare-model internal reconnection, were much cooler than Eruption-2's flare loops (GOES thermal temperatures of approx. 9 MK compared to approx. 14 MK). This eruption sequence produced a strong solar energetic particle (SEP) event (10 MeV protons, >10(exp 3) pfu for 43 hrs), apparently starting when Eruption-2's CME blasted through Eruption-1's CME at 5-10 R_s. This occurred because the two CMEs originated in close proximity and in close time sequence: Eruption-1's fast rise started soon after the TW reconnection; the lid removal by Eruption-1's ejection triggered the slow onset of Eruption 2; and Eruption-2's CME, which started approx. 1 hr later, was three times faster than Eruption-1's CME.

  4. Method for transforming a feature vector

    NARCIS (Netherlands)

    Veldhuis, Raymond N.J.; Chen, C.; Kevenaar, Thomas A.M.; Akkermans, Antonius H.M.

    2007-01-01

    The present invention relates to a method for transforming a feature vector comprising a first and a second feature represented by a first and a second feature value, respectively, into a feature code using an encoder, said feature code usable in an algorithm and having a predetermined number of

  5. Learning Latent Vector Spaces for Product Search

    NARCIS (Netherlands)

    Van Gysel, C.; de Rijke, M.; Kanoulas, E.

    2016-01-01

    We introduce a novel latent vector space model that jointly learns the latent representations of words, e-commerce products and a mapping between the two without the need for explicit annotations. The power of the model lies in its ability to directly model the discriminative relation between

  6. Ecology of parasite-vector interactions

    NARCIS (Netherlands)

    Takken, W.; Koenraadt, C.J.M.

    2013-01-01

    Vector-borne diseases continue to be one of the most important determinants affecting human and animal health. Large numbers of people suffer from diseases like malaria, dengue, filariasis and leishmaniasis, especially in the tropics. Whereas these diseases were eradicated from the temperate climate

  7. Bethe vectors for XXX-spin chain

    Science.gov (United States)

    Burdík, Čestmír; Fuksa, Jan; Isaev, Alexei

    2014-11-01

    The paper deals with algebraic Bethe ansatz for XXX-spin chain. Generators of Yang-Baxter algebra are expressed in basis of free fermions and used to calculate explicit form of Bethe vectors. Their relation to N-component models is used to prove conjecture about their form in general. Some remarks on inhomogeneous XXX-spin chain are included.

  8. Angry Birds Mathematics: Parabolas and Vectors

    Science.gov (United States)

    Lamb, John H.

    2013-01-01

    John Lamb, a professor of mathematics education and a teacher of high school precalculus, describes how he developed a way to use the elements of the game Angry Birds® as a platform to engage his students with the concepts of parabolas and vectors. The game could be categorized as a type of microworld game in which students interact with the…

  9. Vector boson production in hadron nuclear collisions

    Energy Technology Data Exchange (ETDEWEB)

    Walker, W.D. (Duke Univ., Durham, NC (USA)); Whitmore, J. (Pennsylvania State Univ., University Park, PA (USA). Lab. for Elementary Particle Science); Toothacker, W.S. (Pennsylvania State Univ., Mont Alto (USA)); Hill, J.C.; Neale, W.W. (Cambridge Univ. (UK)); Lucas, P.; Voyvodic, L. (Fermi National Accelerator Lab., Batavia, IL (USA)); Ammar, R.; Gress, J. (Kansas Univ., Lawrence (USA)); Bishop, J.M.; Biswas, N.N.; Cason, N.M.; Mattingly, M.C.K.; Ruchti, R.C.; Shephard, W.D. (Notre Dame Univ., IN (USA))

    1991-01-31

    We report a search for the production of light quark vector bosons in hadron-nucleus collisions at 100 GeV bombarding energy. We find surprisingly few of these resonances produced. The lack of these particles is though to be due to the absorption by the many modestly energetic nucleons and the few anti-nucleons in the final state. (orig.).

  10. Malaria vector control: current and future strategies

    NARCIS (Netherlands)

    Takken, W.; Knols, B.G.J.

    2009-01-01

    The recently announced call for malaria eradication represents a new page in the history of this disease. This has been triggered by remarkable reductions in malaria resulting from combined application of effective drugs and vector control. However, this strategy is threatened by development of

  11. Generating and measuring nondiffracting vector Bessel beams

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2013-09-01

    Full Text Available modulator and an azimuthally varying birefringent plate, known as a q-plate. We extend our control of both the geometric and dynamic phases to perform a polarization and modal decomposition on the vector field. We study both single-charged Bessel beams...

  12. NLO vector boson production with light jets

    CERN Document Server

    Bern, Z; Dixon, L J; Cordero, F Febres; Forde, D; Gleisberg, T; Hoeche, S; Ita, H; Kosower, D A; Maitre, D; Ozeren, K

    2012-01-01

    In this contribution we present recent progress in the computation of next-to-leading order (NLO) QCD corrections for the production of an electroweak vector boson in association with jets at hadron colliders. We focus on results obtained using the virtual matrix element library BLACKHAT in conjunction with SHERPA, focusing on results relevant to understanding the background to top production.

  13. Linearization of germs of hyperbolic vector fields

    NARCIS (Netherlands)

    Bonckaert, P; Naudot, [No Value; Yang, JZ

    2003-01-01

    We develop a normal form to express asymptotically a conjugacy between a germ of resonant vector field and its linear part. We show that such an asymptotic expression can be written in terms of functions of the Logarithmic Mourtada type. To cite this article: P Bonckaert et al., C. R. Acad. Sci.

  14. Perturbations of ultralight vector field dark matter

    CERN Document Server

    Cembranos, J A R; Jareño, S J Núñez

    2016-01-01

    We study the dynamics of cosmological perturbations in models of dark matter based on ultralight coherent vector fields. Very much as for scalar field dark matter, we find two different regimes in the evolution: for modes with $k^2\\ll {\\cal H}ma$, we have a particle-like behaviour indistinguishable from cold dark matter, whereas for modes with $k^2\\gg {\\cal H}ma$, we get a wave-like behaviour in which the sound speed is non-vanishing and of order $c_s^2\\simeq k^2/m^2a^2$. This implies that, also in these models, structure formation could be suppressed on small scales. However, unlike the scalar case, the fact that the background evolution contains a non-vanishing homogeneous vector field implies that, in general, the evolution of the three kinds of perturbations (scalar, vector and tensor) can no longer be decoupled at the linear level. More specifically, in the particle regime, the three types of perturbations are actually decoupled, whereas in the wave regime, the three vector field perturbations generate o...

  15. Efficient Multiplicative Updates for Support Vector Machines

    DEFF Research Database (Denmark)

    Potluru, Vamsi K.; Plis, Sergie N; Mørup, Morten

    2009-01-01

    The dual formulation of the support vector machine (SVM) objective function is an instance of a nonnegative quadratic programming problem. We reformulate the SVM objective function as a matrix factorization problem which establishes a connection with the regularized nonnegative matrix factorizati...

  16. Generalized Derivative Based Kernelized Learning Vector Quantization

    NARCIS (Netherlands)

    Schleif, Frank-Michael; Villmann, Thomas; Hammer, Barbara; Schneider, Petra; Biehl, Michael; Fyfe, Colin; Tino, Peter; Charles, Darryl; Garcia-Osoro, Cesar; Yin, Hujun

    2010-01-01

    We derive a novel derivative based version of kernelized Generalized Learning Vector Quantization (KGLVQ) as an effective, easy to interpret, prototype based and kernelized classifier. It is called D-KGLVQ and we provide generalization error bounds, experimental results on real world data, showing

  17. [Conflicts and vector-borne diseases

    DEFF Research Database (Denmark)

    Bygbjerg, Ib Christian

    2010-01-01

    not available for most diseases. Promising preventive methods, including long-lasting impregnated bed-nets and tents, are available. War has been an impetus for disclosing life-cycles of vector-borne diseases and for control methods; peace, reconciliation and poverty reduction are required to achieve lasting...

  18. Closed-chain principal vector linkages

    NARCIS (Netherlands)

    van der Wijk, V.; Flores, Paulo; Viadero, Fernando

    2015-01-01

    For high-speed robotics dynamic balance is an important property for low base vibrations and short cycle times. To consider dynamic balance in the beginning of the design process of a manipulator, mechanism solutions can be synthesized from principal vector linkages, which are fundamental kinematic

  19. Artificial neural networks and support vector mac

    Indian Academy of Sciences (India)

    Quantitative structure-property relationships of electroluminescent materials: Artificial neural networks and support vector machines to predict electroluminescence of organic molecules. ALANA FERNANDES GOLIN and RICARDO STEFANI. ∗. Laboratório de Estudos de Materiais (LEMAT), Instituto de Ciências Exatas e da ...

  20. Creating and decomposing vector Bessel beams

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2013-07-01

    Full Text Available -1 58th Annual SAIP Conference, Richards Bay, 8-12 July 2013 Creating and decomposing vector Bessel beams Angela Dudley1,*, Yanming Li2, Thandeka Mhlanga1, Michael Escuti2 and Andrew Forbes1 1 CSIR National Laser Centre, Pretoria, South...