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Sample records for based gene manipulation

  1. Keratin promoter based gene manipulation in the murine conducting airway

    Directory of Open Access Journals (Sweden)

    Stephen P. Malkoski, Timothy G. Cleaver, Shi-Long Lu, Jessyka G. Lighthall, Xiao-Jing Wang

    2010-01-01

    Full Text Available Systems capable of targeting genetic manipulations to keratin-positive airway basal cells are more poorly developed than systems targeting other airway epithelial cell populations and this has likely hindered development of animal models of diseases such as lung squamous cell carcinoma. Although keratin promoter driven-Cre recombinase constructs are potentially useful for targeting these cells, these constructs have substantially higher activity in the skin and oral epithelium than in the airways. We developed a method for delivering RU486, the conditional activator of Cre recombinase progesterone receptor (CrePR fusion proteins to the lung and then examined the activity of three keratin-driven CrePR constructs in the conducting airways. We also developed a technique for survival bronchioalveolar lavage on non-ventilated animals to examine the effects of the acetone/oil vehicle required to deliver RU486 to the lung. K5CrePR1 and K14CrePR1 constructs differ only in the keratin promoter used to target CrePR1 expression while K5Cre*PR contains a truncated progesterone receptor designed to reduce RU486-independent Cre activity. While all three constructs demonstrate RU486-inducible Cre activity in the conducting airways, both construct activity and tightness of regulation vary considerably. K5Cre*PR is the most tightly regulated Cre driver making it ideal for targeting somatic mutations to the airway epithelia while K5CrePR1 and K14CrePR1 may be better suited to studying diseases of the conducting airways where gene targeting of keratin expressing cells and their derivatives is desired.

  2. New pFA-cassettes for PCR-based gene manipulation in Candida albicans.

    Science.gov (United States)

    Schaub, Yvonne; Dünkler, Alexander; Walther, Andrea; Wendland, Jürgen

    2006-01-01

    Several modules for efficient PCR-based gene disruption have recently been introduced in Candida albicans. These are based on auxotrophic marker genes for deficient strains derived from SC5314/CAI4. Commonly used protocols for the transformation C. albicans are based either on the lithium acetate procedure or on electroporation also used for Saccharomyces cerevisiae. Here we present our updated arsenal of pFA-modules that now include the heterologous marker genes HIS1 from C. dubliniensis and LEU2 from C. maltosa (Noble and Johnson 2005) and the dominant selection marker ca SAT1 (Reuss et al. 2004). We also introduce the Ashbya gossypii TEF1 -promoter as a strong constitutive promoter. With these new elements an enlarged collection of pFA-marker and pFA-marker-promoter modules were generated containing 17 new modules. In addition, N-terminal tagging with GFP-(GA) 6 and epitope-tagging modules using the 6 x-HIS-tag were constructed. This adds to the previous modules that only enabled C-terminal GFP-tagging of genes (Gola et al. 2003). In total 29 pFA-modules are currently freely available from our lab which - together with an update on the diagnostic verification procedure - further enlarge the C. albicans molecular toolbox and enhance our capabilities to use PCR-based gene alteration methods in C. albicans. PMID:17009297

  3. Multi-Homologous Recombination-Based Gene Manipulation in the Rice Pathogen Fusarium fujikuroi

    OpenAIRE

    Hwang, In Sun; Ahn, Il-Pyung

    2016-01-01

    Gene disruption by homologous recombination is widely used to investigate and analyze the function of genes in Fusarium fujikuroi, a fungus that causes bakanae disease and root rot symptoms in rice. To generate gene deletion constructs, the use of conventional cloning methods, which rely on restriction enzymes and ligases, has had limited success due to a lack of unique restriction enzyme sites. Although strategies that avoid the use of restriction enzymes have been employed to overcome this ...

  4. Multi-Homologous Recombination-Based Gene Manipulation in the Rice Pathogen Fusarium fujikuroi

    Directory of Open Access Journals (Sweden)

    In Sun Hwang

    2016-06-01

    Full Text Available Gene disruption by homologous recombination is widely used to investigate and analyze the function of genes in Fusarium fujikuroi, a fungus that causes bakanae disease and root rot symptoms in rice. To generate gene deletion constructs, the use of conventional cloning methods, which rely on restriction enzymes and ligases, has had limited success due to a lack of unique restriction enzyme sites. Although strategies that avoid the use of restriction enzymes have been employed to overcome this issue, these methods require complicated PCR steps or are frequently inefficient. Here, we introduce a cloning system that utilizes multi-fragment assembly by In-Fusion to generate a gene disruption construct. This method utilizes DNA fragment fusion and requires only one PCR step and one reaction for construction. Using this strategy, a gene disruption construct for Fusarium cyclin C1 (FCC1 , which is associated with fumonisin B1 biosynthesis, was successfully created and used for fungal transformation. In vivo and in vitro experiments using confirmed fcc1 mutants suggest that fumonisin production is closely related to disease symptoms exhibited by F. fujikuroi strain B14. Taken together, this multi-fragment assembly method represents a simpler and a more convenient process for targeted gene disruption in fungi.

  5. Molecular genetic techniques for gene manipulation in Candida albicans

    OpenAIRE

    Xu, Qiu-Rong; Yan, Lan; Lv, Quan-zhen; Zhou, Mi; Sui, Xue; Cao, Yong-Bing; Jiang, Yuan-ying

    2014-01-01

    Candida albicans is one of the most common fungal pathogen in humans due to its high frequency as an opportunistic and pathogenic fungus causing superficial as well as invasive infections in immunocompromised patients. An understanding of gene function in C. albicans is necessary to study the molecular basis of its pathogenesis, virulence and drug resistance. Several manipulation techniques have been used for investigation of gene function in C. albicans, including gene disruption, controlled...

  6. Tetracycline inducible gene manipulation in serotonergic neurons.

    Directory of Open Access Journals (Sweden)

    Tillmann Weber

    Full Text Available The serotonergic (5-HT neuronal system has important and diverse physiological functions throughout development and adulthood. Its dysregulation during development or later in adulthood has been implicated in many neuropsychiatric disorders. Transgenic animal models designed to study the contribution of serotonergic susceptibility genes to a pathological phenotype should ideally allow to study candidate gene overexpression or gene knockout selectively in serotonergic neurons at any desired time during life. For this purpose, conditional expression systems such as the tet-system are preferable. Here, we generated a transactivator (tTA mouse line (TPH2-tTA that allows temporal and spatial control of tetracycline (Ptet controlled transgene expression as well as gene deletion in 5-HT neurons. The tTA cDNA was inserted into a 196 kb PAC containing a genomic mouse Tph2 fragment (177 kb by homologous recombination in E. coli. For functional analysis of Ptet-controlled transgene expression, TPH2-tTA mice were crossed to a Ptet-regulated lacZ reporter line (Ptet-nLacZ. In adult double-transgenic TPH2-tTA/Ptet-nLacZ mice, TPH2-tTA founder line L62-20 showed strong serotonergic β-galactosidase expression which could be completely suppressed with doxycycline (Dox. Furthermore, Ptet-regulated gene expression could be reversibly activated or inactivated when Dox was either withdrawn or added to the system. For functional analysis of Ptet-controlled, Cre-mediated gene deletion, TPH2-tTA mice (L62-20 were crossed to double transgenic Ptet-Cre/R26R reporter mice to generate TPH2-tTA/Ptet-Cre/R26R mice. Without Dox, 5-HT specific recombination started at E12.5. With permanent Dox administration, Ptet-controlled Cre-mediated recombination was absent. Dox withdrawal either postnatally or during adulthood induced efficient recombination in serotonergic neurons of all raphe nuclei, respectively. In the enteric nervous system, recombination could not be detected. We

  7. Gene manipulated peritoneal cell patch repairs infarcted myocardium

    OpenAIRE

    Huang, Wei; Zhang, Dongsheng; Millard, Ronald W.; Wang, Tao; Zhao, Tiemin; Fan, Guo-Chang; Ashraf, Atif; Xu, Meifeng; ASHRAF, Muhammad; Wang, Yigang

    2009-01-01

    A gene manipulated cell patch using a homologous peritoneum substrate was developed and applied after myocardial infarction to repair scarred myocardium. We genetically engineered male rat mesenchymal stem cells (MSC) using adenoviral transduction to over-express CXCR4/green fluorescent protein (GFP) (MSCCXCR4) or MSCNull or siRNA targeting CXCR4 (MSCsiRNA). Gene expression was studied by real-time quantitative PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA). Cells were cultured on e...

  8. Manipulating Immune Tolerance with micro-RNA Regulated Gene Therapy

    Directory of Open Access Journals (Sweden)

    KevinScottGoudy

    2011-11-01

    Full Text Available The successful use of in vivo gene therapy depends upon controlling the immune response to the therapeutic transgene to allow stable, long-term transgene expression. Over the last decade several vector-based and pharmacological approaches to control the immune-mediated clearance of transgene expressing cells after viral delivery have been explored. One important outcome from these studies is the concept that expression of transgene in tolerance-promoting organs, such as the liver and tolerogenic antigen presenting cells, can help safeguard transgene expressing cells from immune-mediated clearance. With this in mind, gene therapists are specifically targeting these avenues by manipulating their vectors in three main areas: i incorporating tissue/cell specific promoters, ii viral-capsid engineering to alter tropism and avoid pre-existing immunity, and iii including micro-RNA (miR targets into expression cassettes. The combination of these three layers of vector regulation greatly enhances the targeting of “tolerogenic cells” and limits the off-target expression of the transgene, which can lead to the induction of transgene-specific pathogenic effector T cells. In this review, we discuss the application of using miR transgene regulation to generate tolerogenic responses and speculate on possible mechanisms used by the liver to induce the transgene specific regulatory T cells.

  9. Sound beam manipulation based on temperature gradients

    International Nuclear Information System (INIS)

    Previous research with temperature gradients has shown the feasibility of controlling airborne sound propagation. Here, we present a temperature gradients based airborne sound manipulation schemes: a cylindrical acoustic omnidirectional absorber (AOA). The proposed AOA has high absorption performance which can almost completely absorb the incident wave. Geometric acoustics is used to obtain the refractive index distributions with different radii, which is then utilized to deduce the desired temperature gradients. Since resonant units are not applied in the scheme, its working bandwidth is expected to be broadband. The scheme is temperature-tuned and easy to realize, which is of potential interest to fields such as noise control or acoustic cloaking

  10. Sound beam manipulation based on temperature gradients

    Energy Technology Data Exchange (ETDEWEB)

    Qian, Feng [Key Laboratory of Modern Acoustics, Institute of Acoustics and School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China); School of Physics & Electronic Engineering, Changshu Institute of Technology, Changshu 215500 (China); Quan, Li; Liu, Xiaozhou, E-mail: xzliu@nju.edu.cn; Gong, Xiufen [Key Laboratory of Modern Acoustics, Institute of Acoustics and School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China)

    2015-10-28

    Previous research with temperature gradients has shown the feasibility of controlling airborne sound propagation. Here, we present a temperature gradients based airborne sound manipulation schemes: a cylindrical acoustic omnidirectional absorber (AOA). The proposed AOA has high absorption performance which can almost completely absorb the incident wave. Geometric acoustics is used to obtain the refractive index distributions with different radii, which is then utilized to deduce the desired temperature gradients. Since resonant units are not applied in the scheme, its working bandwidth is expected to be broadband. The scheme is temperature-tuned and easy to realize, which is of potential interest to fields such as noise control or acoustic cloaking.

  11. Manipulators

    International Nuclear Information System (INIS)

    The patent concerns a manipulator, which enables operations to be carried out remotely from the operator. The device is suitable for use in handling of radioactive materials and other hazardous liquids or gases. The specifications are given, and the movements of the manipulator arm described. (U.K.)

  12. Inducible gene manipulations in brain serotonergic neurons of transgenic rats.

    Directory of Open Access Journals (Sweden)

    Tillmann Weber

    Full Text Available The serotonergic (5-HT system has been implicated in various physiological processes and neuropsychiatric disorders, but in many aspects its role in normal and pathologic brain function is still unclear. One reason for this might be the lack of appropriate animal models which can address the complexity of physiological and pathophysiological 5-HT functioning. In this respect, rats offer many advantages over mice as they have been the animal of choice for sophisticated neurophysiological and behavioral studies. However, only recently technologies for the targeted and tissue specific modification of rat genes - a prerequisite for a detailed study of the 5-HT system - have been successfully developed. Here, we describe a rat transgenic system for inducible gene manipulations in 5-HT neurons. We generated a Cre driver line consisting of a tamoxifen-inducible CreERT2 recombinase under the control of mouse Tph2 regulatory sequences. Tissue-specific serotonergic Cre recombinase expression was detected in four transgenic TPH2-CreERT2 rat founder lines. For functional analysis of Cre-mediated recombination, we used a rat Cre reporter line (CAG-loxP.EGFP, in which EGFP is expressed after Cre-mediated removal of a loxP-flanked lacZ STOP cassette. We show an in-depth characterisation of this rat Cre reporter line and demonstrate its applicability for monitoring Cre-mediated recombination in all major neuronal subpopulations of the rat brain. Upon tamoxifen induction, double transgenic TPH2-CreERT2/CAG-loxP.EGFP rats show selective and efficient EGFP expression in 5-HT neurons. Without tamoxifen administration, EGFP is only expressed in few 5-HT neurons which confirms minimal background recombination. This 5-HT neuron specific CreERT2 line allows Cre-mediated, inducible gene deletion or gene overexpression in transgenic rats which provides new opportunities to decipher the complex functions of the mammalian serotonergic system.

  13. Topics in Semantics-based Program Manipulation

    DEFF Research Database (Denmark)

    Grobauer, Bernt

    Programming is at least as much about manipulating existing code as it is about writing new code. Existing code is modified, for example to make inefficient code run faster, or to accommodate for new features when reusing code; existing code is analyzed, for example to verify certain program prop...

  14. SOLVING INVERSE KINEMATICS OF REDUNDANT MANIPULATOR BASED ON NEURAL NETWORK

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    For the redundant manipulators, neural network is used to tackle the velocity inverse kinematics of robot manipulators. The neural networks utilized are multi-layered perceptions with a back-propagation training algorithm. The weight table is used to save the weights solving the inverse kinematics based on the different optimization performance criteria. Simulations verify the effectiveness of using neural network.

  15. A passivity based controller for free base manipulators

    Science.gov (United States)

    Chuang, C.-H.; Mittal, Manoj; Juang, Jer-Nan

    1993-01-01

    A feedback linearization technique is used in conjunction with passivity concepts to design robust controllers for free base robots. It is assumed that bounded modeling uncertainties exist in the inertia matrix and the vector representing the coriolis, centripetal, and friction forces. Under these assumptions, the controller guarantees asymptotic tracking of the joint variables. A Lagrangian approach is used to develop a dynamic model for space robots. Closed-loop simulation results are illustrated for a simple case of a single link planar space manipulator with freely floating base.

  16. Mechatronic Model Based Computed Torque Control of a Parallel Manipulator

    OpenAIRE

    Zhiyong Yang; Jiang Wu; Jiangping Mei; Jian Gao; Tian Huang

    2008-01-01

    With high speed and accuracy the parallel manipulators have wide application in the industry, but there still exist many difficulties in the actual control process because of the time-varying and coupling. Unfortunately, the present-day commercial controlles cannot provide satisfying performance for its single axis linear control only. Therefore, aimed at a novel 2-DOF (Degree of Freedom) parallel manipulator called Diamond 600, a motor-mechanism coupling dynamic model based control scheme em...

  17. A large workspace flexure hinge-based parallel manipulator system

    Institute of Scientific and Technical Information of China (English)

    Dong Wei; Du Zhijiang; Sun Lining

    2005-01-01

    Parallel manipulator systems as promising precision devices are used widely in current researches. A novel large workspace flexure parallel manipulator system utilizing wide-range flexure hinges as passive joints is proposed in this paper, which can attain sub-micron-scale precision over the cubic centimeter motion range. This paper introduces the mechanical system architecture based on the wide-range flexure hinges, analyzes the kinematics via stiffness matrices, presents the control system configuration and control strategy, and finally gives the system performance test results.

  18. A planar parallel manipulator based novel MEMS device bonding system

    Institute of Scientific and Technical Information of China (English)

    Ji Junhong; Sun Lining; Zhu Yuhong

    2006-01-01

    A novel MEMS device boning system is presented. Aiming at the high velocity, high precision and high flexibility requirements, a novel manipulator of planar parallel structure is developed to substitute ordinary X-Y table. In addition, the machine vision is implemented to improve the system's flexibility. The initial angular positions of the joints are estimated by the extended Kalman filter algorithm. As a result, the manipulator's absolute locating accuracy in its workspace is guaranteed indirectly. For any MEMS device, the bonding system itself can be used as measurement equipment to create the device's geometry model, which is the base to do off-line programming. A quite ideal trade-off between the system's flexibility and efficiency is got. Finally, some verified motion specification of the manipulator, the bonding experimental results and the verified qualities of the bonded devices are provided.

  19. Inertial Vibration Damping of a Flexible Base Manipulator

    Science.gov (United States)

    George, Lynnane E.; Book, Wayne J.

    A rigid (micro) robot mounted serially to the tip of a long, flexible (macro) manipulator is often used to increase reach capability, but flexibility in the macromanipulator can make it susceptible to vibration. A rigid manipulator attached to a flexible but unactuated base was used to study a scheme to achieve positioning of the micromanipulator combined with enhanced vibration damping of the base. The interaction forces and torques acting between the robot and its flexible base were modeled and studied. Simulated and measured interactions generated at the base of a three degree of freedom rigid robot are compared. Simulated and experimental results are included that demonstrate with the proper control of these interactions, damping can be added to the base.

  20. Microcystin Biosynthesis in Planktothrix: Genes, Evolution, and Manipulation

    Science.gov (United States)

    Christiansen, Guntram; Fastner, Jutta; Erhard, Marcel; Börner, Thomas; Dittmann, Elke

    2003-01-01

    Microcystins represent an extraordinarily large family of cyclic heptapeptide toxins that are nonribosomally synthesized by various cyanobacteria. Microcystins specifically inhibit the eukaryotic protein phosphatases 1 and 2A. Their outstanding variability makes them particularly useful for studies on the evolution of structure-function relationships in peptide synthetases and their genes. Analyses of microcystin synthetase genes provide valuable clues for the potential and limits of combinatorial biosynthesis. We have sequenced and analyzed 55.6 kb of the potential microcystin synthetase gene (mcy) cluster from the filamentous cyanobacterium Planktothrix agardhii CYA 126. The cluster contains genes for peptide synthetases (mcyABC), polyketide synthases (PKSs; mcyD), chimeric enzymes composed of peptide synthetase and PKS modules (mcyEG), a putative thioesterase (mcyT), a putative ABC transporter (mcyH), and a putative peptide-modifying enzyme (mcyJ). The gene content and arrangement and the sequence of specific domains in the gene products differ from those of the mcy cluster in Microcystis, a unicellular cyanobacterium. The data suggest an evolution of mcy clusters from, rather than to, genes for nodularin (a related pentapeptide) biosynthesis. Our data do not support the idea of horizontal gene transfer of complete mcy gene clusters between the genera. We have established a protocol for stable genetic transformation of Planktothrix, a genus that is characterized by multicellular filaments exhibiting continuous motility. Targeted mutation of mcyJ revealed its function as a gene coding for a O-methyltransferase. The mutant cells produce a novel microcystin variant exhibiting reduced inhibitory activity toward protein phosphatases. PMID:12511503

  1. Multisensor based robotic manipulation in an uncalibrated manufacturing workcell

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, B.K.; Xiao, Di; Xi, Ning; Tarn, Tzyh-Jong [Washington Univ., Saint Louis, MO (United States)

    1997-12-31

    The main problem that we address in this paper is how a robot manipulator is able to track and grasp a part placed arbitrarily on a moving disc conveyor aided by a single CCD camera and fusing information from encoders placed on the conveyor and also from encoders on the robot manipulator. The important assumption that distinguishes our work from what has been previously reported in the literature is that the position and orientation of the camera and the base frame of the robot is apriori assumed to be unknown and is `visually calibrated` during the operation of the manipulator. Moreover the part placed on the conveyor is assumed to be non-planar, i.e. the feature points observed on the part is assumed to be located arbitrarily in IR{sup 3}. The novelties of the proposed approach in this paper includes a (i) multisensor fusion scheme based on complementary data for the purpose of part localization, and (ii) self-calibration between the turntable and the robot manipulator using visual data and feature points on the end-effector. The principle advantages of the proposed scheme are the following. (i) It renders possible to reconfigure a manufacturing workcell without recalibrating the relation between the turntable and the robot. This significantly shortens the setup time of the workcell. (ii) It greatly weakens the requirement on the image processing speed.

  2. Manipulating the Prion Protein Gene Sequence and Expression Levels with CRISPR/Cas9

    Science.gov (United States)

    Kaczmarczyk, Lech; Mende, Ylva; Zevnik, Branko; Jackson, Walker S.

    2016-01-01

    The mammalian prion protein (PrP, encoded by Prnp) is most infamous for its central role in prion diseases, invariably fatal neurodegenerative diseases affecting humans, food animals, and animals in the wild. However, PrP is also hypothesized to be an important receptor for toxic protein conformers in Alzheimer's disease, and is associated with other clinically relevant processes such as cancer and stroke. Thus, key insights into important clinical areas, as well as into understanding PrP functions in normal physiology, can be obtained from studying transgenic mouse models and cell culture systems. However, the Prnp locus is difficult to manipulate by homologous recombination, making modifications of the endogenous locus rarely attempted. Fortunately in recent years genome engineering technologies, like TALENs or CRISPR/Cas9 (CC9), have brought exceptional new possibilities for manipulating Prnp. Herein, we present our observations made during systematic experiments with the CC9 system targeting the endogenous mouse Prnp locus, to either modify sequences or to boost PrP expression using CC9-based synergistic activation mediators (SAMs). It is our hope that this information will aid and encourage researchers to implement gene-targeting techniques into their research program. PMID:27128441

  3. Manipulating the Prion Protein Gene Sequence and Expression Levels with CRISPR/Cas9.

    Science.gov (United States)

    Kaczmarczyk, Lech; Mende, Ylva; Zevnik, Branko; Jackson, Walker S

    2016-01-01

    The mammalian prion protein (PrP, encoded by Prnp) is most infamous for its central role in prion diseases, invariably fatal neurodegenerative diseases affecting humans, food animals, and animals in the wild. However, PrP is also hypothesized to be an important receptor for toxic protein conformers in Alzheimer's disease, and is associated with other clinically relevant processes such as cancer and stroke. Thus, key insights into important clinical areas, as well as into understanding PrP functions in normal physiology, can be obtained from studying transgenic mouse models and cell culture systems. However, the Prnp locus is difficult to manipulate by homologous recombination, making modifications of the endogenous locus rarely attempted. Fortunately in recent years genome engineering technologies, like TALENs or CRISPR/Cas9 (CC9), have brought exceptional new possibilities for manipulating Prnp. Herein, we present our observations made during systematic experiments with the CC9 system targeting the endogenous mouse Prnp locus, to either modify sequences or to boost PrP expression using CC9-based synergistic activation mediators (SAMs). It is our hope that this information will aid and encourage researchers to implement gene-targeting techniques into their research program. PMID:27128441

  4. Manipulating the Prion Protein Gene Sequence and Expression Levels with CRISPR/Cas9.

    Directory of Open Access Journals (Sweden)

    Lech Kaczmarczyk

    Full Text Available The mammalian prion protein (PrP, encoded by Prnp is most infamous for its central role in prion diseases, invariably fatal neurodegenerative diseases affecting humans, food animals, and animals in the wild. However, PrP is also hypothesized to be an important receptor for toxic protein conformers in Alzheimer's disease, and is associated with other clinically relevant processes such as cancer and stroke. Thus, key insights into important clinical areas, as well as into understanding PrP functions in normal physiology, can be obtained from studying transgenic mouse models and cell culture systems. However, the Prnp locus is difficult to manipulate by homologous recombination, making modifications of the endogenous locus rarely attempted. Fortunately in recent years genome engineering technologies, like TALENs or CRISPR/Cas9 (CC9, have brought exceptional new possibilities for manipulating Prnp. Herein, we present our observations made during systematic experiments with the CC9 system targeting the endogenous mouse Prnp locus, to either modify sequences or to boost PrP expression using CC9-based synergistic activation mediators (SAMs. It is our hope that this information will aid and encourage researchers to implement gene-targeting techniques into their research program.

  5. Hybrid Modeling Method for a DEP Based Particle Manipulation

    Directory of Open Access Journals (Sweden)

    Mohamad Sawan

    2013-01-01

    Full Text Available In this paper, a new modeling approach for Dielectrophoresis (DEP based particle manipulation is presented. The proposed method fulfills missing links in finite element modeling between the multiphysic simulation and the biological behavior. This technique is amongst the first steps to develop a more complex platform covering several types of manipulations such as magnetophoresis and optics. The modeling approach is based on a hybrid interface using both ANSYS and MATLAB to link the propagation of the electrical field in the micro-channel to the particle motion. ANSYS is used to simulate the electrical propagation while MATLAB interprets the results to calculate cell displacement and send the new information to ANSYS for another turn. The beta version of the proposed technique takes into account particle shape, weight and its electrical properties. First obtained results are coherent with experimental results.

  6. IMU-based online kinematic calibration of robot manipulator.

    Science.gov (United States)

    Du, Guanglong; Zhang, Ping

    2013-01-01

    Robot calibration is a useful diagnostic method for improving the positioning accuracy in robot production and maintenance. An online robot self-calibration method based on inertial measurement unit (IMU) is presented in this paper. The method requires that the IMU is rigidly attached to the robot manipulator, which makes it possible to obtain the orientation of the manipulator with the orientation of the IMU in real time. This paper proposed an efficient approach which incorporates Factored Quaternion Algorithm (FQA) and Kalman Filter (KF) to estimate the orientation of the IMU. Then, an Extended Kalman Filter (EKF) is used to estimate kinematic parameter errors. Using this proposed orientation estimation method will result in improved reliability and accuracy in determining the orientation of the manipulator. Compared with the existing vision-based self-calibration methods, the great advantage of this method is that it does not need the complex steps, such as camera calibration, images capture, and corner detection, which make the robot calibration procedure more autonomous in a dynamic manufacturing environment. Experimental studies on a GOOGOL GRB3016 robot show that this method has better accuracy, convenience, and effectiveness than vision-based methods. PMID:24302854

  7. IMU-Based Online Kinematic Calibration of Robot Manipulator

    Directory of Open Access Journals (Sweden)

    Guanglong Du

    2013-01-01

    Full Text Available Robot calibration is a useful diagnostic method for improving the positioning accuracy in robot production and maintenance. An online robot self-calibration method based on inertial measurement unit (IMU is presented in this paper. The method requires that the IMU is rigidly attached to the robot manipulator, which makes it possible to obtain the orientation of the manipulator with the orientation of the IMU in real time. This paper proposed an efficient approach which incorporates Factored Quaternion Algorithm (FQA and Kalman Filter (KF to estimate the orientation of the IMU. Then, an Extended Kalman Filter (EKF is used to estimate kinematic parameter errors. Using this proposed orientation estimation method will result in improved reliability and accuracy in determining the orientation of the manipulator. Compared with the existing vision-based self-calibration methods, the great advantage of this method is that it does not need the complex steps, such as camera calibration, images capture, and corner detection, which make the robot calibration procedure more autonomous in a dynamic manufacturing environment. Experimental studies on a GOOGOL GRB3016 robot show that this method has better accuracy, convenience, and effectiveness than vision-based methods.

  8. A practical quality index based on the octahedral manipulator

    International Nuclear Information System (INIS)

    The octahedral manipulator is a 3-3 device that is fully in parallel. It has a linear actuator on each of its six legs. The legs connect an equilateral platform triangle to a similar base triangle in a zigzag pattern between vertices. The proposed quality index takes a maximum value of 1 at a central symmetrical configuration that is shown to correspond to the maximum value of the determinant of the 6 x 6 Jacobian matrix of the manipulator. This matrix is none other than that of the normalized line coordinates of the six leg-lines; for its determinant to be a maximum, the platform triangle is found to be half of the size of the base triangle, and the perpendicular distance between platform and base is equal to the side of the platform triangle. When the manipulator is actuated so that the octahedron departs from this central configuration, the determinant always diminishes, and, as is well known, it becomes zero when a special configuration is reached (the platform then gaining one or more uncontrollable freedoms). The quality index λ, 0 ≤ λ ≤ 1, is a constructive measure of acceptable design proportions. The double-spherical joints (there are six) are the source of the critical practical difficulties. Kinematic substitutions can circumvent this problem, but often there is no reasonable alternative to accepting a reduction of maximum quality index through separation by fairly short distances of some or all of the double-ball joints. Too great a separation easily leads too far toward generality; any fully-in-parallel manipulator of more general proportions should be tested for quality against the octahedral form simply because no different form can be superior to a well-designed octahedron from the points of view of structural soundness and ability to apply both forces and controlled displacements to the end-effector platform

  9. Mechatronic Model Based Computed Torque Control of a Parallel Manipulator

    Directory of Open Access Journals (Sweden)

    Zhiyong Yang

    2008-11-01

    Full Text Available With high speed and accuracy the parallel manipulators have wide application in the industry, but there still exist many difficulties in the actual control process because of the time-varying and coupling. Unfortunately, the present-day commercial controlles cannot provide satisfying performance for its single axis linear control only. Therefore, aimed at a novel 2-DOF (Degree of Freedom parallel manipulator called Diamond 600, a motor-mechanism coupling dynamic model based control scheme employing the computed torque control algorithm are presented in this paper. First, the integrated dynamic coupling model is deduced, according to equivalent torques between the mechanical structure and the PM (Permanent Magnetism servomotor. Second, computed torque controller is described in detail for the above proposed model. At last, a series of numerical simulations and experiments are carried out to test the effectiveness of the system, and the results verify the favourable tracking ability and robustness.

  10. Use of NAP gene to manipulate leaf senescence in plants

    Science.gov (United States)

    Gan, Susheng; Guo, Yongfeng

    2013-04-16

    The present invention discloses transgenic plants having an altered level of NAP protein compared to that of a non-transgenic plant, where the transgenic plants display an altered leaf senescence phenotype relative to a non-transgenic plant, as well as mutant plants comprising an inactivated NAP gene, where mutant plants display a delayed leaf senescence phenotype compared to that of a non-mutant plant. The present invention also discloses methods for delaying leaf senescence in a plant, as well as methods of making a mutant plant having a decreased level of NAP protein compared to that of a non-mutant plant, where the mutant plant displays a delayed leaf senescence phenotype relative to a non-mutant plant. Methods for causing precocious leaf senescence or promoting leaf senescence in a plant are also disclosed. Also disclosed are methods of identifying a candidate plant suitable for breeding that displays a delayed leaf senescence and/or enhanced yield phenotype.

  11. A novel magnetorheological damper based parallel planar manipulator design

    International Nuclear Information System (INIS)

    This paper presents a novel parallel planar robot design which is low cost and simple in structure. The design addresses some of the problems, such as concentration of excessive load on the links and joints, due to wrong commanding signals being given by the controller. In this application two of the conventional actuators are replaced by magnetorheological (MR) dampers, and only one actuator is used to generate motion. The design paradigm is based on the concept that a moving object 'intuitively' follows the path with minimum resistance to its motion. This implies that virtual adoptable constraints can be used effectively to define motion trajectories. In fact, motion generation and adaptive constraints are two elements essential to implementing this strategy. In this paper, MR dampers are used to provide adjustable constraints and to guide the platform that is moved by the linear motor. The model of the MR dampers is derived using the Bouc–Wen model. This model is then used for manipulator simulation and controller design. Two controllers are developed for this manipulator: (1) a closed loop on/off one and (2) a proportional–derivative controller. Also, three different trajectories are defined and used for both the simulations and experiments. The results indicate a good agreement between the simulations and experiments. The experimental results also demonstrate the capability of the manipulator for following sophisticated trajectories

  12. Feasible Human-Spine Motion Simulators Based on Parallel Manipulators

    OpenAIRE

    Zhu, Si-Jun; Huang, Zhen; Zhao, Ming-Yang

    2008-01-01

    Considering the characteristics of a human spine including nearly isotropic kinematical performance, fast speed, available under both active and passive modes and reachable workspace, three 3R2T 5-DoF fully-symmetrical parallel manipulators with base-actuator, including 5-RRR(RR), 5-(RRR)RR, 5-(RRR)(RR) are adopted as feasible human spine motion simulators. To decrease machining difficulty and guarantee the machining precision, 5RRR(RR) is designed and manufactured as the prototype of spine m...

  13. Electroporation-Based Genetic Manipulation in Type I Methanotrophs.

    Science.gov (United States)

    Yan, Xin; Chu, Frances; Puri, Aaron W; Fu, Yanfen; Lidstrom, Mary E

    2016-04-01

    Methane is becoming a major candidate for a prominent carbon feedstock in the future, and the bioconversion of methane into valuable products has drawn increasing attention. To facilitate the use of methanotrophic organisms as industrial strains and accelerate our ability to metabolically engineer methanotrophs, simple and rapid genetic tools are needed. Electroporation is one such enabling tool, but to date it has not been successful in a group of methanotrophs of interest for the production of chemicals and fuels, the gammaproteobacterial (type I) methanotrophs. In this study, we developed electroporation techniques with a high transformation efficiency for three different type I methanotrophs: Methylomicrobium buryatense 5GB1C, Methylomonas sp. strain LW13, and Methylobacter tundripaludum 21/22. We further developed this technique in M. buryatense, a haloalkaliphilic aerobic methanotroph that demonstrates robust growth with a high carbon conversion efficiency and is well suited for industrial use for the bioconversion of methane. On the basis of the high transformation efficiency of M. buryatense, gene knockouts or integration of a foreign fragment into the chromosome can be easily achieved by direct electroporation of PCR-generated deletion or integration constructs. Moreover, site-specific recombination (FLP-FRT [FLP recombination target] recombination) and sacB counterselection systems were employed to perform marker-free manipulation, and two new antibiotics, zeocin and hygromycin, were validated to be antibiotic markers in this strain. Together, these tools facilitate the rapid genetic manipulation of M. buryatense and other type I methanotrophs, promoting the ability to perform fundamental research and industrial process development with these strains. PMID:26801578

  14. A perspective on the economic valorization of gene manipulated biotechnology: Past and future

    Directory of Open Access Journals (Sweden)

    Mirjam Knockaert

    2015-06-01

    Full Text Available Three distinct fields of gene manipulated biotechnology have so far been economically exploited: medical biotechnology, plant biotechnology and industrial biotechnology. This article analyzes the economic evolution and its drivers in the three fields over the past decades, highlighting strong divergences. Product and market characteristics, affecting firms’ financing options, are shown to be important enablers or inhibitors. Subsequently, the lack of commercialization in a fourth type of gene manipulated biotechnology, namely environmental biotechnology, is explained by the existence of strong barriers. Given the latter’s great promises for environmental sustainability, we argue for a need to push the commercial valorization of environmental biotechnology. Our research has strong implications for (technology management research in biotechnology, pointing to a need to control for and/or distinguish between different biotechnology fields.

  15. Velocity observer-based iterative learning control for robot manipulators

    Science.gov (United States)

    Bouakrif, Farah; Boukhetala, Djamel; Boudjema, Farès

    2013-02-01

    This article addresses the problem of designing an iterative learning control for trajectory tracking of rigid robot manipulators subject to external disturbances, and performing repetitive tasks, without using the velocity measurement. For solving this problem, a velocity observer having an iterative form is proposed to reconstruct the velocity signal in the control laws. Under assumptions that the disturbances are repetitive and the velocities are bounded, it has been shown that the whole control system (robot plus controller plus observer) is asymptotically stable and the observation error is globally asymptotically stable, over the whole finite time-interval when the iteration number tends to infinity. This proof is based upon the use of a Lyapunov-like positive definite sequence, which is shown to be monotonically decreasing under the proposed observer-controller schemes.

  16. A modified recombineering protocol for the genetic manipulation of gene clusters in Aspergillus fumigatus.

    Directory of Open Access Journals (Sweden)

    Laura Alcazar-Fuoli

    Full Text Available Genomic analyses of fungal genome structure have revealed the presence of physically-linked groups of genes, termed gene clusters, where collective functionality of encoded gene products serves a common biosynthetic purpose. In multiple fungal pathogens of humans and plants gene clusters have been shown to encode pathways for biosynthesis of secondary metabolites including metabolites required for pathogenicity. In the major mould pathogen of humans Aspergillus fumigatus, multiple clusters of co-ordinately upregulated genes were identified as having heightened transcript abundances, relative to laboratory cultured equivalents, during the early stages of murine infection. The aim of this study was to develop and optimise a methodology for manipulation of gene cluster architecture, thereby providing the means to assess their relevance to fungal pathogenicity. To this end we adapted a recombineering methodology which exploits lambda phage-mediated recombination of DNA in bacteria, for the generation of gene cluster deletion cassettes. By exploiting a pre-existing bacterial artificial chromosome (BAC library of A. fumigatus genomic clones we were able to implement single or multiple intra-cluster gene replacement events at both subtelomeric and telomere distal chromosomal locations, in both wild type and highly recombinogenic A. fumigatus isolates. We then applied the methodology to address the boundaries of a gene cluster producing a nematocidal secondary metabolite, pseurotin A, and to address the role of this secondary metabolite in insect and mammalian responses to A. fumigatus challenge.

  17. Manipulation of Microobjects Based on Dynamic Adhesion Control

    Directory of Open Access Journals (Sweden)

    Tao Chen

    2012-09-01

    Full Text Available Due to scale effects, microoperation, especially the releasing of microobjects, has been a long‐standing challenge in micromanipulation applications. In this paper a micromanipulation method is presented based on dynamic adhesion control with compound vibration. This adhesion control technique employs inertia force to overcome adhesion force achieving 100% repeatability with releasing accuracy of 4± 0.5μm, which was experimentally quantified through the manipulation of 20‐100μm polystyrene spheres under an optical microscope. The micromanipulation system consists of a microgripper and a piezoelectric ceramics module. The compound vibration comes from the electrostatic actuator and the piezoelectrically driven actuator. Surface and bulk micromachining technology is employed to fabricate the microgripper used in the system from a single crystal silicon wafer. Experimental results confirmed that this adhesion control technique is independent of substrate. Theoretical analyses were conducted to understand the picking up and releasing mechanism. Based on this preliminary study, the micromanipulation system proved to be an effective solution for active picking up and releasing of micromanipulation.

  18. AFM-based manipulation of InAs nanowires

    International Nuclear Information System (INIS)

    A controlled method of manipulation of nanowires was found using the tip of an Atomic Force Microscope (AFM). Manipulation is done in the 'Retrace Lift' mode, where feedback is turned off for the reverse scan and the tip follows a nominal path. The effective manipulation force during the reverse scan can be changed by varying an offset in the height of the tip over the surface. Using this method, we have studied InAs nanowires on different substrates. We have also investigated interactions between wires and with gold features patterned onto the substrates

  19. Robotic design analysis based on teleoperated manipulator data collection

    International Nuclear Information System (INIS)

    Extensive data collection was performed on a servomanipulator system (TeleOperator Systems SM-229) to determine the motion range and mechanical power usage of the manipulator under direct human control. More than 50 hours of various manipulation operations were performed while joint positions and motor currents were recorded. Reduction of these data yielded histograms of the manipulator usage patterns revealing areas where future manipulator motion ranges and drive systems could be optimized. This report develops a graphical representation of mechanical power usage that relates torque and velocity to the total usage time. Methods of interpreting this representation are discussed and generalized for use in analyzing robotic systems. The resulting technique will allow designers to reevaluate an operating system and determine how to improve that system's design

  20. Multi-sensor based segmentation of human manipulation tasks

    OpenAIRE

    Hendrich, Norman; Klimentjew, Denis; Zhang, Jianwei

    2010-01-01

    In this paper we present an overview of a multisensor setup designed to record and analyse human in-hand manipulation - tasks consisting of several phases of finger motions following the initial grasp. During the experiments all of the hand, finger, and object positions are recorded, as are the contact forces applied to the manipulated objects. The use of instrumented sensing objects complements the data. The goal is to understand and extract a basic set of finger and ...

  1. From gene engineering to gene modulation and manipulation: can we prevent or detect gene doping in sports?

    Science.gov (United States)

    Fischetto, Giuseppe; Bermon, Stéphane

    2013-10-01

    -carboxamide 1-β-D-ribofuranoside (AICAR), GW1516], might concomitantly improve endurance exercise capacity in ischaemic conditions but also in normal conditions. Undoubtedly, some athletes will attempt to take advantage of these new molecules to increase strength or endurance. Antidoping laboratories are improving detection methods. These are based both on direct identification of new substances or their metabolites and on indirect evaluation of changes in gene, protein or metabolite patterns (genomics, proteomics or metabolomics). PMID:23832852

  2. Automatic calibration of space based manipulators and mechanisms

    Science.gov (United States)

    Everett, Louis J.

    1988-01-01

    Four tasks in manipulator kinematic calibration are summarized. Calibration of a seven degree of freedom manipulator was simulated. A calibration model is presented that can be applied on a closed-loop robot. It is an expansion of open-loop kinematic calibration algorithms subject to constraints. A closed-loop robot with a five-bar linkage transmission was tested. Results show that the algorithm converges within a few iterations. The concept of model differences is formalized. Differences are categorized as structural and numerical, with emphasis on the structural. The work demonstrates that geometric manipulators can be visualized as points in a vector space with the dimension of the space depending solely on the number and type of manipulator joint. Visualizing parameters in a kinematic model as the coordinates locating the manipulator in vector space enables a standard evaluation of the models. Key results include a derivation of the maximum number of parameters necessary for models, a formal discussion on the inclusion of extra parameters, and a method to predetermine a minimum model structure for a kinematic manipulator. A technique is presented that enables single point sensors to gather sufficient information to complete a calibration.

  3. Targeted Gene Manipulation in Plants Using the CRISPR/Cas Technology.

    Science.gov (United States)

    Zhang, Dandan; Li, Zhenxiang; Li, Jian-Feng

    2016-05-20

    The CRISPR/Cas technology is emerging as a revolutionary genome editing tool in diverse organisms including plants, and has quickly evolved into a suite of versatile tools for sequence-specific gene manipulations beyond genome editing. Here, we review the most recent applications of the CRISPR/Cas toolkit in plants and also discuss key factors for improving CRISPR/Cas performance and strategies for reducing the off-target effects. Novel technical breakthroughs in mammalian research regarding the CRISPR/Cas toolkit will also be incorporated into this review in hope to stimulate prospective users from the plant research community to fully explore the potential of these technologies. PMID:27165865

  4. Multisensor-based robotic systems for inspection and manipulation tasks

    International Nuclear Information System (INIS)

    The advanced technology division of the US Department of Energy is sponsoring research at four universities (Florida, Michigan, Tennessee, and Texas) and the Oak Ridge National Laboratory (ORNL) directed toward the development of advanced robotic systems for use in nuclear environments. The primary motivation for using robotic technology in such hazardous environments is to reduce exposure and costs associated with performing tasks such as surveillance, maintenance, and repair. The main focus of research at the University of Tennessee has been to contribute to the development of autonomous inspection and manipulation systems, which utilize a wide array of sensory inputs in controlling the actions of a stationary robot. This involves several important research issues, including selection of sensor modalities, processing and analysis of data acquired by individual sensors, integration of sensory information, control of the robotic arm and end effectors, and efficient computational architectures for implementing various algorithms. Experimental research effort is directed toward design and evaluation of new methodologies using a laboratory-based robotic test bed. A unique feature of this test bed is a multisensor module that is useful in the characterization of the robots work space. In this paper, the authors describe the development of a robotic vision system for automatic spill detection, localization, and cleanup verification and the development of efficient techniques for analyzing range images using a parallel computer. The simulated spill cleanup scenario allows demonstration of the applicability of robotic systems to problems encountered in nuclear environments

  5. Manipulating Neutral Atoms in Chip-Based Magnetic Traps

    Science.gov (United States)

    Aveline, David; Thompson, Robert; Lundblad, Nathan; Maleki, Lute; Yu, Nan; Kohel, James

    2009-01-01

    Several techniques for manipulating neutral atoms (more precisely, ultracold clouds of neutral atoms) in chip-based magnetic traps and atomic waveguides have been demonstrated. Such traps and waveguides are promising components of future quantum sensors that would offer sensitivities much greater than those of conventional sensors. Potential applications include gyroscopy and basic research in physical phenomena that involve gravitational and/or electromagnetic fields. The developed techniques make it possible to control atoms with greater versatility and dexterity than were previously possible and, hence, can be expected to contribute to the value of chip-based magnetic traps and atomic waveguides. The basic principle of these techniques is to control gradient magnetic fields with suitable timing so as to alter a trap to exert position-, velocity-, and/or time-dependent forces on atoms in the trap to obtain desired effects. The trap magnetic fields are generated by controlled electric currents flowing in both macroscopic off-chip electromagnet coils and microscopic wires on the surface of the chip. The methods are best explained in terms of examples. Rather than simply allowing atoms to expand freely into an atomic waveguide, one can give them a controllable push by switching on an externally generated or a chip-based gradient magnetic field. This push can increase the speed of the atoms, typically from about 5 to about 20 cm/s. Applying a non-linear magnetic-field gradient exerts different forces on atoms in different positions a phenomenon that one can exploit by introducing a delay between releasing atoms into the waveguide and turning on the magnetic field.

  6. Nutrition-gene interaction (post-genomics): Changes in gene expression through nutritional manipulations

    International Nuclear Information System (INIS)

    Full text: Consumers in the developed world have demanded quality and consistency from animal products marketed to them, and as a result implementation of quality assurance systems has been a major industry priority. These systems are based on the principle that quality, as defined by the consumer, can be influenced at critical control points in the production chain. Consumer demands for sustainable production practices have also led to adoption of strategies sometimes counter to eating quality objectives. For example, Bos indicus animals are used in extensive grazing systems of northern Australia because of their drought and parasite tolerance, but have inferior eating quality. Given the environmental rigours of this northern production system, cattle producers are attempting to optimise decisions regarding all variables that influence their enterprises. These include breed and genotype, slaughter age, lifetime nutrition, health management strategy, growth promotion strategy, weather predictions, stocking rate, and eating quality criteria. In this paper, we will review what is known about development of the intrinsic factors (those extant at the time of slaughter) of bovine skeletal muscle as they relate to the subsequent eating quality attributes of meat. These attributes include toughness, colour, fat content, and nutritive value, but exclude food safety. We will focus on current understanding of nutritional regulation of the candidate genes known to underlie each of these attributes, and where appropriate draw on understanding developed in other mammalian species. We will discuss two experimental studies that are likely to contribute to our understanding of functional gene networks that are responsive to nutritional restriction. The first investigated the effects of severe nutritional restriction and compensatory growth in Bos indicus cross cattle during the post-weaning period. The study was motivated by our previous finding that nutritional effects on meat

  7. The optimization of global fault tolerant trajectory for redundant manipulator based on self-motion

    Directory of Open Access Journals (Sweden)

    Zhang Jian

    2015-01-01

    Full Text Available The redundancy feature of manipulators provides the possibility for the fault tolerant trajectory planning. Aiming at the completion of the specific task, an algorithm of global fault tolerant trajectory optimization for redundant manipulator based on the self-motion is proposed in this paper. Firstly, inverse kinematics equation of single redundancy manipulator based on self-motion variable and null-space velocity array of Jacobian are analyzed. Secondly, the mathematical description of fault tolerance criteria of the configuration of manipulator is established and the fault tolerance configuration group of manipulator is obtained by using iteration traversal under the fault tolerance criteria. Then, considering the joint limits and minimum the energy consumption as the optimization target, the global fault tolerant joint trajectory is achieved. Finally, simulation for 7 degree of freedom (DOF manipulator is performed, by which the effectiveness of the algorithm is validated.

  8. Comparison of Planar Parallel Manipulator Architectures based on a Multi-objective Design Optimization Approach

    OpenAIRE

    Chablat, Damien; Caro, Stéphane; Ur-Rehman, Raza; Wenger, Philippe

    2010-01-01

    This paper deals with the comparison of planar parallel manipulator architectures based on a multi-objective design optimization approach. The manipulator architectures are compared with regard to their mass in motion and their regular workspace size, i.e., the objective functions. The optimization problem is subject to constraints on the manipulator dexterity and stiffness. For a given external wrench, the displacements of the moving platform have to be smaller than given values throughout t...

  9. Design, Dynamics, and Workspace of a Hybrid-Driven-Based Cable Parallel Manipulator

    OpenAIRE

    Bin Zi; Jianbin Cao; Zhencai Zhu; Peter Mitrouchev

    2013-01-01

    The design, dynamics, and workspace of a hybrid-driven-based cable parallel manipulator (HDCPM) are presented. The HDCPM is able to perform high efficiency, heavy load, and high-performance motion due to the advantages of both the cable parallel manipulator and the hybrid-driven planar five-bar mechanism. The design is performed according to theories of mechanism structure synthesis for cable parallel manipulators. The dynamic formulation of the HDCPM is established on the basis of Newton-Eul...

  10. Manipulation of gene expression by an ecdysone-inducible gene switch in tumor xenografts

    Directory of Open Access Journals (Sweden)

    Gulding Kathryn M

    2001-12-01

    Full Text Available abstract Background Rapid, robust and reversible induction of transgene expression would significantly facilitate cancer gene therapy as well as allow the in vivo functional study of newly discovered genes in tumor formation and progression. The popularity of the ecdysone inducible gene switch system has led us to investigate whether such a system can successfully regulate gene expression in a syngeneic tumor system in vivo. Results MBT-2 and Panc02 carcinoma cells were transfected with components of a modification of the ecdysone switch system driving firefly luciferase (F-Luc. In vitro luciferase expression ± ecdysone analog GS-E indicated a robust induction with minimal baseline activity and complete decay after 24 hours without drug. In vitro selection of MBT-2 transfected cell clones which had complete absence of F-Luc expression in the absence of stimulation but which expressed this gene at high levels in response to GS-E were chosen for in vivo evaluation. Tumors from engineered MBT-2 cells were grown to 5 mm in diameter prior to GS-E administration, animals euthanized and tumors removed at 6, 12 and 24 hours after GS-E administration and assayed for F-Luc activity. GS-E resulted in a maximal induction of F-Luc activity at 6 hours in tumor tissue with almost complete reversion to control levels by 12 hours. Conclusions This study is the first demonstration that robust and reversible transgene expression in tumors is feasible using the ecdysone system, allowing future rapid in vivo functional characterization of gene function or gene therapy applications.

  11. Advanced In vivo Use of CRISPR/Cas9 and Anti-sense DNA Inhibition for Gene Manipulation in the Brain

    Science.gov (United States)

    Walters, Brandon J.; Azam, Amber B.; Gillon, Colleen J.; Josselyn, Sheena A.; Zovkic, Iva B.

    2016-01-01

    Gene editing tools are essential for uncovering how genes mediate normal brain–behavior relationships and contribute to neurodegenerative and neuropsychiatric disorders. Recent progress in gene editing technology now allows neuroscientists unprecedented access to edit the genome efficiently. Although many important tools have been developed, here we focus on approaches that allow for rapid gene editing in the adult nervous system, particularly CRISPR/Cas9 and anti-sense nucleotide-based techniques. CRISPR/Cas9 is a flexible gene editing tool, allowing the genome to be manipulated in diverse ways. For instance, CRISPR/Cas9 has been successfully used to knockout genes, knock-in mutations, overexpress or inhibit gene activity, and provide scaffolding for recruiting specific epigenetic regulators to individual genes and gene regions. Moreover, the CRISPR/Cas9 system may be modified to target multiple genes at one time, affording simultaneous inhibition and overexpression of distinct genetic targets. Although many of the more advanced applications of CRISPR/Cas9 have not been applied to the nervous system, the toolbox is widely accessible, such that it is poised to help advance neuroscience. Anti-sense nucleotide-based technologies can be used to rapidly knockdown genes in the brain. The main advantage of anti-sense based tools is their simplicity, allowing for rapid gene delivery with minimal technical expertise. Here, we describe the main applications and functions of each of these systems with an emphasis on their many potential applications in neuroscience laboratories. PMID:26793235

  12. Trajectory planning and control of a 6 DOF manipulator with Stewart platform-based mechanism

    Science.gov (United States)

    Nguyen, Charles C.; Antrazi, Sami

    1990-01-01

    The trajectory planning and control was studied of a robot manipulator that has 6 degrees of freedom and was designed based on the mechanism of the Stewart Platform. First the main components of the manipulator is described along with its operation. The solutions are briefly prescribed for the forward and inverse kinematics of the manipulator. After that, two trajectory planning schemes are developed using the manipulator inverse kinematics to track straight lines and circular paths. Finally experiments conducted to study the performance of the developed planning schemes in tracking a straight line and a circle are presented and discussed.

  13. Molecular manipulation and modification of the genes encoding the G2 and G4 glycinin subunits

    Directory of Open Access Journals (Sweden)

    Reda H. Sammour

    2006-01-01

    Full Text Available The genes encoding the glycinin subunits G2 and G4 were molecularly manipulated and modified to test the possibility of increasing the nutritional value of soybean seed proteins. The recombinant DNAs pSP65/G2HG4, pSP65/G4HG2, pSP65/248 Metl, pSP65/248 Met2,3 and pSP65/248 Metl.2,3 were used in in vitro translation to produce (i chimeric proteins consisting of reciprocally exchanged acidic and basic G2 and G4 domains and (ii Gy4 point mutants with an increased number of methionine residues. The ability of the recombinant proteins to assemble into proper quaternary structures was investigated using sucrose gradient fractionation. The data produced by this study could provide valuable clues for the potential improvement of genetically modified crops.

  14. A gas bubble-based parallel micro manipulator: conceptual design and kinematics model

    International Nuclear Information System (INIS)

    The parallel mechanism has become an alternative solution when micro manipulators are demanded in the fields of micro manipulation and micro assembly. In this technical note, a three-degree-of-freedom (3-DOF) parallel micro manipulator is presented, which is directly driven by three micro gas bubbles. Since the micro gas bubbles are generated and maintained due to the surface tension between the gas and liquid media, the proposed novel system can be used in the liquid environment which allows for rotation about the X and Y axes and translation along the Z axis. In this technical note, the conceptual design of micro gas bubble-based parallel manipulator is introduced and the input/output characteristic of the actuator is analyzed in detail. The kinematics model of the parallel micro manipulator is also established, based on which the workspace and the system motion resolution are analyzed as a criterion and reference for future prototype development. (technical note)

  15. In ovo gene manipulation of melanocytes and their adjacent keratinocytes during skin pigmentation of chicken embryos.

    Science.gov (United States)

    Murai, Hidetaka; Tadokoro, Ryosuke; Sakai, Ken-Ichiro; Takahashi, Yoshiko

    2015-04-01

    During skin pigmentation in avians and mammalians, melanin is synthesized in the melanocytes, and subsequently transferred to adjacently located keratinocytes, leading to a wide coverage of the body surface by melanin-containing cells. The behavior of melanocytes is influenced by keratinocytes shown mostly by in vitro studies. However, it has poorly been investigated how such intercellular cross-talk is regulated in vivo because of a lack of suitable experimental models. Using chicken embryos, we developed a method that enables in vivo gene manipulations of melanocytes and keratinocytes, where these cells are separately labeled by different genes. Two types of gene transfer techniques were combined: one was a retrovirus-mediated gene infection into the skin/keratinocytes, and the other was the in ovo DNA electroporation into neural crest cells, the origin of melanocytes. Since the Replication-Competent Avian sarcoma-leukosis virus long terminal repeat with Splice acceptor (RCAS) infection was available only for the White leghorn strain showing little pigmentation, melanocytes prepared from the Hypeco nera (pigmented) were back-transplanted into embryos of White leghorn. Prior to the transplantation, enhanced green fluorescent protein (EGFP)(+) Neo(r+) -electroporated melanocytes from Hypeco nera were selectively grown in G418-supplemented medium. In the skin of recipient White leghorn embryos infected with RCAS-mOrange, mOrange(+) keratinocytes and transplanted EGFP(+) melanocytes were frequently juxtaposed each other. High-resolution confocal microscopy also revealed that transplanted melanocytes exhibited normal behaviors regarding distribution patterns of melanocytes, dendrite morphology, and melanosome transfer. The method described in this study will serve as a useful tool to understand the mechanisms underlying intercellular regulations during skin pigmentation in vivo. PMID:25739909

  16. Resolved rate and torque control schemes for large scale space based kinematically redundant manipulators

    Science.gov (United States)

    Bailey, Robert W.; Quiocho, Leslie J.

    1991-01-01

    Resolved rate control of kinematically redundant ground based manipulators is a challenging problem. The structural, actuator, and control loop frequency characteristics of industrial grade robots generally allow operation with resolved rate control; a rate command is achievable with good accuracy. However, space based manipulators are different, typically have less structural stiffness, more motor and joint friction, and lower control loop cycle frequencies. These undesirable characteristics present a considerable Point of Resolution (POR) control problem for space based, kinematically redundant manipulators for the following reason: a kinematically redundant manipulator requires an arbitrary constraint to solve for the joint rate commands. A space manipulator will not respond to joint rate commands because of these characteristics. A space based manipulator simulation, including free end rigid body dynamics, motor dynamics, motor striction/friction, gearbox backlash, joint striction/friction, and Space Station Remote Manipulator System type configuration parameters, is used to evaluate the performance of a documented resolved rate control law. Alternate schemes which include torque control are also evaluated.

  17. SYNTHESIS OF PARALLEL MECHANISM BASED ROBOT MANIPULATORS FROM STRUCTURAL POINT OF VIEW

    Directory of Open Access Journals (Sweden)

    DR. JAGDISH M. PRAJAPATI

    2011-02-01

    Full Text Available Because of their potential merits, the parallel mechanisms are more popular than serial mechanisms based robot manipulators in specific applications. One of the ways of classifying the parallel manipulatorsis according to their platform types and connection between them. Methods for designing different types of parallel manipulators with one or more platforms are presented. The classification of parallel mechanism based manipulators and synthesis of them from structural point of view are presented in this paper. The step by step procedure is presented with help of examples.

  18. Screw-System-Based Mobility Analysis of a Family of Fully Translational Parallel Manipulators

    Directory of Open Access Journals (Sweden)

    Ernesto Rodriguez-Leal

    2013-01-01

    Full Text Available This paper investigates the mobility of a family of fully translational parallel manipulators based on screw system analysis by identifying the common constraint and redundant constraints, providing a case study of this approach. The paper presents the branch motion-screws for the 3-RP̲C-Y parallel manipulator, the 3-RCC-Y (or 3-RP̲RC-Y parallel manipulator, and a newly proposed 3-RP̲C-T parallel manipulator. Then the paper determines the sets of platform constraint-screws for each of these three manipulators. The constraints exerted on the platforms of the 3-RP̲C architectures and the 3-RCC-Y manipulators are analyzed using the screw system approach and have been identified as couples. A similarity has been identified with the axes of couples: they are perpendicular to the R joint axes, but in the former the axes are coplanar with the base and in the latter the axes are perpendicular to the limb. The remaining couples act about the axis that is normal to the base. The motion-screw system and constraint-screw system analysis leads to the insightful understanding of the mobility of the platform that is then obtained by determining the reciprocal screws to the platform constraint screw sets, resulting in three independent instantaneous translational degrees-of-freedom. To validate the mobility analysis of the three parallel manipulators, the paper includes motion simulations which use a commercially available kinematics software.

  19. Control of master-slave manipulator based on virtual internal model

    International Nuclear Information System (INIS)

    This paper presents an alternative control architecture of master-slave manipulators based on the concept of virtual internal model following control. The proposed control architecture realizes the master-salve manipulator system with functions which assist operators based on the external information from sensors as well as bilateral feedback. In this paper, the control problem of a master-slave manipulator is formulated as the realization problem of the desired relation between a master arm and a slave arm. The virtual internal model, whose input includes the external sensory information, is used to describe the desired relation. The control system is designed so that the master arm and the slave arm tracks the desired trajectories generated by the virtual internal model. The proposed control architecture is experimentally applied to the master-slave manipulator system with force sensors and the effectiveness of the control architecture is illustrated through experiments. (author)

  20. A disturbance observer-based adaptive control approach for flexure beam nano manipulators.

    Science.gov (United States)

    Zhang, Yangming; Yan, Peng; Zhang, Zhen

    2016-01-01

    This paper presents a systematic modeling and control methodology for a two-dimensional flexure beam-based servo stage supporting micro/nano manipulations. Compared with conventional mechatronic systems, such systems have major control challenges including cross-axis coupling, dynamical uncertainties, as well as input saturations, which may have adverse effects on system performance unless effectively eliminated. A novel disturbance observer-based adaptive backstepping-like control approach is developed for high precision servo manipulation purposes, which effectively accommodates model uncertainties and coupling dynamics. An auxiliary system is also introduced, on top of the proposed control scheme, to compensate the input saturations. The proposed control architecture is deployed on a customized-designed nano manipulating system featured with a flexure beam structure and voice coil actuators (VCA). Real time experiments on various manipulating tasks, such as trajectory/contour tracking, demonstrate precision errors of less than 1%. PMID:26546099

  1. Evidence-Based Theory of Market Manipulation And Application: The Malaysian Case

    OpenAIRE

    Heong, Yin Yun

    2010-01-01

    According to Part IX Division 1 in Securities Industry Act 1983 of Malaysia Law, stock market manipulation is defined as unlawful action taken either direct or indirectly by any person, to affect the price of securities of the corporation on a stock market in Malaysia for the purpose which may include the purpose of inducing other persons. Extending the framework of Allen and Gale (1992), the Author presents a theory based on the empirical evidence from prosecuted stock market manipulation ca...

  2. Fast Dynamic Model of a Moving-base 6-DOF Parallel Manipulator

    OpenAIRE

    Lopes, Antonio M.

    2010-01-01

    A parallel manipulator is a complex multi-body dynamic system having several closed loops. Typically, it is composed of a (usually) fixed base platform and a moving payload platform, connected by at least two independent open kinematic chains. Dynamic modelling of parallel manipulators presents an inherent difficulty. Despite the intensive study in this topic of robotics, mostly conducted in the last two decades, additional research still has to be done in this area.

  3. Iterative Learning Tracking Control of a Hybrid-Driven Based Three-Cable Parallel Manipulator

    OpenAIRE

    Bin Zi; Jianbin Cao; Sen Qian

    2014-01-01

    The aim of this work was to present iterative learning tracking control of a hybrid-driven based three-cable parallel manipulator (HDCPM). The HDCPM has the advantages of both cable parallel manipulator and hybrid-driven planar five-bar mechanism. Design of the HDCPM is described and dynamic model is developed on the basis of Lagrange method. Consider the HDCPM system with nonlinear, time-varying characteristics and repetitive unknown disturbances; an adaptive iterative learning control strat...

  4. Research on Construction Method of Operational Reliability Control Model for Space Manipulator Based on Particle Filter

    OpenAIRE

    Xin Gao; Yifan Wang; Hanxu Sun; Qingxuan Jia; Xiaojian Yang; Mingtao Du; Jingyu Huang

    2015-01-01

    The operational reliability of the space manipulator is closely related to the control method. However the existing control methods seldom consider the operational reliability from the system level. A method to construct the operational reliability system control model based on particle filter for the space manipulator is presented in this paper. Firstly, the definition of operational reliability and the degree of operational reliability are given and the state space equations of the control ...

  5. Object Structure from Manipulation via Particle Filter and Robot-based Active Learning

    OpenAIRE

    LI, Kun; Meng, Max Q.-H.

    2014-01-01

    To learn object models for robotic manipulation, unsupervised methods cannot provide accurate object structural information and supervised methods require a large amount of manually labeled training samples, thus interactive object segmentation is developed to automate object modeling. In this article, we formulate a novel dynamic process for interactive object segmentation, and develop a solution based on particle filter and active learning so that a robot can manipulate and learn object str...

  6. Alteration of plant meristem function by manipulation of the Retinoblastoma-like plant RRB gene

    Energy Technology Data Exchange (ETDEWEB)

    Durfee, Tim (Madison, WI); Feiler, Heidi (Albany, CA); Gruissem, Wilhelm (Forch, CH); Jenkins, Susan (Martinez, CA); Roe, Judith (Manhattan, KS); Zambryski, Patricia (Berkeley, CA)

    2007-01-16

    This invention provides methods and compositions for altering the growth, organization, and differentiation of plant tissues. The invention is based on the discovery that, in plants, genetically altering the levels of Retinoblastoma-related gene (RRB) activity produces dramatic effects on the growth, proliferation, organization, and differentiation of plant meristem.

  7. Integrating HMM-Based Speech Recognition With Direct Manipulation In A Multimodal Korean Natural Language Interface

    CERN Document Server

    Lee, G; Kim, S; Lee, Geunbae; Lee, Jong-Hyeok; Kim, Sangeok

    1996-01-01

    This paper presents a HMM-based speech recognition engine and its integration into direct manipulation interfaces for Korean document editor. Speech recognition can reduce typical tedious and repetitive actions which are inevitable in standard GUIs (graphic user interfaces). Our system consists of general speech recognition engine called ABrain {Auditory Brain} and speech commandable document editor called SHE {Simple Hearing Editor}. ABrain is a phoneme-based speech recognition engine which shows up to 97% of discrete command recognition rate. SHE is a EuroBridge widget-based document editor that supports speech commands as well as direct manipulation interfaces.

  8. Solution of Inverse Kinematics for 6R Robot Manipulators With Offset Wrist Based on Geometric Algebra.

    Science.gov (United States)

    Fu, Zhongtao; Yang, Wenyu; Yang, Zhen

    2013-08-01

    In this paper, we present an efficient method based on geometric algebra for computing the solutions to the inverse kinematics problem (IKP) of the 6R robot manipulators with offset wrist. Due to the fact that there exist some difficulties to solve the inverse kinematics problem when the kinematics equations are complex, highly nonlinear, coupled and multiple solutions in terms of these robot manipulators stated mathematically, we apply the theory of Geometric Algebra to the kinematic modeling of 6R robot manipulators simply and generate closed-form kinematics equations, reformulate the problem as a generalized eigenvalue problem with symbolic elimination technique, and then yield 16 solutions. Finally, a spray painting robot, which conforms to the type of robot manipulators, is used as an example of implementation for the effectiveness and real-time of this method. The experimental results show that this method has a large advantage over the classical methods on geometric intuition, computation and real-time, and can be directly extended to all serial robot manipulators and completely automatized, which provides a new tool on the analysis and application of general robot manipulators. PMID:23918347

  9. Gene Overexpression and RNA Silencing Tools for the Genetic Manipulation of the S-(+)-Abscisic Acid Producing Ascomycete Botrytis cinerea

    OpenAIRE

    Zhong-Tao Ding; Zhi Zhang; Di Luo; Jin-Yan Zhou; Juan Zhong; Jie Yang; Liang Xiao; Dan Shu; Hong Tan

    2015-01-01

    The phytopathogenic ascomycete Botrytis cinerea produces several secondary metabolites that have biotechnical significance and has been particularly used for S-(+)-abscisic acid production at the industrial scale. To manipulate the expression levels of specific secondary metabolite biosynthetic genes of B. cinerea with Agrobacterium tumefaciens-mediated transformation system, two expression vectors (pCBh1 and pCBg1 with different selection markers) and one RNA silencing vector, pCBSilent1, w...

  10. Terahertz wave manipulation with metamaterials based on metal and graphene

    DEFF Research Database (Denmark)

    Andryieuski, Andrei; Malureanu, Radu; Zalkovskij, Maksim;

    2013-01-01

    The terahertz (THz) technology provides with exciting possibilities for spectroscopy, food quality control, defense, communication and biomedical imaging [1]. Being relatively young (the massive exploitation of the THz range began only in the beginning of 1990-ies), the THz science demands for ac......]. We analyze the limitations and demonstrate numerically and experimentally the chiral and nonchiral thin-film metamaterial based polarization converters [3–5] and graphene total absorbers for THz radiation [6]....

  11. Behavior-based Task Learning by Demonstration on Mobile Manipulation

    Directory of Open Access Journals (Sweden)

    Shu Huang

    2013-03-01

    Full Text Available Users should have the opportunity to teach new tasks on their robot to fit the specific needs in its own environment. Behaviors are good building blocks for complex tasks because they are in charge of a specific control objective and have an intuitive name. After encapsulating controls within a behavior, the task learning problem for behavior-based systems becomes a behavior recognition problem. Behavior-based task learning can be focused on either behavior segmentation, behavior recognition or behavior cooperation. The behavior diagram is expressed by an execution matrix, which consists of only numerical information referring to the parameters of the behaviors or transitions. The parameter values are determined by the behavior classification.A feature space is introduced to extract more meaningful information from sensory data. Geometric features, such as the plane feature or the line feature, detect whether the movement of points fulfills a certain geometric relationship. A combined machine learning approach, which consists of decision tree and support vector machine, is proposed for behavior-based task learning. The decision tree is used to select relevant features from the feature pool, and support vector machine is applied to find the mapping from the feature space to behaviors. This way, corresponding behaviors can be recognized during demonstration. This method also has the ability to handle the diversity of robot configurations and users. Post-processing techniques are proposed to improve the classifi-cation results.

  12. Molecular engineering of manipulated alginate-based polyurethanes.

    Science.gov (United States)

    Daemi, Hamed; Barikani, Mehdi

    2014-11-01

    The novel soluble alginate-based polyurethanes in organic solvents were synthesized by the reaction of NCO-terminated prepolymers and tributylammonium alginate (TBA-Alg) for the first time. The chemical structures of synthesized polyurethanes were characterized using FTIR, (1)H NMR and TGA. The reaction completion was confirmed by disappearing of NCO band in FTIR spectra. Furthermore, a peak at 4.71 ppm and some small peaks at a range of 4.12-4.37 ppm in the (1)H NMR of alginate-based polyurethanes were assigned to the backbone of alginate. The results of both FTIR and (1)H NMR were remarkably confirmed by TGA data. The ionic nature of polyurethane backbone not only affects on thermal properties of samples, but it also changes the chemically-bonded alginate morphology. Both polyether and polyester based non-ionic polyurethanes extended by TBA-Alg illustrated the distinct alginate, whereas those ionomers extended by alginate were appeared as the continuous systems at nanoscale. PMID:25129793

  13. Current Opinions on the Functions of Tocopherol Based on the Genetic Manipulation of Tocopherol Biosynthesis in Plants

    Institute of Scientific and Technical Information of China (English)

    Yin Li; Zinan Wang; Xiaofen Sun; Kexuan Tang

    2008-01-01

    As a member of an important group of lipid soluble antioxidants,tocopherols play a paramount role In the daily diet of humans and animals.Recently,genes required for tocochromanol biosynthesis pathway have been identified and cloned with the help of genomics-based approaches and molecular manipulation in the model organisms: Arabidopsis thaliana and Synechocystis sp.PCC 6803.At the basis of these foundations,genetic manipulation of tocochromanol biosynthesis pathway can give rise to strategies that enhance the level of tocochromanol content or convert the constitution of tocochromanol.In addition,genetic manipulations of the tocochromanol biosynthesis pathway provide help for the study of the function of tocopherol in plant systems.The present article summarizes recent advances and pays special attention to the functions of tocopherol in plants.The roles of tocopherol in the network of reactive oxygen species,antioxidants and phytohormones to maintain redox homeostasis and the functions of tocopherol as a signal molecule in chloroplast-to-nucleus signaling to regulate carbohydrate metabolism are also discussed.

  14. Design, Dynamics, and Workspace of a Hybrid-Driven-Based Cable Parallel Manipulator

    Directory of Open Access Journals (Sweden)

    Bin Zi

    2013-01-01

    Full Text Available The design, dynamics, and workspace of a hybrid-driven-based cable parallel manipulator (HDCPM are presented. The HDCPM is able to perform high efficiency, heavy load, and high-performance motion due to the advantages of both the cable parallel manipulator and the hybrid-driven planar five-bar mechanism. The design is performed according to theories of mechanism structure synthesis for cable parallel manipulators. The dynamic formulation of the HDCPM is established on the basis of Newton-Euler method. The workspace of the manipulator is analyzed additionally. As an example, a completely restrained HDCPM with 3 degrees of freedom is studied in simulation in order to verify the validity of the proposed design, workspace, and dynamic analysis. The simulation results, compared with the theoretical analysis, and the case study previously performed show that the manipulator design is reasonable and the mathematical models are correct, which provides the theoretical basis for future physical prototype and control system design.

  15. Manipulation of orbital angular momentum beams based on space diffraction compensation.

    Science.gov (United States)

    Zhou, Hailong; Dong, Jianji; Yan, Siqi; Zhou, Yifeng; Shi, Lei; Zhang, Xinliang

    2014-07-28

    We put forward a technique to manipulate the size of orbital angular momentum (OAM) beams based on space diffraction compensation. Paraxial Fresnel diffraction which carries a negative spatial quadratic phase distribution can be regarded as a negative diffractive effect. To compensate the negative diffraction, we employ a 4f Fourier lens system containing a phase mask to generate an inverse quadratic phase. The size of OAM beams can be easily controlled by designing the phase mask profile without changing the OAM. The applications of space diffraction compensation in OAM demultiplexing, ring fiber coupling for OAM beams and optical manipulation of micro particles are also discussed. PMID:25089395

  16. Low Speed Motion Optimization of Space Manipulator Based on Gradient Projection Method

    Directory of Open Access Journals (Sweden)

    Peng Junjie

    2015-01-01

    Full Text Available Low-speed crawling phenomenon may occur when space manipulators run at a low speed, which may bring big problem for manipulation work. A kind of low-speed optimization algorithm based on gradient projection method is pro-posed in this paper. The designing of continuous balanced proportional factor can effectively reduce the quantitative differences between the homogeneous solution and the special solution, avoiding the joint velocities oscillations. The low-speed crawling problem can be effectively improved by appropriate increase of joint velocities. And the effectiveness and correctness of the optimization algorithm are confirmed by the simulation.

  17. Fuzzy PID Control Method for Internet-based Tele-operation Manipulators System

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2013-11-01

    Full Text Available Trajectory tracking control problem for internet-based tele-operation system is researched in this paper. The control structure of master and slave tele-operation manipulators adapts bilateral servo control architecture with force deviation feedback. The simulation model of three degrees of freedom (3-DOF manipulator is presented. In order to ensure the synchronization of positions of the master and slave manipulators, a fuzzy PID control method is proposed. This control algorithm is to adjust the three parameters of PID controller online by fuzzy control method. The contrast simulation experiments of PID and fuzzy PID control methods show that the proposed control method can effectively improve the force and position tracking performance and reduce time delay.

  18. Dialogue-Based Activities and Manipulatives to Engage Liberal Arts Majors in Mathematics

    Science.gov (United States)

    Price, James C.

    2015-01-01

    This article presents four inquiry-based learning activities developed for a liberal arts math course. The activities cover four topics: the Pythagorean theorem, interest theory, optimization, and the Monty Hall problem. Each activity consists of a dialogue, with a theme and characters related to the topic, and a manipulative, that allow students…

  19. Defining a Service Angle for Planar Mechanisms of Manipulators based on the Instantaneous States Analysis

    Science.gov (United States)

    Pritykin, F.; Gordeev, O.

    2016-04-01

    The paper provides an algorithm of defining a service angle for planar mechanisms of manipulators having different structures of kinematic chains. The algorithm is based on the motion synthesis in the vector of velocities. The functions defining specified angle determination accuracy by the developed method are obtained.

  20. Dataglove-based interface for impedance control of manipulators in cooperative human–robot environments

    International Nuclear Information System (INIS)

    A dataglove-based interface is presented for tracking the forces applied by the hand during contact tasks with a 6-degree-of-freedom (DOF) manipulator. The interface uses 11 force sensors carefully placed on the palm-side fabric of a 16 DOF dataglove. The force sensors use piezoresistive technology to measure the individual force components from the hand. Based on the dataglove measurements, these components are transformed and summed to assemble the resultant force vector. Finally, this force vector is translated into the manipulator frame using orientation measurements from an inertial measurement unit placed on the dorsal side of the dataglove. Static tests show that the dataglove-based interface can effectively measure the applied hand force, but there are inaccuracies in orientation and magnitude when compared to the load cell measurements used as the reference for error calculation. Promising results were achieved when controlling the 6 DOF manipulator based on the force readings acquired from the dataglove interface; the decoupled dynamics of the dataglove interface with respect to the robot structure yielded smooth force readings of the human intention that could be effectively used in the impedance control of the manipulator. (paper)

  1. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene. Progress report, [April 15, 1987--April 14, 1988

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1988-12-31

    Many agronomically important crops are viewed as significant resources of renewable energy. Overall crop productivity could be increased if the efficiency of photoassimilate conversion into dry matter such as starch were improved in storage tissues. Starch production is controlled by the catalytic activity of ADPglucose pyrophosphorylase in the first step of starch biosynthesis. This research focuses on the genetic structure and molecular mechanisms by which it is controlled during plant development and how it is affected by environmental and hormonal conditions. The current goal is to isolate the genes for this enzyme present in both cereal endosperm and potato tuber tissues, and to elucidate its structure and the controlling sequences responsible for gene expression. The long term goal is the improvement of starch production in storage organs by manipulating this gene so that it encodes an enzyme refractive to inorganic phosphate inhibition.

  2. Dynamic Output Feedback Based Active Decentralized Fault-Tolerant Control for Reconfigurable Manipulator with Concurrent Failures

    Directory of Open Access Journals (Sweden)

    Yuanchun Li

    2015-01-01

    Full Text Available The goal of this paper is to describe an active decentralized fault-tolerant control (ADFTC strategy based on dynamic output feedback for reconfigurable manipulators with concurrent actuator and sensor failures. Consider each joint module of the reconfigurable manipulator as a subsystem, and treat the fault as the unknown input of the subsystem. Firstly, by virtue of linear matrix inequality (LMI technique, the decentralized proportional-integral observer (DPIO is designed to estimate and compensate the sensor fault online; hereafter, the compensated system model could be derived. Then, the actuator fault is estimated similarly by another DPIO using LMI as well, and the sufficient condition of the existence of H∞ fault-tolerant controller in the dynamic output feedback is presented for the compensated system model. Furthermore, the dynamic output feedback controller is presented based on the estimation of actuator fault to realize active fault-tolerant control. Finally, two 3-DOF reconfigurable manipulators with different configurations are employed to verify the effectiveness of the proposed scheme in simulation. The main advantages of the proposed scheme lie in that it can handle the concurrent faults act on the actuator and sensor on the same joint module, as well as there is no requirement of fault detection and isolation process; moreover, it is more feasible to the modularity of the reconfigurable manipulator.

  3. Three knowledge representation formalisms for content-based manipulation of documents

    OpenAIRE

    Al Hulou, Rim; Corby, Olivier; Dieng-Kuntz, Rose; Euzenat, Jérôme; Ramirez, Carolina; Napoli, Amedeo; Troncy, Raphael

    2002-01-01

    Documents accessible from the web or from any document base constitute a significant source of knowledge as soon as the document contents can be represented in an appropriate form. This paper presents the ESCRIRE project, whose objective is to compare three knowledge representation (KR) formalisms, namely conceptual graphs, description logics and objects, for representing and manipulating document contents. The comparison relies on the definition of a pivot language based on XML, allowing the...

  4. Pseudo-inverse Jacobian control with grey relational analysis for robot manipulators mounted on oscillatory bases

    Science.gov (United States)

    Lin, J.; Lin, C. C.; Lo, H.-S.

    2009-10-01

    Interest in complex robotic systems is growing in new application areas. An example of such a robotic system is a dexterous manipulator mounted on an oscillatory base. In literature, such systems are known as macro/micro systems. This work proposes pseudo-inverse Jacobian feedback control laws and applies grey relational analysis for tuning outer-loop PID control parameters of Cartesian computed-torque control law for robotic manipulators mounted on oscillatory bases. The priority when modifying controller parameters should be the top ranking importance among parameters. Grey relational grade is utilized to investigate the sensitivity of tuning the auxiliary signal PID of the Cartesian computed-torque law to achieve desired performance. Results of this study can be feasible to numerous mechanical systems, such as mobile robots, gantry cranes, underwater robots, and other dynamic systems mounted on oscillatory bases, for moving the end-effector to a desired Cartesian position.

  5. xdamp Version 3: An IDL reg-sign-based data and image manipulation program

    International Nuclear Information System (INIS)

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA trademark (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix reg-sign-based workstations, a replacement was needed. This package uses the IDL reg-sign software, available from Research Systems Incorporated in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM reg-sign workstations, Hewlett Packard workstations, SUN reg-sign workstations, Microsoft reg-sign Windows trademark computers, Macintosh reg-sign computers and Digital Equipment Corporation VMS reg-sign and Alpha reg-sign systems. Thus, xdamp is portable across many platforms. The author has verified operation, albeit with some minor IDL bugs, on personal computers using Windows 95 and Windows NT; IBM Unix platforms; and DEC alpha and VMS systems; HP 9000/700 series workstations; and Macintosh computers, both regular and PowerPC trademark versions. Version 3 adds the capability to manipulate images to the original xdamp capabilities

  6. Compact piezoelectric tripod manipulator based on a reverse bridge-type amplification mechanism

    Science.gov (United States)

    Na, Tae-Won; Choi, Jun-Ho; Jung, Jin-Young; Kim, Hyeong-Geon; Han, Jae-Hung; Park, Kwang-Chun; Oh, Il-Kwon

    2016-09-01

    We report a hierarchical piezoelectric tripod manipulator based on a reverse bridge-type displacement amplifier. The reverse bridge-type amplification mechanism is pre-strained by each piezo-stack actuator up to 60 μm and is cross-stacked in a series arrangement to make a compact and high-stroke manipulator having load-bearing characteristics. The designed manipulator with three degrees of freedom is compact with a height of 56.0 mm, a diameter of 48.6 mm and total weight of 115 g. It achieves a translational stroke of up to 880 μm in heaving motion and a tilting angle of up to 2.0° in rotational motion within the operating voltage and power range of the piezoelectric stack actuator. A key feature of the present design is built-in and pre-strained displacement amplification mechanisms integrated with piezoelectric stacked actuators, resulting in a compact tripod manipulator having exceptionally high stroke and load-bearing capacity.

  7. A microcontroller-based three degree-of-freedom manipulator testbed. M.S. Thesis

    Science.gov (United States)

    Brown, Robert Michael, Jr.

    1995-01-01

    A wheeled exploratory vehicle is under construction at the Mars Mission Research Center at North Carolina State University. In order to serve as more than an inspection tool, this vehicle requires the ability to interact with its surroundings. A crane-type manipulator, as well as the necessary control hardware and software, has been developed for use as a sample gathering tool on this vehicle. The system is controlled by a network of four Motorola M68HC11 microcontrollers. Control hardware and software were developed in a modular fashion so that the system can be used to test future control algorithms and hardware. Actuators include three stepper motors and one solenoid. Sensors include three optical encoders and one cable tensiometer. The vehicle supervisor computer provides the manipulator system with the approximate coordinates of the target object. This system maps the workspace surrounding the given location by lowering the claw, along a set of evenly spaced vertical lines, until contact occurs. Based on this measured height information and prior knowledge of the target object size, the system determines if the object exists in the searched area. The system can find and retrieve a 1.25 in. diameter by 1.25 in. tall cylinder placed within the 47.5 sq in search area in less than 12 minutes. This manipulator hardware may be used for future control algorithm verification and serves as a prototype for other manipulator hardware.

  8. xdamp Version 3: An IDL{reg_sign}-based data and image manipulation program

    Energy Technology Data Exchange (ETDEWEB)

    Ballard, W.P.

    1998-05-01

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix{reg_sign}-based workstations, a replacement was needed. This package uses the IDL{reg_sign} software, available from Research Systems Incorporated in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM{reg_sign} workstations, Hewlett Packard workstations, SUN{reg_sign} workstations, Microsoft{reg_sign} Windows{trademark} computers, Macintosh{reg_sign} computers and Digital Equipment Corporation VMS{reg_sign} and Alpha{reg_sign} systems. Thus, xdamp is portable across many platforms. The author has verified operation, albeit with some minor IDL bugs, on personal computers using Windows 95 and Windows NT; IBM Unix platforms; and DEC alpha and VMS systems; HP 9000/700 series workstations; and Macintosh computers, both regular and PowerPC{trademark} versions. Version 3 adds the capability to manipulate images to the original xdamp capabilities.

  9. Study of Automatic Fiber Placement Manipulator’s Robotic Kinematics Manipulability Based on Volume Element

    Directory of Open Access Journals (Sweden)

    Ge Xinfeng

    2013-02-01

    Full Text Available The method is proposed based on volume element in order to measure the manipulator’s robotic kinematics manipulability. Then studied the series redundant automatic fiber placement robotic manipulator’s operation space, draw the conclusion that the greater of the robotic manipulator’s operation space volume, the better of the robotic manipulator’s manipulability, volume element based on redundant robotic manipulator’s kinematics is proposed as an operational performance index. n-DOF serial robotic manipulator’s operation space is n-dimensional Riemannian manifold, the n-dimensional Riemannian manifold volume is calculated using the moving coordinate system and the exterior product definition in differential geometry and get the robotic manipulator’s operation space volume then compared the obtained results with the operation space volume using inner product determinant in the literature, it shows that the volume element as a kinematics operational performance index is feasible.

  10. A Wearable-based and Markerless Human-manipulator Interface with Feedback Mechanism and Kalman Filters

    OpenAIRE

    Zhang, Ping; Li, Bei; Du, Guanglong; Liu, Xin

    2015-01-01

    The objective of this paper is to develop a novel human-manipulator interface which incorporates wearable-based and markerless tracking to interact with the continuous movements of a human operator’s hand. Unlike traditional approaches, which usually include contacting devices or physical markers to track the human-limb movements, this interface enables registration of natural movement through a wireless wearable watch and a leap motion sensor. Due to sensor error and tracking failure, the me...

  11. Manipulation of the fluorescence of nanocrystals by opal-based heterostructures

    OpenAIRE

    Céline, Bourdillon; Ngoc, Hong Phan; de Marcillac Willy, Daney; Laurent, Coolen; Maître, Agnès; Schwob, Catherine

    2015-01-01

    Opal-based photonic crystals are promising materials to engineer complex heterostructures for efficient manipulation of nano-emitters fluorescence. We fabricated and characterized a structure composed of a layer of silica embedded between two silica opals. Thanks to this controlled planar defect which opens a permitted frequency band in the photonic stopband, an increase of emission, depending on angular distribution, is evidenced through photoluminescence spectroscopy. We discuss the use of ...

  12. Solving the dynamic equations of a 3-PRS Parallel Manipulator for efficient model-based designs

    OpenAIRE

    Díaz-Rodríguez, M.; Carretero, J. A.; Bautista-Quintero, R.

    2016-01-01

    Introduction of parallel manipulator systems for different applications areas has influenced many researchers to develop techniques for obtaining accurate and computational efficient inverse dynamic models. Some subject areas make use of these models, such as, optimal design, parameter identification, model based control and even actuation redundancy approaches. In this context, by revisiting some of the current computationally-efficient solutions for obtaining the inverse d...

  13. Manipulation of Original Ideology Through Translation: A Discourse-Based Translation Quality Assessment of Speeches

    OpenAIRE

    Majid Khorsand; Bahloul Salmani

    2014-01-01

    The main focus of this paper is on speeches in literary discourse as the superb ideological displays of propaganda as well as their translations for having an enormous capacity for ideological manipulation. In this paper, the only present English-Azarbaijani Turkish translation of Squealer’s speech from Orwell’s Animal Farm was discoursally analyzed based on House’s revised translation quality assessment (TQA) model. According to this model, speeches as propaganda in literary texts must be tr...

  14. Humidity Dependence of Charge Transport through DNA Revealed by Silicon-Based Nanotweezers Manipulation

    OpenAIRE

    Yamahata, Christophe; Collard, Dominique; Takekawa, Tetsuya; Kumemura, Momoko; Hashiguchi, Gen; Fujita, Hiroyuki

    2007-01-01

    The study of the electrical properties of DNA has aroused increasing interest since the last decade. So far, controversial arguments have been put forward to explain the electrical charge transport through DNA. Our experiments on DNA bundles manipulated with silicon-based actuated tweezers demonstrate undoubtedly that humidity is the main factor affecting the electrical conduction in DNA. We explain the quasi-Ohmic behavior of DNA and the exponential dependence of its conductivity with relati...

  15. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Progress report, [March 15, 1989--April 14, 1990

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1990-12-31

    The long term aim of this project is to assess the feasibility of increasing the conversion of photosynthate into starch via manipulation of the gene that encodes for ADPglucose pyrophosphorylase, a key regulatory enzyme of starch biosynthesis. In developing storage tissues such as cereal seeds and tubers, starch biosynthesis is regulated by the gene activation and expression of ADPglucose pyrophosphorylase, starch synthase, branching enzyme and other ancillary starch modifying enzymes, as well as the allosteric-controlled behavior of ADPglucose pyrophosphorylase activity. During the last two years we have obtained information on the structure of this enzyme from both potato tuber and rice endosperm, using a combination of biochemical and molecular biological approaches. Moreover, we present evidence that this enzyme may be localized at discrete regions of the starch grain within the amyloplast, and plays a role in controlling overall starch biosynthesis in potato tubers.

  16. Gene Overexpression and RNA Silencing Tools for the Genetic Manipulation of the S-(+-Abscisic Acid Producing Ascomycete Botrytis cinerea

    Directory of Open Access Journals (Sweden)

    Zhong-Tao Ding

    2015-05-01

    Full Text Available The phytopathogenic ascomycete Botrytis cinerea produces several secondary metabolites that have biotechnical significance and has been particularly used for S-(+-abscisic acid production at the industrial scale. To manipulate the expression levels of specific secondary metabolite biosynthetic genes of B. cinerea with Agrobacterium tumefaciens-mediated transformation system, two expression vectors (pCBh1 and pCBg1 with different selection markers and one RNA silencing vector, pCBSilent1, were developed with the In-Fusion assembly method. Both expression vectors were highly effective in constitutively expressing eGFP, and pCBSilent1 effectively silenced the eGFP gene in B. cinerea. Bcaba4, a gene suggested to participate in ABA biosynthesis in B. cinerea, was then targeted for gene overexpression and RNA silencing with these reverse genetic tools. The overexpression of bcaba4 dramatically induced ABA formation in the B. cinerea wild type strain Bc-6, and the gene silencing of bcaba4 significantly reduced ABA-production in an ABA-producing B. cinerea strain.

  17. Homoeologous GSL-ELONG gene replacement for manipulation of aliphatic glucosinolates in Brassica rapa L. by marker assisted selection

    Directory of Open Access Journals (Sweden)

    Arvind H. Hirani

    2013-03-01

    Full Text Available Aliphatic glucosinolates are the predominant sulphur-rich plant secondary metabolites in economically important Brassica crops. Glucosinolates and their hydrolysis products are involved in plant-microbe, plant-insect, plant-animal and plant-human interactions. It is, therefore, important to manipulate glucosinolate profiles and contents in Brassica species. In this study, aliphatic glucosinolates were genetically manipulated through homoeologous recombination in backcross lines followed by marker assisted selection in B. rapa. A resynthesized B. napus line, from a cross between B. rapa and B. oleracea, was backcrossed with Chinese cabbage doubled haploid line, RI16. Marker assisted selection for non-functional gene was performed in each backcross generations. Advanced backcross progenies (BC3F2 were developed to identify homoeologous gene replacement and/or introgression. Reduction in 5C aliphatic glucosinolates (gluconapoleiferin, glucoalyssin and glucobrassicanapin was observed in BC3F2 progenies of the recurrent parent that carried the GSL-ELONG gene. The GSL-ELONG positive backcross progenies were also screened by the A-genome and BraGSL-ELONG gene specific marker, which linked with 5C aliphatic glucosinolates. The A-genome specific marker was absent in the plants of advanced backcross progenies which showed reduction in 5C aliphatic glucosinolates. The results suggest that the functional allele had been replaced by the non-functional GSL-ELONG allele from B. oleracea. Some advanced backcross progenies (BC3F2 positive for the GSL-ELONG allele and the A-genome specific SCAR marker BraMAM1-1 did not show reduction in 5C aliphatic glucosinolates, suggesting that GSL-ELONG allele is recessive. Replacement of the functional locus in the A genome by non-functional counterpart in the C genome reduced the content of 5C aliphatic glucosinolates in B. rapa seeds with 20 micromoles per gram.

  18. Quantifying molecule-surface interactions using AFM-based single-molecule manipulation

    Science.gov (United States)

    Tautz, F. S.; Wagner, C.; Temirov, R.; Fournier, N.; Green, M.; Esat, T.; Leinen, P.; Groetsch, A.; Ruiz, V. G.; Tkatchenko, A.; Li, C.; Muellen, K.; Rohlfing, M.

    2015-03-01

    Scanning probe microscopy plays an important role in the investigation of molecular adsorption. Promising, is the possibility to probe the molecule-surface interaction while tuning its strength through AFM tip-induced single-molecule manipulation. Here, we outline a strategy to achieve quantitative understanding of such manipulation experiments. The example of qPlus sensor based PTCDA molecule lifting experiments is used to demonstrate how different aspects of the molecule-surface interaction, namely the short-range adsorption potential, the asymptotic van der Waals potential, local chemical bonds which are the source of the surface corrugation, and molecule-molecule interactions can be measured with SPM and interpreted by the help of force-field simulations.

  19. Neuro-fuzzy and model-based motion control for mobile manipulator among dynamic obstacles

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    This paper focuses on autonomous motion control of a nonholonomic platform with a robotic arm, which is called mobile manipulator. It serves in transportation of loads in imperfectly known industrial environments with unknown dynamic obstacles. A union of both procedures is used to solve the general problems of collision-free motion. The problem of collision-free motion for mobile manipulators has been approached from two directions, Planning and Reactive Control. The dynamic path planning can be used to solve the problem of locomotion of mobile platform, and reactive approaches can be employed to solve the motion planning of the arm. The execution can generate the commands for the servo-systems of the robot so as to follow a given nominal trajectory while reacting in real-time to unexpected events. The execution can be designed as an Adaptive Fuzzy Neural Controller. In real world systems, sensor-based motion control becomes essential to deal with model uncertainties and unexpected obstacles.

  20. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Summary of progress, [April 15, 1991--April 14, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1992-12-31

    The long term aim of this project is to assess the feasibility of increasing the conversion of photosynthate into starch via manipulation of genes encoding enzymes that may be rate-limiting in starch biosynthesis. In developing storage tissues such as tubers, starch biosynthesis is regulated by the gene activation and expression of ADPglucose pyrophosphorylase, starch synthase, branching enzyme and other ancillary starch modifying enzymes, as well as the allosteric-controlled behavior of ADPglucose pyrophosphorylase activity. In view of the regulatory role of ADPglucose pyrophosphorylase in starch biosynthesis at both the genetic and biochemical level, we have focused our attention on the genes that encode for this enzyme in potato tubers. The proposed objectives of the grant were to (1) analyze the structure of the tuber enzyme, (2) isolate and characterize the structure of its genes, and (3) identify the regulatory elements controlling ADPglucose pyrophosphorylase during plant development. During the last two and 1/2 years we have met or have made considerable progress in achieving these objectives as discussed in more detail below.

  1. Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes

    DEFF Research Database (Denmark)

    Zhang, Changyi; Tian, Bin; Li, Suming;

    2013-01-01

    enzymes already impaired cell growth, highlighting their important roles in archaeal DNA repair. Systematically characterizing these mutants and generating mutants lacking two or more DNA repair genes will yield further insights into the genetic mechanisms of DNA repair in this model organism.......Recently, a novel gene-deletion method was developed for the crenarchaeal model Sulfolobus islandicus, which is a suitable tool for addressing gene essentiality in depth. Using this technique, we have investigated functions of putative DNA repair genes by constructing deletion mutants and studying...... their phenotype. We found that this archaeon may not encode a eukarya-type of NER (nucleotide excision repair) pathway because depleting each of the eukaryal NER homologues XPD, XPB and XPF did not impair the DNA repair capacity in their mutants. However, among seven homologous recombination proteins...

  2. Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

    Science.gov (United States)

    Bailey, Andy M.; Alberti, Fabrizio; Kilaru, Sreedhar; Collins, Catherine M.; de Mattos-Shipley, Kate; Hartley, Amanda J.; Hayes, Patrick; Griffin, Alison; Lazarus, Colin M.; Cox, Russell J.; Willis, Christine L.; O’Dwyer, Karen; Spence, David W.; Foster, Gary D.

    2016-05-01

    Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi.

  3. xdamp Version 4: An IDL Based Data and Image Manipulation Program

    International Nuclear Information System (INIS)

    The original DAMP (W t a Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA(trademark) (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix(regsign)-based workstations, a replacement was needed. This package uses the IDL(regsign) software, available from Research Systems Incorporated, a Xerox company, in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM(regsign) workstations, Hewlett Packard workstations, SUN(regsign) workstations, Microsoft(regsign) Windows(trademark) computers, Macintosh(regsign) computers and Digital Equipment Corporation VMS(regsign) and Alpha(regsign) systems. Thus, xdamp is portable across many platforms. We have verified operation, albeit with some minor IDL bugs, on personal computers using Windows 95 and Windows NT; IBM Unix platforms; DEC Alpha and VMS systems; HP 9000/700 series workstations; and Macintosh computers, both regular and PowerPC(trademark) versions. Version 4 is an update that removes some obsolete features and better supports very large arrays and Excel formatted data import

  4. Interactive sculpting of product shape based on constraint manipulation in virtual environment

    Institute of Scientific and Technical Information of China (English)

    LIU Zhen-yu; TAN Jian-rong

    2005-01-01

    In product concept design, not only designers with professional CAD skills, but also final customers take part in the design and evaluation of product shape styling. Because customers usually lack surface modelling background and are not familiar with concrete operations of commercial CAD systems, it is difficult for them to express their change intentions of product shape through professional CAD tools if they are not satisfied with the current shape design. This paper puts forward a method for creating, dragging and manipulating constraint and load represented in form of icon entity in interactive sculpting of product shape in virtual environment. The method supports customers manipulation of sculpting constraints or loads on sculpting shapes in virtual reality interaction to control the deformation of product shape. Constraints management based on icon entity is similar to spline lofting operation that is familiar to engineers, so users do not need to know surface details or have any professional knowledge of surface modelling, by only using their physical and engineering experience, they can manipulate the sculpting of product shape intuitively.

  5. xdamp Version 4 An IDL Based Data and Image Manipulation Program

    CERN Document Server

    William-Ballar, P

    2002-01-01

    The original DAMP (W t a Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA(trademark) (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix(reg sub s ign)-based workstations, a replacement was needed. This package uses the IDL(reg sub s ign) software, available from Research Systems Incorporated, a Xerox company, in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM(reg sub s ign) workstations, Hewlett Packard workstations, SUN(reg sub s ign) workstations, Microsoft(reg sub s ign) Windows(trademark) computers, Macinto...

  6. xdamp Version 6 : an IDL-based data and image manipulation program.

    Energy Technology Data Exchange (ETDEWEB)

    Ballard, William Parker

    2012-04-01

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix(reg sign)-based workstations, a replacement was needed. This package uses the IDL(reg sign) software, available from Research Systems Incorporated, a Xerox company, in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM(reg sign) workstations, Hewlett Packard workstations, SUN(reg sign) workstations, Microsoft(reg sign) Windows{trademark} computers, Macintosh(reg sign) computers and Digital Equipment Corporation VMS(reg sign) and Alpha(reg sign) systems. Thus, xdamp is portable across many platforms. We have verified operation, albeit with some minor IDL bugs, on personal computers using Windows 7 and Windows Vista; Unix platforms; and Macintosh computers. Version 6 is an update that uses the IDL Virtual Machine to resolve the need for licensing IDL.

  7. xdamp Version 2: An IDL{reg_sign}-based data manipulation program

    Energy Technology Data Exchange (ETDEWEB)

    Ballard, W.P. [Sandia National Labs., Albuquerque, NM (United States). Simulation Technology Research Dept.

    1996-12-01

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA{trademark} (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of UNIX{reg_sign}-based workstations, a replacement was needed. This package uses the IDL{reg_sign} software, available from Research Systems Incorporated in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP.IDL is currently supported on a wide variety of UNIX platforms such as IBM{reg_sign} workstations, Hewlett Packard workstations, SUN{reg_sign} workstations, Microsoft{reg_sign} Windows{trademark} computers, Macintosh{reg_sign} computers and Digital Equipment Corporation VMS{reg_sign} systems. Thus, xdamp is portable across many platforms. The authors have verified operation, albeit with some minor IDL bugs, on IBM PC computers using Windows, Windows 95 and Windows NT; IBM UNIX platforms; DEC Alpha and VMS systems; HP 9000/700 series workstations; and Macintosh computers, both regular and PowerPC{trademark} versions. Version 2 updates xdamp to require IDL version 4.0.1, adds many enhancements, and fixes a number of bugs.

  8. Manipulation of Original Ideology Through Translation: A Discourse-Based Translation Quality Assessment of Speeches

    Directory of Open Access Journals (Sweden)

    Majid Khorsand

    2014-09-01

    Full Text Available The main focus of this paper is on speeches in literary discourse as the superb ideological displays of propaganda as well as their translations for having an enormous capacity for ideological manipulation. In this paper, the only present English-Azarbaijani Turkish translation of Squealer’s speech from Orwell’s Animal Farm was discoursally analyzed based on House’s revised translation quality assessment (TQA model. According to this model, speeches as propaganda in literary texts must be translated overtly to meet the standards of an adequate translation. Of the main criteria of an overt translation are co-activating the original discourse world and being equivalent at the levels of text, register, and genre. With respect to covertly and overtly erroneous errors, the findings of the study demonstrated that enormous ideological distortions and manipulation were carried out in the Turkish translation. Therefore, the translation was a covert and inadequate one. Moreover, the social effect the source and target texts’ readerships receive would be radically different from each other. Finally, some implications and suggestions for further studies were proposed.Keywords: Ideology, Manipulation, Squealer’s speech, Discourse analysis, House’s revisited TQA model

  9. [Enhancement of photoassimilate utilization by manipulation of ADP-glucose pyrophosphorylase gene]. Final progress report

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1999-04-01

    Part 1 of this research focuses on patterns of gene expression of ADPG-pyrophosphorylase in native and transgenic potato plants. To elucidate the mechanism controlling AGP expression during plant development, the expression of the potato tuber AGP small subunit (sAGP) gene was analyzed in transgenic potato plants using a promoter-{beta}-glucuronidase expression system. Part II evaluated the structure-function relationships of AGP.

  10. Plasmids as mediators of gene transfer in the genetic manipulation of gram-positive bacteria

    OpenAIRE

    O'Hara, Seamus

    1989-01-01

    Lack of suitable gene transfer techniques hampers genetic improvement and analysis of several industrially and clinically important gram-positive bacteria. Techniques already developed are often difficult to reproduce and limited in application. This study examines the feasibility of expanding the techniques available through the use of conjugation as a broad host range gene transfer mechanism. Such systems have been developed for gram-negative bacteria. Theoretical and practical aspec...

  11. An active damping control of robot manipulators with oscillatory bases by singular perturbation approach

    Science.gov (United States)

    Lin, J.; Huang, Z. Z.; Huang, P. H.

    2007-07-01

    This paper deals with active damping control problems of robot manipulators with oscillatory bases. A first investigation of two-time scale fuzzy logic controller with vibration stabilizer for such structures has been proposed, where the dynamics of a robotic system is strongly affected by disturbances due to the base oscillation. Under the assumption of two-time scale, its stability and design procedures are presented for a multiple link manipulator with multiple dimension oscillation. The fast-subsystem controller will damp out the vibration of the oscillatory bases using a PD control method. Hence, the slow-subsystem fuzzy logic controller dominates the trajectory tracking. It can be guaranteed the stability of the internal dynamics by adding a boundary-layer correction based on singular perturbations approach. Experimental results have shown that the proposed control model offers several implementation advantages such as reduced effect of overshoot and chattering, smaller steady state error, and a fast convergent rate. The results of this study can be feasible to various mechanical systems, such as mobile robot, gantry cranes, underwater robot, and other dynamic systems mounted on oscillatory bases.

  12. Alternative splicing: an important mechanism for myometrial gene regulation that can be manipulated to target specific genes associated with preterm labour

    Directory of Open Access Journals (Sweden)

    Tyson-Capper Alison

    2007-06-01

    Full Text Available Abstract Considerable effort has been expended in attempting to distinguish genes that contribute to initiating the onset of term and preterm labour (PTL from those that change in expression as a consequence of the progression of labour. The ability to define more clearly the genes involved in triggering labour contractions should lead to the development of new effective and safer strategies to prevent preterm birth. There is ample evidence to suggest that specific genes are co-ordinately regulated within the upper and lower regions of the myometrium prior to and during parturition and many of these genes are regulated by alternative pre-mRNA splicing. This mini-review highlights that expression of a range of different splicing factors, with defined roles in pre-mRNA splicing, is both temporally and spatially regulated within the uterine smooth muscle during pregnancy and labour. Moreover, several of these splicing factors play key roles in controlling the differential expression of specific regulatory proteins involved in uterine signalling and uterine quiescence. In addition, antisense morpholino oligonucleotide manipulation of pre-mRNA splicing may have potential in defining and targeting uterine pro-labour genes and thus contribute to the development of new therapeutic approaches to prevent PTL.

  13. Novel integrated optimization algorithm for trajectory planning of robot manipulators based on integrated evolutionary programming

    Institute of Scientific and Technical Information of China (English)

    Xiong LUO; Xiaoping FAN; Heng ZHANG; Tefang CHEN

    2004-01-01

    Optimal trajectory planning for robot manipulators plays an important role in implementing the high productivity for robots.The performance indexes used in optimal trajectory planning are classified into two main categories:optimum traveling time and optimum mechanical energy of the actuators.The current trajectory planning algorithms are designed based on one of the above two performance indexes.So far,there have been few planning algorithms designed to satisfy two performance indexes simultaneously.On the other hand,some deficiencies arise in the existing integrated optimization algorithms of trajectory planning.In order to overcome those deficiencies,the integrated optimization algorithms of trajectory planning are presented based on the complete analysis for trajectory planning of robot manipulators.In the algorithm,two object functions are designed based on the specific weight coefficient method and "ideal point" strategy.Moreover,based on the features of optimization problem,the intensified evolutionary programming is proposed to solve the corresponding optimization model.Especially,for the Stanford Robot,the high-quality solutions are found at a lower cost.

  14. Deployable space manipulator commanded by means of visual-based guidance and navigation

    Science.gov (United States)

    Sabatini, Marco; Monti, Riccardo; Gasbarri, Paolo; Palmerini, Giovanni

    2013-02-01

    On orbit maneuvering of flexible space manipulators requires a special caution. In fact the task of reaching the desired configuration, and at the same time safely preserving the structure integrity and not perturbing the overall spacecraft attitude, is complicated by the extreme flexibility of the structure itself. For studying this problem, an experimental test bed is designed and realized at the Guidance and Navigation Laboratory at La Sapienza, University of Rome. In this paper, visual based techniques are considered as a valid option for the dual purpose of evaluating the control signals and monitoring the flexible behavior of the controlled structure. In fact the joint motors are controlled in order to reach a desired target taking the image of the target as acquired by a mobile camera mounted on the end effector of the manipulator, into account. The Image Based Visual Servoing is introduced together with the simple adaptive algorithm used for processing the acquired images. With respect to a more traditional terrestrial visual servoing, a control system based on a moving camera (a typical configuration in space applications) is particularly sensitive to the flexible vibrations of the arm links. In fact in the closed loop control scheme, an oscillating movement of the camera influences the image processing, which in turn influences control actions. Instability could arise if the flexible dynamics is not separated from the rigid motion. This paper shows that it is possible to evaluate the elastic properties of the complex multibody manipulator (flexibility of the link, elastic behavior of the joints, effects of nonstructural masses) thanks to the analysis of the image acquired.

  15. Force/torque and tactile sensors for sensor-based manipulator control

    Science.gov (United States)

    Vanbrussel, H.; Belieen, H.; Bao, Chao-Ying

    1989-01-01

    The autonomy of manipulators, in space and in industrial environments, can be dramatically enhanced by the use of force/torque and tactile sensors. The development and future use of a six-component force/torque sensor for the Hermes Robot Arm (HERA) Basic End-Effector (BEE) is discussed. Then a multifunctional gripper system based on tactile sensors is described. The basic transducing element of the sensor is a sheet of pressure-sensitive polymer. Tactile image processing algorithms for slip detection, object position estimation, and object recognition are described.

  16. Learning control system design based on 2-D theory - An application to parallel link manipulator

    Science.gov (United States)

    Geng, Z.; Carroll, R. L.; Lee, J. D.; Haynes, L. H.

    1990-01-01

    An approach to iterative learning control system design based on two-dimensional system theory is presented. A two-dimensional model for the iterative learning control system which reveals the connections between learning control systems and two-dimensional system theory is established. A learning control algorithm is proposed, and the convergence of learning using this algorithm is guaranteed by two-dimensional stability. The learning algorithm is applied successfully to the trajectory tracking control problem for a parallel link robot manipulator. The excellent performance of this learning algorithm is demonstrated by the computer simulation results.

  17. Study of Web-based integration of pneumatic manipulator and its vision positioning

    Institute of Scientific and Technical Information of China (English)

    YANG Yuan-zhao; WU Chuan-yu; HU Xu-dong

    2005-01-01

    Pneumatic driven system is widely used in industrial automation, mainly for relatively simple tasks with open-loop control. Because of the pneumatic system's compressibility and few stop positions, it was considered hard to control in a precise motion control system. With the help of newly developed pneumatic servo control technology, using servo-pneumatic positioning controller now is just as easy as using electro-servo system. This article discusses Web-based servo-pneumatic manipulator control and object recognition and positioning. The authors built a three-degrees-of-freedom (3 DOF) pneumatic manipulator with a servo-pneumatic closed-loop control system and machine vision system in their lab. Web-based tele-operation was a basic ability in this experimental system. After installing a CCD camera, video capture card, and related software developed by the authors, the robot could recognize the user specified object through the Web page and find its position. The remote user could command the robot to move to the position and to grab the object. The critical issues of Web-based control are to integrate hybrid open-architecture mechatronic system through the Web and develop a software language environment characterized by the script.The authors' experiment showed that pneumatic devices could serve as accurate position control and be controlled through the Web.

  18. Simple Ontology of Manipulation Actions based on Hand-Object Relations

    DEFF Research Database (Denmark)

    Wörgötter, Florentin; Aksoy, E. E.; Krüger, Norbert;

    2013-01-01

    and time. For this we use as temporal anchor points those moments where two objects (or hand and object) touch or un-touch each other during a manipulation. We show that by this one can define a relatively small tree-like manipulation ontology. We find less than 30 fundamental manipulations. The temporal...

  19. Neuroendocrine-Based Cooperative Intelligent Control System for Multiobjective Integrated Control of a Parallel Manipulator

    Directory of Open Access Journals (Sweden)

    Chongbin Guo

    2012-01-01

    Full Text Available This paper presents a novel multiloop and Multi-objective cooperative intelligent control system (MMCICS used to improve the performance of position, velocity and acceleration integrated control on a complex multichannel plant. Based on regulation mechanism of the neuroendocrine system (NES, a bioinspired motion control approach has been used in the MMCICS which includes four cooperative units. The planning unit outputs the desired signals. The selection unit chooses the real-time dominant control mode. The coordination unit uses the velocity Jacobian matrix to regulate the cooperative control signals. The execution unit achieves the ultimate task based on sub-channel controllers with the proposed hormone regulation self-adaptive Modules (HRSMs. Parameter tuning is given to facilitate the MMCICS implementation. The MMCICS is applied to an actual 2-DOF redundant parallel manipulator where the feasibility of the new control system is demonstrated. The MMCICS keeps its subchannels interacting harmoniously and systematically. Therefore, the plant has fast response, smooth velocity, accurate position, strong self-adaptability, and high stability. The HRSM improves the control performance of the local controllers and the global system as well, especially for manipulators running at high velocities and accelerations.

  20. Data Fusion Based on Optical Technology for Observation of Human Manipulation

    Science.gov (United States)

    Falco, Pietro; De Maria, Giuseppe; Natale, Ciro; Pirozzi, Salvatore

    2012-01-01

    The adoption of human observation is becoming more and more frequent within imitation learning and programming by demonstration approaches (PbD) to robot programming. For robotic systems equipped with anthropomorphic hands, the observation phase is very challenging and no ultimate solution exists. This work proposes a novel mechatronic approach to the observation of human hand motion during manipulation tasks. The strategy is based on the combined use of an optical motion capture system and a low-cost data glove equipped with novel joint angle sensors, based on optoelectronic technology. The combination of the two information sources is obtained through a sensor fusion algorithm based on the extended Kalman filter (EKF) suitably modified to tackle the problem of marker occlusions, typical of optical motion capture systems. This approach requires a kinematic model of the human hand. Another key contribution of this work is a new method to calibrate this model.

  1. A hybrid biogeography-based optimization method for the inverse kinematics problem of an 8-DOF redundant humanoid manipulator

    Institute of Scientific and Technical Information of China (English)

    Zi-wu REN; Zhen-hua WANG; Li-ning SUN

    2015-01-01

    The redundant humanoid manipulator has characteristics of multiple degrees of freedom and complex joint structure, and it is not easy to obtain its inverse kinematics solution. The inverse kinematics problem of a humanoid manipulator can be formulated as an equivalent minimization problem, and thus it can be solved using some numerical optimization methods. Biogeography-based optimization (BBO) is a new biogeography inspired optimization algorithm, and it can be adopted to solve the inverse kinematics problem of a humanoid manipulator. The standard BBO algorithm that uses traditional migration and mutation operators suffers from slow convergence and prematurity. A hybrid biogeography-based optimization (HBBO) algorithm, which is based on BBO and differential evolution (DE), is presented. In this hybrid algorithm, new habitats in the ecosystem are produced through a hybrid migration operator, that is, the BBO migration strategy and DE/best/1/bin differential strategy, to alleviate slow convergence at the later evolution stage of the algorithm. In addition, a Gaussian mutation operator is adopted to enhance the exploration ability and improve the diversity of the population. Based on these, an 8-DOF (degree of freedom) redundant humanoid manipulator is employed as an example. The end-effector error (position and orientation) and the‘away limitation level’ value of the 8-DOF humanoid manipulator constitute the fi tness function of HBBO. The proposed HBBO algorithm has been used to solve the inverse kinematics problem of the 8-DOF redundant humanoid manipulator. Numerical simulation results demonstrate the effectiveness of this method.

  2. Fuzzy Saturated Output Feedback Tracking Control for Robot Manipulators: A Singular Perturbation Theory Based Approach

    Directory of Open Access Journals (Sweden)

    Huashan Liu

    2011-09-01

    Full Text Available To deal with the problem of the output feedback tracking (OFT control with bounded torque inputs of robot manipulators, we propose a generalized fuzzy saturated OFT controller based on singular perturbation theory. First, considering the fact that the output toque of joint actuators is limited, a general expression for a class of saturation functions is given to be applied in the control law. Second, to carry out the whole closed‐loop control with only position measurements, linear and nonlinear filters are optionally involved to generate a pseudo signal to surrogate the actual velocity tracking error. As a third contribution, a fuzzy regulator is added to obtain a self‐tuning performance in tackling the disturbances. Moreover, an explicit but strict stability proof of the system based on the stability theory of singularly perturbed systems is presented. Finally, numerical simulations on several sample controllers are implemented to verify the effectiveness of the proposed approach.

  3. Fuzzy force control of constrained robot manipulators based on impedance model in an unknown environment

    Institute of Scientific and Technical Information of China (English)

    LIU Hongyi; WANG Lei; WANG Fei

    2007-01-01

    To precisely implement the force control of robot manipulators in an unknown environment,a control strategy based on fuzzy prediction of the reference trajectory in the impedance model is developed.The force tracking experiments are executed in an open-architecture control system with different tracking velocities,different desired forces,different contact stiffnesses and different surface figurations.The corresponding force control results are compared and analyzed.The influences of unknown parameters of the environment on the contact force are analyzed based on experimental data,and the tunings of predictive scale factors are illustrated.The experimental results show that the desired trajectory in the impedance model is predicted exactly and rapidly in the cases that the contact surface is unknown,the contact stiffness changes,and the fuzzy force control algorithm has high adaptability to the unknown environment.

  4. Introduction to Gene Editing and Manipulation Using CRISPR/Cas9 Technology.

    Science.gov (United States)

    Newman, Martin; Ausubel, Frederick M

    2016-01-01

    Until very recently, the prospect of introducing mutations or exogenous DNA sequences at precise locations in the genomes of plants and animals was difficult, if not impossible. This rapidly changed with the demonstration that the type II CRISPR-Cas complex, a bacterial anti-viral surveillance system, could be engineered into a simple and robust platform for introducing double-stranded DNA breaks at nearly any position of plant and animal genomes. The prospect of efficiently creating tailored changes to a gene of interest is revolutionizing biomedical research, allowing exciting new questions to be asked. This overview introduces CRISPR-Cas technology as a tool for molecular biology and briefly discusses the advantages of this method over earlier techniques, as well as unique opportunities to create new avenues of research. © 2016 by John Wiley & Sons, Inc. PMID:27366890

  5. Micro magnetofluidics: droplet manipulation of double emulsions based on paramagnetic ionic liquids.

    Science.gov (United States)

    Misuk, Viktor; Mai, Andreas; Giannopoulos, Konstantinos; Alobaid, Falah; Epple, Bernd; Loewe, Holger

    2013-12-01

    The ability to control and manipulate discrete fluid droplets by magnetic fields offers new opportunities in microfluidics. A surfactant-free and easy to realize technique for the continuous generation of double emulsion droplets, composed of an organic solvent and a paramagnetic ionic liquid, is applied. The inner phase of the emulsion droplet consists of imidazolium-based ionic liquids with either iron, manganese, nickel or dysprosium containing anions which provide paramagnetic behaviour. The double emulsion droplets are dispersed in a continuous phase of FC-40. All substances - the organic phase, the paramagnetic ionic liquid and the continuous phase -are immiscible. The magnetic properties of ionic liquids allow, through the influence of external magnetic fields, the manipulation of individual emulsion droplets such as capture and release, rotation and distortion. Arrays of magnets allow a coalescence of emulsion droplets and their subsequent mixing by flowing through an alternating permanent magnetic field. In addition, the double emulsion droplets can be split and reunified, or continuously separated into their original phases. PMID:24108233

  6. A Wearable-based and Markerless Human-manipulator Interface with Feedback Mechanism and Kalman Filters

    Directory of Open Access Journals (Sweden)

    Ping Zhang

    2015-11-01

    Full Text Available The objective of this paper is to develop a novel human-manipulator interface which incorporates wearable-based and markerless tracking to interact with the continuous movements of a human operator’s hand. Unlike traditional approaches, which usually include contacting devices or physical markers to track the human-limb movements, this interface enables registration of natural movement through a wireless wearable watch and a leap motion sensor. Due to sensor error and tracking failure, the measurements are not made with sufficient accuracy. Two Kalman filters are employed to compensate the noisy and incomplete measurements in real time. Furthermore, due to perceptive limitations and abnormal state signals, the operator is unable to achieve high precision and efficiency in robot manipulation; an adaptive multispace transformation method (AMT is therefore introduced, which serves as a secondary treatment. In addition, in order to allow two-way human-robot interaction, the proposed method provides a vibration feedback mechanism triggered by the wearable watch to call the operator’s attention to robot collision incidents or moments where the operator’s hand is in a transboundary state. This improves teleoperation.

  7. The manipulation of miRNA-gene regulatory networks by KSHV induces endothelial cell motility.

    Science.gov (United States)

    Wu, Yu-Hsuan; Hu, Tzu-Fang; Chen, Yu-Chieh; Tsai, Ya-Ni; Tsai, Yuan-Hau; Cheng, Cheng-Chung; Wang, Hsei-Wei

    2011-09-01

    miRNAs have emerged as master regulators of cancer-related events. miRNA dysregulation also occurs in Kaposi sarcoma (KS). Exploring the roles of KS-associated miRNAs should help to identify novel angiogenesis and lymphangiogenesis pathways. In the present study, we show that Kaposi sarcoma-associated herpesvirus (KSHV), the etiological agent of KS, induces global miRNA changes in lymphatic endothelial cells (LECs). Specifically, the miR-221/miR-222 cluster is down-regulated, whereas miR-31 is up-regulated. Both latent nuclear antigen (LANA) and Kaposin B repress the expression of the miR-221/miR-222 cluster, which results in an increase of endothelial cell (EC) migration. In contrast, miR-31 stimulates EC migration, so depletion of miR-31 in KSHV-transformed ECs reduces cell motility. Analysis of the putative miRNA targets among KSHV-affected genes showed that ETS2 and ETS1 are the downstream targets of miR-221 and miR-222, respectively. FAT4 is one of the direct targets of miR-31. Overexpression of ETS1 or ETS2 alone is sufficient to induce EC migration, whereas a reduction in FAT4 enhances EC motility. Our results show that KSHV regulates multiple miRNA-mRNA networks to enhance EC motility, which eventually contributes to KS progression by promoting the spread of malignant KS progenitor cells. Targeting KSHV-regulated miRNAs or genes might allow the development of novel therapeutic strategies that induce angiogenesis or allow the treatment of pathogenic (lymph)angiogenesis. PMID:21715310

  8. Vibrating Manipulation

    Institute of Scientific and Technical Information of China (English)

    SHEN Guo-quan; CUI Yi-jun

    2003-01-01

    @@ As a manipulation with unique therapeutic effect in TCM Tuina manipulations, Vibrating manipulation has significantly stronger effection on viscera, blood vessel, smooth muscle and gland secretion than other Tuina manipulations and it is mainly used in internal medicine, gynecology and miscellaneous diseases.

  9. Polymerase chain reaction-based gene removal from plasmids

    Directory of Open Access Journals (Sweden)

    Vishnu Vardhan Krishnamurthy

    2015-09-01

    Full Text Available This data article contains supplementary figures and methods to the research article entitled, “Multiplex gene removal by two-step polymerase chain reactions” (Krishnamurthy et al., Anal. Biochem., 2015, doi:http://dx.doi.org/10.1016/j.ab.2015.03.033, which presents a restriction-enzyme free method to remove multiple DNA segments from plasmids. Restriction-free cloning methods have dramatically improved the flexibility and speed of genetic manipulation compared to conventional assays based on restriction enzyme digestion (Lale and Valla, 2014. DNA Cloning and Assembly Methods, vol. 1116. Here, we show the basic scheme and characterize the success rate for single and multiplex gene removal from plasmids. In addition, we optimize experimental conditions, including the amount of template, multiple primers mixing, and buffers for DpnI treatment, used in the one-pot reaction for multiplex gene removal.

  10. Modelling, Simulation and Testing of a Reconfigurable Cable-Based Parallel Manipulator as Motion Aiding System

    Directory of Open Access Journals (Sweden)

    Gianni Castelli

    2010-01-01

    Full Text Available This paper presents results on the modelling, simulation and experimental tests of a cable-based parallel manipulator to be used as an aiding or guiding system for people with motion disabilities. There is a high level of motivation for people with a motion disability or the elderly to perform basic daily-living activities independently. Therefore, it is of great interest to design and implement safe and reliable motion assisting and guiding devices that are able to help end-users. In general, a robot for a medical application should be able to interact with a patient in safety conditions, i.e. it must not damage people or surroundings; it must be designed to guarantee high accuracy and low acceleration during the operation. Furthermore, it should not be too bulky and it should exert limited wrenches after close interaction with people. It can be advisable to have a portable system which can be easily brought into and assembled in a hospital or a domestic environment. Cable-based robotic structures can fulfil those requirements because of their main characteristics that make them light and intrinsically safe. In this paper, a reconfigurable four-cable-based parallel manipulator has been proposed as a motion assisting and guiding device to help people to accomplish a number of tasks, such as an aiding or guiding system to move the upper and lower limbs or the whole body. Modelling and simulation are presented in the ADAMS environment. Moreover, experimental tests are reported as based on an available laboratory prototype.

  11. Dynamic Manipulability of 3-RRR Planar Manipulator

    Science.gov (United States)

    Al-Dois, H. A.; Jha, A. K.; Mishra, R. B.

    2012-07-01

    In this paper a simulation study is proposed to study the factors influencing the dynamic manipulability of 3-RRR planar manipulator with and without payload. Different combinations of robot parameters are examined using design of experiment technique while performing variety of tasks. The kinematic and dynamic models are derived symbolically and used to simulate the dynamic performance of 3-RRR planar manipulator while following different trajectories. Finally, the results generated from the simulation of various parameter combinations are analyzed using analysis of variance and discussed to include the optimization of robot's performance based on the dynamic manipulability measure.

  12. Viral vector-based reversible neuronal inactivation and behavioral manipulation in the macaque monkey

    Directory of Open Access Journals (Sweden)

    Kristina Juliane Nielsen

    2012-06-01

    Full Text Available Viral vectors are promising tools for the dissection of neural circuits. In principle, they can manipulate neurons at a level of specificity not otherwise achievable. While many studies have used viral vector-based approaches in the rodent brain, only a few have employed this technique in the non-human primate, despite the importance of this animal model for neuroscience research. Here, we report for the first time that a viral vector-based approach can be used to manipulate a monkey’s behavior in a task. For this purpose, we used the allatostatin receptor/allatostatin (AlstR/AL system, which has previously been shown to allow inactivation of neurons in vivo. The AlstR was expressed in neurons in monkey V1 by injection of an AAV1 vector. Two monkeys were trained in a detection task, in which they had to make a saccade to a faint peripheral target. Injection of AL caused a retinotopic deficit in the detection task in one monkey. Specifically, the monkey showed marked impairment for detection targets placed at the visual field location represented at the virus injection site, but not for targets shown elsewhere. We confirmed that these deficits indeed were due to the interaction of AlstR and AL by injecting saline, or AL at a V1 location without AlstR expression. Post-mortem histology confirmed AlstR expression in this monkey. We failed to replicate the behavioral results in a second monkey, as AL injection did not impair the second monkey’s performance in the detection task. However, post-mortem histology revealed a very low level of AlstR expression in this monkey. Our results demonstrate that viral vector-based approaches can produce effects strong enough to influence a monkey’s performance in a behavioral task, supporting the further development of this approach for studying how neuronal circuits control complex behaviors in non-human primates.

  13. Multipurpose 10 in. manipulator-based optical telescope for Omega and the Trident laser facilities

    International Nuclear Information System (INIS)

    We have recently designed and are building a telescope which acts as an imaging light collector relaying the image to an optical table for experiment dependent analysis and recording. The expected primary use of this instrument is a streaked optical pyrometer for witness plate measurements of the hohlraum drive temperature. The telescope is based on the University of Rochester close-quote s 10 in. manipulator (TIM) which allows compatibility between Omega, Trident, and the NIF lasers. The optics capture a f/7 cone of light, have a field of view of 6 mm, have a spatial resolution of 5 - 7 μm per line pair at the object plane, and are optimized for operation at 280 nm. The image is at a magnification of 11.7x, which is convenient for many experiments, but can be changed using additional optics that reside outside the TIM. copyright 1999 American Institute of Physics

  14. Microparticles manipulation and enhancement of their separation in pinched flow fractionation by insulator-based dielectrophoresis.

    Science.gov (United States)

    Khashei, Hesamodin; Latifi, Hamid; Seresht, Mohsen Jamshidi; Ghasemi, Amir Hossein Baradaran

    2016-03-01

    The separation and manipulation of microparticles in lab on a chip devices have importance in point of care diagnostic tools and analytical applications. The separation and sorting of particles from biological and clinical samples can be performed using active and passive techniques. In passive techniques, no external force is applied while in active techniques by applying external force (e.g. electrical), higher separation efficiency is obtained. In this article, passive (pinched flow fractionation) and active (insulator-based dielectrophoresis) methods were combined to increase the separation efficiency at lower voltages. First by simulation, appropriate values of geometry and applied voltages for better focusing, separation, and lower Joule heating were obtained. Separation of 1.5 and 6 μm polystyrene microparticles was experimentally obtained at optimized geometry and low total applied voltage (25 V). Also, the trajectory of 1.5 μm microparticles was controlled by adjusting the total applied voltage. PMID:26685118

  15. Tailored-waveguide based photonic chip for manipulating an array of single neutral atoms.

    Science.gov (United States)

    Ke, Min; Zhou, Feng; Li, Xiao; Wang, Jin; Zhan, Mingsheng

    2016-05-01

    We propose a tailored-waveguide based photonic chip with the functions of trapping, coherently manipulating, detecting and individually addressing an array of single neutral atoms. Such photonic chip consists of an array of independent functional units spaced by a few micrometers, each of which is comprised of one silica-on-silicon optical waveguide and one phase Fresnel microlens etched in the middle of the output interface of the optical waveguide. We fabricated a number of photonic chips with 7 functional units and measured optical characteristics of these chips. We further propose feasible schemes to realize the functions of such photonic chip. The photonic chip is stable, scalable and can be combined with other integrated devices, such as atom chips, and can be used in the future hybrid quantum system and photonic quantum devices. PMID:27137532

  16. When action turns into words. Activation of motor-based knowledge during categorization of manipulable objects

    DEFF Research Database (Denmark)

    Gerlach, Christian; Law, Ian; Paulson, Olaf B

    2002-01-01

    utilization (action knowledge). Here we show that the left ventral premotor cortex is activated during categorization of "both" fruit/vegetables and articles of clothing, relative to animals and nonmanipulable man-made objects. This observation suggests that action knowledge may not be important for the...... processing of man-made objects per se, but rather for the processing of manipulable objects in general, whether natural or man-made. These findings both support psycholinguistic theories suggesting that certain lexical categories may evolve from, and the act of categorization rely upon, motor-based knowledge...... of action equivalency, and have important implications for theories of category specificity. Thus, the finding that the processing of vegetables/fruit and articles of clothing give rise to similar activation is difficult to account for should knowledge representations in the brain be truly...

  17. A gas bubble-based parallel micro manipulator : conceptual design and kinematics model.

    OpenAIRE

    Dong, Wei; Gauthier, Michaël; Lenders, Cyrille; Lambert, Pierre

    2012-01-01

    The parallel mechanism has become an alternative solution when micro manipulators are demanded in the fields of micro manipulation and micro assembly. In this paper, a three-Degree-Of-Freedom (3-DOF) parallel micro manipulator is presented, which is directly driven by three micro gas bubbles. Since the micro gas bubbles are generated and maintained due to the surface tension between the gas and liquid media, the proposed novel system can be used in the liquid environment which allows for rota...

  18. Nutrient depletion as a key factor for manipulating gene expression and product formation in different branches of the flavonoid pathway.

    Science.gov (United States)

    Lillo, Cathrine; Lea, Unni S; Ruoff, Peter

    2008-05-01

    The content of flavonoids increases in response to nitrogen and phosphorus depletion in plants. Manipulation of these macronutrients may therefore be used to control the levels of desirable compounds and improve plant quality. Key enzymes in the shikimate pathway, which feeds precursors into the flavonoid pathway, are regulated post-translationally by feedback from aromatic amino acids, and possibly by redox control through photosynthesis. Use of microarrays for global transcript analysis in Arabidopsis has revealed that transcript levels are less influenced by mineral nutrients in the shikimate pathway compared with the flavonoid pathway. The responses in the shikimate pathway appear complex, whereas in the flavonoid pathway, a single gene often responds similarly to mineral depletion, high light intensity and sucrose. MYB [production of anthocyanin pigment 1 (PAP1)/production of anthocyanin pigment 2 (PAP2)] and bHLH [GLABRA3 (GL3)] transcription factors are important for the nutrient depletion response. PAP1/2 stimulate gross activation of the flavonoid pathway, and different investigations support merging signal transduction chains for various abiotic treatments on PAP1/2. Flavonol synthase is not part of the PAP1/2 regulon, and expression is mainly enhanced by high light intensity and sucrose, not mineral depletion. Nevertheless, both cyanidin and flavonol derivatives increase in response to nitrogen depletion. Kaempferols are the dominating flavonols in Arabidopsis leaves under normal cultivation conditions, but quercetin accumulation can be triggered by nitrogen depletion in combination with other abiotic factors. PMID:18031469

  19. MEMS-based clamp with a passive hold function for precision position retaining of micro manipulators

    International Nuclear Information System (INIS)

    In this paper the design, modeling and fabrication of a precision MEMS-based clamp with a relatively large clamping force are presented. The purpose of the clamp is to mechanically fix a six-degree-of-freedom (DOF) MEMS-based sample manipulator (Brouwer et al J. Int. Soc. Precis. Eng. Nanotechnol. submitted) once the sample has been positioned in all DOFs. The clamping force is generated by a rotational electrostatic comb-drive actuator and can be latched passively by a parallel plate type electrostatically driven locking device. The clamp design is based on the principles of exact constraint design, resulting in a high actuation compliance (flexibility) combined with a high suspension stiffness. Therefore, a relatively large blocking force of 1.4 mN in relation to the used area of 1.8 mm2 is obtained. The fabrication is based on silicon bulk micromachining technology and combines a high-aspect-ratio deep reactive ion etching (DRIE), conformal deposition of low-pressure chemical vapor deposition (LPCVD) silicon nitride and an anisotropic potassium hydroxide (KOH) backside etching technology. Special attention is given to void reduction of SixNy trench isolation and reduction of heating phenomena during front-side release etching. Guidelines are given for the applied process. Measurements showed that the clamp was able to fix, hold and release a test actuator. The dynamic behavior was in good agreement with the modal analysis

  20. Cable-based parallel manipulator for rehabilitation of shoulder and elbow movements.

    Science.gov (United States)

    Nunes, Wilgo Moreira; Rodrigues, Lucas Antônio Oliveira; Oliveira, Lucas Paiva; Ribeiro, José Francisco; Carvalho, João Carlos Mendes; Gonçalves, Rogério Sales

    2011-01-01

    In this paper a cable-based system is presented for rehabilitation of the shoulder and elbow movements. Cable-based manipulators have very good kinematic and dynamic characteristics, and they also show other properties such as: transportability and low-cost construction, which make them also suitable for medical applications and rehabilitation. The general robotics structure consists of four cables that allow the movement of vertical flexion-extension, abduction-adduction and horizontal flexion-extension with different limits of movement and speed of the shoulder. The structure can also perform the elbow movements of the flexion-extension. The development of this robotic device is justified by the large number of people with upper limb problems. These problems are due of stroke, polio, arthritis, recovery after accidents or trauma and can be applied to movements of physical therapy. The kinematics model of cable-based parallel robots is obtained similarly to the model obtained from traditional parallel structures. The graphical simulations of the cable-based parallel structure for rehabilitation of the movements of the human arm are presented showing the viability of the proposed structure. Finally preliminary experimental tests are presented. PMID:22275699

  1. Experimental investigations of sensor-based surface following tasks by a mobile manipulator

    Energy Technology Data Exchange (ETDEWEB)

    Reister, D.B.; Unseren, M.A.; Baker, J.E.; Pin, F.G.

    1993-10-01

    This paper discusses experimental investigations of the feasibility and requirements of simultaneous external-sensor-based-control of the wheeled platform and the manipulator of a mobile robot. The experiments involve 3-D arbitrary surface following by the manipulator while the platform moves along a predefined trajectory. A variety of concave and convex surfaces were used in the experiments, during which target and measured values of the platform and arm positions and orientations, together with the surface absolute location and normal estimates, were logged at 10 Hz. For all experiments, the data logs showed significant noise, at high frequency, in the calculated surface normal values despite smooth tracking of their target values by the arm and the platform, with typical closed loop delays between target and achieved values of the order of 100 msec. This high-frequency noise in the calculated values is conjectured to result mainly from the arm`s transmission cables compliance and backlash in the spherical wrist gears. On the other hand, the end-effector distance to the surface showed some low frequency errors of the order of {plus_minus}20%The two major sources of these low frequency errors appeared to reside respectively in the low values of the velocity bound and gain parameters utilized to filter the high frequency noise in the calculated normal values prior to using them as input to the arm control, and in the rolling contact of the platform`s rubber-coated wheels on the ground where significant errors in the platform`s positions and orientations can accumulate.

  2. Rod-based Fabrication of Customizable Soft Robotic Pneumatic Gripper Devices for Delicate Tissue Manipulation.

    Science.gov (United States)

    Low, Jin-Huat; Yeow, Chen-Hua

    2016-01-01

    Soft compliant gripping is essential in delicate surgical manipulation for minimizing the risk of tissue grip damage caused by high stress concentrations at the point of contact. It can be achieved by complementing traditional rigid grippers with soft robotic pneumatic gripper devices. This manuscript describes a rod-based approach that combined both 3D-printing and a modified soft lithography technique to fabricate the soft pneumatic gripper. In brief, the pneumatic featureless mold with chamber component is 3D-printed and the rods were used to create the pneumatic channels that connect to the chamber. This protocol eliminates the risk of channels occluding during the sealing process and the need for external air source or related control circuit. The soft gripper consists of a chamber filled with air, and one or more gripper arms with a pneumatic channel in each arm connected to the chamber. The pneumatic channel is positioned close to the outer wall to create different stiffness in the gripper arm. Upon compression of the chamber which generates pressure on the pneumatic channel, the gripper arm will bend inward to form a close grip posture because the outer wall area is more compliant. The soft gripper can be inserted into a 3D-printed handling tool with two different control modes for chamber compression: manual gripper mode with a movable piston, and robotic gripper mode with a linear actuator. The double-arm gripper with two actuatable arms was able to pick up objects of sizes up to 2 mm and yet generate lower compressive forces as compared to elastomer-coated and non-coated rigid grippers. The feasibility of having other designs, such as single-arm or hook gripper, was also demonstrated, which further highlighted the customizability of the soft gripper device, and it's potential to be used in delicate surgical manipulation to reduce the risk of tissue grip damage. PMID:27584722

  3. 75 FR 68560 - Prohibition Against Fraud, Manipulation, and Deception in Connection With Security-Based Swaps

    Science.gov (United States)

    2010-11-08

    ... Act Release No. 62717 (Aug. 13, 2010), 75 FR 51429 (Aug. 20, 2010). \\13\\ In other words, in contrast... COMMISSION 17 CFR Part 240 RIN 3235-AK77 Prohibition Against Fraud, Manipulation, and Deception in Connection... Securities Exchange Act of 1934 (``Exchange Act'') that is intended to prevent fraud, manipulation,...

  4. Robust motion control of oscillatory-base manipulators h∞-control and sliding-mode-control-based approaches

    CERN Document Server

    Toda, Masayoshi

    2016-01-01

    This book provides readers with alternative robust approaches to control design for an important class of systems characteristically associated with ocean-going vessels and structures. These systems, which include crane vessels, on-board cranes, radar gimbals, and a conductivity temperature and depth winch, are modelled as manipulators with oscillating bases. One design approach is based on the H-infinity control framework exploiting an effective combination of PD control, an extended matrix polytope and a robust stability analysis method with a state-dependent coefficient form. The other is based on sliding-mode control using some novel nonlinear sliding surfaces. The model demonstrates how successful motion control can be achieved by suppressing base oscillations and in the presence of uncertainties. This is important not only for ocean engineering systems in which the problems addressed here originate but more generally as a benchmark platform for robust motion control with disturbance rejection. Researche...

  5. Research on critical technology of micro/nano bioparticles manipulation platform based on light-induced dielectrophoresis

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    On the basis of the research on the status and problems of micro/nano bio-particles manipulation using dielectrophoresis, the theoretical basis and the model simulation of micro/nano bio-particles manipu-lation using light-induced dielectrophoresis were discussed. The space distribution of electric field and dielectrophoresis forces in different heights were also obtained. On this basis, the core component of the micro manipulation system, that is, photoconductive layer of the chip, was completed in the mate-rial selection, fabricating process and performance analysis testing. Then the voltage drop of the sus-pension and the effective voltage frequency spectrum were obtained. Finally, by combining the machine vision detection with real-time tracking system, the micro/nano bio-particles manipulation platform based on the light-induced dielectrophoreisis was established, and then the manipulations for micro/nano bio-particles, such as quick collection, transport, separation, were implemented. This provided a basis for rapid, accurate, and low-cost detection of serious diseases based on the micro-fluidic biochip and early diagnosis.

  6. Manipulative-semantic complications of utterance syntax based on the British parliamentary speeches

    Directory of Open Access Journals (Sweden)

    Zyubina Irina Anatolevna

    2015-12-01

    Full Text Available The article studies the possible impact on the addressee by manipulating. The analysis was applied to the manipulative strategy of the syntax complexity by the targeted and motivated selection of the best linguistic units of semantic pragmatic content. The relevance of the parliamentary discourse study is dictated by the need to search the best ways of speech influence on the audience for the parliament members, on the one hand, and the need to understand the real intentions of the audience and latent methods of language manipulation, on the other hand. The purpose of this article is to consider and identify the peculiarities of the mechanism of linguistic manipulation in the parliamentary speeches of the UK at the syntactic level. The study analyses the texts of the parliamentary political discourse of Britain on the issues related to the situation in the Ukraine in 2015. As a result, it was found out that the most frequent are the following means of manipulation: repetition inside a statement, antithesis, anaphora, syntactic parallelism, ellipse, inversion, rhetorical question, graduation, anadiplosis and epiphora. The study of such a mechanism of manipulation with the help of linguistic means and understanding its laws are important because they help to avoid the psycho-technical effect of speech manipulation, aggression or even speech abuse.

  7. Observation and Manipulation of a Capillary Jet in a Centrifuge-Based Droplet Shooting Device

    Directory of Open Access Journals (Sweden)

    Kazuki Maeda

    2015-10-01

    Full Text Available We report observation and manipulation of a capillary jet under ultra-high centrifugal gravity in a proposed capillary-based fluidic device for the synthesis of microparticles in a centrifugal tube called Centrifuge-Based Droplet Shooting Device (CDSD. Using a high-speed camera, we directly observed the dripping to jetting transition of a viscous capillary jet of water and Sodium alginate solution generated from a glass capillary-orifice of a diameter of O (100 m under centrifugal gravity ranging from 190 to 450 g. A non-dimensional analysis shows that the mechanism of the dripping-jetting transition in the CDSD may follow that previously reported for a dripping faucet under standard gravity. We also fabricated calcium alginate microparticles by gelating droplets of sodium alginate solution obtained in the break-up of the capillary jet in the jetting regime and demonstrated fabrication of microbeads-on-a-string structures. We confirmed that the jetting regime of the capillary jet could be used to fabricate smaller particles than that of the dripping regime. The results show that the CDSD would be a more useful device to fabricate various polymeric structures and understand the physics of fluid jets under ultra-high gravity.

  8. An integrated micro-manipulation and biosensing platform built in glass-based LTPS TFT technology

    International Nuclear Information System (INIS)

    The glass-based low-temperature polycrystalline-silicon (LTPS) thin-film transistor (TFT) process, widely known for making liquid crystal displays, is utilized in this work to realize a fully integrated, microbead-based micro-manipulation and biosensing platform. The operation utilizes arrays of microelectrodes made of transparent iridium tin oxide (ITO) to move the immobilized polystyrene microbeads to the sensor surface by dielectrophoresis (DEP). Detection of remaining microbeads after a specific antigen/antibody reaction is accomplished by photo-detectors under the transparent electrodes. It was found that microbeads can be driven successfully by the 30 × 30 µm2 microelectrodes separated by 10 µm with no more than 6 Vp–p, which is compatible with the operating range of thin-film transistors. Microbeads immobilized with antimouse immunoglobulin (IgG) and prostate-specific antigen (PSA) antibody were successfully detected after specific binding, illustrating the potential of LTPS TFT microarrays for more versatile biosensing applications. (paper)

  9. Adaptive and robust algorithms and tests for visual-based navigation of a space robotic manipulator

    Science.gov (United States)

    Sabatini, Marco; Monti, Riccardo; Gasbarri, Paolo; Palmerini, Giovanni B.

    2013-02-01

    Optical navigation for guidance and control of robotic systems is a well-established technique from both theoretic and practical points of view. According to the positioning of the camera, the problem can be approached in two ways: the first one, "hand-in-eye", deals with a fixed camera, external to the robot, which allows to determine the position of the target object to be reached. The second one, "eye-in-hand", consists in a camera accommodated on the end-effector of the manipulator. Here, the target object position is not determined in an absolute reference frame, but with respect to the image plane of the mobile camera. In this paper, the algorithms and the test campaign applied to the case of the planar multibody manipulator developed in the Guidance and Navigation Lab at the University of Rome La Sapienza are reported with respect to the eye-in-hand case. In fact, being the space environment the target application for this research activity, it is quite difficult to imagine a fixed, non-floating camera in the case of an orbital grasping maneuver. The classic approach of Image Base Visual Servoing considers the evaluation of the control actions directly on the basis of the error between the current image of a feature and the image of the same feature in a final desired configuration. Both simulation and experimental tests show that such a classic approach can fail when navigation errors and actuation delays are included. Moreover, changing light conditions or the presence of unexpected obstacles can lead to a camera failure in target acquisition. In order to overcome these two problems, a Modified Image Based Visual Servoing algorithm and an Extended Kalman Filtering for feature position estimation are developed and applied. In particular, the filtering shows a quite good performance if target's depth information is supplied. A simple procedure for estimating initial target depth is therefore developed and tested. As a result of the application of all the

  10. Magnetic-Field-Assisted Fabrication and Manipulation of Nonspherical Polymer Particles in Ferrofluid-Based Droplet Microfluidics.

    Science.gov (United States)

    Zhu, Taotao; Cheng, Rui; Sheppard, Gareth R; Locklin, Jason; Mao, Leidong

    2015-08-11

    We report a novel magnetic-field-assisted method for the fabrication and manipulation of nonspherical polymer particles within a ferrofluid-based droplet microfluidic device. Shape control and chain assembly of droplets with tunable lengths have been achieved. PMID:26212067

  11. Grasping and manipulation of deformable objects based on internal force requirements

    Directory of Open Access Journals (Sweden)

    Sohil Garg

    2008-11-01

    Full Text Available In this paper an analysis of grasping and manipulation of deformable objects by a three finger robot hand has been carried out. It is proved that the required fingertip grasping forces and velocities vary with change in object size due to deformation. The variation of the internal force with the change in fingertip and object contact angle has been investigated in detail. From the results it is concluded that it is very difficult to manipulate an object if the finger contact angle is not between 30 o and 70 o, as the internal forces or velocities become very large outside this range. Hence even if the object is inside the work volume of the three fingers it would still not be possible to manipulate it. A simple control model is proposed which can control the grasping and manipulation of a deformable object. Experimental results are also presented to prove the proposed method.

  12. Synthesis of a spatial 3-RPS parallel manipulator based on physical constraints

    Indian Academy of Sciences (India)

    Nalluri Mohan Rao

    2010-12-01

    The range of motion of the moving platform of a spatial 3-RPS parallel manipulator will be greatly influenced by the physical constraints such as limits on the lengths of the limbs and the range of motion of the spherical joints. Therefore, while synthesizing the parallel manipulator, the physical constraints have to be considered. Synthesis of the manipulator involves determination of the architectural parameters of the manipulator so that a point on the moving platform passes through a prescribed set of positions in space. This paper presents a synthesis procedure that determines location and direction of revolute joints and location of spherical joints along with orientation of sockets of spherical joints, considering the physical constraints. The synthesis procedure is demonstrated through a numerical example.

  13. A giant magnetoresistance ring-sensor based microsystem for magnetic bead manipulation and detection

    KAUST Repository

    Gooneratne, Chinthaka P.

    2011-03-28

    In this paper a novel spin valvegiant magnetoresistance(GMR) ring-sensor integrated with a microstructure is proposed for concentrating, trapping, and detecting superparamagnetic beads (SPBs). Taking advantage of the fact that SPBs can be manipulated by an external magnetic field, a unique arrangement of conducting microrings is utilized to manipulate the SPBs toward the GMR sensing area in order to increase the reliability of detection. The microrings are arranged and activated in such a manner so as to enable the detection of minute concentrations of SPBs in a sample. Precise manipulation is achieved by applying current sequentially to the microrings. The fabricated ring-shaped GMR element is located underneath the innermost ring and has a magnetoresistance of approximately 5.9%. By the performed experiments it was shown that SPBs could be successfully manipulated toward the GMR sensing zone.

  14. Asymptotically-optimal path planning for manipulation using incremental sampling-based algorithms

    OpenAIRE

    Perez, Alejandro Tomas; Karaman, Sertac; Shkolnik, Alexander C.; Frazzoli, Emilio; Teller, Seth; Walter, Matthew R.

    2011-01-01

    A desirable property of path planning for robotic manipulation is the ability to identify solutions in a sufficiently short amount of time to be usable. This is particularly challenging for the manipulation problem due to the need to plan over high-dimensional configuration spaces and to perform computationally expensive collision checking procedures. Consequently, existing planners take steps to achieve desired solution times at the cost of low quality solutions. This paper presents a planni...

  15. Dielectrophoresis for Bioparticle Manipulation

    OpenAIRE

    Cheng Qian; Haibo Huang; Liguo Chen; Xiangpeng Li; Zunbiao Ge; Tao Chen; Zhan Yang; Lining Sun

    2014-01-01

    As an ideal method to manipulate biological particles, the dielectrophoresis (DEP) technique has been widely used in clinical diagnosis, disease treatment, drug development, immunoassays, cell sorting, etc. This review summarizes the research in the field of bioparticle manipulation based on DEP techniques. Firstly, the basic principle of DEP and its classical theories are introduced in brief; Secondly, a detailed introduction on the DEP technique used for bioparticle manipulation is presente...

  16. Graphene based spin-FET devices: Spin current manipulation through spatially modulated Rashba Field

    Science.gov (United States)

    Souza Diniz, Ginetom; Vernek, Edson; Macedo de Souza, Fabricio

    We have calculated the spin dependent conductance in a two-terminal device made of zigzag graphene nanoribbon in the presence of a spatially modulated Rashba spin-orbit coupling (SOC). The modulated Rashba SOC can be achieved by using local gates that generate strong localized electric fields perpendicular to the plane underneath. We have used the equilibrium surface Green's function technique in real space using tight-binding approximation in order to calculate the electronic transport. We demonstrate that by an appropriate architecture of the gate width, and tuning the strength and direction of the electric field in the gates is possible to effectively control the spin-charge current flow along the device. In addition, we also discuss the effect of uniaxial strain in the spin-resolved conductance profiles, which demonstrates to be an additional tool as an on-off electronic current flow switch. Our results suggest suitable application of graphene-based nanostructures in the spintronic field, using spatially modulated Rashba SOC, and uniaxial strains to effectively manipulate the spin-polarized current in nanoelectronic devices. Supported by CAPES, CNPq and FAPEMIG.

  17. Real Time Web-based Data Monitoring and Manipulation System to Improve Translational Research Quality

    Directory of Open Access Journals (Sweden)

    Matthew Nwokejizie Anyanwu, Venkateswara Ra Nagisetty, Emin Kuscu, Teeradache Viangteeravat

    2011-02-01

    Full Text Available The use of the internet technology and web browser capabilities of the internethas provided researchers/scientists with many advantages, which includes butnot limited to ease of access, platform independence of computer systems,relatively low cost of web access etc. Hence online collaboration like socialnetworks and information/data exchange among individuals and organizationscan now be done seamlessly. In practice, many investigators rely heavily ondifferent data modalities for studying and analyzing their research/study and alsofor producing quality reports. The lack of coherency and inconsistencies in datasets can dramatically reduce the quality of research data. Thus to prevent loss ofdata quality and value and provide the needed functionality of data, we haveproposed a novel approach as an ad-hoc component for data monitoring andmanipulation called RTWebDMM (Real-Time Web-based Data Monitoring andManipulation system to improve the quality of translational research data. TheRTWebDMM is proposed as an auditor, monitor, and explorer for improving theway in which investigators access and interact with the data sets in real-timeusing a web browser. The performance of the proposed approach was evaluatedwith different data sets from various studies. It is demonstrated that the approachyields very promising results for data quality improvement while leveraging on aweb-enabled environment.

  18. A single vector-based strategy for marker-less gene replacement in Synechocystis sp. PCC 6803

    OpenAIRE

    Viola, Stefania; Rühle, Thilo; Leister, Dario

    2014-01-01

    Background The cyanobacterium Synechocystis sp. PCC 6803 is widely used for research on photosynthesis and circadian rhythms, and also finds application in sustainable biotechnologies. Synechocystis is naturally transformable and undergoes homologous recombination, which enables the development of a variety of tools for genetic and genomic manipulations. To generate multiple gene deletions and/or replacements, marker-less manipulation methods based on counter-selection are generally employed....

  19. Thesaurus-based disambiguation of gene symbols

    Directory of Open Access Journals (Sweden)

    Wain Hester M

    2005-06-01

    Full Text Available Abstract Background Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck. Results We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data. The thesaurus comprises the information from five human genetic databases and MeSH. The extent of the homonym problem for human gene symbols is shown to be substantial (33% of the genes in our combined thesaurus had one or more ambiguous symbols, not only because one symbol can refer to multiple genes, but also because a gene symbol can have many non-gene meanings. A test set of 52,529 Medline abstracts, containing 690 ambiguous human gene symbols taken from OMIM, was automatically generated. Overall accuracy of the disambiguation algorithm was up to 92.7% on the test set. Conclusion The ambiguity of human gene symbols is substantial, not only because one symbol may denote multiple genes but particularly because many symbols have other, non-gene meanings. The proposed disambiguation approach resolves most ambiguities in our test set with high accuracy, including the important gene/not a gene decisions. The algorithm is fast and scalable, enabling gene-symbol disambiguation in massive text mining applications.

  20. Inverse kinematics of a heavy duty manipulator with 6-DOF based on dual quaternion

    Institute of Scientific and Technical Information of China (English)

    王恒升; 占德友; 黄平伦; 陈伟锋

    2015-01-01

    An iterative method is introduced successfully to solve the inverse kinematics of a 6-DOF manipulator of a tunnel drilling rig based on dual quaternion, which is difficult to get the solution by Denavit-Hartenberg (D-H) based methods. By the intuitive expression of dual quaternion to the orientation of rigid body, the coordinate frames assigned to each joint are established all in the same orientation, which does not need to use the D-H procedure. The compact and simple form of kinematic equations, consisting of position equations and orientation equations, is also the consequence of dual quaternion calculations. The iterative process is basically of two steps which are related to solving the position equations and orientation equations correspondingly. First, assume an initial value of the iterative variable; then, the position equations can be solved because of the reduced number of unknown variables in the position equations and the orientation equations can be solved by applying the solution from the position equations, which obtains an updated value for the iterative variable; finally, repeat the procedure by using the updated iterative variable to the position equations till the prescribed accuracy is obtained. The method proposed has a clear geometric meaning, and the algorithm is simple and direct. Simulation for 100 poses of the end frame shows that the average running time of inverse kinematics calculation for each demanded pose of end-effector is 7.2 ms on an ordinary laptop, which is good enough for practical use. The iteration counts 2−4 cycles generally, which is a quick convergence. The method proposed here has been successfully used in the project of automating a hydraulic rig.

  1. Micro-particle manipulation by single beam acoustic tweezers based on hydrothermal PZT thick film

    Directory of Open Access Journals (Sweden)

    Benpeng Zhu

    2016-03-01

    Full Text Available Single-beam acoustic tweezers (SBAT, used in laboratory-on-a-chip (LOC device has promising implications for an individual micro-particle contactless manipulation. In this study, a freestanding hydrothermal PZT thick film with excellent piezoelectric property (d33 = 270pC/N and kt = 0.51 was employed for SBAT applications and a press-focusing technology was introduced. The obtained SBAT, acting at an operational frequency of 50MHz, a low f-number (∼0.9, demonstrated the capability to trap and manipulate a micro-particle sized 10μm in the distilled water. These results suggest that such a device has great potential as a manipulator for a wide range of biomedical and chemical science applications.

  2. Intelligent control of an IPMC actuated manipulator using emotional learning-based controller

    Science.gov (United States)

    Shariati, Azadeh; Meghdari, Ali; Shariati, Parham

    2008-08-01

    In this research an intelligent emotional learning controller, Takagi- Sugeno- Kang (TSK) is applied to govern the dynamics of a novel Ionic-Polymer Metal Composite (IPMC) actuated manipulator. Ionic-Polymer Metal Composites are active actuators that show very large deformation in existence of low applied voltage. In this research, a new IPMC actuator is considered and applied to a 2-dof miniature manipulator. This manipulator is designed for miniature tasks. The control system consists of a set of neurofuzzy controller whose parameters are adapted according to the emotional learning rules, and a critic with task to assess the present situation resulted from the applied control action in terms of satisfactory achievement of the control goals and provides the emotional signal (the stress). The controller modifies its characteristics so that the critic's stress decreased.

  3. Obstacle avoidance planning of space manipulator end-effector based on improved ant colony algorithm.

    Science.gov (United States)

    Zhou, Dongsheng; Wang, Lan; Zhang, Qiang

    2016-01-01

    With the development of aerospace engineering, the space on-orbit servicing has been brought more attention to many scholars. Obstacle avoidance planning of space manipulator end-effector also attracts increasing attention. This problem is complex due to the existence of obstacles. Therefore, it is essential to avoid obstacles in order to improve planning of space manipulator end-effector. In this paper, we proposed an improved ant colony algorithm to solve this problem, which is effective and simple. Firstly, the models were established respectively, including the kinematic model of space manipulator and expression of valid path in space environment. Secondly, we described an improved ant colony algorithm in detail, which can avoid trapping into local optimum. The search strategy, transfer rules, and pheromone update methods were all adjusted. Finally, the improved ant colony algorithm was compared with the classic ant colony algorithm through the experiments. The simulation results verify the correctness and effectiveness of the proposed algorithm. PMID:27186473

  4. Minimum-acceleration Trajectory Optimization for Humanoid Manipulator Based on Differential Evolution

    Directory of Open Access Journals (Sweden)

    Ren Ziwu

    2016-04-01

    Full Text Available A humanoid manipulator produces significantly reactive forces against a humanoid body when it operates in a rapid and continuous reaction environment (e.g., playing baseball, ping-pong etc.. This not only disturbs the balance and stability of the humanoid robot, but also influences its operation precision. To solve this problem, a novel approach, which is able to generate a minimum-acceleration and continuous acceleration trajectory for the humanoid manipulator, is presented in this paper. By this method, the whole trajectory of humanoid manipulation is divided into two processes, i.e., the operation process and the return process. Moreover, the target operation point is considered as a particular point that should be passed through. As such, the trajectory of each process is described through a quartic polynomial in the joint space, after which the trajectory planning problem for the humanoid manipulator can be formulated as a global constrained optimization problem. In order to alleviate the reactive force, a fitness function that aims to minimize the maximum acceleration of each joint of the manipulator is defined, while differential evolution is employed to determine the joint accelerations of the target operation point. Thus, a trajectory with a minimum-acceleration and continuous acceleration profile is obtained, which can reduce the effect on the body and be favourable for the balance and stability of the humanoid robot to a certain extent. Finally, a humanoid robot with a 7-DOF manipulator for ping-pong playing is employed as an example. Simulation experiment results show the effectiveness of this method for the trajectory planning problem being studied.

  5. Cell Monitoring and Manipulation Systems (CMMSs based on Glass Cell-Culture Chips (GC3s

    Directory of Open Access Journals (Sweden)

    Sebastian M. Buehler

    2016-06-01

    Full Text Available We developed different types of glass cell-culture chips (GC3s for culturing cells for microscopic observation in open media-containing troughs or in microfluidic structures. Platinum sensor and manipulation structures were used to monitor physiological parameters and to allocate and permeabilize cells. Electro-thermal micro pumps distributed chemical compounds in the microfluidic systems. The integrated temperature sensors showed a linear, Pt1000-like behavior. Cell adhesion and proliferation were monitored using interdigitated electrode structures (IDESs. The cell-doubling times of primary murine embryonic neuronal cells (PNCs were determined based on the IDES capacitance-peak shifts. The electrical activity of PNC networks was detected using multi-electrode arrays (MEAs. During seeding, the cells were dielectrophoretically allocated to individual MEAs to improve network structures. MEA pads with diameters of 15, 20, 25, and 35 µm were tested. After 3 weeks, the magnitudes of the determined action potentials were highest for pads of 25 µm in diameter and did not differ when the inter-pad distances were 100 or 170 µm. Using 25-µm diameter circular oxygen electrodes, the signal currents in the cell-culture media were found to range from approximately −0.08 nA (0% O2 to −2.35 nA (21% O2. It was observed that 60-nm thick silicon nitride-sensor layers were stable potentiometric pH sensors under cell-culture conditions for periods of days. Their sensitivity between pH 5 and 9 was as high as 45 mV per pH step. We concluded that sensorized GC3s are potential animal replacement systems for purposes such as toxicity pre-screening. For example, the effect of mefloquine, a medication used to treat malaria, on the electrical activity of neuronal cells was determined in this study using a GC3 system.

  6. MEMS based 6 degrees-of-freedom parallel kinematic precision micro manipulator

    OpenAIRE

    Brouwer, D.M.; Jong, de, B.R.; Soemers, H.M.J.R.

    2006-01-01

    A design is presented for a 6 Degree-of-freedom parallel kinematic precision micro manipulator comprising 3 translations of 20 μm stroke, and three small correction rotation strokes of 5°. The elastic deformations of the manipulator have been optimized for minimal elastic energy storage at a large guiding stiffness. The parallel kinematics facilitates 6 electrostatic lateral comb-drive actuators to be made in-plane of the wafer, using a mechanism to direct the motion to out-of-plane to obtain...

  7. Extended Model-Based Feedforward Compensation in L1 Adaptive Control for Mechanical Manipulators: Design and Experiments

    Directory of Open Access Journals (Sweden)

    Moussab eBennehar

    2015-12-01

    Full Text Available This paper deals with a new control scheme for Parallel Kinematic Manipulators (PKMs based on the L1 adaptive control theory. The original L1 adaptive controller is extended by including an adaptive loop based on the dynamics of the PKM. The additional model-based term is in charge of the compensation of the modeled nonlinear dynamics in the aim of improving the tracking performance. Moreover, the proposed controller is enhanced to reduce the internal forces, which may appear in the case of Redundantly Actuated PKMs (RA-PKMs. The generated control inputs are first regulated through a projection mechanism that reduces the antagonistic internal forces, before being applied to the manipulator. To validate the proposed controller and to show its effectiveness, real-time experiments are conducted on a new four degrees-of-freedom (4-DOFs RA-PKM developed in our laboratory.

  8. Interactive protein manipulation

    Energy Technology Data Exchange (ETDEWEB)

    SNCrivelli@lbl.gov

    2003-07-01

    We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures.

  9. Interactive protein manipulation

    International Nuclear Information System (INIS)

    We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures

  10. Vibration control of a pneumatic driven piezoelectric flexible manipulator using self-organizing map based multiple models

    Science.gov (United States)

    Zhao, Zhi-li; Qiu, Zhi-cheng; Zhang, Xian-min; Han, Jian-da

    2016-03-01

    A kind of hybrid pneumatic-piezoelectric flexible manipulator system has been presented in the paper. A hybrid driving scheme is achieved by combining of a pneumatic proportional valve based pneumatic drive and a piezoelectric actuator bonded to the flexible beam. The system dynamics models are obtained based on system identification approaches, using the established experimental system. For system identification of the flexible piezoelectric manipulator subsystem, parametric estimation methods are utilized. For the pneumatic driven system, a single global linear model is not accurate enough to describe its dynamics, due to the high nonlinearity of the pneumatic driven system. Therefore, a self-organizing map (SOM) based multi-model system identification approach is used to get multiple local linear models. Then, a SOM based multi-model inverse controller and a variable damping pole-placement controller are applied to the pneumatic drive and piezoelectric actuator, respectively. Experiments on pneumatic driven vibration control, piezoelectric vibration control and hybrid vibration control are conducted, utilized proportional and derivative (PD) control, SOM based multi-model inverse controller, and the variable damping pole-placement controller. Experimental results demonstrate that the investigated control algorithms can improve the vibration control performance of the pneumatic driven flexible piezoelectric manipulator system.

  11. Study on optimum maneuverability in horizontal manipulation of objects with power-assist based on weight perception

    Science.gov (United States)

    Rahman, S. M. Mizanoor; Ikeura, Ryojun; Nobe, Masaya; Sawai, Hideki

    2010-01-01

    This paper presents the design of a 1-DOF (horizontal forward-backward translational motion) power assist system (PAS) for manipulating objects in horizontal direction based on human operator's perception of object weight. We adopt a hypothesis that pertains to human's weight perception. The hypothesis means that the human must consider the mass parameter for the inertial force different from the mass parameter for the gravitational force when programming (feedforward) the load force (tangential to grip surfaces) for manipulating an object with a PAS because the perception and the reality regarding the object weight are different in this case. We simulated the system using Matlab/Simulink. Five subjects manipulated objects of three different sizes with the PAS during the simulation. Subjects subjectively determined the optimum values for the mass parameters of the inertial and the gravitational force components. Optimum mass parameters resulted in optimum maneuverability. Finally, we proposed using the findings to develop humanfriendly PASs for manipulating heavy objects in industries such as manufacturing and assembly, mining, logistics and transport, construction, disaster management, military operations etc.

  12. Neural-network-based two-loop control of robotic manipulators including actuator dynamics in task space

    Institute of Scientific and Technical Information of China (English)

    Liangyong WANG; Tianyou CHAI; Zheng FANG

    2009-01-01

    A neural-network-based motion controller in task space is presented in this paper. The proposed controller is addressed as a two-loop cascade control scheme. The outer loop is given by kinematic control in the task space. It provides a joint velocity reference signal to the inner one. The inner loop implements a velocity servo loop at the robot joint level. A radial basis function network (RBFN) is integrated with proportional-integral (PI) control to construct a velocity tracking control scheme for the inner loop. Finally, a prototype technology based control system is designed for a robotic manipulator. The proposed control scheme is applied to the robotic manipulator. Experimental results confirm the validity of the proposed control scheme by comparing it with other control strategies.

  13. Recent developments in nucleic acid based techniques for use in rumen manipulation

    Directory of Open Access Journals (Sweden)

    Christopher McSweeney

    2009-07-01

    Full Text Available Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi have been superseded and are now used mainly to obtain pure isolates of novel organisms and reference strains that are required for the development and validation of the nucleic acid approaches. These reference strains are also essential for physiological studies of the lifestyle of the organisms as well as sources of genomic DNA and RNA that can be analysed for functional gene activity. The foundation of the molecular ecology techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The use of this marker gene in assays involving the use of single nucleic acid probes or primer sets is rapidly evolving to high throughput approaches such as microarray analysis and new generation sequencing technologies. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The focus of nucleic acid research is now shifting to the functional analysis of the ecosystem which involves the measurement of functional genes and their expression in the predominant or specific members of the rumen microbial community. Functional gene studies are less developed than 16S rDNA-based analysis of community structure. Also for gene expression studies there are inherent problems involved in extracting high quality RNA from digesta, and priming cDNA synthesis from bacterial mRNA. This paper reviews nucleic acid based molecular methods which have recently been developed for studying the structure and function of rumen microbial

  14. Manipulatives-Based Laboratory for Majors Biology – a Hands-On Approach to Understanding Respiration and Photosynthesis

    Directory of Open Access Journals (Sweden)

    Sarah M. Boomer

    2011-09-01

    Full Text Available The first course in our year-long introductory series for Biology majors encompasses four learning units: biological molecules and cells, metabolism, genetics, and evolution. Of these, the metabolism unit, which includes respiration and photosynthesis, has shown the lowest student exam scores, least interest, and lowest laboratory ratings. Consequently, we hypothesized that modeling metabolic processes in the laboratory would improve student content learning during this course unit. Specifically, we developed manipulatives-based laboratory exercises that combined paper cutouts, movable blocks, and large diagrams of the cell. In particular, our novel use of connecting LEGO blocks allowed students to move model electrons and phosphates between molecules and within defined spaces of the cell. We assessed student learning using both formal (content indicators and attitude surveys and informal (the identification of misconceptions or discussions with students approaches. On the metabolism unit content exam, student performance improved by 46% over pretest scores and by the end of the course, the majority of students rated metabolism as their most-improved (43% and favorite (33% subject as compared with other unit topics. The majority of students rated manipulatives-based labs as very helpful, as compared to non-manipulatives-based labs. In this report, we will demonstrate that students made learning gains across all content areas, but most notably in the unit that covered respiration and photosynthesis.

  15. High-Resolution Labeling and Functional Manipulation of Specific Neuron Types in Mouse Brain by Cre-Activated Viral Gene Expression

    OpenAIRE

    Kuhlman, Sandra J.; Huang, Z. Josh

    2008-01-01

    We describe a method that combines Cre-recombinase knockin mice and viral-mediated gene transfer to genetically label and functionally manipulate specific neuron types in the mouse brain. We engineered adeno-associated viruses (AAVs) that express GFP, dsRedExpress, or channelrhodopsin (ChR2) upon Cre/loxP recombination-mediated removal of a transcription-translation STOP cassette. Fluorescent labeling was sufficient to visualize neuronal structures with synaptic resolution in vivo, and ChR2 e...

  16. Irreversible electrical manipulation of magnetization on BiFeO{sub 3}-based heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Qingyu, E-mail: xuqingyu@seu.edu.cn, E-mail: jdu@nju.edu.cn; Xu, Zhenyu [Department of Physics, Southeast University, Nanjing 211189 (China); Key Laboratory of MEMS of the Ministry of Education, Southeast University, Nanjing 210096 (China); Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123 (China); He, Maocheng; Du, Jun, E-mail: xuqingyu@seu.edu.cn, E-mail: jdu@nju.edu.cn [Department of Physics and National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210093 (China); Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China); Cao, Yanqiang [Department of Materials Science and Engineering, Nanjing University, Nanjing 210008 (China)

    2015-05-07

    We prepared several heterostructures, Co/Bi{sub 0.90}La{sub 0.10}FeO{sub 3} on surface oxidized Si or (111) SrTiO{sub 3} and NiFe/Bi{sub 0.90}La{sub 0.10}FeO{sub 3} on (001) SrTiO{sub 3} substrates using LaNiO{sub 3} as bottom electrode. With different strategies of voltage application, the exchange bias field H{sub E} decreased with increasing voltage irreversibly for all the heterostructures at room temperature. The chemical state at the NiFe/Bi{sub 0.90}La{sub 0.10}FeO{sub 3} interface was studied by X-ray photoelectron spectroscopy before and after the electrical manipulation. The oxidization of the metallic ferromagnetic layer at interface after the electrical manipulation has been confirmed, which might explain the irreversibility.

  17. SIMULATION and ANALYSIS of PARALLEL MANIPULATOR for MANOEUVRING LAPAROSCOPIC CAMERA - CAD BASED APPROACH

    Directory of Open Access Journals (Sweden)

    K. Kishore Kumar

    2015-02-01

    Full Text Available The inconvenience of laparoscopic operations lies mainly in the difficulties in mutual understanding between the surgeon and the camera assistant that manoeuvres the laparoscope camera according to the surgeon’s instructions .Another problem arises when the operation had to be performed for many hours.[1] In these cases the camera image tends to become unsteady due to fatigue of the camera assistant. The self-camera control, give more stability of the laparoscopic image, A robotic camera Assistant(parallel manipulator directly under surgeon’s control can help the surgeon control the view better.In this paper a parallel robot is simulated for the manipulation of laparoscopic camera and Two dimentional workspace generated is indicated and velocity ,acceleration ,displacement graphs are shown and analysis is done using ANSYS.

  18. Learning reaching strategies through reinforcement for a sensor-based manipulator.

    Science.gov (United States)

    Martín, P; Millán, J del R

    1998-03-31

    This paper presents a neural controller that learns goal-oriented obstacle-avoiding reaction strategies for a multilink robot arm. It acquires these strategies on-line from local sensory data. The controller consists of two neural modules: an actor-critic module and a module for differential inverse kinematics (DIV). The input codification for the controller exploits the inherent symmetry of the robot arm kinematics. The actor-critic module generates actions with regard to the Shortest Path Vector (SPV) to the closest goal in the configuration space. However, the computation of the SPV is cumbersome for manipulators with more than two links. The DIV module aims to overcome the SPV calculation. This module provides a goal vector by means of the inversion of a neural network that has been trained previously to approximate the manipulator forward kinematics. Results for a two-link robot arm show that the combination of both modules speeds up the learning process. PMID:12662844

  19. Osteopathic Manipulative Treatment

    Science.gov (United States)

    Campbell, Shannon M.; Walkowski, Stevan

    2012-01-01

    Dermatological diseases, such as dysesthesia syndromes, stasis dermatoses, and hyperhidrosis are difficult to treat due to their complex etiologies. Current theories suggest these diseases are caused by physiological imbalances, such as nerve impingement, localized tissue congestion, and impaired autonomic regulation. Osteopathic manipulative therapy targets these physiological dysfunctions and may serve as a beneficial therapeutic option. Osteopathic manipulative therapy techniques include high velocity low amplitude, muscle energy, counterstrain, myofascial release, craniosacral, and lymphatic drainage. An osteopathic manipulative therapy technique is chosen based on its physiological target for a particular disease. Osteopathic manipulative therapy may be useful alone or in combination with standard therapeutic options. However, due to the lack of standardized trials supporting the efficacy of osteopathic manipulative therapy treatment for dermatological disease, randomized, well-controlled studies are necessary to confirm its therapeutic value. PMID:23125887

  20. Microfluidic-Based Droplet and Cell Manipulations Using Artificial Bacterial Flagella

    Directory of Open Access Journals (Sweden)

    Yun Ding

    2016-02-01

    Full Text Available Herein, we assess the functionality of magnetic helical microswimmers as basic tools for the manipulation of soft materials, including microdroplets and single cells. Their ability to perform a range of unit operations is evaluated and the operational challenges associated with their use are established. In addition, we also report on interactions observed between the head of such helical swimmers and the boundaries of droplets and cells and discuss the possibilities of assembling an artificial swimming microorganism or a motorized cell.

  1. A New Experimental Approach for Urban Soundscape Characterization Based on Sound Manipulation : A Pilot Study

    OpenAIRE

    Lafay, G; Rossignol, M.; Misdariis, N; Lagrange, M.; Petiot, Jean-François

    2014-01-01

    In this paper, we aim at better understanding how human mental representations are structured in the specific case of the perception of urban soundscapes. This task is traditionally studied using questionnaires, surveys or categorization tasks followed by a lexical analysis. In contrast, we propose a new experimental approach to tackle this aim. In this approach, the subject is asked to manipulate sound events and textures within a dedicated computer environment in order to recreate two compl...

  2. An Image Processing Approach Based on Gnu Image Manipulation Program Gimp to the Panoramic Radiography

    OpenAIRE

    Sparavigna, Amelia Carolina

    2015-01-01

    International audience We have recently proposed, in a paper published by the International Journal of Sciences, the use of some freely available image processing tools to enhance images of the fundus of the eye. In particular, we have discussed the use of GIMP, the GNU Image Manipulation Program, and of some wavelet filters and fractional gradient methods from other image processing programs. Here we propose GIMP to enhance the images given by panoramic radiography. This approach can prod...

  3. Survey based investigation into general practitioner referral patterns for spinal manipulative therapy

    OpenAIRE

    Kier, Annabel; George, Matthew; McCarthy, Peter W

    2013-01-01

    Background In the UK Physiotherapy, Chiropractic and Osteopathy are all statutory regulated professions. Though guidelines have supported the use of Spinal Manipulative Therapy (SMT) for low back pain (LBP), General Practitioners (GP) referral patterns to the 3 registered professions that perform SMT are generally unknown. Method A short questionnaire was designed and piloted. Demographic information, patient referral to SMT and the GPs own personal utilisation of SMT were obtained. 385 GP’s ...

  4. Path planning with obstacle avoidance as applied to a class of space based flexible manipulators

    Science.gov (United States)

    Karray, F.; Modi, V. J.; Chan, J. K.

    1995-10-01

    The present study is a natural extension to the earlier work carried out by the authors in the area of nonlinear control of flexible structures using the Feedback Linearization Technique (FLT). This procedure accounts for the complete nonlinear dynamics of the system. It develops a rather innovative approach to path planning, for a 2-link flexible manipulator, with a specified target and several arbitrarily positioned obstacles. It is important to point out that the presence of link vibrations makes the problem at least an order of magnitude more complicated rendering the conventional algorithms developed for rigid systems virtually of little use. The problem involves generation of regions (contours) representing spheres of influence around the finite size obstacles, with various degrees of permissible penetrations during path planning to the target. To begin with, equations of motion of an orbiting flexible manipulator, undergoing planar slewing maneuvers, are obtained accounting for a shift in the center of mass during maneuvers. Next, a composite control procedure, involving the FLT together with active vibration suppression using piezo-electric actuators, is developed which promises high degree of tracking accuracy. Depending on the performance requirement of the mission, penalty functions are assigned for a given performance index pertaining to the flexible dynamics of the systems. This permits global improvement of the manipulator operation. Finally, effectiveness of the collision avoidance scheme is illustrated through several examples of increasing complexities.

  5. Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation

    Directory of Open Access Journals (Sweden)

    Golovko Georgiy

    2012-07-01

    Full Text Available Abstract Background The emergence of Next Generation Sequencing technologies has made it possible for individual investigators to generate gigabases of sequencing data per week. Effective analysis and manipulation of these data is limited due to large file sizes, so even simple tasks such as data filtration and quality assessment have to be performed in several steps. This requires (potentially problematic interaction between the investigator and a bioinformatics/computational service provider. Furthermore, such services are often performed using specialized computational facilities. Results We present a Windows-based application, Slim-Filter designed to interactively examine the statistical properties of sequencing reads produced by Illumina Genome Analyzer and to perform a broad spectrum of data manipulation tasks including: filtration of low quality and low complexity reads; filtration of reads containing undesired subsequences (such as parts of adapters and PCR primers used during the sample and sequencing libraries preparation steps; excluding duplicated reads (while keeping each read’s copy number information in a specialized data format; and sorting reads by copy numbers allowing for easy access and manual editing of the resulting files. Slim-Filter is organized as a sequence of windows summarizing the statistical properties of the reads. Each data manipulation step has roll-back abilities, allowing for return to previous steps of the data analysis process. Slim-Filter is written in C++ and is compatible with fasta, fastq, and specialized AS file formats presented in this manuscript. Setup files and a user’s manual are available for download at the supplementary web site (https://www.bioinfo.uh.edu/Slim_Filter/. Conclusion The presented Windows-based application has been developed with the goal of providing individual investigators with integrated sequencing reads analysis, curation, and manipulation capabilities.

  6. Advanced In vivo Use of CRISPR/Cas9 and Anti-sense DNA Inhibition for Gene Manipulation in the Brain

    OpenAIRE

    Walters, Brandon J.; Azam, Amber B.; Gillon, Colleen J.; Josselyn, Sheena A; Zovkic, Iva B.

    2016-01-01

    Gene editing tools are essential for uncovering how genes mediate normal brain–behavior relationships and contribute to neurodegenerative and neuropsychiatric disorders. Recent progress in gene editing technology now allows neuroscientists unprecedented access to edit the genome efficiently. Although many important tools have been developed, here we focus on approaches that allow for rapid gene editing in the adult nervous system, particularly CRISPR/Cas9 and anti-sense nucleotide-based techn...

  7. Torque disturbance attenuation and position/force tracking based on SP-D control method for manipulators; SP-D seigyoho ni motozuku manipulator no ichi/chikara seigyo to torque gairan yokusei

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, N.; Fujita, M. [Japan Advanced Institute of Science and Technology, Hokuriku, Ishikawa (Japan)

    1998-02-01

    This paper is concerned with torque disturbance attenuation for manipulators based on SP-D (Saturated Proportional and Differential) position/force control method. The proposed SP-D position/force control method is derived from quasi-natural potential energy. It is applied to a system which consists of a manipulator and a compliant environment. Without the torque disturbance, the proposed control method can ensure asymptotic stability of the closed-loop system. Even though the torque disturbance exists, stability of the system can be guaranteed in the sense of L2. Furthermore, performance of attenuation against the torque disturbance is analyzed by using L2 gain. The proposed SP-D position/force control method is implemented on a two-link planer manipulator system. Effectiveness of the proposed control method is confirmed experimentally. 11 refs., 6 figs.

  8. xdamp Version 6.100: An IDL(reg sign)-based data and image manipulation program

    International Nuclear Information System (INIS)

    The original DAMP (DAta Manipulation Program) was written by Mark Hedemann of Sandia National Laboratories and used the CA-DISSPLA(trademark) (available from Computer Associates International, Inc., Garden City, NY) graphics package as its engine. It was used to plot, modify, and otherwise manipulate the one-dimensional data waveforms (data vs. time) from a wide variety of accelerators. With the waning of CA-DISSPLA and the increasing popularity of Unix(reg sign)-based workstations, a replacement was needed. This package uses the IDL(reg sign) software, available from Research Systems Incorporated, a Xerox company, in Boulder, Colorado, as the engine, and creates a set of widgets to manipulate the data in a manner similar to the original DAMP and earlier versions of xdamp. IDL is currently supported on a wide variety of Unix platforms such as IBM(reg sign) workstations, Hewlett Packard workstations, SUN(reg sign) workstations, Microsoft(reg sign) Windows(trademark) computers, Macintosh(reg sign) computers and Digital Equipment Corporation VMS(reg sign) and Alpha(reg sign) systems. Thus, xdamp is portable across many platforms. We have verified operation, albeit with some minor IDL bugs, on personal computers using Windows 7 and Windows Vista; Unix platforms; and Macintosh computers. Version 6 is an update that uses the IDL Virtual Machine to resolve the need for licensing IDL.

  9. The GeoDataPortal: A Standards-based Environmental Modeling Data Access and Manipulation Toolkit

    Science.gov (United States)

    Blodgett, D. L.; Kunicki, T.; Booth, N.; Suftin, I.; Zoerb, R.; Walker, J.

    2010-12-01

    (OPeNDAP) standard for gridded time series, the OGC’s Web Coverage Service for high-density static gridded data, and Unidata’s CDM-remote for point time series. OGC WFS and Sensor Observation Service (SOS) are being explored as mechanisms to serve and access static or time series data attributed to vector geometry. A set of standardized XML-based output formats allows easy transformation into a wide variety of “model-ready” formats. Interested users will have the option of submitting custom transformations to the GDP or transforming the XML output as a post-process. The GDP project aims to support simple, rapid development of thin user interfaces (like web portals) to commonly needed environmental modeling-related data access and manipulation tools. Standalone, service-oriented components of the GDP framework provide the metadata cataloging, data subset access, and spatial-statistics calculations needed to support interdisciplinary environmental modeling.

  10. Remote Manipulator System (RMS)-based Controls-Structures Interaction (CSI) flight experiment feasibility study

    Science.gov (United States)

    Demeo, Martha E.

    1990-01-01

    The feasibility of an experiment which will provide an on-orbit validation of Controls-Structures Interaction (CSI) technology, was investigated. The experiment will demonstrate the on-orbit characterization and flexible-body control of large flexible structure dynamics using the shuttle Remote Manipulator System (RMS) with an attached payload as a test article. By utilizing existing hardware as well as establishing integration, operation and safety algorithms, techniques and procedures, the experiment will minimize the costs and risks of implementing a flight experiment. The experiment will also offer spin-off enhancement to both the Shuttle RMS (SRMS) and the Space Station RMS (SSRMS).

  11. Simulation of robot manipulators

    International Nuclear Information System (INIS)

    This paper describes Oak Ridge National Laboratory's development of an environment for the simulation of robotic manipulators. Simulation includes the modeling of kinematics, dynamics, sensors, actuators, control systems, operators, and environments. Models will be used for manipulator design, proposal evaluation, control system design and analysis, graphical preview of proposed motions, safety system development, and training. Of particular interest is the development of models for robotic manipulators having at least one flexible link. As a first application, models have been developed for the Pacific Northwest Laboratories' Flexible Beam Testbed which is a one-Degree-Of-Freedom, flexible arm with a hydraulic base actuator. Initial results show good agreement between model and experiment

  12. Cuspidal and Noncuspidal Robot Manipulators

    CERN Document Server

    Wenger, Philippe

    2010-01-01

    This article synthezises the most important results on the kinematics of cuspidal manipulators i.e. nonredundant manipulators that can change posture without meeting a singularity. The characteristic surfaces, the uniqueness domains and the regions of feasible paths in the workspace are defined. Then, several sufficient geometric conditions for a manipulator to be noncuspidal are enumerated and a general necessary and sufficient condition for a manipulator to be cuspidal is provided. An explicit DH-parameter-based condition for an orthogonal manipulator to be cuspidal is derived. The full classification of 3R orthogonal manipulators is provided and all types of cuspidal and noncuspidal orthogonal manipulators are enumerated. Finally, some facts about cuspidal and noncuspidal 6R manipulators are reported.

  13. Pre-impact trajectory planning for minimizing base attitude disturbance in space manipulator systems for a capture task

    Directory of Open Access Journals (Sweden)

    Zhang Long

    2015-08-01

    Full Text Available Aimed at capture task for a free-floating space manipulator, a scheme of pre-impact trajectory planning for minimizing base attitude disturbance caused by impact is proposed in this paper. Firstly, base attitude disturbance is established as a function of joint angles, collision direction and relative velocity between robotic hand and the target. Secondly, on the premise of keeping correct capture pose, a novel optimization factor in null space is designed to minimize base attitude disturbance and ensure that the joint angles do not exceed their limits simultaneously. After reaching the balance state, a desired configuration is achieved at the contact point. Thereafter, particle swarm optimization (PSO algorithm is employed to solve the pre-impact trajectory planning from its initial configuration to the desired configuration to achieve the minimized base attitude disturbance caused by impact and the correct capture pose simultaneously. Finally, the proposed method is applied to a 7-dof free-floating space manipulator and the simulation results verify the effectiveness.

  14. An Oxidase-Based Electrochemical Fluidic Sensor with High-Sensitivity and Low-Interference by On-Chip Oxygen Manipulation

    OpenAIRE

    Chang-Soo Kim; Jongwon Park; Nitin Radhakrishnan

    2012-01-01

    Utilizing a simple fluidic structure, we demonstrate the improved performance of oxidase-based enzymatic biosensors. Electrolysis of water is utilized to generate bubbles to manipulate the oxygen microenvironment close to the biosensor in a fluidic channel. For the proper enzyme reactions to occur, a simple mechanical procedure of manipulating bubbles was developed to maximize the oxygen level while minimizing the pH change after electrolysis. The sensors show improved sensitivities based on ...

  15. Research on modeling and motion simulation of a spherical space robot with telescopic manipulator based on virtual prototype technology

    Science.gov (United States)

    Shi, Chengkun; Sun, Hanxu; Jia, Qingxuan; Zhao, Kailiang

    2009-05-01

    For realizing omni-directional movement and operating task of spherical space robot system, this paper describes an innovated prototype and analyzes dynamic characteristics of a spherical rolling robot with telescopic manipulator. Based on the Newton-Euler equations, the kinematics and dynamic equations of the spherical robot's motion are instructed detailedly. Then the motion simulations of the robot in different environments are developed with ADAMS. The simulation results validate the mathematics model of the system. And the dynamic model establishes theoretical basis for the latter job.

  16. Recent advances in plasma devices based on plasma lens configuration for manipulating high-current heavy ion beams

    International Nuclear Information System (INIS)

    We describe new results of development of novel generation cylindrical plasma devices based on the electrostatic plasma lens configuration and concept of electrons magnetic insulation. The crossed electric and magnetic fields plasma lens configuration provides us with the attractive and suitable method for establishing a stable plasma discharge at low pressure. Using plasma lens configuration in this way some cost-effective plasma devices were developed for ion treatment and deposition of exotic coatings and the effective lens was first proposed for manipulating high-current beams of negatively charged particles. Here we describe operation and features of these plasma devices, and results of theoretical consideration of mechanisms determining their optimal operation conditions.

  17. Pitfalls of enzyme-based molecular anticancer dietary manipulations: food for thought.

    Science.gov (United States)

    Paolini, Moreno; Nestle, Marion

    2003-06-01

    Dietary approaches to cancer chemoprevention increasingly have focused on single nutrients or phytochemicals to stimulate one or another enzymatic metabolizing system. These procedures, which aim to boost carcinogen detoxification or inhibit carcinogen bioactivation, fail to take into account the multiple and paradoxical biological outcomes of enzyme modulators that make their effects unpredictable. Here, we critically examine the scientific and medical evidence for the idea that the physiological roles of specific enzymes may be manipulated by regular, long-term administration of isolated nutrients and other chemicals derived from food plants. Instead, we argue that consumption of healthful diets is most likely to reduce mutagenesis and cancer risk, and that research efforts and dietary recommendations should be redirected away from single nutrients to emphasize the improvement of dietary patterns as a principal strategy for public health policy. PMID:12787810

  18. The holographic optical micro-manipulation system based on counter-propagating beams

    International Nuclear Information System (INIS)

    We present a system employing a dynamic diffractive optical element to control properties of two counter-propagating beams overlapping within a sample chamber. This system allows us to eliminate optical aberrations along both beam pathways and arbitrarily switch between various numbers of laser beams and their spatial profiles (i.e. Gaussian, Laguerre-Gaussian, Bessel beams, etc.). We successfully tested various counter-propagating dual-beam configurations including optical manipulation of both high and low index particles in water or air, particle delivery in an optical conveyor belt and the formation of colloidal solitons by optical binding. Furthermore, we realized a novel optical mixer created by particles spiraling in counter-propagating interfering optical vortices and a new tool for optical tomography or localized spectroscopy enabling sterile contactless rotation and reorientation of a trapped living cell

  19. A high-throughput liquid bead array-based screening technology for Bt presence in GMO manipulation.

    Science.gov (United States)

    Fu, Wei; Wang, Huiyu; Wang, Chenguang; Mei, Lin; Lin, Xiangmei; Han, Xueqing; Zhu, Shuifang

    2016-03-15

    The number of species and planting areas of genetically modified organisms (GMOs) has been rapidly developed during the past ten years. For the purpose of GMO inspection, quarantine and manipulation, we have now devised a high-throughput Bt-based GMOs screening method based on the liquid bead array. This novel method is based on the direct competitive recognition between biotinylated antibodies and beads-coupled antigens, searching for Bt presence in samples if it contains Bt Cry1 Aa, Bt Cry1 Ab, Bt Cry1 Ac, Bt Cry1 Ah, Bt Cry1 B, Bt Cry1 C, Bt Cry1 F, Bt Cry2 A, Bt Cry3 or Bt Cry9 C. Our method has a wide GMO species coverage so that more than 90% of the whole commercialized GMO species can be identified throughout the world. Under our optimization, specificity, sensitivity, repeatability and availability validation, the method shows a high specificity and 10-50 ng/mL sensitivity of quantification. We then assessed more than 1800 samples in the field and food market to prove capacity of our method in performing a high throughput screening work for GMO manipulation. Our method offers an applicant platform for further inspection and research on GMO plants. PMID:26499065

  20. Dielectrophoresis for Bioparticle Manipulation

    Directory of Open Access Journals (Sweden)

    Cheng Qian

    2014-10-01

    Full Text Available As an ideal method to manipulate biological particles, the dielectrophoresis (DEP technique has been widely used in clinical diagnosis, disease treatment, drug development, immunoassays, cell sorting, etc. This review summarizes the research in the field of bioparticle manipulation based on DEP techniques. Firstly, the basic principle of DEP and its classical theories are introduced in brief; Secondly, a detailed introduction on the DEP technique used for bioparticle manipulation is presented, in which the applications are classified into five fields: capturing bioparticles to specific regions, focusing bioparticles in the sample, characterizing biomolecular interaction and detecting microorganism, pairing cells for electrofusion and separating different kinds of bioparticles; Thirdly, the effect of DEP on bioparticle viability is analyzed; Finally, the DEP techniques are summarized and future trends in bioparticle manipulation are suggested.

  1. High-Resolution Labeling and Functional Manipulation of Specific Neuron Types in Mouse Brain by Cre-Activated Viral Gene Expression

    Science.gov (United States)

    Kuhlman, Sandra J.; Huang, Z. Josh

    2008-01-01

    We describe a method that combines Cre-recombinase knockin mice and viral-mediated gene transfer to genetically label and functionally manipulate specific neuron types in the mouse brain. We engineered adeno-associated viruses (AAVs) that express GFP, dsRedExpress, or channelrhodopsin (ChR2) upon Cre/loxP recombination-mediated removal of a transcription-translation STOP cassette. Fluorescent labeling was sufficient to visualize neuronal structures with synaptic resolution in vivo, and ChR2 expression allowed light activation of neuronal spiking. The structural dynamics of a specific class of neocortical neuron, the parvalbumin-containing (Pv) fast-spiking GABAergic interneuron, was monitored over the course of a week. We found that although the majority of Pv axonal boutons were stable in young adults, bouton additions and subtractions on axonal shafts were readily observed at a rate of 10.10% and 9.47%, respectively, over 7 days. Our results indicate that Pv inhibitory circuits maintain the potential for structural re-wiring in post-adolescent cortex. With the generation of an increasing number of Cre knockin mice and because viral transfection can be delivered to defined brain regions at defined developmental stages, this strategy represents a general method to systematically visualize the structure and manipulate the function of different cell types in the mouse brain. PMID:18414675

  2. High-resolution labeling and functional manipulation of specific neuron types in mouse brain by Cre-activated viral gene expression.

    Directory of Open Access Journals (Sweden)

    Sandra J Kuhlman

    Full Text Available We describe a method that combines Cre-recombinase knockin mice and viral-mediated gene transfer to genetically label and functionally manipulate specific neuron types in the mouse brain. We engineered adeno-associated viruses (AAVs that express GFP, dsRedExpress, or channelrhodopsin (ChR2 upon Cre/loxP recombination-mediated removal of a transcription-translation STOP cassette. Fluorescent labeling was sufficient to visualize neuronal structures with synaptic resolution in vivo, and ChR2 expression allowed light activation of neuronal spiking. The structural dynamics of a specific class of neocortical neuron, the parvalbumin-containing (Pv fast-spiking GABAergic interneuron, was monitored over the course of a week. We found that although the majority of Pv axonal boutons were stable in young adults, bouton additions and subtractions on axonal shafts were readily observed at a rate of 10.10% and 9.47%, respectively, over 7 days. Our results indicate that Pv inhibitory circuits maintain the potential for structural re-wiring in post-adolescent cortex. With the generation of an increasing number of Cre knockin mice and because viral transfection can be delivered to defined brain regions at defined developmental stages, this strategy represents a general method to systematically visualize the structure and manipulate the function of different cell types in the mouse brain.

  3. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase genes. Progress report, [April 15, 1990--April 14, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1990-12-31

    The long term goal of this project is to assess the feasibility of increasing the conversion of photosynthate a key regulatory enzyme in starch biosynthesis. In developing storage tissues such as cereal seeds and tubers, starch biosynthesis is primarily regulated by the gene activation, expression, and allosteric regulation of ADPglucose pyrophosphorylase, as well as starch synthase, and branching enzyme. During the last year we have elucidated the structure of both subunits which compose this tetrameric enzyme and determined the temporal and spatial expression of the genes encoding each subunit as well as their correlation to starch biosynthesis. Genomic clones to both subunits have also been isolated and the gene structure of the small subunit determined. Transgenic potato plants have been produced containing deletions of the small subunit promoter. Currently, cis acting elements and their involvement in spatial and temporal expression are under investigation.

  4. Hydraulic manipulator

    International Nuclear Information System (INIS)

    Successful operation of nuclear plant is largely dependent on safe handling of radio-active material. In order to reduce this handling problem and minimise the exposure of radiation, various handling equipment and manipulators have been developed according to the requirements. Manufacture of nuclear fuel, which is the most important part of the nuclear industry, involves handling of uranium ingots weighing approximately 250 kg. This paper describes a specially designed hydraulic manipulator for handling of the ingots in a limited space. It was designed to grab and handle the ingots in any position. This has following drive motions: (1)gripping and releasing, (2)lifting and lowering (z-motion), (3)rotation about the horizontal axis (azimuth drive), (4)rotation about the job axis, and (5)rotation about the vertical axis. For horizontal motion (X and Y axis motion) this equipment is mounted on a motorised trolley, so that it can move inside the workshop. For all drives except the rotation about the job axis, hydraulic cylinders have been used with a battery operated power pack. Trolley drive is also given power from same battery. This paper describes the design aspects of this manipulator. (author). 4 figs

  5. Gene cloning based on long oligonucleotide probes

    International Nuclear Information System (INIS)

    The most commonly used technique for gene cloning has been to utilize oligonucleotide probe based on protein sequence data. Of course this approach requires characterized and purified protein so that at least a portion of amino acid sequence can be determined and used to infer the corresponding DNA sequence. Based on the amino acid sequence information, either short or long oligonucleotide probes can be synthesized chemically. Long probes are typically 30-100 nucleotides long and are a single sequence based on a best guess for each codon. The long probe approach was first used to screen for three different genes: bovine trypsin inhibitor, human insulin-like growth factor I, and human factor IX. There are three advantages of long probes. (1) Any stretch of amino acid sequence 10 or longer can be used. (2) The amino acid sequence need not be absolutely correct. (3) These probes can be used to screen high-complexity libraries with fewer false positives. In spite of the uncertainties over codon selection, the long probe approach is currently the method of choice in screening for genes based on protein sequence data

  6. Feeling manipulated: cytomegalovirus immune manipulation

    Directory of Open Access Journals (Sweden)

    Sparer Tim E

    2009-01-01

    Full Text Available Abstract No one likes to feel like they have been manipulated, but in the case of cytomegalovirus (CMV immune manipulation, we do not really have much choice. Whether you call it CMV immune modulation, manipulation, or evasion, the bottom line is that CMV alters the immune response in such a way to allow the establishment of latency with lifelong shedding. With millions of years of coevolution within their hosts, CMVs, like other herpesviruses, encode numerous proteins that can broadly influence the magnitude and quality of both innate and adaptive immune responses. These viral proteins include both homologues of host proteins, such as MHC class I or chemokine homologues, and proteins with little similarity to any other known proteins, such as the chemokine binding protein. Although a strong immune response is launched against CMV, these virally encoded proteins can interfere with the host's ability to efficiently recognize and clear virus, while others induce or alter specific immune responses to benefit viral replication or spread within the host. Modulation of host immunity allows survival of both the virus and the host. One way of describing it would be a kind of "mutually assured survival" (as opposed to MAD, Mutually Assured Destruction. Evaluation of this relationship provides important insights into the life cycle of CMV as well as a greater understanding of the complexity of the immune response to pathogens in general.

  7. PCR-based gene synthesis to produce recombinant proteins for crystallization

    Directory of Open Access Journals (Sweden)

    Byrne-Steele Miranda L

    2008-04-01

    Full Text Available Abstract Background Gene synthesis technologies are an important tool for structural biology projects, allowing increased protein expression through codon optimization and facilitating sequence alterations. Existing methods, however, can be complex and not always reproducible, prompting researchers to use commercial suppliers rather than synthesize genes themselves. Results A PCR-based gene synthesis method, referred to as SeqTBIO, is described to efficiently assemble the coding regions of two novel hyperthermophilic proteins, PAZ (Piwi/Argonaute/Zwille domain, a siRNA-binding domain of an Argonaute protein homologue and a deletion mutant of a family A DNA polymerase (PolA. The gene synthesis procedure is based on sequential assembly such that homogeneous DNA products can be obtained after each synthesis step without extensive manipulation or purification requirements. Coupling the gene synthesis procedure to in vivo homologous recombination techniques allows efficient subcloning and site-directed mutagenesis for error correction. The recombinant proteins of PAZ and PolA were subsequently overexpressed in E. coli and used for protein crystallization. Crystals of both proteins were obtained and they were suitable for X-ray analysis. Conclusion We demonstrate, by using PAZ and PolA as examples, the feasibility of integrating the gene synthesis, error correction and subcloning techniques into a non-automated gene to crystal pipeline such that genes can be designed, synthesized and implemented for recombinant expression and protein crystallization.

  8. Optimal search-based gene subset selection for gene array cancer classification.

    Science.gov (United States)

    Li, Jiexun; Su, Hua; Chen, Hsinchun; Futscher, Bernard W

    2007-07-01

    High dimensionality has been a major problem for gene array-based cancer classification. It is critical to identify marker genes for cancer diagnoses. We developed a framework of gene selection methods based on previous studies. This paper focuses on optimal search-based subset selection methods because they evaluate the group performance of genes and help to pinpoint global optimal set of marker genes. Notably, this paper is the first to introduce tabu search (TS) to gene selection from high-dimensional gene array data. Our comparative study of gene selection methods demonstrated the effectiveness of optimal search-based gene subset selection to identify cancer marker genes. TS was shown to be a promising tool for gene subset selection. PMID:17674622

  9. Adaptive-backstepping force/motion control for mobile-manipulator robot based on fuzzy CMAC neural networks

    Institute of Scientific and Technical Information of China (English)

    Thang-Long MAI; Yaonan WANG

    2014-01-01

    In this paper, an adaptive backstepping fuzzy cerebellar-model-articulation-control neural-networks control (ABFCNC) system for motion/force control of the mobile-manipulator robot (MMR) is proposed. By applying the ABFCNC in the tracking-position controller, the unknown dynamics and parameter variation problems of the MMR control system are relaxed. In addition, an adaptive robust compensator is proposed to eliminate uncertainties that consist of approximation errors, uncertain disturbances. Based on the tracking position-ABFCNC design, an adaptive robust control strategy is also developed for the nonholonomic-constraint force of the MMR. The design of adaptive-online learning algorithms is obtained by using the Lyapunov stability theorem. Therefore, the proposed method proves that it not only can guarantee the stability and robustness but also the tracking performances of the MMR control system. The effectiveness and robustness of the proposed control system are verified by comparative simulation results.

  10. Singularity Analysis of a Six-dof Parallel Manipulator using Grassmann-Cayley Algebra and Gröbner Bases

    OpenAIRE

    Caro, Stéphane; Moroz, Guillaume; Gayral, Thibault; Chablat, Damien; Chen, Chao

    2010-01-01

    The subject of this paper deals with the singularity analysis of a six-dof three-legged parallel manipulator for force-feedback interface. To this end, a geometric condition for the manipulator singularities is obtained by means of Grassmann-Cayley algebra; the parallel singularities of the manipulator are computed using Jacobian and Gröbner basis. As a result, the algebraic relations of the singularities satisfied by the orientation variables are reported. Finally, the parallel singularities...

  11. Evidence-based gene predictions in plant genomes

    Science.gov (United States)

    Automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. One of the limitations of evidence-based gene builders, however, is their requirement for gene expression evidence—known proteins, full-length cDNAs, or expressed...

  12. Study on in-vessel ISI for JOYO. Laser based ultra sonic non-destructive inspection and manipulation technique

    International Nuclear Information System (INIS)

    This report describes the feasibility study on the in-vessel inspection technique to be applied for the experimental fast reactor JOYO. Since JOYO is a sodium cooled fast reactor and the core structure components are in high temperature and fast neutron irradiation environment, material strength yields to decrease due to heat fatigue and irradiation induced embrittlement. The present surveillance method of testing structural material mechanical property, monitoring subassembly outlet temperature and sodium leak monitoring are not sufficient to detect abnormalities with a small crack. Therefore, the direct inspection method to confirm the core structure integrity needs to be developed considering the recent innovative technology. Since the core structure has a complicated form and components under sodium are not visible, the manipulator technology is essential which has various positioning functions. The core support plate was selected to be an important inspection item, and the method which combines ultrasonic non-destructive inspection technology and manipulator technology was examined. As a result, the concept of core support plate inspection equipment under sodium condition was obtained by contacting ultrasonic sensor from inner side of the core support plate. Another concept was examined by applying laser based ultrasonic inspection technology. This method has advantage of remote control operation because of no-contacting inspection and it was confirmed to be feasible for JOYO in-vessel inspection method from viewpoint of defective detection accuracy and laser transmission ability by means of fiber cable. This is promising for in-vessel inspection without sodium draining. Based on this study, the development of in-vessel inspection equipment is continued and the proto-type will be demonstrated in JOYO. (author)

  13. KBERG: KnowledgeBase for Estrogen Responsive Genes

    DEFF Research Database (Denmark)

    Tang, Suisheng; Zhang, Zhuo; Tan, Sin Lam;

    2007-01-01

    Estrogen has a profound impact on human physiology affecting transcription of numerous genes. To decipher functional characteristics of estrogen responsive genes, we developed KnowledgeBase for Estrogen Responsive Genes (KBERG). Genes in KBERG were derived from Estrogen Responsive Gene Database...... user-friendly system that provides links to other relevant resources such as ERGDB, UniGene, Entrez Gene, HomoloGene, GO, eVOC and GenBank, and thus offers a platform for functional exploration and potential annotation of genes responsive to estrogen. KBERG database can be accessed at http...

  14. Complexity of and Algorithms for Borda Manipulation

    OpenAIRE

    Davies, Jessica; Katsirelos, Georgios; Narodytska, Nina; Walsh, Toby

    2011-01-01

    We prove that it is NP-hard for a coalition of two manipulators to compute how to manipulate the Borda voting rule. This resolves one of the last open problems in the computational complexity of manipulating common voting rules. Because of this NP-hardness, we treat computing a manipulation as an approximation problem where we try to minimize the number of manipulators. Based on ideas from bin packing and multiprocessor scheduling, we propose two new approximation methods to compute manipulat...

  15. Dynamic Control of Kinematically Redundant Robotic Manipulators

    Directory of Open Access Journals (Sweden)

    Erling Lunde

    1987-07-01

    Full Text Available Several methods for task space control of kinematically redundant manipulators have been proposed in the literature. Most of these methods are based on a kinematic analysis of the manipulator. In this paper we propose a control algorithm in which we are especially concerned with the manipulator dynamics. The algorithm is particularly well suited for the class of redundant manipulators consisting of a relatively small manipulator mounted on a larger positioning part.

  16. Evidence Based Selection of Housekeeping Genes

    OpenAIRE

    de Jonge, Hendrik J.M.; Fehrmann, Rudolf S. N.; Eveline S. J. M. de Bont; Hofstra, Robert M. W.; Gerbens, Frans; Kamps, Willem A.; Vries, Elisabeth G. E.; van der Zee, Ate G.J.; te Meerman, Gerard J.; ter Elst, Arja

    2007-01-01

    For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes (reference or internal control genes) is required. It is known that commonly used housekeeping genes (e.g. ACTB, GAPDH, HPRT1, and B2M) vary considerably under different experimental conditions and therefore their use for normalization is limited. We performed a meta-analysis of 13,629 human gene array samples in order to identify the most stable expressed genes. Here we show n...

  17. A Comparison between Position-Based and Image-Based Dynamic Visual Servoings in the Control of a Translating Parallel Manipulator

    Directory of Open Access Journals (Sweden)

    G. Palmieri

    2012-01-01

    Full Text Available Two different visual servoing controls have been developed to govern a translating parallel manipulator with an eye-in-hand configuration, That is, a position-based and an image-based controller. The robot must be able to reach and grasp a target randomly positioned in the workspace; the control must be adaptive to compensate motions of the target in the 3D space. The trajectory planning strategy ensures the continuity of the velocity vector for both PBVS and IBVS controls, whereas a replanning event is needed. A comparison between the two approaches is given in terms of accuracy, fastness, and stability in relation to the robot peculiar characteristics.

  18. A Comparison between Position-Based and Image-Based Dynamic Visual Servoings in the Control of a Translating Parallel Manipulator

    OpenAIRE

    M. Battistelli; Callegari, M.; M. Palpacelli; Palmieri, G.

    2012-01-01

    Two different visual servoing controls have been developed to govern a translating parallel manipulator with an eye-in-hand configuration, That is, a position-based and an image-based controller. The robot must be able to reach and grasp a target randomly positioned in the workspace; the control must be adaptive to compensate motions of the target in the 3D space. The trajectory planning strategy ensures the continuity of the velocity vector for both PBVS and IBVS controls, whereas a replanni...

  19. Manipulating Attention via Mindfulness Induction Improves P300-based Brain-Computer Interface Performance

    OpenAIRE

    Lakey, Chad E.; Berry, Daniel R.; Sellers, Eric W.

    2011-01-01

    In this study, we examined the effects of a short mindfulness meditation induction (MMI) on the performance of a P300-based brain-computer interface (BCI) task. We expected that MMI would harness present moment attentional resources, resulting in two positive consequences for P300-based BCI use. Specifically, we believed MMI would facilitate increases in task accuracy and promote the production of robust P300 amplitudes. Sixteen-channel electroencephalographic data were recorded from 18 subje...

  20. Manipulating Graphene

    Science.gov (United States)

    Ruyack, Alexander; Blees, Melina; Roberts, Samantha; Martin, Chris; Barnard, Arthur; McEuen, Paul L.

    2013-03-01

    Graphene is both strong and flexible, making it a promising material for nanoscale hinges and other three-dimensional structures. Using sacrificial layers and surfactants, we are able to demonstrate control over the adhesion of monolayer graphene to a substrate. By patterning gold on the surface of the graphene, we created arrays of rigid pads bridged by graphene strips that can be decoupled from the surface in an aqueous environment. The pads allow us to manipulate the graphene both on and off the surface using lasers or micromanipulators. Our methods yield fundamental material data on graphene such as the macroscopic bending stiffness, and demonstrate the feasibility of a graphene hinge. We are currently exploring the use of magnetic control as a method for applying forces to stretch and fold graphene. We have already created micron-sized permanent magnets made of iron and successfully released them from the substrate, and are now integrating them into graphene devices.

  1. Improvement of lower extremity electrodiagnostic findings following a trial of spinal manipulation and motion-based therapy

    Directory of Open Access Journals (Sweden)

    Morningstar Mark W

    2006-09-01

    Full Text Available Abstract Background Lumbar disc herniation is a problem frequently encountered in manual medicine. While manual therapy has shown reasonable success in symptomatic management of these cases, little information is known how manual therapy may affect the structure and function of the lumbar disc itself. In cases where lumbar disc herniation is accompanied by radicular symptoms, electrodiagnostic testing has been used to provide objective clinical information on nerve function. This report examines the treatment rendered for a patient with lower extremity neurological deficit, as diagnosed on electrodiagnostic testing. Patient was treated using spinal manipulation and exercises performed on a Pettibon Wobble Chair™, using electrodiagnostic testing as the primary outcome assessment. Case Presentation An elderly male patient presented to a private spine clinic with right-sided foot drop. He had been prescribed an ankle-foot orthosis for this condition. All sensory, motor, and reflex findings in the right leg and foot were absent. This was validated on prior electromyography and nerve conduction velocity testing, performed by a board certified neurologist. Patient was treated using spinal manipulation twice-weekly and wobble chair exercises three times daily for 90 days total. Following this treatment, the patient was referred for follow-up electrodiagnostic studies. Significant improvements were made in these studies as well as self-rated daily function. Conclusion Motion-based therapies, as part of a comprehensive rehabilitation program, may contribute to the restoration of daily function and the reversal of neurological insult as detected by electrodiagnostic testing. Electrodiagnostic testing may be a useful clinical tool to evaluate the progress of chiropractic patients with lumbar disc herniation and radicular pain syndromes.

  2. Atomic and molecular manipulation

    CERN Document Server

    Mayne, Andrew J

    2011-01-01

    Work with individual atoms and molecules aims to demonstrate that miniaturized electronic, optical, magnetic, and mechanical devices can operate ultimately even at the level of a single atom or molecule. As such, atomic and molecular manipulation has played an emblematic role in the development of the field of nanoscience. New methods based on the use of the scanning tunnelling microscope (STM) have been developed to characterize and manipulate all the degrees of freedom of individual atoms and molecules with an unprecedented precision. In the meantime, new concepts have emerged to design molecules and substrates having specific optical, mechanical and electronic functions, thus opening the way to the fabrication of real nano-machines. Manipulation of individual atoms and molecules has also opened up completely new areas of research and knowledge, raising fundamental questions of "Optics at the atomic scale", "Mechanics at the atomic scale", Electronics at the atomic scale", "Quantum physics at the atomic sca...

  3. Effects of thyroid endocrine manipulation on sex-related gene expression and population sex ratios in Zebrafish.

    Science.gov (United States)

    Sharma, Prakash; Tang, Song; Mayer, Gregory D; Patiño, Reynaldo

    2016-09-01

    Thyroid hormone reportedly induces masculinization of genetic females and goitrogen treatment delays testicular differentiation (ovary-to-testis transformation) in genetic males of Zebrafish. This study explored potential molecular mechanisms of these phenomena. Zebrafish were treated with thyroxine (T4, 2nM), goitrogen [methimazole (MZ), 0.15mM], MZ (0.15mM) and T4 (2nM) (rescue treatment), or reconstituted water (control) from 3 to 33days postfertilization (dpf) and maintained in control water until 45dpf. Whole fish were collected during early (25dpf) and late (45dpf) testicular differentiation for transcript abundance analysis of selected male (dmrt1, amh, ar) and female (cyp19a1a, esr1, esr2a, esr2b) sex-related genes by quantitative RT-PCR, and fold-changes relative to control values were determined. Additional fish were sampled at 45dpf for histological assessment of gonadal sex. The T4 and rescue treatments caused male-biased populations, and T4 alone induced precocious puberty in ∼50% of males. Male-biased sex ratios were accompanied by increased expression of amh and ar and reduced expression of cyp19a1a, esr1, esr2a, and esr2b at 25 and 45dpf and, unexpectedly, reduced expression of dmrt1 at 45dpf. Goitrogen exposure increased the proportion of individuals with ovaries (per previous studies interpreted as delay in testicular differentiation of genetic males), and at 25 and 45dpf reduced the expression of amh and ar and increased the expression of esr1 (only at 25dpf), esr2a, and esr2b. Notably, cyp19a1a transcript was reduced but via non-thyroidal pathways (not restored by rescue treatment). In conclusion, the masculinizing activity of T4 at the population level may be due to its ability to inhibit female and stimulate male sex-related genes in larvae, while the inability of MZ to induce cyp19a1a, which is necessary for ovarian differentiation, may explain why its "feminizing" activity on gonadal sex is not permanent. PMID:27255368

  4. Effects of thyroid endocrine manipulation on sex-related gene expression and population sex ratios in Zebrafish

    Science.gov (United States)

    Sharma, Prakash; Tang, Song; Mayer, Gregory D.; Patino, Reynaldo

    2016-01-01

    Thyroid hormone reportedly induces masculinization of genetic females and goitrogen treatment delays testicular differentiation (ovary-to-testis transformation) in genetic males of Zebrafish. This study explored potential molecular mechanisms of these phenomena. Zebrafish were treated with thyroxine (T4, 2 nM), goitrogen [methimazole (MZ), 0.15 mM], MZ (0.15 mM) and T4 (2 nM) (rescue treatment), or reconstituted water (control) from 3 to 33 days postfertilization (dpf) and maintained in control water until 45 dpf. Whole fish were collected during early (25 dpf) and late (45 dpf) testicular differentiation for transcript abundance analysis of selected male (dmrt1, amh, ar) and female (cyp19a1a, esr1, esr2a, esr2b) sex-related genes by quantitative RT-PCR, and fold-changes relative to control values were determined. Additional fish were sampled at 45 dpf for histological assessment of gonadal sex. The T4 and rescue treatments caused male-biased populations, and T4 alone induced precocious puberty in ∼50% of males. Male-biased sex ratios were accompanied by increased expression of amh and ar and reduced expression of cyp19a1a, esr1, esr2a, and esr2b at 25 and 45 dpf and, unexpectedly, reduced expression of dmrt1 at 45 dpf. Goitrogen exposure increased the proportion of individuals with ovaries (per previous studies interpreted as delay in testicular differentiation of genetic males), and at 25 and 45 dpf reduced the expression of amh and ar and increased the expression of esr1 (only at 25 dpf), esr2a, and esr2b. Notably, cyp19a1a transcript was reduced but via non-thyroidal pathways (not restored by rescue treatment). In conclusion, the masculinizing activity of T4 at the population level may be due to its ability to inhibit female and stimulate male sex-related genes in larvae, while the inability of MZ to induce cyp19a1a, which is necessary for ovarian differentiation, may explain why its “feminizing” activity on gonadal

  5. Manipulation of P450 gene expression in tumours; a novel approach for targeted activation of bioreductive prodrugs

    International Nuclear Information System (INIS)

    We are developing a gene-directed enzyme prodrug therapy (GDEPT) strategy to enhance the metabolism of a novel bioreductive drug, AQ4N. Bioreductive drugs are metabolically activated in the hypoxic cell environment allowing effective targeting of hypoxic radioresistant tumour regions. We aim to achieve additional layers of selectivity by using an X-ray inducible promoter linked to our therapeutic gene (cytochrome P450s). This strategy would enhance metabolism of the drug only within the radiation field. Furthermore, normal tissue would be unaffected as the bioreductive drug is only activated in hypoxic conditions. We have identified several human cytochrome P450s which are important for AQ4N prodrug activation, these include CYP3A4, 1A1 and 2B6. RIF1 murine tumour cells transfected with cDNA from any one of these CYPs displayed increased DNA damage and clonogenic cell kill following treatment with AQ4N under hypoxia compared to controls. We are presently testing the ability of these transfectants to enhance anti-tumour effectiveness of AQ4N in combination with radiation in vivo. We have shown that a single CYP3A4 injection using a simple non-optimized approach can increase metabolism of AQ4N and when used in combination with radiation 3 out of 4 tumours are locally controlled for > 60 days (McCarthy et al., 2002). This result is remarkable considering the large enhancement of the radiation effect achieved by adding AQ4N alone. This implies that the bioreduction of AQ4N by CYPs in this tumour system is sub-optimal and this strategy could therefore be very promising for clinical use where CYP levels are known to be variable. We are now exploring the CYP/AQ4N GDEPT strategy in combination with cyclophosphamide, which is also metabolised by CYPs and aim to link these CYPs to the radiation and hypoxia inducible WAF1 promoter for selective activation in vivo

  6. Kinematics of an in-parallel actuated manipulator based on the Stewart platform mechanism

    Science.gov (United States)

    Williams, Robert L., II

    1992-01-01

    This paper presents kinematic equations and solutions for an in-parallel actuated robotic mechanism based on Stewart's platform. These equations are required for inverse position and resolved rate (inverse velocity) platform control. NASA LaRC has a Vehicle Emulator System (VES) platform designed by MIT which is based on Stewart's platform. The inverse position solution is straight-forward and computationally inexpensive. Given the desired position and orientation of the moving platform with respect to the base, the lengths of the prismatic leg actuators are calculated. The forward position solution is more complicated and theoretically has 16 solutions. The position and orientation of the moving platform with respect to the base is calculated given the leg actuator lengths. Two methods are pursued in this paper to solve this problem. The resolved rate (inverse velocity) solution is derived. Given the desired Cartesian velocity of the end-effector, the required leg actuator rates are calculated. The Newton-Raphson Jacobian matrix resulting from the second forward position kinematics solution is a modified inverse Jacobian matrix. Examples and simulations are given for the VES.

  7. Using case-based reasoning for the reconstitution and manipulation of voxelized phantoms

    International Nuclear Information System (INIS)

    The authors reports the development of the EquiVox platform, the aim of which is to allow a radioprotection expert (physician, biologist or other) to work with a phantom which will be the closest possible to the examined person in order to make an as precise as possible dosimetric assessment. The objective is to help to select the best phantom among those the expert knows depending on the assessment type he wants to make. First, they present the general principles of the case-based reasoning, and then the EquiVox platform which proposes all the steps: formalization, elaboration, comparison, and so on. Based on typical numerical values associated with different morphological characteristics, they present and discuss graphical results obtained by the platform. They also discuss their validity and reliability

  8. Direct Search Based Strategy for Obstacle Avoidance of a Redundant Manipulator

    OpenAIRE

    Cornel Secară; Dan Dumitriu

    2010-01-01

    This paper presents an iterative direct search based strategy for redundancy resolution. The end-effector of the redundant manipulatorachieves the imposed task of following the contour of a curve, whilefulfilling two other performance criteria: obstacle avoidance and minimization of the sum of joint displacements. The objective function to minimize is the sum of joint displacements, while the obstacle avoidance and end-effector task are expressed as non-linear constraints. The proposed direct...

  9. MEMS-based Massively-parallelized Mechanoporation Instrumentation for Ultrahigh Throughput Cellular Manipulation

    OpenAIRE

    Zhang, Yanyan

    2012-01-01

    Many applications in cell biology, genetic engineering, cell-based therapeutics, and drug discovery require precise and safe methods for introducing membrane-impermeable molecules into cells. This can be implemented satisfactorily by microinjection. However, disadvantages of traditional manual microinjection include high degree of operator skill, low throughput and labor-intensiveness. Many studies have focused on developing automated and high-throughput systems for microinjection to address ...

  10. Image-based Visual Servoing of a Gough-Stewart Parallel Manipulator using Leg Observations

    OpenAIRE

    Andreff, Nicolas; Dallej, Tej; Martinet, Philippe

    2007-01-01

    In this paper, a tight coupling between computer vision and paral- lel robotics is exhibited through the projective line geometry. Indeed, contrary to the usual methodology where the robot is modeled indepen- dently from the control law which will be implemented, we take into ac- count, since the early modeling stage, that vision will be used for con- trol. Hence, kinematic modeling and projective geometry are fused into a control-devoted projective kinematic model. Thus, a novel vision-based...

  11. Manipulating attention via mindfulness induction improves P300-based brain-computer interface performance

    Science.gov (United States)

    Lakey, Chad E.; Berry, Daniel R.; Sellers, Eric W.

    2011-04-01

    In this study, we examined the effects of a short mindfulness meditation induction (MMI) on the performance of a P300-based brain-computer interface (BCI) task. We expected that MMI would harness present-moment attentional resources, resulting in two positive consequences for P300-based BCI use. Specifically, we believed that MMI would facilitate increases in task accuracy and promote the production of robust P300 amplitudes. Sixteen-channel electroencephalographic data were recorded from 18 subjects using a row/column speller task paradigm. Nine subjects participated in a 6 min MMI and an additional nine subjects served as a control group. Subjects were presented with a 6 × 6 matrix of alphanumeric characters on a computer monitor. Stimuli were flashed at a stimulus onset asynchrony (SOA) of 125 ms. Calibration data were collected on 21 items without providing feedback. These data were used to derive a stepwise linear discriminate analysis classifier that was applied to an additional 14 items to evaluate accuracy. Offline performance analyses revealed that MMI subjects were significantly more accurate than control subjects. Likewise, MMI subjects produced significantly larger P300 amplitudes than control subjects at Cz and PO7. The discussion focuses on the potential attentional benefits of MMI for P300-based BCI performance.

  12. Design Process Optimization Based on Design Process Gene Mapping

    Institute of Scientific and Technical Information of China (English)

    LI Bo; TONG Shu-rong

    2011-01-01

    The idea of genetic engineering is introduced into the area of product design to improve the design efficiency. A method towards design process optimization based on the design process gene is proposed through analyzing the correlation between the design process gene and characteristics of the design process. The concept of the design process gene is analyzed and categorized into five categories that are the task specification gene, the concept design gene, the overall design gene, the detailed design gene and the processing design gene in the light of five design phases. The elements and their interactions involved in each kind of design process gene signprocess gene mapping is drawn with its structure disclosed based on its function that process gene.

  13. CLIMAN - a mobile manipulator concept

    International Nuclear Information System (INIS)

    With increasing age the integrity of more remote parts of reactors, such as the core restraints, is questioned so there is a need for a means of access to these places to carry out inspection, minor repairs and alterations. Conventional standpipe manipulators are about 20 m long so that extending them further presents difficulties of load capacity, rigidity, dexterity and control which must increase steeply with range. The proposal outlined here is for a mobile manipulator which can climb at the end of a cable (CLImbing MANipulator - CLIMAN) into a reactor and reach well beyond the range of a fixed base machine. In addition to virtually unlimited range such a mobile manipulator has twice as many degrees of freedom as a fixed base machine. Its body or base can be manoeuvred with six degrees of freedom so as to obtain the maximum coverage and obstacle avoidance for its manipulator. It is proposed that it should be manually controlled. (author)

  14. Ideological Manipulation in Translation Practice

    Institute of Scientific and Technical Information of China (English)

    张靖

    2011-01-01

    Lefevere's rewriting theory states that translation is a rewriting of the original text,all rewritings reflect a certain ideology and a poetics and as such manipulate literature to function in a given society.Based on this theory,some translation examples are illustrated and analyzed here to show that political and aesthetic ideology will inevitably manipulate translation in different aspects.

  15. Manipulating fluorescence color and intensity with regular metal nanoparticle-based composite materials

    Energy Technology Data Exchange (ETDEWEB)

    Nikitin, Andrey G., E-mail: nikitin@cinam.univ-mrs.fr [Centre Interdisciplinaire de Nanoscience de Marseille (CINaM, UPR 3118 CNRS), Aix-Marseille University, Campus de Luminy, Case 913, 13288 Marseille, France and Faculty of Physics and Technology, Al-Farabi Kazakh National University, 71 Al-Farabi Ave., 050040 Almaty (Kazakhstan)

    2016-02-01

    This paper first studies the role of structural parameters of ordered metal nanoparticle-based composites in the modification of the spectra and intensity of directional emission from organic molecules. It then investigates the possibilities of white light generation via color conversion using two materials, one emitting in the green and the other one in the red spectral region. The structures under study exhibit enhanced emission within small solid angle in the forward direction due to excitation of the quasiguided modes. These modes modify the angle-dependent local photon density of states and, thus, result in efficient directional outcoupling of radiation.

  16. A versatile computer based system for data acquisition manipulation and presentation

    International Nuclear Information System (INIS)

    A data acquisition system based on the Microdata M 1600L data logger and a Digital Equipment Corporation (DEC) VT103 computer system has been set up for use in a wide range of research and development projects in the field of fission detectors and associated technology. The philosophy underlying the system and its important features are described. Operating instructions for the logger are given, and its application to experimental measurements is considered. Observations on whole system performance, and recommendations for improvements are made. (U.K.)

  17. Manipulating effective spin orbit coupling based on proximity effect in magnetic bilayers

    International Nuclear Information System (INIS)

    A proximity effect of spin orbit coupling (SOC) is proposed in nonmagnetic metal/ferromagnet (NM/FM) bilayers by extending the Crépieux-Bruno (CB) theory. We demonstrate that over 1000% enhancement of the SOC strength can be realized based on this effect (Pt/FM bilayers) and it brings greatly enhanced anomalous Hall effect and anomalous Nernst effect. This work could help maximize the performance of magnetic transport property for the spintronics device using NM/FM as the key structure

  18. Manipulating fluorescence color and intensity with regular metal nanoparticle-based composite materials

    International Nuclear Information System (INIS)

    This paper first studies the role of structural parameters of ordered metal nanoparticle-based composites in the modification of the spectra and intensity of directional emission from organic molecules. It then investigates the possibilities of white light generation via color conversion using two materials, one emitting in the green and the other one in the red spectral region. The structures under study exhibit enhanced emission within small solid angle in the forward direction due to excitation of the quasiguided modes. These modes modify the angle-dependent local photon density of states and, thus, result in efficient directional outcoupling of radiation

  19. Manipulation of partially oriented hydroxyapatite building blocks to form flowerlike bundles without acid-base regulation.

    Science.gov (United States)

    Wen, Zhenliang; Wang, Zihao; Chen, Jingdi; Zhong, Shengnan; Hu, Yimin; Wang, Jianhua; Zhang, Qiqing

    2016-06-01

    The application of hydroxyapatite (HAP) in different fields depends greatly on its morphology, composition and structure. Besides, the main inorganic building blocks of human bones and teeth are also HAP. Therefore, accurate shape and aggregation control and of hydroxyapatite particles will be of great interest. Herein, oriented bundles of flowerlike HAP nanorods were successfully prepared through hydrothermal treatment without acid-base regulation, with the mono-alkyl phosphate (MAP) and sodium citrate as surfactant and chelating agent, respectively. The prepared samples were characterized by the X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM) and zeta potential, the pH value and conductivity value of suspension were characterized by pH meter and conductivity measurement. The results showed that the MAP and citrate play an important role in assembly of HAP nanorods without acid-base regulation. Citrate calcium complex could decompose slowly and release citrate ions at hydrothermal conditions. Besides, the further decomposition of citrate ions could release aconitic acid as the reaction time prolongs. Moreover, the possible scheme for the formation process was discussed in detail. PMID:26930036

  20. Control of Free-floating Space Robotic Manipulators base on Neural Network

    Directory of Open Access Journals (Sweden)

    Zhang Wenhui

    2012-11-01

    Full Text Available For problems of trajectory tracking of the free-floating space robot model with uncertainties in task space, neural networks adaptive control strategy is put forward by this paper. Because the non-linear system model can not be obtained accurately, neural network is used to directly identify all parts of the system parameters through GL matrix and its multiplication operator ".". Robust controller is designed to eliminate the approximation errors of neural network and external disturbances. The control strategy neither requires an estimate of inverse dynamic model, nor calculates the inverse Jacobin matrix. Global asymptotic stability based on Lyapunov theory is proved by the paper. Simulation results show that higher control precision is achieved. The control strategy has great value in engineering applications.

  1. A Kinect-Based Framework For Better User Experience in Real-Time Audiovisual Content Manipulation

    DEFF Research Database (Denmark)

    Potetsianakis, Emmanouil; Ksylakis, Emmanouil; Triantafyllidis, Georgios

    inputs from Microsoft Kinect as a controller interface. Originally introduced as a peripheral of XBox, Kinect is a multimodal device equipped with RGB Camera, Depth Sensor and Microphone Array. We use those inputs in order to provide a non-tactile controller abstraction to the user, targeting multimedia...... content creation. Current Kinect-based solutions, try to recognize natural gestures of the user, and classify them as controller actions. The novelty of our implementation is that instead of extracting gesture features, we directly map the inputs from the Kinect to a suitable set of values for the...... multimedia application. By removing the gesture recognition concept, we are able to create a generic and lightweight framework, with a clear interface to the user. We examine the usability of the framework through the development and evaluation, of a Kinect-controlled real-time multimedia application....

  2. Manipulating Representations.

    Science.gov (United States)

    Recchia-Luciani, Angelo N M

    2012-04-01

    The present paper proposes a definition for the complex polysemic concepts of consciousness and awareness (in humans as well as in other species), and puts forward the idea of a progressive ontological development of consciousness from a state of 'childhood' awareness, in order to explain that humans are not only able to manipulate objects, but also their mental representations. The paper builds on the idea of qualia intended as entities posing regular invariant requests to neural processes, trough the permanence of different properties. The concept of semantic differential introduces the properties of metaphorical qualia as an exclusively human ability. Furthermore this paper proposes a classification of qualia, according to the models-with different levels of abstraction-they are implied in, in a taxonomic perspective. This, in turn, becomes a source of categorization of divergent representations, sign systems, and forms of intentionality, relying always on biological criteria. New emerging image-of-the-world-devices are proposed, whose qualia are likely to be only accessible to humans: emotional qualia, where emotion accounts for the invariant and dominant property; and the qualic self where continuity, combined with the oneness of the self, accounts for the invariant and dominant property. The concept of congruence between different domains in a metaphor introduces the possibility of a general evaluation of truth and falsity of all kinds of metaphorical constructs, while the work of Matte Blanco enables us to classify conscious versus unconscious metaphors, both in individuals and in social organizations. PMID:22347988

  3. Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases

    Science.gov (United States)

    Mori, Takahiro; Zhang, Lihan; Awakawa, Takayoshi; Hoshino, Shotaro; Okada, Masahiro; Morita, Hiroyuki; Abe, Ikuro

    2016-03-01

    Prenylation reactions play crucial roles in controlling the activities of biomolecules. Bacterial prenyltransferases, TleC from Streptomyces blastmyceticus and MpnD from Marinactinospora thermotolerans, catalyse the `reverse' prenylation of (-)-indolactam V at the C-7 position of the indole ring with geranyl pyrophosphate or dimethylallyl pyrophosphate, to produce lyngbyatoxin or pendolmycin, respectively. Using in vitro analyses, here we show that both TleC and MpnD exhibit relaxed substrate specificities and accept various chain lengths (C5-C25) of the prenyl donors. Comparisons of the crystal structures and their ternary complexes with (-)-indolactam V and dimethylallyl S-thiophosphate revealed the intimate structural details of the enzyme-catalysed `reverse' prenylation reactions and identified the active-site residues governing the selection of the substrates. Furthermore, structure-based enzyme engineering successfully altered the preference for the prenyl chain length of the substrates, as well as the regio- and stereo-selectivities of the prenylation reactions, to produce a series of unnatural novel indolactams.

  4. Progress in Chimeric Vector and Chimeric Gene Based Cardiovascular Gene Therapy

    Institute of Scientific and Technical Information of China (English)

    HU Chun-Song; YOON Young-sup; ISNER Jeffrey M.; LOSORDO Douglas W.

    2003-01-01

    Gene therapy for cardiovascular diseases has developed from preliminary animal experiments to clinical trials. However, vectors and target genes used currently in gene therapy are mainly focused on viral, nonviral vector and single target gene or monogene. Each vector system has a series of advantages and limitations. Chimeric vectors which combine the advantages of viral and nonviral vector,chimeric target genes which combine two or more target genes and novel gene delivery modes are being developed. In this article, we summarized the progress in chimeric vectors and chimeric genes based cardiovascular gene therapy, which including proliferative or occlusive vascular diseases such as atheroslerosis and restenosis, hypertonic vascular disease such as hypertension and cardiac diseases such as myocardium ischemia, dilated cardiomyopathy and heart failure, even heart transplantation. The development of chimeric vector, chimeric gene and their cardiovascular gene therapy is promising.

  5. A Method for Improving the Pose Accuracy of a Robot Manipulator Based on Multi-Sensor Combined Measurement and Data Fusion

    Directory of Open Access Journals (Sweden)

    Bailing Liu

    2015-04-01

    Full Text Available An improvement method for the pose accuracy of a robot manipulator by using a multiple-sensor combination measuring system (MCMS is presented. It is composed of a visual sensor, an angle sensor and a series robot. The visual sensor is utilized to measure the position of the manipulator in real time, and the angle sensor is rigidly attached to the manipulator to obtain its orientation. Due to the higher accuracy of the multi-sensor, two efficient data fusion approaches, the Kalman filter (KF and multi-sensor optimal information fusion algorithm (MOIFA, are used to fuse the position and orientation of the manipulator. The simulation and experimental results show that the pose accuracy of the robot manipulator is improved dramatically by 38%~78% with the multi-sensor data fusion. Comparing with reported pose accuracy improvement methods, the primary advantage of this method is that it does not require the complex solution of the kinematics parameter equations, increase of the motion constraints and the complicated procedures of the traditional vision-based methods. It makes the robot processing more autonomous and accurate. To improve the reliability and accuracy of the pose measurements of MCMS, the visual sensor repeatability is experimentally studied. An optimal range of 1 x 0.8 x 1 ~ 2 x 0.8 x 1  m in the field of view (FOV is indicated by the experimental results.

  6. A Method for Improving the Pose Accuracy of a Robot Manipulator Based on Multi-Sensor Combined Measurement and Data Fusion

    Science.gov (United States)

    Liu, Bailing; Zhang, Fumin; Qu, Xinghua

    2015-01-01

    An improvement method for the pose accuracy of a robot manipulator by using a multiple-sensor combination measuring system (MCMS) is presented. It is composed of a visual sensor, an angle sensor and a series robot. The visual sensor is utilized to measure the position of the manipulator in real time, and the angle sensor is rigidly attached to the manipulator to obtain its orientation. Due to the higher accuracy of the multi-sensor, two efficient data fusion approaches, the Kalman filter (KF) and multi-sensor optimal information fusion algorithm (MOIFA), are used to fuse the position and orientation of the manipulator. The simulation and experimental results show that the pose accuracy of the robot manipulator is improved dramatically by 38%∼78% with the multi-sensor data fusion. Comparing with reported pose accuracy improvement methods, the primary advantage of this method is that it does not require the complex solution of the kinematics parameter equations, increase of the motion constraints and the complicated procedures of the traditional vision-based methods. It makes the robot processing more autonomous and accurate. To improve the reliability and accuracy of the pose measurements of MCMS, the visual sensor repeatability is experimentally studied. An optimal range of 1 × 0.8 × 1 ∼ 2 × 0.8 × 1 m in the field of view (FOV) is indicated by the experimental results. PMID:25850067

  7. Kinematic analysis of spatial parallel manipulator

    International Nuclear Information System (INIS)

    In this work we analyses a particularly spatial manipulator, establish initial data and based on fixed geometrical link parameters we conduct a kinematic analysis of manipulator by Denavit-Hartenberg matrix way. (author)

  8. A simple cell-based assay reveals that diverse neuropsychiatric risk genes converge on primary cilia.

    Directory of Open Access Journals (Sweden)

    Aaron Marley

    Full Text Available Human genetic studies are beginning to identify a large number of genes linked to neuropsychiatric disorders. It is increasingly evident that different genes contribute to risk for similar syndromes and, conversely, the same genes or even the same alleles cross over traditional diagnostic categories. A current challenge is to understand the cellular biology of identified risk genes. However, most genes associated with complex neuropsychiatric phenotypes are not related through a known biochemical pathway, and many have an entirely unknown cellular function. One possibility is that diverse disease-linked genes converge at a higher-level cellular structure. The synapse is already known to be one such convergence, and emerging evidence suggests the primary cilium as another. Because many genes associated with neuropsychiatric illness are expressed also outside the nervous system, as are cilia, we tested the hypothesis that such genes affect conserved features of the primary cilium. Using RNA interference to test 41 broadly expressed candidate genes associated with schizophrenia, bipolar affective disorder, autism spectrum disorder and intellectual disability, we found 20 candidates that reduce ciliation in NIH3T3 cells when knocked down, and three whose manipulation increases cilia length. Three of the candidate genes were previously implicated in cilia formation and, altogether, approximately half of the candidates tested produced a ciliary phenotype. Our results support the hypothesis that primary cilia indeed represent a conserved cellular structure at which the effects of diverse neuropsychiatric risk genes converge. More broadly, they suggest a relatively simple cell-based approach that may be useful for exploring the complex biological underpinnings of neuropsychiatric disease.

  9. Recent progress in polymer-based gene delivery vectors

    Institute of Scientific and Technical Information of China (English)

    HUANG Shiwen; ZHUO Renxi

    2003-01-01

    The gene delivery system is one of the three components of a gene medicine, which is the bottle neck of current gene therapy. Nonviral vectors offer advantages over the viral system of safety, ease of manufacturing, etc. As important nonviral vectors, polymer gene delivery systems have gained increasing attention and have begun to show increasing promising. In this review, the fundamental and recent progress of polymer-based gene delivery vectors is reviewed.

  10. Evidence based selection of housekeeping genes.

    Directory of Open Access Journals (Sweden)

    Hendrik J M de Jonge

    Full Text Available For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes (reference or internal control genes is required. It is known that commonly used housekeeping genes (e.g. ACTB, GAPDH, HPRT1, and B2M vary considerably under different experimental conditions and therefore their use for normalization is limited. We performed a meta-analysis of 13,629 human gene array samples in order to identify the most stable expressed genes. Here we show novel candidate housekeeping genes (e.g. RPS13, RPL27, RPS20 and OAZ1 with enhanced stability among a multitude of different cell types and varying experimental conditions. None of the commonly used housekeeping genes were present in the top 50 of the most stable expressed genes. In addition, using 2,543 diverse mouse gene array samples we were able to confirm the enhanced stability of the candidate novel housekeeping genes in another mammalian species. Therefore, the identified novel candidate housekeeping genes seem to be the most appropriate choice for normalizing gene expression data.

  11. Distributed microscopy: toward a 3D computer-graphic-based multiuser microscopic manipulation, imaging, and measurement system

    Science.gov (United States)

    Sulzmann, Armin; Carlier, Jerome; Jacot, Jacques

    1996-10-01

    The aim of this project is to telecontrol the movements in 3D-space of a microscope in order to manipulate and measure microsystems or micro parts aided by multi-user virtual reality (VR) environments. Presently microsystems are gaining in interest. Microsystems are small, independent modules, incorporating various functions, such as electronic, micro mechanical, data processing, optical, chemical, medical and biological functions. Though improving the manufacturing technologies, the measurement of the small structures to insure the quality of the process is a key information for the development. So far to measure the micro structures strong microscopes are needed. The use of highly magnifying computerized microscopes is expensive. To insure high quality measurements and distribute the acquired information to multi-user our proposed system is divided into three parts: the virtual reality microscopic environment (VRME)-based user-interface on a SGI workstation to prepare the manipulations and measurements. Secondly the computerized light microscope with the vision system inspecting the scene and getting the images of the specimen. Newly developed vision algorithms are used to analyze micro structures in the scene corresponding to the known a priori model. This vision is extracting position and shape of the objects and then transmitted as feedback to the user of the VRME-system to update his virtual environment. The internet demon is the third part of the system and distributes the information about the position of the micro structures, their shape and the images to the connected users who themselves may interact with the microscope (turn and displace the specimen on the back of a moving platform, or adding their structures to the scene and compare). The key idea behind our project VRME is to use the intuitiveness and the 3D visualization of VR environments coupled with a vision system to perform measurements of micro structures at a high accuracy. The direct

  12. A tuning fork based wide range mechanical characterization tool with nanorobotic manipulators inside a scanning electron microscope

    International Nuclear Information System (INIS)

    This study proposes a tuning fork probe based nanomanipulation robotic system for mechanical characterization of ultraflexible nanostructures under scanning electron microscope. The force gradient is measured via the frequency modulation of a quartz tuning fork and two nanomanipulators are used for manipulation of the nanostructures. Two techniques are proposed for attaching the nanostructure to the tip of the tuning fork probe. The first technique involves gluing the nanostructure for full range characterization whereas the second technique uses van der Waals and electrostatic forces in order to avoid destroying the nanostructure. Helical nanobelts (HNB) are proposed for the demonstration of the setup. The nonlinear stiffness behavior of HNBs during their full range tensile studies is clearly revealed for the first time. Using the first technique, this was between 0.009 N/m for rest position and 0.297 N/m before breaking of the HNB with a resolution of 0.0031 N/m. For the second experiment, this was between 0.014 N/m for rest position and 0.378 N/m before detaching of the HNB with a resolution of 0.0006 N/m. This shows the wide range sensing of the system for potential applications in mechanical property characterization of ultraflexible nanostructures.

  13. A tuning fork based wide range mechanical characterization tool with nanorobotic manipulators inside a scanning electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Acosta, Juan Camilo; Hwang, Gilgueng; Regnier, Stephane [Institut des Systemes Intelligents et de Robotique Universite Pierre et Marie Curie, CNRS UMR 7222 4 Place Jussieu, 75252 Paris Cedex (France); Polesel-Maris, Jerome [CEA, IRAMIS, Service de Physique et Chimie des Surfaces et Interfaces, F-91191 Gif-sur-Yvette (France)

    2011-03-15

    This study proposes a tuning fork probe based nanomanipulation robotic system for mechanical characterization of ultraflexible nanostructures under scanning electron microscope. The force gradient is measured via the frequency modulation of a quartz tuning fork and two nanomanipulators are used for manipulation of the nanostructures. Two techniques are proposed for attaching the nanostructure to the tip of the tuning fork probe. The first technique involves gluing the nanostructure for full range characterization whereas the second technique uses van der Waals and electrostatic forces in order to avoid destroying the nanostructure. Helical nanobelts (HNB) are proposed for the demonstration of the setup. The nonlinear stiffness behavior of HNBs during their full range tensile studies is clearly revealed for the first time. Using the first technique, this was between 0.009 N/m for rest position and 0.297 N/m before breaking of the HNB with a resolution of 0.0031 N/m. For the second experiment, this was between 0.014 N/m for rest position and 0.378 N/m before detaching of the HNB with a resolution of 0.0006 N/m. This shows the wide range sensing of the system for potential applications in mechanical property characterization of ultraflexible nanostructures.

  14. Noise-based switches and amplifiers for gene expression

    CERN Document Server

    Hasty, J; Dolnik, M; Collins, J J; Hasty, Jeff; Pradines, Joel; Dolnik, Milos

    2000-01-01

    The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network. Engineered control of cellular function through the design and manipulation of such networks lies within the constraints of current technology. Here we develop a model describing the regulation of gene expression, and elucidate the effects of noise on the formulation. We consider a single network derived from bacteriophage $\\lambda$, and construct a two-parameter deterministic model describing the temporal evolution of the concentration of $\\lambda$ repressor protein. Bistability in the steady-state protein concentration arises naturally, and we show how the bistable regime is enhanced with the addition of the first operator site in the promotor region. We then show how additive and multiplicative external noise can be used...

  15. Mesenchymal stem cell-based gene therapy: A promising therapeutic strategy.

    Science.gov (United States)

    Mohammadian, Mozhdeh; Abasi, Elham; Akbarzadeh, Abolfazl

    2016-08-01

    Mesenchymal stem cells (MSCs) are multipotent stromal cells that exist in bone marrow, fat, and so many other tissues, and can differentiate into a variety of cell types including osteoblasts, chondrocytes, and adipocytes, as well as myocytes and neurons. Moreover, they have great capacity for self-renewal while maintaining their multipotency. Their capacity for proliferation and differentiation, in addition to their immunomodulatory activity, makes them very promising candidates for cell-based regenerative medicine. Moreover, MSCs have the ability of mobilization to the site of damage; therefore, they can automatically migrate to the site of injury via their chemokine receptors following intravenous transplantation. In this respect, they can be applied for MSC-based gene therapy. In this new therapeutic method, genes of interest are introduced into MSCs via viral and non-viral-based methods that lead to transgene expression in them. Although stem cell-based gene therapy is a relatively new strategy, it lights a new hope for the treatment of a variety of genetic disorders. In the near future, MSCs can be of use in a vast number of clinical applications, because of their uncomplicated isolation, culture, and genetic manipulation. However, full consideration is still crucial before they are utilized for clinical trials, because the number of studies that signify the advantageous effects of MSC-based gene therapy are still limited. PMID:26148175

  16. A knowledge-based clustering algorithm driven by Gene Ontology.

    Science.gov (United States)

    Cheng, Jill; Cline, Melissa; Martin, John; Finkelstein, David; Awad, Tarif; Kulp, David; Siani-Rose, Michael A

    2004-08-01

    We have developed an algorithm for inferring the degree of similarity between genes by using the graph-based structure of Gene Ontology (GO). We applied this knowledge-based similarity metric to a clique-finding algorithm for detecting sets of related genes with biological classifications. We also combined it with an expression-based distance metric to produce a co-cluster analysis, which accentuates genes with both similar expression profiles and similar biological characteristics and identifies gene clusters that are more stable and biologically meaningful. These algorithms are demonstrated in the analysis of MPRO cell differentiation time series experiments. PMID:15468759

  17. Cell- and region-specific miR30-based gene knock-down with temporal control in the rat brain

    OpenAIRE

    Xu Haibo; Liu Beihui; Paton Julian FR; Kasparov Sergey

    2010-01-01

    Abstract Background RNA interference (RNAi) emerges as a powerful tool to induce loss-of-function phenotypes. In the context of the brain, gene manipulation is best targeted to specific subsets of cells in order to achieve a physiologically relevant outcome. Polymerase II-based viral expression systems can be used to cell-specifically express constructs incorporating flanking and loop sequences from endogenous microRNA (miRNA), which directs the designed hairpins into the endogenous gene sile...

  18. General expression of manipulator kinematics

    International Nuclear Information System (INIS)

    In this paper, a general description for kinematic modelling of all types of manipulators is presented by expanding the concept of the homogeneous transformation (Ai-matrix) based on Denavit-Hartenberg notation. Unlike the previous matrix method, the expression of recursive relationships which is suitable for computer-aided design makes it possible to derive automatically the position and orientation of manipulator hand. Two algorithms which take into consideration of the order of operation result in identical relations with respect to the kinematics between the reference system and the final link, which was proved by an application to a six-link manipulator. (author)

  19. HMM-Based Gene Annotation Methods

    Energy Technology Data Exchange (ETDEWEB)

    Haussler, David; Hughey, Richard; Karplus, Keven

    1999-09-20

    Development of new statistical methods and computational tools to identify genes in human genomic DNA, and to provide clues to their functions by identifying features such as transcription factor binding sites, tissue, specific expression and splicing patterns, and remove homologies at the protein level with genes of known function.

  20. An Oxidase-Based Electrochemical Fluidic Sensor with High-Sensitivity and Low-Interference by On-Chip Oxygen Manipulation

    Directory of Open Access Journals (Sweden)

    Chang-Soo Kim

    2012-06-01

    Full Text Available Utilizing a simple fluidic structure, we demonstrate the improved performance of oxidase-based enzymatic biosensors. Electrolysis of water is utilized to generate bubbles to manipulate the oxygen microenvironment close to the biosensor in a fluidic channel. For the proper enzyme reactions to occur, a simple mechanical procedure of manipulating bubbles was developed to maximize the oxygen level while minimizing the pH change after electrolysis. The sensors show improved sensitivities based on the oxygen dependency of enzyme reaction. In addition, this oxygen-rich operation minimizes the ratio of electrochemical interference signal by ascorbic acid during sensor operation (i.e., amperometric detection of hydrogen peroxide. Although creatinine sensors have been used as the model system in this study, this method is applicable to many other biosensors that can use oxidase enzymes (e.g., glucose, alcohol, phenol, etc. to implement a viable component for in-line fluidic sensor systems.

  1. An oxidase-based electrochemical fluidic sensor with high-sensitivity and low-interference by on-chip oxygen manipulation.

    Science.gov (United States)

    Radhakrishnan, Nitin; Park, Jongwon; Kim, Chang-Soo

    2012-01-01

    Utilizing a simple fluidic structure, we demonstrate the improved performance of oxidase-based enzymatic biosensors. Electrolysis of water is utilized to generate bubbles to manipulate the oxygen microenvironment close to the biosensor in a fluidic channel. For the proper enzyme reactions to occur, a simple mechanical procedure of manipulating bubbles was developed to maximize the oxygen level while minimizing the pH change after electrolysis. The sensors show improved sensitivities based on the oxygen dependency of enzyme reaction. In addition, this oxygen-rich operation minimizes the ratio of electrochemical interference signal by ascorbic acid during sensor operation (i.e., amperometric detection of hydrogen peroxide). Although creatinine sensors have been used as the model system in this study, this method is applicable to many other biosensors that can use oxidase enzymes (e.g., glucose, alcohol, phenol, etc.) to implement a viable component for in-line fluidic sensor systems. PMID:23012527

  2. Force/Position Hybrid Control of 6PUS-UPU Redundant Driven Parallel Manipulator Based on 2-DOF Internal Model Control

    OpenAIRE

    Kuijing Zheng; Chao Wang

    2014-01-01

    To improve control performance of parallel manipulator, servo control is optimized according to 2-DOF control with Internal Model Control. Position loop of the controller is redesigned based on the original current loop and speed loop. The hybrid force/position control strategy on the basis of cross-coupling is proposed. With mechatronic cosimulation system, it is proved that the force/position hybrid control on the basis of 2-DOF Internal Model Control has better stability and position preci...

  3. Identifying disease feature genes based on cellular localized gene functional modules and regulation networks

    Institute of Scientific and Technical Information of China (English)

    ZHANG Min; ZHU Jing; GUO Zheng; LI Xia; YANG Da; WANG Lei; RAO Shaoqi

    2006-01-01

    Identifying disease-relevant genes and functional modules, based on gene expression profiles and gene functional knowledge, is of high importance for studying disease mechanisms and subtyping disease phenotypes. Using gene categories of biological process and cellular component in Gene Ontology, we propose an approach to selecting functional modules enriched with differentially expressed genes, and identifying the feature functional modules of high disease discriminating abilities. Using the differentially expressed genes in each feature module as the feature genes, we reveal the relevance of the modules to the studied diseases. Using three datasets for prostate cancer, gastric cancer, and leukemia, we have demonstrated that the proposed modular approach is of high power in identifying functionally integrated feature gene subsets that are highly relevant to the disease mechanisms. Our analysis has also shown that the critical disease-relevant genes might be better recognized from the gene regulation network, which is constructed using the characterized functional modules, giving important clues to the concerted mechanisms of the modules responding to complex disease states. In addition, the proposed approach to selecting the disease-relevant genes by jointly considering the gene functional knowledge suggests a new way for precisely classifying disease samples with clear biological interpretations, which is critical for the clinical diagnosis and the elucidation of the pathogenic basis of complex diseases.

  4. An overview of gene therapy in head and neck cancer

    OpenAIRE

    Amit Bali; Deepika Bali; Ashutosh Sharma

    2013-01-01

    Gene therapy is a new treatment modality in which new gene is introduced or existing gene is manipulated to cause cancer cell death or slow the growth of the tumor. In this review, we have discussed the different treatment approaches for cancer gene therapy; gene addition therapy, immunotherapy, gene therapy using oncolytic viruses, antisense ribonucleic acid (RNA) and RNA interference-based gene therapy. Clinical trials to date in head and neck cancer have shown evidence of gene transduction...

  5. DNA-energetics-based analyses suggest additional genes in prokaryotes

    Indian Academy of Sciences (India)

    Garima Khandelwal; Jalaj Gupta; B Jayaram

    2012-07-01

    We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of higher thermodynamic stability were identified, which were filtered based on already known annotations to yield a set of potentially new genes. These were then processed for their compatibility with the stereo-chemical properties of proteins and tripeptide frequencies of proteins in Swissprot data, which results in a reliable set of new genes in a genome. Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the methodology can handle genomes of any GC-content, size and number of annotated genes.

  6. Gene Network Biological Validity Based on Gene-Gene Interaction Relevance

    OpenAIRE

    Francisco Gómez-Vela; Norberto Díaz-Díaz

    2014-01-01

    In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in...

  7. Gene-based and semantic structure of the Gene Ontology as a complex network

    Science.gov (United States)

    Coronnello, Claudia; Tumminello, Michele; Miccichè, Salvatore

    2016-09-01

    The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The Gene Ontology (GO) is constantly evolving over time. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. Here we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium. Moreover, the GO is a natural example of bipartite network of terms and genes. Here we are interested in studying the properties of the projected network of terms, i.e. a gene-based weighted network of GO terms, in which a link between any two terms is set if at least one gene is annotated in both terms. One aim of the present paper is to compare the structural properties of the semantic and the gene-based network. The relative importance of terms is very similar in the two networks, but the community structure changes. We show that in some cases GO terms that appear to be distinct from a semantic point of view are instead connected, and appear in the same community when considering their gene content. The identification of such gene-based communities of terms might therefore be the basis of a simple protocol aiming at improving the semantic structure of GO. Information about terms that share large gene content might also be important from a biomedical point of view, as it might reveal how genes over-expressed in a certain term also affect other biological processes, molecular functions and cellular components not directly linked according to GO semantics.

  8. Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation

    OpenAIRE

    Golovko Georgiy; Khanipov Kamil; Rojas Mark; Martinez-Alcántara Antonio; Howard Jesse J; Ballesteros Efren; Gupta Sharu; Widger William; Fofanov Yuriy

    2012-01-01

    Abstract Background The emergence of Next Generation Sequencing technologies has made it possible for individual investigators to generate gigabases of sequencing data per week. Effective analysis and manipulation of these data is limited due to large file sizes, so even simple tasks such as data filtration and quality assessment have to be performed in several steps. This requires (potentially problematic) interaction between the investigator and a bioinformatics/computational service provid...

  9. MFR (Multi-purpose Field Robot) Based on Human-Robot Cooperative Manipulation for Handling Building Materials

    OpenAIRE

    Lee, SeungYeol

    2010-01-01

    The prototype of MFR for handling building materials presented in this study combines a manipulator and a mobile platform standardized in modular form to compose its basic system. Also, the hardware and software necessary for each area of application were composed of additional modules and combined with the robot's basic system. The suggested MFR can execute particular operations in various areas such as construction, national defense and rescue by changing these additional modules. One of th...

  10. Seed-based biclustering of gene expression data.

    Directory of Open Access Journals (Sweden)

    Jiyuan An

    Full Text Available BACKGROUND: Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. METHODS: In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns (a a gene set, and (b the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. CONCLUSIONS: This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

  11. The Increasing Importance of Gene-Based Analyses

    Science.gov (United States)

    Cirulli, Elizabeth T.

    2016-01-01

    In recent years, genome and exome sequencing studies have implicated a plethora of new disease genes with rare causal variants. Here, I review 150 exome sequencing studies that claim to have discovered that a disease can be caused by different rare variants in the same gene, and I determine whether their methods followed the current best-practice guidelines in the interpretation of their data. Specifically, I assess whether studies appropriately assess controls for rare variants throughout the entire gene or implicated region as opposed to only investigating the specific rare variants identified in the cases, and I assess whether studies present sufficient co-segregation data for statistically significant linkage. I find that the proportion of studies performing gene-based analyses has increased with time, but that even in 2015 fewer than 40% of the reviewed studies used this method, and only 10% presented statistically significant co-segregation data. Furthermore, I find that the genes reported in these papers are explaining a decreasing proportion of cases as the field moves past most of the low-hanging fruit, with 50% of the genes from studies in 2014 and 2015 having variants in fewer than 5% of cases. As more studies focus on genes explaining relatively few cases, the importance of performing appropriate gene-based analyses is increasing. It is becoming increasingly important for journal editors and reviewers to require stringent gene-based evidence to avoid an avalanche of misleading disease gene discovery papers. PMID:27055023

  12. Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.

    Directory of Open Access Journals (Sweden)

    Nolan Priedigkeit

    2015-02-01

    Full Text Available Genes involved in the same function tend to have similar evolutionary histories, in that their rates of evolution covary over time. This coevolutionary signature, termed Evolutionary Rate Covariation (ERC, is calculated using only gene sequences from a set of closely related species and has demonstrated potential as a computational tool for inferring functional relationships between genes. To further define applications of ERC, we first established that roughly 55% of genetic diseases posses an ERC signature between their contributing genes. At a false discovery rate of 5% we report 40 such diseases including cancers, developmental disorders and mitochondrial diseases. Given these coevolutionary signatures between disease genes, we then assessed ERC's ability to prioritize known disease genes out of a list of unrelated candidates. We found that in the presence of an ERC signature, the true disease gene is effectively prioritized to the top 6% of candidates on average. We then apply this strategy to a melanoma-associated region on chromosome 1 and identify MCL1 as a potential causative gene. Furthermore, to gain global insight into disease mechanisms, we used ERC to predict molecular connections between 310 nominally distinct diseases. The resulting "disease map" network associates several diseases with related pathogenic mechanisms and unveils many novel relationships between clinically distinct diseases, such as between Hirschsprung's disease and melanoma. Taken together, these results demonstrate the utility of molecular evolution as a gene discovery platform and show that evolutionary signatures can be used to build informative gene-based networks.

  13. Modified gateway system for double shRNA expression and Cre/lox based gene expression

    Directory of Open Access Journals (Sweden)

    Leung Lisa

    2011-03-01

    Full Text Available Abstract Background The growing need for functional studies of genes has set the stage for the development of versatile tools for genetic manipulations. Results Aiming to provide tools for high throughput analysis of gene functions, we have developed a modified short hairpin RNA (shRNA and gene expression system based on Gateway Technology. The system contains a series of entry and destination vectors that enables easy transfer of shRNA or cDNA into lentiviral expression systems with a variety of selection or marker genes (i.e. puromycin, hygromycin, green fluorescent protein-EGFP, yellow fluorescent protein-YFP and red fluorescent protein-dsRed2. Our shRNA entry vector pENTR.hU6.hH1 containing two tandem human shRNA expression promoters, H1 and U6, was capable of co-expressing two shRNA sequences simultaneously. The entry vector for gene overexpression, pENTR.CMV.ON was constructed to contain CMV promoter with a multiple cloning site flanked by loxP sites allowing for subsequent Cre/lox recombination. Both shRNA and cDNA expression vectors also contained attL sites necessary for recombination with attR sites in our destination expression vectors. As proof of principle we demonstrate the functionality and efficiency of this system by testing expression of several cDNA and shRNA sequences in a number of cell lines. Conclusion Our system is a valuable addition to already existing library of Gateway based vectors and can be an essential tool for many aspects of gene functional studies.

  14. AAV-Based Targeting Gene Therapy

    Directory of Open Access Journals (Sweden)

    Wenfang Shi

    2008-01-01

    Full Text Available Since the first parvovirus serotype AAV2 was isolated from human and used as a vector for gene therapy application, there have been significant progresses in AAV vector development. AAV vectors have been extensively investigated in gene therapy for a broad application. AAV vectors have been considered as the first choice of vector due to efficient infectivity, stable expression and non-pathogenicity. However, the untoward events in AAV mediated in vivo gene therapy studies proposed the new challenges for their further applications. Deep understanding of the viral life cycle, viral structure and replication, infection mechanism and efficiency of AAV DNA integration, in terms of contributing viral, host-cell factors and circumstances would promote to evaluate the advantages and disadvantages and provide more insightful information for the possible clinical applications. In this review, main effort will be focused on the recent progresses in gene delivery to the target cells via receptor-ligand interaction and DNA specific integration regulation. Furthermore AAV receptor and virus particle intracellular trafficking are also discussed.

  15. 以颈部推拿为主治疗失眠症的研究概况%Overview of Cervical Manipulation Based Treatment on Insomnia

    Institute of Scientific and Technical Information of China (English)

    谢健

    2014-01-01

    颈部不适患者常见失眠症的发生,其病机不仅与走行于颈部的经络相关,更与颈部的神经肌肉分布有着一定联系。本文综述了以颈部为主要作用部位,单纯推拿和以推拿为主的综合疗法在失眠症临床实践过程中的研究概况,总结特点及优劣,以暨为失眠症的推拿治疗提供新的思路和有益参考。%Insomnia is common among the patients with cervical discomfort, its pathogenesis is not only related to the meridians around the cervical, but also associated with the distribution of nerves and muscles of cervical. This article reviews research situation of simple manipulative therapy and manipulation based comprehensive therapy with cervical as the main action site during the clinical practice of insomnia, summarizes its characteristics, advantages and disadvantages, in order to provide new ideas and useful reference for the manipulative therapy on insomnia.

  16. Control Design Of Robot Manipulator Position Based On Pd-Fuzzy Mamdani Controlled With Computed Torque Control (Pd-Fuzzy-Ctc

    Directory of Open Access Journals (Sweden)

    Duli Ridlo Istriantono

    2015-03-01

    Full Text Available Robotics science has evolved significantly, driven by rapid advances in computer and sensor technology; and theoretical advances in control and computer vision. These development make widespread use of robot manipulators in industrial environments. Major problem in controlling a robot manipulator is to control the robot in order to achieve the desired position. Therefore the design issue of the robot control is to choose the right type controller. Computed Torque Controller (CTC is a powerful nonlinear controllers are widely used in the control of robot manipulators. CTC controller is designed based on feedback linearization and the required torque of the robot arm by using a nonlinear feedback control law. Simulation is done by providing joint trajectory from point to point. The simulation results show that the PD-Fuzzy-CTC controller is able to follow the joint trajectory with The RMSE value of the joint angle position of PD-Fuzzy-CTC controller is 10 times smaller than that of the PD-CTC controller with the end-effector position accuracy is 0.1 mm.  

  17. Increased complexity of gene structure and base composition in vertebrates

    Institute of Scientific and Technical Information of China (English)

    Ying Wu; Huizhong Yuan; Shengjun Tan; Jian-Qun Chen; Dacheng Tian; Haiwang Yang

    2011-01-01

    How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals: human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3' UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results.We also find that GC-content increased in many gene regions (especially 5' UTR) in the evolution of endotherms, except in coding-exons.Analysis of individual genomes shows that 3′ UTR demonstrated stronger length and CC-content correlation with intron than 5' UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.

  18. Triplex inducer-directed self-assembly of single-walled carbon nanotubes: a triplex DNA-based approach for controlled manipulation of nanostructures

    OpenAIRE

    Zhao, Chao; Qu, Konggang; Xu, Can; Ren, Jinsong; Qu, Xiaogang

    2011-01-01

    As a promising strategy for artificially control of gene expression, reversible assembly of nanomaterials and DNA nanomachine, DNA triplex formation has received much attention. Carbon nanotubes as gene and drug delivery vector or as ‘building blocks’ in nano/microelectronic devices have been successfully explored. Therefore, studies on triplex DNA-based carbon nanotube hybrid materials are important for development of smart nanomaterials and for gene therapy. In this report, a small molecule...

  19. Using intron position conservation for homology-based gene prediction.

    Science.gov (United States)

    Keilwagen, Jens; Wenk, Michael; Erickson, Jessica L; Schattat, Martin H; Grau, Jan; Hartung, Frank

    2016-05-19

    Annotation of protein-coding genes is very important in bioinformatics and biology and has a decisive influence on many downstream analyses. Homology-based gene prediction programs allow for transferring knowledge about protein-coding genes from an annotated organism to an organism of interest.Here, we present a homology-based gene prediction program called GeMoMa. GeMoMa utilizes the conservation of intron positions within genes to predict related genes in other organisms. We assess the performance of GeMoMa and compare it with state-of-the-art competitors on plant and animal genomes using an extended best reciprocal hit approach. We find that GeMoMa often makes more precise predictions than its competitors yielding a substantially increased number of correct transcripts. Subsequently, we exemplarily validate GeMoMa predictions using Sanger sequencing. Finally, we use RNA-seq data to compare the predictions of homology-based gene prediction programs, and find again that GeMoMa performs well.Hence, we conclude that exploiting intron position conservation improves homology-based gene prediction, and we make GeMoMa freely available as command-line tool and Galaxy integration. PMID:26893356

  20. Genetic Manipulation of Clostridium difficile

    OpenAIRE

    Bouillaut, Laurent; McBride, Shonna M; Sorg, Joseph A.

    2011-01-01

    Clostridium difficile is a Gram-positive, spore forming, anaerobic, intestinal bacterium and is the most common cause of antibiotic-associated colitis. For many years this organism was considered genetically intractable, but in the past 10 years, multiple methods have been developed or adapted for genetic manipulation of C. difficile. This unit describes the molecular techniques used for genetic modification of this organism, including methods for gene disruption, complementation, plasmid int...

  1. Prediction of Tumor Outcome Based on Gene Expression Data

    Institute of Scientific and Technical Information of China (English)

    Liu Juan; Hitoshi Iba

    2004-01-01

    Gene expression microarray data can be used to classify tumor types. We proposed a new procedure to classify human tumor samples based on microarray gene expressions by using a hybrid supervised learning method called MOEA+WV (Multi-Objective Evolutionary Algorithm+Weighted Voting). MOEA is used to search for a relatively few subsets of informative genes from the high-dimensional gene space, and WV is used as a classification tool. This new method has been applied to predicate the subtypes of lymphoma and outcomes of medulloblastoma. The results are relatively accurate and meaningful compared to those from other methods.

  2. 基于机器视觉的机器人写字技术的设计%Design of Writing by Robot Manipulator Based on Machine Vision

    Institute of Scientific and Technical Information of China (English)

    何薇; 钱增磊; 唐超; 蒋玉兵; 江耿红; 肖文皓; 白瑞林

    2011-01-01

    For the purpose of experiment and teaching, the article proposed a method of writing by manipulator based on machine vision. This method, which uses 6-axis robot manipulator of DENSO VP6242g and machine vision of XINJE as the experimental platform, picks up the image information of the characters by machine vision, programs by VC + + , and transmits the image to computer by user-defined protocol of machine vision; it also makes a series of image processing by the OpenCV libraries, including threshold, close, thinning and character segmentation. The information of coordinates of character coming from image processing can then be used to control the manipulators movement, with the manipulator controller connected to the computer via 0RiN2, thus completing the writing process. The experimental results prove that this method can drive the manipulator to write the character caught by machine vision correctly. And the writing can be recognized easily.%针对教学与实验,提出一种基于机器视觉的机器人写字方法.以六自由度DENSO VP6242G机器人、信捷机器视觉和PC机为实验平台,通过机器视觉获取字符的图像信息,采用VC++编程,利用机器视觉自定义协议将图像传输给PC机;借助OpenCV库对图像进行阈值化、闭运算、细化和笔画分割等一系列的处理;利用图像处理得到字符坐标信息控制机器人的多轴联动,机器人控制器与PC机之间通过ORiN2连接,从而完成字符的书写.实验表明,在字迹清晰条件下该方法能够使机器人准确地写出机器视觉所看到的字符.

  3. Effect of manipulating progesterone before timed artificial insemination on reproductive and endocrine parameters in seasonal-calving, pasture-based Holstein-Friesian cows.

    Science.gov (United States)

    Fricke, P M; Carvalho, P D; Lucy, M C; Curran, F; Herlihy, M M; Waters, S M; Larkin, J A; Crowe, M A; Butler, S T

    2016-08-01

    Fertility to timed AI (TAI) is profoundly affected by progesterone (P4) levels during hormonal synchronization protocols. Holstein-Friesian dairy cows managed in a seasonal-calving, pasture-based production system were randomly assigned to 2 treatments to manipulate P4 before TAI during growth of the preovulatory follicle. Cows in the first treatment (High P4; n=30) were submitted to a Double-Ovsynch protocol {Pre-Ovsynch [GnRH; 7 d, PGF2α; 3 d, GnRH] followed 7 d later by Breeding-Ovsynch [GnRH (G1); 7 d PGF2α; 24 h, PGF2α; 32 h, GnRH (G2); 16 h, TAI]}. Cows in the second treatment (n=30; Low P4) received the same Double-Ovsynch protocol but with an additional PGF2α treatment 24 h after G1. Overall, synchronization rate did not differ between treatments and was 92% (55/60). Unexpectedly, 37% of Low P4 cows were detected in estrus ~24 h before scheduled TAI and were inseminated ~16 h before scheduled TAI. Overall, P4 did not differ between treatments at G1, whereas High P4 cows had greater P4 concentrations at PGF2α and G2 than Low P4 cows. High P4 cows had the smallest mean follicle diameter at G2, whereas Low P4 cows with no estrus before TAI had intermediate mean follicle diameter at G2, and Low P4 cows with estrus before TAI had the largest mean follicle diameter. Low P4 cows with estrus before TAI had larger corpora lutea 15 d after TAI than Low P4 cows without estrus before TAI or High P4 cows. In accordance with corpus luteum size on d 15, High P4 cows and Low P4 cows without estrus before TAI had lower P4 from 4 to 46 d after TAI than Low P4 cows with estrus before TAI. Relative mRNA levels of the interferon-stimulated genes ISG15, MX1, MX2, and OAS1 were greater for Low P4 than for High P4 cows, whereas relative mRNA levels of RTP4 were greater for High P4 than for Low P4 cows 18 d after TAI. Treatment did not affect plasma pregnancy-associated glycoprotein concentrations after TAI; however, pregnancy-associated glycoprotein concentrations were

  4. High precision redundant robotic manipulator

    International Nuclear Information System (INIS)

    A high precision redundant robotic manipulator for overcoming contents imposed by obstacles or imposed by a highly congested work space is disclosed. One embodiment of the manipulator has four degrees of freedom and another embodiment has seven degrees of freedom. Each of the embodiments utilize a first selective compliant assembly robot arm (SCARA) configuration to provide high stiffness in the vertical plane, a second SCARA configuration to provide high stiffness in the horizontal plane. The seven degree of freedom embodiment also utilizes kinematic redundancy to provide the capability of avoiding obstacles that lie between the base of the manipulator and the end effector or link of the manipulator. These additional three degrees of freedom are added at the wrist link of the manipulator to provide pitch, yaw and roll. The seven degrees of freedom embodiment uses one revolute point per degree of freedom. For each of the revolute joints, a harmonic gear coupled to an electric motor is introduced, and together with properly designed based servo controllers provide an end point repeatability of less than 10 microns. 3 figs

  5. High-Speed Tactile Sensing for Array-Type Tactile Sensor and Object Manipulation Based on Tactile Information

    Directory of Open Access Journals (Sweden)

    Wataru Fukui

    2011-01-01

    Full Text Available We have developed a universal robot hand with tactile and other sensors. An array-type tactile sensor is crucial for dexterous manipulation of objects using a robotic hand, since this sensor can measure the pressure distribution on finger pads. The sensor has a very high resolution, and the shape of a grasped object can be classified by using this sensor. The more the number of measurement points provided, the higher the accuracy of the classification, but with a corresponding lengthening of the measurement cycle. In this paper, the problem of slow response time is resolved by using software for an array-type tactile sensor with high resolution that emulates the human sensor system. The validity of the proposed method is demonstrated through experiments.

  6. An ensemble of SVM classifiers based on gene pairs.

    Science.gov (United States)

    Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

    2013-07-01

    In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. PMID:23668348

  7. Identification and Analysis of the Balhimycin Biosynthetic Gene Cluster and Its Use for Manipulating Glycopeptide Biosynthesis in Amycolatopsis mediterranei DSM5908

    OpenAIRE

    Pelzer, S.; Süßmuth, R.; Heckmann, D.; Recktenwald, J.; Huber, P; Jung, G; Wohlleben, W

    1999-01-01

    Seven complete genes and one incomplete gene for the biosynthesis of the glycopeptide antibiotic balhimycin were isolated from the producer, Amycolatopsis mediterranei DSM5908, by a reverse-cloning approach and characterized. Using oligonucleotides derived from glycosyltransferase sequences, a 900-bp glycosyltransferase gene fragment was amplified and used to identify a DNA fragment of 9,882 bp. Of the identified open reading frames, three (oxyA to -C) showed significant sequence similarities...

  8. Modeling of contact theories for the manipulation of biological micro/nanoparticles in the form of circular crowned rollers based on the atomic force microscope

    International Nuclear Information System (INIS)

    This article has dealt with the development and modeling of various contact theories for biological nanoparticles shaped as cylinders and circular crowned rollers for application in the manipulation of different biological micro/nanoparticles based on Atomic Force Microscope. First, the effective contact forces were simulated, and their impact on contact mechanics simulation was investigated. In the next step, the Hertz contact model was simulated and compared for gold and DNA nanoparticles with the three types of spherical, cylindrical, and circular crowned roller type contact geometries. Then by reducing the length of the cylindrical section in the circular crowned roller geometry, the geometry of the body was made to approach that of a sphere, and the results were compared for DNA nanoparticles. To anticipatory validate the developed theories, the results of the cylindrical and the circular crowned roller contacts were compared with the results of the existing spherical contact simulations. Following the development of these contact models for the manipulation of various biological micro/nanoparticles, the cylindrical and the circular crowned roller type contact theories were modeled based on the theories of Lundberg, Dowson, Nikpur, Heoprich, and Hertz for the manipulation of biological micro/nanoparticles. Then, for a more accurate validation, the results obtained from the simulations were compared with those obtained by the finite element method and with the experimental results available in previous articles. The previous research works on the simulation of nanomanipulation have mainly investigated the contact theories used in the manipulation of spherical micro/nanoparticles. However since in real biomanipulation situations, biological micro/nanoparticles of more complex shapes need to be displaced in biological environments, this article therefore has modeled and compared, for the first time, different contact theories for use in the biomanipulation of

  9. Modeling of contact theories for the manipulation of biological micro/nanoparticles in the form of circular crowned rollers based on the atomic force microscope

    Science.gov (United States)

    Korayem, M. H.; Khaksar, H.; Taheri, M.

    2013-11-01

    This article has dealt with the development and modeling of various contact theories for biological nanoparticles shaped as cylinders and circular crowned rollers for application in the manipulation of different biological micro/nanoparticles based on Atomic Force Microscope. First, the effective contact forces were simulated, and their impact on contact mechanics simulation was investigated. In the next step, the Hertz contact model was simulated and compared for gold and DNA nanoparticles with the three types of spherical, cylindrical, and circular crowned roller type contact geometries. Then by reducing the length of the cylindrical section in the circular crowned roller geometry, the geometry of the body was made to approach that of a sphere, and the results were compared for DNA nanoparticles. To anticipatory validate the developed theories, the results of the cylindrical and the circular crowned roller contacts were compared with the results of the existing spherical contact simulations. Following the development of these contact models for the manipulation of various biological micro/nanoparticles, the cylindrical and the circular crowned roller type contact theories were modeled based on the theories of Lundberg, Dowson, Nikpur, Heoprich, and Hertz for the manipulation of biological micro/nanoparticles. Then, for a more accurate validation, the results obtained from the simulations were compared with those obtained by the finite element method and with the experimental results available in previous articles. The previous research works on the simulation of nanomanipulation have mainly investigated the contact theories used in the manipulation of spherical micro/nanoparticles. However since in real biomanipulation situations, biological micro/nanoparticles of more complex shapes need to be displaced in biological environments, this article therefore has modeled and compared, for the first time, different contact theories for use in the biomanipulation of

  10. Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression Network

    Directory of Open Access Journals (Sweden)

    Dajeong Lim

    2014-01-01

    Full Text Available Marbling is an important trait in characterization beef quality and a major factor for determining the price of beef in the Korean beef market. In particular, marbling is a complex trait and needs a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with marbling, we used a weighted gene coexpression network analysis from the expression value of bovine genes. Hub genes were identified; they were topologically centered with large degree and BC values in the global network. We performed gene expression analysis to detect candidate genes in M. longissimus with divergent marbling phenotype (marbling scores 2 to 7 using qRT-PCR. The results demonstrate that transmembrane protein 60 (TMEM60 and dihydropyrimidine dehydrogenase (DPYD are associated with increasing marbling fat. We suggest that the network-based approach in livestock may be an important method for analyzing the complex effects of candidate genes associated with complex traits like marbling or tenderness.

  11. Efficient Gene Transfer Mediated by HIV-1-based Defective Lentivector and Inhibition of HIV-1 Replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Lentiviral vectors have drawn considerable attention recently and show great promise to become important delivery vehicles for future gene transfer manipulation. In the present study we have optimized a protocol for preparation of human immunodeficiency virus type-1 (HIV-1)-based defective lentiviral vectors (DLV) and characterized these vectors in terms of their transduction of different cells. Transient co-transfection of 293T packaging cells with DNA plasmids encoding lentiviral vector constituents resulted in production of high-titer DLV (0.5-1.2 × 107IU/mL), which can be further concentrated over 100-fold through a single step ultracentrifugation. These vectors were capable of transducing a variety of cells from both primate and non-primate sources and high transduction efficiency was achieved using concentrated vectors. Assessment of potential generation of RCV revealed no detection of infection by infectious particles in DLV-transduced CEM, SupT-1 and MT-2 cells. Long-term culture of transduced cells showed a stable expression of transgenes without apparent alteration in cellular morphology and growth kinetics. Vector mobilization to untransduced cells mediated by wild-type HIV-1 infection was confirmed in this test. Challenge of transduced human T-lymphocytes with wild-type HIV-1 showed these cells are totally resistant to the viral infection. Considering the effective gene transfer and stable gene expression, safety and anti-HIV activity, these DLV vectors warrant further exploration for their potential use as a gene transfer vehicle in the development of gene therapy protocols.

  12. Patients, evidence and genes: an exploration of GPs' perspectives on gene-based personalized nutrition advice

    NARCIS (Netherlands)

    Bouwman, L.I.; Molder, te H.F.M.; Hiddink, G.J.

    2008-01-01

    Background. Nutrigenomics science examines the response of individuals to food compounds using post-genomics technology. It is expected that in the future, personalized nutrition advice can be provided based on information about genetic make-up. Objectives. Gene-based personalized nutrition advice e

  13. GOBO: gene expression-based outcome for breast cancer online.

    Directory of Open Access Journals (Sweden)

    Markus Ringnér

    Full Text Available Microarray-based gene expression analysis holds promise of improving prognostication and treatment decisions for breast cancer patients. However, the heterogeneity of breast cancer emphasizes the need for validation of prognostic gene signatures in larger sample sets stratified into relevant subgroups. Here, we describe a multifunctional user-friendly online tool, GOBO (http://co.bmc.lu.se/gobo, allowing a range of different analyses to be performed in an 1881-sample breast tumor data set, and a 51-sample breast cancer cell line set, both generated on Affymetrix U133A microarrays. GOBO supports a wide range of applications including: 1 rapid assessment of gene expression levels in subgroups of breast tumors and cell lines, 2 identification of co-expressed genes for creation of potential metagenes, 3 association with outcome for gene expression levels of single genes, sets of genes, or gene signatures in multiple subgroups of the 1881-sample breast cancer data set. The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform.

  14. Circular-rubbing Manipulation

    Institute of Scientific and Technical Information of China (English)

    SHEN Guo-quan; XIAO Yuan-chun

    2003-01-01

    @@ "Mo" literally means "rubbing between two things"and "eliminating". Circular-rubbing is one of the earliest manipulations used in clinical practice. Circular-rubbing differs from pressing actually. Pressing is a static manipulation and acts to inhibit motion; circular-rubbing is a movable manipulation and serves to eliminate stationary. Circular-rubbing can be performed by either the palm or the finger.

  15. Managing collaboration in the nanoManipulator

    DEFF Research Database (Denmark)

    Hudson, Thomas C.; Heiser, Aron T.; Sonnenwald, Diane H.;

    2003-01-01

    We designed, developed, deployed, and evaluated the Collaborative nanoManipulator (CnM), a system supporting remote collaboration between users of the nanoManipulator interface to atomic force microscopes. To be accepted by users, the shared nanoManipulator application had to have the same high...... level of interactivity as the single user system and the application had to support a user's ability to interleave working privately and working collaboratively. This paper briefly describes the entire collaboration system, but focuses on the shared nanoManipulator application. Based on our experience...

  16. Combined method for parallel manipulator configuration design

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Configuration design is an essential, creative and decision-making step in parallel manipulator design process, in which modeling and assembly are iterative and trivial. Combined approach with automatic parametric modeling and automatic assembly is proposed for parallel manipulator configuration design. The design process and key techniques, such as configuration design, configuration verification, poses calculation of all parts in parallel manipulator, virtual assembly and etc., are discussed and demonstrated by an example. A software package is developed for parallel manipulator configuration design based on the proposed method with Visual C+ + and UG/OPEN on Unigraphics.

  17. The Impact of an Ego Depletion Manipulation on Performance-Based and Self-Report Assessment Measures.

    Science.gov (United States)

    Charek, Daniel B; Meyer, Gregory J; Mihura, Joni L

    2016-10-01

    We investigated the impact of ego depletion on selected Rorschach cognitive processing variables and self-reported affect states. Research indicates acts of effortful self-regulation transiently deplete a finite pool of cognitive resources, impairing performance on subsequent tasks requiring self-regulation. We predicted that relative to controls, ego-depleted participants' Rorschach protocols would have more spontaneous reactivity to color, less cognitive sophistication, and more frequent logical lapses in visualization, whereas self-reports would reflect greater fatigue and less attentiveness. The hypotheses were partially supported; despite a surprising absence of self-reported differences, ego-depleted participants had Rorschach protocols with lower scores on two variables indicative of sophisticated combinatory thinking, as well as higher levels of color receptivity; they also had lower scores on a composite variable computed across all hypothesized markers of complexity. In addition, self-reported achievement striving moderated the effect of the experimental manipulation on color receptivity, and in the Depletion condition it was associated with greater attentiveness to the tasks, more color reactivity, and less global synthetic processing. Results are discussed with an emphasis on the response process, methodological limitations and strengths, implications for calculating refined Rorschach scores, and the value of using multiple methods in research and experimental paradigms to validate assessment measures. PMID:26002059

  18. Genetic manipulation of francisella tularensis.

    Science.gov (United States)

    Zogaj, Xhavit; Klose, Karl E

    2010-01-01

    Francisella tularensis is a facultative intracellular pathogen that causes the disease tularemia. F. tularensis subsp. tularensis causes the most severe disease in humans and has been classified as a Category A select agent and potential bioweapon. There is currently no vaccine approved for human use, making genetic manipulation of this organism critical to unraveling the genetic basis of pathogenesis and developing countermeasures against tularemia. The development of genetic techniques applicable to F. tularensis have lagged behind those routinely used for other bacteria, primarily due to lack of research and the restricted nature of the biocontainment required for studying this pathogen. However, in recent years, genetic techniques, such as transposon mutagenesis and targeted gene disruption, have been developed, that have had a dramatic impact on our understanding of the genetic basis of F. tularensis virulence. In this review, we describe some of the methods developed for genetic manipulation of F. tularensis. PMID:21607086

  19. Manipulators in teleoperation

    International Nuclear Information System (INIS)

    Teleoperated manipulators represent a mature technology which has evolved over nearly 40 years of applications experience. The wide range of manipulator concepts developed thus far reflect differing applications, priorities, and philosophies. The technology of teleoperated manipulators is in a rapid state of change (just as are industrial robotics) fueled by microelectronics and materials advances. Large strides in performance and dexterity are now practical and advantageous. Even though improved controls and sensory feedback will increase functionality, overall costs should be reduced as manipulator fabrication and assembly labor costs are reduced through improved manufacturing technology. As these advances begin to materialize, broader applications in nonnuclear areas should occur

  20. Sucrose ester based cationic liposomes as effective non-viral gene vectors for gene delivery.

    Science.gov (United States)

    Zhao, Yinan; Zhu, Jie; Zhou, Hengjun; Guo, Xin; Tian, Tian; Cui, Shaohui; Zhen, Yuhong; Zhang, Shubiao; Xu, Yuhong

    2016-09-01

    As sucrose esters (SEs) are natural and biodegradable excipients with excellent drug dissolution and drug absorption/permeation in controlled release systems, we firstly incorporated SE into liposomes for gene delivery in this article. A peptide-based lipid (CDO14), Gemini-based quaternary ammonium-based lipid (CTA14), and mono-head quaternary ammonium lipid (CPA14), and SE as helper lipid, were prepared into liposomes which could enhance the interactions between liposomes and pDNA. Most importantly, the liposomes with helper lipid SE showed higher transfection and lower cytotoxicity than those without SE in Hela and A549 cells. It was also found that the transfection efficiency increased with the increase of SE content. The selected liposome, CDO14/SE, was able to deliver siRNA against luciferase for silencing gene in lung tumors of mice, with little in vivo toxicity. The results convincingly demonstrated SEs could be highly desirable candidates for gene delivery systems. PMID:27232309

  1. PCR-based detection of gene transfer vectors: application to gene doping surveillance.

    Science.gov (United States)

    Perez, Irene C; Le Guiner, Caroline; Ni, Weiyi; Lyles, Jennifer; Moullier, Philippe; Snyder, Richard O

    2013-12-01

    Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR. PMID:23912835

  2. 75 FR 67657 - Prohibition of Market Manipulation

    Science.gov (United States)

    2010-11-03

    ... Manipulation, 71 FR 4244, 4253 (Jan. 26, 2006) (`` inal rule prohibits the use or employment of any device... their comment letters. B. Anti-Trust Considerations Section 15(b) of the CEA, 7 U.S.C. 19(b), requires... Commission to protect against fraud-based manipulation. I thank Senator Cantwell for her leadership...

  3. Development of Nano- and Microparticle Technologies for Targeted Gene Silencing through RNA Interference Manipulation of the Immune Response in Inflammatory Lung Disease

    OpenAIRE

    Kelly, Ciara

    2011-01-01

    RNA Interference (RNAi) allows specific and potent knockdown of target genes and interest now lies beyond its use as a molecular biology tool and in its potential as a therapeutic to mediate gene silencing in diseased cells. Targeted local delivery of small interfering RNA (siRNA) to the lungs via inhalation offers a unique opportunity to treat a range of previously unbeatable or poorly controlled respiratory conditions. Alveolar macrophages are the first line of defence against inhaled toxin...

  4. Extensive co-operation between the Epstein-Barr virus EBNA3 proteins in the manipulation of host gene expression and epigenetic chromatin modification.

    Directory of Open Access Journals (Sweden)

    Robert E White

    Full Text Available Epstein-Barr virus (EBV is able to drive the transformation of B-cells, resulting in the generation of lymphoblastoid cell lines (LCLs in vitro. EBV nuclear proteins EBNA3A and EBNA3C are necessary for efficient transformation, while EBNA3B is dispensable. We describe a transcriptome analysis of BL31 cells infected with a series of EBNA3-knockout EBVs, including one deleted for all three EBNA3 genes. Using Affymetrix Exon 1.0 ST microarrays analysed with the MMBGX algorithm, we have identified over 1000 genes whose regulation by EBV requires one of the EBNA3s. Remarkably, a third of the genes identified require more than one EBNA3 for their regulation, predominantly EBNA3C co-operating with either EBNA3B, EBNA3A or both. The microarray was validated by real-time PCR, while ChIP analysis of a selection of co-operatively repressed promoters indicates a role for polycomb group complexes. Targets include genes involved in apoptosis, cell migration and B-cell differentiation, and show a highly significant but subtle alteration in genes involved in mitosis. In order to assess the relevance of the BL31 system to LCLs, we analysed the transcriptome of a set of EBNA3B knockout (3BKO LCLs. Around a third of the genes whose expression level in LCLs was altered in the absence of EBNA3B were also altered in 3BKO-BL31 cell lines.Among these are TERT and TCL1A, implying that EBV-induced changes in the expression of these genes are not required for B-cell transformation. We also identify 26 genes that require both EBNA3A and EBNA3B for their regulation in LCLs. Together, this shows the complexity of the interaction between EBV and its host, whereby multiple EBNA3 proteins co-operate to modulate the behaviour of the host cell.

  5. Master-slave manipulator

    International Nuclear Information System (INIS)

    A remote control master-slave manipulator for performing work on the opposite side of a barrier wall, is described. The manipulator consists of a rotatable horizontal support adapted to extend through the wall and two longitudinally extensible arms, a master and a slave, pivotally connected one to each end of the support. (U.K.)

  6. Calculating Clearances for Manipulators

    Science.gov (United States)

    Copeland, E. L.; Peticolas, J. D.; Ray, L. D.

    1983-01-01

    Set of algorithms rapidly calculates minimum safe clearances for remote manipulators. Such calculations are used in design of trajectories for manipulators to ensure they do not accidentally strike surrounding objects. Structural parts are considered as cylindrical shells having circular plane areas for ends. Clearance calculation method offers special benefits in industrial robotics, particularly in automated machining.

  7. Cell manipulation in microfluidics

    International Nuclear Information System (INIS)

    Recent advances in the lab-on-a-chip field in association with nano/microfluidics have been made for new applications and functionalities to the fields of molecular biology, genetic analysis and proteomics, enabling the expansion of the cell biology field. Specifically, microfluidics has provided promising tools for enhancing cell biological research, since it has the ability to precisely control the cellular environment, to easily mimic heterogeneous cellular environment by multiplexing, and to analyze sub-cellular information by high-contents screening assays at the single-cell level. Various cell manipulation techniques in microfluidics have been developed in accordance with specific objectives and applications. In this review, we examine the latest achievements of cell manipulation techniques in microfluidics by categorizing externally applied forces for manipulation: (i) optical, (ii) magnetic, (iii) electrical, (iv) mechanical and (v) other manipulations. We furthermore focus on history where the manipulation techniques originate and also discuss future perspectives with key examples where available. (topical review)

  8. Manipulator comparative testing program

    International Nuclear Information System (INIS)

    The Manipulator Comparative Testing Program examined differences among manipulator systems from the United States and Japan. The manipulator systems included the Meidensha BILARM 83A, the Model M-2 of Central Research Laboratories Division of Sargent Industries (CRL), and the GCA Corporation PaR Systems Model 6000. The site of testing was the Remote Operations Maintenance Demonstration (ROMD) facility, operated by the Fuel Recycle Division in the Consolidated Fuel Reprocessing Program at the Oak Ridge National Laboratory (ORNL). In all stages of testing, operators using the CRL Model M-2 manipulator had consistently lower times to completion and error rates than they did using other machines. Performance was second best with the Meidensha BILARM 83A in master-slave mode. Performance with the BILARM in switchbox mode and the PaR 6000 manipulator was approximately equivalent in terms of criteria recorded in testing. These data show no impact of force reflection on task performance

  9. PaGenBase: a pattern gene database for the global and dynamic understanding of gene function.

    Directory of Open Access Journals (Sweden)

    Jian-Bo Pan

    Full Text Available Pattern genes are a group of genes that have a modularized expression behavior under serial physiological conditions. The identification of pattern genes will provide a path toward a global and dynamic understanding of gene functions and their roles in particular biological processes or events, such as development and pathogenesis. In this study, we present PaGenBase, a novel repository for the collection of tissue- and time-specific pattern genes, including specific genes, selective genes, housekeeping genes and repressed genes. The PaGenBase database is now freely accessible at http://bioinf.xmu.edu.cn/PaGenBase/. In the current version (PaGenBase 1.0, the database contains 906,599 pattern genes derived from the literature or from data mining of more than 1,145,277 gene expression profiles in 1,062 distinct samples collected from 11 model organisms. Four statistical parameters were used to quantitatively evaluate the pattern genes. Moreover, three methods (quick search, advanced search and browse were designed for rapid and customized data retrieval. The potential applications of PaGenBase are also briefly described. In summary, PaGenBase will serve as a resource for the global and dynamic understanding of gene function and will facilitate high-level investigations in a variety of fields, including the study of development, pathogenesis and novel drug discovery.

  10. A study of nanoparticle manipulation using ultrasonic standing waves

    NARCIS (Netherlands)

    Neer, P.L.M.J. van; Rasidovic, A.; Volker, A.W.F.

    2013-01-01

    There has been considerable interest in the noninvasive manipulation of particles in dispersions during the last 15 years. The manipulation techniques based on acoustic radiation forces are particularly interesting as they allow for the manipulation of particles based on their density, compressibili

  11. Cytochrome P450-based cancer gene therapy: current status.

    Science.gov (United States)

    Kan, On; Kingsman, Susan; Naylor, Stuart

    2002-12-01

    Results from a number of preclinical studies have demonstrated that a P450-based gene-directed enzyme prodrug therapy (GDEPT) strategy for the treatment of cancer is both safe and efficacious. This strategy has now moved forward into the clinic. At least two different approaches using different delivery methods (retroviral vector MetXia [Oxford BioMedica] and encapsulated P450 expressing cells), different cytochrome P450 isoforms (human CYP2B6 versus rat CYP2B1) and different prodrugs (cyclophosphamide [CPA] versus ifosfamide [IFA]) have concluded Phase I/II clinical trial with encouraging results. In the future, P450-based GDEPT can potentially be further enhanced by improved vectors for P450 gene delivery and disease-targeted promoters for focused gene expression at the target site. In addition, there is scope for developing synthetic P450s and their respective prodrugs to improve both enzyme kinetics and the profile of the active moiety. PMID:12517265

  12. Manipulation of carbon flux into fatty acid biosynthesis pathway in Dunaliella salina using AccD and ME genes to enhance lipid content and to improve produced biodiesel quality

    Directory of Open Access Journals (Sweden)

    Ahmad Farhad Talebi

    2014-08-01

    Full Text Available Advanced generations of biofuels basically revolve around non-agricultural energy crops. Among those, microalgae owing to its unique characteristics i.e. natural tolerance to waste and saline water, sustainable biomass production and high lipid content (LC, is regarded by many as the ultimate choice for the production of various biofuels such as biodiesel. In the present study, manipulation of carbon flux into fatty acid biosynthesis pathway in Dunaliella salina was achieved using pGH plasmid harboring AccD and ME genes to enhance lipid content and to improve produced biodiesel quality. The stability of transformation was confirmed by PCR after several passages. Southern hybridization of AccD probe with genomic DNA revealed stable integration of the cassette in the specific positions in the chloroplast genome with no read through transcription by indigenous promoters. Comparison of the LC and fatty acid profile of the transformed algal cell line and the control revealed the over-expression of the ME/AccD genes in the transformants leading to 12% increase in total LC and significant improvements in biodiesel properties especially by increasing algal oil oxidation stability. The whole process successfully implemented herein for transforming algal cells by genes involved in lipid production pathway could be helpful for large scale biodiesel production from microalgae.

  13. Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

    OpenAIRE

    Lida Zhang; Shunwu Yu; Kaijing Zuo; Lijun Luo; Kexuan Tang

    2012-01-01

    Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene ...

  14. Manipulation of Biofilm Microbial Ecology

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C.; Palmer, R.J., Jr.; Zinn, M.; Smith, C.A.; Burkhalter, R.; Macnaughton, S.J.; Whitaker, K.W.; Kirkegaard, R.D.

    1998-08-15

    The biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms be generated. The most effective monitoring of biofilm formation, succession and desaturation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  15. Detection of Gene Interactions Based on Syntactic Relations

    Directory of Open Access Journals (Sweden)

    Mi-Young Kim

    2008-01-01

    Full Text Available Interactions between proteins and genes are considered essential in the description of biomolecular phenomena, and networks of interactions are applied in a system's biology approach. Recently, many studies have sought to extract information from biomolecular text using natural language processing technology. Previous studies have asserted that linguistic information is useful for improving the detection of gene interactions. In particular, syntactic relations among linguistic information are good for detecting gene interactions. However, previous systems give a reasonably good precision but poor recall. To improve recall without sacrificing precision, this paper proposes a three-phase method for detecting gene interactions based on syntactic relations. In the first phase, we retrieve syntactic encapsulation categories for each candidate agent and target. In the second phase, we construct a verb list that indicates the nature of the interaction between pairs of genes. In the last phase, we determine direction rules to detect which of two genes is the agent or target. Even without biomolecular knowledge, our method performs reasonably well using a small training dataset. While the first phase contributes to improve recall, the second and third phases contribute to improve precision. In the experimental results using ICML 05 Workshop on Learning Language in Logic (LLL05 data, our proposed method gave an F-measure of 67.2% for the test data, significantly outperforming previous methods. We also describe the contribution of each phase to the performance.

  16. MODULAR MANIPULATOR FOR ROBOTICS APPLICATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Joseph W. Geisinger, Ph.D.

    2001-07-31

    ARM Automation, Inc. is developing a framework of modular actuators that can address the DOE's wide range of robotics needs. The objective of this effort is to demonstrate the effectiveness of this technology by constructing a manipulator from these actuators within a glovebox for Automated Plutonium Processing (APP). At the end of the project, the system of actuators was used to construct several different manipulator configurations, which accommodate common glovebox tasks such as repackaging. The modular nature and quickconnects of this system simplify installation into ''hot'' boxes and any potential modifications or repair therein. This work focused on the development of self-contained robotic actuator modules including the embedded electronic controls for the purpose of building a manipulator system. Both of the actuators developed under this project contain the control electronics, sensors, motor, gear train, wiring, system communications and mechanical interfaces of a complete robotics servo device. Test actuators and accompanying DISC{trademark}s underwent validation testing at The University of Texas at Austin and ARM Automation, Inc. following final design and fabrication. The system also included custom links, an umbilical cord, an open architecture PC-based system controller, and operational software that permitted integration into a completely functional robotic manipulator system. The open architecture on which this system is based avoids proprietary interfaces and communication protocols which only serve to limit the capabilities and flexibility of automation equipment. The system was integrated and tested in the contractor's facility for intended performance and operations. The manipulator was tested using the full-scale equipment and process mock-ups. The project produced a practical and operational system including a quantitative evaluation of its performance and cost.

  17. MODULAR MANIPULATOR FOR ROBOTICS APPLICATIONS

    International Nuclear Information System (INIS)

    ARM Automation, Inc. is developing a FR-amework of modular actuators that can address the DOE's wide range of robotics needs. The objective of this effort is to demonstrate the effectiveness of this technology by constructing a manipulator FR-om these actuators within a glovebox for Automated Plutonium Processing (APP). At the end of the project, the system of actuators was used to construct several different manipulator configurations, which accommodate common glovebox tasks such as repackaging. The modular nature and quickconnects of this system simplify installation into ''hot'' boxes and any potential modifications or repair therein. This work focused on the development of self-contained robotic actuator modules including the embedded electronic controls for the purpose of building a manipulator system. Both of the actuators developed under this project contain the control electronics, sensors, motor, gear train, wiring, system communications and mechanical interfaces of a complete robotics servo device. Test actuators and accompanying DISC(trademark)s underwent validation testing at The University of Texas at Austin and ARM Automation, Inc. following final design and fabrication. The system also included custom links, an umbilical cord, an open architecture PC-based system controller, and operational software that permitted integration into a completely functional robotic manipulator system. The open architecture on which this system is based avoids proprietary interfaces and communication protocols which only serve to limit the capabilities and flexibility of automation equipment. The system was integrated and tested in the contractor's facility for intended performance and operations. The manipulator was tested using the full-scale equipment and process mock-ups. The project produced a practical and operational system including a quantitative evaluation of its performance and cost

  18. System Integration for Real-time Mobile Manipulation

    OpenAIRE

    Reza Oftadeh; Aref, Mohammad M.; Reza Ghabcheloo; Jouni Mattila

    2014-01-01

    Mobile manipulators are one of the most complicated types of mechatronics systems. The performance of these robots in performing complex manipulation tasks is highly correlated with the synchronization and integration of their low-level components. This paper discusses in detail the mechatronics design of a four wheel steered mobile manipulator. It presents the manipulator ’s mechanical structure and electrical interfaces, designs low-level software architecture based on embedded PC-based con...

  19. Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network

    Directory of Open Access Journals (Sweden)

    Chen Xin

    2012-10-01

    Full Text Available Abstract Background The identification of genes that predict in vitro cellular chemosensitivity of cancer cells is of great importance. Chemosensitivity related genes (CRGs have been widely utilized to guide clinical and cancer chemotherapy decisions. In addition, CRGs potentially share functional characteristics and network features in protein interaction networks (PPIN. Methods In this study, we proposed a method to identify CRGs based on Gene Ontology (GO and PPIN. Firstly, we documented 150 pairs of drug-CCRG (curated chemosensitivity related gene from 492 published papers. Secondly, we characterized CCRGs from the perspective of GO and PPIN. Thirdly, we prioritized CRGs based on CCRGs’ GO and network characteristics. Lastly, we evaluated the performance of the proposed method. Results We found that CCRG enriched GO terms were most often related to chemosensitivity and exhibited higher similarity scores compared to randomly selected genes. Moreover, CCRGs played key roles in maintaining the connectivity and controlling the information flow of PPINs. We then prioritized CRGs using CCRG enriched GO terms and CCRG network characteristics in order to obtain a database of predicted drug-CRGs that included 53 CRGs, 32 of which have been reported to affect susceptibility to drugs. Our proposed method identifies a greater number of drug-CCRGs, and drug-CCRGs are much more significantly enriched in predicted drug-CRGs, compared to a method based on the correlation of gene expression and drug activity. The mean area under ROC curve (AUC for our method is 65.2%, whereas that for the traditional method is 55.2%. Conclusions Our method not only identifies CRGs with expression patterns strongly correlated with drug activity, but also identifies CRGs in which expression is weakly correlated with drug activity. This study provides the framework for the identification of signatures that predict in vitro cellular chemosensitivity and offers a valuable

  20. Design and Implementation of Visual Dynamic Display Software of Gene Expression Based on GTK

    Institute of Scientific and Technical Information of China (English)

    JIANG Wei; MENG Fanjiang; LI Yong; YU Xiao

    2009-01-01

    The paper presented an implement method for a dynamic gene expression display software based on the GTK. This method established the dynamic presentation system of gene expression which according to gene expression data from gene chip hybridize at different time, adopted a linearity combination model and Pearson correlation coefficient algorithm. The system described the gene expression changes in graphic form, the gene expression changes with time and the changes in characteristics of the gene expression, also the changes in relations of the gene expression and regulation relationships among genes. The system also provided an integrated platform for analysis on gene chips data, especially for the research on the network of gene regulation.

  1. Smart Hand For Manipulators

    Science.gov (United States)

    Fiorini, Paolo

    1987-10-01

    Sensor based, computer controlled end effectors for mechanical arms are receiving more and more attention in the robotics industry, because commonly available grippers are only adequate for simple pick and place tasks. This paper describes the current status of the research at JPL on a smart hand for a Puma 560 robot arm. The hand is a self contained, autonomous system, capable of executing high level commands from a supervisory computer. The mechanism consists of parallel fingers, powered by a DC motor, and controlled by a microprocessor embedded in the hand housing. Special sensors are integrated in the hand for measuring the grasp force of the fingers, and for measuring forces and torques applied between the arm and the surrounding environment. Fingers can be exercised under position, velocity and force control modes. The single-chip microcomputer in the hand executes the tasks of communication, data acquisition and sensor based motor control, with a sample cycle of 2 ms and a transmission rate of 9600 baud. The smart hand described in this paper represents a new development in the area of end effector design because of its multi-functionality and autonomy. It will also be a versatile test bed for experimenting with advanced control schemes for dexterous manipulation.

  2. The direct manipulation shell

    International Nuclear Information System (INIS)

    Accelerator controls systems provide parameter display pages which allow the operator to monitor and manipulate selected control points in the system. Display pages are generally implemented as either hand-crafted, purpose-built programs; or by using a specialized display page layout tool. These two methods of display page development exhibit the classic trade-off between functionality vs. ease of implementation. In the Direct Manipulation Shell we approach the process of developing a display page in a manifestly object-oriented manner. This is done by providing a general framework for interactively instantiating and manipulating display objects. (author)

  3. Sound visualization and manipulation

    CERN Document Server

    Kim, Yang-Hann

    2013-01-01

    Unique in addressing two different problems - sound visualization and manipulation - in a unified way Advances in signal processing technology are enabling ever more accurate visualization of existing sound fields and precisely defined sound field production. The idea of explaining both the problem of sound visualization and the problem of the manipulation of sound within one book supports this inter-related area of study.  With rapid development of array technologies, it is possible to do much in terms of visualization and manipulation, among other technologies involved with the spatial dis

  4. Multiclass cancer classification based on gene expression comparison

    OpenAIRE

    Yang Sitan; Naiman Daniel Q.

    2014-01-01

    As the complexity and heterogeneity of cancer is being increasingly appreciated through genomic analyses, microarray-based cancer classification comprising multiple discriminatory molecular markers is an emerging trend. Such multiclass classification problems pose new methodological and computational challenges for developing novel and effective statistical approaches. In this paper, we introduce a new approach for classifying multiple disease states associated with cancer based on gene expre...

  5. Classification of one family of 3R positioning Manipulators

    CERN Document Server

    Baili, Maher; Chablat, Damien

    2003-01-01

    The aim of this paper is to classify one family of 3R serial positioning manipulators. This categorization is based on the number of cusp points of quaternary, binary, generic and non-generic manipulators. It was found three subsets of manipulators with 0, 2 or 4 cusp points and one homotopy class for generic quaternary manipulators. This classification allows us to define the design parameters for which the manipulator is cuspidal or not, i.e., for which the manipulator can or cannot change posture without meeting a singularity, respectively.

  6. Comparative analysis of bacterial essential and nonessential genes with Hurst exponent based on chaos game representation

    International Nuclear Information System (INIS)

    Essential genes are indispensable for the survival of an organism. Investigating features associated with gene essentiality is fundamental to the prediction and identification of essential genes with computational techniques. We use fractal theory approach to make comparative analysis of essential and nonessential genes in bacteria. The Hurst exponents of essential genes and nonessential genes available in the DEG database for 27 bacteria are calculated based on their gene chaos game representations. It is found that for most analyzed bacteria, weak negative correlation exists between Hurst exponent and gene length. Moreover, essential genes generally differ from nonessential genes in their Hurst exponent. For genes of similar length, the average Hurst exponent of essential genes is smaller than that of nonessential genes. The results of our work reveal that gene Hurst exponent is very probably useful gene feature for the algorithm predicting essential genes

  7. Interaction control of a redundant mobile manipulator

    International Nuclear Information System (INIS)

    This paper discusses the modeling and control of a spatial mobile manipulator that consists of a robotic manipulator mounted on a wheeled mobile platform. The Lagrange-d'Alembert formulation is used to obtain a concise description of the dynamics of the system, which is subject to nonholonomic constraints. The complexity of the model is increased by introducing kinematic redundancy, which is created when a multilinked manipulator is used. The kinematic redundancy is resolved by decomposing the mobile manipulator into two subsystems: the mobile platform and the manipulator. The redundancy resolution scheme employs a nonlinear interaction-control algorithm, which is developed and applied to coordinate the two subsystems' controllers. The subsystem controllers are independently designed, based on each subsystem's dynamic characteristics. Simulation results show the promise of the developed algorithm

  8. Laser Diode Beam Basics, Manipulations and Characterizations

    CERN Document Server

    Sun, Haiyin

    2012-01-01

    Many optical design technical books are available for many years which mainly deal with image optics design based on geometric optics and using sequential raytracing technique. Some books slightly touched laser beam manipulation optics design. On the other hand many books on laser diodes have been published that extensively deal with laser diode physics with little touching on laser diode beam manipulations and characterizations. There are some internet resources dealing with laser diode beams. However, these internet resources have not covered enough materials with enough details on laser diode beam manipulations and characterizations. A technical book concentrated on laser diode beam manipulations and characterizations can fit in to the open and provide useful information to laser diode users. Laser Diode Beam Basics, Manipulations and  Characterizations is concentrated on the very practical side of the subject, it only discusses the basic physics and mathematics that are necessary for the readers in order...

  9. Manipulating Strings in Python

    Directory of Open Access Journals (Sweden)

    William J. Turkel

    2012-07-01

    Full Text Available This lesson is a brief introduction to string manipulation techniques in Python. Knowing how to manipulate strings plays a crucial role in most text processing tasks. If you’d like to experiment with the following lessons, you can write and execute short programs as we’ve been doing, or you can open up a Python shell / Terminal to try them out on the command line.

  10. Manipulating Strings in Python

    OpenAIRE

    William J. Turkel; Adam Crymble

    2012-01-01

    This lesson is a brief introduction to string manipulation techniques in Python. Knowing how to manipulate strings plays a crucial role in most text processing tasks. If you’d like to experiment with the following lessons, you can write and execute short programs as we’ve been doing, or you can open up a Python shell / Terminal to try them out on the command line.

  11. Nanoparticle manipulation by dielectrophoresis

    International Nuclear Information System (INIS)

    In the last decades, non-uniform electric field proved to be the most promising technique for nanoparticles manipulation with applications in fields such as medicine, biology, physics or nano technology. The paper presents a set of numerical results concerning the influence of the dielectrophoretic (DEP) forces on a nanoparticle suspension. The DEP force depends on the electric properties of the nanoparticles, as well as their shape, size and mass, and the properties of the surrounding medium. The numerical study was performed in the frame of a mathematical model describing the electric field distribution and the suspended nanoparticle movement in a dense and viscous fluid. The equations are solved, together with the appropriate boundary conditions using a code based on the finite element method. The dielectrophoretic force distribution, the particle trajectories and the nanoparticle concentration profile are computed. This type of analysis leads to the optimization of the control parameters and is crucial in the designing process of an experimental micro fluidic device with application in the separation of submicronic particles. (Author)

  12. Microbial manipulation of host sex determination

    NARCIS (Netherlands)

    Beukeboom, Leo W.

    2012-01-01

    A recent study in the lepidopteran Ostrinia scapulalis shows that endosymbionts can actively manipulate the sex determination mechanism of their host. Wolbachia bacteria alter the sex-specific splicing of the doublesex master switch gene. In ZZ males of this female heterogametic system, the female i

  13. Gene expression-based biomarkers for Anopheles gambiae age grading.

    Science.gov (United States)

    Wang, Mei-Hui; Marinotti, Osvaldo; Zhong, Daibin; James, Anthony A; Walker, Edward; Guda, Tom; Kweka, Eliningaya J; Githure, John; Yan, Guiyun

    2013-01-01

    Information on population age structure of mosquitoes under natural conditions is fundamental to the understanding of vectorial capacity and crucial for assessing the impact of vector control measures on malaria transmission. Transcriptional profiling has been proposed as a method for predicting mosquito age for Aedes and Anopheles mosquitoes, however, whether this new method is adequate for natural conditions is unknown. This study tests the applicability of transcriptional profiling for age-grading of Anopheles gambiae, the most important malaria vector in Africa. The transcript abundance of two An. gambiae genes, AGAP009551 and AGAP011615, was measured during aging under laboratory and field conditions in three mosquito strains. Age-dependent monotonic changes in transcript levels were observed in all strains evaluated. These genes were validated as age-grading biomarkers using the mark, release and recapture (MRR) method. The MRR method determined a good correspondence between actual and predicted age, and thus demonstrated the value of age classifications derived from the transcriptional profiling of these two genes. The technique was used to establish the age structure of mosquito populations from two malaria-endemic areas in western Kenya. The population age structure determined by the transcriptional profiling method was consistent with that based on mosquito parity. This study demonstrates that the transcription profiling method based on two genes is valuable for age determination of natural mosquitoes, providing a new approach for determining a key life history trait of malaria vectors. PMID:23936017

  14. Gene expression-based biomarkers for Anopheles gambiae age grading.

    Directory of Open Access Journals (Sweden)

    Mei-Hui Wang

    Full Text Available Information on population age structure of mosquitoes under natural conditions is fundamental to the understanding of vectorial capacity and crucial for assessing the impact of vector control measures on malaria transmission. Transcriptional profiling has been proposed as a method for predicting mosquito age for Aedes and Anopheles mosquitoes, however, whether this new method is adequate for natural conditions is unknown. This study tests the applicability of transcriptional profiling for age-grading of Anopheles gambiae, the most important malaria vector in Africa. The transcript abundance of two An. gambiae genes, AGAP009551 and AGAP011615, was measured during aging under laboratory and field conditions in three mosquito strains. Age-dependent monotonic changes in transcript levels were observed in all strains evaluated. These genes were validated as age-grading biomarkers using the mark, release and recapture (MRR method. The MRR method determined a good correspondence between actual and predicted age, and thus demonstrated the value of age classifications derived from the transcriptional profiling of these two genes. The technique was used to establish the age structure of mosquito populations from two malaria-endemic areas in western Kenya. The population age structure determined by the transcriptional profiling method was consistent with that based on mosquito parity. This study demonstrates that the transcription profiling method based on two genes is valuable for age determination of natural mosquitoes, providing a new approach for determining a key life history trait of malaria vectors.

  15. Versatile Supramolecular Gene Vector Based on Host-Guest Interaction.

    Science.gov (United States)

    Liu, Jia; Hennink, Wim E; van Steenbergen, Mies J; Zhuo, Renxi; Jiang, Xulin

    2016-04-20

    It is a great challenge to arrange multiple functional components into one gene vector system to overcome the extra- and intracellular obstacles for gene therapy. In this study, we developed a supramolecular approach for constructing a versatile gene delivery system composed of adamantyl-terminated functional polymers and a β-cyclodextrin based polymer. Adamantyl-functionalized low molecular weight PEIs (PEI-Ad) and PEG (Ad-PEG) as well as poly(β-cyclodextrin) (PCD) were synthesized by one-step chemical reactions. The supramolecular inclusion complex formed from PCD to assemble LMW PEI-Ad4 via host-guest interactions can condense plasmid DNA to form nanopolyplexes by electrostatic interactions. The supramolecular polyplexes can be further PEGylated with Ad-PEG to form inclusion complexes, which showed increased salt and serum stability. In vitro experiments revealed that these supramolecular assembly polyplexes had good cytocompatibility and showed high transfection activity close to that of the commercial ExGen 500 at high dose of DNA. Also, the supramolecular vector system exhibited about 60% silencing efficiency as a siRNA vector. Thus, a versatile effective supramolecular gene vector based on host-guest complexes was fabricated with good cytocompatbility and transfection activity. PMID:27019340

  16. Nanoparticle-based targeted gene therapy for lung cancer

    Science.gov (United States)

    Lee, Hung-Yen; Mohammed, Kamal A; Nasreen, Najmunnisa

    2016-01-01

    Despite striking insights on lung cancer progression, and cutting-edge therapeutic approaches the survival of patients with lung cancer, remains poor. In recent years, targeted gene therapy with nanoparticles is one of the most rapidly evolving and extensive areas of research for lung cancer. The major goal of targeted gene therapy is to bring forward a safe and efficient treatment to cancer patients via specifically targeting and deterring cancer cells in the body. To achieve high therapeutic efficacy of gene delivery, various carriers have been engineered and developed to provide protection to the genetic materials and efficient delivery to targeted cancer cells. Nanoparticles play an important role in the area of drug delivery and have been widely applied in cancer treatments for the purposes of controlled release and cancer cell targeting. Nanoparticles composed of artificial polymers, proteins, polysaccharides and lipids have been developed for the delivery of therapeutic deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequences to target cancer. In addition, the effectiveness of cancer targeting has been enhanced by surface modification or conjugation with biomolecules on the surface of nanoparticles. In this review article we provide an overview on the latest developments in nanoparticle-based targeted gene therapy for lung cancers. Firstly, we outline the conventional therapies and discuss strategies for targeted gene therapy using nanoparticles. Secondly, we provide the most representative and recent researches in lung cancers including malignant pleural mesothelioma, mainly focusing on the application of Polymeric, Lipid-based, and Metal-based nanoparticles. Finally, we discuss current achievements and future challenges. PMID:27294004

  17. Numeric processor and text manipulator for the ''MASTER CONTROL'' data-base-management system

    Energy Technology Data Exchange (ETDEWEB)

    Kuhn, R.W.

    1976-02-10

    The numeric and text processor of the MASTER CONTROL (MCP) data-base-management system permits the user to define fields and arrays that are functionally dependent on the data retained in a data base. This allows the storage of only the essential and unique information and data, and the calculation of derivable quantities as required. The derived quantity can be expressed as an arithmetic expression, that is, a functional relationship. Functions can be multiply subscripted and can be embedded within other functions at up to 58 levels. They can be stored either semi-permanently in a repertoire of functional relations, or they can be defined interactively from a terminal and used immediately for searching on the derived value. The processor also permits the conversion of literal strings into numbers, and vice versa. In addition, the user can define dictionaries that allow the expansion of keyed sentinels associated with records in the data base into fully descriptive expressions. This option can be used for cost-effective searching and data compaction. The functional definitions are reduced to Polish notation and stored in a disk file from which they are either retrieved on demand and evaluated according to the data of records specified or used in any given MASTER CONTROL command. The language used for the definitions of the numeric processor is essentially FORTRAN; most of the standard functions and over two dozen special functions are thus available. The functional processor provides a powerful technique for the integration of text and data for energy research and for scientific and technological work in general. MASTER CONTROL is operational at the Lawrence Livermore Laboratory (LLL) and at the Los Alamos Scientific Laboratory (LASL). 6 figures, 1 table.

  18. Real-time compensation of static deflections in robotic manipulators

    OpenAIRE

    Calkins, Joseph M

    1994-01-01

    The focus of this work is the real-time prediction and compensation of static deflections in robotic manipulator arms. A general manipulator deflection model is developed based on static beam theory and robot kinematics. An optimization technique is proposed to determine the stiffness of the manipulator components using end-effector deflection measurements. Strategies for incorporating this modeling approach into a manipulator controller are also presented along with the results of a successf...

  19. FAO/IAEA international symposium on applications of gene-based technologies for improving animal production and health in developing countries. Book of extended synopses

    International Nuclear Information System (INIS)

    Genetic engineering is at the forefront of much biological research - basic, adaptive and applied or near market. Manipulation of genes to bring about the expression of a specific product, or to produce a characteristic or trait, offers exciting possibilities within both the plant and the animal kingdom. The opportunities, in terms of improving livestock productivity or reducing losses from disease, lie in a number of areas. In almost all areas of this research, isotopic markers are extensively used and are in most cases essential for achieving the levels of sensitivity required for genetic characterization and manipulation. Genetic engineering has the potential to solve many problems relating to animal productivity and health. At present the focus is on the problems that face livestock producers in the developed world. If the full benefit of this technology is to be realized globally, the problems confronting livestock farmers in developing countries will have to be considered. The characterization and application of methods in these regions has to be managed and exploited. It is hoped that this Symposium will stimulate the international exchange of information and ideas that contribute to greater accessibility and enhanced use of gene based technologies in animal agriculture in developing countries. OBJECTIVES: To create an interactive environment to discuss the role and future potential of gene based technologies for improving animal production and health; To identify constraints in the use of gene based technologies in developing countries and to determine how to use these technologies in a simple, practical way; To identify and prioritize specific research needs; To explore the possibility of international co-ordination in the area of gene based technologies in animal agriculture; To examine ethical, technological, policy and environmental issues and the role of nuclear techniques in the further development and application of gene based technologies with

  20. Development of gene diagnosis for diabetes and cholecystitis based on gene analysis of CCK-A receptor

    International Nuclear Information System (INIS)

    Base sequence analysis of CCKAR gene (a gene of A-type receptor for cholecystokinin) from OLETF rat, a model rat for insulin-independent diabetes was made based on the base sequence of wild CCKAR gene, which had been clarified in the previous year. From the pancreas of OLETF rat, DNA was extracted and transduced into λphage after fragmentation to construct the gene library of OLETF. Then, λphage DNA clone bound with labelled cDNA of CCKAR gene was analyzed and the gene structure was compared with that of the wild gene. It was demonstrated that CCKAR gene of OLETF had a deletion (6800 b.p.) ranging from the promoter region to the Exon 2, suggesting that CCKAR gene is not functional in OLETF rat. The whole sequence of this mutant gene was registered into Japan DNA Bank (D 50610). Then, F2 offspring rats were obtained through crossing OLETF (female) and F344 (male) and the time course-changes in the blood glucose level after glucose loading were compared among them. The blood glucose level after glucose loading was significantly higher in the homo-mutant F2 (CCKAR,-/-) as well as the parent OLETF rat than hetero-mutant F2 (CCKARm-/+) or the wild rat (CCKAR,+/+). This suggests that CCKAR gene might be involved in the control of blood glucose level and an alteration of the expression level or the functions of CCKAR gene might affect the blood glucose level. (M.N.)

  1. An all fiber apparatus for microparticles selective manipulation based on a variable ratio coupler and a microfiber

    Science.gov (United States)

    Li, Baoli; Luo, Wei; Xu, Fei; Lu, Yanqing

    2016-09-01

    We propose an all fiber apparatus based on a variable ratio coupler which can transport microparticles controllably and trap particles one by one along a microfiber. By connecting two output ports of a variable ratio coupler with two end pigtails of a microfiber and launching a 980 nm laser into the variable ratio coupler, particles in suspension were trapped to the waist of microfiber due to a gradient force and then transported along the microfiber due to a total scattering force generated by two counter-propagating beams. The direction of transportation was controlled by altering the coupling ratio of the variable ratio coupler. When the intensities of two output ports were equivalent, trapped particles stayed at fixed positions. With time going, another particle around the micro fiber was trapped onto the microfiber. There were three particles trapped in total in our experiment. This technique combines with the function of conventional tweezers and optical conveyor.

  2. Identification of crucial genes in intracranial aneurysm based on weighted gene coexpression network analysis.

    Science.gov (United States)

    Zheng, X; Xue, C; Luo, G; Hu, Y; Luo, W; Sun, X

    2015-05-01

    The rupture of intracranial aneurysm (IA) is the leading cause for devastating subarachnoid hemorrhage. This study aimed to investigate genes related to IA and potential diagnosis targets. Two data sets (GSE15629 and GSE54083) were downloaded from Gene Expression Omnibus database. GSE15629 contained eight RI (ruptured IA), six UI (unruptured IA) and five control IA samples. GSE54083 included 8 RI, 5 UI and 10 superficial temporal artery samples. In total, 452 differentially expressed genes (DEGs) between RI and control, and 570 DEGs between UI and control, were identified. Protein-protein interaction networks for two kinds of DEGs related to RI and UI were constructed, respectively. Module networks were searched for DEGs related to RI or UI based on WGCNA (weighted gene coexpression network analysis). In the significant modules, FOS, CCL2, COL4A2 and CXCL5 were screened as crucial nodes with high degrees. Among them, FOS and CCL2 were enriched in immune response and COL4A2 was involved in the ECM (extracellular matrix) pathway, whereas CXCL5 was related to cytokine-cytokine receptor pathway. Taken together, FOS, CCL2, COL4A2 and CXCL5 might participate in the pathogenesis of RI or UI, and could serve as potential diagnosis targets. PMID:25721208

  3. Autonomous Industrial Mobile Manipulation (AIMM)

    DEFF Research Database (Denmark)

    Hvilshøj, Mads; Bøgh, Simon; Nielsen, Oluf Skov;

    2012-01-01

    ; sustainability, configuration, adaptation, autonomy, positioning, manipulation and grasping, robot-robot interaction, human-robot interaction, process quality, dependability, and physical properties. Findings - The concise yet comprehensive review provides both researchers (academia) and practitioners (industry......Purpose - The purpose of this paper is to provide a review of the interdisciplinary research field Autonomous Industrial Mobile Manipulation (AIMM), with an emphasis on physical implementations and applications. Design/methodology/approach - Following an introduction to AIMM, this paper...... investigates the missing links and gaps between the research and developments efforts and the real-world application requirements, in order to bring the AIMM technology from laboratories to manufacturing environments. The investigation is based on 12 general application requirements for robotics...

  4. Improved Wood Properties Through Genetic Manipulation: Engineering of Syringyl Lignin in Softwood Species Through Xylem-Specific Expression of Hardwood Syringyl Monolignol Pathway Genes

    Energy Technology Data Exchange (ETDEWEB)

    Chandrashekhar P. Joshi; Vincent L. Chiang

    2009-01-29

    Project Objective: Our long-term goal is to genetically engineer higher value raw materials with desirable wood properties to promote energy efficiency, international competitiveness, and environmental responsiveness of the U.S. forest products industry. The immediate goal of this project was to produce the first higher value softwood raw materials engineered with a wide range of syringyl lignin quantities. Summary: The most important wood property affecting directly the levels of energy, chemical and bleaching requirements for kraft pulp production is lignin. Softwoods contain almost exclusively chemically resistant guaiacyl (G) lignin, whereas hardwoods have more reactive or easily degradable lignins of the guaiacyl (G)-syringyl (S) type. It is also well established that the reactive S lignin component is the key factor that permits much lower effective alkali and temperature, shorter pulping time and less bleaching stages for processing hardwoods than for softwoods. Furthermore, our pulping kinetic study explicitly demonstrated that every increase in one unit of the lignin S/G ratio would roughly double the rate of lignin removal. These are clear evidence that softwoods genetically engineered with S lignin are keys to revolutionizing the energy efficiency and enhancing the environmental performance of this industry. Softwoods and hardwoods share the same genetic mechanisms for the biosynthesis of G lignin. However, in hardwoods, three additional genes branch out from the G-lignin pathway and become specifically engaged in regulating S lignin biosynthesis. In this research, we simultaneously transferred aspen S-specific genes into a model softwood, black spruce, to engineer S lignin.

  5. A fisheye viewer for microarray-based gene expression data

    Directory of Open Access Journals (Sweden)

    Munson Ethan V

    2006-10-01

    Full Text Available Abstract Background Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface – an electronic table (E-table that uses fisheye distortion technology. Results The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. Conclusion This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

  6. A modular positive feedback-based gene amplifier

    Directory of Open Access Journals (Sweden)

    Bhalerao Kaustubh D

    2010-02-01

    Full Text Available Abstract Background Positive feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, positive feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. Results We developed a modular positive feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorum-sensing regulator LuxR. We experimentally tested the ability of the positive feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the positive feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. Conclusions The advantage of our design is that the actual feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.

  7. PGMA-based gene carriers with lipid molecules.

    Science.gov (United States)

    Xu, Chen; Yu, Bingran; Hu, Hao; Nizam, Muhammad Naeem; Yuan, Wei; Ma, Jie; Xu, Fu-Jian

    2016-08-19

    Lipids, as the greatest constituent in cell membranes, have been widely used for biomedical applications because of their excellent biological properties. The introduction of membrane lipid molecules into gene vectors would embody greater biocompatibility, cellular uptake and transfection efficiency. In this work, one flexible strategy for readily conjugating lipid molecules with polycations was proposed based on atom transfer radical polymerization to produce a series of cholesterol (CHO)- and phosphatidylinositol (PI)-terminated ethanolamine-functionalized poly(glycidyl methacrylate)s, namely CHO-PGEAs and PI-PGEAs, as effective gene carriers. CHO-PGEAs and PI-PGEAs truly demonstrated much better transfection performances compared to linear ethanolamine-functionalized poly(glycidyl methacrylate) (denoted as BUCT-PGEA) counterparts and traditional standard branched polythylenimine (PEI, 25 kDa). In addition, the good antitumor effects of CHO-PGEA and PI-PGEA were confirmed with suppressor tumor gene p53 systems in vitro and in vivo. The present work could provide a new strategy to develop effective cationic conjugation of lipid molecules for gene therapy. PMID:27374783

  8. The individual-cell-based cryo-chip for the cryopreservation, manipulation and observation of spatially identifiable cells. I: Methodology

    Directory of Open Access Journals (Sweden)

    Thaele Michael

    2010-07-01

    Full Text Available Abstract Background Cryopreservation is the only widely applicable method of storing vital cells for nearly unlimited periods of time. Successful cryopreservation is essential for reproductive medicine, stem cell research, cord blood storage and related biomedical areas. The methods currently used to retrieve a specific cell or a group of individual cells with specific biological properties after cryopreservation are quite complicated and inefficient. Results The present study suggests a new approach in cryopreservation, utilizing the Individual Cell-based Cryo-Chip (i3C. The i3C is made of materials having appropriate durability for cryopreservation conditions. The core of this approach is an array of picowells, each picowell designed to maintain an individual cell during the severe conditions of the freezing - thawing cycle and accompanying treatments. More than 97% of cells were found to retain their position in the picowells throughout the entire freezing - thawing cycle and medium exchange. Thus the comparison between pre-freezing and post-thawing data can be achieved at an individual cell resolution. The intactness of cells undergoing slow freezing and thawing, while residing in the i3C, was found to be similar to that obtained with micro-vials. However, in a fast freezing protocol, the i3C was found to be far superior. Conclusions The results of the present study offer new opportunities for cryopreservation. Using the present methodology, the cryopreservation of individual identifiable cells, and their observation and retrieval, at an individual cell resolution become possible for the first time. This approach facilitates the correlation between cell characteristics before and after the freezing - thawing cycle. Thus, it is expected to significantly enhance current cryopreservation procedures for successful regenerative and reproductive medicine.

  9. Position-Singularity Analysis of a Class of the 3/6-Gough-Stewart Manipulators based on Singularity-Equivalent-Mechanism

    Directory of Open Access Journals (Sweden)

    Hui Zhou

    2012-03-01

    this class of 3/6‐Gough‐Stewart manipulators for general orientations in parallel principal‐sections are all quadratic expressions, including a parabola, four pairs of intersecting lines and infinite hyperbolas. Finally, the properties of the position‐singularity loci of this class of 3/6‐Gough‐Stewart parallel manipulators in a three‐ dimensional space for all orientations are presented.

  10. KINEMATICS AND DYNAMICS MANIPULATOR

    OpenAIRE

    Квасніков, В. П.; Національний авіаційний університет; Вохмянін, М. М.; Національний авіаційний університет

    2013-01-01

    Robots which must work in the real world require some way to manipulate objects; pick up, modify, destroy or otherwise have an effect. Thus the ‘hands’ of a robot are often referred to as end-effectors, while the arm is referred to as a manipulator. A common effector is the gripper. In its simplest manifestation it consists of just two fingers which can open and close to pick up and let go of a range of small objects. Some advanced robots are beginning to use fully humanoid hands. These highl...

  11. A Resampling Based Clustering Algorithm for Replicated Gene Expression Data.

    Science.gov (United States)

    Li, Han; Li, Chun; Hu, Jie; Fan, Xiaodan

    2015-01-01

    In gene expression data analysis, clustering is a fruitful exploratory technique to reveal the underlying molecular mechanism by identifying groups of co-expressed genes. To reduce the noise, usually multiple experimental replicates are performed. An integrative analysis of the full replicate data, instead of reducing the data to the mean profile, carries the promise of yielding more precise and robust clusters. In this paper, we propose a novel resampling based clustering algorithm for genes with replicated expression measurements. Assuming those replicates are exchangeable, we formulate the problem in the bootstrap framework, and aim to infer the consensus clustering based on the bootstrap samples of replicates. In our approach, we adopt the mixed effect model to accommodate the heterogeneous variances and implement a quasi-MCMC algorithm to conduct statistical inference. Experiments demonstrate that by taking advantage of the full replicate data, our algorithm produces more reliable clusters and has robust performance in diverse scenarios, especially when the data is subject to multiple sources of variance. PMID:26671802

  12. Information dimension analysis of bacterial essential and nonessential genes based on chaos game representation

    International Nuclear Information System (INIS)

    Essential genes are indispensable for the survival of an organism. Investigating features associated with gene essentiality is fundamental to the prediction and identification of the essential genes. Selecting features associated with gene essentiality is fundamental to predict essential genes with computational techniques. We use fractal theory to make comparative analysis of essential and nonessential genes in bacteria. The information dimensions of essential genes and nonessential genes available in the DEG database for 27 bacteria are calculated based on their gene chaos game representations (CGRs). It is found that weak positive linear correlation exists between information dimension and gene length. Moreover, for genes of similar length, the average information dimension of essential genes is larger than that of nonessential genes. This indicates that essential genes show less regularity and higher complexity than nonessential genes. Our results show that for bacterium with a similar number of essential genes and nonessential genes, the CGR information dimension is helpful for the classification of essential genes and nonessential genes. Therefore, the gene CGR information dimension is very probably a useful gene feature for a genetic algorithm predicting essential genes. (paper)

  13. Active learning of manipulation sequences

    OpenAIRE

    Martínez Martínez, David; Alenyà Ribas, Guillem; Jimenez Schlegl, Pablo; Torras, Carme; Rossmann, Jürgen; Wantia, Nils; Eren Erdal, Aksoy; Haller, Simon; Piater, Justus

    2014-01-01

    We describe a system allowing a robot to learn goal-directed manipulation sequences such as steps of an assembly task. Learning is based on a free mix of exploration and instruction by an external teacher, and may be active in the sense that the system tests actions to maximize learning progress and asks the teacher if needed. The main component is a symbolic planning engine that operates on learned rules, defined by actions and their pre- and postconditions. Learned by model-based reinforcem...

  14. Fuzzy logic control of telerobot manipulators

    Science.gov (United States)

    Franke, Ernest A.; Nedungadi, Ashok

    1992-01-01

    Telerobot systems for advanced applications will require manipulators with redundant 'degrees of freedom' (DOF) that are capable of adapting manipulator configurations to avoid obstacles while achieving the user specified goal. Conventional methods for control of manipulators (based on solution of the inverse kinematics) cannot be easily extended to these situations. Fuzzy logic control offers a possible solution to these needs. A current research program at SRI developed a fuzzy logic controller for a redundant, 4 DOF, planar manipulator. The manipulator end point trajectory can be specified by either a computer program (robot mode) or by manual input (teleoperator). The approach used expresses end-point error and the location of manipulator joints as fuzzy variables. Joint motions are determined by a fuzzy rule set without requiring solution of the inverse kinematics. Additional rules for sensor data, obstacle avoidance and preferred manipulator configuration, e.g., 'righty' or 'lefty', are easily accommodated. The procedure used to generate the fuzzy rules can be extended to higher DOF systems.

  15. Gene ontology based transfer learning for protein subcellular localization

    Directory of Open Access Journals (Sweden)

    Zhou Shuigeng

    2011-02-01

    Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

  16. Integrated microfluidic device for droplet manipulation

    OpenAIRE

    Basova, E.

    2013-01-01

    Droplets based microfluidic systems have a big potential for the miniaturization of processes for bioanalysis. In the form of droplets, reagents are used in discrete volume, enabling high-throughput chemical reactions as well as single-cell encapsulation. Microreactors of this type can be manipulated and applied in bio-testing. In this work we present a platform for droplet generation and manipulation by using dielectrophoresis force. This platform is an integrated microfluidic device wit...

  17. INTEGRATED MICROFLUIDIC DEVICE FOR DROPLET MANIPULATION

    OpenAIRE

    Basova Evgenia; Drs Jakub; Zemanek Jiri; Hurak Zdenek; Foret František

    2013-01-01

    Droplets based microfluidic systems have a big potential for the miniaturization of processes for bioanalysis. In the form of droplets, reagents are used in discrete volume, enabling high-throughput chemical reactions as well as single-cell encapsulation. Microreactors of this type can be manipulated and applied in bio-testing. In this work we present a platform for droplet generation and manipulation by using dielectrophoresis force. This platform is an integrated microfluidic device wit...

  18. Efficient Computation Of Manipulator Inertia Matrix

    Science.gov (United States)

    Fijany, Amir; Bejczy, Antal K.

    1991-01-01

    Improved method for computation of manipulator inertia matrix developed, based on concept of spatial inertia of composite rigid body. Required for implementation of advanced dynamic-control schemes as well as dynamic simulation of manipulator motion. Motivated by increasing demand for fast algorithms to provide real-time control and simulation capability and, particularly, need for faster-than-real-time simulation capability, required in many anticipated space teleoperation applications.

  19. Genetic Manipulation in Δku80 Strains for Functional Genomic Analysis of Toxoplasma gondii

    OpenAIRE

    Rommereim, Leah M.; Hortua Triana, Miryam A.; Falla, Alejandra; Sanders, Kiah L; Guevara, Rebekah B.; Bzik, David J.; Fox, Barbara A.

    2013-01-01

    Targeted genetic manipulation using homologous recombination is the method of choice for functional genomic analysis to obtain a detailed view of gene function and phenotype(s). The development of mutant strains with targeted gene deletions, targeted mutations, complemented gene function, and/or tagged genes provides powerful strategies to address gene function, particularly if these genetic manipulations can be efficiently targeted to the gene locus of interest using integration mediated by ...

  20. GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms

    Directory of Open Access Journals (Sweden)

    Argraves W Scott

    2010-04-01

    Full Text Available Abstract Background An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions, cellular components, signaling pathways, physiologic processes and diseases. Results Here we describe GeneMesh, a web-based program that facilitates analysis of DNA microarray gene expression data. GeneMesh relates genes in a query set to categories available in the Medical Subject Headings (MeSH hierarchical index. The interface enables hypothesis driven relational analysis to a specific MeSH subcategory (e.g., Cardiovascular System, Genetic Processes, Immune System Diseases etc. or unbiased relational analysis to broader MeSH categories (e.g., Anatomy, Biological Sciences, Disease etc.. Genes found associated with a given MeSH category are dynamically linked to facilitate tabular and graphical depiction of Entrez Gene information, Gene Ontology information, KEGG metabolic pathway diagrams and intermolecular interaction information. Expression intensity values of groups of genes that cluster in relation to a given MeSH category, gene ontology or pathway can be displayed as heat maps of Z score-normalized values. GeneMesh operates on gene expression data derived from a number of commercial microarray platforms including Affymetrix, Agilent and Illumina. Conclusions GeneMesh is a versatile web-based tool for testing and developing new hypotheses through relating genes in a query set (e.g., differentially expressed genes from a DNA microarray experiment to descriptors making up the hierarchical structure of the National Library of Medicine controlled vocabulary thesaurus, MeSH. The system further enhances the discovery process by providing links between sets of genes associated with a given MeSH category to a rich set of html linked tabular and graphic information including Entrez Gene summaries, gene ontologies

  1. Development of gene diagnosis for diabetes and cholecystis based on gene analysis of CCK-A receptor

    International Nuclear Information System (INIS)

    The gene structures of CCK, A type receptor in human, the rat and the mouse were investigated aiming to clarify that the aberration of the gene is involved in the incidences of diabetes and cholecystis. In this fiscal year, 1997, the normal structure of the gene and the accurate base sequence were analyzed using DNA fragments bound to 32P-labelled cDNA of human CCKAR originated from the gene library of leucocyte. This gene contained about 2.2 x 105 base pairs and the base sequence was completely determined and registered to Japan DNA data bank (D85606). In addition, the genome structures and base sequences of mouse and rat CCKAR were analyzed and registered (D 85605 and D 50608, respectively). The differences in the base sequence of CCKAR among the species were found in the promotor region and the intron regions, suggesting that there might be differences in splicing among species. (M.N.)

  2. Group II intron-based gene targeting reactions in eukaryotes.

    Directory of Open Access Journals (Sweden)

    Marta Mastroianni

    Full Text Available Mobile group II introns insert site-specifically into DNA target sites by a mechanism termed retrohoming in which the excised intron RNA reverse splices into a DNA strand and is reverse transcribed by the intron-encoded protein. Retrohoming is mediated by a ribonucleoprotein particle that contains the intron-encoded protein and excised intron RNA, with target specificity determined largely by base pairing of the intron RNA to the DNA target sequence. This feature enabled the development of mobile group II introns into bacterial gene targeting vectors ("targetrons" with programmable target specificity. Thus far, however, efficient group II intron-based gene targeting reactions have not been demonstrated in eukaryotes.By using a plasmid-based Xenopus laevis oocyte microinjection assay, we show that group II intron RNPs can integrate efficiently into target DNAs in a eukaryotic nucleus, but the reaction is limited by low Mg(2+ concentrations. By supplying additional Mg(2+, site-specific integration occurs in up to 38% of plasmid target sites. The integration products isolated from X. laevis nuclei are sensitive to restriction enzymes specific for double-stranded DNA, indicating second-strand synthesis via host enzymes. We also show that group II intron RNPs containing either lariat or linear intron RNA can introduce a double-strand break into a plasmid target site, thereby stimulating homologous recombination with a co-transformed DNA fragment at frequencies up to 4.8% of target sites. Chromatinization of the target DNA inhibits both types of targeting reactions, presumably by impeding RNP access. However, by using similar RNP microinjection methods, we show efficient Mg(2+-dependent group II intron integration into plasmid target sites in zebrafish (Danio rerio embryos and into plasmid and chromosomal target sites in Drosophila melanogster embryos, indicating that DNA replication can mitigate effects of chromatinization.Our results provide an

  3. Genetic manipulation of Methanosarcina spp.

    Directory of Open Access Journals (Sweden)

    PetraRegine AdelheidKohler

    2012-07-01

    Full Text Available The discovery of the third domain of life, the Archaea, is one of the most exciting findings of the last century. These remarkable prokaryotes are well known for their adaptations to extreme environments; however, Archaea have also conquered moderate environments. Many of the archaeal biochemical processes, such as methane production, are unique in nature and therefore of great scientific interest. Although formerly restricted to biochemical and physiological studies, sophisticated systems for genetic manipulation have been developed during the last two decades for methanogenic archaea, halophilic archaea and thermophilic, sulfur-metabolizing archaea. The availability of these tools has allowed for more complete studies of archaeal physiology and metabolism and most importantly provides the basis for the investigation of gene expression, regulation and function. In this review we provide an overview of methods for genetic manipulation of Methanosarcina spp., a group of methanogenic archaea that are key players in the global carbon cycle and which can be found in a variety of anaerobic environments.

  4. Manipulating Combinatorial Structures.

    Science.gov (United States)

    Labelle, Gilbert

    This set of transparencies shows how the manipulation of combinatorial structures in the context of modern combinatorics can easily lead to interesting teaching and learning activities at every level of education from elementary school to university. The transparencies describe: (1) the importance and relations of combinatorics to science and…

  5. Data manipulation with R

    CERN Document Server

    Abedin, Jaynal

    2015-01-01

    This book is for all those who wish to learn about data manipulation from scratch and excel at aggregating data effectively. It is expected that you have basic knowledge of R and have previously done some basic administration work with R.

  6. MANIPULATING CONSUMERS THROUGH ADVERTISING

    Directory of Open Access Journals (Sweden)

    Nicoleta -Andreea Neacşu

    2012-12-01

    Full Text Available Marketing communication has evolved steadily in the direction of increasing complexity and increasing volume of funds needed to run their own actions. More than ever, consumers are exposed to an overwhelming variety of sources and communication tehniques, the information received being numerous, diverse and polyvalent. The desire to make more efficient the marketing communication activity urges the broadcasters to encode messages, to use effective means of propagation in order to obtain a high degree of control on receptors and to influence the consumption attitudes. Between the means used for this purpose, manipulation tehniques are well known. This paper highlights the main conclusions drawn as a result of a quantitative marketing research on the adult population from Braşov in order to identify the attitudes and opinions of consumers from Braşov regarding the manipulation techniques used by commercial practices and advertising.The results of the research have shown that 82% of the respondents buy products in promotional offers, and 18% choose not to buy these products and 61% of the respondents consider that they have not been manipulated not even once, while only 39% believe that they have been manipulated at least once through advertising or commercial practices. Advertisements on TV have a strong influence on consumers, 81% of the respondents considering that at least once they have bought a product because of a TV commercial.

  7. Manipulating the Gradient

    Science.gov (United States)

    Gaze, Eric C.

    2005-01-01

    We introduce a cooperative learning, group lab for a Calculus III course to facilitate comprehension of the gradient vector and directional derivative concepts. The lab is a hands-on experience allowing students to manipulate a tangent plane and empirically measure the effect of partial derivatives on the direction of optimal ascent. (Contains 7…

  8. Genetic manipulation of Porphyromonas gingivalis.

    Science.gov (United States)

    Bélanger, Myriam; Rodrigues, Paulo; Progulske-Fox, Ann

    2007-06-01

    Porphyromonas gingivalis, an oral anaerobic bacterium, is an important etiological agent of periodontal disease and may contribute to cardiovascular disease, preterm birth, and diabetes as well. Therefore, genetic studies are of crucial importance in investigating molecular mechanisms of P. gingivalis virulence. Although molecular genetic tools have been available for many bacterial species for some time, genetic manipulations of Porphyromonas species were not developed until more recently and remain limited. In this unit, current molecular genetic approaches for mutant construction in P. gingivalis using the suicide vector pPR-UF1 and the transposon Tn4351 are described, as are protocols for performing electroporation and conjugation. Furthermore, a technique to restore the wild-type phenotype of the mutant by complementation using vector pT-COW is provided. Finally, a description of a noninvasive reporter system allowing the study of gene expression and regulation in P. gingivalis completes this unit. PMID:18770611

  9. Door breaching robotic manipulator

    Science.gov (United States)

    Schoenfeld, Erik; Parrington, Lawrence; von Muehlen, Stephan

    2008-04-01

    As unmanned systems become more commonplace in military, police, and other security forces, they are tasked to perform missions that the original hardware was not designed for. Current military robots are built for rough outdoor conditions and have strong inflexible manipulators designed to handle a wide range of operations. However, these manipulators are not well suited for some essential indoor tasks, including opening doors. This is a complicated kinematic task that places prohibitively difficult control challenges on the robot and the operator. Honeybee and iRobot have designed a modular door-breaching manipulator that mechanically simplifies the demands upon operator and robot. The manipulator connects to the existing robotic arm of the iRobot PackBot EOD. The gripper is optimized for grasping a variety of door knobs, levers, and car-door handles. It works in conjunction with a compliant wrist and magnetic lock-out mechanism that allows the wrist to remain rigid until the gripper has a firm grasp of the handle and then bend with its rotation and the swing of the door. Once the door is unlatched, the operator simply drives the robot through the doorway while the wrist compensates for the complex, multiple degree-of-freedom motion of the door. Once in the doorway the operator releases the handle, the wrist pops back into place, and the robot is ready for the next door. The new manipulator dramatically improves a robot's ability to non-destructively breach doors and perform an inspection of a room's content, a capability that was previously out of reach of unmanned systems.

  10. IL-12 based gene therapy in veterinary medicine

    Directory of Open Access Journals (Sweden)

    Pavlin Darja

    2012-11-01

    Full Text Available Abstract The use of large animals as an experimental model for novel treatment techniques has many advantages over the use of laboratory animals, so veterinary medicine is becoming an increasingly important translational bridge between preclinical studies and human medicine. The results of preclinical studies show that gene therapy with therapeutic gene encoding interleukin-12 (IL-12 displays pronounced antitumor effects in various tumor models. A number of different studies employing this therapeutic plasmid, delivered by either viral or non-viral methods, have also been undertaken in veterinary oncology. In cats, adenoviral delivery into soft tissue sarcomas has been employed. In horses, naked plasmid DNA has been delivered by direct intratumoral injection into nodules of metastatic melanoma. In dogs, various types of tumors have been treated with either local or systemic IL-12 electrogene therapy. The results of these studies show that IL-12 based gene therapy elicits a good antitumor effect on spontaneously occurring tumors in large animals, while being safe and well tolerated by the animals. Hopefully, such results will lead to further investigation of this therapy in veterinary medicine and successful translation into human clinical trials.

  11. Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies

    Directory of Open Access Journals (Sweden)

    Lehr Thorsten

    2011-03-01

    Full Text Available Abstract Background Several methods have been presented for the analysis of complex interactions between genetic polymorphisms and/or environmental factors. Despite the available methods, there is still a need for alternative methods, because no single method will perform well in all scenarios. The aim of this work was to evaluate the performance of three selected rule based classifier algorithms, RIPPER, RIDOR and PART, for the analysis of genetic association studies. Methods Overall, 42 datasets were simulated with three different case-control models, a varying number of subjects (300, 600, SNPs (500, 1500, 3000 and noise (5%, 10%, 20%. The algorithms were applied to each of the datasets with a set of algorithm-specific settings. Results were further investigated with respect to a the Model, b the Rules, and c the Attribute level. Data analysis was performed using WEKA, SAS and PERL. Results The RIPPER algorithm discovered the true case-control model at least once in >33% of the datasets. The RIDOR and PART algorithm performed poorly for model detection. The RIPPER, RIDOR and PART algorithm discovered the true case-control rules in more than 83%, 83% and 44% of the datasets, respectively. All three algorithms were able to detect the attributes utilized in the respective case-control models in most datasets. Conclusions The current analyses substantiate the utility of rule based classifiers such as RIPPER, RIDOR and PART for the detection of gene-gene/gene-environment interactions in genetic association studies. These classifiers could provide a valuable new method, complementing existing approaches, in the analysis of genetic association studies. The methods provide an advantage in being able to handle both categorical and continuous variable types. Further, because the outputs of the analyses are easy to interpret, the rule based classifier approach could quickly generate testable hypotheses for additional evaluation. Since the algorithms are

  12. Dynamics of a multimodule variable geometry manipulator

    Science.gov (United States)

    Caron, M.; Modi, V. J.; Misra, A. K.

    2002-05-01

    As robotic manipulators gain more importance in space operations, it is becoming imperative to understand their distinctive dynamics and control characteristics. With the increasing complexity of space robot, efficient algorithms are required for their simulation. The present study uses an order- N algorithm, based on the Lagrangian approach and velocity transformations, to simulate the planar dynamics of a novel orbiting manipulator with arbitrary number of slewing and deployable flexible links. The relatively general formulation accounts for the interactions between orbital, librational, slewing, deployment, and vibrational degrees of freedom, and thus is applicable to a large class of manipulator systems of contemporary interest. A parametric analysis of the system dynamics is carried out to investigate effects of initial disturbances, system parameters and maneuver profiles. The study suggests considerable coupling between the rigid body motion and structural vibrations. Obviously, this would significantly affect the manipulator's performance in tracking a prescribed trajectory.

  13. Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology

    Institute of Scientific and Technical Information of China (English)

    Shun-Liang CAO; Lei QIN; Wei-Zhong HE; Yang ZHONG; Yang-Yong ZHU; Yi-Xue LI

    2004-01-01

    Semantic search is a key issue in integration of heterogeneous biological databases. In thispaper, we present a methodology for implementing semantic search in BioDW, an integrated biological datawarehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entriesfrom BioDW data sources with GO, and the semantic similarity table to record similarity scores derived fromany pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and thecorresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

  14. A comprehensive family-based replication study of schizophrenia genes

    DEFF Research Database (Denmark)

    Aberg, Karolina A; Liu, Youfang; Bukszár, Jozsef;

    2013-01-01

     768 control subjects from 6 databases and, after quality control 6298 individuals (including 3286 cases) from 1811 nuclear families. MAIN OUTCOMES AND MEASURES Case-control status for SCZ. RESULTS Replication results showed a highly significant enrichment of SNPs with small P values. Of the SNPs with...... independent family-based replication study that, after quality control, consisted of 8107 SNPs. SETTING Linkage meta-analysis, brain transcriptome meta-analysis, candidate gene database, OMIM, relevant mouse studies, and expression quantitative trait locus databases. PATIENTS We included 11 185 cases and 10...

  15. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th. PMID:18820292

  16. Improving gene expression similarity measurement using pathway-based analytic dimension

    OpenAIRE

    2009-01-01

    Background Gene expression similarity measuring methods were developed and applied to search rapidly growing public microarray databases. However, current expression similarity measuring methods need to be improved to accurately measure similarity between gene expression profiles from different platforms or different experiments. Results We devised new gene expression similarity measuring method based on pathway information. In short, newly devised method measure similarity between gene expre...

  17. Spin-manipulating polarized deuterons

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, V S; Krisch, A D; Leonova, M A; Raymond, R S; Sivers, D W; Wong, V K; Hinterberger, F; Kondratenko, A M

    2011-03-01

    Spin dynamics of polarized deuteron beams near depolarization resonances, including a new polarization preservation concept based on specially-designed multiple resonance crossings, has been tested in a series of experiments in the COSY synchrotron. Intricate spin dynamics with sophisticated pre-programmed patterns as well as effects of multiple crossings of a resonance were studied both theoretically and experimentally with excellent agreement. Possible applications of these results to preserve, manipulate and spin-flip polarized beams in synchrotrons and storage rings are discussed.

  18. From Micro- to Nanoparticle Manipulation

    International Nuclear Information System (INIS)

    The precise manipulation of small particles is not a trivial task. In a first effort, a nanorobot system was built based on a robot with vision feedback and a micromachined gripper. It was suitable for handling particles down to 100 μ with submicron accuracy in a normal environment. For smaller particles stiction effects prohibit the release of the particles in a controlled way. Stiction effects are avoided in a fluid environment. As an example, a system of channels is described in detail that is able to feed micron sized particles in a fluid environment to the desired places

  19. Efficient manipulation of the human adenovirus genome as an infectious yeast artificial chromosome clone.

    OpenAIRE

    Ketner, G; Spencer, F; Tugendreich, S; C. Connelly; Hieter, P

    1994-01-01

    A yeast artificial chromosome (YAC) containing a complete human adenovirus type 2 genome was constructed, and viral DNA derived from the YAC was shown to be infectious upon introduction into mammalian cells. The adenovirus YAC could be manipulated efficiently using homologous recombination-based methods in the yeast host, and mutant viruses, including a variant that expresses the human analog of the Saccharomyces cerevisiae CDC27 gene, were readily recovered from modified derivatives of the Y...

  20. Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects

    OpenAIRE

    Chang Maw-Shang; Wang Feng-Sheng; Wu Wu-Hsiung

    2011-01-01

    Abstract Background Improving the synthesis rate of desired metabolites in metabolic systems is one of the main tasks in metabolic engineering. In the last decade, metabolic engineering approaches based on the mathematical optimization have been used extensively for the analysis and manipulation of metabolic networks. Experimental evidence shows that mutants reflect resilience phenomena against gene alterations. Although researchers have published many studies on the design of metabolic syste...

  1. Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data

    OpenAIRE

    Yang, Zuozhang; Chen, Yongbin; Fu, Yu; Yang, Yihao; Zhang, Ya; Chen, Yanjin; Li, Dongqi

    2014-01-01

    Background To uncover the genes involved in the development of osteosarcoma (OS), we performed a meta-analysis of OS microarray data to identify differentially expressed genes (DEGs) and biological functions associated with gene expression changes between OS and normal control (NC) tissues. Methods We used publicly available GEO datasets of OS to perform a meta-analysis. We performed Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Pr...

  2. Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression Network

    OpenAIRE

    Dajeong Lim; Nam-Kuk Kim; Seung-Hwan Lee; Hye-Sun Park; Yong-Min Cho; Han-Ha Chai; Heebal Kim

    2014-01-01

    Marbling is an important trait in characterization beef quality and a major factor for determining the price of beef in the Korean beef market. In particular, marbling is a complex trait and needs a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with marbling, we used a weighted gene coexpression network analysis from the expression value of bovine genes. Hub genes were identified; they were topologically centered with large d...

  3. Inference of Gene Regulatory Network Based on Local Bayesian Networks

    Science.gov (United States)

    Liu, Fei; Zhang, Shao-Wu; Guo, Wei-Feng; Chen, Luonan

    2016-01-01

    The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. During past decades, numerous computational approaches have been introduced for inferring the GRNs. However, many of them still suffer from various problems, e.g., Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory-based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. To overcome the limitations, in this work we present a novel algorithm, namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. Then, BN method is employed to generate a series of local BNs by selecting the k-nearest neighbors of each gene as its candidate regulatory genes, which significantly reduces the exponential search space from all possible GRN structures. Integrating these local BNs forms a tentative network or GRN by performing CMI, which reduces redundant regulations in the GRN and thus alleviates the false positive problem. The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative process, the false or redundant regulations are gradually removed. When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E.coli, our results suggest that LBN outperforms other state-of-the-art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. In particular, the decomposition strategy with local Bayesian networks not only effectively reduce

  4. Inference of Gene Regulatory Network Based on Local Bayesian Networks.

    Science.gov (United States)

    Liu, Fei; Zhang, Shao-Wu; Guo, Wei-Feng; Wei, Ze-Gang; Chen, Luonan

    2016-08-01

    The inference of gene regulatory networks (GRNs) from expression data can mine the direct regulations among genes and gain deep insights into biological processes at a network level. During past decades, numerous computational approaches have been introduced for inferring the GRNs. However, many of them still suffer from various problems, e.g., Bayesian network (BN) methods cannot handle large-scale networks due to their high computational complexity, while information theory-based methods cannot identify the directions of regulatory interactions and also suffer from false positive/negative problems. To overcome the limitations, in this work we present a novel algorithm, namely local Bayesian network (LBN), to infer GRNs from gene expression data by using the network decomposition strategy and false-positive edge elimination scheme. Specifically, LBN algorithm first uses conditional mutual information (CMI) to construct an initial network or GRN, which is decomposed into a number of local networks or GRNs. Then, BN method is employed to generate a series of local BNs by selecting the k-nearest neighbors of each gene as its candidate regulatory genes, which significantly reduces the exponential search space from all possible GRN structures. Integrating these local BNs forms a tentative network or GRN by performing CMI, which reduces redundant regulations in the GRN and thus alleviates the false positive problem. The final network or GRN can be obtained by iteratively performing CMI and local BN on the tentative network. In the iterative process, the false or redundant regulations are gradually removed. When tested on the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in E.coli, our results suggest that LBN outperforms other state-of-the-art methods (ARACNE, GENIE3 and NARROMI) significantly, with more accurate and robust performance. In particular, the decomposition strategy with local Bayesian networks not only effectively reduce

  5. Development of gene diagnosis for diabetes and cholecystitis based on gene analysis of CCK-A receptor

    Energy Technology Data Exchange (ETDEWEB)

    Kono, Akira [National Kyushu Cancer Center, Fukuoka (Japan)

    1999-02-01

    Base sequence analysis of CCKAR gene (a gene of A-type receptor for cholecystokinin) from OLETF rat, a model rat for insulin-independent diabetes was made based on the base sequence of wild CCKAR gene, which had been clarified in the previous year. From the pancreas of OLETF rat, DNA was extracted and transduced into {lambda}phage after fragmentation to construct the gene library of OLETF. Then, {lambda}phage DNA clone bound with labelled cDNA of CCKAR gene was analyzed and the gene structure was compared with that of the wild gene. It was demonstrated that CCKAR gene of OLETF had a deletion (6800 b.p.) ranging from the promoter region to the Exon 2, suggesting that CCKAR gene is not functional in OLETF rat. The whole sequence of this mutant gene was registered into Japan DNA Bank (D 50610). Then, F{sub 2} offspring rats were obtained through crossing OLETF (female) and F344 (male) and the time course-changes in the blood glucose level after glucose loading were compared among them. The blood glucose level after glucose loading was significantly higher in the homo-mutant F{sub 2} (CCKAR,-/-) as well as the parent OLETF rat than hetero-mutant F{sub 2} (CCKARm-/+) or the wild rat (CCKAR,+/+). This suggests that CCKAR gene might be involved in the control of blood glucose level and an alteration of the expression level or the functions of CCKAR gene might affect the blood glucose level. (M.N.)

  6. Microradiographic microsphere manipulator

    International Nuclear Information System (INIS)

    A method and apparatus are provided for radiographic characterization of small hollow spherical members (microspheres), constructed of either optically transparent or opaque materials. The apparatus involves a microsphere manipulator which holds a batch of microspheres between two parallel thin plastic films for contact microradiographic characterization or projection microradiography thereof. One plastic film is translated to relative to and parallel to the other to roll the microspheres through any desired angle to allow different views of the microspheres

  7. MANIPULATOR FOR SLAVE ROBOT

    Science.gov (United States)

    Goertz, R.C.; Grimson, J.H.; Kohut, F.A.

    1961-04-01

    A remote-control manipulator comprising two stationary master units, two slave units on a movable vehicle, and electrical connections between the master and slave units is reported. The slave units are side by side with a minimum over-all width, which is made feasible by an arrangement of transducers producing most movements of each slave unit to one side of the support of said slave unit.

  8. Microradiographic microsphere manipulator

    Science.gov (United States)

    Singleton, Russell M.

    1980-01-01

    A method and apparatus for radiographic characterization of small hollow spherical members (microspheres), constructed of either optically transparent or opaque materials. The apparatus involves a microsphere manipulator which holds a batch of microspheres between two parallel thin plastic films for contact microradiographic characterization or projection microradiography thereof. One plastic film is translated to relative to and parallel to the other to roll the microspheres through any desired angle to allow different views of the microspheres.

  9. Seed-Based Biclustering of Gene Expression Data

    OpenAIRE

    Jiyuan An; Alan Wee-Chung Liew; Colleen C Nelson

    2012-01-01

    BACKGROUND: Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar e...

  10. Novel RNA-based Strategies for Therapeutic Gene Silencing

    OpenAIRE

    Sibley, Christopher R.; Seow, Yiqi; Wood, Matthew JA

    2010-01-01

    The past decade has seen intense scientific interest in non-coding RNAs. In particular, the discovery and subsequent exploitation of gene silencing via RNA interference (RNAi) has revolutionized the way in which gene expression is now studied and understood. It is now well established that post-transcriptional gene silencing (PTGS) by the microRNA (miRNA) and other RNAi-associated pathways represents an essential layer of complexity to gene regulation. Gene silencing using RNAi additionally d...

  11. Gene network-based cancer prognosis analysis with sparse boosting

    OpenAIRE

    Ma, Shuangge; Huang, Yuan; Huang, Jian; Fang, Kuangnan

    2012-01-01

    High-throughput gene profiling studies have been extensively conducted, searching for markers associated with cancer development and progression. In this study, we analyse cancer prognosis studies with right censored survival responses. With gene expression data, we adopt the weighted gene co-expression network analysis (WGCNA) to describe the interplay among genes. In network analysis, nodes represent genes. There are subsets of nodes, called modules, which are tightly connected to each othe...

  12. Parallel microassembly with a robotic manipulation system

    International Nuclear Information System (INIS)

    This paper proposes a methodology to assemble multiple micro-components simultaneously with a robotic manipulator using a parallel assembly method. Through manipulating and assembling the micro-components, intricate, out-of-plane, three-dimensional micro-devices can now be fabricated. Use of a parallel microassembly process rather that a serial approach can significantly increase the productivity and reduce the cost of assembling micro-devices. The parallel microassembly operation proposed in this work was developed and implemented on a 6-DOF robot manipulator to attain considerable manufacturing flexibility. In this study, three passive microgrippers were bonded in parallel to the end-effector of the manipulator. Three microparts were then grasped by the grippers from the worktable of the manipulator, rotated 90°, and assembled onto the base substrate simultaneously. During the parallel microassembly operation, the visual image may not be able to monitor all three gripper-part pairs simultaneously due to the limited field of view of the microscope. Through the use of an alignment-calibration algorithm with only one gripper-part set, the remaining two sets were successfully manipulated and inserted onto the desired assembly location

  13. Multi-agent Architecture Model for Driving Mobile Manipulator Robots

    OpenAIRE

    Hentout, A.; Bouzouia, B.; Z. Toukal

    2008-01-01

    In this article, we present generic hierarchical behavior-based architecture model for driving mobile manipulator robots. Two behaviors are of high-level. They constitute the Supervisory agent, which manages the global system. Two others are of intermediate-level and finally one behavior is of low-level. These last ones constitute the Mobile Robot agent and the Manipulator Robot agent controlling, respectively, the mobile base and the manipulator arm. The choice of the suggest...

  14. Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

    Science.gov (United States)

    Kibinge, Nelson; Ono, Naoaki; Horie, Masafumi; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Saito, Akira; Kanaya, Shigehiko

    2016-06-01

    Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation. The pipeline implements pathway-based modularization of expression profiles into functional units to improve biological interpretation. The integrated workflow was implemented as a web application software (TransReguloNet) with functions that enable pathway visualization and comparison of transcription factor activity between sample conditions defined in the experimental design. The pipeline merges differential expression, network construction, pathway-based abstraction, clustering and visualization. The framework was applied in analysis of actual expression datasets related to lung, breast and prostrate cancer. PMID:27064123

  15. Gene-based analysis of regionally enriched cortical genes in GWAS data sets of cognitive traits and psychiatric disorders.

    Directory of Open Access Journals (Sweden)

    Kari M Ersland

    Full Text Available BACKGROUND: Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes in three different cortical areas (frontomedial, temporal and occipital cortices of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used the regionally enriched cortical genes to mine a genome-wide association study (GWAS of the Norwegian Cognitive NeuroGenetics (NCNG sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ (n = 3 samples and bipolar affective disorder (BP (n = 3 samples, to which cognitive impairment is linked. PRINCIPAL FINDINGS: At the single gene level, the temporal cortex enriched gene RAR-related orphan receptor B (RORB showed the strongest overall association, namely to a test of verbal intelligence (Vocabulary, P = 7.7E-04. We also applied gene set enrichment analysis (GSEA to test the candidate genes, as gene sets, for enrichment of association signal in the NCNG GWAS and in GWASs of BP and of SCZ. We found that genes differentially expressed in the temporal cortex showed a significant enrichment of association signal in a test measure of non-verbal intelligence (Reasoning in the NCNG sample. CONCLUSION: Our gene-based approach suggests that RORB could be involved in verbal intelligence differences, while the genes enriched in the temporal cortex might be important to intellectual functions as measured by a test of reasoning in the healthy population. These findings warrant further replication in independent samples on cognitive traits.

  16. Milestones in Candida albicans Gene Manipulation

    OpenAIRE

    Samaranayake, Dhanushki P.; Hanes, Steven D.

    2011-01-01

    In the United States, candidemia is one of the most common hospital-acquired infections and is estimated to cause 10,000 deaths per year. The species Candida albicans is responsible for the majority of these cases. As C. albicans is capable of developing resistance against the currently available drugs, understanding the molecular basis of drug resistance, finding new cellular targets, and further understanding the overall mechanism of C. albicans pathogenesis are important goals. To study th...

  17. The effects of cervical joint manipulation, based on passive motion analysis, on cervical lordosis, forward head posture, and cervical ROM in university students with abnormal posture of the cervical spine

    OpenAIRE

    Gong, Wontae

    2015-01-01

    [Purpose] The aim of this study was to determine the effect of cervical posture manipulation, based on passive motion analysis (MBPMA) and general mobilization, on cervical lordosis, forward head posture (FHP), and cervical ROM in university students with problems in cervical posture and range of motion (ROM). [Subjects] The Subjects were 40 university students in their 20s who displayed problems in cervical posture and ROM; they were divided into an MBPMA group (n=20) and a mobilization grou...

  18. Spatial manipulation with microfluidics

    Directory of Open Access Journals (Sweden)

    Benjamin eLin

    2015-04-01

    Full Text Available Biochemical gradients convey information through space, time, and concentration, and are ultimately capable of spatially resolving distinct cellular phenotypes, such as differentiation, proliferation, and migration. How these gradients develop, evolve, and function during development, homeostasis, and various disease states is a subject of intense interest across a variety of disciplines. Microfluidic technologies have become essential tools for investigating gradient sensing in vitro due to their ability to precisely manipulate fluids on demand in well controlled environments at cellular length scales. This minireview will highlight their utility for studying gradient sensing along with relevant applications to biology.

  19. Performance measurement of mobile manipulators

    Science.gov (United States)

    Bostelman, Roger; Hong, Tsai; Marvel, Jeremy

    2015-05-01

    This paper describes a concept for measuring the reproducible performance of mobile manipulators to be used for assembly or other similar tasks. An automatic guided vehicle with an onboard robot arm was programmed to repeatedly move to and stop at a novel, reconfigurable mobile manipulator artifact (RMMA), sense the RMMA, and detect targets on the RMMA. The manipulator moved a laser retroreflective sensor to detect small reflectors that can be reconfigured to measure various manipulator positions and orientations (poses). This paper describes calibration of a multi-camera, motion capture system using a 6 degree-of-freedom metrology bar and then using the camera system as a ground truth measurement device for validation of the reproducible mobile manipulator's experiments and test method. Static performance measurement of a mobile manipulator using the RMMA has proved useful for relatively high tolerance pose estimation and other metrics that support standard test method development for indexed and dynamic mobile manipulator applications.

  20. Design and Transmission Analysis of an Asymmetrical Spherical Parallel Manipulator

    DEFF Research Database (Denmark)

    Wu, Guanglei; Caro, Stéphane; Wang, Jiawei

    2015-01-01

    This paper presents an asymmetrical spherical parallel manipulator and its transmissibility analysis. This manipulator contains a center shaft to both generate a decoupled unlimited-torsion motion and support the mobile platform for high positioning accuracy. This work addresses the transmission...... analysis and optimal design of the proposed manipulator based on its kinematic analysis. The input and output transmission indices of the manipulator are defined for its optimum design based on the virtual coefficient between the transmission wrenches and twist screws. The sets of optimal parameters are...... identified and the distribution of the transmission index is visualized. Moreover, a comparative study regarding to the performances with the symmetrical spherical parallel manipulators is conducted and the comparison shows the advantages of the proposed manipulator with respect to its spherical parallel...

  1. Cell- and region-specific miR30-based gene knock-down with temporal control in the rat brain

    Directory of Open Access Journals (Sweden)

    Xu Haibo

    2010-12-01

    Full Text Available Abstract Background RNA interference (RNAi emerges as a powerful tool to induce loss-of-function phenotypes. In the context of the brain, gene manipulation is best targeted to specific subsets of cells in order to achieve a physiologically relevant outcome. Polymerase II-based viral expression systems can be used to cell-specifically express constructs incorporating flanking and loop sequences from endogenous microRNA (miRNA, which directs the designed hairpins into the endogenous gene silencing machinery. While many studies have documented non-cell-selective gene knock-down in the brain, it has not been tested whether different cell types or different areas of the central nervous system (CNS are equally amenable to this approach. We have evaluated this issue using a tetracycline (Tet-controllable and cell-specific miRNA 30 (miR30-based short hairpin (shRNA interference system. Results To achieve targeted expression two cell type-specific promoters were used; the enhanced compact glial fibrillary acidic protein (GfaABC1D promoter and the enhanced human synapsin-1 (SYN promoter. Powerful luciferase (Luc and the neuronal isoform of nitric oxide synthase (nNOS gene knock-down were achieved both in vitro and in vivo. Administration of doxycycline (Dox abrogated gene silencing. However, the efficacy of gene knock-down in both neurones and astrocytes in the hippocampus (HIP was lower than that in the dorsal vagal complex of the brainstem (DVC. This was not due to regional differences in the expression of the the key enzymes involved in miRNA processing. Conclusions The results from the presented experiments demonstrated that selective gene knock-down in subsets of brain cells is achievable. However, there are some presently unknown regional factors which affect either the processing of miRNA-based cassettes or their potency for gene silencing.

  2. Density based pruning for identification of differentially expressed genes from microarray data

    Directory of Open Access Journals (Sweden)

    Xu Jia

    2010-11-01

    Full Text Available Abstract Motivation Identification of differentially expressed genes from microarray datasets is one of the most important analyses for microarray data mining. Popular algorithms such as statistical t-test rank genes based on a single statistics. The false positive rate of these methods can be improved by considering other features of differentially expressed genes. Results We proposed a pattern recognition strategy for identifying differentially expressed genes. Genes are mapped to a two dimension feature space composed of average difference of gene expression and average expression levels. A density based pruning algorithm (DB Pruning is developed to screen out potential differentially expressed genes usually located in the sparse boundary region. Biases of popular algorithms for identifying differentially expressed genes are visually characterized. Experiments on 17 datasets from Gene Omnibus Database (GEO with experimentally verified differentially expressed genes showed that DB pruning can significantly improve the prediction accuracy of popular identification algorithms such as t-test, rank product, and fold change. Conclusions Density based pruning of non-differentially expressed genes is an effective method for enhancing statistical testing based algorithms for identifying differentially expressed genes. It improves t-test, rank product, and fold change by 11% to 50% in the numbers of identified true differentially expressed genes. The source code of DB pruning is freely available on our website http://mleg.cse.sc.edu/degprune

  3. Design PID-Like Fuzzy Controller With Minimum Rule Base and Mathematical Proposed On-line Tunable Gain: Applied to Robot Manipulator

    Directory of Open Access Journals (Sweden)

    Farzin Piltan

    2011-10-01

    Full Text Available In this study, an on-line tunable gain model free PID-like fuzzy controller (GTFLC is designed for three degrees of freedom (3DOF robot manipulator to rich the best performance. Fuzzy logic controller is studied because of its model free and high performance. Today, robot manipulators are used in unknown and unstructured environment and caused to provide sophisticated systems, therefore strong mathematical tools are used in new control methodologies to design adaptive nonlinear robust controller with acceptable performance (e.g., minimum error, good trajectory, disturbance rejection. The strategies of control robot manipulator are classified into two main groups: classical and non-classical methods, however non linear classical theories have been applied successfully in many applications, but they also have some limitation. One of the most important nonlinear non classical robust controller that can used in uncertainty nonlinear systems, are fuzzy logic controller. This paper is focuses on applied mathematical tunable gain method in robust non classical method to reduce the fuzzy logic controller limitations. Therefore on-line tunable PID like fuzzy logic controller will be presented in this paper.

  4. Citrus plastid-related gene profiling based on expressed sequence tag analyses

    Directory of Open Access Journals (Sweden)

    Tercilio Calsa Jr.

    2007-01-01

    Full Text Available Plastid-related sequences, derived from putative nuclear or plastome genes, were searched in a large collection of expressed sequence tags (ESTs and genomic sequences from the Citrus Biotechnology initiative in Brazil. The identified putative Citrus chloroplast gene sequences were compared to those from Arabidopsis, Eucalyptus and Pinus. Differential expression profiling for plastid-directed nuclear-encoded proteins and photosynthesis-related gene expression variation between Citrus sinensis and Citrus reticulata, when inoculated or not with Xylella fastidiosa, were also analyzed. Presumed Citrus plastome regions were more similar to Eucalyptus. Some putative genes appeared to be preferentially expressed in vegetative tissues (leaves and bark or in reproductive organs (flowers and fruits. Genes preferentially expressed in fruit and flower may be associated with hypothetical physiological functions. Expression pattern clustering analysis suggested that photosynthesis- and carbon fixation-related genes appeared to be up- or down-regulated in a resistant or susceptible Citrus species after Xylella inoculation in comparison to non-infected controls, generating novel information which may be helpful to develop novel genetic manipulation strategies to control Citrus variegated chlorosis (CVC.

  5. Partially flagged parallel manipulators: singularity charting and avoidance

    OpenAIRE

    Alberich-Carramiñana, Maria; Garolera, Marçal; Thomas, Federico; Torras, Carme

    2009-01-01

    There are only three 6-SPS parallel manipulators with triangular base and platform: the octahedral, the flagged, and the partially-flagged studied in this paper. The forward kinematics of the octahedral manipulator is algebraically intricate, while those of the other two can be solved by three trilaterations. As an additional nice feature, the flagged manipulator is the only parallel platform for which a cell decomposition of its singularity locus has been derived. Here we prove that the part...

  6. A Dynamic Manipulation Strategy for an Intervention Autonomous Underwater Vehicle

    OpenAIRE

    Ridolfi, Alessandro; Conti, Roberto; Costanzi, Riccardo; Fanelli, Francesco; Meli, Enrico

    2015-01-01

    This paper presents the modelling and the control architecture of an Autonomous Underwater Vehicle for Intervention (I-AUV). Autonomous underwater manipulation with free-floating base is still an open topic of research, far from reaching an industrial product. Dynamic manipulation tasks, where relevant vehicle velocities are required during manipulation, over an additional challenge. In this paper, the accurate modelling of an I-AUV is described, not neglecting the interaction wit...

  7. Simulation Results for Manipulation of Unknown Objects in Hand

    OpenAIRE

    Li, Qiang; Haschke, Robert; Ritter, Helge; Bolder, Bram

    2011-01-01

    In this paper, the authors proposed a novel reactive strategy to solve a unknown object local manipulation problem with an multifingered robot hand. In this method, the micro manipulation assumption is proposed and the object can be manipulated within the robot hand workspace without the active and explicit controlling about the rolling and sliding of the fingertips on the object. A 6 D.O.F reactive controller based on the hybrid of the contact force and the contact posit...

  8. The market manipulation regime in the European Union

    OpenAIRE

    Li, Xue

    2015-01-01

    Market manipulation is an illegal practice that enables a person can profit from practices that artificially raise or lower the prices of an instrument in the financial markets. Its prohibition is based on the 2003 Market Abuse Directive in the EU. The current market manipulation regime was broadly considered as a big success except for enforcement and supervisory inconsistencies in the Member States at the initial. A review of the market manipulation regime began at the end of 2007, which...

  9. 基于VB的气动复合式康复机械手单片机控制系统%Pneumatic Composite Rehabilitation Manipulators' Microcontroller Control System Based on VB

    Institute of Scientific and Technical Information of China (English)

    王领; 张志军; 王利波

    2012-01-01

    This paper introduces a new type of pneumatic composite rehabilitation manipulators, the design of the corresponding pneumatic schematic diagram. Based on the Visual Basic language environment,using MSComm control communications , through the friendly man - machine interface control,the low cost,high performance of manipulator control system is built,also analyzed the open control system structure and component.%介绍了一种新型气动复合式康复机械手,设计了相应的气动原理图.建立了基于VB语言环境,采用MSComm控件通讯,通过友好的人机界面控制低成本、高性能的机械手控制系统,分析了这种开放式控制系统的结构组成.

  10. Gene-Expression-Based Predictors for Breast Cancer.

    Science.gov (United States)

    Gupta, Arjun; Mutebi, Miriam; Bardia, Aditya

    2015-10-01

    An important and often complicated management decision in early stage hormone receptor (HR)-positive breast cancer relates to the use of adjuvant systemic chemotherapy. Although traditional clinicopathologic markers exist, tremendous progress has been achieved in the field of predictive biomarkers and genomics with both prognostic and predictive capabilities to identify patients who will potentially benefit from additional therapy. The use of these genomic tests in the neoadjuvant setting is also being studied and may lead to these tests providing clinical benefit even earlier in the disease course. Landmark articles published in the last few years have expanded our knowledge of breast cancer genomics to an unprecedented level, and mutational analysis via next-generation sequencing methods allows the identification of molecular targets for novel targeted therapeutic agents and clinical trials testing efficacy of targeted therapies, such as PI3K inhibitors, in addition to endocrine therapy for HR-positive breast cancer, are ongoing. We provide an in-depth review on the role of gene expression-based predictors in early stage breast cancer and an overview of future directions, including next-generation sequencing. Over the coming years, we anticipate a significant increase in utilization of genomic-based predictors for individualized selection and duration of endocrine therapy with and without genotype-driven targeted therapy, and a major decrease in the use of chemotherapy, possibly even leading to a chemotherapy-free road for early stage HR-positive breast cancer. PMID:26215189

  11. Hydraulic manipulator research at ORNL

    International Nuclear Information System (INIS)

    Recently, task requirements have dictated that manipulator payload capacity increase to accommodate greater payloads, greater manipulator length, and larger environmental interaction forces. General tasks such as waste storage tank cleanup and facility dismantlement and decommissioning require manipulator life capacities in the range of hundreds of pounds rather than tens of pounds. To meet the increased payload capacities demanded by present-day tasks, manipulator designers have turned once again to hydraulics as a means of actuation. In order to successfully design, build, and deploy a new hydraulic manipulator (or subsystem), sophisticated modeling, analysis, and control experiments are usually needed. Oak Ridge National Laboratory (ORNL) has a history of projects that incorporate hydraulics technology, including mobile robots, teleoperated manipulators, and full-scale construction equipment. In addition, to support the development and deployment of new hydraulic manipulators, ORNL has outfitted a significant experimental laboratory and has developed the software capability for research into hydraulic manipulators, hydraulic actuators, hydraulic systems, modeling of hydraulic systems, and hydraulic controls. The purpose of this article is to describe the past hydraulic manipulator developments and current hydraulic manipulator research capabilities at ORNL. Included are example experimental results from ORNL's flexible/prismatic test stand

  12. Hydraulic manipulator research at ORNL

    Energy Technology Data Exchange (ETDEWEB)

    Kress, R.L.; Jansen, J.F. [Oak Ridge National Lab., TN (United States); Love, L.J. [Oak Ridge Inst. for Science and Education, TN (United States)

    1997-03-01

    Recently, task requirements have dictated that manipulator payload capacity increase to accommodate greater payloads, greater manipulator length, and larger environmental interaction forces. General tasks such as waste storage tank cleanup and facility dismantlement and decommissioning require manipulator life capacities in the range of hundreds of pounds rather than tens of pounds. To meet the increased payload capacities demanded by present-day tasks, manipulator designers have turned once again to hydraulics as a means of actuation. In order to successfully design, build, and deploy a new hydraulic manipulator (or subsystem), sophisticated modeling, analysis, and control experiments are usually needed. Oak Ridge National Laboratory (ORNL) has a history of projects that incorporate hydraulics technology, including mobile robots, teleoperated manipulators, and full-scale construction equipment. In addition, to support the development and deployment of new hydraulic manipulators, ORNL has outfitted a significant experimental laboratory and has developed the software capability for research into hydraulic manipulators, hydraulic actuators, hydraulic systems, modeling of hydraulic systems, and hydraulic controls. The purpose of this article is to describe the past hydraulic manipulator developments and current hydraulic manipulator research capabilities at ORNL. Included are example experimental results from ORNL`s flexible/prismatic test stand.

  13. Sleeping Beauty transposon-based system for cellular reprogramming and targeted gene insertion in induced pluripotent stem cells

    Science.gov (United States)

    Grabundzija, Ivana; Wang, Jichang; Sebe, Attila; Erdei, Zsuzsanna; Kajdi, Robert; Devaraj, Anantharam; Steinemann, Doris; Szuhai, Károly; Stein, Ulrike; Cantz, Tobias; Schambach, Axel; Baum, Christopher; Izsvák, Zsuzsanna; Sarkadi, Balázs; Ivics, Zoltán

    2013-01-01

    The discovery of direct cell reprogramming and induced pluripotent stem (iPS) cell technology opened up new avenues for the application of non-viral, transposon-based gene delivery systems. The Sleeping Beauty (SB) transposon is highly advanced for versatile genetic manipulations in mammalian cells. We established iPS cell reprogramming of mouse embryonic fibroblasts and human foreskin fibroblasts by transposition of OSKM (Oct4, Sox2, Klf4 and c-Myc) and OSKML (OSKM + Lin28) expression cassettes mobilized by the SB100X hyperactive transposase. The efficiency of iPS cell derivation with SB transposon system was in the range of that obtained with retroviral vectors. Co-expression of the miRNA302/367 cluster together with OSKM significantly improved reprogramming efficiency and accelerated the temporal kinetics of reprogramming. The iPS cells displayed a stable karyotype, and hallmarks of pluripotency including expression of stem cell markers and the ability to differentiate into embryoid bodies in vitro. We demonstrate Cre recombinase-mediated exchange allowing simultaneous removal of the reprogramming cassette and targeted knock-in of an expression cassette of interest into the transposon-tagged locus in mouse iPS cells. This strategy would allow correction of a genetic defect by site-specific insertion of a therapeutic gene construct into ‘safe harbor’ sites in the genomes of autologous, patient-derived iPS cells. PMID:23275558

  14. Concurrent Manipulation of Expanded AVL Trees

    Institute of Scientific and Technical Information of China (English)

    章寅; 许卓群

    1998-01-01

    The concurrent manipulation of an expanded AVL tree(EAVL tree)s considered in this paper.The presented system can support any number of concurrent processes which perform searching,insertion and deletion on the tree.Simulation results indicate the high performance of the system.Elaborate techniques are used to achieve such a system unavailable based on any known algorithms.Methods developed in this paper may provide new insights into other problems in the area of concurrent search structure manipulation.

  15. Gene identification and analysis: an application of neural network-based information fusion

    Energy Technology Data Exchange (ETDEWEB)

    Matis, S.; Xu, Y.; Shah, M.B.; Mural, R.J.; Einstein, J.R.; Uberbacher, E.C.

    1996-10-01

    Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. We describe a gene localization and modeling system called GRAIL. GRAIL is a multiple sensor-neural network based system. It localizes genes in anonymous DNA sequence by recognizing gene features related to protein-coding slice sites, and then combines the recognized features using a neural network system. Localized coding regions are then optimally parsed into a gene mode. RNA polymerase II promoters can also be predicted. Through years of extensive testing, GRAIL consistently localizes about 90 percent of coding portions of test genes with a false positive rate of about 10 percent. A number of genes for major genetic diseases have been located through the use of GRAIL, and over 1000 research laboratories worldwide use GRAIL on regular bases for localization of genes on their newly sequenced DNA.

  16. Mixing in manipulated turbulence

    CERN Document Server

    Kuczaj, A K; Geurts, Bernard J.; Kuczaj, Arkadiusz K.

    2006-01-01

    A new computational framework for the simulation of turbulent flow through complex objects and along irregular boundaries is presented. This is motivated by the application of metal foams in compact heat-transfer devices, or as catalyst substrates in process-engineering. The flow-consequences of such complicated objects are incorporated by adding explicit multiscale forcing to the Navier-Stokes equations. The forcing represents the simultaneous agitation of a wide spectrum of length-scales when flow passes through the complex object. It is found that a considerable modulation of the traditional energy cascading can be introduced with a specific forcing strategy. In spectral space, forcing yields strongly localized deviations from the common Kolmogorov scaling law, directly associated with the explicitly forced scales. In addition, the accumulated effect of forcing induces a significant non-local alteration of the kinetic energy including the spectrum for the large scales. Consequently, a manipulation of turbu...

  17. Manipulation with molecules

    Directory of Open Access Journals (Sweden)

    M.D Barnes

    2002-09-01

    For many years now, researchers in materials and photonics have been keenly interested in the design and fabrication of structures that confine and manipulate electromagnetic fields on length scales comparable to optical wavelengths. The ultimate goal is an all-optical information processing and computation platform using photons in ways analogous to electrons in silicon devices on similar length scales. Specific focus areas such as wafer-scale integration, parallel processing, and frequency management (e.g. add-drop filters, on micron or sub-micron length scales are active areas of photonics research. While a great deal of progress has been made in the burgeoning field of microphotonics, we are still a long way off from realizing important goals such as the optical transistor and all-optical integrated circuits1.

  18. Force reflecting hand controller for manipulator teleoperation

    Science.gov (United States)

    Bryfogle, Mark D.

    1991-12-01

    A force reflecting hand controller based upon a six degree of freedom fully parallel mechanism, often termed a Stewart Platform, has been designed, constructed, and tested as an integrated system with a slave robot manipulator test bed. A force reflecting hand controller comprises a kinesthetic device capable of transmitting position and orientation commands to a slave robot manipulator while simultaneously representing the environmental interaction forces of the slave manipulator back to the operator through actuators driving the hand controller mechanism. The Stewart Platform was chosen as a novel approach to improve force reflecting teleoperation because of its inherently high ratio of load generation capability to system mass content and the correspondingly high dynamic bandwidth. An additional novelty of the program was to implement closed loop force and torque control about the hand controller mechanism by equipping the handgrip with a six degree of freedom force and torque measuring cell. The mechanical, electrical, computer, and control systems are discussed and system tests are presented.

  19. Design of multivariable controllers for robot manipulators

    Science.gov (United States)

    Seraji, H.

    1986-01-01

    The paper presents a simple method for the design of linear multivariable controllers for multi-link robot manipulators. The control scheme consists of multivariable feedforward and feedback controllers. The feedforward controller is the minimal inverse of the linearized model of robot dynamics and contains only proportional-double-derivative (PD2) terms. This controller ensures that the manipulator joint angles track any reference trajectories. The feedback controller is of proportional-integral-derivative (PID) type and achieves pole placement. This controller reduces any initial tracking error to zero as desired and also ensures that robust steady-state tracking of step-plus-exponential trajectories is achieved by the joint angles. The two controllers are independent of each other and are designed separately based on the linearized robot model and then integrated in the overall control scheme. The proposed scheme is simple and can be implemented for real-time control of robot manipulators.

  20. Robotic manipulator systems for FMF-extension

    International Nuclear Information System (INIS)

    FMF-Extension, an intelligent hot laboratory is going to conduct immediate and accurate Post-Irradiation-Examination by using computers. This facility is also aiming to establish a comprehensive intelligent system with an entire networking by computers, test equipment and machineries under a unified control. Based on the concept, the primary function of the robotic manipulator is focused on automatic and safety transfer of a pin rack containing the fuel pins ready for testing after the irradiation. For that purpose, the automatic mode system for the facility and the robotic manipulator systems are combined together by a local area networking and are able to work collaboratively. In addition to the remote maintainability, the automated transfer function is given to the installed robotic manipulator systems. (author)

  1. Spider management in agroecosystems: Habitat manipulation

    Science.gov (United States)

    Mansour, Fadel; Richman, David B.; Whitcomb, W. H.

    1983-01-01

    Based on the literature and on work conducted in Israel, the management of spider populations through habitat manipulation was found to be very helpful in controlling pest insects in various crops. Spiders were found to be reduced or eliminated by non-selective insecticides, although some resistance has been noted

  2. A new gene co-expression network analysis based on Core Structure Detection (CSD)

    OpenAIRE

    Brunet, A-C; Azais, J-M; Loubes, J-M; Amar, J; Burcelin, R

    2016-01-01

    We propose a novel method to cluster gene networks. Based on a dissimilarity built using correlation structures, we consider networks that connect all the genes based on the strength of their dissimilarity. The large number of genes require the use of the threshold to find sparse structures in the graph. in this work, using the notion of graph coreness, we identify clusters of genes which are central in the network. Then we estimate a network that has these genes as main hubs. We use this new...

  3. Multidiscipline simulation of elastic manipulators

    Directory of Open Access Journals (Sweden)

    T. Rølvåg

    1992-10-01

    Full Text Available This paper contributes to multidiscipline simulation of elastic robot manipulators in FEDEM. All developments presented in this paper are based on the formulations in FEDEM, a simulation system developed by the authors which combines finite element, mechanism and control analysis. In order to establish this general simulation system as an efficient multidiscipline robot design tool a robot control system including a high level robot programming language, interpolation algorithms, path generation algorithms, forward and inverse kinematics, control systems, gear and transmission models are implemented. These new features provide a high level of integration between traditionally separate design disciplines from the very beginning of the design and optimization process. Several simulations have shown that high fidelity mathematical models can be derived and used as a basis for dynamic analysis and controller design in FEDEM.

  4. Symbolic Manipulation of Code Properties

    OpenAIRE

    Konstantinidis, Stavros; Meijer, Casey; Moreira, Nelma; Reis, Rogério

    2015-01-01

    The FAdo system is a symbolic manipulator of formal languages objects, implemented in Python. In this work, we extend its capabilities by implementing methods to manipulate transducers and we go one level higher than existing formal language systems and implement methods to manipulate objects representing classes of independent languages (widely known as code properties). Our methods allow users to define their own code properties and combine them between themselves or with fixed properties s...

  5. Mobile Manipulation: A Case Study

    OpenAIRE

    Hentout, A.; Bouzouia, B.; Akli, I.; Toumi, R.

    2010-01-01

    This chapter presented a multi-agent control architecture of mobile manipulators. The architecture consists of six agents: Supervisory Agent (SA), Local Mobile Robot Agent (LMRA), Local Manipulator Robot Agent (LARA), Vision System Agent (VSA), Remote Mobile Robot Agent (RMRA) and Remote Manipulator Robot Agent (RARA). The first four agents are installed on an off-board PC while the two other agents are installed on the on-board PC of the robot. The controller was applied successfully to foll...

  6. Screening for genes and subnetworks associated with pancreatic cancer based on the gene expression profile.

    Science.gov (United States)

    Long, Jin; Liu, Zhe; Wu, Xingda; Xu, Yuanhong; Ge, Chunlin

    2016-05-01

    The present study aimed to screen for potential genes and subnetworks associated with pancreatic cancer (PC) using the gene expression profile. The expression profile GSE 16515 was downloaded from the Gene Expression Omnibus database, which included 36 PC tissue samples and 16 normal samples. Limma package in R language was used to screen differentially expressed genes (DEGs), which were grouped as up‑ and downregulated genes. Then, PFSNet was applied to perform subnetwork analysis for all the DEGs. Moreover, Gene Ontology (GO) and REACTOME pathway enrichment analysis of up‑ and downregulated genes was performed, followed by protein‑protein interaction (PPI) network construction using Search Tool for the Retrieval of Interacting Genes Search Tool for the Retrieval of Interacting Genes. In total, 1,989 DEGs including 1,461 up‑ and 528 downregulated genes were screened out. Subnetworks including pancreatic cancer in PC tissue samples and intercellular adhesion in normal samples were identified, respectively. A total of 8 significant REACTOME pathways for upregulated DEGs, such as hemostasis and cell cycle, mitotic were identified. Moreover, 4 significant REACTOME pathways for downregulated DEGs, including regulation of β‑cell development and transmembrane transport of small molecules were screened out. Additionally, DEGs with high connectivity degrees, such as CCNA2 (cyclin A2) and PBK (PDZ binding kinase), of the module in the protein‑protein interaction network were mainly enriched with cell‑division cycle. CCNA2 and PBK of the module and their relative pathway cell‑division cycle, and two subnetworks (pancreatic cancer and intercellular adhesion subnetworks) may be pivotal for further understanding of the molecular mechanism of PC. PMID:27035224

  7. Graph theory-based measures as predictors of gene morbidity.

    Science.gov (United States)

    Massanet-Vila, Raimon; Caminal, Pere; Perera, Alexandre

    2010-01-01

    Previous studies have suggested that some graph properties of protein interaction networks might be related with gene morbidity. In particular, it has been suggested that when a polymorphism affects a gene, it is more likely to produce a disease if the node degree in the interaction network is higher than for other genes. However, these results do not take into account the possible bias introduced by the variance in the amount of information available for different genes. This work models the relationship between the morbidity associated with a gene and the degrees of the nodes in the protein interaction network controlling the amount of information available in the literature. A set of 7461 genes and 3665 disease identifiers reported in the Online Mendelian Inheritance in Man (OMIM) was mined jointly with 9630 nodes and 38756 interactions of the Human Proteome Resource Database (HPRD). The information available from a gene was measured through PubMed mining. Results suggest that the correlation between the degree of a node in the protein interaction network and its morbidity is largely contributed by the information available from the gene. Even though the results suggest a positive correlation between the degree of a node and its morbidity while controlling the information factor, we believe this correlation has to be taken with caution for it can be affected by other factors not taken into account in this study. PMID:21096114

  8. TXTGate: profiling gene groups with text-based information

    DEFF Research Database (Denmark)

    Glenisson, P.; Coessens, B.; Van Vooren, S.;

    2004-01-01

    We implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, term-as well as gene-centric views are offered on selected textual...

  9. GEDA: new knowledge base of gene expression in drug addiction.

    Science.gov (United States)

    Suh, Young Ju; Yang, Moon Hee; Yoon, Suk Joon; Park, Jong Hoon

    2006-07-31

    Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and nonredundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain. PMID:16889689

  10. Assessment of gene set analysis methods based on microarray data.

    Science.gov (United States)

    Alavi-Majd, Hamid; Khodakarim, Soheila; Zayeri, Farid; Rezaei-Tavirani, Mostafa; Tabatabaei, Seyyed Mohammad; Heydarpour-Meymeh, Maryam

    2014-01-25

    Gene set analysis (GSA) incorporates biological information into statistical knowledge to identify gene sets differently expressed between two or more phenotypes. It allows us to gain an insight into the functional working mechanism of cells beyond the detection of differently expressed gene sets. In order to evaluate the competence of GSA approaches, three self-contained GSA approaches with different statistical methods were chosen; Category, Globaltest and Hotelling's T(2) together with their assayed power to identify the differences expressed via simulation and real microarray data. The Category does not take care of the correlation structure, while the other two deal with correlations. In order to perform these methods, R and Bioconductor were used. Furthermore, venous thromboembolism and acute lymphoblastic leukemia microarray data were applied. The results of three GSAs showed that the competence of these methods depends on the distribution of gene expression in a dataset. It is very important to assay the distribution of gene expression data before choosing the GSA method to identify gene sets differently expressed between phenotypes. On the other hand, assessment of common genes among significant gene sets indicated that there was a significant agreement between the result of GSA and the findings of biologists. PMID:24012817

  11. Flexible manipulator control experiments and analysis

    Science.gov (United States)

    Yurkovich, S.; Ozguner, U.; Tzes, A.; Kotnik, P. T.

    1987-01-01

    Modeling and control design for flexible manipulators, both from an experimental and analytical viewpoint, are described. From the application perspective, an ongoing effort within the laboratory environment at the Ohio State University, where experimentation on a single link flexible arm is underway is described. Several unique features of this study are described here. First, the manipulator arm is slewed by a direct drive dc motor and has a rigid counterbalance appendage. Current experimentation is from two viewpoints: (1) rigid body slewing and vibration control via actuation with the hub motor, and (2) vibration suppression through the use of structure-mounted proof-mass actuation at the tip. Such an application to manipulator control is of interest particularly in design of space-based telerobotic control systems, but has received little attention to date. From an analytical viewpoint, parameter estimation techniques within the closed-loop for self-tuning adaptive control approaches are discussed. Also introduced is a control approach based on output feedback and frequency weighting to counteract effects of spillover in reduced-order model design. A model of the flexible manipulator based on experimental measurements is evaluated for such estimation and control approaches.

  12. Blood-based gene expression signatures of medication-free outpatients with major depressive disorder: integrative genome-wide and candidate gene analyses

    OpenAIRE

    Hiroaki Hori; Daimei Sasayama; Toshiya Teraishi; Noriko Yamamoto; Seiji Nakamura; Miho Ota; Kotaro Hattori; Yoshiharu Kim; Teruhiko Higuchi; Hiroshi Kunugi

    2016-01-01

    Several microarray-based studies have investigated gene expression profiles in major depressive disorder (MDD), yet with highly variable findings. We examined blood-based genome-wide expression signatures of MDD, focusing on molecular pathways and networks underlying differentially expressed genes (DEGs) and behaviours of hypothesis-driven, evidence-based candidate genes for depression. Agilent human whole-genome arrays were used to measure gene expression in 14 medication-free outpatients wi...

  13. Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders

    DEFF Research Database (Denmark)

    Ersland, Kari M; Christoforou, Andrea; Stansberg, Christine;

    2012-01-01

    Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes in...... three different cortical areas (frontomedial, temporal and occipital cortices) of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used the...... regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n...

  14. Manipulating and Visualizing Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Horst D.

    2003-12-05

    ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore and model data in a more intuitive fashion. With this in mind, researchers at Lawrence Berkeley National Laboratory and the University of California, Davis, have developed ProteinShop, a visualization and modeling program which allows researchers to manipulate protein structures with pinpoint control, guided in large part by their own biological and experimental instincts. Biologists have spent the last half century trying to unravel the ''protein folding problem,'' which refers to the way chains of amino acids physically fold themselves into three-dimensional proteins. This final shape, which resembles a crumpled ribbon or piece of origami, is what determines how the protein functions and translates genetic information. Understanding and modeling this geometrically complex formation is no easy matter. ProteinShop takes a given sequence of amino acids and uses visualization guides to help generate predictions about the secondary structures, identifying alpha helices and flat beta strands, and the coil regions that bind them. Once secondary structures are in place, researchers can twist and turn these pre-configurations until they come up with a number of possible tertiary structure conformations. In turn, these are fed into a computationally intensive optimization procedure that tries to find the final, three-dimensional protein structure. Most importantly, ProteinShop allows users to add human knowledge and intuition to the protein structure prediction process, thus bypassing bad configurations that would otherwise be fruitless for optimization. This saves compute cycles and accelerates

  15. Design PID-Like Fuzzy Controller With Minimum Rule Base and Mathematical Proposed On-line Tunable Gain: Applied to Robot Manipulator

    Directory of Open Access Journals (Sweden)

    Farzin Piltan, N. Sulaiman, Arash Zargari, Mohammad Keshavarz & Ali Badri

    2011-10-01

    Full Text Available In this study, an on-line tunable gain model free PID-like fuzzy controller (GTFLC is designed forthree degrees of freedom (3DOF robot manipulator to rich the best performance. Fuzzy logiccontroller is studied because of its model free and high performance. Today, robot manipulatorsare used in unknown and unstructured environment and caused to provide sophisticated systems,therefore strong mathematical tools are used in new control methodologies to design adaptivenonlinear robust controller with acceptable performance (e.g., minimum error, good trajectory,disturbance rejection. The strategies of control robot manipulator are classified into two maingroups: classical and non-classical methods, however non linear classical theories have beenapplied successfully in many applications, but they also have some limitation. One of the mostimportant nonlinear non classical robust controller that can used in uncertainty nonlinear systems,are fuzzy logic controller. This paper is focuses on applied mathematical tunable gain method inrobust non classical method to reduce the fuzzy logic controller limitations. Therefore on-linetunable PID like fuzzy logic controller will be presented in this paper.

  16. Gene-based Association Approach Identify Genes Across Stress Traits in Fruit Flies

    DEFF Research Database (Denmark)

    Rohde, Palle Duun; Edwards, Stefan McKinnon; Sarup, Pernille Merete; Sørensen, Peter

    Identification of genes explaining variation in quantitative traits or genetic risk factors of human diseases requires both good phenotypic- and genotypic data, but also efficient statistical methods. Genome-wide association studies may reveal association between phenotypic variation and variatio...

  17. Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling

    Directory of Open Access Journals (Sweden)

    Guo Zheng

    2006-01-01

    Full Text Available Abstract Background It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that propel and characterize the progression of versatile life phenomena, to name a few, cell cycling, developmental biology, aging, and the progressive and recurrent pathogenesis of complex diseases. The vast amount of large-scale and genome-wide time-resolved data is becoming increasing available, which provides the golden opportunity to unravel the challenging reverse-engineering problem of time-delayed gene regulatory networks. Results In particular, this methodological paper aims to reconstruct regulatory networks from temporal gene expression data by using delayed correlations between genes, i.e., pairwise overlaps of expression levels shifted in time relative each other. We have thus developed a novel model-free computational toolbox termed TdGRN (Time-delayed Gene Regulatory Network to address the underlying regulations of genes that can span any unit(s of time intervals. This bioinformatics toolbox has provided a unified approach to uncovering time trends of gene regulations through decision analysis of the newly designed time-delayed gene expression matrix. We have applied the proposed method to yeast cell cycling and human HeLa cell cycling and have discovered most of the underlying time-delayed regulations that are supported by multiple lines of experimental evidence and that are remarkably consistent with the current knowledge on phase characteristics for the cell cyclings. Conclusion We established a usable and powerful model-free approach to dissecting high-order dynamic trends of gene-gene interactions. We have carefully validated the proposed algorithm by applying it to two publicly available cell cycling datasets. In addition to uncovering the time trends of gene regulations for cell cycling, this unified approach can also be used to study the complex

  18. A sight on the current nanoparticle-based gene delivery vectors

    Science.gov (United States)

    Dizaj, Solmaz Maleki; Jafari, Samira; Khosroushahi, Ahmad Yari

    2014-05-01

    Nowadays, gene delivery for therapeutic objects is considered one of the most promising strategies to cure both the genetic and acquired diseases of human. The design of efficient gene delivery vectors possessing the high transfection efficiencies and low cytotoxicity is considered the major challenge for delivering a target gene to specific tissues or cells. On this base, the investigations on non-viral gene vectors with the ability to overcome physiological barriers are increasing. Among the non-viral vectors, nanoparticles showed remarkable properties regarding gene delivery such as the ability to target the specific tissue or cells, protect target gene against nuclease degradation, improve DNA stability, and increase the transformation efficiency or safety. This review attempts to represent a current nanoparticle based on its lipid, polymer, hybrid, and inorganic properties. Among them, hybrids, as efficient vectors, are utilized in gene delivery in terms of materials (synthetic or natural), design, and in vitro/ in vivo transformation efficiency.

  19. Kinematic analysis of platform-type robotic manipulators

    Science.gov (United States)

    Shi, Xiaolun

    New methods are developed for the kinematic analysis of serial and platform-type parallel robotic manipulators, including forward and inverse kinematic solutions, singularity identifications and workspace evaluation. Differences between serial and platform-type parallel manipulators, which can provide substantially improved end-point rigidity compared with the conventional serial robotic arms, are addressed. The problem of determining the screw parameters of rigid body motion from initial and final position data is discussed, as a basis to search for a general and efficient procedure to solve the complex forward kinematics problem of platform-type manipulators. Several Screw-Theory based approaches for solving the inverse instantaneous problem of 6 DOF serial manipulators are studied and compared in terms of their computational efficiency, accuracy, sensitivity to data error and capability of dealing with singularities. A modified Vector Decomposition method is then proposed for solving the IIK problem and for singularity analysis of serial kinematic chains, the method is especially effective when applied to the wrist partitioned serial manipulators, which are essential components to any platform-type parallel manipulators. By using the data of three point positions, velocities, and accelerations of the end effector a general method is developed for solving the forward kinematics problem, including position, velocity and acceleration kinematics, of platform-type manipulators. The solution procedure can be applied to a wide variety of platform-type manipulators such as the 6 DOF Steward Platform manipulator and other models. It is found that while the solution for the forward position kinematics of a platform-type manipulator can be obtained by solving a non-linear system of equations, the closed-form solutions for forward rate and acceleration kinematics can be found by solving a system of linear equations. Based on the proposed kinematic formulations, an algorithm

  20. Stereoscopically Observing Manipulative Actions.

    Science.gov (United States)

    Ferri, S; Pauwels, K; Rizzolatti, G; Orban, G A

    2016-08-01

    The purpose of this study was to investigate the contribution of stereopsis to the processing of observed manipulative actions. To this end, we first combined the factors "stimulus type" (action, static control, and dynamic control), "stereopsis" (present, absent) and "viewpoint" (frontal, lateral) into a single design. Four sites in premotor, retro-insular (2) and parietal cortex operated specifically when actions were viewed stereoscopically and frontally. A second experiment clarified that the stereo-action-specific regions were driven by actions moving out of the frontoparallel plane, an effect amplified by frontal viewing in premotor cortex. Analysis of single voxels and their discriminatory power showed that the representation of action in the stereo-action-specific areas was more accurate when stereopsis was active. Further analyses showed that the 4 stereo-action-specific sites form a closed network converging onto the premotor node, which connects to parietal and occipitotemporal regions outside the network. Several of the specific sites are known to process vestibular signals, suggesting that the network combines observed actions in peripersonal space with gravitational signals. These findings have wider implications for the function of premotor cortex and the role of stereopsis in human behavior. PMID:27252350

  1. Configurable pattern-based evolutionary biclustering of gene expression data

    OpenAIRE

    Pontes Balanza, Beatriz; Giráldez Rojo, Raúl; Aguilar Ruiz, Jesús Salvador

    2013-01-01

    Background Biclustering algorithms for microarray data aim at discovering functionally related gene sets under different subsets of experimental conditions. Due to the problem complexity and the characteristics of microarray datasets, heuristic searches are usually used instead of exhaustive algorithms. Also, the comparison among different techniques is still a challenge. The obtained results vary in relevant features such as the number of genes or conditions, which makes it difficult to carr...

  2. Stem Cell Based Gene Therapy in Prostate Cancer

    OpenAIRE

    Jae Heon Kim; Hong Jun Lee; Yun Seob Song

    2014-01-01

    Current prostate cancer treatment, especially hormone refractory cancer, may create profound iatrogenic outcomes because of the adverse effects of cytotoxic agents. Suicide gene therapy has been investigated for the substitute modality for current chemotherapy because it enables the treatment targeting the cancer cells. However the classic suicide gene therapy has several profound side effects, including immune-compromised due to viral vector. Recently, stem cells have been regarded as a new ...

  3. Nanoparticle-based targeted gene therapy for lung cancer

    OpenAIRE

    Lee, Hung-Yen; Mohammed, Kamal A; Nasreen, Najmunnisa

    2016-01-01

    Despite striking insights on lung cancer progression, and cutting-edge therapeutic approaches the survival of patients with lung cancer, remains poor. In recent years, targeted gene therapy with nanoparticles is one of the most rapidly evolving and extensive areas of research for lung cancer. The major goal of targeted gene therapy is to bring forward a safe and efficient treatment to cancer patients via specifically targeting and deterring cancer cells in the body. To achieve high therapeuti...

  4. Manipulation of Carotenoid Content in Plants to Improve Human Health.

    Science.gov (United States)

    Alós, Enriqueta; Rodrigo, Maria Jesús; Zacarias, Lorenzo

    2016-01-01

    Carotenoids are essential components for human nutrition and health, mainly due to their antioxidant and pro-vitamin A activity. Foods with enhanced carotenoid content and composition are essential to ensure carotenoid feasibility in malnourished population of many countries around the world, which is critical to alleviate vitamin A deficiency and other health-related disorders. The pathway of carotenoid biosynthesis is currently well understood, key steps of the pathways in different plant species have been characterized and the corresponding genes identified, as well as other regulatory elements. This enables the manipulation and improvement of carotenoid content and composition in order to control the nutritional value of a number of agronomical important staple crops. Biotechnological and genetic engineering-based strategies to manipulate carotenoid metabolism have been successfully implemented in many crops, with Golden rice as the most relevant example of β-carotene improvement in one of the more widely consumed foods. Conventional breeding strategies have been also adopted in the bio-fortification of carotenoid in staple foods that are highly consumed in developing countries, including maize, cassava and sweet potatoes, to alleviate nutrition-related problems. The objective of the chapter is to summarize major breakthroughs and advances in the enhancement of carotenoid content and composition in agronomical and nutritional important crops, with special emphasis to their potential impact and benefits in human nutrition and health. PMID:27485228

  5. Web-based interrogation of gene expression signatures using EXALT

    Directory of Open Access Journals (Sweden)

    Yu Jian

    2009-12-01

    Full Text Available Abstract Background Widespread use of high-throughput techniques such as microarrays to monitor gene expression levels has resulted in an explosive growth of data sets in public domains. Integration and exploration of these complex and heterogeneous data have become a major challenge. Results The EXALT (EXpression signature AnaLysis Tool online program enables meta-analysis of gene expression profiles derived from publically accessible sources. Searches can be executed online against two large databases currently containing more than 28,000 gene expression signatures derived from GEO (Gene Expression Omnibus and published expression profiles of human cancer. Comparisons among gene expression signatures can be performed with homology analysis and co-expression analysis. Results can be visualized instantly in a plot or a heat map. Three typical use cases are illustrated. Conclusions The EXALT online program is uniquely suited for discovering relationships among transcriptional profiles and searching gene expression patterns derived from diverse physiological and pathological settings. The EXALT online program is freely available for non-commercial users from http://seq.mc.vanderbilt.edu/exalt/.

  6. The Manipulative Discourse of Gandalf

    Directory of Open Access Journals (Sweden)

    Farid Mohammadi

    2014-07-01

    Full Text Available The aim of this essay is to investigate discursive, cognitive and social aspects of manipulation in regard to the dialogues of the literary fictional character of Gandalf in the trilogy of The Lord of the Rings. Accordingly, the researcher has taken a multidisciplinary approach to an account of discursive manipulation, and focuses on the cognitive dimensions of manipulation. As a result, the researcher demonstrates meticulously how manipulation involves intensifying the power, moral superiority and the credibility of the speaker(s, while abusing the others (recipients, along with an emotional and attractive way of expression, and supplemented by reasonable facts and documents in regard to a specific issue.Keywords: Manipulation, Discourse, Cognitive, Power Abuse, Persuasion, Social representation, J.R.R. Tolkien

  7. 基于轮廓图元边缘检测的新式秸秆上料机械手设计%Manipulator Design of a New Straw Feeding Based on Contour Map Edge Detection

    Institute of Scientific and Technical Information of China (English)

    黄力刚; 朱文琦; 刘志刚

    2016-01-01

    为了解决秸秆粉碎机自动上料问题,设计了一种新的秸秆上料机械手装置,提高了秸秆粉碎机作业的精度和自动化水平. 该装置使用Canny算子对秸秆图像进行分割, 并对弱边缘进行提取,将提取信息传递给机械手PC处理中心,发出控制机械手的动作的指令;并利用PLC闭环系统控制,完成了秸秆上料机械手的自动化控制,优化了伺服电机的启停时间和上料的工作效率. 同时,对装置进行了秸秆上料试验,结果表明:与人工上料相比,使用自动化控制的机械手可以提高工作效率及秸秆的粉碎质量,且可降低上料过程对人造成的损害,是一种安全高效的上料装置.%In order to solve the problem of straw crusher automatic feeding, we design a new straw stalk feeding manipu-lator device, precision and automation level of the straw crusher is improved.The device using canny operator of straw image segmentation, and the weak edge extraction, extracted information to manipulator PC processing center, a control action of the manipulator's instructions, and a closed-loop control system based on PLC, completes the straw stalk feed-ing automatic control of the manipulator, and optimize the servo motor start-stop time, improve loading efficiency.The last straw is for device feeding experiment, the experimental results can be seen that,compared with the artificial feeding, use of automatic control of the manipulator can improve work efficiency and improve the quality of the shattering of the straw, and can reduce the feeding process of damage,which is a safe and efficient feeding device.

  8. Kinect平台上使用机器学习的非接触式GUI操控方式%Non-Contact GUI Manipulation Approach Based on Machine Learning and Kinect

    Institute of Scientific and Technical Information of China (English)

    曾繁江; 李涛; 黎铭

    2014-01-01

    People are gradually abandoning the mouse and keyboard since touch screens come into their lives, however the shortcomings and limitations of touch manipulation emerge subsequently, thus non-contact manipulations are becoming the new trend of human-computer interaction in the future due to its unique advantages. There are many problems in existing non-contact manipulation approaches, e.g. improper definitions of gestures, complex algo-rithms, low recognition accuracy, etc. This paper proposes RemoteControl, a non-contact manipulation approach based on machine learning and the Kinect device. Users can finish most fundamental GUI (graphical user interface) manipulations in the 3-dimensional space by the two actions,“grab”and“put”. RemoteControl utilizes SVM (support vector machine) and random forest to recognize hand shapes in hand images. The experimental results show that RemoteControl achieves high accuracy in hand gesture recognition.%触摸屏的出现使人们逐渐摒弃鼠标和键盘,而触摸操作的不便和局限性也随之显现,非接触式操作凭借其独特的优势正逐渐成为未来人机交互方式的新潮流。针对现有的非接触式操作方式存在的手势定义不合理,方法复杂难解,识别精度低等许多问题,提出了使用“抓”和“放”这两个手势的非接触式操控方式RemoteControl,用户可在三维空间中做出操控动作来完成大部分基础图形用户界面(graphical user interface,GUI)操作。RemoteControl使用支持向量机(support vector machine,SVM)和随机森林来从手部图像中识别出手的形状。实验结果表明RemoteControl的操控动作识别取得了较高的精确度。

  9. Randomized parallel motion planning for robot manipulators.

    OpenAIRE

    Qin, Caigong; Henrich, Dominik

    2007-01-01

    We present a novel approach to parallel motion planning for robot manipulators in 3D workspaces. The approach is based on a randomized parallel search algorithm and focuses on solving the path planning problem for industrial robot arms working in a reasonably cluttered workspace.The path planning system works in the discretized configuration space, which needs not to be represented explicitly. The parallel search is conducted by a number of rule-based sequential search pr...

  10. Adaptive Control of Flexible Redundant Manipulators Using Neural Networks

    Institute of Scientific and Technical Information of China (English)

    SONG Yimin; LI Jianxin; WANG Shiyu; LIU Jianping

    2006-01-01

    An investigation on the neural networks based active vibration control of flexible redundant manipulators was conducted.The smart links of the manipulator were synthesized with the flexible links to which were attached piezoceramic actuators and strain gauge sensors.A nonlinear adaptive control strategy named neural networks based indirect adaptive control (NNIAC) was employed to improve the dynamic performance of the manipulator.The mathematical model of the 4-layered dynamic recurrent neural networks (DRNN) was introduced.The neuro-identifier and the neurocontroller featuring the DRNN topology were designed off line so as to enhance the initial robustness of the NNIAC.By adjusting the neuro-identifier and the neuro-controller alternatively,the manipulator was controlled on line for achieving the desired dynamic performance.Finally,a planar 3R redundant manipulator with one smart link was utilized as an illustrative example.The simulation results proved the validity of the control strategy.

  11. Dexterous Manipulation: Making Remote Manipulators Easy to Use

    International Nuclear Information System (INIS)

    Perhaps the most basic barrier to the widespread deployment of remote manipulators is that they are very difficult to use. Remote manual operations are fatiguing and tedious, while fully autonomous systems are seldom able to function in changing and unstructured environments. An alternative approach to these extremes is to exploit computer control while leaving the operator in the loop to take advantage of the operator's perceptual and decision-making capabilities. This report describes research that is enabling gradual introduction of computer control and decision making into operator-supervised robotic manipulation systems, and its integration on a commercially available, manually controlled mobile manipulator

  12. Manipulability, force, and compliance analysis for planar continuum manipulators

    Science.gov (United States)

    Gravagne, Ian A.; Walker, Ian D.

    2002-01-01

    Continuum manipulators, inspired by the natural capabilities of elephant trunks and octopus tentacles, may find niche applications in areas like human-robot interaction, multiarm manipulation, and unknown environment exploration. However, their true capabilities will remain largely inaccessible without proper analytical tools to evaluate their unique properties. Ellipsoids have long served as one of the foremost analytical tools available to the robotics researcher, and the purpose of this paper is to first formulate, and then to examine, three types of ellipsoids for continuum robots: manipulability, force, and compliance.

  13. Testing gene-environment interactions in family-based association studies using trait-based ascertained samples

    OpenAIRE

    Zhang, Weiming; Langefeld, Carl D.; Grunwald, Gary K; Fingerlin, Tasha E

    2013-01-01

    The study of gene-environment interactions is an increasingly important aspect of genetic epidemiological investigation. Historically, it has been difficult to study gene-environment interactions using a family-based design for quantitative traits or when parent-offspring trios were incomplete. The QBAT-I[1] provides researchers a tool to estimate and test for a gene-environment interaction in families of arbitrary structure that are sampled without regard to the phenotype of interest, but is...

  14. Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway.

    Directory of Open Access Journals (Sweden)

    Jing Yang

    Full Text Available Cancer is a serious disease that causes many deaths every year. We urgently need to design effective treatments to cure this disease. Tumor suppressor genes (TSGs are a type of gene that can protect cells from becoming cancerous. In view of this, correct identification of TSGs is an alternative method for identifying effective cancer therapies. In this study, we performed gene ontology (GO and pathway enrichment analysis of the TSGs and non-TSGs. Some popular feature selection methods, including minimum redundancy maximum relevance (mRMR and incremental feature selection (IFS, were employed to analyze the enrichment features. Accordingly, some GO terms and KEGG pathways, such as biological adhesion, cell cycle control, genomic stability maintenance and cell death regulation, were extracted, which are important factors for identifying TSGs. We hope these findings can help in building effective prediction methods for identifying TSGs and thereby, promoting the discovery of effective cancer treatments.

  15. Identification of Genes Related to Nasopharyngeal Carcinoma with the Help of Pathway-based Networks

    Institute of Scientific and Technical Information of China (English)

    Hui LI; Cai-Ping REN; Xiao-Jun TAN; Xu-Yu YANG; Hong-Bo ZHANG; Wen ZHOU; Kai-Tai YAO

    2006-01-01

    cDNA microarray is a powerful tool to analyze simultaneously the expression levels of tens of thousands of genes. Compared with normal nasopharynx (NP) tissues, 2210 genes were highly differentially expressed in nasopharyngeal carcinoma (NPC) tissues detected by cDNA microarray. Since signal pathway is widely used to describe the complex relationship between genes, a pathway-based network was constructed to visualize the connection between the genes obtained from microarray data in this report. We analyzed the targeted genes that may have more important influence on this gene network with statistical methods and found that some genes might have significant influence on this network, especially Ras-related nuclear protein (RAN), carboxyl ester lipase (CEL), v-rel reticuloendotheliosis viral oncogene homolog A (RELA) genes. To verify the results from pathway-based selection, reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR were performed to detect the expression levels of RAN, CEL and RELA genes and it was found that the RAN and CEL genes were significantly up-regulated in more than 80%of NPC tissues. To further elucidate the function of the RAN gene, RAN expression was specifically suppressed in a 5-8F NPC cell line by RNA interference (RNAi). As expected, the depletion of RAN could effectively block the proliferation of tumor cells. Therefore, our study may open up a new way to analyze the vast microarray data.

  16. Estimation of growth rate of Skeletonema costatum based on relative expression amount of PCNA gene

    Institute of Scientific and Technical Information of China (English)

    HE Shanying; YU Zhigang

    2008-01-01

    Partial sequence of Skeletonema costatum proliferating cell nuclear antigen (PCNA) gene was obtained by reverse transcriptase PCR(RT-PCR) and 3' rapid amplification of cDNA ends (3'-RACE) techniques.Based on the obtained PCNA and cytochrome b gene(Cyt b gene) sequences,a real-time fluorescent quantitative PCR (FQ-PCR) method was developed to detect the expres-sion S.costatum PCNA gene,and this method was applied to study the relationship between the growth rate of S.costatum and the average expression amount of PCNA gene in a single cell.The expression amount of PCNA gene had large variation in cells col-lected at different culture phases,and the trend was well consistent with the growth rate,which suggested that the expression amount of PCNA gene correlated well with the cell division,and the PCNA could be a promising indicator for the S.costatum cell proliferation.Furthermore,using the PCNA gene as the objective gene and the Cyt b gene as the house-keeping gene,a new method for estimating the in situ growth rate of S.costatum was established by analysis of the relative expression quantity (REQ) of the PCNA gene.

  17. Automatic camera tracking for remote manipulators

    International Nuclear Information System (INIS)

    The problem of automatic camera tracking of mobile objects is addressed with specific reference to remote manipulators and using either fixed or mobile cameras. The technique uses a kinematic approach employing 4 x 4 coordinate transformation matrices to solve for the needed camera PAN and TILT angles. No vision feedback systems are used, as the required input data are obtained entirely from position sensors from the manipulator and the camera-positioning system. All hardware requirements are generally satisfied by currently available remote manipulator systems with a supervisory computer. The system discussed here implements linear plus on/off (bang-bang) closed-loop control with a +-2-deg deadband. The deadband area is desirable to avoid operator seasickness caused by continuous camera movement. Programming considerations for camera control, including operator interface options, are discussed. The example problem presented is based on an actual implementation using a PDP 11/34 computer, a TeleOperator Systems SM-229 manipulator, and an Oak Ridge National Laboratory (ORNL) camera-positioning system. 3 references, 6 figures, 2 tables

  18. Passivity analysis for flexible multilink space manipulators

    Science.gov (United States)

    Damaren, Christopher J.

    1995-03-01

    The important input-output property of passivity is explored for a general flexible space manipulator with chain topology. The manipulator is assumed to consist of rigid and/or flexible links interconnected via revolute joints, and a free rigid spacecraft and cantilevered payload are modeled at the base and tip, respectively. Actuation on the spacecraft and torques at the joints serve as control inputs and a suitably modified input variable is constructed. The notion of reflected tip position introduced by Wang and Vidyasagar for a single flexible link is extended to the multilink case and used to define a corresponding modified output variable. The dynamics governing the system are developed using a Lagrangian approach and both linearized and nonlinear forms of the mapping relating modified inputs to modified outputs are examined. Our major result shows that the transfer function in the linear case is positive real when the spacecraft and payload are much more massive than the manipulator links. The corresponding nonlinear analysis shows that the mapping is, in fact, passive and uncovers an approximate static relationship between the elastic coordinates and applied torques. A numerical example employing the Space Shuttle, remote manipulator system, and payload is used to demonstrate the validity of the theoretical results. Applications to control system design are indicated.

  19. Automatic camera tracking for remote manipulators

    International Nuclear Information System (INIS)

    The problem of automatic camera tracking of mobile objects is addressed with specific reference to remote manipulators and using either fixed or mobile cameras. The technique uses a kinematic approach employing 4 x 4 coordinate transformation matrices to solve for the needed camera PAN and TILT angles. No vision feedback systems are used, as the required input data are obtained entirely from position sensors from the manipulator and the camera-positioning system. All hardware requirements are generally satisfied by currently available remote manipulator systems with a supervisory computer. The system discussed here implements linear plus on/off (''bang-bang'') closed-loop control with a +-2-deg deadband. The deadband area is desirable to avoid operator ''seasickness'' caused by continuous camera movement. Programming considerations for camera control, including operator interface options, are discussed. The example problem presented is based on an actual implementation using a PDP 11/34 computer, a TeleOperator System SM-229 manipulator, and an Oak Ridge National Laboratory (ORNL) camera-positioning system

  20. Automatic camera tracking for remote manipulators

    International Nuclear Information System (INIS)

    The problem of automatic camera tracking of mobile objects is addressed with specific reference to remote manipulators and using either fixed or mobile cameras. The technique uses a kinematic approach employing 4 x 4 coordinate transformation matrices to solve for the needed camera PAN and TILT angles. No vision feedback systems are used, as the required input data are obtained entirely from position sensors from the manipulator and the camera-positioning system. All hardware requirements are generally satisfied by currently available remote manipulator systems with a supervisory computer. The system discussed here implements linear plus on/off (bang-bang) closed-loop control with a +-20 deadband. The deadband area is desirable to avoid operator seasickness caused by continuous camera movement. Programming considerations for camera control, including operator interface options, are discussed. The example problem presented is based on an actual implementation using a PDP 11/34 computer, a TeleOperator Systems SM-229 manipulator, and an Oak Ridge National Laboratory (ORNL) camera-positioning system. 3 references, 6 figures, 2 tables

  1. Bubble Manipulation by Self Organization of Bubbles inside Ultrasonic Wave

    Science.gov (United States)

    Yamakoshi, Yoshiki; Koganezawa, Masato

    2005-06-01

    Microbubble manipulation using ultrasonic waves is a promising technology in the fields of future medicine and biotechnology. For example, it is considered that bubble trapping using ultrasonic waves may play an important role in drug or gene delivery systems in order to trap the drugs or genes in the diseased tissue. Usually, when bubbles are designed so that they carry payloads, such as drug or gene, they tend to be harder than free bubbles. These hard bubbles receive a small acoustic radiation force, which is not sufficient for bubble manipulation. In this paper, a novel method of microbubble manipulation using ultrasonic waves is proposed. This method uses seed bubbles in order to manipulate target bubbles. When the seed bubbles are introduced into the ultrasonic wave field, they start to oscillate to produce a bubble aggregation of a certain size. Then the target bubbles are introduced, the target bubbles attach around the seed bubbles producing a bubble mass with bilayers (inner layer: seed bubbles, outer layer: target bubbles). The target bubbles are manipulated as a bilayered bubble mass. Basic experiments are carried out using polyvinyl chloride (PVC) shell bubbles. No target bubbles are trapped when only the target bubbles are introduced. However, they are trapped if the seed bubbles are introduced in advance.

  2. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  3. Excel® : importer, mettre en forme et manipuler des données de génotypage microsatellites produites par le logiciel GeneMapper® V4.1. avec l'aide de macros codées en langage visual basic for application

    OpenAIRE

    2014-01-01

    Cet article présente les fonctionnalités d’un fichier Excel® permettant par le biais de plusieurs Macros VBA d’importer, mettre en forme et manipuler des données de génotypage issues de l’analyse faite par le logiciel GeneMapper® en Version 4.1. Les différentes fonctionnalités et outils seront exposés. Le fichier est en téléchargement libre.

  4. Stabilization system for a manipulator

    International Nuclear Information System (INIS)

    A patent is claimed for the invention of a stabilization system for a manipulator. The invention proposes a low cost, functional and easily operated device. The system can be used in a manipulator carried by an equipment which is in motion in a working area and is equipped with a moving arm and a prehension tool at one end. The manipulator system is suspended to the displacement device and equipped with several coils and cables ended with fixation systems. The diagrams, the advantages and the operation of the invention are described

  5. Towards gene therapy based on femtosecond optical transfection

    Science.gov (United States)

    Antkowiak, M.; Torres-Mapa, M. L.; McGinty, J.; Chahine, M.; Bugeon, L.; Rose, A.; Finn, A.; Moleirinho, S.; Okuse, K.; Dallman, M.; French, P.; Harding, S. E.; Reynolds, P.; Gunn-Moore, F.; Dholakia, K.

    2012-06-01

    Gene therapy poses a great promise in treatment and prevention of a variety of diseases. However, crucial to studying and the development of this therapeutic approach is a reliable and efficient technique of gene and drug delivery into primary cell types. These cells, freshly derived from an organ or tissue, mimic more closely the in vivo state and present more physiologically relevant information compared to cultured cell lines. However, primary cells are known to be difficult to transfect and are typically transfected using viral methods, which are not only questionable in the context of an in vivo application but rely on time consuming vector construction and may also result in cell de-differentiation and loss of functionality. At the same time, well established non-viral methods do not guarantee satisfactory efficiency and viability. Recently, optical laser mediated poration of cell membrane has received interest as a viable gene and drug delivery technique. It has been shown to deliver a variety of biomolecules and genes into cultured mammalian cells; however, its applicability to primary cells remains to be proven. We demonstrate how optical transfection can be an enabling technique in research areas, such as neuropathic pain, neurodegenerative diseases, heart failure and immune or inflammatory-related diseases. Several primary cell types are used in this study, namely cardiomyocytes, dendritic cells, and neurons. We present our recent progress in optimizing this technique's efficiency and post-treatment cell viability for these types of cells and discuss future directions towards in vivo applications.

  6. Gene expression module-based chemical function similarity search

    OpenAIRE

    Li, Yun; Hao, Pei; Zheng, Siyuan; Tu, Kang; Fan, Haiwei; Zhu, Ruixin; Ding, Guohui; Dong, Changzheng; Wang, Chuan; Li, Xuan; Thiesen, H.-J.; Chen, Y. Eugene; Jiang, HuaLiang; Liu, Lei; Li, Yixue

    2008-01-01

    Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of chemical related expression profiles, and introduced similarity comparison into chemical induced transcriptome analysis. Resembling sequence similarity alignment, expression pat...

  7. Human-like Manipulation Planning for Articulated Manipulator

    Institute of Scientific and Technical Information of China (English)

    Yahui Gan; Xianzhong Dai

    2012-01-01

    A new method based on human-likeness assessment and optimization concept to solve the problem of human-like manipulation planning for articulated robot is proposed in this paper.This method intrinsically formulates the problem as a constrained optimization problem in robot configuration space.The robot configuration space is divided into different subregions by human likeness assessment.A widely used strategy,Rapid Upper Limb Assessment (RULA) in applied ergonomics,is adopted here to evaluate the human likeness of robot configuration.A task compatibility measurement of the robot velocity transmission ratio along a specified direction is used as the target function for the optimization problem.Simple illustrative examples of this method applied to a two Degree of Freedom (DOF) planar robot that resembles the upper limb of a human are presented.Further applications to a humanoid industrial robot SDA10D are also presented.The reasonable planning results for these applications assert the effectiveness of our method.

  8. Taking behavioralism seriously: some evidence of market manipulation.

    Science.gov (United States)

    Hanson, J D; Kysar, D A

    1999-05-01

    Over the last ten to fifteen years, economists and legal scholars have become increasingly interested in and sensitive to behavioralist insights. In a companion article, Jon Hanson and Douglas Kysar argued that those scholars have nevertheless given short shrift to what is, at least for policymaking purposes, perhaps the most important lesson of the behavioralist research: individuals' perceptions and preferences are highly manipulable. According to Hanson and Kysar, one theoretical implication of that insight for products liability law is that manufacturers and marketers will manipulate the risk perceptions of consumers. Indeed, to survive in a competitive market, manufacturers and marketers must do so. In this Article, Hanson and Kysar present empirical evidence of market manipulation--a previously unrecognized source of market failure. The Article begins by surveying the extensive qualitative and quantitative marketing research and consumer behavioral studies that discern and influence consumer perceptions. It then provides evidence of market manipulation by reviewing common practices in everyday market settings, such as gas stations and supermarkets, and by examining familiar marketing approaches, such as environmentally oriented and fear-based advertising. Although consumers may be well-aware of those practices and approaches, they appear to be generally unaware of the extent to which those tactics are manipulative. The Article then focuses on the industry that has most depended upon market manipulation: the cigarette industry. Through decades of sophisticated marketing and public relations efforts, cigarette manufacturers have heightened consumer demand and lowered consumer risk perceptions. Because consumers are aware that smoking may pose significant health risks, the tobacco industry's success in manipulating risk perceptions constitutes especially strong evidence of the power of market manipulation. The Article concludes by arguing that the evidence of

  9. A population-based gene signature is predictive of breast cancer survival and chemoresponse

    OpenAIRE

    Rathnagiriswaran, Shruti; Wan, Ying-Wooi; Abraham, Jame; Castranova, Vincent; Qian, Yong; Guo, Nancy L.

    2010-01-01

    It remains a critical issue to improve the survival rate in patients with recurrent or metastatic breast cancer. This study sought to develop a prognostic scheme based on a 28-gene signature in a broad patient population, including those with advanced disease. Clinically annotated transcriptional profiles of 1,734 breast cancer patients were obtained to validate the 28-gene signature in prognostic categorization. The 28-gene signature generated significant patient stratification with regard t...

  10. Signaling pathway-based identification of extensive prognostic gene signatures for lung adenocarcinoma

    OpenAIRE

    Wan, Ying-Wooi; Beer, David G.; Guo, Nancy Lan

    2011-01-01

    Tumor recurrence is the major cause of death in lung cancer treatment. To date, there is no clinically applied gene expression-based model to predict the risk for tumor recurrence in non-small cell lung cancer (NSCLC). We sought to embed crosstalk with major signaling pathways into biomarker identification. Three approaches were used to identify prognostic gene signatures from 442 lung adenocarcinoma samples. Candidate genes co-expressed with 6 or 7 major NSCLC signaling hallmarks were identi...

  11. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining

    OpenAIRE

    Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

    2012-01-01

    Background Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genome-wide, Centrality and Ontology-based Network Discovery using Literature data (CONDL) approach to analyse the genes and gene interaction networks associated with fever or vaccine-related fever responses. Results Over 170,000 fever-related articles from PubMed abstracts and tit...

  12. Comparative study between recent methods manipulating ratio spectra and classical methods based on two-wavelength selection for the determination of binary mixture of antazoline hydrochloride and tetryzoline hydrochloride

    Science.gov (United States)

    Abdel-Halim, Lamia M.; Abd-El Rahman, Mohamed K.; Ramadan, Nesrin K.; EL Sanabary, Hoda F. A.; Salem, Maissa Y.

    2016-04-01

    A comparative study was developed between two classical spectrophotometric methods (dual wavelength method and Vierordt's method) and two recent methods manipulating ratio spectra (ratio difference method and first derivative of ratio spectra method) for simultaneous determination of Antazoline hydrochloride (AN) and Tetryzoline hydrochloride (TZ) in their combined pharmaceutical formulation and in the presence of benzalkonium chloride as a preservative without preliminary separation. The dual wavelength method depends on choosing two wavelengths for each drug in a way so that the difference in absorbance at those two wavelengths is zero for the other drug. While Vierordt's method, is based upon measuring the absorbance and the absorptivity values of the two drugs at their λmax (248.0 and 219.0 nm for AN and TZ, respectively), followed by substitution in the corresponding Vierordt's equation. Recent methods manipulating ratio spectra depend on either measuring the difference in amplitudes of ratio spectra between 255.5 and 269.5 nm for AN and 220.0 and 273.0 nm for TZ in case of ratio difference method or computing first derivative of the ratio spectra for each drug then measuring the peak amplitude at 250.0 nm for AN and at 224.0 nm for TZ in case of first derivative of ratio spectrophotometry. The specificity of the developed methods was investigated by analyzing different laboratory prepared mixtures of the two drugs. All methods were applied successfully for the determination of the selected drugs in their combined dosage form proving that the classical spectrophotometric methods can still be used successfully in analysis of binary mixture using minimal data manipulation rather than recent methods which require relatively more steps. Furthermore, validation of the proposed methods was performed according to ICH guidelines; accuracy, precision and repeatability are found to be within the acceptable limits. Statistical studies showed that the methods can be

  13. Optogenetic Control of Gene Expression in Drosophila.

    Directory of Open Access Journals (Sweden)

    Yick-Bun Chan

    Full Text Available To study the molecular mechanism of complex biological systems, it is important to be able to artificially manipulate gene expression in desired target sites with high precision. Based on the light dependent binding of cryptochrome 2 and a cryptochrome interacting bHLH protein, we developed a split lexA transcriptional activation system for use in Drosophila that allows regulation of gene expression in vivo using blue light or two-photon excitation. We show that this system offers high spatiotemporal resolution by inducing gene expression in tissues at various developmental stages. In combination with two-photon excitation, gene expression can be manipulated at precise sites in embryos, potentially offering an important tool with which to examine developmental processes.

  14. Dominating Manipulations in Voting with Partial Information

    CERN Document Server

    Conitzer, Vincent; Xia, Lirong

    2011-01-01

    We consider manipulation problems when the manipulator only has partial information about the votes of the nonmanipulators. Such partial information is described by an information set, which is the set of profiles of the nonmanipulators that are indistinguishable to the manipulator. Given such an information set, a dominating manipulation is a non-truthful vote that the manipulator can cast which makes the winner at least as preferable (and sometimes more preferable) as the winner when the manipulator votes truthfully. When the manipulator has full information, computing whether or not there exists a dominating manipulation is in P for many common voting rules (by known results). We show that when the manipulator has no information, there is no dominating manipulation for many common voting rules. When the manipulator's information is represented by partial orders and only a small portion of the preferences are unknown, computing a dominating manipulation is NP-hard for many common voting rules. Our results t...

  15. Osteopathic manipulative treatment: novel application to dermatological disease.

    Science.gov (United States)

    Campbell, Shannon M; Winkelmann, Richard R; Walkowski, Stevan

    2012-10-01

    Dermatological diseases, such as dysesthesia syndromes, stasis dermatoses, and hyperhidrosis are difficult to treat due to their complex etiologies. Current theories suggest these diseases are caused by physiological imbalances, such as nerve impingement, localized tissue congestion, and impaired autonomic regulation. Osteopathic manipulative therapy targets these physiological dysfunctions and may serve as a beneficial therapeutic option. Osteopathic manipulative therapy techniques include high velocity low amplitude, muscle energy, counterstrain, myofascial release, craniosacral, and lymphatic drainage. An osteopathic manipulative therapy technique is chosen based on its physiological target for a particular disease. Osteopathic manipulative therapy may be useful alone or in combination with standard therapeutic options. However, due to the lack of standardized trials supporting the efficacy of osteopathic manipulative therapy treatment for dermatological disease, randomized, well-controlled studies are necessary to confirm its therapeutic value. PMID:23125887

  16. Nonlinear Effects in Stiffness Modeling of Robotic Manipulators

    CERN Document Server

    Pashkevich, Anatoly; Chablat, Damien

    2009-01-01

    The paper focuses on the enhanced stiffness modeling of robotic manipulators by taking into account influence of the external force/torque acting upon the end point. It implements the virtual joint technique that describes the compliance of manipulator elements by a set of localized six-dimensional springs separated by rigid links and perfect joints. In contrast to the conventional formulation, which is valid for the unloaded mode and small displacements, the proposed approach implicitly assumes that the loading leads to the non-negligible changes of the manipulator posture and corresponding amendment of the Jacobian. The developed numerical technique allows computing the static equilibrium and relevant force/torque reaction of the manipulator for any given displacement of the end-effector. This enables designer detecting essentially nonlinear effects in elastic behavior of manipulator, similar to the buckling of beam elements. It is also proposed the linearization procedure that is based on the inversion of ...

  17. Spatial-Operator Algebra For Flexible-Link Manipulators

    Science.gov (United States)

    Jain, Abhinandan; Rodriguez, Guillermo

    1994-01-01

    Method of computing dynamics of multiple-flexible-link robotic manipulators based on spatial-operator algebra, which originally applied to rigid-link manipulators. Aspects of spatial-operator-algebra approach described in several previous articles in NASA Tech Briefs-most recently "Robot Control Based on Spatial-Operator Algebra" (NPO-17918). In extension of spatial-operator algebra to manipulators with flexible links, each link represented by finite-element model: mass of flexible link apportioned among smaller, lumped-mass rigid bodies, coupling of motions expressed in terms of vibrational modes. This leads to operator expression for modal-mass matrix of link.

  18. The evolution of teleoperated manipulators at ORNL

    Energy Technology Data Exchange (ETDEWEB)

    Kress, R.L.; Jansen, J.F.; Noakes, M.W.; Herndon, J.N.

    1996-12-31

    ORNL has made significant contributions to teleoperator and telerobotics technology for two decades and continues with an aggressive program today. Examples of past projects are: (1) the M2 servomanipulator, which was the first digitally controlled teleoperator; (2) the Advanced Servomanipulator (ASM), which was the first remotely maintainable teleoperator; (3) the CESARm/Kraft dissimilar teleoperated system; and (4) the Laboratory Telerobotic Manipulator (LTM), a 7-Degree-of-Freedom (7-DOF) telerobot built as a prototype for work in space. More recently, ORNL has become heavily involved with Environmental Restoration and Waste Management (ERWM) robotics programs funded by the Department of Energy (DOE). The ERWM program requires high payloads and high dexterity. As a result, a hydraulically actuated, dual-arm system comprised of two 6-DOF arms mounted on a 5-DOF base has been constructed and is being used today for various research tasks and for decontamination and dismantlement activities. All of these teleoperated manipulator systems build upon the experiences gained throughout the almost two decades of development. Each system incorporates not only the latest technology in computers, sensors, and electronics, but each new . system also adds at least one new feature to the technologies already developed and demonstrated in the previous system(s). As a result of this process, a serious study of these manipulator systems is a study in the evolution of teleoperated manipulator the systems in general. This provides insight not only into the research and development paths chosen in the past, but also into the appropriate directions for future teleoperator and telerobotics research. This paper examines each of the teleoperated/telerobotic systems developed at ORNL, summarizes their features and capabilities, examines the state of the most current telerobotic system (the Dual Arm Work Module), PM provides direction for a Next Generation Telerobotic Manipulator system.

  19. The evolution of teleoperated manipulators at ORNL

    International Nuclear Information System (INIS)

    ORNL has made significant contributions to teleoperator and telerobotics technology for two decades and continues with an aggressive program today. Examples of past projects are: (1) the M2 servomanipulator, which was the first digitally controlled teleoperator; (2) the Advanced Servomanipulator (ASM), which was the first remotely maintainable teleoperator; (3) the CESARm/Kraft dissimilar teleoperated system; and (4) the Laboratory Telerobotic Manipulator (LTM), a 7-Degree-of-Freedom (7-DOF) telerobot built as a prototype for work in space. More recently, ORNL has become heavily involved with Environmental Restoration and Waste Management (ERWM) robotics programs funded by the Department of Energy (DOE). The ERWM program requires high payloads and high dexterity. As a result, a hydraulically actuated, dual-arm system comprised of two 6-DOF arms mounted on a 5-DOF base has been constructed and is being used today for various research tasks and for decontamination and dismantlement activities. All of these teleoperated manipulator systems build upon the experiences gained throughout the almost two decades of development. Each system incorporates not only the latest technology in computers, sensors, and electronics, but each new . system also adds at least one new feature to the technologies already developed and demonstrated in the previous system(s). As a result of this process, a serious study of these manipulator systems is a study in the evolution of teleoperated manipulator the systems in general. This provides insight not only into the research and development paths chosen in the past, but also into the appropriate directions for future teleoperator and telerobotics research. This paper examines each of the teleoperated/telerobotic systems developed at ORNL, summarizes their features and capabilities, examines the state of the most current telerobotic system (the Dual Arm Work Module), PM provides direction for a Next Generation Telerobotic Manipulator system

  20. Chiropractic Manipulation: Reasons for Concern?

    OpenAIRE

    Gouveia, LO; Castanho, P.; Ferreira, JJ; Guedes, MM; Falcão, F; Pinho e Melo, T

    2007-01-01

    Chiropractic's popularity is rising among the general population. Moreover, few studies have been conducted to properly evaluate its safety. We report three cases of serious neurological adverse events in patients treated with chiropractic manipulation. The first case is a 41 years old woman who developed a vertebro-basilar stroke 48 h after cervical manipulation. The second case represents a 68 years old woman who presented a neuropraxic injury of both radial nerves after three sessions of s...

  1. Preparation of hybrid soda-lime/quartz glass chips with wettability-patterned channels for manipulation of flow profiles in droplet-based analytical systems.

    Science.gov (United States)

    Bai, Zeqing; He, Qiaohong; Huang, Shanshi; Hu, Xianqiao; Chen, Hengwu

    2013-03-12

    Profile switching of two-phase flows is often required in microfluidic systems. Manipulation of flow profiles can be realized by control of local surface energy of micro channel through wettability-patterning of channel surface. This article presents a facile approach for wettability-patterning of the micro channels of glass chips. Commercially available octadecyltrichlorosilane (OTS) was used to hydrophobilize the channels via the formation of OTS self-assembly monolayer (SAM), and a UV-source that mainly emits deep UV-light of 254 and 185 nm was employed to degrade the in-channel formed OTS-SAM. The architecture of soda-lime glass/quartz glass hybrid chip was designed to facilitate the deep UV-light effective degrading the OTS-SAM. The established approach, together with the side-by-side laminar-flow patterning technique, was applied to prepare various finely patterned channel networks for different tasks of flow profile switching. The micro device capable of conducting the profile switch from W/O droplets to two separated continuous phases was demonstrated to perform on-chip quick liquid-liquid extraction for the determination of partition coefficients of pharmaceuticals. PMID:23452792

  2. Design-Based Learning for Biology: Genetic Engineering Experience Improves Understanding of Gene Expression

    Science.gov (United States)

    Ellefson, Michelle R.; Brinker, Rebecca A.; Vernacchio, Vincent J.; Schunn, Christian D.

    2008-01-01

    Gene expression is a difficult topic for students to learn and comprehend, at least partially because it involves various biochemical structures and processes occurring at the microscopic level. Designer Bacteria, a design-based learning (DBL) unit for high-school students, applies principles of DBL to the teaching of gene expression. Throughout…

  3. Neural network predicts sequence of TP53 gene based on DNA chip

    DEFF Research Database (Denmark)

    Spicker, J.S.; Wikman, F.; Lu, M.L.;

    2002-01-01

    We have trained an artificial neural network to predict the sequence of the human TP53 tumor suppressor gene based on a p53 GeneChip. The trained neural network uses as input the fluorescence intensities of DNA hybridized to oligonucleotides on the surface of the chip and makes between zero and...

  4. Evaluation of gene importance in microarray data based upon probability of selection

    Directory of Open Access Journals (Sweden)

    Fu Li M

    2005-03-01

    Full Text Available Abstract Background Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking to metabolic characteristics that contribute to disease development and progression. The microarray approach offers an expedited solution to this problem. However, it has posed a challenging issue to recognize disease-related genes expression patterns embedded in the microarray data. In selecting a small set of biologically significant genes for classifier design, the nature of high data dimensionality inherent in this problem creates substantial amount of uncertainty. Results Here we present a model for probability analysis of selected genes in order to determine their importance. Our contribution is that we show how to derive the P value of each selected gene in multiple gene selection trials based on different combinations of data samples and how to conduct a reliability analysis accordingly. The importance of a gene is indicated by its associated P value in that a smaller value implies higher information content from information theory. On the microarray data concerning the subtype classification of small round blue cell tumors, we demonstrate that the method is capable of finding the smallest set of genes (19 genes with optimal classification performance, compared with results reported in the literature. Conclusion In classifier design based on microarray data, the probability value derived from gene selection based on multiple combinations of data samples enables an effective mechanism for reducing the tendency of fitting local data particularities.

  5. MASS MEDIA'S MANIPULATIVE POTENTIAL IN POLITICAL DISCOURSE

    OpenAIRE

    GUSHCHINA L.V.; AGAPOVA S.G.; AGAPOVA E.A.

    2015-01-01

    Since the invention of telegraph, radio and television which enable contacts with a large audience, the social impact of communication via the mass media has been a subject of intense research by political and social scientists. Thus the paper discusses the nature of manipulation in political discourse and its ambivalent role in the modern society. The solution of the research tasks is carried out on the basis of the complex methodological base which defines the general orientation and the pr...

  6. Evolution of the Space Station Robotic Manipulator

    Science.gov (United States)

    Razvi, Shakeel; Burns, Susan H.

    2007-01-01

    The Space Station Remote Manipulator System (SSRMS), Canadarm2, was launched in 2001 and deployed on the International Space Station (ISS). The Canadarm2 has been instrumental in ISS assembly and maintenance. Canadarm2 shares its heritage with the Space Shuttle Arm (Canadarm). This article explores the evolution from the Shuttle Canadarm to the Space Station Canadarm2 design, which incorporates a 7 degree of freedom design, larger joints, and changeable operating base. This article also addresses phased design, redundancy, life and maintainability requirements. The design of Canadarm2 meets unique ISS requirements, including expanded handling capability and the ability to be maintained on orbit. The size of ISS necessitated a mobile manipulator, resulting in the unique capability of Canadarm2 to relocate by performing a walk off to base points located along the Station, and interchanging the tip and base of the manipulator. This provides the manipulator with reach and access to a large part of the Station, enabling on-orbit assembly of the Station and providing support to Extra-Vehicular Activity (EVA). Canadarm2 is evolving based on on-orbit operational experience and new functionality requirements. SSRMS functionality is being developed in phases to support evolving ISS assembly and operation as modules are added and the Station becomes more complex. Changes to sustaining software, hardware architecture, and operations have significantly enhanced SSRMS capability to support ISS mission requirements. As a result of operational experience, SSRMS changes have been implemented for Degraded Joint Operations, Force Moment Sensor Thermal Protection, Enabling Ground Controlled Operations, and Software Commutation. Planned Canadarm2 design modifications include: Force Moment Accommodation, Smart Safing, Separate Safing, and Hot Backup. In summary, Canadarm2 continues to evolve in support of new ISS requirements and improved operations. It is a tribute to the design that

  7. Identification of putative gene based markers of renal toxicity.

    OpenAIRE

    Amin, Rupesh P; Vickers, Alison E; Sistare, Frank; Thompson, Karol L.; Roman, Richard J.; Lawton, Michael; Kramer, Jeffrey; Hamadeh, Hisham K.; Collins, Jennifer; Grissom, Sherry; Bennett, Lee; Tucker, C Jeffrey; Wild, Stacie; Kind, Clive; Oreffo, Victor

    2004-01-01

    This study, designed and conducted as part of the International Life Sciences Institute working group on the Application of Genomics and Proteomics, examined the changes in the expression profile of genes associated with the administration of three different nephrotoxicants--cisplatin, gentamicin, and puromycin--to assess the usefulness of microarrays in the understanding of mechanism(s) of nephrotoxicity. Male Sprague-Dawley rats were treated with daily doses of puromycin (5-20 mg/kg/day for...

  8. Component Thermodynamical Selection Based Gene Expression Programming for Function Finding

    OpenAIRE

    Zhaolu Guo; Zhijian Wu; Xiaojian Dong; Kejun Zhang; Shenwen Wang; Yuanxiang Li

    2014-01-01

    Gene expression programming (GEP), improved genetic programming (GP), has become a popular tool for data mining. However, like other evolutionary algorithms, it tends to suffer from premature convergence and slow convergence rate when solving complex problems. In this paper, we propose an enhanced GEP algorithm, called CTSGEP, which is inspired by the principle of minimal free energy in thermodynamics. In CTSGEP, it employs a component thermodynamical selection (CTS) operator to quantitativel...

  9. Queueing-Based Synchronization and Entrainment for Synthetic Gene Oscillators

    Science.gov (United States)

    Mather, William; Butzin, Nicholas; Hochendoner, Philip; Ogle, Curtis

    Synthetic gene oscillators have been a major focus of synthetic biology research since the beginning of the field 15 years ago. They have proven to be useful both for biotechnological applications as well as a testing ground to significantly develop our understanding of the design principles behind synthetic and native gene oscillators. In particular, the principles governing synchronization and entrainment of biological oscillators have been explored using a synthetic biology approach. Our work combines experimental and theoretical approaches to specifically investigate how a bottleneck for protein degradation, which is present in most if not all existing synthetic oscillators, can be leveraged to robustly synchronize and entrain biological oscillators. We use both the terminology and mathematical tools of queueing theory to intuitively explain the role of this bottleneck in both synchronization and entrainment, which extends prior work demonstrating the usefulness of queueing theory in synthetic and native gene circuits. We conclude with an investigation of how synchronization and entrainment may be sensitive to the presence of multiple proteolytic pathways in a cell that couple weakly through crosstalk. This work was supported by NSF Grant #1330180.

  10. 番茄收获机械手轨迹跟踪模糊控制仿真与试验%Simulation and test of trajectory tracking control for tomato harvesting manipulator based on fuzzy logic compensation

    Institute of Scientific and Technical Information of China (English)

    梁喜凤; 杨犇; 王永维

    2013-01-01

      针对番茄收获机械手动力学模型不精确和外界扰动问题,该文采用计算力矩-模糊补偿相结合的控制方法进行了番茄收获机械手轨迹跟踪控制研究。通过自适应模糊逻辑系统补偿机械手动力学模型中的不确定部分,模糊逻辑系统的参数基于Lynaponv稳定性理论自适应调节,并利用ADAMS与MATLAB进行仿真试验。结果表明,对比计算力矩法,计算力矩-模糊补偿控制算法中各关节轨迹跟踪误差明显减小且收敛趋势明显。关节1至关节7平均轨迹跟踪精度分别提高了70.29%、94.72%、0.61%、74.29%、89.75%、86.41%和67.14%。该控制方案中各关节控制力(矩)均呈规律性变化,增加扰动信号亦未使输出力(力矩)出现抖振和突变,启动力(矩)最大出现在移动关节2和转动关节4,分别为453N和98.33 N·m。研究结果可为番茄收获机械手轨迹跟踪控制系统的深入研究奠定基础。%The tomato harvesting manipulator is apt to work in a complicated and unstructured production environment. The research on the trajectory tracking control is a key task. The tomato harvesting manipulator studied in the paper is a redundant manipulator with 7-DOF including two prismatic joints and five revolute joints, which is a multivariable nonlinear system. It is difficult to obtain its accurate dynamic model during control due to the external disturbance and the nonlinear friction, etc. The traditional control algorithm based on this model has poor robustness and cannot achieve global asymptotic stability. A fuzzy logic system can approximate a nonlinear function with arbitrary precision, which has more and more application in the manipulator control. To realize trajectory tracking with high accuracy and stability, a control method based on compute torque-fuzzy logic compensation is proposed to control trajectory tracking for a tomato harvesting manipulator. This method compensates the

  11. A Design of Truss Manipulator Monitoring System Based on MAP library functions%基于西门子MAP库的桁架机械手监控系统设计

    Institute of Scientific and Technical Information of China (English)

    许仙珍; 徐进富

    2016-01-01

    A monitoring system of truss manipulator based on S7-200 PLC and Kingview software is designed for digital flexible manufacturing line in this paper. MAP library functions are applied to control the manipulator X axis and Z axis servo motion, so as to accomplish accurate positioning control of material handling. The experi⁃mental results show that the designed system is accurate and stable, which can realize parameter setting, control mode switching and real-time dynamic monitoring, so it meets the design requirements.%以数字化柔性制造生产线中的桁架机械手为控制对象,基于S7-200PLC和组态王软件设计了机械手监控系统。采用MAP库函数控制桁架机械手x轴、z轴的伺服运动,从而实现物料加工搬运的精确定位。运行结果表明,桁架机械手运行准确可靠,可以实现参数设置及系统运行状态的实时、动态监控,达到了设计要求。

  12. Genome-based versus gene-based theory of cancer: Possible implications for clinical practice

    Indian Academy of Sciences (India)

    Nataša Todorović-Raković

    2011-09-01

    The current state in oncology research indicates that the attempts to explain such complex process as cancerogenesis by a single or several genetic mutations were not successful enough. On the other hand, chromosomal/genomic instability – almost universal features of malignant tumours which influence a global pattern of gene expression and, subsequently, many oncogenic pathways – were often disregarded and considered nonessential to clinical application. However, a new arising field of system biology including ‘new forms’ of genome diversity such as copy number variations (CNV) and high-throughput oncogene mutation profiling now reveal all the complexity of cancer and provide the final explanation of the oncogenic pathways, based on stochastic (onco)genomic variation rather than on (onco)genic concepts.

  13. Multiobjective Optimum Design of a 3-RRR Spherical Parallel Manipulator with Kinematic and Dynamic Dexterities

    OpenAIRE

    Guanglei Wu

    2012-01-01

    This paper deals with the kinematic synthesis problem of a 3-underlineRRR spherical parallel manipulator, based on the evaluation criteria of the kinematic, kinetostatic and dynamic performances of the manipulator. A multiobjective optimization problem is formulated to optimize the structural and geometric parameters of the spherical parallel manipulator. The proposed approach is illustrated with the optimum design of a special spherical parallel manipulator with unlimited rolling motion. The...

  14. CONSTRUCTION AND EXPRESSION OF ADENOASSOCIATED VIRUS- BASED PLASMID EXPRESSING VECTORS CONTAINING hIL- 2 GENE OR mIFN-γ GENE

    Institute of Scientific and Technical Information of China (English)

    张景迎; 梁宏立; 陈诗书

    2000-01-01

    Objective To improve the plasmid vectors in gene therapy, adeno - associated virus (AA V) based plasmid expressing vectors containing hIL-2 gene or mIFN-γ gene were constructed and its expression in transfected cells was studied. Methods By means of step to step cloning, promoter CMVp was placed at the downstream of 5' inverted terminal repeat from AA V (AA V- ITR) of pAP, hIL- 2 gene or mIFN- γ gene inserted into pAC between CMVp and poly A. Then intron A was inserted into pAC- hIL - 2 or pAC- mIFN- γ between CMVp and IL - 2 gene or IFNγ gene to construct pAI- hIL - 2 or pAI- mIFN - γ. Liposome -plasmid complexes were formed by mixing Dosper with these AAV-based plasmids containing hIL-2 gene or mIFN-γgene. Results High biological activities of IL - 2 or IFN- γ could be detected in the supernatants of NIH3T3 and MM45T. Li cells after transfection. Insertion of intron A into pAC-hIL-2 or pAC-mIFN-γ improved the expression of IL- 2 or IFN- γ. Conclusion These data demonstrated that the constructed AA V- based plasmid expressing vectors could efficiently express therapeutic genes in cultured cells and could be used as a nonviral gene transfer system in human gene therapy.

  15. Repetitive motion planning and control of redundant robot manipulators

    CERN Document Server

    Zhang, Yunong

    2013-01-01

    Repetitive Motion Planning and Control of Redundant Robot Manipulators presents four typical motion planning schemes based on optimization techniques, including the fundamental RMP scheme and its extensions. These schemes are unified as quadratic programs (QPs), which are solved by neural networks or numerical algorithms. The RMP schemes are demonstrated effectively by the simulation results based on various robotic models; the experiments applying the fundamental RMP scheme to a physical robot manipulator are also presented. As the schemes and the corresponding solvers presented in the book have solved the non-repetitive motion problems existing in redundant robot manipulators, it is of particular use in applying theoretical research based on the quadratic program for redundant robot manipulators in industrial situations. This book will be a valuable reference work for engineers, researchers, advanced undergraduate and graduate students in robotics fields. Yunong Zhang is a professor at The School of Informa...

  16. Multi-label literature classification based on the Gene Ontology graph

    Directory of Open Access Journals (Sweden)

    Lu Xinghua

    2008-12-01

    Full Text Available Abstract Background The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification. Results In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community. Conclusion Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate

  17. Analysis of regulatory networks constructed based on gene coexpression in pituitary adenoma

    Indian Academy of Sciences (India)

    Jie Gong; Bo Diao; Guo Jie Yao; Ying Liu; Guo Zheng Xu

    2013-12-01

    Gene coexpression patterns can reveal gene collections with functional consistency. This study systematically constructs regulatory networks for pituitary tumours by integrating gene coexpression, transcriptional and posttranscriptional regulation. Through network analysis, we elaborate the incidence mechanism of pituitary adenoma. The Pearson’s correlation coefficient was utilized to calculate the level of gene coexpression. By comparing pituitary adenoma samples with normal samples, pituitary adenoma-specific gene coexpression patterns were identified. For pituitary adenoma-specific coexpressed genes, we integrated transcription factor (TF) and microRNA (miRNA) regulation to construct a complex regulatory network from the transcriptional and posttranscriptional perspectives. Network module analysis identified the synergistic regulation of genes by miRNAs and TFs in pituitary adenoma. We identified 142 pituitary adenoma-specific active genes, including 43 TFs and 99 target genes of TFs. Functional enrichment of these 142 genes revealed that the occurrence of pituitary adenoma induced abnormalities in intracellular metabolism and angiogenesis process. These 142 genes were also significantly enriched in adenoma pathway. Module analysis of the systematic regulatory network found that three modules contained elements that were closely related to pituitary adenoma, such as FGF2 and SP1, as well as transcription factors and miRNAs involved in the tumourigenesis. These results show that in the occurrence of pituitary adenoma, miRNA, TF and genes interact with each other. Based on gene expression, the proposed method integrates interaction information from different levels and systematically explains the occurrence of pituitary tumours. It facilitates the tracing of the origin of the disease and can provide basis for early diagnosis of complex diseases or cancer without obvious symptoms.

  18. Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

    OpenAIRE

    Costanzo, Maria C.; Park, Julie; Balakrishnan, Rama; Cherry, J. Michael; Hong, Eurie L.

    2011-01-01

    Annotation using Gene Ontology (GO) terms is one of the most important ways in which biological information about specific gene products can be expressed in a searchable, computable form that may be compared across genomes and organisms. Because literature-based GO annotations are often used to propagate functional predictions between related proteins, their accuracy is critically important. We present a strategy that employs a comparison of literature-based annotations with computational pre...

  19. Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes

    OpenAIRE

    Milinkovitch, M C; Meyer., A; Powell, J R

    1994-01-01

    Traditionally, living cetaceans (order Cetacea) are classified into two highly distinct suborders: the echolocating toothed whales, Odontoceti, and the filter-feeding baleen whales, Mysticeti. A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome b gene for all major groups of cetaceans contradicts this long-accepted taxonomic subdivision. One group of toothed whales, the sperm whales, is more closely related to the morph...

  20. RNA-guided gene activation by CRISPR-Cas9-based transcription factors

    OpenAIRE

    Perez-Pinera, Pablo; Kocak, D. Dewran; Vockley, Christopher M.; Adler, Andrew F; Kabadi, Ami M.; Polstein, Lauren R.; Thakore, Pratiksha I; Glass, Katherine A.; Ousterout, David G.; Leong, Kam W.; Guilak, Farshid; Crawford, Gregory E.; Reddy, Timothy E.; Gersbach, Charles A

    2013-01-01

    Technologies for engineering synthetic transcription factors have enabled many advances in medicine and science. In contrast to existing methods based on engineering of new DNA-binding proteins, we created a Cas9-based transactivator that is targeted to DNA sequences by guide RNA molecules. Co-expression of this transactivator and combinations of guide RNAs in human cells induced specific expression of endogenous target genes, demonstrating a simple and versatile approach for RNA-guided gene ...