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Sample records for based gene manipulation

  1. 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.

  2. Inducible Gene Manipulations in Serotonergic Neurons

    Science.gov (United States)

    Weber, Tillmann; Böhm, Gerald; Hermann, Elke; Schütz, Günther; Schönig, Kai; Bartsch, Dusan

    2009-01-01

    An impairment of the serotonergic (5-HT) system has been implicated in the etiology of many neuropsychiatric disorders. Despite the considerable genetic evidence, the exact molecular and pathophysiological mechanisms underlying this dysfunction remain largely unknown. To address the lack of instruments for the molecular dissection of gene function in serotonergic neurons we have developed a new mouse transgenic tool that allows inducible Cre-mediated recombination of genes selectively in 5-HT neurons of all raphe nuclei. In this transgenic mouse line, the tamoxifen-inducible CreERT2 recombinase is expressed under the regulatory control of the mouse tryptophan hydroxylase 2 (Tph2) gene locus (177 kb). Tamoxifen treatment efficiently induced recombination selectively in serotonergic neurons with minimal background activity in vehicle-treated mice. These genetic manipulations can be initiated at any desired time during embryonic development, neonatal stage or adulthood. To illustrate the versatility of this new tool, we show that Brainbow-1.0LTPH2-CreERT2 mice display highly efficient recombination in serotonergic neurons with individual 5-HT neurons labeling with multiple distinct fluorescent colors. This labeling is well suited for visualization and tracing of serotonergic neurons and their network architecture. Finally, the applicability of TPH2-CreERT2 for loxP-flanked candidate gene manipulation is evidenced by our successful knockout induction of the ubiquitously expressed glucocorticoid-receptor exclusively in 5-HT neurons of adult mice. The TPH2-CreERT2 line will allow detailed analysis of gene function in both developing and adult serotonergic neurons. PMID:19936315

  3. Molecular genetic techniques for gene manipulation in Candida albicans

    Science.gov (United States)

    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 gene expression, protein tagging, gene reintegration, and overexpression. In this review, the main cassettes containing selectable markers used for gene manipulation in C. albicans are summarized; the advantages and limitations of these cassettes are discussed concerning the influences on the target gene expression and the virulence of the mutant strains. PMID:24759671

  4. 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

  5. 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...... properties, or to use the analysis information for code modifications. Semanticsbased program manipulation addresses methods for program modifications and program analyses that are formally defined and therefore can be verified with respect to the programming-language semantics. This dissertation comprises...... four articles in the field of semantics-based techniques for program manipulation: three articles are about partial evaluation, a method for program specialization; the fourth article treats an approach to automatic cost analysis. Partial evaluation optimizes programs by specializing them with respect...

  6. Radiation application on development of marker genes for genetic manipulation

    International Nuclear Information System (INIS)

    Lee, Young Il

    1997-04-01

    This state of art report was dealt with the recent progress of genetic engineering techniques and prospect of gene manipulation. Especially the selection of new genetic marker genes such as variants to environmental stress, pest or insect resistance, herbicide resistance and nutritional requirement was reviewed by using plant cell and tissue culture combined with radiation mutation induction. Biotechnology has taken us from the era hybrid plants to the era of transgenic plants. Although there are still many problems to solve in transformation method and the regeneration of transformed cell and tissue. Genetic marker genes are very important material to improve the technique of genetic manipulation. Most of the genes have been developed by radiation. (author). 180 refs., 6 tabs

  7. Gene-manipulated embryonic stem cells for rat transgenesis.

    Science.gov (United States)

    Kawamata, Masaki; Ochiya, Takahiro

    2011-06-01

    Embryonic stem cells (ESCs) are derived from blastocysts and are capable of differentiating into whole tissues and organs. Transplantation of ESCs into recipient blastocysts leads to the generation of germline-competent chimeras in mice. Transgenic, knockin, and knockout gene manipulations are available in mouse ESCs, enabling the production of genetically modified animals. Rats have important advantages over mice as an experimental system for physiological and pharmacological investigations. However, in contrast to mouse ESCs, rat ESCs were not established until 2008 because of the difficulty of maintaining pluripotency. Although the use of signaling inhibitors has allowed the generation of rat ESCs, the production of genetically modified rats has been difficult due to problems in rat ESCs after gene introduction. In this review, we will focus on some well-documented examples of gene manipulation in rat ESCs.

  8. Manipulation of particles based on swirl

    Science.gov (United States)

    Zhang, Qin; Fan, Jibin; Aoyama, Hisayuki

    2018-01-01

    A method of manipulating particles based on swirl was proposed in this article. The pressure and velocity distributions of swirling flow field were analyzed theoretically. The mechanism of particle trapping and controlling based on swirling flow was discussed, and the feasibility of the proposed method was verified by experiments. The results show that a swirling flow can be generated by placing two microtubules in parallel and jetting fluid in opposite directions. Particles with arbitrary size and shape can be trapped and controlled to rotate and move directionally and quantitatively with proper swirling flow parameters.

  9. 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.

  10. Sound beam manipulation based on temperature gradients

    International Nuclear Information System (INIS)

    Qian, Feng; Quan, Li; Liu, Xiaozhou; Gong, Xiufen

    2015-01-01

    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. Physics Based Vision Systems for Robotic Manipulation

    Data.gov (United States)

    National Aeronautics and Space Administration — With the increase of robotic manipulation tasks (TA4.3), specifically dexterous manipulation tasks (TA4.3.2), more advanced computer vision algorithms will be...

  12. Manipulators

    International Nuclear Information System (INIS)

    Wilcock, P.D.

    1984-01-01

    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.)

  13. Automated Fictional Ideation via Knowledge Base Manipulation.

    Science.gov (United States)

    Llano, Maria Teresa; Colton, Simon; Hepworth, Rose; Gow, Jeremy

    The invention of fictional ideas (ideation) is often a central process in the creative production of artefacts such as poems, music and paintings, but has barely been studied in the computational creativity community. We present here a general approach to automated fictional ideation that works by manipulating facts specified in knowledge bases. More specifically, we specify a number of constructions which, by altering and combining facts from a knowledge base, result in the generation of fictions. Moreover, we present an instantiation of these constructions through the use of ConceptNet, a database of common sense knowledge. In order to evaluate the success of these constructions, we present a curation analysis that calculates the proportion of ideas which pass a typicality judgement. We further evaluate the output of this approach through a crowd-sourcing experiment in which participants were asked to rank ideas. We found a positive correlation between the participant's rankings and a chaining inference technique that automatically assesses the value of the fictions generated through our approach. We believe that these results show that this approach constitutes a firm basis for automated fictional ideation with evaluative capacity.

  14. Manipulators

    International Nuclear Information System (INIS)

    Andre, Y.; Routelous, F.; Spina, G.; Perpina, J.; Suquet, J.; Rossi, M.; Zanca, M.; Billiet, A.; Madec, L.; Lemoine, T.; Gaboriaud, G.; Aubert, B.; Rosenwald, J.C.; Neuenschwander, S.; Brisse, H.; Rehel, J.L.; Rebibo, G.; Bensimon, J.L.; Kulski, A.; Serhal, M.; Nguyen, K.V.; Lescure, R.; Cymbalista, M.

    2005-01-01

    Three articles have for purpose the radiation doses optimization in medical imaging. The first one concerns the radiation protection of manipulators working at a PET scan post, the second one concerns more particularly the optimization of doses delivered in pediatric computerized tomography, the third one is devoted to a comparison between radiation dose and image quality through scanners of adult temporal bone. (N.C.)

  15. 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.

  16. Implementation of vision based 2-DOF underwater Manipulator

    Directory of Open Access Journals (Sweden)

    Geng Jinpeng

    2015-01-01

    Full Text Available Manipulator is of vital importance to the remotely operated vehicle (ROV, especially when it works in the nuclear reactor pool. Two degrees of freedom (2-DOF underwater manipulator is designed to the ROV, which is composed of control cabinet, buoyancy module, propellers, depth gauge, sonar, a monocular camera and other attitude sensors. The manipulator can be used to salvage small parts like bolts and nuts to accelerate the progress of the overhaul. It can move in the vertical direction alone through the control of the second joint, and can grab object using its unique designed gripper. A monocular vision based localization algorithm is applied to help the manipulator work independently and intelligently. Eventually, field experiment is conducted in the swimming pool to verify the effectiveness of the manipulator and the monocular vision based algorithm.

  17. Faults and Failures in SQL-based Data Manipulation Programming

    OpenAIRE

    Leitão Júnior, Plínio de Sá; Universidade Federal de Lavras; Vilela, Plínio Robert Souza; Universidade Metodista de Piracicaba; Jino, Mario; Unicamp

    2007-01-01

    Database applications, including SQL-based applications, have received little attention directed towards improving the knowledge of their possible faults. This paper deals with issues related to software faults and failures aiming at understanding what types of faults occur in SQL manipulation commands, and how they are propagated to the output of command execution. SQL manipulation commands are studied and their structure is organized into structural items, a step towards understanding and g...

  18. Application of model based control to robotic manipulators

    Science.gov (United States)

    Petrosky, Lyman J.; Oppenheim, Irving J.

    1988-01-01

    A robot that can duplicate humam motion capabilities in such activities as balancing, reaching, lifting, and moving has been built and tested. These capabilities are achieved through the use of real time Model-Based Control (MBC) techniques which have recently been demonstrated. MBC accounts for all manipulator inertial forces and provides stable manipulator motion control even at high speeds. To effectively demonstrate the unique capabilities of MBC, an experimental robotic manipulator was constructed, which stands upright, balancing on a two wheel base. The mathematical modeling of dynamics inherent in MBC permit the control system to perform functions that are impossible with conventional non-model based methods. These capabilities include: (1) Stable control at all speeds of operation; (2) Operations requiring dynamic stability such as balancing; (3) Detection and monitoring of applied forces without the use of load sensors; (4) Manipulator safing via detection of abnormal loads. The full potential of MBC has yet to be realized. The experiments performed for this research are only an indication of the potential applications. MBC has no inherent stability limitations and its range of applicability is limited only by the attainable sampling rate, modeling accuracy, and sensor resolution. Manipulators could be designed to operate at the highest speed mechanically attainable without being limited by control inadequacies. Manipulators capable of operating many times faster than current machines would certainly increase productivity for many tasks.

  19. Evaluation of phantom-based education system for acupuncture manipulation.

    Science.gov (United States)

    Lee, In-Seon; Lee, Ye-Seul; Park, Hi-Joon; Lee, Hyejung; Chae, Younbyoung

    2015-01-01

    Although acupuncture manipulation has been regarded as one of the important factors in clinical outcome, it has been difficult to train novice students to become skillful experts due to a lack of adequate educational program and tools. In the present study, we investigated whether newly developed phantom acupoint tools would be useful to practice-naïve acupuncture students for practicing the three different types of acupuncture manipulation to enhance their skills. We recruited 12 novice students and had them practice acupuncture manipulations on the phantom acupoint (5% agarose gel). We used the Acusensor 2 and compared their acupuncture manipulation techniques, for which the target criteria were depth and time factors, at acupoint LI11 in the human body before and after 10 training sessions. The outcomes were depth of needle insertion, depth error from target criterion, time of rotating, lifting, and thrusting, time error from target criteria and the time ratio. After 10 training sessions, the students showed significantly improved outcomes in depth of needle, depth error (rotation, reducing lifting/thrusting), thumb-forward time error, thumb-backward time error (rotation), and lifting time (reinforcing lifting/thrusting). The phantom acupoint tool could be useful in a phantom-based education program for acupuncture-manipulation training for students. For advanced education programs for acupuncture manipulation, we will need to collect additional information, such as patient responses, acupoint-specific anatomical characteristics, delicate tissue-like modeling, haptic and visual feedback, and data from an acupuncture practice simulator.

  20. KINEMATIC ANALYSIS OF MODULAR, TRUSS-BASED MANIPULATOR UNITS

    Energy Technology Data Exchange (ETDEWEB)

    Salerno, R. J.

    1994-06-01

    Decontamination and Dismantling (D&D) activities within the U.S. Department of Energy (DOE) require a long reach manipulator with a large load capacity. Variable Geometry Trusses (VGTs) are a unique class of mechanical structures which allow the advantages of truss structures for large scale applications to be applied to large robotic manipulators. Individual VGT units may be assembled to create a modular, long-reach, truss-type manipulator. Each module of such a manipulator system is either a static truss section or one of several possible VGT geometries. While many potential applications exist for this technology, the present work is largely motivated by the need for generic robotic systems for remote manipulation. A manipulator system based on VGT modules provides several advantages. The reconfigurable nature of the manipulator system allows it to be adapted on site to unforeseen conditions. The kinematic redundancy of the manipulator enables it to work effectively even in a highly obstructed workspace. The parallel structure of the truss modules enables the manipulator to be withdrawn in the event of a structural failure. Finally, the open framework of the modules provides a clear, protected passageway for control and power cabling, waste conveyance, or other services required at the end effector. As is implied in a truss structure, all primary members of a VGT are ideally loaded in pure tension or compression. This results in an extremely stiff and strong manipulator system with minimal overall weight. Careful design of the joints of a VGT is very important to the overall stiffness and accuracy of the structure, as several links (as many as six) are joined together at each joint. The greatest disadvantage to this approach to manipulator design has traditionally been that the kinematics of VGT structures are complex and poorly understood. This report specifically addresses the kinematics of several possible geometries for the individual VGT units. Equations and

  1. Bidirectional manipulation of gene expression in adipocytes using CRISPRa and siRNA

    DEFF Research Database (Denmark)

    Lundh, Morten; Pluciñska, Kaja; Isidor, Marie S

    2017-01-01

    " system and siRNAs to simultaneously overexpress and silence selected genes in the same cell populations. METHODS: We introduced a stable expression of dCas9-VP64 and MS2-P65, the core components of the CRIPSRa SAM system, in mesenchymal C3H/10T1/2 cells through viral delivery and used guide RNAs...... targeting Pparγ2, Prdm16, Zfp423, or Ucp1 to control the expression of key genes involved in adipocyte differentiation and function. We additionally co-transfected mature adipocytes with sgRNA plasmids and siRNA to simultaneously up-regulate and silence selected genes. Quantitative gene expression, oxygen...... gene silencing using siRNA, allowing for bidirectional manipulation of gene expression in the same cell populations. CONCLUSIONS: We demonstrate that the CRISPRa SAM system can be easily adopted and used to efficiently manipulate gene expression in pre- and mature adipocytes in vitro. Moreover, we...

  2. 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.

  3. Manipulation of Cell Physiology Enables Gene Silencing in Well-differentiated Airway Epithelia

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    Sateesh Krishnamurthy

    2012-01-01

    Full Text Available The application of RNA interference-based gene silencing to the airway surface epithelium holds great promise to manipulate host and pathogen gene expression for therapeutic purposes. However, well-differentiated airway epithelia display significant barriers to double-stranded small-interfering RNA (siRNA delivery despite testing varied classes of nonviral reagents. In well-differentiated primary pig airway epithelia (PAE or human airway epithelia (HAE grown at the air–liquid interface (ALI, the delivery of a Dicer-substrate small-interfering RNA (DsiRNA duplex against hypoxanthine–guanine phosphoribosyltransferase (HPRT with several nonviral reagents showed minimal uptake and no knockdown of the target. In contrast, poorly differentiated cells (2–5-day post-seeding exhibited significant oligonucleotide internalization and target knockdown. This finding suggested that during differentiation, the barrier properties of the epithelium are modified to an extent that impedes oligonucleotide uptake. We used two methods to overcome this inefficiency. First, we tested the impact of epidermal growth factor (EGF, a known enhancer of macropinocytosis. Treatment of the cells with EGF improved oligonucleotide uptake resulting in significant but modest levels of target knockdown. Secondly, we used the connectivity map (Cmap database to correlate gene expression changes during small molecule treatments on various cells types with genes that change upon mucociliary differentiation. Several different drug classes were identified from this correlative assessment. Well-differentiated epithelia treated with DsiRNAs and LY294002, a PI3K inhibitor, significantly improved gene silencing and concomitantly reduced target protein levels. These novel findings reveal that well-differentiated airway epithelia, normally resistant to siRNA delivery, can be pretreated with small molecules to improve uptake of synthetic oligonucleotide and RNA interference (RNAi responses.

  4. 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.

  5. 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.

  6. 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.

  7. Adaptive control of a Stewart platform-based manipulator

    Science.gov (United States)

    Nguyen, Charles C.; Antrazi, Sami S.; Zhou, Zhen-Lei; Campbell, Charles E., Jr.

    1993-01-01

    A joint-space adaptive control scheme for controlling noncompliant motion of a Stewart platform-based manipulator (SPBM) was implemented in the Hardware Real-Time Emulator at Goddard Space Flight Center. The six-degrees of freedom SPBM uses two platforms and six linear actuators driven by dc motors. The adaptive control scheme is based on proportional-derivative controllers whose gains are adjusted by an adaptation law based on model reference adaptive control and Liapunov direct method. It is concluded that the adaptive control scheme provides superior tracking capability as compared to fixed-gain controllers.

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

    Directory of Open Access Journals (Sweden)

    Zhiyong Yang

    2008-03-01

    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.

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

    OpenAIRE

    Knockaert, Mirjam; Manigart, Sophie; Cattoir, Sofie; Verstraete, Willy

    2015-01-01

    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...

  11. Closed-loop physics-based manipulation under uncertainty

    Data.gov (United States)

    National Aeronautics and Space Administration — Robotic manipulation has wide applications both on Earth and in space. Dexterous manipulators have been carefully designed to assist astronauts with dangerous and...

  12. 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.

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

    Science.gov (United States)

    Knockaert, Mirjam; Manigart, Sophie; Cattoir, Sofie; Verstraete, Willy

    2015-06-01

    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.

  14. Manipulation of MKS1 gene expression affects Kalanchoe blossfeldiana and Petunia hybrida phenotypes

    OpenAIRE

    Gargul, Joanna Maria; Mibus, Heiko; Serek, Margrethe

    2015-01-01

    The establishment of alternative methods to chemical treatments for growth retardation and pathogen protection in ornamental plant production has become a major goal in recent breeding programmes. This study evaluates the effect of manipulating MAP kinase 4 nuclear substrate 1 (MKS1) expression in Kalanchoe blossfeldiana and Petunia hybrida. The Arabidopsis thaliana MKS1 gene was overexpressed in both species via Agrobacterium-mediated transformation, resulting in dwarfed phenotypes and delay...

  15. SVM-Based Control System for a Robot Manipulator

    Directory of Open Access Journals (Sweden)

    Foudil Abdessemed

    2012-12-01

    Full Text Available Real systems are usually non-linear, ill-defined, have variable parameters and are subject to external disturbances. Modelling these systems is often an approximation of the physical phenomena involved. However, it is from this approximate system of representation that we propose - in this paper - to build a robust control, in the sense that it must ensure low sensitivity towards parameters, uncertainties, variations and external disturbances. The computed torque method is a well-established robot control technique which takes account of the dynamic coupling between the robot links. However, its main disadvantage lies on the assumption of an exactly known dynamic model which is not realizable in practice. To overcome this issue, we propose the estimation of the dynamics model of the nonlinear system with a machine learning regression method. The output of this regressor is used in conjunction with a PD controller to achieve the tracking trajectory task of a robot manipulator. In cases where some of the parameters of the plant undergo a change in their values, poor performance may result. To cope with this drawback, a fuzzy precompensator is inserted to reinforce the SVM computed torque-based controller and avoid any deterioration. The theory is developed and the simulation results are carried out on a two-degree of freedom robot manipulator to demonstrate the validity of the proposed approach.

  16. In vitro manipulation of gene expression in larval Schistosoma: a model for postgenomic approaches in Trematoda

    Science.gov (United States)

    YOSHINO, TIMOTHY P.; DINGUIRARD, NATHALIE; DE MORAES MOURÃO, MARINA

    2013-01-01

    SUMMARY With rapid developments in DNA and protein sequencing technologies, combined with powerful bioinformatics tools, a continued acceleration of gene identification in parasitic helminths is predicted, potentially leading to discovery of new drug and vaccine targets, enhanced diagnostics and insights into the complex biology underlying host-parasite interactions. For the schistosome blood flukes, with the recent completion of genome sequencing and comprehensive transcriptomic datasets, there has accumulated massive amounts of gene sequence data, for which, in the vast majority of cases, little is known about actual functions within the intact organism. In this review we attempt to bring together traditional in vitro cultivation approaches and recent emergent technologies of molecular genomics, transcriptomics and genetic manipulation to illustrate the considerable progress made in our understanding of trematode gene expression and function during development of the intramolluscan larval stages. Using several prominent trematode families (Schistosomatidae, Fasciolidae, Echinostomatidae), we have focused on the current status of in vitro larval isolation/cultivation as a source of valuable raw material supporting gene discovery efforts in model digeneans that include whole genome sequencing, transcript and protein expression profiling during larval development, and progress made in the in vitro manipulation of genes and their expression in larval trematodes using transgenic and RNA interference (RNAi) approaches. PMID:19961646

  17. Adaptive Control for Robotic Manipulators Base on RBF Neural Network

    Directory of Open Access Journals (Sweden)

    MA Jing

    2013-09-01

    Full Text Available An adaptive neural network controller is brought forward by the paper to solve trajectory tracking problems of robotic manipulators with uncertainties. The first scheme consists of a PD feedback and a dynamic compensator which is composed by neural network controller and variable structure controller. Neutral network controller is designed to adaptive learn and compensate the unknown uncertainties, variable structure controller is designed to eliminate approach errors of neutral network. The adaptive weight learning algorithm of neural network is designed to ensure online real-time adjustment, offline learning phase is not need; Global asymptotic stability (GAS of system base on Lyapunov theory is analysised to ensure the convergence of the algorithm. The simulation result s show that the kind of the control scheme is effective and has good robustness.

  18. Regulation of gene expression by manipulating transcriptional repressor activity using a novel CoSRI technology.

    Science.gov (United States)

    Xu, Yue; Li, Song Feng; Parish, Roger W

    2017-07-01

    Targeted gene manipulation is a central strategy for studying gene function and identifying related biological processes. However, a methodology for manipulating the regulatory motifs of transcription factors is lacking as these factors commonly possess multiple motifs (e.g. repression and activation motifs) which collaborate with each other to regulate multiple biological processes. We describe a novel approach designated conserved sequence-guided repressor inhibition (CoSRI) that can specifically reduce or abolish the repressive activities of transcription factors in vivo. The technology was evaluated using the chimeric MYB80-EAR transcription factor and subsequently the endogenous WUS transcription factor. The technology was employed to develop a reversible male sterility system applicable to hybrid seed production. In order to determine the capacity of the technology to regulate the activity of endogenous transcription factors, the WUS repressor was chosen. The WUS repression motif could be inhibited in vivo and the transformed plants exhibited the wus-1 phenotype. Consequently, the technology can be used to manipulate the activities of transcriptional repressor motifs regulating beneficial traits in crop plants and other eukaryotic organisms. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  19. From gene manipulation to forest establishment: shoot cultures of woody plants can be a central tool

    Energy Technology Data Exchange (ETDEWEB)

    McCown, B.H.

    1985-05-01

    Establishing germplasm of woody plants in microculture as shoot cultures has proved to be an effective method of overcoming many of the obstacles in working with these crops. Shoot cultures eliminate the changes associated with seasonal growth cycles and phase change and put large plants into a more manageable form. Well-established shoot cultures are central to successful clonal propagation systems for forest trees as well as to genetic improvement based on the use of cellular techniques such as protoplast manipulation. The physiological basis as to why tissues from shoot cultures are so readily manipulated is not well understood.

  20. A minimally invasive, lentiviral based method for the rapid and sustained genetic manipulation of renal tubules.

    Science.gov (United States)

    Espana-Agusti, Judit; Tuveson, David A; Adams, David J; Matakidou, Athena

    2015-06-05

    The accelerated discovery of disease-related genes emerging from genomic studies has strained the capacity of traditional genetically engineered mouse models (GEMMs) to provide in-vivo validation. Direct, somatic, genetic engineering approaches allow for accelerated and flexible genetic manipulation and represent an attractive alternative to GEMMs. In this study we investigated the feasibility, safety and efficiency of a minimally invasive, lentiviral based approach for the sustained in-vivo modification of renal tubular epithelial cells. Using ultrasound guidance, reporter vectors were directly injected into the mouse renal parenchyma. We observed transgene expression confined to the renal cortex (specifically proximal and distal tubules) and sustained beyond 2 months post injection. Furthermore, we demonstrate the ability of this methodology to induce long-term, in-vivo knockdown of candidate genes either through somatic recombination of floxed alleles or by direct delivery of specific shRNA sequences. This study demonstrates that ultrasound-guided injection of lentiviral vectors provides a safe and efficient method for the genetic manipulation of renal tubules, representing a quick and versatile alternative to GEMMs for the functional characterisation of disease-related genes.

  1. Modification of flower colour via manipulation of P450 gene expression in transgenic plants.

    Science.gov (United States)

    Holton, T A

    1995-01-01

    Unlike animals, which synthesise cytochrome P450 enzymes mostly for the degradation of xenobiotics, plants have evolved a large number of different P450 enzymes for the synthesis of secondary metabolites. Probably the most conspicuous of these secondary metabolites are anthocyanins, which are important flower pigments. The types of anthocyanins synthesised in plants are controlled by the cytochrome P450 enzymes flavonoid 3'-hydroxylase and flavonoid 3',5'-hydroxylase. Cloning of flavonoid 3',5'-hydroxylase genes has enabled the manipulation of anthocyanin synthesis in transgenic plants and enabled the production of novel pigments and flower colours.

  2. I Have a Dream: Organic Movements Include Gene Manipulation to Improve Sustainable Farming

    Directory of Open Access Journals (Sweden)

    Gerhart U. Ryffel

    2017-03-01

    Full Text Available Several papers in a Special Issue of Sustainability have recently discussed various aspects to evaluate whether organic farming and gene manipulation are compatible. A special emphasis was given to new plant breeding techniques (NPBTs. These new approaches allow the most predictable genetic alterations of crop plants in ways that the genetically modified plant is identical to a plant generated by conventional breeding. The articles of the Special Issue present the arguments pro and contra the inclusion of the plants generated by NPBTs in organic farming. Organic movements have not yet made a final decision whether some of these techniques should be accepted or banned. In my view these novel genetically manipulated (GM crops could be used in such a way as to respect the requirements for genetically manipulated organisms (GMOs formulated by the International Federation of Organic Movements (IFOAM. Reviewing the potential benefits of disease-resistant potatoes and bananas, it seems possible that these crops support organic farming. To this end, I propose specific requirements that the organic movements should proactively formulate as their standards to accept specific GM crops.

  3. Robotic design analysis based on teleoperated manipulator data collection

    Energy Technology Data Exchange (ETDEWEB)

    Stoughton, R.S.; Martin, H.L.

    1985-01-01

    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.

  4. Robotic design analysis based on teleoperated manipulator data collection

    International Nuclear Information System (INIS)

    Stoughton, R.S.; Martin, H.L.

    1985-01-01

    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

  5. Manipulating the membrane penetration mechanism of helical polypeptides via aromatic modification for efficient gene delivery.

    Science.gov (United States)

    Zheng, Nan; Song, Ziyuan; Yang, Jiandong; Liu, Yang; Li, Fangfang; Cheng, Jianjun; Yin, Lichen

    2017-08-01

    The delivery performance of non-viral gene vectors is greatly related to their intracellular kinetics. Cationic helical polypeptides with potent membrane penetration properties and gene transfection efficiencies have been recently developed by us. However, they suffer from severe drawbacks in terms of their membrane penetration mechanisms that mainly include endocytosis and pore formation. The endocytosis mechanism leads to endosomal entrapment of gene cargos, while the charge- and helicity-induced pore formation causes appreciable cytotoxicity at high concentrations. With the attempt to overcome such critical challenges, we incorporated aromatic motifs into the design of helical polypeptides to enhance their membrane activities and more importantly, to manipulate their membrane penetration mechanisms. The aromatically modified polypeptides exhibited higher cellular internalization level than the unmodified analogue by up to 2.5 folds. Such improvement is possibly because aromatic domains promoted the polypeptides to penetrate cell membranes via direct transduction, a non-endocytosis and non-pore formation mechanism. As such, gene cargos were more efficiently delivered into cells by bypassing endocytosis and subsequently avoiding endosomal entrapment, and the material toxicity associated with excessive pore formation was also reduced. The top-performing aromatic polypeptide containing naphthyl side chains at the incorporated content of 20mol% revealed notably higher transfection efficiencies than commercial reagents in melanoma cells in vitro (by 11.7 folds) and in vivo (by 9.1 folds), and thus found potential utilities toward topical gene delivery for cancer therapy. Cationic helical polypeptides, as efficient gene delivery materials, suffer from severe drawbacks in terms of their membrane penetration mechanisms. The main cell penetration mechanisms involved are endocytosis and pore formation. However, the endocytosis mechanism has the limitation of endosomal

  6. Micromirror-based manipulation of synchrotron x-ray beams

    Science.gov (United States)

    Walko, D. A.; Chen, Pice; Jung, I. W.; Lopez, D.; Schwartz, C. P.; Shenoy, G. K.; Wang, Jin

    2017-08-01

    Synchrotron beamlines typically use macroscopic, quasi-static optics to manipulate x-ray beams. We present the use of dynamic microelectromechanical systems-based optics (MEMS) to temporally modulate synchrotron x-ray beams. We demonstrate this concept using single-crystal torsional MEMS micromirrors oscillating at frequencies of 75 kHz. Such a MEMS micromirror, with lateral dimensions of a few hundred micrometers, can interact with x rays by operating in grazing-incidence reflection geometry; x rays are deflected only when an x-ray pulse is incident on the rotating micromirror under appropriate conditions, i.e., at an angle less than the critical angle for reflectivity. The time window for such deflections depends on the frequency and amplitude of the MEMS rotation. We demonstrate that reflection geometry can produce a time window of a few microseconds. We further demonstrate that MEMS optics can isolate x rays from a selected synchrotron bunch or group of bunches. With ray-trace simulations we explain the currently achievable time windows and suggest a path toward improvements.

  7. 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.

  8. Manipulation of regulatory genes reveals complexity and fidelity in hormaomycin biosynthesis.

    Science.gov (United States)

    Cai, Xiaofeng; Teta, Roberta; Kohlhaas, Christoph; Crüsemann, Max; Ueoka, Reiko; Mangoni, Alfonso; Freeman, Michael F; Piel, Jörn

    2013-06-20

    Hormaomycin (HRM) is a structurally remarkable peptide produced by Streptomyces griseoflavus W-384 that acts as a Streptomyces signaling metabolite and exhibits potent antibiotic activity against coryneform actinomycetes. HRM biosynthetic studies have been hampered by inconsistent and low production. To enhance fermentation titers, the role of its cluster-encoded regulatory genes was investigated. Extra copies of the putative regulators hrmA and hrmB were introduced into the wild-type strain, resulting in an increase of HRM production and its analogs up to 135-fold. For the HrmB overproducer, six bioactive analogs were isolated and characterized. This study demonstrates that HrmA and HrmB are positive regulators in HRM biosynthesis. A third gene, hrmH, was identified as encoding a protein capable of shifting the metabolic profile of HRM and its derivatives. Its manipulation resulted in the generation of an additional HRM analog. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Modeling and Manipulating Human Diseases with Induced Pluripotent Stem Cells, Pig Models and Precision Gene Editing.

    Directory of Open Access Journals (Sweden)

    Yonglun Luo

    2016-06-01

    Full Text Available We have developed systems, e.g. C-Check, that can be used to rapidly select and quantify CRISPR/Cas9 nuclease activity and enrichment of genetically modified cells with desired mutations (Zhou et al., 2016. To facilitate the simultaneous manipulation of multiple genes in cells, we have developed a system that allows concordant delivery of up to 30 sgRNAs into one cell [Johan Vad-Nielsen et al., under review]. Targeted insertion, fluorescent tagging or correction of endogenous genes is of great interest but greatly hampered by the technical difficulties and relatively low homology directed repair efficiency compared to the higher efficiency of NHEJ. Thus, we have developed systems for rapid generation of gene targeting vectors (Luo et al., 2014, lentivirus-mediated gene targeting [Yujia Cai et al., Elife, in revision], and recombinant Cas9s to enhance HDR in mammalian cells. Furthermore, to recapitulate the pathogenesis of human diseases, we have developed pig models of breast cancer and diabetes using gene editing and SCNT, as well as human induced pluripotent stem cell models of MCADD.

  10. Tip displacement variance of manipulator to simultaneous horizontal and vertical stochastic base excitations

    International Nuclear Information System (INIS)

    Rahi, A.; Bahrami, M.; Rastegar, J.

    2002-01-01

    The tip displacement variance of an articulated robotic manipulator to simultaneous horizontal and vertical stochastic base excitation is studied. The dynamic equations for an n-links manipulator subjected to both horizontal and vertical stochastic excitations are derived by Lagrangian method and decoupled for small displacement of joints. The dynamic response covariance of the manipulator links is computed in the coordinate frame attached to the base and then the principal variance of tip displacement is determined. Finally, simulation for a two-link planner robotic manipulator under base excitation is developed. Then sensitivity of the principal variance of tip displacement and tip velocity to manipulator configuration, damping, excitation parameters and manipulator links length are investigated

  11. Parallel manipulators with two end-effectors : Getting a grip on Jacobian-based stiffness analysis

    NARCIS (Netherlands)

    Hoevenaars, A.G.L.

    2016-01-01

    Robots that are developed for applications which require a high stiffness-over-inertia ratio, such as pick-and-place robots, machining robots, or haptic devices, are often based on parallel manipulators. Parallel manipulators connect an end-effector to an inertial base using multiple serial

  12. Workflow automation based on OSI job transfer and manipulation

    NARCIS (Netherlands)

    van Sinderen, Marten J.; Joosten, Stef M.M.; Guareis de farias, Cléver

    1999-01-01

    This paper shows that Workflow Management Systems (WFMS) and a data communication standard called Job Transfer and Manipulation (JTM) are built on the same concepts, even though different words are used. The paper analyses the correspondence of workflow concepts and JTM concepts. Besides, the

  13. Non-classic multiscale modeling of manipulation based on AFM, in aqueous and humid ambient

    Science.gov (United States)

    Korayem, M. H.; Homayooni, A.; Hefzabad, R. N.

    2018-05-01

    To achieve a precise manipulation, it is important that an accurate model consisting the size effect and environmental conditions be employed. In this paper, the non-classical multiscale modeling is developed to investigate the manipulation in a vacuum, aqueous and humid ambient. The manipulation structure is considered into two parts as a macro-field (MF) and a nano-field (NF). The governing equations of the AFM components (consist of the cantilever and tip) in the MF are derived based on the modified couple stress theory. The material length scale parameter is used to study the size effect. The fluid flow in the MF is assumed as the Couette and Creeping flows. Moreover, the NF is modeled using the molecular dynamics. The Electro-Based (ELBA) model is considered to model the ambient condition in the NF. The nanoparticle in the different conditions is taken into account to study the manipulation. The results of the manipulation indicate that the predicted deflection of the non-classical model is less than the classical one. Comparison of the nanoparticle travelled distance on substrate shows that the manipulation in the submerged condition is close to the ideal manipulation. The results of humid condition illustrate that by increasing the relative humidity (RH) the manipulation force decreases. Furthermore, Root Mean Square (RMS) as a criterion of damage demonstrates that the submerged nanoparticle has the minimum damage, however, the minimum manipulation force occurs in superlative humid ambient.

  14. 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. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  15. A novel DC therapy with manipulation of MKK6 gene on nickel allergy in mice.

    Directory of Open Access Journals (Sweden)

    Megumi Watanabe

    Full Text Available BACKGROUND: Although the activation of dermal dendritic cells (DCs or Langerhans cells (LCs via p38 mitogen-activated protein kinase (MAPK plays a crucial role in the pathogenesis of metal allergy, the in vivo molecular mechanisms have not been identified and a possible therapeutic strategy using the control of dermal DCs or LCs has not been established. In this study, we focused on dermal DCs to define the in vivo mechanisms of metal allergy pathogenesis in a mouse nickel (Ni allergy model. The effects of DC therapy on Ni allergic responses were also investigated. METHODS AND FINDING: The activation of dermal DCs via p38 MAPK triggered a T cell-mediated allergic immune response in this model. In the MAPK signaling cascade in DCs, Ni potently phosphorylated MAP kinase kinase 6 (MKK6 following increased DC activation. Ni-stimulated DCs could prime T cell activation to induce Ni allergy. Interestingly, when MKK6 gene-transfected DCs were transferred into the model mice, a more pronounced allergic reaction was observed. In addition, injection of short interfering (si RNA targeting the MKK6 gene protected against a hypersensitivity reaction after Ni immunization. The cooperative action between T cell activation and MKK6-mediated DC activation by Ni played an important role in the development of Ni allergy. CONCLUSIONS: DC activation by Ni played an important role in the development of Ni allergy. Manipulating the MKK6 gene in DCs may be a good therapeutic strategy for dermal Ni allergy.

  16. A novel DC therapy with manipulation of MKK6 gene on nickel allergy in mice.

    Science.gov (United States)

    Watanabe, Megumi; Ishimaru, Naozumi; Ashrin, Meinar Nur; Arakaki, Rieko; Yamada, Akiko; Ichikawa, Tetsuo; Hayashi, Yoshio

    2011-04-22

    Although the activation of dermal dendritic cells (DCs) or Langerhans cells (LCs) via p38 mitogen-activated protein kinase (MAPK) plays a crucial role in the pathogenesis of metal allergy, the in vivo molecular mechanisms have not been identified and a possible therapeutic strategy using the control of dermal DCs or LCs has not been established. In this study, we focused on dermal DCs to define the in vivo mechanisms of metal allergy pathogenesis in a mouse nickel (Ni) allergy model. The effects of DC therapy on Ni allergic responses were also investigated. The activation of dermal DCs via p38 MAPK triggered a T cell-mediated allergic immune response in this model. In the MAPK signaling cascade in DCs, Ni potently phosphorylated MAP kinase kinase 6 (MKK6) following increased DC activation. Ni-stimulated DCs could prime T cell activation to induce Ni allergy. Interestingly, when MKK6 gene-transfected DCs were transferred into the model mice, a more pronounced allergic reaction was observed. In addition, injection of short interfering (si) RNA targeting the MKK6 gene protected against a hypersensitivity reaction after Ni immunization. The cooperative action between T cell activation and MKK6-mediated DC activation by Ni played an important role in the development of Ni allergy. DC activation by Ni played an important role in the development of Ni allergy. Manipulating the MKK6 gene in DCs may be a good therapeutic strategy for dermal Ni allergy.

  17. Trajectory Planning of 7-DOF Space Manipulator for Minimizing Base Disturbance

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    2016-03-01

    Full Text Available In the free-floating mode, there is intense dynamic coupling existing between the space manipulator and the base, and the base attitude may change while performing a motion with its manipulator. Therefore, it is necessary to reduce the interference that resulted from the manipulator movement. For planning trajectories of the space manipulator with 7 degrees of freedom (7-DOF, simulated annealing particle swarm optimization (SAPSO algorithm is presented in the paper. Firstly, kinematics equations are setup. Secondly, the joint functions are parameterized by sinusoidal functions, and the objective function is defined according to the motion constraints of manipulator and accuracy requirements of the base attitude. Finally, SAPSO algorithm is used to search the optimal trajectory. The simulation results verify the proposed method.

  18. Nutrition-gene interactions (post-genomics). Changes in gene expression through nutritional manipulations

    International Nuclear Information System (INIS)

    Harper, G.S.; Lehnert, S.A.; Greenwood, P.L.

    2005-01-01

    This paper discusses the effects of severe nutritional restriction, both pre- and post-weaning, on development of skeletal muscle in food animals. Given recent predictions about growth in demand for muscle-foods in developing countries, the global community will need to face the food-feed dilemma, and balance efficiency of production against the quality-of-life aspects of local livestock husbandry. It is likely that production animals will be grown in successively more marginal environments and at higher stocking rates on unimproved pastures. Understanding the nutritional limits to animal growth at the level of muscle gene networks will help us find optima for nutrition, growth rate and meat yield. Genomic approaches give us unprecedented capacity to map the networks of control under nutritionally restricted conditions, though the challenges remain of identifying steps that regulate substrate flux. The paper describes some approaches currently being taken to understanding muscle development, and concludes that the genes contributing to two ruminant phenotypes should be mapped and characterized. These are: the capacity to depress metabolic rate in response to nutritional restriction; and the capacity to exhibit compensatory growth after restriction is relieved. (author)

  19. Design and modeling of a six DOF's MEMS-based precision manipulators

    NARCIS (Netherlands)

    Brouwer, Dannis Michel; de Jong, B.R.; Soemers, Herman

    2010-01-01

    In this paper a design is presented for a precision MEMS-based six degrees-of-freedom (DOFs) manipulator. The purpose of the manipulator is to position a small sample (10 μm × 20 μm × 0.2 μm) in a transmission electron microscope. A parallel kinematic mechanism with slanted leaf-springs is used to

  20. Graphene based gene transfection

    Science.gov (United States)

    Feng, Liangzhu; Zhang, Shuai; Liu, Zhuang

    2011-03-01

    Graphene as a star in materials research has been attracting tremendous attentions in the past few years in various fields including biomedicine. In this work, for the first time we successfully use graphene as a non-toxic nano-vehicle for efficient gene transfection. Graphene oxide (GO) is bound with cationic polymers, polyethyleneimine (PEI) with two different molecular weights at 1.2 kDa and 10 kDa, forming GO-PEI-1.2k and GO-PEG-10k complexes, respectively, both of which are stable in physiological solutions. Cellular toxicity tests reveal that our GO-PEI-10k complex exhibits significantly reduced toxicity to the treated cells compared to the bare PEI-10k polymer. The positively charged GO-PEI complexes are able to further bind with plasmid DNA (pDNA) for intracellular transfection of the enhanced green fluorescence protein (EGFP) gene in HeLa cells. While EGFP transfection with PEI-1.2k appears to be ineffective, high EGFP expression is observed using the corresponding GO-PEI-1.2k as the transfection agent. On the other hand, GO-PEI-10k shows similar EGFP transfection efficiency but lower toxicity compared with PEI-10k. Our results suggest graphene to be a novel gene delivery nano-vector with low cytotoxicity and high transfection efficiency, promising for future applications in non-viral based gene therapy.Graphene as a star in materials research has been attracting tremendous attentions in the past few years in various fields including biomedicine. In this work, for the first time we successfully use graphene as a non-toxic nano-vehicle for efficient gene transfection. Graphene oxide (GO) is bound with cationic polymers, polyethyleneimine (PEI) with two different molecular weights at 1.2 kDa and 10 kDa, forming GO-PEI-1.2k and GO-PEG-10k complexes, respectively, both of which are stable in physiological solutions. Cellular toxicity tests reveal that our GO-PEI-10k complex exhibits significantly reduced toxicity to the treated cells compared to the bare PEI

  1. Design Issues and Application of Cable-Based Parallel Manipulators for Rehabilitation Therapy

    Directory of Open Access Journals (Sweden)

    E. Ottaviano

    2008-01-01

    Full Text Available In this study, cable-based manipulators are proposed for application in rehabilitation therapies. Cable-based manipulators show good features that are very useful when the system has to interact with humans. In particular, they can be used to aid motion or as monitoring/training systems in rehabilitation therapies. Modelling and simulation of both active and passive cable-based parallel manipulators are presented for an application to help older people, patients or disabled people in the sit-to-stand transfer and as a monitoring/training system. Experimental results are presented by using built prototypes.

  2. Model-based remote handling with the MAESTRO hydraulic manipulator

    International Nuclear Information System (INIS)

    Gravez, Philippe; Leroux, C.; Irving, M.; Galbiati, L.; Raneda, A.; Siuko, M.; Maisonnier, D.; Palmer, J.D.

    2003-01-01

    A powerful hydraulic manipulator may be a useful tool to deal efficiently with the remote handling, dexterous operations required during the Divertor maintenance. Its main advantages are a good weight capacity, the large range of tasks that can be addressed and its capability to recover from unforeseen situations. On the other hand, it implies intensive video monitoring and the use of hydraulics technology that is not currently suited to nuclear environments. This paper describes the developments and experiments performed in conjunction with CEA/LIST, IHA and ENEA in the frame of task T329-5 to enhance the benefits of computer-assisted hydraulic remote operation, while minimising its shortcomings

  3. On Enzyme-Based Anticancer Molecular Dietary Manipulations

    Directory of Open Access Journals (Sweden)

    Andrea Sapone

    2012-01-01

    Full Text Available Evidence from both epidemiological and experimental observations has fuelled the belief that the high consumption of fruits and vegetables rich in nutrients and phytochemicals may help prevent cancer and heart disease in humans. This concept has been drastically simplified from the dietary approaches to the use of single bioactive components both as a single supplement or in functional foods to manipulate xenobiotic metabolism. These procedures, which aim to induce mutagen/carcinogen detoxification or inhibit their bioactivation, fail to take into account the multiple and paradoxical biological outcomes of enzyme modulators that make their effects unpredictable. Here, we show that the idea that the physiological roles of specific catalysts may be easily manipulated by regular long-term administration of isolated nutrients and other chemicals derived from food plants is not viable. In contrast, we claim that the consumption of healthy diets is most likely to reduce mutagenesis and cancer risk, and that both research endeavours and dietary recommendations should be redirected away from single molecules to dietary patterns as a main strategy for public health policy.

  4. Thermal Manipulation Mid-term Broiler Chicken Embryogenesis: Effect on Muscle Growth Factors and Muscle Marker Genes

    Directory of Open Access Journals (Sweden)

    MB Al-Zghoul

    Full Text Available ABSTRACT Thermal manipulation (TM during broiler chicken embryogenesis has been shown to promote muscle development and growth. However, the molecular bases of promoting broiler muscle development and growth are not fully understood. The aim of this study was to investigate the molecular bases of muscle growth and development in broiler chickens subjected to TM. This included the investigating of the changes in mRNA expression levels of muscle marker genes, namely MyoD, myogenin, paired box transcription factor (Pax7 and proliferating cell nuclear antigen (PCNA, and muscle growth factors namely insulin-like growth factor 1 (IGF-1, myostatin and growth hormone (GH during embryogenesis and on posthatch days 10 and 28. Fertile Cobb eggs (n=1500 were divided into four groups. Eggs in the first group (control were incubated at 37.8°C and 56% RH, whereas, eggs in the second group (TM1, third group (TM2, and fourth group (TM3 were subjected to 39 ºC and 65% RH daily during embryonic days (ED 12-18 for 9, 12, and 18 hours, respectively. Body weight (BW during embryogenesis and posthatch days (1, 3, 5, 7, 14, 21, 28 and 35 was recorded. mRNA expression levels of muscle marker genes and muscle growth factor genes during ED 12, 14, 16 and 18 and on posthatch days 10 and 28 were analyzed using real-time RT-PCR. TM upregulated the mRNA expressions of muscle marker and growth factors genes. This upregulation was accompanied by improvement of body weight near and at market age.

  5. Manipulation of MKS1 gene expression affects Kalanchoë blossfeldiana and Petunia hybrida phenotypes.

    Science.gov (United States)

    Gargul, Joanna Maria; Mibus, Heiko; Serek, Margrethe

    2015-01-01

    The establishment of alternative methods to chemical treatments for growth retardation and pathogen protection in ornamental plant production has become a major goal in recent breeding programmes. This study evaluates the effect of manipulating MAP kinase 4 nuclear substrate 1 (MKS1) expression in Kalanchoë blossfeldiana and Petunia hybrida. The Arabidopsis thaliana MKS1 gene was overexpressed in both species via Agrobacterium-mediated transformation, resulting in dwarfed phenotypes and delayed flowering in both species and increased tolerance to Pseudomonas syringae pv. tomato in transgenic Petunia plants. The lengths of the stems and internodes were decreased, while the number of nodes in the transgenic plants was similar to that of the control plants in both species. The transgenic Kalanchoë flowers had an increased anthocyanin concentration, and the length of the inflorescence stem was decreased. The morphology of transgenic Petunia flowers was not altered. The results of the Pseudomonas syringae tolerance test showed that Petunia plants with one copy of the transgene reacted similarly to the nontransgenic control plants; however, plants with four copies of the transgene exhibited considerably higher tolerance to bacterial attack. Transgene integration and expression was determined by Southern blot hybridization and RT-PCR analyses. MKS1 in wild-type Petunia plants was down-regulated through a virus-induced gene silencing (VIGS) method using tobacco rattle virus vectors. There were no significant phenotypic differences between the plants with silenced MKS1 genes and the controls. The relative concentration of the MKS1 transcript in VIGS-treated plants was estimated by quantitative RT-PCR. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  6. CRISPR/Cas9-loxP-Mediated Gene Editing as a Novel Site-Specific Genetic Manipulation Tool.

    Science.gov (United States)

    Yang, Fayu; Liu, Changbao; Chen, Ding; Tu, Mengjun; Xie, Haihua; Sun, Huihui; Ge, Xianglian; Tang, Lianchao; Li, Jin; Zheng, Jiayong; Song, Zongming; Qu, Jia; Gu, Feng

    2017-06-16

    Cre-loxP, as one of the site-specific genetic manipulation tools, offers a method to study the spatial and temporal regulation of gene expression/inactivation in order to decipher gene function. CRISPR/Cas9-mediated targeted genome engineering technologies are sparking a new revolution in biological research. Whether the traditional site-specific genetic manipulation tool and CRISPR/Cas9 could be combined to create a novel genetic tool for highly specific gene editing is not clear. Here, we successfully generated a CRISPR/Cas9-loxP system to perform gene editing in human cells, providing the proof of principle that these two technologies can be used together for the first time. We also showed that distinct non-homologous end-joining (NHEJ) patterns from CRISPR/Cas9-mediated gene editing of the targeting sequence locates at the level of plasmids (episomal) and chromosomes. Specially, the CRISPR/Cas9-mediated NHEJ pattern in the nuclear genome favors deletions (64%-68% at the human AAVS1 locus versus 4%-28% plasmid DNA). CRISPR/Cas9-loxP, a novel site-specific genetic manipulation tool, offers a platform for the dissection of gene function and molecular insights into DNA-repair pathways. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  7. MEMS-based platforms for mechanical manipulation and characterization of cells

    Science.gov (United States)

    Pan, Peng; Wang, Wenhui; Ru, Changhai; Sun, Yu; Liu, Xinyu

    2017-12-01

    Mechanical manipulation and characterization of single cells are important experimental techniques in biological and medical research. Because of the microscale sizes and highly fragile structures of cells, conventional cell manipulation and characterization techniques are not accurate and/or efficient enough or even cannot meet the more and more demanding needs in different types of cell-based studies. To this end, novel microelectromechanical systems (MEMS)-based technologies have been developed to improve the accuracy, efficiency, and consistency of various cell manipulation and characterization tasks, and enable new types of cell research. This article summarizes existing MEMS-based platforms developed for cell mechanical manipulation and characterization, highlights their specific design considerations making them suitable for their designated tasks, and discuss their advantages and limitations. In closing, an outlook into future trends is also provided.

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

    International Nuclear Information System (INIS)

    Furuta, Katsuhisa; Kosuge, Kazuhiro; Shiote, Yoshinori; Hatano, Hiromu.

    1988-01-01

    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)

  9. Manipulator inverse kinematics control based on particle swarm optimization neural network

    Science.gov (United States)

    Wen, Xiulan; Sheng, Danghong; Guo, Jing

    2008-10-01

    The inverse kinematics control of a robotic manipulator requires solving non-linear equations having transcendental functions and involving time-consuming calculations. Particle Swarm Optimization (PSO), which is based on the behaviour of insect swarms and exploits the solution space by taking into account the experience of the single particle as well as that of the entire swarm, is similar to the genetic algorithm (GA) in that it performs a structured randomized search of an unknown parameter space by manipulating a population of parameter estimates to converge on a suitable solution. In this paper, PSO is firstly proposed to optimize feed-forward neural network for manipulator inverse kinematics. Compared with the results of the fast back propagation learning algorithm (FBP), conventional GA genetic algorithm based elitist reservation (EGA), improved GA (IGA) and immune evolutionary computation (IEC), the simulation results verify the particle swarm optimization neural network (PSONN) is effective for manipulator inverse kinematics control.

  10. Kinematics and dynamics Hessian matrices of manipulators based on screw theory

    Science.gov (United States)

    Zhao, Tieshi; Geng, Mingchao; Chen, Yuhang; Li, Erwei; Yang, Jiantao

    2015-03-01

    The complexity of the kinematics and dynamics of a manipulator makes it necessary to simplify the modeling process. However, the traditional representations cannot achieve this because of the absence of coordinate invariance. Therefore, the coordinate invariant method is an important research issue. First, the rigid-body acceleration, the time derivative of the twist, is proved to be a screw, and its physical meaning is explained. Based on the twist and the rigid-body acceleration, the acceleration of the end-effector is expressed as a linear-bilinear form, and the kinematics Hessian matrix of the manipulator(represented by Lie bracket) is deduced. Further, Newton-Euler's equation is rewritten as a linear-bilinear form, from which the dynamics Hessian matrix of a rigid body is obtained. The formulae and the dynamics Hessian matrix are proved to be coordinate invariant. Referring to the principle of virtual work, the dynamics Hessian matrix of the parallel manipulator is gotten and the detailed dynamic model is derived. An index of dynamical coupling based on dynamics Hessian matrix is presented. In the end, a foldable parallel manipulator is taken as an example to validate the deduced kinematics and dynamics formulae. The screw theory based method can simplify the kinematics and dynamics of a manipulator, also the corresponding dynamics Hessian matrix can be used to evaluate the dynamical coupling of a manipulator.

  11. Structure Comparison and Optimal Design of 6-RUS Parallel Manipulator Based on Kinematic and Dynamic Performances

    Directory of Open Access Journals (Sweden)

    Erfan Mirshekari

    Full Text Available Abstract The effects of distinctive parameters such as revolute joint angle or spherical joint location of mobile platform in a 6-DOF 6-RUS parallel manipulators on workspace, kinematic, and dynamic indices are investigated in this study to select proper structure commensurate with performance. Intelligent multi-objective optimization method is used to design the manipulator. Considering distinctive parameters, relevant relations for developing inverse kinematic and Jacobin matrix are obtained. In order to study dynamic properties, mass matrix is obtained from calculating the total kinetic energy of the manipulator. After modifying multi-objective Bees algorithm, it used to optimize the manipulator structure considering all geometrical parameters with proper constraints. In addition of comparison of three well known 6-RUS manipulators' types, variation diagram of workspace, local and global dynamics and kinematics performance indices have been drawn with respect to structural parameters variation and limitation of these parameters with proper value are determined. Moreover, considering all dimensional parameters, Pareto front line of multi objective optimization of structure is presented based on dynamic and kinematic performance in pre-determined workspace. Based on the results, a fairly comparison among various types of 6-RUS manipulators can be conducted and the most appropriate set of dimensional parameters are selected based on specific demand.

  12. Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio).

    Science.gov (United States)

    Robison, Barrie D; Drew, Robert E; Murdoch, Gordon K; Powell, Madison; Rodnick, Kenneth J; Settles, Matt; Stone, David; Churchill, Erin; Hill, Rodney A; Papasani, Madhusudhan R; Lewis, Solange S; Hardy, Ronald W

    2008-06-01

    In this study, we tested for the presence of sexual dimorphism in the hepatic transcriptome of the adult zebrafish and examined the effect of long term manipulation of dietary carbohydrate on gene expression in both sexes. Zebrafish were fed diets comprised of 0%, 15%, 25%, or 35% carbohydrate from the larval stage through sexual maturity, then sampled for hepatic tissue, growth, proximate body composition, and retention efficiencies. Using Affymetrix microarrays and qRT-PCR, we observed substantial sexual dimorphism in the hepatic transcriptome. Males up-regulated genes associated with oxidative metabolism, carbohydrate metabolism, energy production, and amelioration of oxidative stress, while females had higher expression levels of genes associated with translation. Restriction of dietary carbohydrate (0% diet) significantly affected hepatic gene expression, growth performance, retention efficiencies of protein and energy, and percentages of moisture, lipid, and ash. The response of some genes to dietary manipulation varied by sex; with increased dietary carbohydrate, males up-regulated genes associated with oxidative metabolism (e.g. hadhbeta) while females up-regulated genes associated with glucose phosphorylation (e.g. glucokinase). Our data support the use of the zebrafish model for the study of fish nutritional genomics, but highlight the importance of accounting for sexual dimorphism in these studies.

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

    Directory of Open Access Journals (Sweden)

    M. Díaz-Rodríguez

    2016-01-01

    Full Text Available 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 dynamic model of parallel manipulators, this paper compares three different methods for inverse dynamic modelling of a general, lower mobility, 3-PRS parallel manipulator. The first method obtains the inverse dynamic model by describing the manipulator as three open kinematic chains. Then, vector-loop closure constraints are introduced for obtaining the relationship between the dynamics of the open kinematic chains (such as a serial robot and the closed chains (such as a parallel robot. The second method exploits certain characteristics of parallel manipulators such that the platform and the links are considered as independent subsystems. The proposed third method is similar to the second method but it uses a different Jacobian matrix formulation in order to reduce computational complexity. Analysis of these numerical formulations will provide fundamental software support for efficient model-based designs. In addition, computational cost reduction presented in this paper can also be an effective guideline for optimal design of this type of manipulator and for real-time embedded control.

  14. Power-Based Setpoint Control : Experimental Results on a Planar Manipulator

    NARCIS (Netherlands)

    Dirksz, D. A.; Scherpen, J. M. A.

    In the last years the power-based modeling framework, developed in the sixties to model nonlinear electrical RLC networks, has been extended for modeling and control of a larger class of physical systems. In this brief we apply power-based integral control to a planar manipulator experimental setup.

  15. Enriching Project-Based Learning Environments with Virtual Manipulatives: A Comparative Study

    Science.gov (United States)

    Çakiroglu, Ünal

    2014-01-01

    Problem statement: Although there is agreement on the potential of project based learning (PBL) and virtual manipulatives (VMs), their positive impact depends on how they are used. This study was based on supporting the use of online PBL environments and improving the efficacy of the instructional practices in PBL by combining the potentials of…

  16. An XML-Based Manipulation and Query Language for Rule-Based Information

    Science.gov (United States)

    Mansour, Essam; Höpfner, Hagen

    Rules are utilized to assist in the monitoring process that is required in activities, such as disease management and customer relationship management. These rules are specified according to the application best practices. Most of research efforts emphasize on the specification and execution of these rules. Few research efforts focus on managing these rules as one object that has a management life-cycle. This paper presents our manipulation and query language that is developed to facilitate the maintenance of this object during its life-cycle and to query the information contained in this object. This language is based on an XML-based model. Furthermore, we evaluate the model and language using a prototype system applied to a clinical case study.

  17. CRISPR-based technologies for the manipulation of eukaryotic genomes

    Science.gov (United States)

    Komor, Alexis C.; Badran, Ahmed H.; Liu, David R.

    2016-01-01

    The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this review we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and some of the remarkable advancements in basic research, biotechnology, and therapeutics development that these developments have facilitated. PMID:27866654

  18. Two-Link Flexible Manipulator Control Using Sliding Mode Control Based Linear Matrix Inequality

    Science.gov (United States)

    Zulfatman; Marzuki, Mohammad; Alif Mardiyah, Nur

    2017-04-01

    Two-link flexible manipulator is a manipulator robot which at least one of its arms is made of lightweight material and not rigid. Flexible robot manipulator has some advantages over the rigid robot manipulator, such as lighter, requires less power and costs, and to result greater payload. However, suitable control algorithm to maintain the two-link flexible robot manipulator in accurate positioning is very challenging. In this study, sliding mode control (SMC) was employed as robust control algorithm due to its insensitivity on the system parameter variations and the presence of disturbances when the system states are sliding on a sliding surface. SMC algorithm was combined with linear matrix inequality (LMI), which aims to reduce the effects of chattering coming from the oscillation of the state during sliding on the sliding surface. Stability of the control algorithm is guaranteed by Lyapunov function candidate. Based on simulation works, SMC based LMI resulted in better performance improvements despite the disturbances with significant chattering reduction. This was evident from the decline of the sum of squared tracking error (SSTE) and the sum of squared of control input (SSCI) indexes respectively 25.4% and 19.4%.

  19. Investigation of geometrical effects in the carbon allotropes manipulation based on AFM: multiscale approach

    Energy Technology Data Exchange (ETDEWEB)

    Korayem, M. H., E-mail: hkorayem@iust.ac.ir; Hefzabad, R. N.; Homayooni, A.; Aslani, H. [Iran University of Science and Technology, Robotic Research Laboratory, Center of Excellence in Experimental Solid Mechanics and Dynamics, School of Mechanical Engineering (Iran, Islamic Republic of)

    2017-01-15

    Carbon allotropes are used as nanocarriers for drug and cell delivery. To obtain an accurate result in the nanoscale, it is important to use a precise model. In this paper, a multiscale approach is presented to investigate the manipulation process of carbon allotropes based on atomic force microscopy (AFM). For this purpose, the AFM setup is separated into two parts with different sizes as macro field (MF) and nano field (NF). Using Kirchhoff’s plate model, the cantilever (the main part of MF) is modeled. The molecular dynamics method is applied to model the NF part, and then the MF and NF are coupled with the multiscale algorithm. With this model, by considering the effect of size and shape, the manipulation of carbon allotropes is carried out. The manipulations of armchair CNTs and fullerenes are performed to study the diameter changing effects. The result shows that the manipulation and friction force increases by increasing the diameter. The result of the indentation depth for the armchair CNTs indicates that decreasing the diameter causes the indentation depth to reduce. Moreover, the manipulations of four kinds of carbon allotropes with the same number of atoms have been studied to investigate the geometrical effects. The shapes of these nanoparticles change from sphere to cylinder. The results illustrate that the manipulation and the friction force decrease as the nanoparticle shape varies from sphere to cylinder. The Von-Mises results demonstrate that by changing the nanoparticle shape from the spherical to the cylindrical form, the stress increases, although the manipulation force reduces.

  20. Investigation of geometrical effects in the carbon allotropes manipulation based on AFM: multiscale approach

    International Nuclear Information System (INIS)

    Korayem, M. H.; Hefzabad, R. N.; Homayooni, A.; Aslani, H.

    2017-01-01

    Carbon allotropes are used as nanocarriers for drug and cell delivery. To obtain an accurate result in the nanoscale, it is important to use a precise model. In this paper, a multiscale approach is presented to investigate the manipulation process of carbon allotropes based on atomic force microscopy (AFM). For this purpose, the AFM setup is separated into two parts with different sizes as macro field (MF) and nano field (NF). Using Kirchhoff’s plate model, the cantilever (the main part of MF) is modeled. The molecular dynamics method is applied to model the NF part, and then the MF and NF are coupled with the multiscale algorithm. With this model, by considering the effect of size and shape, the manipulation of carbon allotropes is carried out. The manipulations of armchair CNTs and fullerenes are performed to study the diameter changing effects. The result shows that the manipulation and friction force increases by increasing the diameter. The result of the indentation depth for the armchair CNTs indicates that decreasing the diameter causes the indentation depth to reduce. Moreover, the manipulations of four kinds of carbon allotropes with the same number of atoms have been studied to investigate the geometrical effects. The shapes of these nanoparticles change from sphere to cylinder. The results illustrate that the manipulation and the friction force decrease as the nanoparticle shape varies from sphere to cylinder. The Von-Mises results demonstrate that by changing the nanoparticle shape from the spherical to the cylindrical form, the stress increases, although the manipulation force reduces.

  1. Inertial measurement unit–based iterative pose compensation algorithm for low-cost modular manipulator

    Directory of Open Access Journals (Sweden)

    Yunhan Lin

    2016-01-01

    Full Text Available It is a necessary mean to realize the accurate motion control of the manipulator which uses end-effector pose correction method and compensation method. In this article, first, we established the kinematic model and error model of the modular manipulator (WUST-ARM, and then we discussed the measurement methods and precision of the inertial measurement unit sensor. The inertial measurement unit sensor is mounted on the end-effector of modular manipulator, to get the real-time pose of the end-effector. At last, a new inertial measurement unit–based iterative pose compensation algorithm is proposed. By applying this algorithm in the pose compensation experiment of modular manipulator which is composed of low-cost rotation joints, the results show that the inertial measurement unit can obtain a higher precision when in static state; it will accurately feedback to the control system with an accurate error compensation angle after a brief delay when the end-effector moves to the target point, and after compensation, the precision errors of roll angle, pitch angle, and yaw angle are reached at 0.05°, 0.01°, and 0.27° respectively. It proves that this low-cost method provides a new solution to improve the end-effector pose of low-cost modular manipulator.

  2. Optimum selection of mechanism type for heavy manipulators based on particle swarm optimization method

    Science.gov (United States)

    Zhao, Yong; Chen, Genliang; Wang, Hao; Lin, Zhongqin

    2013-07-01

    The mechanism type plays a decisive role in the mechanical performance of robotic manipulators. Feasible mechanism types can be obtained by applying appropriate type synthesis theory, but there is still a lack of effective and efficient methods for the optimum selection among different types of mechanism candidates. This paper presents a new strategy for the purpose of optimum mechanism type selection based on the modified particle swarm optimization method. The concept of sub-swarm is introduced to represent the different mechanisms generated by the type synthesis, and a competitive mechanism is employed between the sub-swarms to reassign their population size according to the relative performances of the mechanism candidates to implement the optimization. Combining with a modular modeling approach for fast calculation of the performance index of the potential candidates, the proposed method is applied to determine the optimum mechanism type among the potential candidates for the desired manipulator. The effectiveness and efficiency of the proposed method is demonstrated through a case study on the optimum selection of mechanism type of a heavy manipulator where six feasible candidates are considered with force capability as the specific performance index. The optimization result shows that the fitness of the optimum mechanism type for the considered heavy manipulator can be up to 0.578 5. This research provides the instruction in optimum selection of mechanism types for robotic manipulators.

  3. 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.

  4. Dimension Synthesis of a Spatial Parallel Kinematic Manipulator Based on S-shaped Test Specimen

    Directory of Open Access Journals (Sweden)

    Liu Yuzhe

    2017-01-01

    Full Text Available With the development of the aerospace industry, the hybrid machine tool for machining the complicated curved surface is becoming a research hotspot. The S-shaped test specimen proposed by Chengdu Aircraft Industrial Company is an effective test method to verify the ability of machining the complicated curved surface for a machine tool. Considering the spatial parallel kinematic manipulator in a hybrid machine tool provides the complicated orientation motion and its design of structure dimension affects the accuracy of the machine tool, this paper investigates the issue about dimension synthesis of the manipulator based on S-shaped test specimen. By establishing models of the S-shaped test specimen and parallel kinematic manipulator, the motion trajectory of the parallel kinematic manipulator for machining S-shaped test specimen is obtained. According to the motion trajectory and expected performance indices, the result of dimension synthesis for the manipulator is plotted and a set of suitable dimensions is achieved. With the analysis result in this paper, it is helpful to improving the accuracy of machining the S-shaped test specimen.

  5. Novel PID Tracking Controller for 2DOF Robotic Manipulator System Based on Artificial Bee Colony Algorithm

    Directory of Open Access Journals (Sweden)

    Elkhateeb Nasr A.

    2017-12-01

    Full Text Available This study presents a well-developed optimization methodology based on the dynamic inertia weight Artificial Bee Colony algorithm (ABC to design an optimal PID controller for a robotic arm manipulator. The dynamical analysis of robotic arm manipulators investigates a coupling relation between the joint torques applied by the actuators and the position and acceleration of the robot arm. An optimal PID control law is obtained from the proposed (ABC algorithm and applied to the robotic system. The designed controller optimizes the trajectory of the robot’s end effector for a time-variant input and makes the robot robust in the presence of external disturbance.

  6. Sliding Mode Tracking Control of Manipulator Based on the Improved Reaching Law

    Directory of Open Access Journals (Sweden)

    Wei-Na ZHAI

    2013-04-01

    Full Text Available Due to the mechanical hand often have serious uncertainty, as the state in which the different and external changes, also its parameters are changing, this is very adverse to achieve precise control. In this paper, the traditional sliding mode variable structure was improved, the sign function is replaced by saturated function based on the double power reaching law, by adjusting the values of e1, e2, a, b, g and k to effectively improve the manipulator joint reaching speed, track expected trajectory fast and shorten the system response time. Finally, the method is used for simulation of manipulator trajectory tracking, compared to two reaching law control algorithms. The simulation results show that the control algorithm has good dynamic performance, which can effectively restrain the chattering and quickly track the desired trajectory. Therefore, the improved reaching law can effectively improve the performance of robotic manipulator.

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

    International Nuclear Information System (INIS)

    Paredes-Madrid, L; Gonzalez de Santos, P

    2013-01-01

    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)

  8. 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.

  9. 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…

  10. Design and modeling of a precision 6 DOF MEMS-based parallel kinematic TEM sample manipulator

    NARCIS (Netherlands)

    Brouwer, Dannis Michel; de Jong, B.R.; Soemers, Herman

    2006-01-01

    A design for a 6 Degree-of-freedom precision MEMS-based manipulator for a TEM will is presented. The elastic mechanism is designed and modeled with the specific design considerations regarding kinematic constraint design and elastic energy storage. The typical relatively large deformations of

  11. Kinematic Calibration of a Six DOF Flexure-based Parallel Manipulator

    NARCIS (Netherlands)

    Timmer Arends, J.H.; Voss, K.H.J.; Hakvoort, W.K.; Aarts, R.G.K.M.

    2017-01-01

    The absence of friction, hysteresis and backlash makes flexure-based mechanisms well-suited for high precision manipulators. However, the (inverse) kinematic relation between actuators and end-effector is far from trivial due to the non-linear behaviour of the deforming compliant joints. In this

  12. Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation

    NARCIS (Netherlands)

    de Bekker, Charissa; Ohm, Robin A; Loreto, Raquel G; Sebastian, Aswathy; Albert, Istvan; Merrow, Martha; Brachmann, Andreas; Hughes, David P

    2015-01-01

    BACKGROUND: Adaptive manipulation of animal behavior by parasites functions to increase parasite transmission through changes in host behavior. These changes can range from slight alterations in existing behaviors of the host to the establishment of wholly novel behaviors. The biting behavior

  13. 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.

  14. Vector magnetometer based on synchronous manipulation of nitrogen-vacancy centers in all crystal directions

    Science.gov (United States)

    Zhang, Chen; Yuan, Heng; Zhang, Ning; Xu, Lixia; Zhang, Jixing; Li, Bo; Fang, Jiancheng

    2018-04-01

    Negatively charged nitrogen vacancy (NV‑) centers in diamond have been extensively studied as high-sensitivity magnetometers, showcasing a wide range of applications. This study experimentally demonstrates a vector magnetometry scheme based on synchronous manipulation of NV‑ center ensembles in all crystal directions using double frequency microwaves (MWs) and multi-coupled-strip-lines (mCSL) waveguide. The application of the mCSL waveguide ensures a high degree of synchrony (99%) for manipulating NV‑ centers in multiple orientations in a large volume. Manipulation with double frequency MWs makes NV‑ centers of all four crystal directions involved, and additionally leads to an enhancement of the manipulation field. In this work, by monitoring the changes in the slope of the resonance line consisting of multi-axes NV‑ centers, measurement of the direction of the external field vector was demonstrated with a sensitivity of {{10}\\prime}/\\sqrt{Hz} . Based on the scheme, the fluorescence signal contrast was improved by four times higher and the sensitivity to the magnetic field strength was improved by two times. The method provides a more practical way of achieving vector sensors based on NV‑ center ensembles in diamond.

  15. 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.

  16. A systematic meta-review of manipulative and body-based CAM for cancer

    DEFF Research Database (Denmark)

    Lunde, Anita; Johannessen, Helle

    another review warns against the use of massage for fragile patients. Conclusion: There is fairly good evidence that massage can help to reduce stress and anxiety in cancer patients if it is provided by well qualified practitioners. Massage can safely be combined with conventional cancer treatment......  Background: There is a need for high-level evidence on the effects of CAM for cancer. 36% of European cancer patients have used CAM, and CAM is increasing integrated in oncology without a firm evidence base. This presentation provides a meta review of effects of manipulative and body......-based complementary medicine for cancer. Methods: Pubmed, the Cochrane library, AMED and Science citation index were systematically searched for reviews of quantitative and qualitative studies on effects of CAM for cancer or cancer related systems published 2000-2007. All reviews on manipulative and body-based CAM...

  17. 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.

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

    International Nuclear Information System (INIS)

    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

  19. CircleBoard-Pro: Concrete manipulative-based learning cycle unit for learning geometry

    Science.gov (United States)

    Jamhari, Wongkia, Wararat

    2018-01-01

    Currently, a manipulative is commonly used in mathematics education as a supported tool for teaching and learning. With engaging natural interaction of a concrete manipulative and advantages of a learning cycle approach, we proposed the concrete manipulative-based learning cycle unit to promote mathematics learning. Our main objectives are to observe possibilities on the use of a concrete manipulative in learning geometry, and to assess students' understanding of a specific topic, angle properties in a circle, of secondary level students. To meet the first objective, the concrete manipulative, called CricleBoard-Pro, was designed. CircleBoard-Pro is built for easy to writing on or deleting from, accurate angle measurement, and flexible movement. Besides, learning activities and worksheets were created for helping students to learn angle properties in a circle. Twenty eighth graders on a lower secondary school in Indonesia were voluntarily involved to learn mathematics using CircleBoard-Pro with the designed learning activities and worksheets. We informally observed students' performance by focusing on criteria of using manipulative tools in learning mathematics while the learning activities were also observed in terms of whether they work and which step of activities need to be improved. The results of this part showed that CircleBoard-Pro complied the criteria of the use of the manipulative in learning mathematics. Nevertheless, parts of learning activities and worksheets need to be improved. Based on the results of the observation, CircleBoard-Pro, learning activities, and worksheets were merged together and became the CircleBoardPro embedded on 5E (Engage - Explore - Explain - Elaborate - Evaluate) learning cycle unit. Then, students understanding were assessed to reach the second objective. Six ninth graders from an Indonesian school in Thailand were recruited to participate in this study. Conceptual tests for both pre-and post-test, and semi

  20. [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.

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

    Science.gov (United States)

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

    2015-05-06

    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.

  2. Development of a Web-Enabled Informatics Platform for Manipulation of Gene Expression Data

    National Research Council Canada - National Science Library

    Peel, Sheila A; Kopydlowski, Karen; Carel, Roland

    2004-01-01

    High-throughput gene expression technologies such as Affymetrix and De Novo 2-Color Microarrays generate large scale measurements that require sophisticated bioinformatic platforms for data archival...

  3. 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.

  4. Manipulation of biliary lipids by gene therapy: potential consequences for patients with progressive familial intrahepatic cholestasis

    NARCIS (Netherlands)

    Oude Elferink, Ronald P. J.

    2005-01-01

    Gene therapy constitutes a great promise for the treatment of inherited diseases as well as cancer. Although the principle is extremely elegant, reality proves that several important problems remain to be solved before gene therapy becomes a standard application for these conditions. Meanwhile, and

  5. 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.

  6. PSO based neuro fuzzy sliding mode control for a robot manipulator

    Directory of Open Access Journals (Sweden)

    M. Vijay

    2017-05-01

    Full Text Available This paper presents the control strategy of two degrees of freedom (2DOF rigid robot manipulator based on the coupling of artificial neuro fuzzy inference system (ANFIS with sliding mode control (SMC. Initially SMC with proportional integral derivative (PID sliding surface is adapted to control the robot manipulator. The parameters of the sliding surface are obtained by minimizing a quadratic performance indices using particle swarm optimization (PSO. Variations of SMC i.e. boundary sliding mode control (BSMC and boundary sliding mode control with PID sliding surface (PIDBSMC are developed for optimized performance index. Finally an ANFIS adaptive controller is proposed to generate the adaptive control signal and found to be more robust with regard to disturbances in input torque.

  7. DNA manipulation by means of insulator-based dielectrophoresis employing direct current electric fields.

    Science.gov (United States)

    Gallo-Villanueva, Roberto C; Rodríguez-López, Carlos E; Díaz-de-la-Garza, Rocío I; Reyes-Betanzo, Claudia; Lapizco-Encinas, Blanca H

    2009-12-01

    Electrokinetic techniques offer a great potential for biological particle manipulation. Among these, dielectrophoresis (DEP) has been successfully utilized for the concentration of bioparticles. Traditionally, DEP is performed employing microelectrodes, an approach with attractive characteristics but expensive due to microelectrode fabrication costs. An alternative is insulator-based DEP, a method where non-uniform electric fields are created with arrays of insulating structures. This study presents the concentration of linear DNA particles (pET28b) employing a microchannel, with an array of cylindrical insulating structures and direct current electric fields. Results showed manipulation of DNA particles with a combination of electroosmotic, electrophoretic, and dielectrophoretic forces. Employing suspending media with conductivity of 104 muS/cm and pH of 11.15, under applied fields between 500 and 1500 V/cm, DNA particles were observed to be immobilized due to negative dielectrophoretic trapping. The observation of DNA aggregates that occurred at higher applied fields, and dispersed once the field was removed is also included. Finally, concentration factors varying from 8 to 24 times the feed concentration were measured at 2000 V/cm after concentration time-periods of 20-40 s. The results presented here demonstrate the potential of insulator-based DEP for DNA concentration, and open the possibility for fast DNA manipulation for laboratory and large-scale applications.

  8. Improvement of a Robotic Manipulator Model Based on Multivariate Residual Modeling

    Directory of Open Access Journals (Sweden)

    Serge Gale

    2017-07-01

    Full Text Available A new method is presented for extending a dynamic model of a six degrees of freedom robotic manipulator. A non-linear multivariate calibration of input–output training data from several typical motion trajectories is carried out with the aim of predicting the model systematic output error at time (t + 1 from known input reference up till and including time (t. A new partial least squares regression (PLSR based method, nominal PLSR with interactions was developed and used to handle, unmodelled non-linearities. The performance of the new method is compared with least squares (LS. Different cross-validation schemes were compared in order to assess the sampling of the state space based on conventional trajectories. The method developed in the paper can be used as fault monitoring mechanism and early warning system for sensor failure. The results show that the suggested methods improves trajectory tracking performance of the robotic manipulator by extending the initial dynamic model of the manipulator.

  9. Design principles for six degrees-of-freedom MEMS-based precision manipulators

    NARCIS (Netherlands)

    Brouwer, Dannis Michel

    2007-01-01

    In the future, the precision manipulation of small objects will become more and more important for appliances such as data storage, micro assembly, sample manipulation in microscopes, cell manipulation, and manipulation of beam paths by micro mirrors. At the same time, there is a drive towards

  10. Generation of Elf5-Cre knockin mouse strain for trophoblast-specific gene manipulation.

    Science.gov (United States)

    Kong, Shuangbo; Liang, Guixian; Tu, Zhaowei; Chen, Dunjin; Wang, Haibin; Lu, Jinhua

    2018-04-01

    Placental development is a complex and highly controlled process during which trophoblast stem cells differentiate to various trophoblast subtypes. The early embryonic death of systemic gene knockout models hampers the investigation of these genes that might play important roles during placentation. A trophoblast specific Cre mouse model would be of great help for dissecting out the potential roles of these genes during placental development. For this purpose, we generate a transgenic mouse with the Cre recombinase inserted into the endogenous locus of Elf5 gene that is expressed specifically in placental trophoblast cells. To analyze the specificity and efficiency of Cre recombinase activity in Elf5-Cre mice, we mated Elf5-Cre mice with Rosa26 mT/mG reporter mice, and found that Elf5-Cre transgene is expressed specifically in the trophoectoderm as early as embryonic day 4.5 (E4.5). By E12.5, the activity of Elf5-Cre transgene was detected exclusively in all derivatives of trophoblast lineages, including spongiotrophoblast, giant cells, and labyrinth trophoblasts. In addition, Elf5-Cre transgene was also active during spermatogenesis, from spermatids to mature sperms, which is consistent with the endogenous Elf5 expression in testis. Collectively, our results provide a unique tool to delete specific genes selectively and efficiently in trophoblast lineage during placentation. © 2018 Wiley Periodicals, Inc.

  11. Admittance Control of a Multi-Finger Arm Based on Manipulability of Fingers

    Directory of Open Access Journals (Sweden)

    Takayuki Hori

    2011-09-01

    Full Text Available In the previous studies, admittance control and impedance control for a finger‐arm robot using the manipulability of the finger were studied and methods of realizing the controls have been proposed. In this study, two 3‐DOF fingers are attached to the end‐effector of a 6‐DOF arm to configure a multi‐finger arm robot. Based on the previous methods, the authors have proposed an admittance control for a multi‐finger arm robot using the manipulability of the fingers in this study. Algorithms of the averaging method and the mini‐max method were introduced to establish a manipulability criterion of the two fingers in order to generate a cooperative movement of the arm. Comparison of the admittance controls combined with the top search method and local optimization method for the multi‐finger arm robot was made and features of the control methods were also discussed. The stiffness control and damping control were experimentally evaluated to demonstrate the effectiveness of the proposed methods.

  12. Admittance Control of a Multi-Finger Arm Based on Manipulability of Fingers

    Directory of Open Access Journals (Sweden)

    Jian Huang

    2011-09-01

    Full Text Available In the previous studies, admittance control and impedance control for a finger-arm robot using the manipulability of the finger were studied and methods of realizing the controls have been proposed. In this study, two 3-DOF fingers are attached to the end-effector of a 6-DOF arm to configure a multi-finger arm robot. Based on the previous methods, the authors have proposed an admittance control for a multi-finger arm robot using the manipulability of the fingers in this study. Algorithms of the averaging method and the mini-max method were introduced to establish a manipulability criterion of the two fingers in order to generate a cooperative movement of the arm. Comparison of the admittance controls combined with the top search method and local optimization method for the multi-finger arm robot was made and features of the control methods were also discussed. The stiffness control and damping control were experimentally evaluated to demonstrate the effectiveness of the proposed methods.

  13. DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.

    Science.gov (United States)

    Hendriks, Bart S; Espelin, Christopher W

    2010-02-01

    DataPflex is a MATLAB-based application that facilitates the manipulation and visualization of multidimensional datasets. The strength of DataPflex lies in the intuitive graphical user interface for the efficient incorporation, manipulation and visualization of high-dimensional data that can be generated by multiplexed protein measurement platforms including, but not limited to Luminex or Meso-Scale Discovery. Such data can generally be represented in the form of multidimensional datasets [for example (time x stimulation x inhibitor x inhibitor concentration x cell type x measurement)]. For cases where measurements are made in a combinational fashion across multiple dimensions, there is a need for a tool to efficiently manipulate and reorganize such data for visualization. DataPflex accepts data consisting of up to five arbitrary dimensions in addition to a measurement dimension. Data are imported from a simple .xls format and can be exported to MATLAB or .xls. Data dimensions can be reordered, subdivided, merged, normalized and visualized in the form of collections of line graphs, bar graphs, surface plots, heatmaps, IC50's and other custom plots. Open source implementation in MATLAB enables easy extension for custom plotting routines and integration with more sophisticated analysis tools. DataPflex is distributed under the GPL license (http://www.gnu.org/licenses/) together with documentation, source code and sample data files at: http://code.google.com/p/datapflex. Supplementary data available at Bioinformatics online.

  14. 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.

  15. 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...

  16. 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.

  17. Bidirectional manipulation of gene expression in adipocytes using CRISPRa and siRNA

    DEFF Research Database (Denmark)

    Lundh, Morten; Pluciñska, Kaja; Isidor, Marie S

    2017-01-01

    fold); this induction was long lasting and sufficient to promote adipogenesis. Furthermore, co-activation of Pparγ2 with either Prdm16 or Zfp423 transcripts drove distinct thermogenic gene expression patterns associated with increased or decreased oxygen consumption, respectively, mimicking typical...

  18. Bacillus subtilis genome vector-based complete manipulation and reconstruction of genomic DNA for mouse transgenesis.

    Science.gov (United States)

    Iwata, Tetsuo; Kaneko, Shinya; Shiwa, Yuh; Enomoto, Takayuki; Yoshikawa, Hirofumi; Hirota, Junji

    2013-05-03

    The Bacillus subtilis genome (BGM) vector is a novel cloning system for large DNA fragments, in which the entire 4.2 Mb genome of B. subtilis functions as a vector. The BGM vector system has several attractive properties, such as a large cloning capacity of over 3 Mb, stable propagation of cloned DNA and various modification strategies using RecA-mediated homologous recombination. However, genetic modifications using the BGM vector system have not been fully established, and this system has not been applied to transgenesis. In this study, we developed important additions to the genetic modification methods of the BGM vector system. To explore the potential of the BGM vector, we focused on the fish-like odorant receptor (class I OR) gene family, which consists of 158 genes and forms a single gene cluster. Although a cis-acting locus control region is expected to regulate transcription, this has not yet been determined experimentally. Using two contiguous bacterial artificial chromosome clones containing several class I OR genes, we constructed two transgenes in the BGM vector by inserting a reporter gene cassette into one class I OR gene. Because they were oriented in opposite directions, we performed an inversion modification to align their orientation and then fused them to enlarge the genomic structure. DNA sequencing revealed that no mutations occurred during gene manipulations with the BGM vector. We further demonstrated that the modified, reconstructed genomic DNA fragments could be used to generate transgenic mice. Transgenic mice carrying the enlarged transgene recapitulated the expression and axonal projection patterns of the target class I OR gene in the main olfactory system. We offer a complete genetic modification method for the BGM vector system, including insertion, deletion, inversion and fusion, to engineer genomic DNA fragments without any trace of modifications. In addition, we demonstrate that this system can be used for mouse transgenesis. Thus

  19. Interactive Web-based e-learning for Studying Flexible Manipulator Systems

    Directory of Open Access Journals (Sweden)

    Abul K. M. Azad

    2008-03-01

    Full Text Available Abstract— This paper presents a web-based e-leaning facility for simulation, modeling, and control of flexible manipulator systems. The simulation and modeling part includes finite difference and finite element simulations along with neural network and genetic algorithm based modeling strategies for flexible manipulator systems. The controller part constitutes a number of open-loop and closed-loop designs. Closed loop control designs include the classical, adaptive, and neuro-model based strategies. Matlab software package and its associated toolboxes are used to implement these. The Matlab web server is used as the gateway between the facility and web-access. ASP.NET technology and SQL database are utilized to develop web applications for access control, user account and password maintenance, administrative management, and facility utilization monitoring. The reported facility provides a flexible but effective approach of web-based interactive e-learning facility of an engineering system. This can be extended to incorporate additional engineering systems within the e-learning framework.

  20. 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.

  1. A vision-based end-point control for a two-link flexible manipulator

    Science.gov (United States)

    Obergfell, Klaus

    1991-08-01

    The measurement and control of the end-effector position of a large two-link flexible manipulator are investigated. The system implementation is described and an initial algorithm for static end-point positioning is discussed. Most existing robots are controlled through independent joint controllers, while the end-effector position is estimated from the joint positions using a kinematic relation. End-point position feedback can be used to compensate for uncertainty and structural deflections. Such feedback is especially important for flexible robots. Computer vision is utilized to obtain end-point position measurements. A look-and-move control structure alleviates the disadvantages of the slow and variable computer vision sampling frequency. This control structure consists of an inner joint-based loop and an outer vision-based loop. A static positioning algorithm was implemented and experimentally verified. This algorithm utilizes the manipulator Jacobian to transform a tip position error to a joint error. The joint error is then used to give a new reference input to the joint controller. The convergence of the algorithm is demonstrated experimentally under payload variation. A Landmark Tracking System (Dickerson, et al 1990) is used for vision-based end-point measurements. This system was modified and tested. A real-time control system was implemented on a PC and interfaced with the vision system and the robot.

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

    Science.gov (United States)

    Newman, Martin; Ausubel, Frederick M

    2016-07-01

    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. Copyright © 2016 John Wiley & Sons, Inc.

  3. Gallium-Based Room-Temperature Liquid Metals: Actuation and Manipulation of Droplets and Flows

    Directory of Open Access Journals (Sweden)

    Leily Majidi

    2017-08-01

    Full Text Available Gallium-based room-temperature liquid metals possess extremely valuable properties, such as low toxicity, low vapor pressure, and high thermal and electrical conductivity enabling them to become suitable substitutes for mercury and beyond in wide range of applications. When exposed to air, a native oxide layer forms on the surface of gallium-based liquid metals which mechanically stabilizes the liquid. By removing or reconstructing the oxide skin, shape and state of liquid metal droplets and flows can be manipulated/actuated desirably. This can occur manually or in the presence/absence of a magnetic/electric field. These methods lead to numerous useful applications such as soft electronics, reconfigurable devices, and soft robots. In this mini-review, we summarize the most recent progresses achieved on liquid metal droplet generation and actuation of gallium-based liquid metals with/without an external force.

  4. 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......Humans can perform a multitude of different actions with their hands (manipulations). In spite of this, so far there have been only a few attempts to represent manipulation types trying to understand the underlying principles. Here we first discuss how manipulation actions are structured in space...... anchors also provide us with information about when to pay attention to additional important information, for example when to consider trajectory shapes and relative poses between objects. As a consequence a highly condensed representation emerges by which different manipulations can be recognized...

  5. Image-Based Visual Servoing for Manipulation Via Predictive Control – A Survey of Some Results

    Directory of Open Access Journals (Sweden)

    Corneliu Lazăr

    2016-09-01

    Full Text Available In this paper, a review of predictive control algorithms developed by the authors for visual servoing of robots in manipulation applications is presented. Using these algorithms, a control predictive framework was created for image-based visual servoing (IBVS systems. Firstly, considering the point features, in the year 2008 we introduced an internal model predictor based on the interaction matrix. Secondly, distinctly from the set-point trajectory, we introduced in 2011 the reference trajectory using the concept from predictive control. Finally, minimizing a sum of squares of predicted errors, the optimal input trajectory was obtained. The new concept of predictive control for IBVS systems was employed to develop a cascade structure for motion control of robot arms. Simulation results obtained with a simulator for predictive IBVS systems are also presented.

  6. 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.

  7. 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.

  8. 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.

  9. Soft object deformation monitoring and learning for model-based robotic hand manipulation.

    Science.gov (United States)

    Cretu, Ana-Maria; Payeur, Pierre; Petriu, Emil M

    2012-06-01

    This paper discusses the design and implementation of a framework that automatically extracts and monitors the shape deformations of soft objects from a video sequence and maps them with force measurements with the goal of providing the necessary information to the controller of a robotic hand to ensure safe model-based deformable object manipulation. Measurements corresponding to the interaction force at the level of the fingertips and to the position of the fingertips of a three-finger robotic hand are associated with the contours of a deformed object tracked in a series of images using neural-network approaches. The resulting model captures the behavior of the object and is able to predict its behavior for previously unseen interactions without any assumption on the object's material. The availability of such models can contribute to the improvement of a robotic hand controller, therefore allowing more accurate and stable grasp while providing more elaborate manipulation capabilities for deformable objects. Experiments performed for different objects, made of various materials, reveal that the method accurately captures and predicts the object's shape deformation while the object is submitted to external forces applied by the robot fingers. The proposed method is also fast and insensitive to severe contour deformations, as well as to smooth changes in lighting, contrast, and background.

  10. 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

    2013-12-07

    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.

  11. 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.

  12. A Method on Dynamic Path Planning for Robotic Manipulator Autonomous Obstacle Avoidance Based on an Improved RRT Algorithm.

    Science.gov (United States)

    Wei, Kun; Ren, Bingyin

    2018-02-13

    In a future intelligent factory, a robotic manipulator must work efficiently and safely in a Human-Robot collaborative and dynamic unstructured environment. Autonomous path planning is the most important issue which must be resolved first in the process of improving robotic manipulator intelligence. Among the path-planning methods, the Rapidly Exploring Random Tree (RRT) algorithm based on random sampling has been widely applied in dynamic path planning for a high-dimensional robotic manipulator, especially in a complex environment because of its probability completeness, perfect expansion, and fast exploring speed over other planning methods. However, the existing RRT algorithm has a limitation in path planning for a robotic manipulator in a dynamic unstructured environment. Therefore, an autonomous obstacle avoidance dynamic path-planning method for a robotic manipulator based on an improved RRT algorithm, called Smoothly RRT (S-RRT), is proposed. This method that targets a directional node extends and can increase the sampling speed and efficiency of RRT dramatically. A path optimization strategy based on the maximum curvature constraint is presented to generate a smooth and curved continuous executable path for a robotic manipulator. Finally, the correctness, effectiveness, and practicability of the proposed method are demonstrated and validated via a MATLAB static simulation and a Robot Operating System (ROS) dynamic simulation environment as well as a real autonomous obstacle avoidance experiment in a dynamic unstructured environment for a robotic manipulator. The proposed method not only provides great practical engineering significance for a robotic manipulator's obstacle avoidance in an intelligent factory, but also theoretical reference value for other type of robots' path planning.

  13. 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.

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

    International Nuclear Information System (INIS)

    Oertel, J.A.; Murphy, T.J.; Berggren, R.R.; Faulkner, J.; Schmell, R.; Little, D.; Archuleta, T.; Lopez, J.; Velarde, J.; Horton, R.F.

    1999-01-01

    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

  15. From bioseparation to artificial micro-organs: microfluidic chip based particle manipulation techniques

    Science.gov (United States)

    Stelzle, Martin

    2010-02-01

    Microfluidic device technology provides unique physical phenomena which are not available in the macroscopic world. These may be exploited towards a diverse array of applications in biotechnology and biomedicine ranging from bioseparation of particulate samples to the assembly of cells into structures that resemble the smallest functional unit of an organ. In this paper a general overview of chip-based particle manipulation and separation is given. In the state of the art electric, magnetic, optical and gravitational field effects are utilized. Also, mechanical obstacles often in combination with force fields and laminar flow are employed to achieve separation of particles or molecules. In addition, three applications based on dielectrophoretic forces for particle manipulation in microfluidic systems are discussed in more detail. Firstly, a virus assay is demonstrated. There, antibody-loaded microbeads are used to bind virus particles from a sample and subsequently are accumulated to form a pico-liter sized aggregate located at a predefined position in the chip thus enabling highly sensitive fluorescence detection. Secondly, subcellular fractionation of mitochondria from cell homogenate yields pure samples as was demonstrated by Western Blot and 2D PAGE analysis. Robust long-term operation with complex cell homogenate samples while avoiding electrode fouling is achieved by a set of dedicated technical means. Finally, a chip intended for the dielectrophoretic assembly of hepatocytes and endothelial cells into a structure resembling a liver sinusoid is presented. Such "artificial micro organs" are envisioned as substance screening test systems providing significantly higher predictability with respect to the in vivo response towards a substance under test.

  16. Do Bodybuilders Use Evidence-Based Nutrition Strategies to Manipulate Physique?

    Directory of Open Access Journals (Sweden)

    Lachlan Mitchell

    2017-09-01

    Full Text Available Competitive bodybuilders undergo strict dietary and training practices to achieve an extremely lean and muscular physique. The purpose of this study was to identify and describe different dietary strategies used by bodybuilders, their rationale, and the sources of information from which these strategies are gathered. In-depth interviews were conducted with seven experienced (10.4 ± 3.4 years bodybuilding experience, male, natural bodybuilders. Participants were asked about training, dietary and supplement practices, and information resources for bodybuilding strategies. Interviews were transcribed verbatim and analyzed using qualitative content analysis. During the off-season, energy intake was higher and less restricted than during the in-season to aid in muscle hypertrophy. There was a focus on high protein intake with adequate carbohydrate to permit high training loads. To create an energy deficit and loss of fat mass, energy intake was gradually and progressively reduced during the in-season via a reduction in carbohydrate and fat intake. The rationale for weekly higher carbohydrate refeed days was to offset declines in metabolic rate and fatigue, while in the final “peak week” before competition, the reasoning for fluid and sodium manipulation and carbohydrate loading was to enhance the appearance of leanness and vascularity. Other bodybuilders, coaches and the internet were significant sources of information. Despite the common perception of extreme, non-evidence-based regimens, these bodybuilders reported predominantly using strategies which are recognized as evidence-based, developed over many years of experience. Additionally, novel strategies such as weekly refeed days to enhance fat loss, and sodium and fluid manipulation, warrant further investigation to evaluate their efficacy and safety.

  17. A Method on Dynamic Path Planning for Robotic Manipulator Autonomous Obstacle Avoidance Based on an Improved RRT Algorithm

    Directory of Open Access Journals (Sweden)

    Kun Wei

    2018-02-01

    Full Text Available In a future intelligent factory, a robotic manipulator must work efficiently and safely in a Human–Robot collaborative and dynamic unstructured environment. Autonomous path planning is the most important issue which must be resolved first in the process of improving robotic manipulator intelligence. Among the path-planning methods, the Rapidly Exploring Random Tree (RRT algorithm based on random sampling has been widely applied in dynamic path planning for a high-dimensional robotic manipulator, especially in a complex environment because of its probability completeness, perfect expansion, and fast exploring speed over other planning methods. However, the existing RRT algorithm has a limitation in path planning for a robotic manipulator in a dynamic unstructured environment. Therefore, an autonomous obstacle avoidance dynamic path-planning method for a robotic manipulator based on an improved RRT algorithm, called Smoothly RRT (S-RRT, is proposed. This method that targets a directional node extends and can increase the sampling speed and efficiency of RRT dramatically. A path optimization strategy based on the maximum curvature constraint is presented to generate a smooth and curved continuous executable path for a robotic manipulator. Finally, the correctness, effectiveness, and practicability of the proposed method are demonstrated and validated via a MATLAB static simulation and a Robot Operating System (ROS dynamic simulation environment as well as a real autonomous obstacle avoidance experiment in a dynamic unstructured environment for a robotic manipulator. The proposed method not only provides great practical engineering significance for a robotic manipulator’s obstacle avoidance in an intelligent factory, but also theoretical reference value for other type of robots’ path planning.

  18. A Method on Dynamic Path Planning for Robotic Manipulator Autonomous Obstacle Avoidance Based on an Improved RRT Algorithm

    Science.gov (United States)

    Wei, Kun; Ren, Bingyin

    2018-01-01

    In a future intelligent factory, a robotic manipulator must work efficiently and safely in a Human–Robot collaborative and dynamic unstructured environment. Autonomous path planning is the most important issue which must be resolved first in the process of improving robotic manipulator intelligence. Among the path-planning methods, the Rapidly Exploring Random Tree (RRT) algorithm based on random sampling has been widely applied in dynamic path planning for a high-dimensional robotic manipulator, especially in a complex environment because of its probability completeness, perfect expansion, and fast exploring speed over other planning methods. However, the existing RRT algorithm has a limitation in path planning for a robotic manipulator in a dynamic unstructured environment. Therefore, an autonomous obstacle avoidance dynamic path-planning method for a robotic manipulator based on an improved RRT algorithm, called Smoothly RRT (S-RRT), is proposed. This method that targets a directional node extends and can increase the sampling speed and efficiency of RRT dramatically. A path optimization strategy based on the maximum curvature constraint is presented to generate a smooth and curved continuous executable path for a robotic manipulator. Finally, the correctness, effectiveness, and practicability of the proposed method are demonstrated and validated via a MATLAB static simulation and a Robot Operating System (ROS) dynamic simulation environment as well as a real autonomous obstacle avoidance experiment in a dynamic unstructured environment for a robotic manipulator. The proposed method not only provides great practical engineering significance for a robotic manipulator’s obstacle avoidance in an intelligent factory, but also theoretical reference value for other type of robots’ path planning. PMID:29438320

  19. 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. © 2011 IEEE

  20. Design of mechanical coxa joints based on three-degree-of-freedom spherical parallel manipulators

    International Nuclear Information System (INIS)

    Li, Yanbiao; Ji, Shiming; Wang, Zhongfei; Jin, Mingsheng; Liu, Yi; Jin, Zhenlin

    2013-01-01

    We addressed the issue of the design of mechanical coxa joints based on three-degree-of-freedom spherical parallel manipulators using the parameter statistics optimum method based on index atlases. The coxa joints have the advantages of high payload, high accuracy, and good technological efficiency. The first step of the design and prototyping used in this paper develops the direct and inverse displacement equations from the layout feature of the mechanical coxa joints. Then, the shapes of a constant-orientation workspace of the mechanical coxa joints are described, and the effects of the design parameters on the workspace volume are studied quantitatively. The next step deals with the graphical representation of the atlases that illustrates the relationship between performance evaluation index and design parameters based on the kinematics and torque analysis of the mechanical coxa joints. Finally, the geometric parameters of the coxa joints are obtained by the parameter statistics optimum method based on the index atlases. Considering assembly conditions, the design scheme of the mechanical coxa joints is developed, which provides a theoretical basis for the application of the mechanical coxa joints.

  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. Improved Laser Manipulation for On-chip Fabricated Microstructures Based on Solution Replacement and Its Application in Single Cell Analysis

    Directory of Open Access Journals (Sweden)

    Tao Yue

    2014-02-01

    Full Text Available In this paper, we present the fabrication and assembly of microstructures inside a microfluidic device based on a photocrosslinkable resin and optical tweezers. We also report a method of solution replacement inside the microfluidic channel in order to improve the manipulation performance and apply the assembled microstructures for single cell cultivation. By the illumination of patterned ultraviolet (UV through a microscope, microstructures of arbitrary shape were fabricated by the photocrosslinkable resin inside a microfluidic channel. Based on the microfluidic channel with both glass and polydimethylsiloxane (PDMS surfaces, immovable and movable microstructures were fabricated and manipulated. The microstructures were fabricated at the desired places and manipulated by the optical tweezers. A rotational microstructure including a microgear and a rotation axis was assembled and rotated in demonstrating this technique. The improved laser manipulation of microstructures was achieved based on the on-chip solution replacement method. The manipulation speed of the microstructures increased when the viscosity of the solvent decreased. The movement efficiency of the fabricated microstructures inside the lower viscosity solvent was evaluated and compared with those microstructures inside the former high viscosity solvent. A novel cell cage was fabricated and the cultivation of a single yeast cell (w303 was demonstrated in the cell cage, inside the microfluidic device.

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

    NARCIS (Netherlands)

    Brouwer, Dannis Michel; de Jong, B.R.; Soemers, Herman

    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

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

    Indian Academy of Sciences (India)

    IEEE International Conference on Robotics and Automation 1: 345–350. Lee K, Shah D K 1988 Dynamic analysis of a three degrees of freedom in-parallel actuated manipulator. IEEE Tran. Rob. Autom. 4: 361–367. Rao N M, Rao K M 2006 Multi-position dimensional synthesis of a spatial 3-RPS parallel manipulator.

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

    Indian Academy of Sciences (India)

    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 ...

  6. Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins.

    Science.gov (United States)

    de Bekker, Charissa; Ohm, Robin A; Evans, Harry C; Brachmann, Andreas; Hughes, David P

    2017-10-02

    Much can be gained from revealing the mechanisms fungal entomopathogens employ. Especially intriguing are fungal parasites that manipulate insect behavior because, presumably, they secrete a wealth of bioactive compounds. To gain more insight into their strategies, we compared the genomes of five ant-infecting Ophiocordyceps species from three species complexes. These species were collected across three continents, from five different ant species in which they induce different levels of manipulation. A considerable number of (small) secreted and pathogenicity-related proteins were only found in these ant-manipulating Ophiocordyceps species, and not in other ascomycetes. However, few of those proteins were conserved among them, suggesting that several different methods of behavior modification have evolved. This is further supported by a relatively fast evolution of previously reported candidate manipulation genes associated with biting behavior. Moreover, secondary metabolite clusters, activated during biting behavior, appeared conserved within a species complex, but not beyond. The independent co-evolution between these manipulating parasites and their respective hosts might thus have led to rather diverse strategies to alter behavior. Our data indicate that specialized, secreted enterotoxins may play a major role in one of these strategies.

  7. 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...

  8. Characteristics of manipulative in mathematics laboratory

    Science.gov (United States)

    Istiandaru, A.; Istihapsari, V.; Prahmana, R. C. I.; Setyawan, F.; Hendroanto, A.

    2017-12-01

    A manipulative is a teaching aid designed such that students could understand mathematical concepts by manipulating it. This article aims to provide an insight to the characteristics of manipulatives produced in the mathematics laboratory of Universitas Ahmad Dahlan, Indonesia. A case study was conducted to observe the existing manipulatives produced during the latest three years and classified the manipulatives based on the characteristics found. There are four kinds of manipulatives: constructivism manipulative, virtual manipulative, informative manipulative, and game-based manipulative. Each kinds of manipulative has different characteristics and impact towards the mathematics learning.

  9. Performance evaluation of 3D vision-based semi-autonomous control method for assistive robotic manipulator.

    Science.gov (United States)

    Ka, Hyun W; Chung, Cheng-Shiu; Ding, Dan; James, Khara; Cooper, Rory

    2018-02-01

    We developed a 3D vision-based semi-autonomous control interface for assistive robotic manipulators. It was implemented based on one of the most popular commercially available assistive robotic manipulator combined with a low-cost depth-sensing camera mounted on the robot base. To perform a manipulation task with the 3D vision-based semi-autonomous control interface, a user starts operating with a manual control method available to him/her. When detecting objects within a set range, the control interface automatically stops the robot, and provides the user with possible manipulation options through audible text output, based on the detected object characteristics. Then, the system waits until the user states a voice command. Once the user command is given, the control interface drives the robot autonomously until the given command is completed. In the empirical evaluations conducted with human subjects from two different groups, it was shown that the semi-autonomous control can be used as an alternative control method to enable individuals with impaired motor control to more efficiently operate the robot arms by facilitating their fine motion control. The advantage of semi-autonomous control was not so obvious for the simple tasks. But, for the relatively complex real-life tasks, the 3D vision-based semi-autonomous control showed significantly faster performance. Implications for Rehabilitation A 3D vision-based semi-autonomous control interface will improve clinical practice by providing an alternative control method that is less demanding physically as well cognitively. A 3D vision-based semi-autonomous control provides the user with task specific intelligent semiautonomous manipulation assistances. A 3D vision-based semi-autonomous control gives the user the feeling that he or she is still in control at any moment. A 3D vision-based semi-autonomous control is compatible with different types of new and existing manual control methods for ARMs.

  10. 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.

  11. Stability Analysis of a Voltage-Based Controller for Robot Manipulators

    Directory of Open Access Journals (Sweden)

    Jorge Orrante-Sakanassi

    2013-01-01

    Full Text Available A voltage-based control scheme for robot manipulators has been presented in recent literature, where feedback linearization is applied in the electrical equations of the DC motors in order to cancel the electrical current terms. However, in this paper we show that this control technique generates a system of the form Ex = Ax + Bu, where E is a singular matrix, that is to say, a generalized state-space system or singular system. This paper introduces a formal stability analysis of the respective system by considering the state-space equation as a singular system. Furthermore, in order to avoid the singularity of the closed-loop system, modified voltage-based control schemes are proposed, whose Lyapunov stability analyses conclude semiglobal asymptotic stability for the set-point control case and uniform boundedness of the solutions and semiglobal convergence of the position, as well as velocity errors for the tracking control case. The proposed control systems are simulated for the tracking and set-point cases using the CICESE Pelican robot driven by DC motors.

  12. Tip position control of a two-link flexible robot manipulator based on nonlinear deflection feedback

    CERN Document Server

    Oke, G

    2003-01-01

    The control of flexible link manipulators has gained an increasing importance in robotics, in recent years. To control the tip of a flexible manipulator, the joint angles should converge to the desired positions fast and elastic deflections must be effectively suppressed. In this study, a two-link flexible manipulator is controlled by three methods and the results are compared. These methods are, Pd control, PD control augmented by a nonlinear correction term feedback, where the correction term is a function of the deflection of each link, and an adaptive fuzzy controller with the nonlinear correction term feedback. Simulations have been carried out to compare the performances of all three methods.

  13. 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.

  14. [An Introduction to A Newly-developed "Acupuncture Needle Manipulation Training-evaluation System" Based on Optical Motion Capture Technique].

    Science.gov (United States)

    Zhang, Ao; Yan, Xing-Ke; Liu, An-Guo

    2016-12-25

    In the present paper, the authors introduce a newly-developed "Acupuncture Needle Manipulation Training-evaluation System" based on optical motion capture technique. It is composed of two parts, sensor and software, and overcomes some shortages of mechanical motion capture technique. This device is able to analyze the data of operations of the pressing-hand and needle-insertion hand during acupuncture performance and its software contains personal computer (PC) version, Android version, and Internetwork Operating System (IOS) Apple version. It is competent in recording and analyzing information of any ope-rator's needling manipulations, and is quite helpful for teachers in teaching, training and examining students in clinical practice.

  15. 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.

  16. 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.

  17. Flexible DWDM Grid Manipulation Using Four Wave Mixing-based Time Lenses

    DEFF Research Database (Denmark)

    Røge, Kasper Meldgaard; Guan, Pengyu; Mulvad, Hans Christian Hansen

    2014-01-01

    An experimental demonstration of dense wavelength-division multiplexing (DWDM) grid manipulation is carried out using two time lenses. A DWDM spectrum is compressed from a 100-GHz to a 28-GHz grid with error-free performance.......An experimental demonstration of dense wavelength-division multiplexing (DWDM) grid manipulation is carried out using two time lenses. A DWDM spectrum is compressed from a 100-GHz to a 28-GHz grid with error-free performance....

  18. Optimal design of a spherical parallel manipulator based on kinetostatic performance using evolutionary techniques

    Energy Technology Data Exchange (ETDEWEB)

    Daneshmand, Morteza [University of Tartu, Tartu (Estonia); Saadatzi, Mohammad Hossein [Colorado School of Mines, Golden (United States); Kaloorazi, Mohammad Hadi [École de Technologie Supérieur, Montréal (Canada); Masouleh, Mehdi Tale [University of Tehran, Tehran (Iran, Islamic Republic of); Anbarjafari, Gholamreza [Hasan Kalyoncu University, Gaziantep (Turkmenistan)

    2016-03-15

    This study aims to provide an optimal design for a Spherical parallel manipulator (SPM), namely, the Agile Eye. This aim is approached by investigating kinetostatic performance and workspace and searching for the most promising design. Previously recommended designs are examined to determine whether they provide acceptable kinetostatic performance and workspace. Optimal designs are provided according to different kinetostatic performance indices, especially kinematic sensitivity. The optimization process is launched based on the concept of the genetic algorithm. A single-objective process is implemented in accordance with the guidelines of an evolutionary algorithm called differential evolution. A multi-objective procedure is then provided following the reasoning of the nondominated sorting genetic algorithm-II. This process results in several sets of Pareto points for reconciliation between kinetostatic performance indices and workspace. The concept of numerous kinetostatic performance indices and the results of optimization algorithms are elaborated. The conclusions provide hints on the provided set of designs and their credibility to provide a well-conditioned workspace and acceptable kinetostatic performance for the SPM under study, which can be well extended to other types of SPMs.

  19. Neonatal manipulation of oxytocin prevents lipopolysaccharide-induced decrease in gene expression of growth factors in two developmental stages of the female rat.

    Science.gov (United States)

    Bakos, Jan; Lestanova, Zuzana; Strbak, Vladimir; Havranek, Tomas; Bacova, Zuzana

    2014-10-01

    Oxytocin production and secretion is important for early development of the brain. Long-term consequences of manipulation of oxytocin system might include changes in markers of brain plasticity - cytoskeletal proteins and neurotrophins. The aim of the present study was (1) to determine whether neonatal oxytocin administration affects gene expression of nestin, microtubule-associated protein-2 (MAP-2), brain derived neurotrophic factor (BDNF) and nerve growth factor (NGF) in the brain of two developmental stages of rat and (2) to evaluate whether neonatal oxytocin administration protects against lipopolysaccharide (LPS) induced inflammation. Neonatal oxytocin did not prevent a decrease of body weight in the LPS treated animals. Oxytocin significantly increased gene expression of BDNF in the right hippocampus in 21-day and 2-month old rats of both sexes. Gene expression of NGF and MAP-2 significantly increased in males treated with oxytocin. Both, growth factors and intermediate filament-nestin mRNA levels, were reduced in females exposed to LPS. Oxytocin treatment prevented a decrease in the gene expression of only growth factors. In conclusion, neonatal manipulation of oxytocin has developmental and sex-dependent effect on markers of brain plasticity. These results also indicate, that oxytocin may be protective against inflammation particularly in females. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

    Zhu, Benpeng; Xu, Jiong; Yang, Xiaofei; Li, Ying; Lee, Changyang; Zhou, Qifa; Shung, K. Kirk; Wang, Tian; Xiong, Ke; Shiiba, Michihisa; Takeuchi, Shinichi

    2016-01-01

    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 (d 33 = 270 pC/N and k t = 0.51) was employed for SBAT applications and a press-focusing technology was introduced. The obtained SBAT, acting at an operational frequency of 50 MHz, 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.

  1. 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.

  2. Optimization and limit of a tilt manipulation stage based on the electrowetting-on-dielectric principle

    Science.gov (United States)

    Tan, Xiao; Tao, Zhi; Suzuki, Kenji; Li, Haiwang

    2017-12-01

    This work designed a new tilt manipulation stage based on the electrowetting-on-dielectric (EWOD) principle as the actuating mechanism and investigated the performance of that stage. The stage was fabricated using a universal MEMS (Micro-Electro-Mechanical System) fabrication method. In the previously demonstrated form of this device, the tilt stage consisted of a top plate that functions as a mirror, a bottom plate that was designed for changing the shape of water droplets, and supporters that were fixed between the top and bottom plate. That device was actuated by a voltage applied to the bottom plate, resulting in a static electric force actuating the shape change in the droplets by moving the top plate in the vertical direction. Previous experimental results indicated that that device can tilt at up to ±1.8°, with a resolution of 7 μm in displacement and 0.05° in angle. By selecting the best combination of the dielectric layer, the tilt angle was maximized. The new device, fabricated using a common and straightforward fabrication method, avoids deflection of the top plate and grounding in the bottom plate. Because of the limit of Teflon and other MEMS materials, this device has a tilt angle in the range of 3.2-3.5° according to the experimental data for friction and the EWOD device limit, which is close to 1.8°. This paper also describe the investigation of the effects of various parameters, e.g., various dielectric materials, thicknesses, and droplet type and volume, on the performance of the stage. The results indicate that the apparent frictions coefficient of the solid-liquid interface may remain constant, i.e., the friction force is proportional to the normal support force and the apparent frictions coefficient.

  3. 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.

  4. 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.

  5. Interactive protein manipulation

    International Nuclear Information System (INIS)

    2003-01-01

    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

  6. 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.

  7. Dynamic modeling of dual-arm cooperating manipulators based on Udwadia–Kalaba equation

    Directory of Open Access Journals (Sweden)

    Jia Liu

    2016-07-01

    Full Text Available Dual-arm cooperating manipulators subject to a certain constraint brought about by the desired trajectory and geometric constraint show high nonlinearity and coupling in their dynamic characteristic. Therefore, it is hard to build dynamical equation with traditional Lagrange equation. The Udwadia–Kalaba equation presents a new idea of dynamic modeling of multi-body systems. However, the dynamic modeling of the unconstrained systems still depends on the traditional Lagrange equation and is quite tedious for dual-arm cooperating manipulators. A generalized dynamical equation of multi-link planar manipulators is thus presented and proven to make modeling conveniently. The constraint relationship is established from a new perspective, and the dynamical equation of dual-arm cooperating manipulator subject to the desired trajectory is acquired with the Udwadia–Kalaba equation. The simple approach overcomes the disadvantage of obtaining dynamical equation from traditional Lagrange equation by Lagrange multiplier. The simulation results of varying law of the joint angles and the motion path of the bar prove that the dynamical equation established by this method conforms to reality.

  8. Design and Fabrication of a Planar Three-DOFs MEMS-Based Manipulator

    NARCIS (Netherlands)

    de Jong, B.R.; Brouwer, Dannis Michel; de Boer, Meint J.; Jansen, Henricus V.; Soemers, Herman; Krijnen, Gijsbertus J.M.

    2010-01-01

    This paper presents the design, modeling, and fabrication of a planar three-degrees-of-freedom parallel kinematic manipulator, fabricated with a simple two-mask process in conventional highly doped single-crystalline silicon (SCS) wafers (100). The manipulator’s purpose is to provide accurate and

  9. Adverse events after cervical spinal manipulative therapy: consensus based classification and definitions

    NARCIS (Netherlands)

    Dr. C.P. van der Schans; M. Schmitt; dr. S.E. Lakke; H.A. Kranenburg

    2015-01-01

    Cervical spinal manipulations (CSM) are frequently employed techniques to alleviate neck pain and headache. Minor and major complications following CSM have been described, though clear consensus on definition and the classification of the complications had not yet been achieved. As a result,

  10. The Importance of the Secure Base Effect for Domestic Dogs – Evidence from a Manipulative Problem-Solving Task

    Science.gov (United States)

    Horn, Lisa; Huber, Ludwig; Range, Friederike

    2013-01-01

    Background It has been suggested that dogs display a secure base effect similar to that found in human children (i.e., using the owner as a secure base for interacting with the environment). In children, this effect influences their daily lives and importantly also their performance in cognitive testing. Here, we investigate the importance of the secure base effect for dogs in a problem-solving task. Methodology/Principal Findings Using a manipulative task, we tested dogs in three conditions, in which we varied the owner's presence and behavior (Experiment 1: “Absent owner”, “Silent owner”, “Encouraging owner”) and in one additional condition, in which the owner was replaced by an unfamiliar human (Experiment 2: “Replaced owner”). We found that the dogs' duration of manipulating the apparatus was longer when their owner was present than absent, irrespective of the owner's behavior. The presence of an unfamiliar human however did not increase their manipulation. Furthermore, the reduced manipulation during the absence of the owner was not correlated with the dog's degree of separation distress scored in a preceding attachment experiment. Conclusions/Significance Our study is the first to provide evidence for an owner-specific secure base effect in dogs that extends from attachment tests to other areas of dogs' lives and also manifests itself in cognitive testing – thereby confirming the remarkable similarity between the secure base effect in dogs and in human children. These results also have important implications for behavioral testing in dogs, because the presence or absence of the owner during a test situation might substantially influence dogs' motivation and therefore the outcome of the test. PMID:23734243

  11. The importance of the secure base effect for domestic dogs - evidence from a manipulative problem-solving task.

    Directory of Open Access Journals (Sweden)

    Lisa Horn

    Full Text Available It has been suggested that dogs display a secure base effect similar to that found in human children (i.e., using the owner as a secure base for interacting with the environment. In children, this effect influences their daily lives and importantly also their performance in cognitive testing. Here, we investigate the importance of the secure base effect for dogs in a problem-solving task.Using a manipulative task, we tested dogs in three conditions, in which we varied the owner's presence and behavior (Experiment 1: "Absent owner", "Silent owner", "Encouraging owner" and in one additional condition, in which the owner was replaced by an unfamiliar human (Experiment 2: "Replaced owner". We found that the dogs' duration of manipulating the apparatus was longer when their owner was present than absent, irrespective of the owner's behavior. The presence of an unfamiliar human however did not increase their manipulation. Furthermore, the reduced manipulation during the absence of the owner was not correlated with the dog's degree of separation distress scored in a preceding attachment experiment.Our study is the first to provide evidence for an owner-specific secure base effect in dogs that extends from attachment tests to other areas of dogs' lives and also manifests itself in cognitive testing - thereby confirming the remarkable similarity between the secure base effect in dogs and in human children. These results also have important implications for behavioral testing in dogs, because the presence or absence of the owner during a test situation might substantially influence dogs' motivation and therefore the outcome of the test.

  12. 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

  13. Performance and characterization of a MEMS-based device for alignment and manipulation of x-ray nanofocusing optics

    Directory of Open Access Journals (Sweden)

    Weihe Xu

    2015-03-01

    Full Text Available X-ray microscopy is a powerful, non-invasive tool used for nanometer-scale resolution imaging, and it is widely applied in various areas of science and technology. To push the spatial resolution of x-ray microscopy studies in the hard x-ray regime below 10 nm, Multilayer Laue Lenses (MLL can be used as nanofocusing elements. To ensure distortion-free x-ray imaging, high-stability microscopy systems are required. MEMS-based manipulators are a promising route to achieve high stability when used for alignment and manipulation of nanofocusing optics. In this work, we present a tip-tilt MEMS-based device suitable for MLL alignment. We fully characterize the device and demonstrate better-than 10 millidegree angular positioning resolution when utilizing capacitive displacement sensors, and better-than 0.8 millidegree resolution when using laser interferometry.

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

    OpenAIRE

    Sandra J Kuhlman; Z Josh Huang

    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...

  15. A Hierarchical Reliability Control Method for a Space Manipulator Based on the Strategy of Autonomous Decision-Making

    OpenAIRE

    Gao, Xin; Wang, Yifan; Sun, Hanxu; Jia, Qingxuan; Chen, Gang; Du, Mingtao; Yang, Yukun

    2016-01-01

    In order to maintain and enhance the operational reliability of a robotic manipulator deployed in space, an operational reliability system control method is presented in this paper. First, a method to divide factors affecting the operational reliability is proposed, which divides the operational reliability factors into task-related factors and cost-related factors. Then the models describing the relationships between the two kinds of factors and control variables are established. Based on th...

  16. 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.

  17. Inner-Learning Mechanism Based Control Scheme for Manipulator with Multitasking and Changing Load

    Directory of Open Access Journals (Sweden)

    Fangzheng Xue

    2014-05-01

    Full Text Available With the rapid development of robot technology and its application, manipulators may face complex tasks and dynamic environments in the coming future, which leads to two challenges of control: multitasking and changing load. In this paper, a novel multicontroller strategy is presented to meet such challenges. The presented controller is composed of three parts: subcontrollers, inner-learning mechanism, and switching rules. Each subcontroller is designed with self-learning skills to fit the changing load under a special task. When a new task comes, switching rule reselects the most suitable subcontroller as the working controller to handle current task instead of the older one. Inner-learning mechanism makes the subcontrollers learn from the working controller when load changes so that the switching action causes smaller tracking error than the traditional switch controller. The results of the simulation experiments on two-degree manipulator show the proposed method effect.

  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.

  19. A Dynamic Model for GPS Based Attitude Determination and Testing using a Serial Robotic Manipulator

    OpenAIRE

    Raskaliyev, Almat; Patel, Sarosh; Sobh, Tarek

    2017-01-01

    A computational algorithm is developed for estimating accurately the attitude of a robotic arm which moves along a predetermined path. This algorithm requires preliminary input data obtained in the static mode to yield phase observables for the precise, 3-axis attitude determination of a swinging manipulator in the dynamic mode. Measurements are recorded simultaneously by three GPS L1 receivers and then processed in several steps to accomplish this task. First, artkconv batch executable conve...

  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. Design of safety mechanism for an industrial manipulator based on passive compliance

    International Nuclear Information System (INIS)

    Kim, Hwi Su; Park, Jung Jun; Song, Jae Bok; Kyung, Jin Ho

    2010-01-01

    In recent years, collision safety between humans and robots has drawn much attention since human-robot cooperation is increasingly needed in various fields. Since positioning accuracy and collision safety are both important, an industrial manipulator should maintain very high stiffness for positioning accuracy in a normal situation, but exhibit very low stiffness when subjected to a collision force greater than the tolerance for human injury. To satisfy these requirements, we proposed in our previous research a safety mechanism composed of a linear spring and a double-slider mechanism for a service robot with a small payload. We modified this device to meet more stringent requirements for an industrial manipulator which usually has a payload higher than a service robot. Several experiments on static and dynamic collisions showed high stiffness of the safety mechanism in response to an external torque that was less than a predetermined threshold torque, but low stiffness that enabled absorption of the collision force when the external torque exceeded the threshold. Thus, positioning accuracy and collision safety were improved using the proposed design. Furthermore, a new safety criterion is suggested to verify the collision safety of a manipulator that uses the proposed safety mechanism

  2. Uncertainty analysis and allocation of joint tolerances in robot manipulators based on interval analysis

    International Nuclear Information System (INIS)

    Wu Weidong; Rao, S.S.

    2007-01-01

    Many uncertain factors influence the accuracy and repeatability of robots. These factors include manufacturing and assembly tolerances and deviations in actuators and controllers. The effects of these uncertain factors must be carefully analyzed to obtain a clear insight into the manipulator performance. In order to ensure the position and orientation accuracy of a robot end effector as well as to reduce the manufacturing cost of the robot, it is necessary to quantify the influence of the uncertain factors and optimally allocate the tolerances. This involves a study of the direct and inverse kinematics of robot end effectors in the presence of uncertain factors. This paper focuses on the optimal allocation of joint tolerances with consideration of the positional and directional errors of the robot end effector and the manufacturing cost. The interval analysis is used for predicting errors in the performance of robot manipulators. The Stanford manipulator is considered for illustration. The unknown joint variables are modeled as interval parameters due to the inherent uncertainty. The cost-tolerance model is assumed to be of an exponential form during optimization. The effects of the upper bounds on the minimum cost and relative deviations of the directional and positional errors of the end effector are also studied

  3. Robot Manipulators

    Science.gov (United States)

    1988-01-01

    Space Shuttle's Remote Manipulator System (Canadarm) is a 50 foot robot arm used to deploy, retrieve or repair satellites in orbit. Initial spinoff version is designed to remove, inspect and replace large components of Ontario Hydro's CANDU nuclear reactors, which supply 50 percent of Ontario Hydro's total power reduction. CANDU robot is the first of SPAR's Remote Manipulator Systems intended for remote materials handling operations in nuclear servicing, chemical processing, smelting and manufacturing. Inco Limited used remote manipulator for remote control mining equipment to enhance safety and productivity of Inco's hardrock mining operations. System not only improves safety in a hazardous operation that costs more than a score of lives annually, it also increases productivity fourfold. Remote Manipulator System Division is also manufacturing a line of industrial robots and developing additional system for nuclear servicing, mining, defense and space operations.

  4. Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

    Science.gov (United States)

    Sun, Jingchun; Han, Leng; Zhao, Zhongming

    2010-01-01

    Schizophrenia is a chronic psychiatric disorder that affects about 1% of the population globally. A tremendous amount of effort has been expended in the past decade, including more than 2400 association studies, to identify genes influencing susceptibility to the disorder. However, few genes or markers have been reliably replicated. The wealth of this information calls for an integration of gene association data, evidence-based gene ranking, and follow-up replication in large sample. The objective of this study is to develop and evaluate evidence-based gene ranking methods and to examine the features of top-ranking candidate genes for schizophrenia. We proposed a gene-based approach for selecting and prioritizing candidate genes by combining odds ratios (ORs) of multiple markers in each association study and then combining ORs in multiple studies of a gene. We named it combination-combination OR method (CCOR). CCOR is similar to our recently published method, which first selects the largest OR of the markers in each study and then combines these ORs in multiple studies (i.e., selection-combination OR method, SCOR), but differs in selecting representative OR in each study. Features of top-ranking genes were examined by Gene Ontology terms and gene expression in tissues. Our evaluation suggested that the SCOR method overall outperforms the CCOR method. Using the SCOR, a list of 75 top-ranking genes was selected for schizophrenia candidate genes (SZGenes). We found that SZGenes had strong correlation with neuro-related functional terms and were highly expressed in brain-related tissues. The scientific landscape for schizophrenia genetics and other complex disease studies is expected to change dramatically in the next a few years, thus, the gene-based combined OR method is useful in candidate gene selection for follow-up association studies and in further artificial intelligence in medicine. This method for prioritization of candidate genes can be applied to other

  5. TensorPack: a Maple-based software package for the manipulation of algebraic expressions of tensors in general relativity

    International Nuclear Information System (INIS)

    Huf, P A; Carminati, J

    2015-01-01

    In this paper we: (1) introduce TensorPack, a software package for the algebraic manipulation of tensors in covariant index format in Maple; (2) briefly demonstrate the use of the package with an orthonormal tensor proof of the shearfree conjecture for dust. TensorPack is based on the Riemann and Canon tensor software packages and uses their functions to express tensors in an indexed covariant format. TensorPack uses a string representation as input and provides functions for output in index form. It extends the functionality to basic algebra of tensors, substitution, covariant differentiation, contraction, raising/lowering indices, symmetry functions and other accessory functions. The output can be merged with text in the Maple environment to create a full working document with embedded dynamic functionality. The package offers potential for manipulation of indexed algebraic tensor expressions in a flexible software environment. (paper)

  6. Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity

    Directory of Open Access Journals (Sweden)

    Thomas Marshall

    2011-02-01

    Full Text Available Abstract Background In addition to determining static states of gene expression (high vs. low, it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before. Results We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs and other genes. Responsive genes (N = 4746, which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF and our new data for 15 organs and tissues. Non-responsive genes (N = 9562, which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters. Conclusions We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.

  7. Synergy-Based Bilateral Port: A Universal Control Module for Tele-Manipulation Frameworks Using Asymmetric Master-Slave Systems.

    Science.gov (United States)

    Brygo, Anais; Sarakoglou, Ioannis; Grioli, Giorgio; Tsagarakis, Nikos

    2017-01-01

    Endowing tele-manipulation frameworks with the capability to accommodate a variety of robotic hands is key to achieving high performances through permitting to flexibly interchange the end-effector according to the task considered. This requires the development of control policies that not only cope with asymmetric master-slave systems but also whose high-level components are designed in a unified space in abstraction from the devices specifics. To address this dual challenge, a novel synergy port is developed that resolves the kinematic, sensing, and actuation asymmetries of the considered system through generating motion and force feedback references in the hardware-independent hand postural synergy space. It builds upon the concept of the Cartesian-based synergy matrix, which is introduced as a tool mapping the fingertips Cartesian space to the directions oriented along the grasp principal components. To assess the effectiveness of the proposed approach, the synergy port has been integrated into the control system of a highly asymmetric tele-manipulation framework, in which the 3-finger hand exoskeleton HEXOTRAC is used as a master device to control the SoftHand, a robotic hand whose transmission system relies on a single motor to drive all joints along a soft synergistic path. The platform is further enriched with the vision-based motion capture system Optitrack to monitor the 6D trajectory of the user's wrist, which is used to control the robotic arm on which the SoftHand is mounted. Experiments have been conducted with the humanoid robot COMAN and the KUKA LWR robotic manipulator. Results indicate that this bilateral interface is highly intuitive and allows users with no prior experience to reach, grasp, and transport a variety of objects exhibiting very different shapes and impedances. In addition, the hardware and control solutions proved capable of accommodating users with different hand kinematics. Finally, the proposed control framework offers a

  8. Nonlinear modelling and dynamic stability analysis of a flexible Cartesian robotic manipulator with base disturbance and terminal load

    Directory of Open Access Journals (Sweden)

    J. Ju

    2017-07-01

    Full Text Available The flexible Cartesian robotic manipulator (FCRM is coming into widespread application in industry. Because of the feeble rigidity and heavy deflection, the dynamic characteristics of the FCRM are easily influenced by external disturbances which mainly concentrate in the driving end and the load end. Thus, with the influence of driving base disturbance and terminal load considered, the motion differential equations of the FCRM under the plane motion of the base are constructed, which contain the forced and non-linear parametric excitations originated from the disturbances of base lateral and axial motion respectively. Considering the relationship between the coefficients of the motion differential equations and the mode shapes of the flexible manipulator, the analytic expressions of the mode shapes with terminal load are deduced. Then, based on multiple scales method and rectangular coordinate transformation, the average equations of the FCRM are derived to analyze the influence mechanism of base disturbance and terminal load on the system parametric vibration stability. The results show that terminal load mainly affects the node locations of mode shapes and mode frequencies of the FCRM, and the axial motion disturbance of the driving base introduces parametric excitation while the lateral motion disturbance generates forced excitation for the transverse vibration model of the FCRM. Furthermore, with the increase of the base excitation acceleration and terminal load, the parametric vibration instability region of the FCRM increases significantly. This study will be helpful for the dynamic characteristics analysis and vibration control of the FCRM.

  9. Dual-mode optical fiber-based tweezers for robust trapping and manipulation of absorbing particles in air

    Science.gov (United States)

    Sil, Souvik; Kanti Saha, Tushar; Kumar, Avinash; Bera, Sudipta K.; Banerjee, Ayan

    2017-12-01

    We develop an optical tweezers system using a single dual-mode optical fiber where mesoscopic absorbing particles can be trapped in three dimensions and manipulated employing photophoretic forces. We generate a superposition of fundamental and first order Hermite-Gaussian beam modes by the simple innovation of coupling a laser into a commercial optical fiber designed to be single mode for a wavelength higher than that of the laser. We achieve robust trapping of the absorbing particles for hours using both the pure fundamental and superposition mode beams and attain large manipulation velocities of ˜5 mm s-1 in the axial direction and ˜0.75 mm s-1 in the radial direction. We then demonstrate that the superposition mode is more effective in trapping and manipulation compared to the fundamental mode by around 80%, which may be increased several times by the use of a pure first order Hermite-Gaussian mode. The work has promising implications for trapping and spectroscopy of aerosols in air using simple optical fiber-based traps.

  10. Physiological hemostasis based intelligent integrated cooperative controller for precise fault-tolerant control of redundant parallel manipulator

    Science.gov (United States)

    Hao, Kuangrong; Guo, Chongbin; Ding, Yongsheng

    2014-10-01

    This paper focuses on precise fault-tolerant control for actual redundant parallel manipulator. Based on kinematic redundancy, some unnoticed influences such as mechanical clearance have been considered to design a more precise and intelligent fault-tolerant plan for actual plants. According to regulation principles in human hemostasis system, a bio-inspired intelligent integrated cooperative controller (BIICC) is developed including system structure, algorithm and step in parameter tuning. The proposed BIICC optimises partial error signal and improves control performance in each sub-channel. Moreover, the new controller transfers and disposes cooperative control signals among different sub-channels to achieve an intelligent integrated fault-tolerant system. The proposed BIICC is applied to an actual 2-DOF (degrees of freedom) redundant parallel manipulator where the feasibility of the new controller is demonstrated. The BIICC is beneficial to control precision and fault-tolerant capability of redundant plant. The improvements are more obvious in cases where extra actuators of redundant manipulator are broken.

  11. Fabrication of a pen-shaped portable biochemical reaction system based on magnetic bead manipulation

    International Nuclear Information System (INIS)

    Shikida, Mitsuhiro; Inagaki, Noriyuki; Okochi, Mina; Honda, Hiroyuki; Sato, Kazuo

    2011-01-01

    A pen-shaped platform that is similar to a mechanical pencil is proposed for producing a portable reaction system. A reaction unit, as the key component in the system, was produced by using a heat shrinkable tube. A mechanical pencil supplied by Mitsubishi Pencil Co. Ltd was used as the pen-shaped platform for driving the reaction cylinder. It was actuated using an inchworm motion. We confirmed that the magnetic beads were successfully manipulated in the droplet in the cylinder-shaped reaction units. (technical note)

  12. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization.

    Science.gov (United States)

    Senturk, Serif; Shirole, Nitin H; Nowak, Dawid G; Corbo, Vincenzo; Pal, Debjani; Vaughan, Alexander; Tuveson, David A; Trotman, Lloyd C; Kinney, Justin B; Sordella, Raffaella

    2017-02-22

    The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter. In particular, when co-expressed with inducible Cre-ER T2 , our system enables parallel, independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic characterization and identification of essential genes, as well as the investigation of the interactions between functional genes.

  13. Optimization-based design of heat flux manipulation devices with emphasis on fabricability.

    Science.gov (United States)

    Peralta, Ignacio; Fachinotti, Víctor D

    2017-07-24

    In this work, we present a new method for the design of heat flux manipulating devices, with emphasis on their fabricability. The design is obtained as solution of a nonlinear optimization problem where the objective function represents the given heat flux manipulation task, and the design variables define the material distribution in the device. In order to facilitate the fabrication of the device, the material at a given point is chosen from a set of predefined metamaterials. Each candidate material is assumed to be a laminate of materials with high conductivity contrast, so it is a metamaterial with a highly anisotropic effective conductivity. Following the discrete material optimization (DMO) approach, the fraction of each material at a given finite element of the mesh is defined as a function of continuous variables, which are ultimately the design variables. This DMO definition forces the fraction of each candidate to tend to either zero or one at the optimal solution. As an application example, we designed an easy-to-make device for heat flux concentration and cloaking.

  14. Laser-ablation-based ion source characterization and manipulation for laser-driven ion acceleration

    Science.gov (United States)

    Sommer, P.; Metzkes-Ng, J.; Brack, F.-E.; Cowan, T. E.; Kraft, S. D.; Obst, L.; Rehwald, M.; Schlenvoigt, H.-P.; Schramm, U.; Zeil, K.

    2018-05-01

    For laser-driven ion acceleration from thin foils (∼10 μm–100 nm) in the target normal sheath acceleration regime, the hydro-carbon contaminant layer at the target surface generally serves as the ion source and hence determines the accelerated ion species, i.e. mainly protons, carbon and oxygen ions. The specific characteristics of the source layer—thickness and relevant lateral extent—as well as its manipulation have both been investigated since the first experiments on laser-driven ion acceleration using a variety of techniques from direct source imaging to knife-edge or mesh imaging. In this publication, we present an experimental study in which laser ablation in two fluence regimes (low: F ∼ 0.6 J cm‑2, high: F ∼ 4 J cm‑2) was applied to characterize and manipulate the hydro-carbon source layer. The high-fluence ablation in combination with a timed laser pulse for particle acceleration allowed for an estimation of the relevant source layer thickness for proton acceleration. Moreover, from these data and independently from the low-fluence regime, the lateral extent of the ion source layer became accessible.

  15. Underwater manipulator

    Science.gov (United States)

    Schrum, P.B.; Cohen, G.H.

    1993-04-20

    Self-contained, waterproof, water-submersible, remote-controlled apparatus is described for manipulating a device, such as an ultrasonic transducer for measuring crack propagation on an underwater specimen undergoing shock testing. The subject manipulator includes metal bellows for transmittal of angular motions without the use of rotating shaft seals or O-rings. Inside the manipulator, a first stepper motor controls angular movement. In the preferred embodiment, the bellows permit the first stepper motor to move an ultrasonic transducer [plus minus]45 degrees in a first plane and a second bellows permit a second stepper motor to move the transducer [plus minus]10 degrees in a second plane orthogonal to the first. In addition, an XY motor-driven table provides XY motion.

  16. Underwater manipulator

    International Nuclear Information System (INIS)

    Schrum, P.B.; Cohen, G.H.

    1993-01-01

    Self-contained, waterproof, water-submersible, remote-controlled apparatus is described for manipulating a device, such as an ultrasonic transducer for measuring crack propagation on an underwater specimen undergoing shock testing. The subject manipulator includes metal bellows for transmittal of angular motions without the use of rotating shaft seals or O-rings. Inside the manipulator, a first stepper motor controls angular movement. In the preferred embodiment, the bellows permit the first stepper motor to move an ultrasonic transducer ±45 degrees in a first plane and a second bellows permit a second stepper motor to move the transducer ±10 degrees in a second plane orthogonal to the first. In addition, an XY motor-driven table provides XY motion

  17. Higher growth rate and gene expression in male zebra finch embryos are independent of manipulation of maternal steroids in the eggs.

    Science.gov (United States)

    Lutyk, Dorota; Tagirov, Makhsud; Drobniak, Szymon; Rutkowska, Joanna

    2017-12-01

    Sexual dimorphism in prenatal development is widespread among vertebrates, including birds. Its mechanism remains unclear, although it has been attributed to the effect of maternal steroid hormones. The aim of this study was to investigate how increased levels of steroid hormones in the eggs influence early embryonic development of male and female offspring. We also asked whether maternal hormones take part in the control of sex-specific expression of the genes involved in prenatal development. We experimentally manipulated hormones' concentrations in the egg yolk by injecting zebra finch females prior to ovulation with testosterone or corticosterone. We assessed growth rate and expression levels of CDK7, FBP1 and GHR genes in 37h-old embryos. We found faster growth and higher expression of two studied genes in male compared to female embryos. Hormonal treatment, despite clearly differentiating egg steroid levels, had no effect on the sex-specific pattern of the embryonic gene expression, even though we confirmed expression of receptors of androgens and glucocorticoids at such an early stage of development. Thus, our study shows high stability of the early sex differences in the embryonic development before the onset of sexual differentiation and indicates their independence of maternal hormones in the egg. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Nanoparticles for siRNA-Based Gene Silencing in Tumor Therapy.

    Science.gov (United States)

    Babu, Anish; Muralidharan, Ranganayaki; Amreddy, Narsireddy; Mehta, Meghna; Munshi, Anupama; Ramesh, Rajagopal

    2016-12-01

    Gene silencing through RNA interference (RNAi) has emerged as a potential strategy in manipulating cancer causing genes by complementary base-pairing mechanism. Small interfering RNA (siRNA) is an important RNAi tool that has found significant application in cancer therapy. However due to lack of stability, poor cellular uptake and high probability of loss-of-function due to degradation, siRNA therapeutic strategies seek safe and efficient delivery vehicles for in vivo applications. The current review discusses various nanoparticle systems currently used for siRNA delivery for cancer therapy, with emphasis on liposome based gene delivery systems. The discussion also includes various methods availed to improve nanoparticle based-siRNA delivery with target specificity and superior efficiency. Further this review describes challenges and perspectives on the development of safe and efficient nanoparticle based-siRNA-delivery systems for cancer therapy.

  19. Computationally efficient dynamic modeling of robot manipulators with multiple flexible-links using acceleration-based discrete time transfer matrix method

    DEFF Research Database (Denmark)

    Zhang, Xuping; Sørensen, Rasmus; RahbekIversen, Mathias

    2018-01-01

    This paper presents a novel and computationally efficient modeling method for the dynamics of flexible-link robot manipulators. In this method, a robot manipulator is decomposed into components/elements. The component/element dynamics is established using Newton–Euler equations, and then is linea......This paper presents a novel and computationally efficient modeling method for the dynamics of flexible-link robot manipulators. In this method, a robot manipulator is decomposed into components/elements. The component/element dynamics is established using Newton–Euler equations......, and then is linearized based on the acceleration-based state vector. The transfer matrices for each type of components/elements are developed, and used to establish the system equations of a flexible robot manipulator by concatenating the state vector from the base to the end-effector. With this strategy, the size...... manipulators, and only involves calculating and transferring component/element dynamic equations that have small size. The numerical simulations and experimental testing of flexible-link manipulators are conducted to validate the proposed methodologies....

  20. Manipulatives Work!

    Science.gov (United States)

    Moch, Peggy L.

    2001-01-01

    Fifth graders (n=16) engaged in manipulative activities to improve their grasp of math concepts; one-third were identified as exceptional children. Posttest results after 12 lessons showed the overall class average increased from 49% to 59% and all areas improved compared to pretest scores. Attitude changes were also apparent. (Contains 24…

  1. Cloning and manipulation of the Schizosaccharomyces pombe his7+ gene as a new selectable marker for molecular genetic studies

    Science.gov (United States)

    Apolinario, Ethel; Nocero, Mary; Jin, Mei; Hoffman, Charles S.

    2015-01-01

    We have cloned the his7+ gene of the fission yeast Schizosaccharomyces pombe by complementation of the recessive mutant allele his7-366. The his7+ gene is able to complement a mutation of the Escherichia coli hisI gene, suggesting that his7+ encodes a phosphoribosyl-AMP cyclohydrase. Subcloning experiments localize the gene to a 1.9-kb XbaI-BglII fragment. We describe the construction of plasmids to facilitate the use of his7+ as a selectable marker in S. pombe studies. Plasmid pEA2 carries his7+ cloned into the pUC18 polylinker. From either pEA2 or the original his7+ clone, pMN1, fragments carrying his7+ can be isolated using a variety of restriction enzymes for the construction of gene disruptions. Plasmid pEA500 is a cloning vector that carries his7+ and ars1, yet retains the ability to use the blue/white color screen to identify recombinants. PMID:8299169

  2. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. 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

    2008-04-01

    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.

  4. Manipulation of DET1 expression in tomato results in photomorphogenic phenotypes caused by post-transcriptional gene silencing.

    Science.gov (United States)

    Davuluri, Ganga Rao; van Tuinen, Ageeth; Mustilli, Anna Chiara; Manfredonia, Alessandro; Newman, Robert; Burgess, Diane; Brummell, David A; King, Stephen R; Palys, Joe; Uhlig, John; Pennings, Henk M J; Bowler, Chris

    2004-11-01

    The tomato HIGH PIGMENT-2 gene encodes an orthologue of the Arabidopsis nuclear protein DE-ETIOLATED 1 (DET1). From genetic analyses it has been proposed that DET1 is a negative regulator of light signal transduction, and recent results indicate that it may control light-regulated gene expression at the level of chromatin remodelling. To gain further understanding about the function of DET1 during plant development, we generated a range of overexpression constructs and introduced them into tomato. Unexpectedly, we only observed phenotypes characteristic of DET1 inactivation, i.e. hyper-responsiveness to light. Molecular analysis indicated in all cases that these phenotypes were a result of suppression of endogenous DET1 expression, due to post-transcriptional gene silencing. DET1 silencing was often lethal when it occurred at relatively early stages of plant development, whereas light hyper-responsive phenotypes were obtained when silencing occurred later on. The appearance of phenotypes correlated with the generation of siRNAs but not DNA hypermethylation, and was most efficient when using constructs with mutations in the DET1 coding sequence or with constructs containing only the 3'-terminal portion of the gene. These results indicate an important function for DET1 throughout plant development and demonstrate that silencing of DET1 in fruits results in increased carotenoids, which may have biotechnological potential.

  5. Social context affects behavior, preoptic area gene expression, and response to D2 receptor manipulation during territorial defense in a cichlid fish.

    Science.gov (United States)

    Weitekamp, C A; Nguyen, J; Hofmann, H A

    2017-07-01

    Social context often has profound effects on behavior, yet the neural and molecular mechanisms which mediate flexible behavioral responses to different social environments are not well understood. We used the African cichlid fish, Astatotilapia burtoni, to examine aggressive defense behavior across three social contexts representing different motivational states: a reproductive opportunity, a familiar male and a neutral context. To elucidate how differences in behavior across contexts may be mediated by neural gene expression, we examined gene expression in the preoptic area, a brain region known to control male aggressive and sexual behavior. We show that social context has broad effects on preoptic gene expression. Specifically, we found that the expression of genes encoding nonapeptides and sex steroid receptors are upregulated in the familiar male context. Furthermore, circulating levels of testosterone and cortisol varied markedly depending on social context. We also manipulated the D2 receptor (D2R) in each social context, given that it has been implicated in mediating context-dependent behavior. We found that a D2R agonist reduced intruder-directed aggression in the reproductive opportunity and familiar male contexts, while a D2R antagonist inhibited intruder-directed aggression in the reproductive opportunity context and increased aggression in the neutral context. Our results demonstrate a critical role for preoptic gene expression, as well as circulating steroid hormone levels, in encoding information from the social environment and in shaping adaptive behavior. In addition, they provide further evidence for a role of D2R in context-dependent behavior. © 2017 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  6. Synergy-Based Bilateral Port: A Universal Control Module for Tele-Manipulation Frameworks Using Asymmetric Master–Slave Systems

    Science.gov (United States)

    Brygo, Anais; Sarakoglou, Ioannis; Grioli, Giorgio; Tsagarakis, Nikos

    2017-01-01

    Endowing tele-manipulation frameworks with the capability to accommodate a variety of robotic hands is key to achieving high performances through permitting to flexibly interchange the end-effector according to the task considered. This requires the development of control policies that not only cope with asymmetric master–slave systems but also whose high-level components are designed in a unified space in abstraction from the devices specifics. To address this dual challenge, a novel synergy port is developed that resolves the kinematic, sensing, and actuation asymmetries of the considered system through generating motion and force feedback references in the hardware-independent hand postural synergy space. It builds upon the concept of the Cartesian-based synergy matrix, which is introduced as a tool mapping the fingertips Cartesian space to the directions oriented along the grasp principal components. To assess the effectiveness of the proposed approach, the synergy port has been integrated into the control system of a highly asymmetric tele-manipulation framework, in which the 3-finger hand exoskeleton HEXOTRAC is used as a master device to control the SoftHand, a robotic hand whose transmission system relies on a single motor to drive all joints along a soft synergistic path. The platform is further enriched with the vision-based motion capture system Optitrack to monitor the 6D trajectory of the user’s wrist, which is used to control the robotic arm on which the SoftHand is mounted. Experiments have been conducted with the humanoid robot COMAN and the KUKA LWR robotic manipulator. Results indicate that this bilateral interface is highly intuitive and allows users with no prior experience to reach, grasp, and transport a variety of objects exhibiting very different shapes and impedances. In addition, the hardware and control solutions proved capable of accommodating users with different hand kinematics. Finally, the proposed control framework offers a

  7. Perception-based effects of clinical exposure to osteopathic manipulative treatment on first- and second-year osteopathic medical students.

    Science.gov (United States)

    Vazzana, Kathleen M; Yao, Sheldon C; Jung, Min-Kyung; Terzella, Michael J

    2014-07-01

    Little research has been done regarding osteopathic medical students' clinical exposure to osteopathic manipulative treatment (OMT). Most existing research focuses on third- and fourth-year students. To determine the effects of clinical exposure to OMT on first- and second-year osteopathic medical students by assessing the same population's perceptions of OMT. In the present survey-based study, conducted at the New York Institute of Technology College of Osteopathic Medicine, first- and second-year osteopathic medical students were administered an electronic survey containing 18 multiple-choice questions. The first 2 questions were demographic. The next 6 questions had participants identify what, if any, clinical exposure to OMT they had, including clinical shadowing, the MedPrep program, and the Summer Student American Academy of Osteopathy Osteopathic Manipulative Medicine Preceptorship program. The 10 questions that followed assessed the participant's perception of OMT: (1) understanding, (2) attitude toward OMT, (3) scope of practice of OMT, and (4) intention to use OMT in future clinical practice. The survey used the statistically validated Likert scale for all of the scaled questions. Analysis was performed using the Pearson χ(2) test and the Fisher exact test. Of the 600 students who were sent surveys, 364 replied, for a response rate of 60.7%. There was an association with students' anticipated use of OMT in their future clinical practice and the following types of clinical exposures to OMT: MedPrep (P=.04), Summer Student American Academy of Osteopathy Osteopathic Manipulative Medicine Preceptorship (P=.04), extracurricular OMT didactics (P=.048), and shadowing a physician performing OMT before attending osteopathic medical school (P=.007). Being treated with OMT had no association with anticipated future use of OMT. More OMT clinical exposures were associated with more positive responses to the perception questions ([Formula: see text], Pperception of

  8. A dynamic model for GPS based attitude determination and testing using a serial robotic manipulator.

    Science.gov (United States)

    Raskaliyev, Almat; Patel, Sarosh; Sobh, Tarek

    2017-07-01

    A computational algorithm is developed for estimating accurately the attitude of a robotic arm which moves along a predetermined path. This algorithm requires preliminary input data obtained in the static mode to yield phase observables for the precise, 3-axis attitude determination of a swinging manipulator in the dynamic mode. Measurements are recorded simultaneously by three GPS L1 receivers and then processed in several steps to accomplish this task. First, artkconv batch executable converts GPS receiver readings into RINEX format to generate GPS observables and ephemeris for multiple satellites. Then baseline vectors determination is carried out by baseline constrained Least-Squares Ambiguity Decorrelation (LAMBDA) method that uses double difference carrier phase estimates as input to calculate integer solution for each baseline. Finally, attitude determination is made by employing alternatively Least-squares attitude determination (LSAD) in the static mode and extended Kalman filter in the dynamic mode. The algorithm presented in this paper is applied to recorded data on Mitsubishi RV-M1 robotic arm in order to produce attitude estimates. These results are confirmed by another set of Euler angles independently evaluated from robotic arm postures obtained along the predefined trajectory.

  9. A dynamic model for GPS based attitude determination and testing using a serial robotic manipulator

    Directory of Open Access Journals (Sweden)

    Almat Raskaliyev

    2017-07-01

    Full Text Available A computational algorithm is developed for estimating accurately the attitude of a robotic arm which moves along a predetermined path. This algorithm requires preliminary input data obtained in the static mode to yield phase observables for the precise, 3-axis attitude determination of a swinging manipulator in the dynamic mode. Measurements are recorded simultaneously by three GPS L1 receivers and then processed in several steps to accomplish this task. First, artkconv batch executable converts GPS receiver readings into RINEX format to generate GPS observables and ephemeris for multiple satellites. Then baseline vectors determination is carried out by baseline constrained Least-Squares Ambiguity Decorrelation (LAMBDA method that uses double difference carrier phase estimates as input to calculate integer solution for each baseline. Finally, attitude determination is made by employing alternatively Least-squares attitude determination (LSAD in the static mode and extended Kalman filter in the dynamic mode. The algorithm presented in this paper is applied to recorded data on Mitsubishi RV-M1 robotic arm in order to produce attitude estimates. These results are confirmed by another set of Euler angles independently evaluated from robotic arm postures obtained along the predefined trajectory.

  10. Improved Alkane Production in Nitrogen-Fixing and Halotolerant Cyanobacteria via Abiotic Stresses and Genetic Manipulation of Alkane Synthetic Genes.

    Science.gov (United States)

    Kageyama, Hakuto; Waditee-Sirisattha, Rungaroon; Sirisattha, Sophon; Tanaka, Yoshito; Mahakhant, Aparat; Takabe, Teruhiro

    2015-07-01

    Cyanobacteria possess the unique capacity to produce alkane. In this study, effects of nitrogen deficiency and salt stress on biosynthesis of alkanes were investigated in three kinds of cyanobacteria. Intracellular alkane accumulation was increased in nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, but decreased in non-diazotrophic cyanobacterium Synechococcus elongatus PCC7942 and constant in a halotolerant cyanobacterium Aphanothece halophytica under nitrogen-deficient condition. We also found that salt stress increased alkane accumulation in Anabaena sp. PCC7120 and A. halophytica. The expression levels of two alkane synthetic genes were not upregulated significantly under nitrogen deficiency or salt stress in Anabaena sp. PCC7120. The transformant Anabaena sp. PCC7120 cells with additional alkane synthetic gene set from A. halophytica increased intracellular alkane accumulation level compared to control cells. These results provide a prospect to improve bioproduction of alkanes in nitrogen-fixing halotolerant cyanobacteria via abiotic stresses and genetic engineering.

  11. Hydraulic manipulator

    International Nuclear Information System (INIS)

    Sinha, A.K.; Srikrishnamurty, G.

    1990-01-01

    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

  12. 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.

  13. Improvement of Hydrodynamics-Based Gene Transfer of Nonviral DNA Targeted to Murine Hepatocytes

    Directory of Open Access Journals (Sweden)

    Shingo Nakamura

    2013-01-01

    Full Text Available The liver is an important organ for supporting the life of an individual. Gene transfer toward this organ has been attempted in many laboratories to date; however, there have been few reports on improved liver-targeted gene delivery by using a nonviral vector. In this study, we examined the effect of various types of gene delivery carriers on enhancing the uptake and gene expression of exogenous DNA in murine hepatocytes when a hydrodynamics-based gene delivery (HGD is performed via tail-vein injection. Mice were singly injected with a large amount of phosphate-buffered saline containing reporter plasmid DNA and/or with a gene delivery carrier. One day after the gene delivery, the animals' livers were dissected and subjected to biochemical, histochemical, and molecular biological analyses. The strongest signal from the reporter plasmid DNA was observed when the DNA was mixed with a polyethylenimine- (PEI- based reagent. Coinjection with pCRTEIL (a loxP-floxed reporter construct and pTR/NCre (a liver-specific Cre expression vector resulted in the liver-specific recombination of pCRTEIL. The combination of PEI with HGD would thus be a valuable tool for liver-specific manipulation to examine the function of a gene of interest in the liver and for creating liver disease models.

  14. Paper-based Synthetic Gene Networks

    Science.gov (United States)

    Pardee, Keith; Green, Alexander A.; Ferrante, Tom; Cameron, D. Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J.

    2014-01-01

    Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides a new venue for synthetic biologists to operate, and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze-dried onto paper, enabling the inexpensive, sterile and abiotic distribution of synthetic biology-based technologies for the clinic, global health, industry, research and education. For field use, we create circuits with colorimetric outputs for detection by eye, and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors. PMID:25417167

  15. Evidence based selection of housekeeping genes

    NARCIS (Netherlands)

    de Jonge, Hendrik J. M.; Fehrmann, Rudolf S. N.; de Bont, Eveline S. J. M.; Hofstra, Robert M. W.; Gerbens, Frans; Kamps, Willem A.; de 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

  16. Calibration and Motion Control of a Cable-Driven Parallel Manipulator Based Triple-Level Spatial Positioner

    Directory of Open Access Journals (Sweden)

    Xuechao Duan

    2014-02-01

    Full Text Available This paper deals with the kinematic calibration and motion control of a triple-level spatial positioner consisting of the cable-driven parallel manipulator (CDPM, active gyro stabilizer (AGS, and the Stewart platform. A six-degree-of-freedom laser tracker is employed when calibrating the benchmark positions and measuring the real-time position and orientation in motion control, which makes it a straightforward solution to tackle with hierarchical mechatronic system actuated by servomotors with incremental encoders. Then the trajectory planning and motion control of the triple-level robotic spatial positioner are explored to verify the correctness and to what extent the calibration improves the system. This CDPM based spatial positioner has an accuracy of several millimeters though it has a ten-meter workspace.

  17. 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

  18. Manipulating galectin expression in zebrafish (Danio rerio)

    Digital Repository Service at National Institute of Oceanography (India)

    Feng, C.; Nita-Lazar, M.; Gonzalez-Montalban, N.; Wang, J.; Mancini, J.; Ravindran, C.; Ahmed, H.; Vasta, G.R.

    , autoimmunity and cancer, thus making them potential molecular targets for innovative drug discovery. Here, we provide a review of the current methods available for the manipulation of gene expression in the zebrafish, with a focus on gene knockdown [morpholino...

  19. 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.

  20. 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.

  1. 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...

  2. 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

    Functional imaging studies have demonstrated that processing of man-made objects activate the left ventral premotor cortex, which is known to be concerned with motor function. This has led to the suggestion that the comprehension of man-made objects may rely on motor-based knowledge of object uti...

  3. 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.

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

    International Nuclear Information System (INIS)

    Henriet, J.; Fontaine, E.; Bopp, M.; Makovicka, L.; Farah, J.; Broggio, D.; Franck, D.; Chebel-Morello, B.

    2010-01-01

    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

  5. Manipulation of Gap Nodes by Uniaxial Strain in Iron-Based Superconductors

    Science.gov (United States)

    Kang, Jian; Kemper, Alexander F.; Fernandes, Rafael M.

    2014-11-01

    In the iron pnictides and chalcogenides, multiple orbitals participate in the superconducting state, enabling different gap structures to be realized in distinct materials. Here we argue that the spectral weights of these orbitals can, in principle, be controlled by a tetragonal symmetry-breaking uniaxial strain, due to the enhanced nematic susceptibility of many iron-based superconductors. By investigating multiorbital microscopic models in the presence of orbital order, we show that not only Tc can be enhanced, but pairs of accidental gap nodes can be annihilated and created in the Fermi surface by an increasing external strain. We explain our results as a mixture of nearly degenerate superconducting states promoted by strain, and show that the annihilation and creation of nodes can be detected experimentally via anisotropic penetration depth measurements. Our results provide a promising framework to externally control the superconducting properties of iron-based materials.

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

    Indian Academy of Sciences (India)

    A revolute joint R at Ai (i = 1,2,3) connects the lower member of each limb to the fixed base and a spherical joint S at Bi connects the upper member to the moving platform. The axes of the revolute joints are J1,J2 and J3. ai = [ax ay az]T is the position vector of the revolute joint Ai (i = 1,2,3) with respect to the fixed frame XYZ ...

  7. 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.

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

    International Nuclear Information System (INIS)

    Kuhn, R.W.

    1976-01-01

    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

  9. 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.

  10. Optimal trajectory planning of a 5-axis machine tool based on a 6-axis parallel manipulator.

    OpenAIRE

    Merlet, Jean-Pierre; Perng, M.-W.; Daney, David

    2000-01-01

    International audience; Many new machine-tool are based on a hexapod structure, a parallel robot with 6 DOF, While only 5 of them are needed for the machining operations as the rotation of the end-effector around its normal is not used. We have therefore an extra DoF: we propose an algorithm which is able to determine for almost any trajectory of the machine the values of the extra DoF to ensure that the trajectory lie within the workspace of the robot is singularity -free and furthermore opt...

  11. Multiobjective differential evolution-based multifactor dimensionality reduction for detecting gene-gene interactions.

    Science.gov (United States)

    Yang, Cheng-Hong; Chuang, Li-Yeh; Lin, Yu-Da

    2017-10-09

    Epistasis within disease-related genes (gene-gene interactions) was determined through contingency table measures based on multifactor dimensionality reduction (MDR) using single-nucleotide polymorphisms (SNPs). Most MDR-based methods use the single contingency table measure to detect gene-gene interactions; however, some gene-gene interactions may require identification through multiple contingency table measures. In this study, a multiobjective differential evolution method (called MODEMDR) was proposed to merge the various contingency table measures based on MDR to detect significant gene-gene interactions. Two contingency table measures, namely the correct classification rate and normalized mutual information, were selected to design the fitness functions in MODEMDR. The characteristics of multiobjective optimization enable MODEMDR to use multiple measures to efficiently and synchronously detect significant gene-gene interactions within a reasonable time frame. Epistatic models with and without marginal effects under various parameter settings (heritability and minor allele frequencies) were used to assess existing methods by comparing the detection success rates of gene-gene interactions. The results of the simulation datasets show that MODEMDR is superior to existing methods. Moreover, a large dataset obtained from the Wellcome Trust Case Control Consortium was used to assess MODEMDR. MODEMDR exhibited efficiency in identifying significant gene-gene interactions in genome-wide association studies.

  12. [Study on force feedback of acupuncture manipulation at Jianliao (TE 14) based on VOXEL-MAN].

    Science.gov (United States)

    Wang, Hai-sheng; Yan, Zhen-guo; Cheng, Zhuo; Shao, Shui-jin; Zhuang, Tian-ge

    2009-09-01

    To discuss the mechanical virtual reality when acupuncture on Jianliao (TE 14) so as to get perform perceptual knowledge of acupuncture for beginners through studying 3D reconstruction of surrounding tissues of this acupoint. Related tissues were segmented and reconstructed by establishing mathematics model based on the operational platform of VOXEL-MAN (vision reappearance); and mechanical model was constructed and fused with related data of virtual human (touch reappearance); data communication between the force feedback apparatus and the operational platform of virtual human were set up by interchanging vision reappearance module and touch reappearance module. In Linux system, the operator could experience the mechanical changes while needle-tip passing various tissues of Jianliao (TE 14) as well as lifting and thrusting evenly in needling process through the force feedback apparatus. Based on the platform of VOXEL-MAN, the sensation of needling at jianliao (TE 14) could be reappeared idealy by strength feedback instrument, so that the beginners could imitate, learn and practice the virtual acupuncture.

  13. Mapping of bionic array electric field focusing in plasmid DNA-based gene electrotransfer.

    Science.gov (United States)

    Browne, C J; Pinyon, J L; Housley, D M; Crawford, E N; Lovell, N H; Klugmann, M; Housley, G D

    2016-04-01

    Molecular medicine through gene therapy is challenged to achieve targeted action. This is now possible utilizing bionic electrode arrays for focal delivery of naked (plasmid) DNA via gene electrotransfer. Here, we establish the properties of array-based electroporation affecting targeted gene delivery. An array with eight 300 μm platinum ring electrodes configured as a cochlear implant bionic interface was used to transduce HEK293 cell monolayers with a plasmid-DNA green fluorescent protein (GFP) reporter gene construct. Electroporation parameters were pulse intensity, number, duration, separation and electrode configuration. The latter determined the shape of the electric fields, which were mapped using a voltage probe. Electrode array-based electroporation was found to require ~100 × lower applied voltages for cell transduction than conventional electroporation. This was found to be due to compression of the field lines orthogonal to the array. A circular area of GFP-positive cells was created when the electrodes were ganged together as four adjacent anodes and four cathodes, whereas alternating electrode polarity created a linear area of GFP-positive cells. The refinement of gene delivery parameters was validated in vivo in the guinea pig cochlea. These findings have significant clinical ramifications, where spatiotemporal control of gene expression can be predicted by manipulation of the electric field via current steering at a cellular level.

  14. Stabilisation of a three-dimensional boundary layer by base-flow manipulation using plasma actuators

    International Nuclear Information System (INIS)

    Dörr, P C; Kloker, M J

    2015-01-01

    The applicability of dielectric barrier discharge plasma actuators for controlling the crossflow-vortex-induced laminar breakdown in a three-dimensional swept-wing-type boundary-layer flow is investigated using direct numerical simulation. Similar to the classical application of suction at the wall the aim is to modify the quasi two-dimensional base flow and to weaken primary crossflow (CF) instability, mainly due to a reduction of the basic CF. Not only localised volumetric forcing by plasma actuators but also CF counter-blowing and spots with a moving wall are investigated to identify effective fundamental mechanisms. It is found that counter blowing always results in partial blockage of the flow and eventually increased CF velocity, whereas moving-wall spots can slightly reduce the CF and the amplitude of crossflow vortices. Using discrete volumetric forcing a significant attenuation even of finite-amplitude crossflow vortices and thus a distinct transition delay is achieved. (paper)

  15. Far-field high resolution effects and manipulating of electromagnetic waves based on transformation optics

    Science.gov (United States)

    Ji, XueBin; Zang, XiaoFei; Li, Zhou; Shi, Cheng; Chen, Lin; Cai, Bin; Zhu, YiMing

    2015-05-01

    Based on the transformation optics (TO) and the effective medium theory (EMT), a new illusion media with homogeneous and isotropic materials is proposed to realize the far-field high resolution effects. When two point sources with the separation distance of λ0 / 4 are covered with the illusion media (λ0 is the free-space wavelength), the corresponding far-field pattern is equivalent to the case of two point sources with the separation distance larger than λ0 / 2 in free space, leading to the far-field high resolution effects (in free space, the separation distance of λ0 / 4 is less than half-wavelength, and thus the two point sources cannot be distinguished from each other). Furthermore, such illusion media can be applied to design tunable high-directivity antenna and an angle-dependent floating carpet cloak. Full wave simulations are carried out to verify the performance of our device.

  16. A metasurface-based prism analogue for terahertz rainbow spectrum manipulation

    Science.gov (United States)

    Zheng, Shen; Li, Chao; Li, Shichao; Zhang, Xiaojuan; Fang, Guangyou

    2017-06-01

    Optical prisms can spread compound light spatially into a rainbow and have widespread applications in spectroscopy and imaging. Limited by the natural materials as well as technologies, there has been no natural counterpart of the optical prism that works in the Terahertz (THz) band so far. In this letter, a THz prism analogue based on metasurfaces working in the transmission diffraction mechanism is first proposed to generate the THz rainbow spectrum. The physics of different modes excited by the interaction between the incident wave and the metasurface is investigated in theory and simulation. A coherent enhancement method was developed to improve the mode competition of the rainbow spectrum over other unwanted leaky modes to guarantee the high transfer efficiency of the wavelength dependent transmission diffraction. The experimental results show that the prism analogue can spread the incident spectrum from 0.15 to 0.22 THz in an angular scope of about 30.8° with comparatively high transferring efficiency.

  17. Nonlinear model-based control of the Czochralski process III: Proper choice of manipulated variables and controller parameter scheduling

    Science.gov (United States)

    Neubert, M.; Winkler, J.

    2012-12-01

    This contribution continues an article series [1,2] about the nonlinear model-based control of the Czochralski crystal growth process. The key idea of the presented approach is to use a sophisticated combination of nonlinear model-based and conventional (linear) PI controllers for tracking of both, crystal radius and growth rate. Using heater power and pulling speed as manipulated variables several controller structures are possible. The present part tries to systematize the properties of the materials to be grown in order to get unambiguous decision criteria for a most profitable choice of the controller structure. For this purpose a material specific constant M called interface mobility and a more process specific constant S called system response number are introduced. While the first one summarizes important material properties like thermal conductivity and latent heat the latter one characterizes the process by evaluating the average axial thermal gradients at the phase boundary and the actual growth rate at which the crystal is grown. Furthermore these characteristic numbers are useful for establishing a scheduling strategy for the PI controller parameters in order to improve the controller performance. Finally, both numbers give a better understanding of the general thermal system dynamics of the Czochralski technique.

  18. Multi-modal particle manipulator to enhance bead-based bioassays

    Science.gov (United States)

    Glynne-Jones, P.; Boltryk, R. J.; Hill, M.; Zhang, F.; Dong, L.; Wilkinson, J. S.; Brown, T.; Melvin, T.; Harris, N. R.

    2010-01-01

    By sequentially pushing micro-beads towards and away from a sensing surface, we show that ultrasonic radiation forces can be used to enhance the interaction between a functionalized glass surface and polystyrene micro-beads, and distinguish those that bind to the surface, ultimately by using an integrated optical waveguide implanted in the reflector to facilitate optical detection. The movement towards and immobilization of streptavidin coated beads onto a biotin functionalized waveguide surface is achieved by using a quarter-wavelength mode pushing beads onto the surface, while the removal of non-specifically bound beads uses a second quarter-wavelength mode which exhibits a kinetic energy maxima at the boundary between the carrier layer and fluid, drawing beads towards this surface. This has been achieved using a multi-modal acoustic device which exhibits both these quarter-wavelength resonances. Both 1-D acoustic modeling and finite element analysis has been used to design this device and investigate the spatial uniformity of the field. We demonstrate experimentally that 90% of specifically bound beads remain attached after applying ultrasound, with 80% of non-specifically bound control beads being successfully removed acoustically. This approach overcomes problems associated with lengthy sedimentation processes used for bead-based bioassays and surface (electrostatic) forces, which delay or prevent immobilization. We explain the potential of this technique in the development of DNA and protein assays in terms of detection speed and multiplexing.

  19. Efficient Disk-Based Techniques for Manipulating Very Large String Databases

    KAUST Repository

    Allam, Amin

    2017-05-18

    Indexing and processing strings are very important topics in database management. Strings can be database records, DNA sequences, protein sequences, or plain text. Various string operations are required for several application categories, such as bioinformatics and entity resolution. When the string count or sizes become very large, several state-of-the-art techniques for indexing and processing such strings may fail or behave very inefficiently. Modifying an existing technique to overcome these issues is not usually straightforward or even possible. A category of string operations can be facilitated by the suffix tree data structure, which basically indexes a long string to enable efficient finding of any substring of the indexed string, and can be used in other operations as well, such as approximate string matching. In this document, we introduce a novel efficient method to construct the suffix tree index for very long strings using parallel architectures, which is a major challenge in this category. Another category of string operations require clustering similar strings in order to perform application-specific processing on the resulting possibly-overlapping clusters. In this document, based on clustering similar strings, we introduce a novel efficient technique for record linkage and entity resolution, and a novel method for correcting errors in a large number of small strings (read sequences) generated by the DNA sequencing machines.

  20. Determining workspace parameters for a new type of 6RSS parallel manipulator based on structural and geometric models

    Directory of Open Access Journals (Sweden)

    Milica Lucian

    2017-01-01

    Full Text Available Workspace geometric modelling of a new type of 6RSS parallel manipulator is described below. In the beginning, the researches undertaken in this area by other authors are highlighted and then a definition of this type of mechanisms is provided. The structural model of the 6RSS manipulator is briefly described. Inverse geometric model and translation subspace methods are used in order to determine the dimensions that define the workspace volume of the parallel manipulator. The reachable workspace is defined as a subset of the whole workspace in relation with the positions achieved by the characteristic point.

  1. CRISPR/Cas9-based genome editing for simultaneous interference with gene expression and protein stability

    DEFF Research Database (Denmark)

    Martinez, Virginia; Lauritsen, Ida; Hobel, Tonja

    2017-01-01

    Interference with genes is the foundation of reverse genetics and is key to manipulation of living cells for biomedical and biotechnological applications. However, classical genetic knockout and transcriptional knockdown technologies have different drawbacks and offer no control over existing pro...

  2. 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.

  3. Role of an ultrathin platinum seed layer in antiferromagnet-based perpendicular exchange coupling and its electrical manipulation

    International Nuclear Information System (INIS)

    Wang, Y.Y.; Song, C.; Zhang, J.Y.; Pan, F.

    2017-01-01

    The requirement for low-power consumption advances the development of antiferromagnetic (AFM) spintronics manipulated by electric fields. Here we report an electrical manipulation of metallic AFM moments within IrMn/[Co/Pt] by interface engineering, where ultrathin non-magnetic metals are highlighted between IrMn and ferroelectric substrates. Ultrathin Pt seed layers are proved to be vital in elevating the blocking temperature and enhancing the perpendicular exchange coupling through modulating the domain structures of as-prepared IrMn AFM. Further electrical manipulations of perpendicular magnetic anisotropy crucially verify the indispensable role of pre-deposited ultrathin Pt layers in modulating IrMn antiferromagnetic moments, which is confirmed by the intimate correlation between the electrically manipulating AFM and improving its blocking temperature. Instead of immediate contact between IrMn AFM and ferroelectric substrates in a conventional way, interface engineering by adopting ultrathin seed layers here adds a new twist to the electrical modulation of AFM metals. This would provide scientific basis on how to manipulate AFM moments and optimize the design of practical AFM spintronics. - Highlights: • An alternative for manipulating antiferromagnet by interface engineering is provided. • Ultrathin Pt seed layers are vital in elevating the blocking temperature of IrMn. • Perpendicular exchange coupling in IrMn/[Co/Pt] can be modulated by seed layers. • Ultrathin Pt seed layers enable electrical control of perpendicular exchange coupling.

  4. Role of an ultrathin platinum seed layer in antiferromagnet-based perpendicular exchange coupling and its electrical manipulation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.Y., E-mail: wangyy@buaa.edu.cn [Department of Physics, Beihang University, Beijing 100191 (China); Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Song, C., E-mail: songcheng@mail.tsinghua.edu.cn [Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Zhang, J.Y. [Department of Physics, Beihang University, Beijing 100191 (China); Pan, F. [Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China)

    2017-04-15

    The requirement for low-power consumption advances the development of antiferromagnetic (AFM) spintronics manipulated by electric fields. Here we report an electrical manipulation of metallic AFM moments within IrMn/[Co/Pt] by interface engineering, where ultrathin non-magnetic metals are highlighted between IrMn and ferroelectric substrates. Ultrathin Pt seed layers are proved to be vital in elevating the blocking temperature and enhancing the perpendicular exchange coupling through modulating the domain structures of as-prepared IrMn AFM. Further electrical manipulations of perpendicular magnetic anisotropy crucially verify the indispensable role of pre-deposited ultrathin Pt layers in modulating IrMn antiferromagnetic moments, which is confirmed by the intimate correlation between the electrically manipulating AFM and improving its blocking temperature. Instead of immediate contact between IrMn AFM and ferroelectric substrates in a conventional way, interface engineering by adopting ultrathin seed layers here adds a new twist to the electrical modulation of AFM metals. This would provide scientific basis on how to manipulate AFM moments and optimize the design of practical AFM spintronics. - Highlights: • An alternative for manipulating antiferromagnet by interface engineering is provided. • Ultrathin Pt seed layers are vital in elevating the blocking temperature of IrMn. • Perpendicular exchange coupling in IrMn/[Co/Pt] can be modulated by seed layers. • Ultrathin Pt seed layers enable electrical control of perpendicular exchange coupling.

  5. Geometrical effect characterization of femtosecond-laser manufactured glass microfluidic chips based on optical manipulation of submicroparticles

    Science.gov (United States)

    Kotsifaki, Domna G.; Mackenzie, Mark D.; Polydefki, Georgia; Kar, Ajoy K.; Makropoulou, Mersini; Serafetinides, Alexandros A.

    2017-12-01

    Microfluidic devices provide a platform with wide ranging applications from environmental monitoring to disease diagnosis. They offer substantive advantages but are often not optimized or designed to be used by nonexpert researchers. Microchannels of a microanalysis platform and their geometrical characterization are of eminent importance when designing such devices. We present a method that is used to optimize each microchannel within a device using high-throughput particle manipulation. For this purpose, glass-based microfluidic devices, with three-dimensional channel networks of several geometrical sizes, were fabricated by employing laser fabrication techniques. The effect of channel geometry was investigated by employing an optical tweezer. The optical trapping force depends on the flow velocity that is associated with the dimensions of the microchannel. We observe a linear dependence of the trapping efficiency and of the fluid flow velocity, with the channel dimensions. We determined that the highest trapping efficiency was achieved for microchannels with aspect ratio equal to one. Numerical simulation validated the impact of the device design dimensions on the trapping efficiency. This investigation indicates that the geometrical characteristics, the flow velocity, and trapping efficiency are crucial and should be considered when fabricating microfluidic devices for cell studies.

  6. 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.

  7. Correlation-based linear discriminant classification for gene expression data.

    Science.gov (United States)

    Pan, M; Zhang, J

    2017-01-23

    Microarray gene expression technology provides a systematic approach to patient classification. However, microarray data pose a great computational challenge owing to their large dimensionality, small sample sizes, and potential correlations among genes. A recent study has shown that gene-gene correlations have a positive effect on the accuracy of classification models, in contrast to some previous results. In this study, a recently developed correlation-based classifier, the ensemble of random subspace (RS) Fisher linear discriminants (FLDs), was utilized. The impact of gene-gene correlations on the performance of this classifier and other classifiers was studied using simulated datasets and real datasets. A cross-validation framework was used to evaluate the performance of each classifier using the simulated datasets or real datasets, and misclassification rates (MRs) were computed. Using the simulated data, the average MRs of the correlation-based classifiers decreased as the correlations increased when there were more correlated genes. Using real data, the correlation-based classifiers outperformed the non-correlation-based classifiers, especially when the gene-gene correlations were high. The ensemble RS-FLD classifier is a potential state-of-the-art computational method. The correlation-based ensemble RS-FLD classifier was effective and benefited from gene-gene correlations, particularly when the correlations were high.

  8. A Synthetic Algorithm for Tracking a Moving Object in a Multiple-Dynamic Obstacles Environment Based on Kinematically Planar Redundant Manipulators

    Directory of Open Access Journals (Sweden)

    Hongzhe Jin

    2017-01-01

    Full Text Available This paper presents a synthetic algorithm for tracking a moving object in a multiple-dynamic obstacles environment based on kinematically planar manipulators. By observing the motions of the object and obstacles, Spline filter associated with polynomial fitting is utilized to predict their moving paths for a period of time in the future. Several feasible paths for the manipulator in Cartesian space can be planned according to the predicted moving paths and the defined feasibility criterion. The shortest one among these feasible paths is selected as the optimized path. Then the real-time path along the optimized path is planned for the manipulator to track the moving object in real-time. To improve the convergence rate of tracking, a virtual controller based on PD controller is designed to adaptively adjust the real-time path. In the process of tracking, the null space of inverse kinematic and the local rotation coordinate method (LRCM are utilized for the arms and the end-effector to avoid obstacles, respectively. Finally, the moving object in a multiple-dynamic obstacles environment is thus tracked via real-time updating the joint angles of manipulator according to the iterative method. Simulation results show that the proposed algorithm is feasible to track a moving object in a multiple-dynamic obstacles environment.

  9. 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...... (ERGDB) and were analyzed from multiple aspects. We explored the possible transcription regulation mechanism by capturing highly conserved promoter motifs across orthologous genes, using promoter regions that cover the range of [-1200, +500] relative to the transcription start sites. The motif detection...... is based on ab initio discovery of common cis-elements from the orthologous gene cluster from human, mouse and rat, thus reflecting a degree of promoter sequence preservation during evolution. The identified motifs are linked to transcription factor binding sites based on the TRANSFAC database. In addition...

  10. A Direct Kinematics Problem Solution for the Three-degree-of-freedom Parallel Structure Manipulator Based on Crank Mechanism

    Directory of Open Access Journals (Sweden)

    V. N. Paschenko

    2015-01-01

     to state the possibility to use the constructed model for the further development of control systems based on it.The paper shows the possibilities to use the presented solution to determine the working area of the mechanism. Computer simulation methods allowed us to find a working area of the manipulator without restrictions on the physical characteristics of a real model.

  11. Manipulating scattering features by metamaterials

    Directory of Open Access Journals (Sweden)

    Lu Cui

    2016-01-01

    Full Text Available We present a review on manipulations of electromagnetic scattering features by using metamaterials or metasurfaces. Several approaches in controlling the scattered fields of objects are presented, including invisibility cloaks and radar illusions based on transformation optics, carpet cloak using gradient metamaterials, dc cloaks, mantle cloaks based on scattering cancellation, “skin” cloaks using phase compensation, scattering controls with coding/programmable metasurfaces, and scattering reductions by multilayered structures. Finally, the future development of metamaterials on scattering manipulation is predicted.

  12. Numerical studies of manipulation and separation of Janus particles in nano-orifice based DC-dielectrophoretic microfluidic chips

    International Nuclear Information System (INIS)

    Zhao, Kai; Li, Dongqing

    2017-01-01

    The direct current dielectrophoretic (DC-DEP) manipulation and separation of polystyrene-based Janus particles and the homogeneous polystyrene particles in microchannels are numerically investigated. To induce the DEP force, a small electric potential difference is applied across the microchannel via a smaller nano-orifice on one side of the channel walls and a larger micro-orifice on the opposite channel wall. A strong non-uniform electric field gradient is generated by the asymmetric orifices, and the particles will undergo the DEP forces when moving with the flow through the vicinity of the small orifice, where the strongest electrical field gradient exists. By adjusting the electrical conductivity of the suspending solution, one kind of the particles will experience the negative DEP force while another will undergo the positive DEP force. In this way, the separation of 5 µ m Janus particles and homogeneous polystyrene particles, and the separation of 3 µ m and 5 µ m Janus particles were numerically demonstrated. Moreover, in order to further understand the dielectrophoretic motion of the Janus particles, the DC-DEP force on the Janus particles was analyzed and the effects of the electric fields, as well as the coating coverage, thickness, and electric conductivity of the Janus particles were studied. The results show that the Janus particles with gold coating coverage over 50% will experience positive DEP forces and be attracted towards the maximum electric fields. It is also found that the effect of the gold coating thickness of the Janus particles on their trajectories can be neglected when using the DC-DEP method. (paper)

  13. Progress in Nano-Electro-Optics VI Nano-Optical Probing, Manipulation, Analysis, and Their Theoretical Bases

    CERN Document Server

    Ohtsu, Motoichi

    2008-01-01

    This volume focuses on nano-optical probing, manipulation, and analysis. It begins with recent developments in near-field optical spectroscopy that clarify quantum states at the nanoscale, followed by a theory for a photon-electron-phonon interacting system at the nanoscale. Further topics include: visible laser desorption/ionization mass spectroscopy exhibiting near-field effects; a practical nanofabrication method with optical near fields applied to a SHG device; a theory and experimental achievements on optical transport of nanoparticles, selectively manipulated by resonant radiation force. Taken as a whole, this overview will be a valuable resource for engineers and scientists working in the field of nano-electro-optics.

  14. A Girl With Multiple Disabilities Increases Object Manipulation and Reduces Hand Mouthing Through a Microswitch-Based Program

    NARCIS (Netherlands)

    Lancioni, G.E.; Singh, N.N.; O'Reilly, M.F.; Sigafoos, J.; Didden, H.C.M.; Oliva, D.; Cingolani, E.

    2008-01-01

    The study was an effort to help a girl with multiple disabilities increase object manipulation responses and reduce hand mouthing, carried out according to an ABAB sequence (in which A represented baseline phases; B, treatment phases) and including a 3-month follow-up. During the baseline phases, a

  15. Contact State Estimation by Vision-based Tactile Sensors for Dexterous Manipulation with Robot Hands Based on Shape-Sensing

    Directory of Open Access Journals (Sweden)

    Yuji Ito

    2011-09-01

    Full Text Available We propose a new method for estimating the contact state of objects with varying shapes on a vision‐ based fluid‐type tactile sensor, which touch pad is an elastic transparent membrane of silicon rubber with dotted pattern printed on its inner side. The membrane is filled with translucent red colored water. The proposed method leads to better understanding of the object

  16. Contact State Estimation by Vision-Based Tactile Sensors for Dexterous Manipulation with Robot Hands Based on Shape-Sensing

    Directory of Open Access Journals (Sweden)

    Yuji Ito

    2011-09-01

    Full Text Available We propose a new method for estimating the contact state of objects with varying shapes on a vision-based fluid-type tactile sensor, which touch pad is an elastic transparent membrane of silicon rubber with dotted pattern printed on its inner side. The membrane is filled with translucent red colored water. The proposed method leads to better understanding of the object's shape and movement, and can be applied for accomplishing reliable and dexterous handling tasks by robot hands.

  17. Manipulating duckweed through genome duplication.

    Science.gov (United States)

    Vunsh, R; Heinig, U; Malitsky, S; Aharoni, A; Avidov, A; Lerner, A; Edelman, M

    2015-01-01

    Significant inter- and intraspecific genetic variation exists in duckweed, thus the potential for genome plasticity and manipulation is high. Polyploidy is recognised as a major mechanism of adaptation and speciation in plants. We produced several genome-duplicated lines of Landoltia punctata (Spirodela oligorrhiza) from both whole plants and regenerating explants using a colchicine-based cocktail. These lines stably maintained an enlarged frond and root morphology. DNA ploidy levels determined by florescence-activated cell sorting indicated genome duplication. Line A4 was analysed after 75 biomass doublings. Frond area, fresh and dry weights, rhizoid number and length were significantly increased versus wild type, while the growth rate was unchanged. This resulted in accumulation of biomass 17-20% faster in the A4 plants. We sought to determine if specific differences in gene products are found in the genome duplicated lines. Non-targeted ultra performance LC-quadrupole time of flight mass spectrometry was employed to compare some of the lines and the wild type to seek identification of up-regulated metabolites. We putatively identified differential metabolites in Line A65 as caffeoyl hexoses. The combination of directed genome duplication and metabolic profiling might offer a path for producing stable gene expression, leading to altered production of secondary metabolites. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  18. Heterologous Reconstitution of the Intact Geodin Gene Cluster in Aspergillus nidulans through a Simple and Versatile PCR Based Approach

    DEFF Research Database (Denmark)

    Nielsen, Morten Thrane; Nielsen, Jakob Blæsbjerg; Anyaogu, Dianna Chinyere

    2013-01-01

    was transferred in a two step procedure to an expression platform in A. nidulans. The individual cluster fragments were generated by PCR and assembled via efficient USER fusion prior to ransformation and integration via re-iterative gene targeting. A total of 13 open reading frames contained in 25 kb of DNA were...... of solid methodology for genetic manipulation of most species severely hampers pathway haracterization. Here we present a simple PCR based approach for heterologous reconstitution of intact gene clusters. Specifically, the putative gene cluster responsible for geodin production from Aspergillus terreus...... successfully transferred between the two species enabling geodin synthesis in A. nidulans. Subsequently, functions of three genes in the cluster were validated by genetic and chemical analyses. Specifically, ATEG_08451 (gedC) encodes a polyketide synthase, ATEG_08453 (gedR) encodes a transcription factor...

  19. 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.

  20. Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules

    Directory of Open Access Journals (Sweden)

    Ettore Mosca

    2017-09-01

    Full Text Available Autism spectrum disorder (ASD is marked by a strong genetic heterogeneity, which is underlined by the low overlap between ASD risk gene lists proposed in different studies. In this context, molecular networks can be used to analyze the results of several genome-wide studies in order to underline those network regions harboring genetic variations associated with ASD, the so-called “disease modules.” In this work, we used a recent network diffusion-based approach to jointly analyze multiple ASD risk gene lists. We defined genome-scale prioritizations of human genes in relation to ASD genes from multiple studies, found significantly connected gene modules associated with ASD and predicted genes functionally related to ASD risk genes. Most of them play a role in synapsis and neuronal development and function; many are related to syndromes that can be in comorbidity with ASD and the remaining are involved in epigenetics, cell cycle, cell adhesion and cancer.

  1. 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.

  2. A transgenic Neospora caninum strain based on mutations of the dihydrofolate reductase-thymidylate synthase gene.

    Science.gov (United States)

    Pereira, Luiz Miguel; Baroni, Luciana; Yatsuda, Ana Patrícia

    2014-03-01

    Neospora caninum is an Apicomplexa parasite related to abortion and losses of fertility in cattle. The amenability of Toxoplasma gondii and Plasmodium to genetic manipulation offers several tools to determine the invasion and replication processes, which support posterior strategies related to the combat of these diseases. For Plasmodium the use of pyrimethamine as an auxiliary drug on malaria treatment has been affected by the rise of resistant strains and the analyses on Dihydrofolate reductase-thymidylate synthase (DHFR-TS) gene indicated several point mutations. In this work we developed a method for stable insertion of genes based on resistance to pyrimethamine. For that, the coding sequence of NcDHFR-TS (Dihydrofolate reductase-thymidylate synthase) was point mutated in two amino acids, generating DHFRM2M3. The DHFRM2M3 flanked by the promoter and 3'UTR of Ncdhfr-ts (Ncdhfr-DHFRM2M3) conferred resistance to pyrimethamine after transfection. For illustration of stability and expression, the cassette Ncdhfr-DHFRM2M3 was ligated to the reporter gene Lac-Z (β-galactosidase enzyme) controlled by the N. caninum tubulin promoter and was transfected and selected in N. caninum. The cassette was integrated into the genome and the selected tachyzoites expressed Lac-Z, allowing the detection of tachyzoites by the CPRG reaction and X-gal precipitation. The obtainment of transgenic N. caninum resistant to pyrimethamine confirms the effects on DHFR-TS among the Apicomplexa members and will support future approaches on pholate inhibitors for N. caninum prophylaxis. The construction of stable tachyzoites based on vectors with N. caninum promoters initiates the molecular manipulation of this parasite independently of T. gondii. Copyright © 2014. Published by Elsevier Inc.

  3. The Dubbing of Gay-themed TV Series in Italy: Corpus-based Evidence of Manipulation and Censorship

    Directory of Open Access Journals (Sweden)

    Annalisa Sandrelli

    2016-02-01

    Full Text Available The manipulation and censorship of taboo and sensitive references in AVT has attracted the interest of several scholars over the last few years, but systematic studies of the impact of such practices on different genres in different countries are still needed. The paper analyses the Italian dubbing of three gay-themed TV series, Queer as Folk, Queer as Folk (US remake, and The L Word. Gay-themed series are less mainstream on Italian TV channels than in the UK and the USA, and gayspeak as a linguistic phenomenon is not well-known to Italian audiences. Consequently, the Italian dubbed dialogues are the product of different degrees of manipulation and even censorship. The paper finds empirical evidence of such alterations in data from the DubTalk corpus and attempts a tentative evaluation of the impact of such practices on the Italian versions of the above-mentioned series.

  4. Regulated expression of human A γ-, β-, and hybrid γ β-globin genes in transgenic mice: manipulation of the developmental expression patterns.

    NARCIS (Netherlands)

    G. Kollias (George); N. Wrighton; J. Hurst; F.G. Grosveld (Frank)

    1986-01-01

    textabstractWe have introduced the human fetal gamma- and adult beta-globin genes into the germ line of mice. Analysis of the resulting transgenic mice shows that the human gamma-globin gene is expressed like an embryonic mouse globin gene; the human beta-globin gene is expressed (as previously

  5. 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.

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

    Science.gov (United States)

    Radulovich, Nikolina; Leung, Lisa; Tsao, Ming-Sound

    2011-03-22

    The growing need for functional studies of genes has set the stage for the development of versatile tools for genetic manipulations. 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. 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.

  7. RNAi-based silencing of genes encoding the vacuolar- ATPase ...

    African Journals Online (AJOL)

    RNAi-based silencing of genes encoding the vacuolar- ATPase subunits a and c in pink bollworm (Pectinophora gossypiella). Ahmed M. A. Mohammed. Abstract. RNA interference is a post- transcriptional gene regulation mechanism that is predominantly found in eukaryotic organisms. RNAi demonstrated a successful ...

  8. DNA-energetics-based analyses suggest additional genes in ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... [Khandelwal G, Gupta J and Jayaram B 2012 DNA-energetics-based analyses suggest additional genes in prokaryotes. J. Biosci. 37 433–444] DOI ..... illustration for detecting potential new genes in 12 different genomes with varied GC ..... maps and genetic map of DNA double strand. J. Phys. Soc. Jpn.

  9. Nanotechnology-based gene-eluting stents.

    Science.gov (United States)

    Goh, Debbie; Tan, Aaron; Farhatnia, Yasmin; Rajadas, Jayakumar; Alavijeh, Mohammad S; Seifalian, Alexander M

    2013-04-01

    Cardiovascular disease is one of the major causes of death in the world. Coronary stenting in percutaneous coronary intervention (PCI) has revolutionized the field of cardiology. Coronary stenting is seen as a less invasive procedure compared to coronary artery bypass graft (CABG) surgery. Two main types of stents currently exist in the market: bare-metal stents (BMS) and drug-eluting stents (DES). DES were developed in response to problems associated with BMS use, like neointimal hyperplasia leading to restenosis. However, the use of DES engendered other problems as well, like late stent thrombosis (ST), which is a serious and lethal complication. Gene-eluting stents (GES) have recently been proposed as a novel method of circumventing problems seen in BMS and DES. Utilizing nanotechnology, sustained and localized delivery of genes can mitigate problems of restenosis and late ST by accelerating the regenerative capacity of re-endothelialization. Therefore this review seeks to explore the realm of GES as a novel alternative to BMS and DES, and its potential implications in the field of nanotechnology and regenerative medicine.

  10. Evaluation of Gene-Based Family-Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease

    Directory of Open Access Journals (Sweden)

    Maria V. Fernández

    2018-04-01

    Full Text Available Gene-based tests to study the combined effect of rare variants on a particular phenotype have been widely developed for case-control studies, but their evolution and adaptation for family-based studies, especially studies of complex incomplete families, has been slower. In this study, we have performed a practical examination of all the latest gene-based methods available for family-based study designs using both simulated and real datasets. We examined the performance of several collapsing, variance-component, and transmission disequilibrium tests across eight different software packages and 22 models utilizing a cohort of 285 families (N = 1,235 with late-onset Alzheimer disease (LOAD. After a thorough examination of each of these tests, we propose a methodological approach to identify, with high confidence, genes associated with the tested phenotype and we provide recommendations to select the best software and model for family-based gene-based analyses. Additionally, in our dataset, we identified PTK2B, a GWAS candidate gene for sporadic AD, along with six novel genes (CHRD, CLCN2, HDLBP, CPAMD8, NLRP9, and MAS1L as candidate genes for familial LOAD.

  11. 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.  

  12. Identifying key genes in glaucoma based on a benchmarked dataset and the gene regulatory network.

    Science.gov (United States)

    Chen, Xi; Wang, Qiao-Ling; Zhang, Meng-Hui

    2017-10-01

    The current study aimed to identify key genes in glaucoma based on a benchmarked dataset and gene regulatory network (GRN). Local and global noise was added to the gene expression dataset to produce a benchmarked dataset. Differentially-expressed genes (DEGs) between patients with glaucoma and normal controls were identified utilizing the Linear Models for Microarray Data (Limma) package based on benchmarked dataset. A total of 5 GRN inference methods, including Zscore, GeneNet, context likelihood of relatedness (CLR) algorithm, Partial Correlation coefficient with Information Theory (PCIT) and GEne Network Inference with Ensemble of Trees (Genie3) were evaluated using receiver operating characteristic (ROC) and precision and recall (PR) curves. The interference method with the best performance was selected to construct the GRN. Subsequently, topological centrality (degree, closeness and betweenness) was conducted to identify key genes in the GRN of glaucoma. Finally, the key genes were validated by performing reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 176 DEGs were detected from the benchmarked dataset. The ROC and PR curves of the 5 methods were analyzed and it was determined that Genie3 had a clear advantage over the other methods; thus, Genie3 was used to construct the GRN. Following topological centrality analysis, 14 key genes for glaucoma were identified, including IL6 , EPHA2 and GSTT1 and 5 of these 14 key genes were validated by RT-qPCR. Therefore, the current study identified 14 key genes in glaucoma, which may be potential biomarkers to use in the diagnosis of glaucoma and aid in identifying the molecular mechanism of this disease.

  13. DriverFinder: A Gene Length-Based Network Method to Identify Cancer Driver Genes

    Directory of Open Access Journals (Sweden)

    Pi-Jing Wei

    2017-01-01

    Full Text Available Integration of multi-omics data of cancer can help people to explore cancers comprehensively. However, with a large volume of different omics and functional data being generated, there is a major challenge to distinguish functional driver genes from a sea of inconsequential passenger genes that accrue stochastically but do not contribute to cancer development. In this paper, we present a gene length-based network method, named DriverFinder, to identify driver genes by integrating somatic mutations, copy number variations, gene-gene interaction network, tumor expression, and normal expression data. To illustrate the performance of DriverFinder, it is applied to four cancer types from The Cancer Genome Atlas including breast cancer, head and neck squamous cell carcinoma, thyroid carcinoma, and kidney renal clear cell carcinoma. Compared with some conventional methods, the results demonstrate that the proposed method is effective. Moreover, it can decrease the influence of gene length in identifying driver genes and identify some rare mutated driver genes.

  14. Algorithm For Control Of Underactuated Manipulators

    Science.gov (United States)

    Jain, Abhinandan; Rodriguez, Guillermo

    1994-01-01

    Algorithm for improved control of underactuated multiple-link robotic manipulators developed via spatial-algebra-operator approach. Aspects of this approach described in several previous articles in NASA Tech Briefs-most recently "Robot Control Based on Spatial-Operator Algebra" (NPO-17918). Underactuated manipulator has fewer actuators than it has degrees of freedom. Complexity of underactuated systems managed by unified analysis. It has implications for fault-tolerant control, and many practical manipulators underactuated. Examples include manipulators with flexible joints and/or flexible links; space/underwater robots; manipulators that operate with some actuators that turned off because of failure or because of need to conserve energy; manipulators that grasp objects loosely, and manipulators that grasp objects with internal degrees of freedom (e.g., plungers, rollers).

  15. A Nonlinear Model for Gene-Based Gene-Environment Interaction

    Directory of Open Access Journals (Sweden)

    Jian Sa

    2016-06-01

    Full Text Available A vast amount of literature has confirmed the role of gene-environment (G×E interaction in the etiology of complex human diseases. Traditional methods are predominantly focused on the analysis of interaction between a single nucleotide polymorphism (SNP and an environmental variable. Given that genes are the functional units, it is crucial to understand how gene effects (rather than single SNP effects are influenced by an environmental variable to affect disease risk. Motivated by the increasing awareness of the power of gene-based association analysis over single variant based approach, in this work, we proposed a sparse principle component regression (sPCR model to understand the gene-based G×E interaction effect on complex disease. We first extracted the sparse principal components for SNPs in a gene, then the effect of each principal component was modeled by a varying-coefficient (VC model. The model can jointly model variants in a gene in which their effects are nonlinearly influenced by an environmental variable. In addition, the varying-coefficient sPCR (VC-sPCR model has nice interpretation property since the sparsity on the principal component loadings can tell the relative importance of the corresponding SNPs in each component. We applied our method to a human birth weight dataset in Thai population. We analyzed 12,005 genes across 22 chromosomes and found one significant interaction effect using the Bonferroni correction method and one suggestive interaction. The model performance was further evaluated through simulation studies. Our model provides a system approach to evaluate gene-based G×E interaction.

  16. Locally linear embedding and neighborhood rough set-based gene selection for gene expression data classification.

    Science.gov (United States)

    Sun, L; Xu, J-C; Wang, W; Yin, Y

    2016-08-30

    Cancer subtype recognition and feature selection are important problems in the diagnosis and treatment of tumors. Here, we propose a novel gene selection approach applied to gene expression data classification. First, two classical feature reduction methods including locally linear embedding (LLE) and rough set (RS) are summarized. The advantages and disadvantages of these algorithms were analyzed and an optimized model for tumor gene selection was developed based on LLE and neighborhood RS (NRS). Bhattacharyya distance was introduced to delete irrelevant genes, pair-wise redundant analysis was performed to remove strongly correlated genes, and the wavelet soft threshold was determined to eliminate noise in the gene datasets. Next, prior optimized search processing was carried out. A new approach combining dimension reduction of LLE and feature reduction of NRS (LLE-NRS) was developed for selecting gene subsets, and then an open source software Weka was applied to distinguish different tumor types and verify the cross-validation classification accuracy of our proposed method. The experimental results demonstrated that the classification performance of the proposed LLE-NRS for selecting gene subset outperforms those of other related models in terms of accuracy, and our proposed approach is feasible and effective in the field of high-dimensional tumor classification.

  17. 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.

  18. The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes

    Directory of Open Access Journals (Sweden)

    Fu-Liu Casey S

    2007-05-01

    Full Text Available Abstract Background Tuberculosis remains a leading infectious disease with global public health threat. Its control and management have been complicated by multi-drug resistance and latent infection, which prompts scientists to find new and more effective drugs. With the completion of the genome sequence of the etiologic bacterium, Mycobacterium tuberculosis, it is now feasible to search for new drug targets by sieving through a large number of gene products and conduct genome-scale experiments based on microarray technology. However, the full potential of genome-wide microarray analysis in configuring interrelationships among all genes in M. tuberculosis has yet to be realized. To date, it is only possible to assign a function to 52% of proteins predicted in the genome. Results We conducted a functional-genomics study using the high-resolution Affymetrix oligonucleotide GeneChip. Approximately one-half of the genes were found to be always expressed, including more than 100 predicted conserved hypotheticals, in the genome of M. tuberculosis during the log phase of in vitro growth. The gene expression profiles were analyzed and visualized through cluster analysis to epitomize the full details of genomic behavior. Broad patterns derived from genome-wide expression experiments in this study have provided insight into the interrelationships among genes in the basic cellular processes of M. tuberculosis. Conclusion Our results have confirmed several known gene clusters in energy production, information pathways, and lipid metabolism, and also hinted at potential roles of hypothetical and regulatory proteins.

  19. New Genome Similarity Measures based on Conserved Gene Adjacencies.

    Science.gov (United States)

    Doerr, Daniel; Kowada, Luis Antonio B; Araujo, Eloi; Deshpande, Shachi; Dantas, Simone; Moret, Bernard M E; Stoye, Jens

    2017-06-01

    Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, for example, to elucidate the phylogenetic relationships between species. The power of different genome comparison methods varies with the underlying formal model of a genome. The simplest models impose the strong restriction that each genome under study must contain the same genes, each in exactly one copy. More realistic models allow several copies of a gene in a genome. One speaks of gene families, and comparative genomic methods that allow this kind of input are called gene family-based. The most powerful-but also most complex-models avoid this preprocessing of the input data and instead integrate the family assignment within the comparative analysis. Such methods are called gene family-free. In this article, we study an intermediate approach between family-based and family-free genomic similarity measures. Introducing this simpler model, called gene connections, we focus on the combinatorial aspects of gene family-free genome comparison. While in most cases, the computational costs to the general family-free case are the same, we also find an instance where the gene connections model has lower complexity. Within the gene connections model, we define three variants of genomic similarity measures that have different expression powers. We give polynomial-time algorithms for two of them, while we show NP-hardness for the third, most powerful one. We also generalize the measures and algorithms to make them more robust against recent local disruptions in gene order. Our theoretical findings are supported by experimental results, proving the applicability and performance of our newly defined similarity measures.

  20. 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

  1. Cancer classification based on gene expression using neural networks.

    Science.gov (United States)

    Hu, H P; Niu, Z J; Bai, Y P; Tan, X H

    2015-12-21

    Based on gene expression, we have classified 53 colon cancer patients with UICC II into two groups: relapse and no relapse. Samples were taken from each patient, and gene information was extracted. Of the 53 samples examined, 500 genes were considered proper through analyses by S-Kohonen, BP, and SVM neural networks. Classification accuracy obtained by S-Kohonen neural network reaches 91%, which was more accurate than classification by BP and SVM neural networks. The results show that S-Kohonen neural network is more plausible for classification and has a certain feasibility and validity as compared with BP and SVM neural networks.

  2. High precision redundant robotic manipulator

    International Nuclear Information System (INIS)

    Young, K.K.D.

    1998-01-01

    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

  3. Gene-Expression Profiles in Generalized Aggressive Periodontitis: A Gene Network-Based Microarray Analysis.

    Science.gov (United States)

    Guzeldemir-Akcakanat, Esra; Sunnetci-Akkoyunlu, Deniz; Orucguney, Begum; Cine, Naci; Kan, Bahadır; Yılmaz, Elif Büsra; Gümüşlü, Esen; Savli, Hakan

    2016-01-01

    In this study, molecular biomarkers that play a role in the development of generalized aggressive periodontitis (GAgP) are investigated using gingival tissue samples through omics-based whole-genome transcriptomics while using healthy individuals as background controls. Gingival tissue biopsies from 23 patients with GAgP and 25 healthy individuals were analyzed using gene-expression microarrays with network and pathway analyses to identify gene-expression patterns. To substantiate the results of the microarray studies, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to assess the messenger RNA (mRNA) expression of MZB1 and DSC1. The microarrays and qRT-PCR resulted in similar gene-expression changes, confirming the reliability of the microarray results at the mRNA level. As a result of the gene-expression microarray studies, four significant gene networks were identified. The most upregulated genes were found as MZB1, TNFRSF17, PNOC, FCRL5, LAX1, BMS1P20, IGLL5, MMP7, SPAG4, and MEI1; the most downregulated genes were found as LOR, LAMB4, AADACL2, MAPT, ARG1, NPR3, AADAC, DSC1, LRRC4, and CHP2. Functions of the identified genes that were involved in gene networks were cellular development, cell growth and proliferation, cellular movement, cell-cell signaling and interaction, humoral immune response, protein synthesis, cell death and survival, cell population and organization, organismal injury and abnormalities, molecular transport, and small-molecule biochemistry. The data suggest new networks that have important functions as humoral immune response and organismal injury/abnormalities. Future analyses may facilitate proteomic profiling analyses to identify gene-expression patterns related to clinical outcome.

  4. Comparison of the Efficacy and Efficiency of the Use of Virtual Reality Simulation With High-Fidelity Mannequins for Simulation-Based Training of Fiberoptic Bronchoscope Manipulation.

    Science.gov (United States)

    Jiang, Bailin; Ju, Hui; Zhao, Ying; Yao, Lan; Feng, Yi

    2018-04-01

    This study compared the efficacy and efficiency of virtual reality simulation (VRS) with high-fidelity mannequin in the simulation-based training of fiberoptic bronchoscope manipulation in novices. Forty-six anesthesia residents with no experience in fiberoptic intubation were divided into two groups: VRS (group VRS) and mannequin (group M). After a standard didactic teaching session, group VRS trained 25 times on VRS, whereas group M performed the same process on a mannequin. After training, participants' performance was assessed on a mannequin five consecutive times. Procedure times during training were recorded as pooled data to construct learning curves. Procedure time and global rating scale scores of manipulation ability were compared between groups, as well as changes in participants' confidence after training. Plateaus in the learning curves were achieved after 19 (95% confidence interval = 15-26) practice sessions in group VRS and 24 (95% confidence interval = 20-32) in group M. There was no significant difference in procedure time [13.7 (6.6) vs. 11.9 (4.1) seconds, t' = 1.101, P = 0.278] or global rating scale [3.9 (0.4) vs. 3.8 (0.4), t = 0.791, P = 0.433] between groups. Participants' confidence increased after training [group VRS: 1.8 (0.7) vs. 3.9 (0.8), t = 8.321, P < 0.001; group M = 2.0 (0.7) vs. 4.0 (0.6), t = 13.948, P < 0.001] but did not differ significantly between groups. Virtual reality simulation is more efficient than mannequin in simulation-based training of flexible fiberoptic manipulation in novices, but similar effects can be achieved in both modalities after adequate training.

  5. IGENT: efficient entropy based algorithm for genome-wide gene-gene interaction analysis.

    Science.gov (United States)

    Kwon, Min-Seok; Park, Mira; Park, Taesung

    2014-01-01

    With the development of high-throughput genotyping and sequencing technology, there are growing evidences of association with genetic variants and complex traits. In spite of thousands of genetic variants discovered, such genetic markers have been shown to explain only a very small proportion of the underlying genetic variance of complex traits. Gene-gene interaction (GGI) analysis is expected to unveil a large portion of unexplained heritability of complex traits. In this work, we propose IGENT, Information theory-based GEnome-wide gene-gene iNTeraction method. IGENT is an efficient algorithm for identifying genome-wide gene-gene interactions (GGI) and gene-environment interaction (GEI). For detecting significant GGIs in genome-wide scale, it is important to reduce computational burden significantly. Our method uses information gain (IG) and evaluates its significance without resampling. Through our simulation studies, the power of the IGENT is shown to be better than or equivalent to that of that of BOOST. The proposed method successfully detected GGI for bipolar disorder in the Wellcome Trust Case Control Consortium (WTCCC) and age-related macular degeneration (AMD). The proposed method is implemented by C++ and available on Windows, Linux and MacOSX.

  6. Finding gene regulatory network candidates using the gene expression knowledge base.

    Science.gov (United States)

    Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin

    2014-12-10

    Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of 'omics' data can be interpreted. The background information required for the construction of such networks is often dispersed across a multitude of knowledge bases in a variety of formats. The seamless integration of this information is one of the main challenges in bioinformatics. The Semantic Web offers powerful technologies for the assembly of integrated knowledge bases that are computationally comprehensible, thereby providing a potentially powerful resource for constructing biological networks and network-based analysis. We have developed the Gene eXpression Knowledge Base (GeXKB), a semantic web technology based resource that contains integrated knowledge about gene expression regulation. To affirm the utility of GeXKB we demonstrate how this resource can be exploited for the identification of candidate regulatory network proteins. We present four use cases that were designed from a biological perspective in order to find candidate members relevant for the gastrin hormone signaling network model. We show how a combination of specific query definitions and additional selection criteria derived from gene expression data and prior knowledge concerning candidate proteins can be used to retrieve a set of proteins that constitute valid candidates for regulatory network extensions. Semantic web technologies provide the means for processing and integrating various heterogeneous information sources. The GeXKB offers biologists such an integrated knowledge resource, allowing them to address complex biological questions pertaining to gene expression. This work illustrates how GeXKB can be used in combination with gene expression results and literature information to identify new potential candidates that may be considered for extending a gene regulatory network.

  7. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks.

    Science.gov (United States)

    Xiang, Zuoshuang; Qin, Tingting; Qin, Zhaohui S; He, Yongqun

    2013-10-16

    The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. The GenoMesh algorithm and web program provide the first genome-wide, MeSH-based literature mining

  8. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

    Science.gov (United States)

    2013-01-01

    Background The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. Results The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. Conclusions The GenoMesh algorithm and web program provide the first genome

  9. A Gene-Based Analysis of Acoustic Startle Latency

    Science.gov (United States)

    Smith, Alicia K.; Jovanovic, Tanja; Kilaru, Varun; Lori, Adriana; Gensler, Lauren; Lee, Samuel S.; Norrholm, Seth Davin; Massa, Nicholas; Cuthbert, Bruce; Bradley, Bekh; Ressler, Kerry J.; Duncan, Erica

    2017-01-01

    Latency of the acoustic startle response is the time required from the presentation of startling auditory stimulus until the startle response is elicited and provides an index of neural processing speed. Latency is prolonged in subjects with schizophrenia compared to controls in some but not all studies and is 68–90% heritable in baseline startle trials. In order to determine the genetic association with latency as a potential inroad into genetically based vulnerability to psychosis, we conducted a gene-based study of latency followed by an independent replication study of significant gene findings with a single-nucleotide polymorphism (SNP)-based analysis of schizophrenia and control subjects. 313 subjects from an urban population of low socioeconomic status with mixed psychiatric diagnoses were included in the gene-based study. Startle testing was conducted using a Biopac M150 system according to our published methods. Genotyping was performed with the Omni-Quad 1M or the Omni Express BeadChip. The replication study was conducted on 154 schizophrenia subjects and 123 psychiatric controls. Genetic analyses were conducted with Illumina Human Omni1-Quad and OmniExpress BeadChips. Twenty-nine SNPs were selected from four genes that were significant in the gene-based analysis and also associated with startle and/or schizophrenia in the literature. Linear regressions on latency were conducted, controlling for age, race, and diagnosis as a dichotomous variable. In the gene-based study, 2,870 genes demonstrated the evidence of association after correction for multiple comparisons (false discovery rate < 0.05). Pathway analysis of these genes revealed enrichment for relevant biological processes including neural transmission (p = 0.0029), synaptic transmission (p = 0.0032), and neuronal development (p = 0.024). The subsequent SNP-based replication analysis revealed a strong association of onset latency with the SNP rs901561 on the neuregulin gene (NRG1

  10. Two-Time Scale Virtual Sensor Design for Vibration Observation of a Translational Flexible-Link Manipulator Based on Singular Perturbation and Differential Games.

    Science.gov (United States)

    Ju, Jinyong; Li, Wei; Wang, Yuqiao; Fan, Mengbao; Yang, Xuefeng

    2016-10-28

    Effective feedback control requires all state variable information of the system. However, in the translational flexible-link manipulator (TFM) system, it is unrealistic to measure the vibration signals and their time derivative of any points of the TFM by infinite sensors. With the rigid-flexible coupling between the global motion of the rigid base and the elastic vibration of the flexible-link manipulator considered, a two-time scale virtual sensor, which includes the speed observer and the vibration observer, is designed to achieve the estimation for the vibration signals and their time derivative of the TFM, as well as the speed observer and the vibration observer are separately designed for the slow and fast subsystems, which are decomposed from the dynamic model of the TFM by the singular perturbation. Additionally, based on the linear-quadratic differential games, the observer gains of the two-time scale virtual sensor are optimized, which aims to minimize the estimation error while keeping the observer stable. Finally, the numerical calculation and experiment verify the efficiency of the designed two-time scale virtual sensor.

  11. Compliant Aerial Manipulators

    DEFF Research Database (Denmark)

    Bartelds, T.; Capra, A.; Hamaza, S.

    2016-01-01

    This letter focuses on the problem of handling impacts by means of an aerial manipulator and proposes a solution that combines the control of the aerial manipulator's end-effector position with an innovative design approach of aerial manipulation systems, consisting of both active and passive...... joints. The approach aims at limiting the influence of impacts on the controlled attitude dynamics in order to allow the aerial manipulator to remain stable during and after impact. The developed concept is intended to convert kinetic energy into potential energy, which is permanently stored into elastic...... elements by means of directional locking mechanisms. The proposed approach has been tested on a 2 d.o.f. manipulator mounted on a quadrotor UAV. The manipulation system has one active rotational d.o.f. compensating for pitch movements of the UAV and one passive linear joint which is in charge of absorbing...

  12. Survey of gene splicing algorithms based on reads.

    Science.gov (United States)

    Si, Xiuhua; Wang, Qian; Zhang, Lei; Wu, Ruo; Ma, Jiquan

    2017-11-02

    Gene splicing is the process of assembling a large number of unordered short sequence fragments to the original genome sequence as accurately as possible. Several popular splicing algorithms based on reads are reviewed in this article, including reference genome algorithms and de novo splicing algorithms (Greedy-extension, Overlap-Layout-Consensus graph, De Bruijn graph). We also discuss a new splicing method based on the MapReduce strategy and Hadoop. By comparing these algorithms, some conclusions are drawn and some suggestions on gene splicing research are made.

  13. Getting Manipulative about Math.

    Science.gov (United States)

    Scheer, Janet K.; And Others

    1984-01-01

    Math manipulatives that are made from inexpensive, common items help students understand basic mathematics concepts. Learning activities using Cheerios, jellybeans, and clay as teaching materials are suggested. (DF)

  14. Manipulators in teleoperation

    International Nuclear Information System (INIS)

    Hamel, W.R.

    1985-01-01

    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

  15. Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach.

    Directory of Open Access Journals (Sweden)

    Morten Thrane Nielsen

    Full Text Available Fungal natural products are a rich resource for bioactive molecules. To fully exploit this potential it is necessary to link genes to metabolites. Genetic information for numerous putative biosynthetic pathways has become available in recent years through genome sequencing. However, the lack of solid methodology for genetic manipulation of most species severely hampers pathway characterization. Here we present a simple PCR based approach for heterologous reconstitution of intact gene clusters. Specifically, the putative gene cluster responsible for geodin production from Aspergillus terreus was transferred in a two step procedure to an expression platform in A. nidulans. The individual cluster fragments were generated by PCR and assembled via efficient USER fusion prior to transformation and integration via re-iterative gene targeting. A total of 13 open reading frames contained in 25 kb of DNA were successfully transferred between the two species enabling geodin synthesis in A. nidulans. Subsequently, functions of three genes in the cluster were validated by genetic and chemical analyses. Specifically, ATEG_08451 (gedC encodes a polyketide synthase, ATEG_08453 (gedR encodes a transcription factor responsible for activation of the geodin gene cluster and ATEG_08460 (gedL encodes a halogenase that catalyzes conversion of sulochrin to dihydrogeodin. We expect that our approach for transferring intact biosynthetic pathways to a fungus with a well developed genetic toolbox will be instrumental in characterizing the many exciting pathways for secondary metabolite production that are currently being uncovered by the fungal genome sequencing projects.

  16. Nano-manipulation of single DNA molecules

    International Nuclear Information System (INIS)

    Hu Jun; Shanghai Jiaotong Univ., Shanghai; Lv Junhong; Wang Guohua; Wang Ying; Li Minqian; Zhang Yi; Li Bin; Li Haikuo; An Hongjie

    2004-01-01

    Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotechnology. This review paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM). Precise manipulation has been realized including varied manipulating modes such as 'cutting', 'pushing', 'folding', 'kneading', 'picking up', 'dipping', etc. The cutting accuracy is dominated by the size of the AFM tip, which is usually 10 nm or less. Single DNA fragments can be cut and picked up and then amplified by single molecule PCR. Thus positioning isolation and sequencing can be performed. (authors)

  17. A genetic map of Blumeria graminis based on functional genes, avirulence genes, and molecular markers.

    Science.gov (United States)

    Pedersen, Carsten; Rasmussen, Søren W; Giese, Henriette

    2002-04-01

    A genetic map of the powdery mildew fungus, Blumeria graminis f. sp. hordei, an obligate biotrophic pathogen of barley, is presented. The linkage analysis was conducted on 81 segregating haploid progeny isolates from a cross between 2 isolates differing in seven avirulence genes. A total of 359 loci were mapped, comprising 182 amplified fragment length polymorphism markers, 168 restriction fragment length polymorphism markers including 42 LTR-retrotransposon loci and 99 expressed sequence tags (ESTs), all the seven avirulence genes, and a marker closely linked to the mating type gene. The markers are distributed over 34 linkage groups covering a total of 2114 cM. Five avirulence genes were found to be linked and mapped in clusters of three and two, and two were unlinked. The Avr(a6) gene was found to be closely linked to markers suitable for a map-based cloning approach. A linkage between ESTs allowed us to demonstrate examples of synteny between genes in B. graminis and Neurospora crassa.

  18. 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.

  19. Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.

    Science.gov (United States)

    Richards, Adam J; Muller, Brian; Shotwell, Matthew; Cowart, L Ashley; Rohrer, Bäerbel; Lu, Xinghua

    2010-06-15

    The results of initial analyses for many high-throughput technologies commonly take the form of gene or protein sets, and one of the ensuing tasks is to evaluate the functional coherence of these sets. The study of gene set function most commonly makes use of controlled vocabulary in the form of ontology annotations. For a given gene set, the statistical significance of observing these annotations or 'enrichment' may be tested using a number of methods. Instead of testing for significance of individual terms, this study is concerned with the task of assessing the global functional coherence of gene sets, for which novel metrics and statistical methods have been devised. The metrics of this study are based on the topological properties of graphs comprised of genes and their Gene Ontology annotations. A novel aspect of these methods is that both the enrichment of annotations and the relationships among annotations are considered when determining the significance of functional coherence. We applied our methods to perform analyses on an existing database and on microarray experimental results. Here, we demonstrated that our approach is highly discriminative in terms of differentiating coherent gene sets from random ones and that it provides biologically sensible evaluations in microarray analysis. We further used examples to show the utility of graph visualization as a tool for studying the functional coherence of gene sets. The implementation is provided as a freely accessible web application at: http://projects.dbbe.musc.edu/gosteiner. Additionally, the source code written in the Python programming language, is available under the General Public License of the Free Software Foundation. Supplementary data are available at Bioinformatics online.

  20. Log-linear model-based multifactor dimensionality reduction method to detect gene gene interactions.

    Science.gov (United States)

    Lee, Seung Yeoun; Chung, Yujin; Elston, Robert C; Kim, Youngchul; Park, Taesung

    2007-10-01

    The identification and characterization of susceptibility genes that influence the risk of common and complex diseases remains a statistical and computational challenge in genetic association studies. This is partly because the effect of any single genetic variant for a common and complex disease may be dependent on other genetic variants (gene-gene interaction) and environmental factors (gene-environment interaction). To address this problem, the multifactor dimensionality reduction (MDR) method has been proposed by Ritchie et al. to detect gene-gene interactions or gene-environment interactions. The MDR method identifies polymorphism combinations associated with the common and complex multifactorial diseases by collapsing high-dimensional genetic factors into a single dimension. That is, the MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups based on a comparison of the ratios of the numbers of cases and controls. When a high-order interaction model is considered with multi-dimensional factors, however, there may be many sparse or empty cells in the contingency tables. The MDR method cannot classify an empty cell as high risk or low risk and leaves it as undetermined. In this article, we propose the log-linear model-based multifactor dimensionality reduction (LM MDR) method to improve the MDR in classifying sparse or empty cells. The LM MDR method estimates frequencies for empty cells from a parsimonious log-linear model so that they can be assigned to high-and low-risk groups. In addition, LM MDR includes MDR as a special case when the saturated log-linear model is fitted. Simulation studies show that the LM MDR method has greater power and smaller error rates than the MDR method. The LM MDR method is also compared with the MDR method using as an example sporadic Alzheimer's disease.

  1. A Model-Based Joint Identification of Differentially Expressed Genes and Phenotype-Associated Genes.

    Directory of Open Access Journals (Sweden)

    Samuel Sunghwan Cho

    Full Text Available Over the last decade, many analytical methods and tools have been developed for microarray data. The detection of differentially expressed genes (DEGs among different treatment groups is often a primary purpose of microarray data analysis. In addition, association studies investigating the relationship between genes and a phenotype of interest such as survival time are also popular in microarray data analysis. Phenotype association analysis provides a list of phenotype-associated genes (PAGs. However, it is sometimes necessary to identify genes that are both DEGs and PAGs. We consider the joint identification of DEGs and PAGs in microarray data analyses. The first approach we used was a naïve approach that detects DEGs and PAGs separately and then identifies the genes in an intersection of the list of PAGs and DEGs. The second approach we considered was a hierarchical approach that detects DEGs first and then chooses PAGs from among the DEGs or vice versa. In this study, we propose a new model-based approach for the joint identification of DEGs and PAGs. Unlike the previous two-step approaches, the proposed method identifies genes simultaneously that are DEGs and PAGs. This method uses standard regression models but adopts different null hypothesis from ordinary regression models, which allows us to perform joint identification in one-step. The proposed model-based methods were evaluated using experimental data and simulation studies. The proposed methods were used to analyze a microarray experiment in which the main interest lies in detecting genes that are both DEGs and PAGs, where DEGs are identified between two diet groups and PAGs are associated with four phenotypes reflecting the expression of leptin, adiponectin, insulin-like growth factor 1, and insulin. Model-based approaches provided a larger number of genes, which are both DEGs and PAGs, than other methods. Simulation studies showed that they have more power than other methods

  2. The manipulation of gene expression and the biosynthesis of Vitamin C, E and folate in light-and dark-germination of sweet corn seeds.

    Science.gov (United States)

    Liu, Fengyuan; Xiang, Nan; Hu, Jian Guang; Shijuan, Yan; Xie, Lihua; Brennan, Charles Stephen; Huang, Wenjie; Guo, Xinbo

    2017-08-08

    This study investigates the potential interrelationship between gene expression and biosynthesis of vitamin C, E and folate in sweet corn sprouts. Germination of sweet corn kernels was conducted in light and dark environments to determine if this relationship was regulated by photo-illumination. Results indicated that light and dark environments affected the DHAR, TMT and GTPCH expression and that these genes were the predominant genes of vitamin C, E and folate biosynthesis pathways respectively during the germination. Levels of vitamin C and folate increased during the germination of sweet corn seeds while vitamin E had a declining manner. Sweet corn sprouts had higher vitamin C and E levels as well as relevant gene expression levels in light environment while illumination had little influence on the folate contents and the gene expression levels during the germination. These results indicate that there might be a collaborative relationship between vitamin C and folate regulation during sweet corn seed germination, while an inhibitive regulation might exist between vitamin C and E.

  3. Electrodeposition of compact zinc from the hydrophobic Brønsted acidic ionic liquid-based electrolytes and the study of zinc stability along with the acidity manipulation

    International Nuclear Information System (INIS)

    Chen, Yi-Han; Yeh, Hsin-Wen; Lo, Nai-Chang; Chiu, Chen-Wei; Sun, I-Wen; Chen, Po-Yu

    2017-01-01

    Highlights: • Compact Zn with no crack is deposited from protic ionic liquid-based electrolytes. • The ionic liquid is composed of the protonated betaine ion. • This ionic liquid is hydrophobic and zinc oxide is soluble in it. • The effects of co-solvents, propylene carbonate and water, are studied. • The Zn stripping/deposition efficiency can be manipulated via acidity adjustment. - Abstract: Compact crystalline zinc was electrodeposited on stainless-steel electrode (SS) via potentiostatic/galvanostatic electrolysis from the hydrophobic Brønsted acidic ionic liquid, protonated betaine bis((trifluoromethyl)sulfonyl)imide (IL [Hbet][TFSI]), −based electrolytes containing ZnCl 2 or ZnO under argon or ambient air atmosphere. Approximate 10 wt% of propylene carbonate and water, respectively, were used as the co-solvents for [Hbet][TFSI] to form the IL-based electrolytes. The efficiency of zinc deposition/stripping, which is significantly affected by the Brønsted acidity of the IL-based electrolytes, was studied at glassy carbon electrode (GC) to evaluate the stability of the zinc electrodeposits along with the electrolyte acidity. The stability is very poor for the zinc electrodeposits obtained from ZnCl 2 solution. However, it increases with increasing the quantity of ZnO or urea in the electrolytes; the former neutralize the dissociable protons in [Hbet] cations to form water, and the latter may form H-bonding with [Hbet] or be protonated to form the weakly acidic cations [HUrea]. Both suppress the reaction between the Zn electrodeposits and protons. The stability of the Zn electrodeposits, therefore, can be improved via the manipulation of the IL acidity.

  4. Degradable Polyethylenimine-Based Gene Carriers for Cancer Therapy.

    Science.gov (United States)

    Jiang, Hu-Lin; Islam, Mohammad Ariful; Xing, Lei; Firdous, Jannatul; Cao, Wuji; He, Yu-Jing; Zhu, Yong; Cho, Ki-Hyun; Li, Hui-Shan; Cho, Chong-Su

    2017-04-01

    Gene therapy using recombinant DNA or gene silencing using siRNA have become a prominent area of research in cancer therapy. However, their use in clinical applications is limited due to overall safety concerns and suboptimal efficacy. Although non-viral vectors such as polycationic polymers do not offer the same level of transfection efficiency as their viral counterparts, they still demonstrate immense potential as alternatives to viral vectors, given their versatility, low immunogenicity, ease of large-scale production, and ability to accelerate gene transfer with well-designed delivery platforms. Among these polymers, polyethylenimine (PEI) is considered a state-of-the-art gene carrier, owing to its ability to improve gene transfer capacity and intracellular delivery. Nonetheless, PEI suffers from the critical shortcoming of non-degradability that can lead to severe cytotoxic effects, despite the fact that the level of this toxicity decreases with molecular weight (MW). As a result, a considerable amount of effort has been devoted to designing low-MW PEI derivatives with degradable linkages. This review will categorize the recent advances in these degradable PEI derivatives based on their degradable chemistries, including ester, disulfide, imine, carbamate, amide, and ketal linkages, and summarize their application in gene therapies against various major cancer malignancies.

  5. Construction of coffee transcriptome networks based on gene annotation semantics

    Directory of Open Access Journals (Sweden)

    Castillo Luis F.

    2012-12-01

    Full Text Available Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  6. Maximum allowable load on wheeled mobile manipulators

    International Nuclear Information System (INIS)

    Habibnejad Korayem, M.; Ghariblu, H.

    2003-01-01

    This paper develops a computational technique for finding the maximum allowable load of mobile manipulator during a given trajectory. The maximum allowable loads which can be achieved by a mobile manipulator during a given trajectory are limited by the number of factors; probably the dynamic properties of mobile base and mounted manipulator, their actuator limitations and additional constraints applied to resolving the redundancy are the most important factors. To resolve extra D.O.F introduced by the base mobility, additional constraint functions are proposed directly in the task space of mobile manipulator. Finally, in two numerical examples involving a two-link planar manipulator mounted on a differentially driven mobile base, application of the method to determining maximum allowable load is verified. The simulation results demonstrates the maximum allowable load on a desired trajectory has not a unique value and directly depends on the additional constraint functions which applies to resolve the motion redundancy

  7. Global Regulatory Differences for Gene- and Cell-Based Therapies

    DEFF Research Database (Denmark)

    Coppens, Delphi G M; De Bruin, Marie L; Leufkens, Hubert G M

    2017-01-01

    Gene- and cell-based therapies (GCTs) offer potential new treatment options for unmet medical needs. However, the use of conventional regulatory requirements for medicinal products to approve GCTs may impede patient access and therapeutic innovation. Furthermore, requirements differ between juris...

  8. GeneNetwork: framework for web-based genetics

    NARCIS (Netherlands)

    Sloan, Zachary; Arends, Danny; Broman, Karl W.; Centeno, Arthur; Furlotte, Nicholas; Nijveen, H.; Yan, Lei; Zhou, Xiang; Williams, Robert W.; Prins, Pjotr

    2016-01-01

    GeneNetwork (GN) is a free and open source (FOSS) framework for web-based genetics that can be deployed anywhere. GN allows biologists to upload high-throughput experimental data, such as expression data from microarrays and RNA-seq, and also `classic' phenotypes, such as disease phenotypes. These

  9. Analysis of singularity in redundant manipulators

    International Nuclear Information System (INIS)

    Watanabe, Koichi

    2000-03-01

    In the analysis of arm positions and configurations of redundant manipulators, the singularity avoidance problems are important themes. This report presents singularity avoidance computations of a 7 DOF manipulator by using a computer code based on human-arm models. The behavior of the arm escaping from the singular point can be identified satisfactorily through the use of 3-D plotting tools. (author)

  10. Revisiting Mathematics Manipulative Materials

    Science.gov (United States)

    Swan, Paul; Marshall, Linda

    2010-01-01

    It is over 12 years since "APMC" published Bob Perry and Peter Howard's research on the use of mathematics manipulative materials in primary mathematics classrooms. Since then the availability of virtual manipulatives and associated access to computers and interactive whiteboards have caused educators to rethink the use of mathematics…

  11. Mascot servo-manipulator

    CERN Multimedia

    1972-01-01

    The Mascot servo-manipulator on its test rails. In the foreground is the slave unit, which, in normal use, operates in the "hot" area with television observation. In the background the operator is manipulating arms which the slave arms follow, and which also convey back to him the "feel" of what is being handled.

  12. Master-slave manipulator

    International Nuclear Information System (INIS)

    Haaker, L.W.; Jelatis, D.G.

    1981-01-01

    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.)

  13. 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.

  14. Cell manipulation in microfluidics

    International Nuclear Information System (INIS)

    Yun, Hoyoung; Kim, Kisoo; Lee, Won Gu

    2013-01-01

    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)

  15. Manipulator comparative testing program

    International Nuclear Information System (INIS)

    Draper, J.V.; Handel, S.J.; Sundstrom, E.; Herndon, J.N.; Fujita, Y.; Maeda, M.

    1986-01-01

    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

  16. Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria.

    Directory of Open Access Journals (Sweden)

    Mario Fruzangohar

    Full Text Available The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO, which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria from different sources simultaneously. Comparing GO protein distribution among up- or down-regulated genes from different samples can improve understanding of biological pathways, and mechanism(s of infection. It can also aid in the discovery of genes associated with specific function(s for investigation as a novel vaccine or therapeutic targets.http://turing.ersa.edu.au/BacteriaGO.

  17. Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria.

    Science.gov (United States)

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Ogunniyi, Abiodun D; Mahdi, Layla K; Paton, James C; Adelson, David L

    2013-01-01

    The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO), which defines genes/proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns in multiple datasets using visually comprehensible and user-friendly statistical reports. Importantly, while there are many GO resources available for eukaryotes, there are none suitable for simultaneous, graphical and statistical comparison between multiple datasets. In addition, none of them supports comprehensive resources for bacteria. By using Streptococcus pneumoniae as a model, we identified and collected GO resources including genes, proteins, taxonomy and GO relationships from NCBI, UniProt and GO organisations. Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. We developed a PHP web application based on Model-View-Control architecture, used a specific data structure as well as current and novel algorithms to estimate GO graphs parameters. We designed different navigation and visualization methods on the graphs and integrated these into graphical reports. This tool is particularly significant when comparing GO groups between multiple samples (including those of pathogenic bacteria) from different sources simultaneously. Comparing GO protein distribution among up- or down-regulated genes from different samples can improve understanding of biological pathways, and mechanism(s) of infection. It can also aid in the discovery of genes associated with specific function(s) for investigation as a novel vaccine or therapeutic targets. http://turing.ersa.edu.au/BacteriaGO.

  18. [Detecting gene-gene/environment interactions by model-based multifactor dimensionality reduction].

    Science.gov (United States)

    Fan, Wei; Shen, Chao; Guo, Zhirong

    2015-11-01

    This paper introduces a method called model-based multifactor dimensionality reduction (MB-MDR), which was firstly proposed by Calle et al., and can be applied for detecting gene-gene or gene-environment interactions in genetic studies. The basic principle and characteristics of MB-MDR as well as the operation in R program are briefly summarized. Besides, the detailed procedure of MB-MDR is illustrated by using example. Compared with classical MDR, MB-MDR has similar principle, which merges multi-locus genotypes into a one-dimensional construct and can be used in the study with small sample size. However, there is some difference between MB-MDR and classical MDR. First, it has higher statistical power than MDR and other MDR in the presence of different noises due to the different way the genotype cells merged. Second, compared with MDR, it can deal with all binary and quantitative traits, adjust marginal effects of factors and confounders. MBMDR could be a useful method in the analyses of gene-gene/environment interactions.

  19. VEGAS2: Software for More Flexible Gene-Based Testing.

    Science.gov (United States)

    Mishra, Aniket; Macgregor, Stuart

    2015-02-01

    Gene-based tests such as versatile gene-based association study (VEGAS) are commonly used following per-single nucleotide polymorphism (SNP) GWAS (genome-wide association studies) analysis. Two limitations of VEGAS were that the HapMap2 reference set was used to model the correlation between SNPs and only autosomal genes were considered. HapMap2 has now been superseded by the 1,000 Genomes reference set, and whereas early GWASs frequently ignored the X chromosome, it is now commonly included. Here we have developed VEGAS2, an extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X. VEGAS2 allows greater flexibility when defining gene boundaries. VEGAS2 offers both a user-friendly, web-based front end and a command line Linux version. The online version of VEGAS2 can be accessed through https://vegas2.qimrberghofer.edu.au/. The command line version can be downloaded from https://vegas2.qimrberghofer.edu.au/zVEGAS2offline.tgz. The command line version is developed in Perl, R and shell scripting languages; source code is available for further development.

  20. Improving Adenovirus Based Gene Transfer: Strategies to Accomplish Immune Evasion

    Directory of Open Access Journals (Sweden)

    Andrea Amalfitano

    2010-09-01

    Full Text Available Adenovirus (Ad based gene transfer vectors continue to be the platform of choice for an increasing number of clinical trials worldwide. In fact, within the last five years, the number of clinical trials that utilize Ad based vectors has doubled, indicating growing enthusiasm for the numerous positive characteristics of this gene transfer platform. For example, Ad vectors can be easily and relatively inexpensively produced to high titers in a cGMP compliant manner, can be stably stored and transported, and have a broad applicability for a wide range of clinical conditions, including both gene therapy and vaccine applications. Ad vector based gene transfer will become more useful as strategies to counteract innate and/or pre-existing adaptive immune responses to Ads are developed and confirmed to be efficacious. The approaches attempting to overcome these limitations can be divided into two broad categories: pre-emptive immune modulation of the host, and selective modification of the Ad vector itself. The first category of methods includes the use of immunosuppressive drugs or specific compounds to block important immune pathways, which are known to be induced by Ads. The second category comprises several innovative strategies inclusive of: (1 Ad-capsid-display of specific inhibitors or ligands; (2 covalent modifications of the entire Ad vector capsid moiety; (3 the use of tissue specific promoters and local administration routes; (4 the use of genome modified Ads; and (5 the development of chimeric or alternative serotype Ads. This review article will focus on both the promise and the limitations of each of these immune evasion strategies, and in the process delineate future directions in developing safer and more efficacious Ad-based gene transfer strategies.

  1. Improving adenovirus based gene transfer: strategies to accomplish immune evasion.

    Science.gov (United States)

    Seregin, Sergey S; Amalfitano, Andrea

    2010-09-01

    Adenovirus (Ad) based gene transfer vectors continue to be the platform of choice for an increasing number of clinical trials worldwide. In fact, within the last five years, the number of clinical trials that utilize Ad based vectors has doubled, indicating growing enthusiasm for the numerous positive characteristics of this gene transfer platform. For example, Ad vectors can be easily and relatively inexpensively produced to high titers in a cGMP compliant manner, can be stably stored and transported, and have a broad applicability for a wide range of clinical conditions, including both gene therapy and vaccine applications. Ad vector based gene transfer will become more useful as strategies to counteract innate and/or pre-existing adaptive immune responses to Ads are developed and confirmed to be efficacious. The approaches attempting to overcome these limitations can be divided into two broad categories: pre-emptive immune modulation of the host, and selective modification of the Ad vector itself. The first category of methods includes the use of immunosuppressive drugs or specific compounds to block important immune pathways, which are known to be induced by Ads. The second category comprises several innovative strategies inclusive of: (1) Ad-capsid-display of specific inhibitors or ligands; (2) covalent modifications of the entire Ad vector capsid moiety; (3) the use of tissue specific promoters and local administration routes; (4) the use of genome modified Ads; and (5) the development of chimeric or alternative serotype Ads. This review article will focus on both the promise and the limitations of each of these immune evasion strategies, and in the process delineate future directions in developing safer and more efficacious Ad-based gene transfer strategies.

  2. Thermodynamics-based models of transcriptional regulation with gene sequence.

    Science.gov (United States)

    Wang, Shuqiang; Shen, Yanyan; Hu, Jinxing

    2015-12-01

    Quantitative models of gene regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled or heuristic approximations of the underlying regulatory mechanisms. In this work, we have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence. The proposed model relies on a continuous time, differential equation description of transcriptional dynamics. The sequence features of the promoter are exploited to derive the binding affinity which is derived based on statistical molecular thermodynamics. Experimental results show that the proposed model can effectively identify the activity levels of transcription factors and the regulatory parameters. Comparing with the previous models, the proposed model can reveal more biological sense.

  3. Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression

    Science.gov (United States)

    Ivanov, Maxim; Kals, Mart; Lauschke, Volker; Barragan, Isabel; Ewels, Philip; Käller, Max; Axelsson, Tomas; Lehtiö, Janne; Milani, Lili; Ingelman-Sundberg, Magnus

    2016-01-01

    To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications. PMID:27131363

  4. 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.

  5. Manipulation, salience, and nudges.

    Science.gov (United States)

    Noggle, Robert

    2018-03-01

    Cass Sunstein and Richard Thaler recommend helping people make better decisions by employing 'nudges', which they define as noncoercive methods of influencing choice for the better. Not surprisingly, healthcare practitioners and public policy professionals have become interested in whether nudges might be a promising method of improving health-related behaviors without resorting to heavy-handed methods such as coercion, deception, or government regulation. Many nudges seem unobjectionable as they merely improve the quality and quantity available for the decision-maker. However, other nudges influence decision-making in ways that do not involve providing more and better information. Nudges of this sort raise concerns about manipulation. This paper will focus on noninformational nudges that operate by changing the salience of various options. It will survey two approaches to understanding manipulation, one which sees manipulation as a kind of pressure, and one that sees it as a kind of trickery. On the pressure view, salience nudges do not appear to be manipulative. However, on the trickery view (which the author favors), salience nudges will be manipulative if they increase the salience so that it is disproportionate to that fact's true relevance and importance for the decision at hand. By contrast, salience nudges will not be manipulative if they merely highlight some fact that is true and important for the decision at hand. The paper concludes by providing examples of both manipulative and nonmanipulative salience nudges. © 2017 John Wiley & Sons Ltd.

  6. Manipulators for production and research

    International Nuclear Information System (INIS)

    Munro, Ian

    1987-01-01

    The development of caves or cells and master-slave manipulators to handle radioactive materials is discussed. Some of the most recent advances are described. A manipulator arm, a master-slave manipulator and a servomanipulator mounted on a manipulator are illustrated. Future developments are discussed - these include resolved tip control for the manipulator. (UK)

  7. 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.

  8. MODULAR MANIPULATOR FOR ROBOTICS APPLICATIONS

    International Nuclear Information System (INIS)

    Geisinger, Joseph W. Ph.D.

    2001-01-01

    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

  9. 3D investigation of dynamic behavior and sensitivity analysis of the parameters of spherical biological particles in the first phase of AFM-based manipulations with the consideration of humidity effect.

    Science.gov (United States)

    Korayem, M H; Mahmoodi, Z; Mohammadi, M

    2018-01-07

    The imaging and manipulation tools being the same in an AFM has necessitated the modeling and simulation of the AFM-based manipulation processes. In earlier studies, the dynamic behavior of biological particles in the course of manipulation has been modeled and simulated two-dimensionally. Now, with the advancements made in the modeling techniques, a 3D model of the manipulation of biological particles is more accurate than its 2D counterpart. In this paper, the effect of humidity has been taken into consideration in the three-dimensional modeling of the manipulation. By employing this model, the equations for the motion modes of particles (sliding, rolling, and spinning) at the onset of movement have been derived and the critical force magnitude has been obtained. In order to reduce the potential damage to the manipulated biological particle, the maximum radius of the tip has been determined. The effective parameters in this process have been extracted by performing sensitivity analysis using the Sobol method. In comparison to the results obtained for a dry environment, the results obtained by simulating the manipulation of a yeast particle in a wet environment shows that the critical force for the onset of particle movement diminishes by considering the moisture effect (high humidity levels). The parameters influencing the magnitude of the critical force include the particle radius, particle material, surface energy of the chosen substrate, amount of preload and the contact angle. Also, the results of the performed sensitivity analysis indicate a very high influence of particle radius on the critical manipulation force and a very low impact of cantilever width on the critical force. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. 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.

  11. Local-Nearest-Neighbors-Based Feature Weighting for Gene Selection.

    Science.gov (United States)

    An, Shuai; Wang, Jun; Wei, Jinmao

    2017-06-07

    Selecting functional genes is essential for analyzing microarray data. Among many available feature (gene) selection approaches, the ones on the basis of the large margin nearest neighbor receive more attention due to their low computational costs and high accuracies in analyzing the high-dimensional data. Yet there still exist some problems that hamper the existing approaches in sifting real target genes, including selecting erroneous nearest neighbors, high sensitivity to irrelevant genes, and inappropriate evaluation criteria. Previous pioneer works have partly addressed some of the problems, but none of them are capable of solving these problems simultaneously. In this paper, we propose a new local-nearest-neighbors-based feature weighting approach to alleviate the above problems. The proposed approach is based on the trick of locally minimizing the within-class distances and maximizing the between-class distances with the k nearest neighbors rule. We further define a feature weight vector, and construct it by minimizing the cost function with a regularization term. The proposed approach can be applied naturally to the multi-class problems and does not require extra modification. Experimental results on the UCI and the open microarray data sets validate the effectiveness and efficiency of the new approach.

  12. Powered manipulator control arm

    International Nuclear Information System (INIS)

    Le Mouee, Theodore; Vertut, Jean; Marchal, Paul; Germon, J.C.; Petit, Michel

    1975-01-01

    A remote operated control arm for powered manipulators is described. It includes an assembly allowing several movements with position sensors for each movement. The number of possible arm movements equals the number of possible manipulator movements. The control systems may be interrupted as required. One part of the arm is fitted with a system to lock it with respect to another part of the arm without affecting the other movements, so long as the positions of the manipulator and the arm have not been brought into complete coincidence. With this system the locking can be ended when complete concordance is achieved [fr

  13. The direct manipulation shell

    International Nuclear Information System (INIS)

    Allen, M.E.; Christiansen, M.

    1992-01-01

    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)

  14. Manipulating early pig embryos.

    Science.gov (United States)

    Niemann, H; Reichelt, B

    1993-01-01

    On the basis of established surgical procedures for embryo recovery and transfer, the early pig embryo can be subjected to various manipulations aimed at a long-term preservation of genetic material, the generation of identical multiplets, the early determination of sex or the alteration of the genetic make-up. Most of these procedures are still at an experimental stage and despite recent considerable progress are far from practical application. Normal piglets have been obtained after cryopreservation of pig blastocysts hatched in vitro, whereas all attempts to freeze embryos with intact zona pellucida have been unsuccessful. Pig embryos at the morula and blastocyst stage can be bisected microsurgically and the resulting demi-embryos possess a high developmental potential in vitro, whereas their development in vivo is impaired. Pregnancy rates are similar (80%) but litter size is reduced compared with intact embryos and twinning rate is approximately 2%. Pig blastomeres isolated from embryos up to the 16-cell stage can be grown in culture and result in normal blastocysts. Normal piglets have been born upon transfer of blastocysts derived from isolated eight-cell blastomeres, clearly underlining the totipotency of this developmental stage. Upon nuclear transfer the developmental capacity of reconstituted pig embryos is low and culture. Sex determination can be achieved either by separation of X and Y chromosome bearing spermatozoa by flow cytometry or by analysing the expression of the HY antigen in pig embryos from the eight-cell to morula stage. Microinjection of foreign DNA has been successfully used to alter growth and development of transgenic pigs, and to produce foreign proteins in the mammary gland or in the bloodstream, indicating that pigs can be used as donors for valuable human pharmaceutical proteins. Another promising area of gene transfer is the increase of disease resistance in transgenic lines of pigs. Approximately 30% of pig spermatozoa bind

  15. A faster pedigree-based generalized multifactor dimensionality reduction method for detecting gene-gene interactions.

    Science.gov (United States)

    Chen, Guo-Bo; Zhu, Jun; Lou, Xiang-Yang

    2011-01-01

    We proposed a faster pedigree-based generalized multifactor dimensionality reduction algorithm, called PedG-MDR II (PII), to detect gene-gene interactions underlying complex traits. Inherited from our previous framework of PedGMDR (PI), PII can handle both dichotomous and continuous traits in pedigree-based designs and allows for covariate adjustment. Compared with PI, this faster version can theoretically halve the computing burden and memory requirement. To evaluate the performance of PII, we performed comprehensive simulations across a wide variety of experimental scenarios, in which we considered two study designs, discordant sib pairs and mixed families of varying size, and, for each study design, we considered five common factors that may potentially affect statistical power: minor allele frequency, missing rate of parental genotypes, covariate effect, gene-gene interaction, and scheme to adjust phenotypic outcomes. Simulations showed that PII gave well controlled type I error rates against population admixture. Under a total of 4,096 scenarios simulated, PII, in general, had a higher average power than PI for both dichotomous and continuous traits, and the advantage was more pronounced for continuous traits. PII also appeared to be less sensitive than PI to changes in the other four factors than the magnitude of genetic effects considered in this study. Applied to the Mid-South Tobacco Family study, PII detected a significant interaction with a p value of 5.4 × 10(-5) between two taster receptor genes, TAS2R16 and TAS2R38, responsible for nicotine dependence. In conclusion, PII is a faster supplementary version of our previous PI for detecting multifactor interactions.

  16. GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics.

    Science.gov (United States)

    Piovesan, Allison; Caracausi, Maria; Antonaros, Francesca; Pelleri, Maria Chiara; Vitale, Lorenza

    2016-01-01

    We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a 'mean' human protein-coding gene is 67 kbp long, has eleven 309 bp long exons and ten 6355 bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves.Database URL: http://apollo11.isto.unibo.it/software/. © The Author(s) 2016. Published by Oxford University Press.

  17. Manipulation of surface plasmon resonance of a graphene-based Au aperture antenna in visible and near-infrared regions

    Science.gov (United States)

    Wan, Yuan; An, Yashuai; Tao, Zhi; Deng, Luogen

    2018-03-01

    Behaviors of surface plasmon resonance (SPR) of a graphene-based Au aperture antenna are investigated in visible and near-infrared (vis-NIR) regions. Compared with the SPR wavelength of a traditional Au aperture antenna, the SPR wavelength of the graphene-based Au aperture antenna shows a remarkable blue shift due to the redistribution of the electric field in the proposed structure. The electric field of the graphene-based Au aperture antenna is highly localized on the surface of the graphene in the aperture and redistributed to be a standing wave. Moreover, the SPR of a graphene-based Au aperture antenna is sensitive to the thickness and the refractive index of the dielectric layer, the graphene Fermi energy, the refractive index of the environment and the polarization direction of the incident light. Finally, we find the wavelength, intensity and phase of the reflected light of the graphene-based Au aperture antenna array can be actively modulated by varying the graphene Fermi energy. The proposed structure provides a promising platform for realizing a tunable optical filter, a highly sensitive refractive index sensor, and other actively tunable optical and optoelectronic devices.

  18. A novel evolution-based method for detecting gene-gene interactions.

    Directory of Open Access Journals (Sweden)

    Shaoqi Rao

    Full Text Available BACKGROUND: The rapid advance in large-scale SNP-chip technologies offers us great opportunities in elucidating the genetic basis of complex diseases. Methods for large-scale interactions analysis have been under development from several sources. Due to several difficult issues (e.g., sparseness of data in high dimensions and low replication or validation rate, development of fast, powerful and robust methods for detecting various forms of gene-gene interactions continues to be a challenging task. METHODOLOGY/PRINCIPAL FINDINGS: In this article, we have developed an evolution-based method to search for genome-wide epistasis in a case-control design. From an evolutionary perspective, we view that human diseases originate from ancient mutations and consider that the underlying genetic variants play a role in differentiating human population into the healthy and the diseased. Based on this concept, traditional evolutionary measure, fixation index (Fst for two unlinked loci, which measures the genetic distance between populations, should be able to reveal the responsible genetic interplays for disease traits. To validate our proposal, we first investigated the theoretical distribution of Fst by using extensive simulations. Then, we explored its power for detecting gene-gene interactions via SNP markers, and compared it with the conventional Pearson Chi-square test, mutual information based test and linkage disequilibrium based test under several disease models. The proposed evolution-based method outperformed these compared methods in dominant and additive models, no matter what the disease allele frequencies were. However, its performance was relatively poor in a recessive model. Finally, we applied the proposed evolution-based method to analysis of a published dataset. Our results showed that the P value of the Fst -based statistic is smaller than those obtained by the LD-based statistic or Poisson regression models. CONCLUSIONS/SIGNIFICANCE: With

  19. Canonical correlation analysis for gene-based pleiotropy discovery.

    Directory of Open Access Journals (Sweden)

    Jose A Seoane

    2014-10-01

    Full Text Available Genome-wide association studies have identified a wealth of genetic variants involved in complex traits and multifactorial diseases. There is now considerable interest in testing variants for association with multiple phenotypes (pleiotropy and for testing multiple variants for association with a single phenotype (gene-based association tests. Such approaches can increase statistical power by combining evidence for association over multiple phenotypes or genetic variants respectively. Canonical Correlation Analysis (CCA measures the correlation between two sets of multidimensional variables, and thus offers the potential to combine these two approaches. To apply CCA, we must restrict the number of attributes relative to the number of samples. Hence we consider modules of genetic variation that can comprise a gene, a pathway or another biologically relevant grouping, and/or a set of phenotypes. In order to do this, we use an attribute selection strategy based on a binary genetic algorithm. Applied to a UK-based prospective cohort study of 4286 women (the British Women's Heart and Health Study, we find improved statistical power in the detection of previously reported genetic associations, and identify a number of novel pleiotropic associations between genetic variants and phenotypes. New discoveries include gene-based association of NSF with triglyceride levels and several genes (ACSM3, ERI2, IL18RAP, IL23RAP and NRG1 with left ventricular hypertrophy phenotypes. In multiple-phenotype analyses we find association of NRG1 with left ventricular hypertrophy phenotypes, fibrinogen and urea and pleiotropic relationships of F7 and F10 with Factor VII, Factor IX and cholesterol levels.

  20. Manipulating cognitive reserve: Pre-injury environmental conditions influence the severity of concussion symptomology, gene expression, and response to melatonin treatment in rats.

    Science.gov (United States)

    Yamakawa, Glenn R; Salberg, Sabrina; Barlow, Karen M; Brooks, Brian L; Esser, Michael J; Yeates, Keith Owen; Mychasiuk, Richelle

    2017-09-01

    In an effort to understand the factors that contribute to heterogeneity in outcomes often associated with mTBI in youth, this study examined the role of premorbid differences in cognitive reserve on post-concussive symptoms (PCS), molecular markers, and treatment response. Male and female rats matured in one of three environmental conditions (Stress, Enrichment, Control), received a mTBI in adolescence, and were randomized to melatonin or placebo treatment. All animals underwent a behavioural test battery designed to examine PCS. Using prefrontal cortex and hippocampus tissue, expression of 9 genes was assessed in an effort to determine how the brain's epigenome was influenced by cognitive reserve, mTBI, and melatonin. Enrichment increased cognitive reserve (CR) and prevented lingering symptoms. Conversely, stress was associated with progressive worsening and manifestation of PCS in the longer-term. Melatonin was able to restore baseline function for control and enriched animals, but was ineffective for the stress condition. Epigenetic change in the prefrontal cortex was largely driven by the injury, while gene expression changes in the hippocampus were dependent upon cognitive reserve. The occurrence and severity of PCS is dependent upon a complex and multifaceted array of factors that modify behavioural and epigenetic responses to mTBI and its treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    International Nuclear Information System (INIS)

    Kono, Akira

    1999-01-01

    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 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, F 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 2 (CCKAR,-/-) as well as the parent OLETF rat than hetero-mutant F 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.)

  2. Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

    Directory of Open Access Journals (Sweden)

    Olszewski Kellen L

    2007-07-01

    Full Text Available Abstract Background The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrated workings of the cell. However, translating this amount of data into biological insight remains a daunting task. An important initial step in the analysis of microarray data is clustering of genes with similar behavior. A number of classical techniques are commonly used to perform this task, particularly hierarchical and K-means clustering, and many novel approaches have been suggested recently. While these approaches are useful, they are not without drawbacks; these methods can find clusters in purely random data, and even clusters enriched for biological functions can be skewed towards a small number of processes (e.g. ribosomes. Results We developed Nearest Neighbor Networks (NNN, a graph-based algorithm to generate clusters of genes with similar expression profiles. This method produces clusters based on overlapping cliques within an interaction network generated from mutual nearest neighborhoods. This focus on nearest neighbors rather than on absolute distance measures allows us to capture clusters with high connectivity even when they are spatially separated, and requiring mutual nearest neighbors allows genes with no sufficiently similar partners to remain unclustered. We compared the clusters generated by NNN with those generated by eight other clustering methods. NNN was particularly successful at generating functionally coherent clusters with high precision, and these clusters generally represented a much broader selection of biological processes than those recovered by other methods. Conclusion The Nearest Neighbor Networks algorithm is a valuable clustering method that effectively groups genes that are likely to be functionally related. It is particularly attractive due to its simplicity, its success in the

  3. Schema-Based Instruction with Concrete and Virtual Manipulatives to Teach Problem Solving to Students with Autism

    Science.gov (United States)

    Root, Jenny R.; Browder, Diane M.; Saunders, Alicia F.; Lo, Ya-yu

    2017-01-01

    The current study evaluated the effects of modified schema-based instruction on the mathematical word problem solving skills of three elementary students with autism spectrum disorders and moderate intellectual disability. Participants learned to solve compare problem type with themes that related to their interests and daily experiences. In…

  4. 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.

  5. Manipulation of choice behavior

    OpenAIRE

    Manzini, Paola; Mariotti, Marco; Tyson, Christopher J.

    2011-01-01

    We introduce and study the problem of manipulation of choice behavior. In a class of two-stage models of decision making, with the agent's choices determined by three "psychological variables," we imagine that a subset of these variables can be selected by a "manipulator." To what extent does this confer control of the agent's behavior? Within the specified framework, which overlaps with two existing models of choice under cognitive constraints, we provide a complete answer to this question.

  6. 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...

  7. A Fisheye Viewer for microarray-based gene expression data.

    Science.gov (United States)

    Wu, Min; Thao, Cheng; Mu, Xiangming; Munson, Ethan V

    2006-10-13

    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. 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. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Microbial manipulation of host sex determination

    NARCIS (Netherlands)

    Beukeboom, Leo W.

    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

  12. Identifying the optimal gene and gene set in hepatocellular carcinoma based on differential expression and differential co-expression algorithm.

    Science.gov (United States)

    Dong, Li-Yang; Zhou, Wei-Zhong; Ni, Jun-Wei; Xiang, Wei; Hu, Wen-Hao; Yu, Chang; Li, Hai-Yan

    2017-02-01

    The objective of this study was to identify the optimal gene and gene set for hepatocellular carcinoma (HCC) utilizing differential expression and differential co-expression (DEDC) algorithm. The DEDC algorithm consisted of four parts: calculating differential expression (DE) by absolute t-value in t-statistics; computing differential co-expression (DC) based on Z-test; determining optimal thresholds on the basis of Chi-squared (χ2) maximization and the corresponding gene was the optimal gene; and evaluating functional relevance of genes categorized into different partitions to determine the optimal gene set with highest mean minimum functional information (FI) gain (Δ*G). The optimal thresholds divided genes into four partitions, high DE and high DC (HDE-HDC), high DE and low DC (HDE-LDC), low DE and high DC (LDE‑HDC), and low DE and low DC (LDE-LDC). In addition, the optimal gene was validated by conducting reverse transcription-polymerase chain reaction (RT-PCR) assay. The optimal threshold for DC and DE were 1.032 and 1.911, respectively. Using the optimal gene, the genes were divided into four partitions including: HDE-HDC (2,053 genes), HED-LDC (2,822 genes), LDE-HDC (2,622 genes), and LDE-LDC (6,169 genes). The optimal gene was microtubule‑associated protein RP/EB family member 1 (MAPRE1), and RT-PCR assay validated the significant difference between the HCC and normal state. The optimal gene set was nucleoside metabolic process (GO\\GO:0009116) with Δ*G = 18.681 and 24 HDE-HDC partitions in total. In conclusion, we successfully investigated the optimal gene, MAPRE1, and gene set, nucleoside metabolic process, which may be potential biomarkers for targeted therapy and provide significant insight for revealing the pathological mechanism underlying HCC.

  13. Creating and Manipulating a Domain-Specific Formal Object Base to Support a Domain-Oriented Application Composition System

    Science.gov (United States)

    1992-12-01

    Weide. A special thanks goes to Chuck Wright who was always there to offer support (or an offer to go get ice cream and/or chocolate which was even...technology base: "LOAD-SWITCH" "TEST- STR -SUB" "AID-i" Enter the object name: load-switch Enter the application name: (DEMO): Rule successfully applied...51 function Read-String(Prompt : string) : string = (if "empty(Prompt) then format(t, "A: ", Prompt) let ( str : any

  14. Design and Simulation of 5-DOF Vision-Based Manipulator to Increase Radiation Safety for Industrial Cobalt-60 Irradiators

    International Nuclear Information System (INIS)

    Solyman, A.E.; Keshk, A.B.; Sharshar, K.A.; Roman, M.R.

    2016-01-01

    Robotics has proved its efficiency in nuclear and radiation fields. Computer vision is one of the advanced approaches used to enhance robotic efficiency. The current work investigates the possibility of using a vision-based controlled arm robot to collect the fallen hot Cobalt-60 capsules inside wet storage pool of industrial irradiator. A 5-DOF arm robot is designed and vision algorithms are established to pick the fallen capsules on the bottom surface of the storage pool, read the information printed on its edge (cap) and move it to a safe storage place. Two object detection approaches are studied; RGB-based filter and background subtraction technique. Vision algorithms and camera calibration are done using MATLAB/SIMULINK program. Robot arm forward and inverse kinematics are developed and programmed using an embedded micro controller system. Experiments show the validity of the proposed system and prove its success. The collecting process will be done without interference of operators, hence radiation safety will be increased.

  15. Mesenchymal Stem Cell-Based Cartilage Regeneration Approach and Cell Senescence: Can We Manipulate Cell Aging and Function?

    Science.gov (United States)

    Szychlinska, Marta A; Stoddart, Martin J; D'Amora, Ugo; Ambrosio, Luigi; Alini, Mauro; Musumeci, Giuseppe

    2017-12-01

    Aging is the most prominent risk factor triggering several degenerative diseases, such as osteoarthritis (OA). Due to its poor self-healing capacity, once injured cartilage needs to be reestablished. This process might be approached through resorting to cell-based therapies and/or tissue engineering. Human mesenchymal stem cells (MSCs) represent a promising approach due to their chondrogenic differentiation potential. Presently, in vitro chondrogenic differentiation of MSCs is limited by two main reasons as follows: aging of MSCs, which determines the loss of cell proliferative and differentiation capacity and MSC-derived chondrocyte hypertrophic differentiation, which limits the use of these cells in cartilage tissue regeneration approach. The effect of aging on MSCs is fundamental for stem cell-based therapy development, especially in older subjects. In the present review we focus on homeostasis alterations occurring in MSC-derived chondrocytes during in vitro aging. Moreover, we deal with potential cell aging regulation approaches, such as cell stimulation through telomerase activators, mechanical strain, and epigenetic regulation. Future investigations in this field might provide new insights into innovative strategies for cartilage regeneration and potentially inspire novel therapeutic approaches for OA treatment.

  16. Polymorphism of the DNA Base Excision Repair Genes in Keratoconus

    Science.gov (United States)

    Wojcik, Katarzyna A.; Synowiec, Ewelina; Sobierajczyk, Katarzyna; Izdebska, Justyna; Blasiak, Janusz; Szaflik, Jerzy; Szaflik, Jacek P.

    2014-01-01

    Keratoconus (KC) is a degenerative corneal disorder for which the exact pathogenesis is not yet known. Oxidative stress is reported to be associated with this disease. The stress may damage corneal biomolecules, including DNA, and such damage is primarily removed by base excision repair (BER). Variation in genes encoding BER components may influence the effectiveness of corneal cells to cope with oxidative stress. In the present work we genotyped 5 polymorphisms of 4 BER genes in 284 patients and 353 controls. The A/A genotype of the c.–1370T>A polymorphism of the DNA polymerase γ (POLG) gene was associated with increased occurrence of KC, while the A/T genotype was associated with decreased occurrence of KC. The A/G genotype and the A allele of the c.1196A>G polymorphism of the X-ray repair cross-complementing group 1 (XRCC1) were associated with increased, and the G/G genotype and the G allele, with decreased KC occurrence. Also, the C/T and T as well as C/C genotypes and alleles of the c.580C>T polymorphism of the same gene displayed relationship with KC occurrence. Neither the g.46438521G>C polymorphism of the Nei endonuclease VIII-like 1 (NEIL1) nor the c.2285T>C polymorphism of the poly(ADP-ribose) polymerase-1 (PARP-1) was associated with KC. In conclusion, the variability of the XRCC1 and POLG genes may play a role in KC pathogenesis and determine the risk of this disease. PMID:25356504

  17. Polymorphism of the DNA Base Excision Repair Genes in Keratoconus

    Directory of Open Access Journals (Sweden)

    Katarzyna A. Wojcik

    2014-10-01

    Full Text Available Keratoconus (KC is a degenerative corneal disorder for which the exact pathogenesis is not yet known. Oxidative stress is reported to be associated with this disease. The stress may damage corneal biomolecules, including DNA, and such damage is primarily removed by base excision repair (BER. Variation in genes encoding BER components may influence the effectiveness of corneal cells to cope with oxidative stress. In the present work we genotyped 5 polymorphisms of 4 BER genes in 284 patients and 353 controls. The A/A genotype of the c.–1370T>A polymorphism of the DNA polymerase γ (POLG gene was associated with increased occurrence of KC, while the A/T genotype was associated with decreased occurrence of KC. The A/G genotype and the A allele of the c.1196A>G polymorphism of the X-ray repair cross-complementing group 1 (XRCC1 were associated with increased, and the G/G genotype and the G allele, with decreased KC occurrence. Also, the C/T and T as well as C/C genotypes and alleles of the c.580C>T polymorphism of the same gene displayed relationship with KC occurrence. Neither the g.46438521G>C polymorphism of the Nei endonuclease VIII-like 1 (NEIL1 nor the c.2285T>C polymorphism of the poly(ADP-ribose polymerase-1 (PARP-1 was associated with KC. In conclusion, the variability of the XRCC1 and POLG genes may play a role in KC pathogenesis and determine the risk of this disease.

  18. 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

  19. Design of Knowledge Bases for Plant Gene Regulatory Networks.

    Science.gov (United States)

    Mukundi, Eric; Gomez-Cano, Fabio; Ouma, Wilberforce Zachary; Grotewold, Erich

    2017-01-01

    Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary information and resources, and outline the methods for obtaining data. The second stage consists of designing the schema, which involves defining the entire arrangement of the database in a systematic plan. The third stage is the implementation, defined by actualization of the database by using software according to a predefined schema. The final stage is development, where the database is made available to users in a web-accessible system. The result is a knowledgebase that integrates all the information pertaining to gene regulation, and which is easily expandable and transferable.

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

    International Nuclear Information System (INIS)

    Zhou, Qian; Yu, Yong-ming

    2014-01-01

    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)

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

    Science.gov (United States)

    Zhou, Qian; Yu, Yong-ming

    2014-11-01

    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.

  2. Inferring nonlinear gene regulatory networks from gene expression data based on distance correlation.

    Directory of Open Access Journals (Sweden)

    Xiaobo Guo

    Full Text Available Nonlinear dependence is general in regulation mechanism of gene regulatory networks (GRNs. It is vital to properly measure or test nonlinear dependence from real data for reconstructing GRNs and understanding the complex regulatory mechanisms within the cellular system. A recently developed measurement called the distance correlation (DC has been shown powerful and computationally effective in nonlinear dependence for many situations. In this work, we incorporate the DC into inferring GRNs from the gene expression data without any underling distribution assumptions. We propose three DC-based GRNs inference algorithms: CLR-DC, MRNET-DC and REL-DC, and then compare them with the mutual information (MI-based algorithms by analyzing two simulated data: benchmark GRNs from the DREAM challenge and GRNs generated by SynTReN network generator, and an experimentally determined SOS DNA repair network in Escherichia coli. According to both the receiver operator characteristic (ROC curve and the precision-recall (PR curve, our proposed algorithms significantly outperform the MI-based algorithms in GRNs inference.

  3. A novel fuzzy set based multifactor dimensionality reduction method for detecting gene-gene interaction.

    Science.gov (United States)

    Jung, Hye-Young; Leem, Sangseob; Lee, Sungyoung; Park, Taesung

    2016-12-01

    Gene-gene interaction (GGI) is one of the most popular approaches for finding the missing heritability of common complex traits in genetic association studies. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGIs. In order to identify the best interaction model associated with disease susceptibility, MDR compares all possible genotype combinations in terms of their predictability of disease status from a simple binary high(H) and low(L) risk classification. However, this simple binary classification does not reflect the uncertainty of H/L classification. We regard classifying H/L as equivalent to defining the degree of membership of two risk groups H/L. By adopting the fuzzy set theory, we propose Fuzzy MDR which takes into account the uncertainty of H/L classification. Fuzzy MDR allows the possibility of partial membership of H/L through a membership function which transforms the degree of uncertainty into a [0,1] scale. The best genotype combinations can be selected which maximizes a new fuzzy set based accuracy measure. Two simulation studies are conducted to compare the power of the proposed Fuzzy MDR with that of MDR. Our results show that Fuzzy MDR has higher power than MDR. We illustrate the proposed Fuzzy MDR by analysing bipolar disorder (BD) trait of the WTCCC dataset to detect GGI associated with BD. We propose a novel Fuzzy MDR method to detect gene-gene interaction by taking into account the uncertainly of H/L classification and show that it has higher power than MDR. Fuzzy MDR can be easily extended to handle continuous phenotypes as well. The program written in R for the proposed Fuzzy MDR is available at https://statgen.snu.ac.kr/software/FuzzyMDR. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Gene-disease relationship discovery based on model-driven data integration and database view definition.

    Science.gov (United States)

    Yilmaz, S; Jonveaux, P; Bicep, C; Pierron, L; Smaïl-Tabbone, M; Devignes, M D

    2009-01-15

    Computational methods are widely used to discover gene-disease relationships hidden in vast masses of available genomic and post-genomic data. In most current methods, a similarity measure is calculated between gene annotations and known disease genes or disease descriptions. However, more explicit gene-disease relationships are required for better insights into the molecular bases of diseases, especially for complex multi-gene diseases. Explicit relationships between genes and diseases are formulated as candidate gene definitions that may include intermediary genes, e.g. orthologous or interacting genes. These definitions guide data modelling in our database approach for gene-disease relationship discovery and are expressed as views which ultimately lead to the retrieval of documented sets of candidate genes. A system called ACGR (Approach for Candidate Gene Retrieval) has been implemented and tested with three case studies including a rare orphan gene disease.

  5. Manipulator gaiter system

    International Nuclear Information System (INIS)

    Cole, G.V.

    1991-01-01

    A manipulator is described which comprises a throughtube and a slave arm which is provided with a retainer ring to retain a gaiter enclosing the slave arm while the manipulator is installed in a through-wall liner in a wall of a hot cell. The manipulator also incorporates a cam and spring-loaded pin arranged to push the toggle of the gaiter ring into its expanded position, clamped to the liner. The cam is operated by bending the slave arm relative to the throughtube. Since the gaiter is fitted over the slave arm before installation of the slave arm in the liner, the gaiter is less likely to be damaged or to be knocked out of the liner during installation. (author)

  6. IL-12 based gene therapy in veterinary medicine.

    Science.gov (United States)

    Pavlin, Darja; Cemazar, Maja; Sersa, Gregor; Tozon, Natasa

    2012-11-21

    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.

  7. SVM-based generalized multifactor dimensionality reduction approaches for detecting gene-gene interactions in family studies.

    Science.gov (United States)

    Fang, Yao-Hwei; Chiu, Yen-Feng

    2012-02-01

    Gene-gene interaction plays an important role in the etiology of complex diseases, which may exist without a genetic main effect. Most current statistical approaches, however, focus on assessing an interaction effect in the presence of the gene's main effects. It would be very helpful to develop methods that can detect not only the gene's main effects but also gene-gene interaction effects regardless of the existence of the gene's main effects while adjusting for confounding factors. In addition, when a disease variant is rare or when the sample size is quite limited, the statistical asymptotic properties are not applicable; therefore, approaches based on a reasonable and applicable computational framework would be practical and frequently applied. In this study, we have developed an extended support vector machine (SVM) method and an SVM-based pedigree-based generalized multifactor dimensionality reduction (PGMDR) method to study interactions in the presence or absence of main effects of genes with an adjustment for covariates using limited samples of families. A new test statistic is proposed for classifying the affected and the unaffected in the SVM-based PGMDR approach to improve performance in detecting gene-gene interactions. Simulation studies under various scenarios have been performed to compare the performances of the proposed and the original methods. The proposed and original approaches have been applied to a real data example for illustration and comparison. Both the simulation and real data studies show that the proposed SVM and SVM-based PGMDR methods have great prediction accuracies, consistencies, and power in detecting gene-gene interactions. © 2012 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    Bouwman, Laura; Te Molder, Hedwig; Hiddink, Gerrit

    2008-12-01

    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. Gene-based personalized nutrition advice emerges at the junction of different disciplines and technologies and may directly influence people's lives. Therefore, public concern is to be expected. Because GPs are gatekeepers of health care, their involvement in early stages of the development process is desirable. In 2006, 15 GPs were interviewed to collect their perceived barriers and opportunities towards involvement in gene-based nutrition advice. The interviews were qualitatively analysed with use of Atlas.ti, a qualitative analysis programme. The participants held a mostly critical view towards such personalized nutrition advice. They argued that findings of nutritional studies lacked robustness, were not based on patients' needs and were often equivocal. And that a patient central perspective urges them to question consequences for patients. Participants argued that GPs should be involved in selecting and monitoring patients in nutrigenomics studies. Early involvement of GPs in the development process is needed to allow for the integration of their practical, social and ethical considerations in the technical and scientific agendas. However, the background of their critical attitude towards nutrigenomics-based personalized nutrition, and nutrition advice more generally, has to be explored further. To facilitate a joint learning process and to improve socio-technical decision making with respect to this innovation, initiatives that allow different stakeholders to exchange their perspectives should be organized.

  9. Reporter Gene-Based Screening for TPP Riboswitch Activators.

    Science.gov (United States)

    Lünse, Christina E; Mayer, Günter

    2017-01-01

    With the rise of multidrug resistant bacteria and a growing number of nosocomial infections, there has been an increased interest in finding new antibacterial drugs and drug targets. Riboswitches represent attractive new antibacterial drug targets, because they not only inherently recognize a specific metabolite or ion with their RNA aptamer domain, but also often regulate essential metabolic pathways. Here, we describe a reporter gene-based screen to identify compounds that activate the thiamine pyrophosphate (TPP) riboswitch in bacteria. This assay can be easily adapted for different riboswitch classes and thus has the potential to target many essential metabolic pathways and a broad spectrum of bacterial pathogens.

  10. Data manipulation with R

    CERN Document Server

    Abedin, Jaynal

    2014-01-01

    This book is a step-by step, example-oriented tutorial that will show both intermediate and advanced users how data manipulation is facilitated smoothly using R.This book is aimed at intermediate to advanced level users of R who want to perform data manipulation with R, and those who want to clean and aggregate data effectively. Readers are expected to have at least an introductory knowledge of R and some basic administration work in R, such as installing packages and calling them when required.

  11. ELECTRONIC MASTER SLAVE MANIPULATOR

    Science.gov (United States)

    Goertz, R.C.; Thompson, Wm.M.; Olsen, R.A.

    1958-08-01

    A remote control manipulator is described in which the master and slave arms are electrically connected to produce the desired motions. A response signal is provided in the master unit in order that the operator may sense a feel of the object and may not thereby exert such pressures that would ordinarily damage delicate objects. This apparatus will permit the manipulation of objects at a great distance, that may be viewed over a closed TV circuit, thereby permitting a remote operator to carry out operations in an extremely dangerous area with complete safety.

  12. Stock Market Manipulation on the Hong Kong Stock Exchange

    Directory of Open Access Journals (Sweden)

    Dionigi Gerace

    2014-10-01

    Full Text Available This study is the first to empirically examine stock market manipulation on the Hong Kong Stock Exchange. The dataset contains 40 cases of market manipulation from 1996 to 2009 that were successfully prosecuted by the Hong Kong Securities & Futures Commission. Manipulation is found to negatively impact market efficiency measures such as the bid-ask spread and volatility. Markets appear incapable of efficiently responding to the presence of manipulators and are characterised by information asymmetry. Manipulators were successfully able to raise prices and exit the market. This finding contradicts views that trade-based manipulation is entirely unprofitable and self-deterring. The victimisation of information-seeking investors and the market as a whole provides a strong rationale for all jurisdictions, including Australia, to have effective laws that prohibit manipulation and for robust enforcement of those laws to further deter market manipulation.

  13. Gene-based therapy for alpha-1 antitrypsin deficiency.

    Science.gov (United States)

    Mueller, Christian; Flotte, Terence R

    2013-03-01

    Alpha-1 antitrypsin Deficiency (AATD) has been an attractive target for the development of gene therapy because it is a common single gene disorder, for which there would appear to be significant benefit to be gained for lung disease patients by augmentation of plasma levels of wild-type (M) alpha-1 antitrypsin (AAT). While a significant proportion of patients also have liver disease, which is unlikely to be benefitted by augmentation, the potential to treat or prevent lung disease by replacement of plasma levels to at least 11 microMolar (571 mcg/ml) is the basis upon which several protein replacement therapies have been licensed for human use. Further enhancing the likelihood of success of gene therapy is the fact that the AAT coding sequence is relatively short and the protein appears to function primarily in the plasma and extracellular space. This means that AAT production from any cell or tissue capable of secreting it could be useful therapeutically for augmentation. Based on these considerations, attempts have been made to develop AAT therapies using nonviral gene transfer, gammaretrovirus, recombinant adenovirus (rAd), and recombinant adeno-associated virus (rAAV) vectors. These have resulted in three phase I clinical trials (one of cationic liposome, one of rAAV2, and one of rAAV1) and one phase II clinical trial (with rAAV1). The results of the latter trial, while promising, demonstrated levels were only 3 to 5% of the target range. This indicates the need to further increase the dose of the vector and/or to increase the levels to within the therapeutic range.

  14. Improved RBF Neural Network Based Soft Sensor: Application to the Optimal Robust Calibration of a Six Degrees of Freedom Parallel Kinematics Manipulator

    Directory of Open Access Journals (Sweden)

    Dan ZHANG

    2010-10-01

    Full Text Available Accuracy is paramount for the further development of parallel mechanism in real world, especially in industry. Previous research was focused on the improvement of rigidity and load capacity which is related with the stiffness matrix of closed loop kinematic structure. However, if the mechanical structure has been predefined or fabricated, stiffness matrix only can search for the optimal configuration in the workspace, but fails to enhance the accuracy at a given pose. In this research, the concept of optimal robust calibration is developed as an effective approach to largely reduce various errors of the predefined parallel mechanism. A novel coevolutionary radial basis function (RBF neural network based soft sensor is proposed to implement the optimal robust calibration procedure. A six- degrees-of-freedom parallel kinematics manipulator is selected as the case study to verify the proposed methodology. The results demonstrate that the coevolutionary neural network possesses the excellent performance as a smart soft sensor for the calibration of closed loop kinematic structure.

  15. Giant voltage manipulation of MgO-based magnetic tunnel junctions via localized anisotropic strain: A potential pathway to ultra-energy-efficient memory technology

    Science.gov (United States)

    Zhao, Zhengyang; Jamali, Mahdi; D'Souza, Noel; Zhang, Delin; Bandyopadhyay, Supriyo; Atulasimha, Jayasimha; Wang, Jian-Ping

    2016-08-01

    Voltage control of magnetization via strain in piezoelectric/magnetostrictive systems is a promising mechanism to implement energy-efficient straintronic memory devices. Here, we demonstrate giant voltage manipulation of MgO magnetic tunnel junctions (MTJ) on a Pb(Mg1/3Nb2/3)0.7Ti0.3O3 piezoelectric substrate with (001) orientation. It is found that the magnetic easy axis, switching field, and the tunnel magnetoresistance (TMR) of the MTJ can be efficiently controlled by strain from the underlying piezoelectric layer upon the application of a gate voltage. Repeatable voltage controlled MTJ toggling between high/low-resistance states is demonstrated. More importantly, instead of relying on the intrinsic anisotropy of the piezoelectric substrate to generate the required strain, we utilize anisotropic strain produced using a local gating scheme, which is scalable and amenable to practical memory applications. Additionally, the adoption of crystalline MgO-based MTJ on piezoelectric layer lends itself to high TMR in the strain-mediated MRAM devices.

  16. Herpes simplex virus type 1-based amplicon vectors for fundamental research in neurosciences and gene therapy of neurological diseases.

    Science.gov (United States)

    Jerusalinsky, Diana; Baez, María Verónica; Epstein, Alberto Luis

    2012-01-01

    Somatic manipulation of the nervous system without the involvement of the germinal line appears as a powerful counterpart of the transgenic strategy. The use of viral vectors to produce specific, transient and localized knockout, knockdown, ectopic expression or overexpression of a gene, leads to the possibility of analyzing both in vitro and in vivo molecular basis of neural function. In this approach, viral particles engineered to carry transgenic sequences are delivered into discrete brain regions, to transduce cells that will express the transgenic products. Amplicons are replication-incompetent helper-dependent vectors derived from herpes simplex virus type 1 (HSV-1), with several advantages that potentiate their use in neurosciences: (1) minimal toxicity: amplicons do not encode any virus proteins, are neither toxic for the infected cells nor pathogenic for the inoculated animals and elicit low levels of adaptive immune responses; (2) extensive transgene capacity to carry up to 150-kb of foreign DNA; i.e., entire genes with regulatory sequences could be delivered; (3) widespread cellular tropism: amplicons can experimentally infect several cell types including glial cells, though naturally the virus infects mainly neurons and epithelial cells; (4) since the viral genome does not integrate into cellular chromosomes there is low probability to induce insertional mutagenesis. Recent investigations on gene transfer into the brain using these vectors, have focused on gene therapy of inherited genetic diseases affecting the nervous system, such as ataxias, or on neurodegenerative disorders using experimental models of Parkinson's or Alzheimer's disease. Another group of studies used amplicons to investigate complex neural functions such as neuroplasticity, anxiety, learning and memory. In this short review, we summarize recent data supporting the potential of HSV-1 based amplicon vector model for gene delivery and modulation of gene expression in primary cultures

  17. A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer

    Directory of Open Access Journals (Sweden)

    Mary Qu Yang

    Full Text Available Clear cell renal cell carcinoma (ccRCC is the most common and most aggressive form of renal cell cancer (RCC. The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to prioritize the somatic mutated genes that lead to dysregulation of pathways in ccRCC. The method integrated multi-layer information to infer causative mutations and disease genes. First, we identified differential gene modules in ccRCC by coupling transcriptome and protein-protein interactions. Each of these modules consisted of interacting genes that were involved in similar biological processes and their combined expression alterations were significantly associated with disease type. Then, subsequent gene module-based eQTL analysis revealed somatic mutated genes that had driven the expression alterations of differential gene modules. Our study yielded a list of candidate disease genes, including several known ccRCC causative genes such as BAP1 and PBRM1, as well as novel genes such as NOD2, RRM1, CSRNP1, SLC4A2, TTLL1 and CNTN1. The differential gene modules and their driver genes revealed by our study provided a new perspective for understanding the molecular mechanisms underlying the disease. Moreover, we validated the results in independent ccRCC patient datasets. Our study provided a new method for prioritizing disease genes and pathways. Keywords: ccRCC, Causative mutation, Pathways, Protein-protein interaction, Gene module, eQTL

  18. 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.

  19. Genetic manipulation of Methanosarcina spp.

    Directory of Open Access Journals (Sweden)

    Petra Regine Adelheid Kohler

    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.

  20. A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information.

    Science.gov (United States)

    Han, Fei; Yang, Chun; Wu, Ya-Qi; Zhu, Jian-Sheng; Ling, Qing-Hua; Song, Yu-Qing; Huang, De-Shuang

    2017-01-01

    Traditional gene selection methods for microarray data mainly considered the features' relevance by evaluating their utility for achieving accurate predication or exploiting data variance and distribution, and the selected genes were usually poorly explicable. To improve the interpretability of the selected genes as well as prediction accuracy, an improved gene selection method based on binary particle swarm optimization (BPSO) and prior information is proposed in this paper. In the proposed method, BPSO encoding gene-to-class sensitivity (GCS) information is used to perform gene selection. The gene-to-class sensitivity information, extracted from the samples by extreme learning machine (ELM), is encoded into the selection process in four aspects: initializing particles, updating the particles, modifying maximum velocity, and adopting mutation operation adaptively. Constrained by the gene-to-class sensitivity information, the new method can select functional gene subsets which are significantly sensitive to the samples' classes. With the few discriminative genes selected by the proposed method, ELM, K-nearest neighbor and support vector machine classifiers achieve much high prediction accuracy on five public microarray data, which in turn verifies the efficiency and effectiveness of the proposed gene selection method.

  1. 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.

  2. Automated visual attention manipulation

    NARCIS (Netherlands)

    Bosse, T.; Lambalgen, R. van; Maanen, P.P. van; Treur, J.

    2009-01-01

    In this paper a system for visual attention manipulation is introduced and formally described. This system is part of the design of a software agent that supports naval crew in her task to compile a tactical picture of the situation in the field. A case study is described in hich the system is used

  3. 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.

  4. Microrobots to Manipulate Cells

    DEFF Research Database (Denmark)

    Glückstad, Jesper

    At DTU Fotonik we developed and harnessed the new and emerging research area of so-called Light Robotics including the 3D-printed micro-tools coined Wave-guided Optical Waveguides that can be real-time laser-manipulated in a 3D-volume with six-degrees-of-freedom. To be exploring the full potentia...

  5. Control of two Wheeled Welding Mobile Manipulator

    Directory of Open Access Journals (Sweden)

    M. D. Ngo

    2007-09-01

    Full Text Available A three-linked manipulator mounted on a two-wheeled mobile platform is used to weld a long curved welding path. A welding torch mounted at the end of a manipulator of the welding mobile manipulator (WMM must be controlled for tracking a welding path with constant velocity and constant welding angle of torch. In this paper, a decentralized control method is applied to control the WMM considered as two separate subsystems such as a mobile platform and a manipulator. Two decentralized motion controllers are designed to control two subsystems of WMM, respectively. Firstly, based on a tracking error vector of the manipulator and a feedback motion of the mobile platform, a kinematic controller is designed for manipulator. Secondly, based on an another tracking error vector of the mobile platform and a feedback angular velocities of revolution joints of three-link, a sliding mode controller is designed for the mobile platform. These controllers are obtained based on the Lyapunov's function and its stability condition to ensure for the tracking error vectors to be asymptotically stable. Furthermore, simulation and experimental results are presented to illustrate the effectiveness of the proposed algorithm.

  6. 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.

  7. 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.)

  8. Increasing the open-circuit voltage of photoprotein-based photoelectrochemical cells by manipulation of the vacuum potential of the electrolytes.

    Science.gov (United States)

    Tan, Swee Ching; Crouch, Lucy I; Mahajan, Sumeet; Jones, Michael R; Welland, Mark E

    2012-10-23

    The innately highly efficient light-powered separation of charge that underpins natural photosynthesis can be exploited for applications in photoelectrochemistry by coupling nanoscale protein photoreaction centers to man-made electrodes. Planar photoelectrochemical cells employing purple bacterial reaction centers have been constructed that produce a direct current under continuous illumination and an alternating current in response to discontinuous illumination. The present work explored the basis of the open-circuit voltage (V(OC)) produced by such cells with reaction center/antenna (RC-LH1) proteins as the photovoltaic component. It was established that an up to ~30-fold increase in V(OC) could be achieved by simple manipulation of the electrolyte connecting the protein to the counter electrode, with an approximately linear relationship being observed between the vacuum potential of the electrolyte and the resulting V(OC). We conclude that the V(OC) of such a cell is dependent on the potential difference between the electrolyte and the photo-oxidized bacteriochlorophylls in the reaction center. The steady-state short-circuit current (J(SC)) obtained under continuous illumination also varied with different electrolytes by a factor of ~6-fold. The findings demonstrate a simple way to boost the voltage output of such protein-based cells into the hundreds of millivolts range typical of dye-sensitized and polymer-blend solar cells, while maintaining or improving the J(SC). Possible strategies for further increasing the V(OC) of such protein-based photoelectrochemical cells through protein engineering are discussed.

  9. Indentation analysis of nano-particle using nano-contact mechanics models during nano-manipulation based on atomic force microscopy

    International Nuclear Information System (INIS)

    Daeinabi, Khadijeh; Korayem, Moharam Habibnejad

    2011-01-01

    Atomic force microscopy is applied to measure intermolecular forces and mechanical properties of materials, nano-particle manipulation, surface scanning and imaging with atomic accuracy in the nano-world. During nano-manipulation process, contact forces cause indentation in contact area between nano-particle and tip/substrate which is considerable at nano-scale and affects the nano-manipulation process. Several nano-contact mechanics models such as Hertz, Derjaguin–Muller–Toporov (DMT), Johnson–Kendall–Roberts–Sperling (JKRS), Burnham–Colton–Pollock (BCP), Maugis–Dugdale (MD), Carpick–Ogletree–Salmeron (COS), Pietrement–Troyon (PT), and Sun et al. have been applied as the continuum mechanics approaches at nano-scale. In this article, indentation depth and contact radius between tip and substrate with nano-particle for both spherical and conical tip shape during nano-manipulation process are analyzed and compared by applying theoretical, semiempirical, and empirical nano-contact mechanics models. The effects of adhesion force, as the main contrast point in different nano-contact mechanics models, on nano-manipulation analysis is investigated for different contact radius, and the critical point is discussed for mentioned models.

  10. The modelling of industrial robot manipulator vibration

    Energy Technology Data Exchange (ETDEWEB)

    Marcham, L.J.; Rao, B.K.N.; Noroozi, S.; Penson, R.P. [Southampton Inst. (United Kingdom). Systems Engineering Research Centre

    1996-11-01

    The work reported in this paper addresses the modelling of robot manipulator vibration, with the specific aim of producing a model suitable to be employed within an active compensation controller. An overview of existing work on the modelling of robot dynamics, both mathematically and empirically, is reported. A model of the dynamics of an industrial manipulator, inclusive of vibration, derived using Lagrangian mechanics is presented and further developed through the application of experimental modal analysis, by which the position dependent modal parameters of an industrial robot manipulator are determined. The model results are compared with experimental vibration data taken from the end-effector of a PUMA562C industrial manipulator using laser interferometry. Control of an end-effector located, active compensator for vibration suppression, based upon the derived model is discussed and recommendations which form the basis of further investigations, currently being undertaken, are presented.

  11. Unifying the genomics-based classes of cancer fusion gene partners: large cancer fusion genes are evolutionarily conserved.

    Science.gov (United States)

    Pava, Libia M; Morton, Daniel T; Chen, Ren; Blanck, George

    2012-11-01

    Genes that fuse to cause cancer have been studied to determine molecular bases for proliferation, to develop diagnostic tools, and as targets for drugs. To facilitate identification of additional, cancer fusion genes, following observation of a chromosomal translocation, we have characterized the genomic features of the fusion gene partners. Previous work indicated that cancer fusion gene partners, are either large or evolutionarily conserved in comparison to the neighboring genes in the region of a chromosomal translocation. These results raised the question of whether large cancer fusion gene partners were also evolutionarily conserved. We developed two methods for quantifying evolutionary conservation values, allowing the conclusion that both large and small cancer fusion gene partners are more evolutionarily conserved than their neighbors. Additionally, we determined that cancer fusion gene partners have more 3' untranslated region secondary structures than do their neighbors. Coupled with previous algorithms, with or without transcriptome approaches, we expect these results to assist in the rapid and efficient use of chromosomal translocations to identify cancer fusion genes. The above parameters for any gene of interest can be accessed at www.cancerfusiongenes.com.

  12. A nanoparticle-based epigenetic modulator for efficient gene modulation

    Science.gov (United States)

    Pongkulapa, Thanapat

    Modulation of gene expression through chromatin remodeling involves epigenetic mechanisms, such as histone acetylation. Acetylation is tightly regulated by two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). Molecules that can regulate these enzymes by altering (activating or inhibiting) their functions have become a valuable tool for understanding cell development and diseases. HAT activators, i.e. N-(4-Chloro-(3-trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB), have shown a therapeutic potential for many diseases, including cancer and neurodegeneration. However, these compounds encounter a solubility and a membrane permeability issue, which restricts their full potential for practical usage, especially for in vivo applications. To address this issue, in this work, we developed a nanoparticle-based HAT activator CTB, named Au-CTB, by incorporating a new CTB analogue onto gold nanoparticles (AuNPs) along with a poly(ethylene glycol) moiety and a nuclear localization signal (NLS) peptide to assist with solubility and membrane permeability. We found that our new CTB analogue and Au-CTB could activate HAT activity. Significantly, an increase in potency to activate HAT activity by Au-CTB proved the effectiveness of using the nanoparticle delivery platform. In addition, the versatility of Au-CTB platform permits the attachment of multiple ligands with tunable ratios on the nanoparticle surface via facile surface functionalization of gold nanoparticles. Due to its high delivery efficiency and versatility, Au-CTB can be a powerful platform for applications in epigenetic regulation of gene expression.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    (P = 9.01 × 10-7), CNNM2 (P = 6.07 × 10-7), and NT5C2 (P = 4.09 × 10-7). To explore the many small effects, we performed pathway analyses. The most significant pathways involved neuronal function (axonal guidance, neuronal systems, and L1 cell adhesion molecule interaction) and the immune system...... genes. DESIGN We integrated results from a meta-analysis of 18 genome-wide association studies (GWAS) involving 1 085 772 single-nucleotide polymorphisms (SNPs) and 6 databases that showed significant informativeness for SCZ. The 9380 most promising SNPs were then specifically genotyped...... in an 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...

  14. Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

    Science.gov (United States)

    Saraee, Mahdieh B; Korayem, Moharam H

    2015-08-07

    Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. A universal microscope manipulator

    Directory of Open Access Journals (Sweden)

    Peter S. Boyadzhiev

    2012-03-01

    Full Text Available A modified and improved model of a mechanical manipulator for observation of pinned and mounted insects is described. This device allows movement of the observed object around three perpendicular axes in the field of vision at all magnifications of stereomicroscopes. The main improvement of this new model is positioning of the guiding knobs for rotating around two of the axes next to each other, allowing faster and easier manipulation of the studied object. Thus, one of the main advantages of this device is the possibility to rotate the specimen without the need to refocus. The device enables easily reaching a precession deviation in the intersection point of axes up to 0.5 mm in the process of assembling.

  16. A dictionary-based approach for gene annotation.

    Science.gov (United States)

    Pachter, L; Batzoglou, S; Spitkovsky, V I; Banks, E; Lander, E S; Kleitman, D J; Berger, B

    1999-01-01

    This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.

  17. Gene-Based Antibody Strategies for Prion Diseases

    Directory of Open Access Journals (Sweden)

    Alessio Cardinale

    2013-01-01

    Full Text Available Prion diseases or transmissible spongiform encephalopathies (TSE are a group of neurodegenerative and infectious disorders characterized by the conversion of a normal cellular protein PrPC into a pathological abnormally folded form, termed PrPSc. There are neither available therapies nor diagnostic tools for an early identification of individuals affected by these diseases. New gene-based antibody strategies are emerging as valuable therapeutic tools. Among these, intrabodies are chimeric molecules composed by recombinant antibody fragments fused to intracellular trafficking sequences, aimed at inhibiting, in vivo, the function of specific therapeutic targets. The advantage of intrabodies is that they can be selected against a precise epitope of target proteins, including protein-protein interaction sites and cytotoxic conformers (i.e., oligomeric and fibrillar assemblies. Herein, we address and discuss in vitro and in vivo applications of intrabodies in prion diseases, focussing on their therapeutic potential.

  18. Gene manipulation: churches against germ changes.

    Science.gov (United States)

    Budiansky, S

    An immediate ban on human genetic engineering that alters germ cells is called for in a resolution, written by activist Jeremy Rifkin, that was released last week over the signatures of 21 Catholic bishops, a broad spectrum of Protestant and Jewish religious leaders, and three scientists. The resolution takes a much harder line than was espoused by religious leaders in a letter to the now-defunct President's Commission for the Study of Ethical Problems in Medicine and Biomedical and Behavioral Research. Several of the signers indicated that they did not fully agree with the resolution, but saw it as a good vehicle to encourage public discussion.

  19. A positive feedback-based gene circuit to increase the production of a membrane protein

    Directory of Open Access Journals (Sweden)

    Gennis Robert B

    2010-05-01

    Full Text Available Abstract Background Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult to produce in large quantities for the purpose of crystallographic or biochemical analyses. Results In this paper, we demonstrate that synthetic gene circuits designed specifically to overexpress certain genes can be applied to manipulate the expression kinetics of a model membrane protein, cytochrome bd quinol oxidase in E. coli, resulting in increased expression rates. The synthetic circuit involved is an engineered, autoinducer-independent variant of the lux operon activator LuxR from V. fischeri in an autoregulatory, positive feedback configuration. Conclusions Our proof-of-concept experiments indicate a statistically significant increase in the rate of production of the bd oxidase membrane protein. Synthetic gene networks provide a feasible solution for the problem of membrane protein production.

  20. Manipulation of quantum evolution

    Science.gov (United States)

    Cabera, David Jose Fernandez; Mielnik, Bogdan

    1994-01-01

    The free evolution of a non-relativistic charged particle is manipulated using time-dependent magnetic fields. It is shown that the application of a programmed sequence of magnetic pulses can invert the free evolution process, forcing an arbitrary wave packet to 'go back in time' to recover its past shape. The possibility of more general operations upon the Schrodinger wave packet is discussed.

  1. Microradiographic microsphere manipulator

    Science.gov (United States)

    Singleton, R.M.

    A method and apparatus is disclosed 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 relative to and parallel to the other to roll the microspheres through any desired angle to allow different views of the microspheres.

  2. 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.

  3. Optimization of conditions for gene delivery system based on PEI

    Directory of Open Access Journals (Sweden)

    Roya Cheraghi

    2017-01-01

    Full Text Available Objective(s: PEI based nanoparticle (NP due to dual capabilities of proton sponge and DNA binding is known as powerful tool for nucleic acid delivery to cells. However, serious cytotoxicity and complicated conditions, which govern NPs properties and its interactions with cells practically, hindered achievement to high transfection efficiency. Here, we have tried to optimize the properties of PEI/ firefly luciferase plasmid complexes and cellular condition to improve transfection efficiency. Materials and Methods: For this purpose, firefly luciferase, as a robust gene reporter, was complexed with PEI to prepare NPs with different size and charge. The physicochemical properties of nanoparticles were evaluated using agarose gel retardation and dynamic light scattering.  MCF7 and BT474 cells at different confluency were also transfected with prepared nanoparticles at various concentrations for short and long times. Results: The branched PEI can instantaneously bind to DNA and form cationic NPs. The results demonstrated the production of nanoparticles with size about 100-500 nm dependent on N/P ratio. Moreover, increase of nanoparticles concentration on the cell surface drastically improved the transfection rate, so at a concentration of 30 ng/ìl, the highest transfection efficiency was achieved. On the other side, at confluency between 40-60%, the maximum efficiency was obtained. The result demonstrated that N/P ratio of 12 could establish an optimized ratio between transfection efficiency and cytotoxicity of PEI/plasmid nanoparticles. The increase of NPs N/P ratio led to significant cytotoxicity. Conclusion: Obtained results verified the optimum conditions for PEI based gene delivery in different cell lines.

  4. Manipulator type book

    International Nuclear Information System (INIS)

    Koehler, G.W.

    1981-01-01

    Manipulators and similar equipment operated by personnel constitute one of the two major branches of handling technology besides program controlled units (industrial robots and feeding machines). Despite the widespread use of remote handling equipment in nuclear engineering, its growing importance and increasing application also in other areas, a comprehensive treatment of the field has so far been missing. This gap is now filled with the manipulator type book. The bulk of the volume is reserved to remote handling equipment for nuclear purposes available in the international market. However, the survey would be incomplete, also for potential interactions, without manipulators now used also for purposes other than nuclear technology, and without a reference to experimental units and developments which may be assumed to reach practical application one day. This book has been written to help all those who are involved in remote handling technology in one way or the other - plant designers, public authorities and users of such equipment. The text is printed both in German and English for the benefit of foreign readers. A standardized language is proposed to improve communication. (orig./HP) [de

  5. Prediction of autism susceptibility genes based on association rules.

    Science.gov (United States)

    Gong, Lejun; Yan, Yunyang; Xie, Jianming; Liu, Hongde; Sun, Xiao

    2012-06-01

    Autism is a complex neuropsychiatric disorder with high heritability and an unclear etiology. The identification of key genes related to autism may elucidate its etiology. The current study provides an approach to predicting autism susceptibility genes. Genes are first extracted from the biomedical literature, and some autism susceptibility genes are then recognized as seeds by the prior knowledge. As candidates, the remaining genes are predicted by creating association rules between the seeds and candidates. In an evaluated data set, 27 autism susceptibility genes (type "Y") are extracted and 43 possible autism susceptibility genes (type "P") are predicted. The sum of "Y" and "P" genes accounts for 93.3% of the data set that are not contained in the typical database of autism susceptibility genes. Our approach can effectively extract and predict autism susceptibility genes from the biomedical literature. These predicted results complement the typical database of autism susceptibility genes. The web portal for the predicted results, which is freely available at http://biolab.hyit.edu.cn/ar, can be a valuable resource in studies of diseases related to genes. Copyright © 2012 Wiley Periodicals, Inc.

  6. An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods.

    Science.gov (United States)

    Valentini, Giorgio; Paccanaro, Alberto; Caniza, Horacio; Romero, Alfonso E; Re, Matteo

    2014-06-01

    In the context of "network medicine", gene prioritization methods represent one of the main tools to discover candidate disease genes by exploiting the large amount of data covering different types of functional relationships between genes. Several works proposed to integrate multiple sources of data to improve disease gene prioritization, but to our knowledge no systematic studies focused on the quantitative evaluation of the impact of network integration on gene prioritization. In this paper, we aim at providing an extensive analysis of gene-disease associations not limited to genetic disorders, and a systematic comparison of different network integration methods for gene prioritization. We collected nine different functional networks representing different functional relationships between genes, and we combined them through both unweighted and weighted network integration methods. We then prioritized genes with respect to each of the considered 708 medical subject headings (MeSH) diseases by applying classical guilt-by-association, random walk and random walk with restart algorithms, and the recently proposed kernelized score functions. The results obtained with classical random walk algorithms and the best single network achieved an average area under the curve (AUC) across the 708 MeSH diseases of about 0.82, while kernelized score functions and network integration boosted the average AUC to about 0.89. Weighted integration, by exploiting the different "informativeness" embedded in different functional networks, outperforms unweighted integration at 0.01 significance level, according to the Wilcoxon signed rank sum test. For each MeSH disease we provide the top-ranked unannotated candidate genes, available for further bio-medical investigation. Network integration is necessary to boost the performances of gene prioritization methods. Moreover the methods based on kernelized score functions can further enhance disease gene ranking results, by adopting both

  7. Statistics on gene-based laser speckles with a small number of scatterers: implications for the detection of polymorphism in the Chlamydia trachomatis omp1 gene

    Science.gov (United States)

    Ulyanov, Sergey S.; Ulianova, Onega V.; Zaytsev, Sergey S.; Saltykov, Yury V.; Feodorova, Valentina A.

    2018-04-01

    The transformation mechanism for a nucleotide sequence of the Chlamydia trachomatis gene into a speckle pattern has been considered. The first and second-order statistics of gene-based speckles have been analyzed. It has been demonstrated that gene-based speckles do not obey Gaussian statistics and belong to the class of speckles with a small number of scatterers. It has been shown that gene polymorphism can be easily detected through analysis of the statistical characteristics of gene-based speckles.

  8. Automatic Guidance for Remote Manipulator

    Science.gov (United States)

    Johnston, A. R.

    1986-01-01

    Position sensor and mirror guides manipulator toward object. Grasping becomes automatic when sensor begins to receive signal from reflector on object to be manipulated. Light-emitting diodes on manipulator produce light signals for reflector, which is composite of plane and corner reflectors. Proposed scheme especially useful when manipulator arm tends to flex or when object is moving. Sensor and microprocessor designed to compensate for manipulatorarm oscillation.

  9. On-demand Droplet Manipulation via Triboelectrification

    Science.gov (United States)

    Wang, Wei; Vahabi, Hamed; Cackovic, Matthew; Jiang, Rui; Kota, Arun

    2017-11-01

    Controlled manipulation of liquid droplets has attracted tremendous interest across different scientific fields over the past two decades. To date, a variety of external stimuli-mediated methods such as magnetic field, electric field, and light have been developed for manipulating droplets on surfaces. However, these methods usually have drawbacks such as complex fabrication of manipulation platform, low droplet motility, expensive actuation system and lack of precise control. In this work, we demonstrate the controlled manipulation of liquid droplet with both high (e.g., water) and low (e.g., n-hexadecane) dielectric strengths on a smooth, slippery surface via triboelectric effect. Our highly simple, facile and portable methodology enables on-demand, precise manipulation of droplets using solely the electrostatic attraction or repulsion force, which is exerted on the droplet by a simple charged actuator (e.g., Teflon film). We envision that our triboelectric effect enabled droplet manipulation methodology will open a new avenue for droplet based lab-on-a-chip systems, energy harvesting devices and biomedical applications.

  10. An Exploratory Study of Fifth-Grade Students' Reasoning about the Relationship between Fractions and Decimals When Using Number Line-Based Virtual Manipulatives

    Science.gov (United States)

    Smith, Scott

    2017-01-01

    Understanding the relationship between fractions and decimals is an important step in developing an overall understanding of rational numbers. Research has demonstrated the feasibility of technology in the form of virtual manipulatives for facilitating students' meaningful understanding of rational number concepts. This exploratory dissertation…

  11. Gene Ontology based housekeeping gene selection for RNA-seq normalization.

    Science.gov (United States)

    Chen, Chien-Ming; Lu, Yu-Lun; Sio, Chi-Pong; Wu, Guan-Chung; Tzou, Wen-Shyong; Pai, Tun-Wen

    2014-06-01

    RNA-seq analysis provides a powerful tool for revealing relationships between gene expression level and biological function of proteins. In order to identify differentially expressed genes among various RNA-seq datasets obtained from different experimental designs, an appropriate normalization method for calibrating multiple experimental datasets is the first challenging problem. We propose a novel method to facilitate biologists in selecting a set of suitable housekeeping genes for inter-sample normalization. The approach is achieved by adopting user defined experimentally related keywords, GO annotations, GO term distance matrices, orthologous housekeeping gene candidates, and stability ranking of housekeeping genes. By identifying the most distanced GO terms from query keywords and selecting housekeeping gene candidates with low coefficients of variation among different spatio-temporal datasets, the proposed method can automatically enumerate a set of functionally irrelevant housekeeping genes for pratical normalization. Novel and benchmark testing RNA-seq datasets were applied to demostrate that different selections of housekeeping gene lead to strong impact on differential gene expression analysis, and compared results have shown that our proposed method outperformed other traditional approaches in terms of both sensitivity and specificity. The proposed mechanism of selecting appropriate houskeeping genes for inter-dataset normalization is robust and accurate for differential expression analyses. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Using Manipulatives in Math Instruction.

    Science.gov (United States)

    Marzola, Eileen S.

    1987-01-01

    Guidelines for teachers to better use manipulatives in the teaching of mathematics to learning disabled learners are offered including a rationale for manipulatives, selection crteria, principles underlying productive use of manipulatives, and making the transition from the concrete to the symbolic. Suggested materials and distributors are listed.…

  13. Genetic manipulation system in propionibacteria.

    Science.gov (United States)

    Kiatpapan, Pornpimon; Murooka, Yoshikatsu

    2002-01-01

    Members of the genus Propionibacterium are widely used in the production of vitamin B12, tetrapyrrole compounds, and propionic acid as well as in probiotic and cheese industries. Shuttle vectors were developed in propionibacteria using replicons from endogenous plasmids in Propionibacterium and Escherichia coli and an appropriate selection marker. The efficient transformation was achieved using the shuttle vector prepared from Propionibacterium freudenreichii to overcome the high restriction modification system in propionibacteria. Expression vectors with native promoters for use in propionibacteria were also developed. Using this system, cholesterol oxidase, which is used as a diagnostic enzyme, was produced in P. freudenreichii. Genes involved in 5-aminolevulinic acid (ALA) and vitamin B12 biosynthesis in propionibacteria were isolated. ALA in propionibacteria could be synthesized via both the C4 pathway (condensation of glycine and succinyl CoA) and the C5 pathway (from glutamate). The hemA gene encoding ALA synthase from Rhodobacter spheroides, was overexpressed and ALA accumulated in P. freudenreichii. Thus, the genetic manipulation systems in propionibacteria will facilitate genetic studies of probiotics and the vitamin B12 biosynthetic pathway.

  14. 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

  15. A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions.

    Science.gov (United States)

    Yu, Wenbao; Lee, Seungyeoun; Park, Taesung

    2016-09-01

    Gene-gene interaction (GGI) is one of the most popular approaches for finding and explaining the missing heritability of common complex traits in genome-wide association studies. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGI effects. However, there are several disadvantages of the existing MDR-based approaches, such as the lack of an efficient way of evaluating the significance of multi-locus models and the high computational burden due to intensive permutation. Furthermore, the MDR method does not distinguish marginal effects from pure interaction effects. We propose a two-step unified model based MDR approach (UM-MDR), in which, the significance of a multi-locus model, even a high-order model, can be easily obtained through a regression framework with a semi-parametric correction procedure for controlling Type I error rates. In comparison to the conventional permutation approach, the proposed semi-parametric correction procedure avoids heavy computation in order to achieve the significance of a multi-locus model. The proposed UM-MDR approach is flexible in the sense that it is able to incorporate different types of traits and evaluate significances of the existing MDR extensions. The simulation studies and the analysis of a real example are provided to demonstrate the utility of the proposed method. UM-MDR can achieve at least the same power as MDR for most scenarios, and it outperforms MDR especially when there are some single nucleotide polymorphisms that only have marginal effects, which masks the detection of causal epistasis for the existing MDR approaches. UM-MDR provides a very good supplement of existing MDR method due to its efficiency in achieving significance for every multi-locus model, its power and its flexibility of handling different types of traits. A R package "umMDR" and other source codes are freely available at http://statgen.snu.ac.kr/software/umMDR/ CONTACT: tspark

  16. Virus manipulation of cell cycle.

    Science.gov (United States)

    Nascimento, R; Costa, H; Parkhouse, R M E

    2012-07-01

    Viruses depend on host cell resources for replication and access to those resources may be limited to a particular phase of the cell cycle. Thus manipulation of cell cycle is a commonly employed strategy of viruses for achieving a favorable cellular environment. For example, viruses capable of infecting nondividing cells induce S phase in order to activate the host DNA replication machinery and provide the nucleotide triphosphates necessary for viral DNA replication (Flemington in J Virol 75:4475-4481, 2001; Sullivan and Pipas in Microbiol Mol Biol Rev 66:179-202, 2002). Viruses have developed several strategies to subvert the cell cycle by association with cyclin and cyclin-dependent kinase complexes and molecules that regulate their activity. Viruses tend to act on cellular proteins involved in a network of interactions in a way that minimal protein-protein interactions lead to a major effect. The complex and interactive nature of intracellular signaling pathways controlling cell division affords many opportunities for virus manipulation strategies. Taking the maxim "Set a thief to catch a thief" as a counter strategy, however, provides us with the very same virus evasion strategies as "ready-made tools" for the development of novel antivirus therapeutics. The most obvious are attenuated virus vaccines with critical evasion genes deleted. Similarly, vaccines against viruses causing cancer are now being successfully developed. Finally, as viruses have been playing chess with our cell biology and immune responses for millions of years, the study of their evasion strategies will also undoubtedly reveal new control mechanisms and their corresponding cellular intracellular signaling pathways.

  17. 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.

  18. Using Virtual Manipulatives with and without Symbolic Representation to Teach First Grade Multi-Digit Addition

    Science.gov (United States)

    Haistings, Jeanine L.

    2009-01-01

    Technology and mathematics. manipulatives have been brought together in a new format. This joining has resulted in virtual manipulatives that are available on the Internet for students. Virtual manipulatives have been defined as computer based renditions of common mathematics manipulatives and tools. Just as a physical object can be flipped,…

  19. Gene-based segregation method for identifying rare variants in family-based sequencing studies.

    Science.gov (United States)

    Qiao, Dandi; Lange, Christoph; Laird, Nan M; Won, Sungho; Hersh, Craig P; Morrow, Jarrett; Hobbs, Brian D; Lutz, Sharon M; Ruczinski, Ingo; Beaty, Terri H; Silverman, Edwin K; Cho, Michael H

    2017-05-01

    Whole-exome sequencing using family data has identified rare coding variants in Mendelian diseases or complex diseases with Mendelian subtypes, using filters based on variant novelty, functionality, and segregation with the phenotype within families. However, formal statistical approaches are limited. We propose a gene-based segregation test (GESE) that quantifies the uncertainty of the filtering approach. It is constructed using the probability of segregation events under the null hypothesis of Mendelian transmission. This test takes into account different degrees of relatedness in families, the number of functional rare variants in the gene, and their minor allele frequencies in the corresponding population. In addition, a weighted version of this test allows incorporating additional subject phenotypes to improve statistical power. We show via simulations that the GESE and weighted GESE tests maintain appropriate type I error rate, and have greater power than several commonly used region-based methods. We apply our method to whole-exome sequencing data from 49 extended pedigrees with severe, early-onset chronic obstructive pulmonary disease (COPD) in the Boston Early-Onset COPD study (BEOCOPD) and identify several promising candidate genes. Our proposed methods show great potential for identifying rare coding variants of large effect and high penetrance for family-based sequencing data. The proposed tests are implemented in an R package that is available on CRAN (https://cran.r-project.org/web/packages/GESE/). © 2017 WILEY PERIODICALS, INC.

  20. Master/slave manipulators

    International Nuclear Information System (INIS)

    Luxmoore, R.J.

    1987-01-01

    For detecting a fault in a flexible gaiter enclosing the slave arm of a master/slave manipulator used in the nuclear industry, valve means comprising oppositely acting non-return valves are arranged in the wall of the gaiter. On extension and retraction of the slave arm the valves operate to equalise pressure differences at opposite sides of the gaiter. Failure of the valves to function during extension and retraction of the slave arm can indicate a fault, such as a tear, in the gaiter. (author)

  1. 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.

  2. Manipulating structured light

    CSIR Research Space (South Africa)

    Dudley, Angela

    2016-07-01

    Full Text Available stream_source_info Dudley_2016a.pdf.txt stream_content_type text/plain stream_size 4579 Content-Encoding UTF-8 stream_name Dudley_2016a.pdf.txt Content-Type text/plain; charset=UTF-8 10/10/2016 1 Manipulating Structured... The City College of New York, New York, USA 5 July 2016 We are tied together by Structured Light Classical Quantum Resonators TweezingFibres Structured Light 10/10/2016 2 Bright Dark Reference beam Hologram Object Light reflected from object Conventional...

  3. 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.

  4. An analysis of interpersonal manipulation.

    Science.gov (United States)

    Kligman, M; Culver, C M

    1992-04-01

    The term 'manipulation' is frequently employed but rarely discussed or defined in psychiatric circles. This paper reviews previous conceptual analyses of the term by philosophers and psychiatrists, and examines its use in ordinary discourse. A series of characteristics which comprise the conceptual core of the term when it is unambiguously applied in interpersonal settings are proposed. Manipulation is contrasted with other behavior control methods such as rational persuasion and coercion, with emphasis on the role played by deception and the communicative context in which the manipulative transaction occurs. It is argued that manipulative behavior is fundamentally intentional, and the usefulness of the concept of 'unconscious manipulation' is questioned. Though the proposal that Manipulative Personality Disorder be formally recognized as a new diagnostic category is rejected, it is urged that the concept of manipulation receive wider attention and discussion within the mental health community.

  5. Gene-based interaction analysis shows GABAergic genes interacting with parenting in adolescent depressive symptoms

    NARCIS (Netherlands)

    Van Assche, Evelien; Moons, Tim; Cinar, Ozan; Viechtbauer, Wolfgang; Oldehinkel, Albertine J.; Van Leeuwen, Karla; Verschueren, Karine; Colpin, Hilde; Lambrechts, Diether; Van den Noortgate, Wim; Goossens, Luc; Claes, Stephan; van Winkel, Ruud

    2017-01-01

    BACKGROUND: Most gene-environment interaction studies (G × E) have focused on single candidate genes. This approach is criticized for its expectations of large effect sizes and occurrence of spurious results. We describe an approach that accounts for the polygenic nature of most psychiatric

  6. Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions.

    Science.gov (United States)

    Chung, Yujin; Lee, Seung Yeoun; Elston, Robert C; Park, Taesung

    2007-01-01

    The identification and characterization of genes that increase the susceptibility to common complex multifactorial diseases is a challenging task in genetic association studies. The multifactor dimensionality reduction (MDR) method has been proposed and implemented by Ritchie et al. (2001) to identify the combinations of multilocus genotypes and discrete environmental factors that are associated with a particular disease. However, the original MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups in an ad hoc manner based on a simple comparison of the ratios of the number of cases and controls. Hence, the MDR approach is prone to false positive and negative errors when the ratio of the number of cases and controls in a combination of genotypes is similar to that in the entire data, or when both the number of cases and controls is small. Hence, we propose the odds ratio based multifactor dimensionality reduction (OR MDR) method that uses the odds ratio as a new quantitative measure of disease risk. While the original MDR method provides a simple binary measure of risk, the OR MDR method provides not only the odds ratio as a quantitative measure of risk but also the ordering of the multilocus combinations from the highest risk to lowest risk groups. Furthermore, the OR MDR method provides a confidence interval for the odds ratio for each multilocus combination, which is extremely informative in judging its importance as a risk factor. The proposed OR MDR method is illustrated using the dataset obtained from the CDC Chronic Fatigue Syndrome Research Group. The program written in R is available.

  7. Screening key genes for abdominal aortic aneurysm based on gene expression omnibus dataset.

    Science.gov (United States)

    Wan, Li; Huang, Jingyong; Ni, Haizhen; Yu, Guanfeng

    2018-02-13

    Abdominal aortic aneurysm (AAA) is a common cardiovascular system disease with high mortality. The aim of this study was to identify potential genes for diagnosis and therapy in AAA. We searched and downloaded mRNA expression data from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) from AAA and normal individuals. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, transcriptional factors (TFs) network and protein-protein interaction (PPI) network were used to explore the function of genes. Additionally, immunohistochemical (IHC) staining was used to validate the expression of identified genes. Finally, the diagnostic value of identified genes was accessed by receiver operating characteristic (ROC) analysis in GEO database. A total of 1199 DEGs (188 up-regulated and 1011 down-regulated) were identified between AAA and normal individual. KEGG pathway analysis displayed that vascular smooth muscle contraction and pathways in cancer were significantly enriched signal pathway. The top 10 up-regulated and top 10 down-regulated DEGs were used to construct TFs and PPI networks. Some genes with high degrees such as NELL2, CCR7, MGAM, HBB, CSNK2A2, ZBTB16 and FOXO1 were identified to be related to AAA. The consequences of IHC staining showed that CCR7 and PDGFA were up-regulated in tissue samples of AAA. ROC analysis showed that NELL2, CCR7, MGAM, HBB, CSNK2A2, ZBTB16, FOXO1 and PDGFA had the potential diagnostic value for AAA. The identified genes including NELL2, CCR7, MGAM, HBB, CSNK2A2, ZBTB16, FOXO1 and PDGFA might be involved in the pathology of AAA.

  8. AFM-based nanolithography : manipulating poly(dimethylsiloxane) : loading force, scan speed and image resolution dependence on stick-slip outcomes in the slow and fast scan directions

    International Nuclear Information System (INIS)

    Watson, J.A.; Brown, C.L.; Myhra, S.; Watson, G.S.

    2005-01-01

    The various properties of a polymer will affect its functionality in a wide range of applications including biosensors, tissue engineering and biomaterials technology. Some of those require precise manipulation of laterally differentiated regions, currently taking place on the μm-scale. It is now apparent that this need must now be driven into the nm-regime. Using the AFM, the principal objective is to explore and investigate lithographic outcomes during tip-induced manipulation with the aid of work on poly(dimethylsiloxane), (PDMS). The frictional effects (including any in-plane relaxation), and their dependence on the loading force, scan speed and image resolution are examined. (author). 3 refs., 5 figs

  9. The Integrative Method Based on the Module-Network for Identifying Driver Genes in Cancer Subtypes

    Directory of Open Access Journals (Sweden)

    Xinguo Lu

    2018-01-01

    Full Text Available With advances in next-generation sequencing(NGS technologies, a large number of multiple types of high-throughput genomics data are available. A great challenge in exploring cancer progression is to identify the driver genes from the variant genes by analyzing and integrating multi-types genomics data. Breast cancer is known as a heterogeneous disease. The identification of subtype-specific driver genes is critical to guide the diagnosis, assessment of prognosis and treatment of breast cancer. We developed an integrated frame based on gene expression profiles and copy number variation (CNV data to identify breast cancer subtype-specific driver genes. In this frame, we employed statistical machine-learning method to select gene subsets and utilized an module-network analysis method to identify potential candidate driver genes. The final subtype-specific driver genes were acquired by paired-wise comparison in subtypes. To validate specificity of the driver genes, the gene expression data of these genes were applied to classify the patient samples with 10-fold cross validation and the enrichment analysis were also conducted on the identified driver genes. The experimental results show that the proposed integrative method can identify the potential driver genes and the classifier with these genes acquired better performance than with genes identified by other methods.

  10. NDRC: A Disease-Causing Genes Prioritized Method Based on Network Diffusion and Rank Concordance.

    Science.gov (United States)

    Fang, Minghong; Hu, Xiaohua; Wang, Yan; Zhao, Junmin; Shen, Xianjun; He, Tingting

    2015-07-01

    Disease-causing genes prioritization is very important to understand disease mechanisms and biomedical applications, such as design of drugs. Previous studies have shown that promising candidate genes are mostly ranked according to their relatedness to known disease genes or closely related disease genes. Therefore, a dangling gene (isolated gene) with no edges in the network can not be effectively prioritized. These approaches tend to prioritize those genes that are highly connected in the PPI network while perform poorly when they are applied to loosely connected disease genes. To address these problems, we propose a new disease-causing genes prioritization method that based on network diffusion and rank concordance (NDRC). The method is evaluated by leave-one-out cross validation on 1931 diseases in which at least one gene is known to be involved, and it is able to rank the true causal gene first in 849 of all 2542 cases. The experimental results suggest that NDRC significantly outperforms other existing methods such as RWR, VAVIEN, DADA and PRINCE on identifying loosely connected disease genes and successfully put dangling genes as potential candidate disease genes. Furthermore, we apply NDRC method to study three representative diseases, Meckel syndrome 1, Protein C deficiency and Peroxisome biogenesis disorder 1A (Zellweger). Our study has also found that certain complex disease-causing genes can be divided into several modules that are closely associated with different disease phenotype.

  11. Model tracking controller design of robot manipulator system with disturbances

    Directory of Open Access Journals (Sweden)

    Dazhong Wang

    2015-06-01

    Full Text Available In the model tracking control of robot manipulator system, the treatment of nonlinear uncertainty in the system has always been an active research field. This article establishes a kinetic equation for robot manipulator system based on Lagrange equation and proposes a model tracking control system based on differential divisor. On this basis, this article proposes a model tracking control scheme for robot manipulator systems with disturbances. The proposed scheme is robust stable under the external disturbances. At last, the system simulation approach is employed to verify the effectiveness of this scheme on robot manipulator control.

  12. A hybrid network-based method for the detection of disease-related genes

    Science.gov (United States)

    Cui, Ying; Cai, Meng; Dai, Yang; Stanley, H. Eugene

    2018-02-01

    Detecting disease-related genes is crucial in disease diagnosis and drug design. The accepted view is that neighbors of a disease-causing gene in a molecular network tend to cause the same or similar diseases, and network-based methods have been recently developed to identify novel hereditary disease-genes in available biomedical networks. Despite the steady increase in the discovery of disease-associated genes, there is still a large fraction of disease genes that remains under the tip of the iceberg. In this paper we exploit the topological properties of the protein-protein interaction (PPI) network to detect disease-related genes. We compute, analyze, and compare the topological properties of disease genes with non-disease genes in PPI networks. We also design an improved random forest classifier based on these network topological features, and a cross-validation test confirms that our method performs better than previous similar studies.

  13. Dual-MWCNT Probe Thermal Sensor Assembly and Evaluation Based on Nanorobotic Manipulation inside a Field-Emission-Scanning Electron Microscope

    Directory of Open Access Journals (Sweden)

    Zhan Yang

    2015-03-01

    Full Text Available We report a thermal sensor composed of two multiwalled carbon nano-tubes (MWCNTs inside a field-emission-scanning electron microscope. The sensor was assembled using a nanorobotic manipulation system, which was used to construct a probe tip in order to detect the local environment of a single cell. An atomic force microscopy (AFM cantilever was used as a substrate; the cantilever was composed of Si3N4 and both sides were covered with a gold layer. MWCNTs were individually assembled on both sides of the AFM cantilever by employing nanorobotic manipulation. Another AFM cantilever was subsequently used as an end effector to manipulate the MWCNTs to touch each other. Electron-beam-induced deposition (EBID was then used to bond the two MWCNTs. The MWCNT probe thermal sensor was evaluated inside a thermostated container in the temperature range from 25°C to 60°C. The experimental results show the positive characteristics of the temperature coefficient of resistance (TCR.

  14. Analysis of regulatory networks constructed based on gene ...

    Indian Academy of Sciences (India)

    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 ...

  15. Ecdysone Receptor-Based Gene Switches for Applications in Plants

    Science.gov (United States)

    There are a number of circumstances in which it is advantageous to use an inducible gene regulation system, the most obvious being when introducing transgenes whose constitutive expression is detrimental or even lethal to the host plants. The selective induction of gene expression is typically accom...

  16. Microarray-based Detection of Antibiotic Resisteance Genes in Salmonella

    NARCIS (Netherlands)

    Hoek, van A.H.A.M.; Aarts, H.J.M.

    2008-01-01

    In the presented study, 143 Salmonella isolates belonging to 26 different serovars were screened for the presence of antibiotic resistance genes by microarray analysis. The microarray contained a total of 223 oligonucleotides representing genes encoding for resistance to the following antibiotic

  17. DNA-energetics-based analyses suggest additional genes in ...

    Indian Academy of Sciences (India)

    Permanent link: http://www.ias.ac.in/article/fulltext/jbsc/037/03/0433-0444 ... We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of ... Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the ...

  18. 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...

  19. 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...

  20. 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

  1. RNAi-Based Identification of Gene-Specific Nuclear Cofactor Networks Regulating Interleukin-1 Target Genes

    Directory of Open Access Journals (Sweden)

    Johanna Meier-Soelch

    2018-04-01

    Full Text Available The potent proinflammatory cytokine interleukin (IL-1 triggers gene expression through the NF-κB signaling pathway. Here, we investigated the cofactor requirements of strongly regulated IL-1 target genes whose expression is impaired in p65 NF-κB-deficient murine embryonic fibroblasts. By two independent small-hairpin (shRNA screens, we examined 170 genes annotated to encode nuclear cofactors for their role in Cxcl2 mRNA expression and identified 22 factors that modulated basal or IL-1-inducible Cxcl2 levels. The functions of 16 of these factors were validated for Cxcl2 and further analyzed for their role in regulation of 10 additional IL-1 target genes by RT-qPCR. These data reveal that each inducible gene has its own (quantitative requirement of cofactors to maintain basal levels and to respond to IL-1. Twelve factors (Epc1, H2afz, Kdm2b, Kdm6a, Mbd3, Mta2, Phf21a, Ruvbl1, Sin3b, Suv420h1, Taf1, and Ube3a have not been previously implicated in inflammatory cytokine functions. Bioinformatics analysis indicates that they are components of complex nuclear protein networks that regulate chromatin functions and gene transcription. Collectively, these data suggest that downstream from the essential NF-κB signal each cytokine-inducible target gene has further subtle requirements for individual sets of nuclear cofactors that shape its transcriptional activation profile.

  2. A new measure for functional similarity of gene products based on Gene Ontology

    Directory of Open Access Journals (Sweden)

    Lengauer Thomas

    2006-06-01

    Full Text Available Abstract Background Gene Ontology (GO is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. Results We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; simRel and funSim. One measure (simRel is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. Conclusion The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

  3. Gene-based SNP discovery and genetic mapping in pea.

    Science.gov (United States)

    Sindhu, Anoop; Ramsay, Larissa; Sanderson, Lacey-Anne; Stonehouse, Robert; Li, Rong; Condie, Janet; Shunmugam, Arun S K; Liu, Yong; Jha, Ambuj B; Diapari, Marwan; Burstin, Judith; Aubert, Gregoire; Tar'an, Bunyamin; Bett, Kirstin E; Warkentin, Thomas D; Sharpe, Andrew G

    2014-10-01

    Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world's oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.

  4. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

    Science.gov (United States)

    Liu, Fang; Jenssen, Tor-Kristian; Trimarchi, Jeff; Punzo, Claudio; Cepko, Connie L; Ohno-Machado, Lucila; Hovig, Eivind; Kuo, Winston Patrick

    2007-06-07

    High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies. As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing). The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery. Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive alternatives for measuring gene expression, and currently, both are important tools for transcriptome profiling.

  5. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates

    Directory of Open Access Journals (Sweden)

    Cepko Connie L

    2007-06-01

    Full Text Available Abstract Background High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies. As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing. Results The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery. Conclusion Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive alternatives for measuring gene expression, and currently, both are important tools for transcriptome profiling.

  6. Targeted delivery of genes to endothelial cells and cell- and gene-based therapy in pulmonary vascular diseases.

    Science.gov (United States)

    Suen, Colin M; Mei, Shirley H J; Kugathasan, Lakshmi; Stewart, Duncan J

    2013-10-01

    Pulmonary arterial hypertension (PAH) is a devastating disease that, despite significant advances in medical therapies over the last several decades, continues to have an extremely poor prognosis. Gene therapy is a method to deliver therapeutic genes to replace defective or mutant genes or supplement existing cellular processes to modify disease. Over the last few decades, several viral and nonviral methods of gene therapy have been developed for preclinical PAH studies with varying degrees of efficacy. However, these gene delivery methods face challenges of immunogenicity, low transduction rates, and nonspecific targeting which have limited their translation to clinical studies. More recently, the emergence of regenerative approaches using stem and progenitor cells such as endothelial progenitor cells (EPCs) and mesenchymal stem cells (MSCs) have offered a new approach to gene therapy. Cell-based gene therapy is an approach that augments the therapeutic potential of EPCs and MSCs and may deliver on the promise of reversal of established PAH. These new regenerative approaches have shown tremendous potential in preclinical studies; however, large, rigorously designed clinical studies will be necessary to evaluate clinical efficacy and safety. © 2013 American Physiological Society. Compr Physiol 3:1749-1779, 2013.

  7. Hydraulic manipulator research at ORNL

    International Nuclear Information System (INIS)

    Kress, R.L.; Jansen, J.F.; Love, L.J.

    1997-01-01

    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

  8. 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.

  9. Media and manipulation

    Directory of Open Access Journals (Sweden)

    Kovačević Braco

    2013-01-01

    Full Text Available The role and importance of the media are huge, both in everyday life and in cultural, spiritual and political life of modern man. Their power in the sense of political shaping of people and shaping of public opinion is very distinctive. In the process of propaganda to influence public opinion, they use various manipulative procedures in order to accomplish certain interests and objectives. Through the media, politics realizes its economic, ideological, political and even military activities. The war in the former Yugoslavia and former Bosnia and Herzegovina was also waged through the media. This media war still is spreading the hate speech, thus still causing conflicts and disintegration processes in the Balkans.

  10. Manipulation et information fictionnelle

    OpenAIRE

    Dufiet, Jean-Paul

    2012-01-01

    Le 13 décembre 2006, la Radio Télévision Belge Francophone (RTBF) annonçait, dans un vrai journal télévisé spécial, la fausse nouvelle que la Flandre venait de déclarer son indépendance. Par l’analyse des caractéristiques du journal télévisé, l’auteur décrypte le rapport entre mise en scène linguistique et sémiotique d’une part, et manipulation médiatique d’autre part. On December 13, 2006, Radio Télévision Belge Francophone (RTBF) interrupted its regular programming with a special bulleti...

  11. Reconfigurable metamaterials for terahertz wave manipulation

    Science.gov (United States)

    Hashemi, Mohammed R.; Cakmakyapan, Semih; Jarrahi, Mona

    2017-09-01

    Reconfigurable metamaterials have emerged as promising platforms for manipulating the spectral and spatial properties of terahertz waves without being limited by the characteristics of naturally existing materials. Here, we present a comprehensive overview of various types of reconfigurable metamaterials that are utilized to manipulate the intensity, phase, polarization, and propagation direction of terahertz waves. We discuss various reconfiguration mechanisms based on optical, electrical, thermal, and mechanical stimuli while using semiconductors, superconductors, phase-change materials, graphene, and electromechanical structures. The advantages and disadvantages of different reconfigurable metamaterial designs in terms of modulation efficiency, modulation bandwidth, modulation speed, and system complexity are discussed in detail.

  12. Gene therapy prospects--intranasal delivery of therapeutic genes.

    Science.gov (United States)

    Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

    2012-01-01

    Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

  13. Embryo quality predictive models based on cumulus cells gene expression

    Directory of Open Access Journals (Sweden)

    Devjak R

    2016-06-01

    Full Text Available Since the introduction of in vitro fertilization (IVF in clinical practice of infertility treatment, the indicators for high quality embryos were investigated. Cumulus cells (CC have a specific gene expression profile according to the developmental potential of the oocyte they are surrounding, and therefore, specific gene expression could be used as a biomarker. The aim of our study was to combine more than one biomarker to observe improvement in prediction value of embryo development. In this study, 58 CC samples from 17 IVF patients were analyzed. This study was approved by the Republic of Slovenia National Medical Ethics Committee. Gene expression analysis [quantitative real time polymerase chain reaction (qPCR] for five genes, analyzed according to embryo quality level, was performed. Two prediction models were tested for embryo quality prediction: a binary logistic and a decision tree model. As the main outcome, gene expression levels for five genes were taken and the area under the curve (AUC for two prediction models were calculated. Among tested genes, AMHR2 and LIF showed significant expression difference between high quality and low quality embryos. These two genes were used for the construction of two prediction models: the binary logistic model yielded an AUC of 0.72 ± 0.08 and the decision tree model yielded an AUC of 0.73 ± 0.03. Two different prediction models yielded similar predictive power to differentiate high and low quality embryos. In terms of eventual clinical decision making, the decision tree model resulted in easy-to-interpret rules that are highly applicable in clinical practice.

  14. 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 textu...... fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database. Subclustering and links to external resources allow for in-depth analysis of the resulting term profiles....

  15. 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.

  16. New Approaches to Manipulation of Microbiological Objects

    Science.gov (United States)

    Kamantsev, Alexander; Mashirov, Alexey; Dilmieva, Elvina; Zakharov, Dmitry; Zhikharev, Alexey; Koledov, Victor; Shavrov, Vladimir; Irzhak, Artemy; Shelyakov, Alexander; Albertiti, Franca

    The new concept of nanotweezers based on bimetallic composite Ti50Ni25Cu25/Pt with shape memory effect have recently demonstrated the ability to manipulate real nanoobjects, such as CNTs, graphene layers, etc., when heated to 40-60 °C by laser radiation. We demonstrate possibility of manipulation of microbiological objects - fibers from the body of Culex pipiens in vacuum chamber of FIB device. Composite microactuator controlled by magnetic field at constant temperature was produced using rapidly quenched ferromagnetic shape memory Heusler alloy Ni53Mn24Ga23. The experiments on control of this microactuator by applying magnetic field of 8 T prove the possibility of manipulation of living objects.

  17. Coordinated Control Of Mobile Robotic Manipulators

    Science.gov (United States)

    Seraji, Homayoun

    1995-01-01

    Computationally efficient scheme developed for on-line coordinated control of both manipulation and mobility of robots that include manipulator arms mounted on mobile bases. Applicable to variety of mobile robotic manipulators, including robots that move along tracks (typically, painting and welding robots), robots mounted on gantries and capable of moving in all three dimensions, wheeled robots, and compound robots (consisting of robots mounted on other robots). Theoretical basis discussed in several prior articles in NASA Tech Briefs, including "Increasing the Dexterity of Redundant Robots" (NPO-17801), "Redundant Robot Can Avoid Obstacles" (NPO-17852), "Configuration-Control Scheme Copes With Singularities" (NPO-18556), "More Uses for Configuration Control of Robots" (NPO-18607/NPO-18608).

  18. 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.

  19. Spin tunneling and manipulation in nanostructures.

    Science.gov (United States)

    Sherman, E Ya; Ban, Yue; Gulyaev, L V; Khomitsky, D V

    2012-09-01

    The results for joint effects of tunneling and spin-orbit coupling on spin dynamics in nanostructures are presented for systems with discrete and continuous spectra. We demonstrate that tunneling plays the crucial role in the spin dynamics and the abilities of spin manipulation by external electric field. This result can be important for design of nanostructures-based spintronics devices.

  20. Motion planning for gantry mounted manipulators

    DEFF Research Database (Denmark)

    Olsen, Anders Lau; Petersen, Henrik Gordon

    2007-01-01

    We present a roadmap based planner for finding robot motions for gantry mounted manipulators for a line welding application at Odense Steel Shipyard (OSS). The robot motions are planned subject to constraints on when the gantry may be moved. We show that random sampling of gantry configurations...

  1. Impedance Control of a Redundant Parallel Manipulator

    DEFF Research Database (Denmark)

    Méndez, Juan de Dios Flores; Schiøler, Henrik; Madsen, Ole

    2017-01-01

    This paper presents the design of Impedance Control to a redundantly actuated Parallel Kinematic Manipulator. The proposed control is based on treating each limb as a single system and their connection through the internal interaction forces. The controller introduces a stiffness and damping...

  2. Motorized manipulator for positioning a TEM specimen

    Science.gov (United States)

    Schmid, Andreas Karl; Andresen, Nord

    2010-12-14

    The invention relates to a motorized manipulator for positioning a TEM specimen holder with sub-micron resolution parallel to a y-z plane and rotating the specimen holder in the y-z plane, the manipulator comprising a base (2), and attachment means (30) for attaching the specimen holder to the manipulator, characterized in that the manipulator further comprises at least three nano-actuators (3.sup.a, 3.sup.b, 3.sup.c) mounted on the base, each nano-actuator showing a tip (4.sup.a, 4.sup.b, 4.sup.c), the at least three tips defining the y-z plane, each tip capable of moving with respect to the base in the y-z plane; a platform (5) in contact with the tips of the nano-actuators; and clamping means (6) for pressing the platform against the tips of the nano-actuators; as a result of which the nano-actuators can rotate the platform with respect to the base in the y-z plane and translate the platform parallel to the y-z plane.

  3. 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.

  4. Prioritizing Genes Related to Nicotine Addiction Via a Multi-source-Based Approach.

    Science.gov (United States)

    Liu, Xinhua; Liu, Meng; Li, Xia; Zhang, Lihua; Fan, Rui; Wang, Ju

    2015-08-01

    Nicotine has a broad impact on both the central and peripheral nervous systems. Over the past decades, an increasing number of genes potentially involved in nicotine addiction have been identified by different technical approaches. However, the molecular mechanisms underlying nicotine addiction remain largely unknown. Under such situation, prioritizing the candidate genes for further investigation is becoming increasingly important. In this study, we presented a multi-source-based gene prioritization approach for nicotine addiction by utilizing the vast amounts of information generated from for nicotine addiction study during the past years. In this approach, we first collected and curated genes from studies in four categories, i.e., genetic association analysis, genetic linkage analysis, high-throughput gene/protein expression analysis, and literature search of single gene/protein-based studies. Based on these resources, the genes were scored and a weight value was determined for each category. Finally, the genes were ranked by their combined scores, and 220 genes were selected as the prioritized nicotine addiction-related genes. Evaluation suggested the prioritized genes were promising targets for further analysis and replication study.

  5. Manipulating stored phonological input during verbal working memory

    Science.gov (United States)

    Cogan, Gregory B.; Iyer, Asha; Melloni, Lucia; Thesen, Thomas; Friedman, Daniel; Doyle, Werner; Devinsky, Orrin; Pesaran, Bijan

    2016-01-01

    Verbal working memory (vWM), involves storing and manipulating information in phonological sensory input. An influential theory of vWM proposes that manipulation is carried out by a central executive while storage is performed by two interacting systems: A phonological input buffer that captures sound-based information and an articulatory rehearsal system that controls speech motor output. Whether, when, and how neural activity in the brain encodes these components remains unknown. Here, we read-out the contents of vWM from neural activity in human subjects as they manipulate stored speech sounds. As predicted, we identify storage systems that contain both phonological sensory and articulatory motor representations. Surprisingly however, we find that manipulation does not involve a single central executive but rather involves two systems with distinct contributions to successful manipulation. We propose, therefore, that multiple subsystems comprise the central executive needed to manipulate stored phonological input for articulatory motor output in vWM. PMID:27941789

  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.

  7. Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

    Science.gov (United States)

    Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

    2017-10-01

    Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

  8. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.

    Science.gov (United States)

    Hur, Junguk; Özgür, Arzucan; He, Yongqun

    2017-03-14

    Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks. In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E. coli vaccines and genes used in the vaccine development. We also normalized E. coli gene names compiled from the annotations of various E. coli strains using a pan-genome-based annotation strategy. The Interaction Network Ontology (INO) includes a hierarchy of various interaction-related keywords useful for literature mining. Using VO, INO, and normalized E. coli gene names, we applied an ontology-based SciMiner literature mining strategy to mine all PubMed abstracts and retrieve E. coli vaccine-associated E. coli gene interactions. Four centrality metrics (i.e., degree, eigenvector, closeness, and betweenness) were calculated for identifying highly ranked genes and interaction types. Using vaccine-related PubMed abstracts, our study identified 11,350 sentences that contain 88 unique INO interactions types and 1,781 unique E. coli genes. Each sentence contained at least one interaction type and two unique E. coli genes. An E. coli gene interaction network of genes and INO interaction types was created. From this big network, a sub-network consisting of 5 E. coli vaccine genes, including carA, carB, fimH, fepA, and vat, and 62 other E. coli genes, and 25 INO interaction types was identified. While many interaction types represent direct interactions between two indicated genes, our study has also shown that many of these retrieved interaction types are indirect in that the two genes participated in the specified interaction process in a required but indirect process. Our centrality analysis of

  9. 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,...

  10. YAGM: a web tool for mining associated genes in yeast based on diverse biological associations.

    Science.gov (United States)

    Wu, Wei-Sheng; Wang, Chung-Ching; Jhou, Meng-Jhun; Wang, Yu-Cheng

    2015-01-01

    Investigating association between genes can be used in understanding the relations of genes in biological processes. STRING and GeneMANIA are two well-known web tools which can provide a list of associated genes of a query gene based on diverse biological associations such as co-expression, co-localization, co-citation and so on. However, the transcriptional regulation association and mutant phenotype association have not been used in these two web tools. Since the comprehensive transcription factor (TF)-gene binding data, TF-gene regulation data and mutant phenotype data are available in yeast, we developed a web tool called YAGM (Yeast Associated Genes Miner) which constructed the transcriptional regulation association, mutant phenotype association and five commonly used biological associations to mine a list of associated genes of a query yeast gene. In YAGM, we collected seven kinds of datasets including TF-gene binding (TFB) data, TF-gene regulation (TFR) data, mutant phenotype (MP) data, functional annotation (FA) data, physical interaction (PI) data, genetic interaction (GI) data, and literature evidence (LE) data. Then by using the hypergeometric test to calculate the association scores of all gene pairs in yeast, we constructed seven biological associations including two transcriptional regulation associations (TFB association and TFR association), MP association, FA association, PI association, GI association, and LE association. Moreover, the expression profile association from SPELL database was also included in YAGM. When using YAGM, users can input a query gene and choose any possible subsets of the eight biological associations, then a list of associated genes of the query gene will be returned based on the chosen biological associations. In this study, we presented the YAGM which provides eight biological associations for mining associated genes of a query gene in yeast. Among the eight biological associations constructed in YAGM, three (TFB

  11. Tree manipulation experiment

    Science.gov (United States)

    Nishina, K.; Takenaka, C.; Ishizuka, S.; Hashimoto, S.; Yagai, Y.

    2012-12-01

    Some forest operations such as thinning and harvesting management could cause changes in N cycling and N2O emission from soils, since thinning and harvesting managements are accompanied with changes in aboveground environments such as an increase of slash falling and solar radiation on the forest floor. However, a considerable uncertainty exists in effects of thinning and harvesting on N2O fluxes regarding changes in belowground environments by cutting trees. To focus on the effect of changes in belowground environments on the N2O emissions from soils, we conducted a tree manipulation experiment in Japanese cedar (Cryptomeria japonica) stand without soil compaction and slash falling near the chambers and measured N2O flux at 50 cm and 150 cm distances from the tree trunk (stump) before and after cutting. We targeted 5 trees for the manipulation and established the measurement chambers to the 4 directions around each targeted tree relative to upper slope (upper, left, right, lower positions). We evaluated the effect of logging on the emission by using hierarchical Bayesian model. HB model can evaluate the variability in observed data and their uncertainties in the estimation with various probability distributions. Moreover, the HB model can easily accommodate the non-linear relationship among the N2O emissions and the environmental factors, and explicitly take non-independent data (nested structure of data) for the estimation into account by using random effects in the model. Our results showed tree cutting stimulated N2O emission from soils, and also that the increase of N2O flux depended on the distance from the trunk (stump): the increase of N2O flux at 50 cm from the trunk (stump) was greater than that of 150 cm from the trunk. The posterior simulation of the HB model indicated that the stimulation of N2O emission by tree cut- ting could reach up to 200 cm in our experimental plot. By tree cutting, the estimated N2O emission at 0-40 cm from the trunk doubled

  12. An Entropy-based gene selection method for cancer classification using microarray data

    Directory of Open Access Journals (Sweden)

    Krishnan Arun

    2005-03-01

    Full Text Available Abstract Background Accurate diagnosis of cancer subtypes remains a challenging problem. Building classifiers based on gene expression data is a promising approach; yet the selection of non-redundant but relevant genes is difficult. The selected gene set should be small enough to allow diagnosis even in regular clinical laboratories and ideally identify genes involved in cancer-specific regulatory pathways. Here an entropy-based method is proposed that selects genes related to the different cancer classes while at the same time reducing the redundancy among the genes. Results The present study identifies a subset of features by maximizing the relevance and minimizing the redundancy of the selected genes. A merit called normalized mutual information is employed to measure the relevance and the redundancy of the genes. In order to find a more representative subset of features, an iterative procedure is adopted that incorporates an initial clustering followed by data partitioning and the application of the algorithm to each of the partitions. A leave-one-out approach then selects the most commonly selected genes across all the different runs and the gene selection algorithm is applied again to pare down the list of selected genes until a minimal subset is obtained that gives a satisfactory accuracy of classification. The algorithm was applied to three different data sets and the results obtained were compared to work done by others using the same data sets Conclusion This study presents an entropy-based iterative algorithm for selecting genes from microarray data that are able to classify various cancer sub-types with high accuracy. In addition, the feature set obtained is very compact, that is, the redundancy between genes is reduced to a large extent. This implies that classifiers can be built with a smaller subset of genes.

  13. Accurate Gene Expression-Based Biodosimetry Using a Minimal Set of Human Gene Transcripts

    Energy Technology Data Exchange (ETDEWEB)

    Tucker, James D., E-mail: jtucker@biology.biosci.wayne.edu [Department of Biological Sciences, Wayne State University, Detroit, Michigan (United States); Joiner, Michael C. [Department of Radiation Oncology, Wayne State University, Detroit, Michigan (United States); Thomas, Robert A.; Grever, William E.; Bakhmutsky, Marina V. [Department of Biological Sciences, Wayne State University, Detroit, Michigan (United States); Chinkhota, Chantelle N.; Smolinski, Joseph M. [Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan (United States); Divine, George W. [Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan (United States); Auner, Gregory W. [Department of Electrical and Computer Engineering, Wayne State University, Detroit, Michigan (United States)

    2014-03-15

    Purpose: Rapid and reliable methods for conducting biological dosimetry are a necessity in the event of a large-scale nuclear event. Conventional biodosimetry methods lack the speed, portability, ease of use, and low cost required for triaging numerous victims. Here we address this need by showing that polymerase chain reaction (PCR) on a small number of gene transcripts can provide accurate and rapid dosimetry. The low cost and relative ease of PCR compared with existing dosimetry methods suggest that this approach may be useful in mass-casualty triage situations. Methods and Materials: Human peripheral blood from 60 adult donors was acutely exposed to cobalt-60 gamma rays at doses of 0 (control) to 10 Gy. mRNA expression levels of 121 selected genes were obtained 0.5, 1, and 2 days after exposure by reverse-transcriptase real-time PCR. Optimal dosimetry at each time point was obtained by stepwise regression of dose received against individual gene transcript expression levels. Results: Only 3 to 4 different gene transcripts, ASTN2, CDKN1A, GDF15, and ATM, are needed to explain ≥0.87 of the variance (R{sup 2}). Receiver-operator characteristics, a measure of sensitivity and specificity, of 0.98 for these statistical models were achieved at each time point. Conclusions: The actual and predicted radiation doses agree very closely up to 6 Gy. Dosimetry at 8 and 10 Gy shows some effect of saturation, thereby slightly diminishing the ability to quantify higher exposures. Analyses of these gene transcripts may be advantageous for use in a field-portable device designed to assess exposures in mass casualty situations or in clinical radiation emergencies.

  14. Integrating Concrete and Virtual Manipulatives in Early Childhood Mathematics

    Science.gov (United States)

    Rosen, Dina; Hoffman, Jo

    2009-01-01

    Early childhood teachers around the country and the world guide children's mathematical learning through the use of manipulatives--pattern blocks, base blocks, geoboards, Unifx cubes, Cuisenaire rods, coins, clocks, and so on. Manipulatives allow concrete, hands-on exploration and representation of mathematical concepts. In the past few years,…

  15. Comparative study on gene set and pathway topology-based enrichment methods.

    Science.gov (United States)

    Bayerlová, Michaela; Jung, Klaus; Kramer, Frank; Klemm, Florian; Bleckmann, Annalen; Beißbarth, Tim

    2015-10-22

    Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both

  16. LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

    Science.gov (United States)

    Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

    2012-01-01

    Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene

  17. Stud manipulating device

    International Nuclear Information System (INIS)

    Bunyan, T.W.

    1980-01-01

    A device for inserting and removing studs from bores in a workpiece, for example a nuclear reactor vessel, comprises manipulating devices for operating on individual studs, each capable of tensioning a stud slackening a working nut on the stud, and subsequently removing the stud from the bore. A ring has dogs which can engage working nut recesses to interlock with the nut against relative rotation. Motors coupled to the ring rotate the working nut. A top nut is coupled to the motors to rotate the nut and screw it onto the stud. The top nut with other device parts can be raised and lowered on a tube by a hydraulic actuator. A hydraulic load cell between the top nut and a stool on the workpiece is pressurised to tension the stud by means of the top nut and thus facilitate rotation of the working nut when tightening or slackening. A dog clutch mechanism engages a stud end fitting against relative axial and rotational movement. The mechanism is raised and lowered on a guide member by an actuator. The mechanism has a tubular member and the drive coupling for the motors to the top nut includes a tubular member. Tubular members carry teeth which are engaged when the top nut is raised and the clutch mechanism is lowered, to provide a coupling between the motors and the mechanism for rotating the stud. (U.K.)

  18. Image Manipulation: Then and Now.

    Science.gov (United States)

    Sutton, Ronald E.

    The images of photography have been manipulated almost from the moment of their discovery. The blending together in the studio and darkroom of images not found in actual scenes from life has been a regular feature of modern photography in both art and advertising. Techniques of photograph manipulation include retouching; blocking out figures or…

  19. Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data.

    Directory of Open Access Journals (Sweden)

    Enrico Glaab

    Full Text Available Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic diseases. Although classical machine learning techniques have successfully been applied to find informative genes and to predict class labels for new samples, common restrictions of microarray analysis such as small sample sizes, a large attribute space and high noise levels still limit its scientific and clinical applications. Increasing the interpretability of prediction models while retaining a high accuracy would help to exploit the information content in microarray data more effectively. For this purpose, we evaluate our rule-based evolutionary machine learning systems, BioHEL and GAssist, on three public microarray cancer datasets, obtaining simple rule-based models for sample classification. A comparison with other benchmark microarray sample classifiers based on three diverse feature selection algorithms suggests that these evolutionary learning techniques can compete with state-of-the-art methods like support vector machines. The obtained models reach accuracies above 90% in two-level external cross-validation, with the added value of facilitating interpretation by using only combinations of simple if-then-else rules. As a further benefit, a literature mining analysis reveals that prioritizations of informative genes extracted from BioHEL's classification rule sets can outperform gene rankings obtained from a conventional ensemble feature selection in terms of the pointwise mutual information between relevant disease terms and the standardized names of top-ranked genes.

  20. Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data.

    Science.gov (United States)

    Glaab, Enrico; Bacardit, Jaume; Garibaldi, Jonathan M; Krasnogor, Natalio

    2012-01-01

    Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic diseases. Although classical machine learning techniques have successfully been applied to find informative genes and to predict class labels for new samples, common restrictions of microarray analysis such as small sample sizes, a large attribute space and high noise levels still limit its scientific and clinical applications. Increasing the interpretability of prediction models while retaining a high accuracy would help to exploit the information content in microarray data more effectively. For this purpose, we evaluate our rule-based evolutionary machine learning systems, BioHEL and GAssist, on three public microarray cancer datasets, obtaining simple rule-based models for sample classification. A comparison with other benchmark microarray sample classifiers based on three diverse feature selection algorithms suggests that these evolutionary learning techniques can compete with state-of-the-art methods like support vector machines. The obtained models reach accuracies above 90% in two-level external cross-validation, with the added value of facilitating interpretation by using only combinations of simple if-then-else rules. As a further benefit, a literature mining analysis reveals that prioritizations of informative genes extracted from BioHEL's classification rule sets can outperform gene rankings obtained from a conventional ensemble feature selection in terms of the pointwise mutual information between relevant disease terms and the standardized names of top-ranked genes.

  1. Whole genome homology-based identification of candidate genes ...

    African Journals Online (AJOL)

    Sesame (Sesamum indicum L.) is one of the most important oilseed crops. It is mainly grown in arid and semi-arid regions with occurrence of unpredictable drought which is one of the major constraints of its production. However, the lack of gene resources associated with drought tolerance hinders sesame genetic ...

  2. RNAi-based silencing of genes encoding the vacuolar- ATPase ...

    African Journals Online (AJOL)

    2016-11-09

    Nov 9, 2016 ... Spodoptera exigua larval development by silencing chitin synthase gene with RNA interference. Bull. Entomol. Res. 98:613-619. Dow JAT (1999). The Multifunctional Drosophila melanogaster V-. ATPase is encoded by a multigene family. J. Bioenerg. Biomembr. 31:75-83. Fire A, Xu SQ, Montgomery MK, ...

  3. Whole genome homology-based identification of candidate genes ...

    African Journals Online (AJOL)

    Josephine Erhiakporeh

    2016-07-06

    Jul 6, 2016 ... Phylogenetic relationships of the species studied and number of sequences downloaded. genes and proteins sequences of these ... stage, all plants were transferred under a plastic rain shelter. Total. RNA of drought-stressed sesame seedlings were extracted from leaves using Trizol Reagent (Invitrogen, ...

  4. Advanced teleoperators. [remote manipulation system

    Science.gov (United States)

    Bejczy, A. K.

    1979-01-01

    Advanced teleoperators are discussed, with emphasis on the remote manipulation system designed to perform such actions as grasping, orienting, moving, placing, and inserting objects. Geometrical performance dimensions are considered, indicating that a manipulator is limited to three-orders-of-magnitude ratio of workspace extension to positioning accuracy. The control system is examined, showing that a manipulative task requires coordination of several joints, with the relationship between the task definers and the joint variables given by complex trigonometrical transformations. Control modes developed in the last 30 years are noted, including program controlled industrial 'robots' which can endlessly repeat a fixed sequence of motions without operator intervention, and the sensor-referenced/computer-controlled mode manipulators. Advanced proximity sensor systems are taken into account, with emphasis on the applications of the force-torque and slip models. The proximity sensor system for the shuttle-size manipulator is described.

  5. 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

  6. Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?

    Science.gov (United States)

    Zhao, Shanrong; Xi, Li; Zhang, Baohong

    2015-01-01

    In recent years, RNA-seq is emerging as a powerful technology in estimation of gene and/or transcript expression, and RPKM (Reads Per Kilobase per Million reads) is widely used to represent the relative abundance of mRNAs for a gene. In general, the methods for gene quantification can be largely divided into two categories: transcript-based approach and 'union exon'-based approach. Transcript-based approach is intrinsically more difficult because different isoforms of the gene typically have a high proportion of genomic overlap. On the other hand, 'union exon'-based approach method is much simpler and thus widely used in RNA-seq gene quantification. Biologically, a gene is expressed in one or more transcript isoforms. Therefore, transcript-based approach is logistically more meaningful than 'union exon'-based approach. Despite the fact that gene quantification is a fundamental task in most RNA-seq studies, however, it remains unclear whether 'union exon'-based approach for RNA-seq gene quantification is a good practice or not. In this paper, we carried out a side-by-side comparison of 'union exon'-based approach and transcript-based method in RNA-seq gene quantification. It was found that the gene expression levels are significantly underestimated by 'union exon'-based approach, and the average of RPKM from 'union exons'-based method is less than 50% of the mean expression obtained from transcript-based approach. The difference between the two approaches is primarily affected by the number of transcripts in a gene. We performed differential analysis at both gene and transcript levels, respectively, and found more insights, such as isoform switches, are gained from isoform differential analysis. The accuracy of isoform quantification would improve if the read coverage pattern and exon-exon spanning reads are taken into account and incorporated into EM (Expectation Maximization) algorithm. Our investigation discourages the use of 'union exons'-based approach in gene

  7. Manipulating Quantum Coherence in Solid State Systems

    CERN Document Server

    Flatté, Michael E; The NATO Advanced Study Institute "Manipulating Quantum Coherence in Solid State Systems"

    2007-01-01

    The NATO Advanced Study Institute "Manipulating Quantum Coherence in Solid State Systems", in Cluj-Napoca, Romania, August 29-September 9, 2005, presented a fundamental introduction to solid-state approaches to achieving quantum computation. This proceedings volume describes the properties of quantum coherence in semiconductor spin-based systems and the behavior of quantum coherence in superconducting systems. Semiconductor spin-based approaches to quantum computation have made tremendous advances in the past several years. Coherent populations of spins can be oriented, manipulated and detected experimentally. Rapid progress has been made towards performing the same tasks on individual spins (nuclear, ionic, or electronic) with all-electrical means. Superconducting approaches to quantum computation have demonstrated single qubits based on charge eigenstates as well as flux eigenstates. These topics have been presented in a pedagogical fashion by leading researchers in the fields of semiconductor-spin-based qu...

  8. 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.

  9. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.

    Science.gov (United States)

    Hur, Junguk; Ozgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

    2012-12-20

    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. Over 170,000 fever-related articles from PubMed abstracts and titles were retrieved and analysed at the sentence level using natural language processing techniques to identify genes and vaccines (including 186 Vaccine Ontology terms) as well as their interactions. This resulted in a generic fever network consisting of 403 genes and 577 gene interactions. A vaccine-specific fever sub-network consisting of 29 genes and 28 gene interactions was extracted from articles that are related to both fever and vaccines. In addition, gene-vaccine interactions were identified. Vaccines (including 4 specific vaccine names) were found to directly interact with 26 genes. Gene set enrichment analysis was performed using the genes in the generated interaction networks. Moreover, the genes in these networks were prioritized using network centrality metrics. Making scientific discoveries and generating new hypotheses were possible by using network centrality and gene set enrichment analyses. For example, our study found that the genes in the generic fever network were more enriched in cell death and responses to wounding, and the vaccine sub-network had more gene enrichment in leukocyte activation and phosphorylation regulation. The most central genes in the vaccine-specific fever network are predicted to be highly relevant to vaccine-induced fever, whereas genes that are central only in the generic fever network are likely to be highly relevant to generic fever responses. Interestingly, no Toll-like receptors (TLRs) were found in the gene-vaccine interaction network. Since

  10. Gene-based testing of interactions in association studies of quantitative traits.

    Directory of Open Access Journals (Sweden)

    Li Ma

    Full Text Available Various methods have been developed for identifying gene-gene interactions in genome-wide association studies (GWAS. However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene-gene interaction (GGG tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein-protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies.

  11. Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling–A Feasibility Study

    Directory of Open Access Journals (Sweden)

    Sandra Weißenborn

    2017-10-01

    Full Text Available Despite many developed experimental and computational approaches, functional gene annotation remains challenging. With the rapidly growing number of sequenced genomes, the concept of phylogenetic profiling, which predicts functional links between genes that share a common co-occurrence pattern across different genomes, has gained renewed attention as it promises to annotate gene functions based on presence/absence calls alone. We applied phylogenetic profiling to the problem of metabolic pathway assignments of plant genes with a particular focus on secondary metabolism pathways. We determined phylogenetic profiles for 40,960 metabolic pathway enzyme genes with assigned EC numbers from 24 plant species based on sequence and pathway annotation data from KEGG and Ensembl Plants. For gene sequence family assignments, needed to determine the presence or absence of particular gene functions in the given plant species, we included data of all 39 species available at the Ensembl Plants database and established gene families based on pairwise sequence identities and annotation information. Aside from performing profiling comparisons, we used machine learning approaches to predict pathway associations from phylogenetic profiles alone. Selected metabolic pathways were indeed found to be composed of gene families of greater than expected phylogenetic profile similarity. This was particularly evident for primary metabolism pathways, whereas for secondary pathways, both the available annotation in different species as well as the abstraction of functional association via distinct pathways proved limiting. While phylogenetic profile similarity was generally not found to correlate with gene co-expression, direct physical interactions of proteins were reflected by a significantly increased profile similarity suggesting an application of phylogenetic profiling methods as a filtering step in the identification of protein-protein interactions. This feasibility

  12. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jing; Ma, Zihao; Carr, Steven A.; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W.; Ellis, Matthew J. C.; Townsend, R. Reid; Smith, Richard D.; McDermott, Jason E.; Chen, Xian; Paulovich, Amanda G.; Boja, Emily S.; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Rodland, Karin D.; Liebler, Daniel C.; Zhang, Bing

    2016-11-11

    Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

  13. Literature-Based Discovery of IFN-γ and Vaccine-Mediated Gene Interaction Networks

    Directory of Open Access Journals (Sweden)

    Arzucan Özgür

    2010-01-01

    Full Text Available Interferon-gamma (IFN-γ regulates various immune responses that are often critical for vaccine-induced protection. In order to annotate the IFN-γ-related gene interaction network from a large amount of IFN-γ research reported in the literature, a literature-based discovery approach was applied with a combination of natural language processing (NLP and network centrality analysis. The interaction network of human IFN-γ (Gene symbol: IFNG and its vaccine-specific subnetwork were automatically extracted using abstracts from all articles in PubMed. Four network centrality metrics were further calculated to rank the genes in the constructed networks. The resulting generic IFNG network contains 1060 genes and 26313 interactions among these genes. The vaccine-specific subnetwork contains 102 genes and 154 interactions. Fifty six genes such as TNF, NFKB1, IL2, IL6, and MAPK8 were ranked among the top 25 by at least one of the centrality methods in one or both networks. Gene enrichment analysis indicated that these genes were classified in various immune mechanisms such as response to extracellular stimulus, lymphocyte activation, and regulation of apoptosis. Literature evidence was manually curated for the IFN-γ relatedness of 56 genes and vaccine development relatedness for 52 genes. This study also generated many new hypotheses worth further experimental studies.

  14. Network-Based Method for Identifying Co- Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues.

    Science.gov (United States)

    Chen, Lei; Pan, Hongying; Zhang, Yu-Hang; Feng, Kaiyan; Kong, XiangYin; Huang, Tao; Cai, Yu-Dong

    2017-10-02

    Bone and dental diseases are serious public health problems. Most current clinical treatments for these diseases can produce side effects. Regeneration is a promising therapy for bone and dental diseases, yielding natural tissue recovery with few side effects. Because soft tissues inside the bone and dentin are densely populated with nerves and vessels, the study of bone and dentin regeneration should also consider the co-regeneration of nerves and vessels. In this study, a network-based method to identify co-regeneration genes for bone, dentin, nerve and vessel was constructed based on an extensive network of protein-protein interactions. Three procedures were applied in the network-based method. The first procedure, searching, sought the shortest paths connecting regeneration genes of one tissue type with regeneration genes of other tissues, thereby extracting possible co-regeneration genes. The second procedure, testing, employed a permutation test to evaluate whether possible genes were false discoveries; these genes were excluded by the testing procedure. The last procedure, screening, employed two rules, the betweenness ratio rule and interaction score rule, to select the most essential genes. A total of seventeen genes were inferred by the method, which were deemed to contribute to co-regeneration of at least two tissues. All these seventeen genes were extensively discussed to validate the utility of the method.

  15. 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.

  16. Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

    Science.gov (United States)

    Wada, Masayoshi; Takahashi, Hiroki; Altaf-Ul-Amin, Md; Nakamura, Kensuke; Hirai, Masami Y; Ohta, Daisaku; Kanaya, Shigehiko

    2012-07-15

    Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene clusters are defined by their co-regulation or neighboring positions within immediate vicinity of chromosomal regions. A comprehensive analysis of the expression of neighboring genes therefore accounts a crucial step to reveal the complete set of operon-like gene clusters within a genome. Genome-wide prediction of operon-like gene clusters should contribute to functional annotation efforts and provide novel insight into evolutionary aspects acquiring certain biological functions as well. We predicted co-expressed gene clusters by comparing the Pearson correlation coefficient of neighboring genes and randomly selected gene pairs, based on a statistical method that takes false discovery rate (FDR) into consideration for 1469 microarray gene expression datasets of A. thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters in total. We predicted 34 statistically significant gene clusters consisting of 3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional relationships among genes in individual clusters were estimated by sequence similarity and functional annotation of genes. Duplicated gene pairs (determined based on BLAST with a cutoff of EOperon-like clusters tend to include genes encoding bio-machinery associated with ribosomes, the ubiquitin/proteasome system, secondary metabolic pathways, lipid and fatty-acid metabolism, and the lipid transfer system. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Direct Manipulation in Virtual Reality

    Science.gov (United States)

    Bryson, Steve

    2003-01-01

    Virtual Reality interfaces offer several advantages for scientific visualization such as the ability to perceive three-dimensional data structures in a natural way. The focus of this chapter is direct manipulation, the ability for a user in virtual reality to control objects in the virtual environment in a direct and natural way, much as objects are manipulated in the real world. Direct manipulation provides many advantages for the exploration of complex, multi-dimensional data sets, by allowing the investigator the ability to intuitively explore the data environment. Because direct manipulation is essentially a control interface, it is better suited for the exploration and analysis of a data set than for the publishing or communication of features found in that data set. Thus direct manipulation is most relevant to the analysis of complex data that fills a volume of three-dimensional space, such as a fluid flow data set. Direct manipulation allows the intuitive exploration of that data, which facilitates the discovery of data features that would be difficult to find using more conventional visualization methods. Using a direct manipulation interface in virtual reality, an investigator can, for example, move a data probe about in space, watching the results and getting a sense of how the data varies within its spatial volume.

  18. 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.

  19. 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...

  20. 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…